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|---|---|---|---|---|---|
Rift Valley fever ( RVF ) outbreaks in Kenya have increased in frequency and range to include northeastern Kenya where viruses are increasingly being isolated from known ( Aedes mcintoshi ) and newly-associated ( Ae . ochraceus ) vectors . The factors contributing to these changing outbreak patterns are unclear and the... | Despite the threat posed by Rift Valley fever ( RVF ) , poor understanding of the disease epidemiology exists with respect to vector population structure in relation to differential outbreak patterns and future vector genetic control . Here , nuclear and mtDNA data reveal genetic complexities of RVF key vectors ( Aedes... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"ecology",
"and",
"environmental",
"sciences"
] | 2014 | Population Genetics of Two Key Mosquito Vectors of Rift Valley Fever Virus Reveals New Insights into the Changing Disease Outbreak Patterns in Kenya |
Enteropathies such as Crohn’s disease are associated with enteric inflammation characterized by impaired TGF-β signaling , decreased expression of phosphorylated ( p ) -SMAD2 , 3 and increased expression of SMAD7 ( an inhibitor of SMAD3 phosphorylation ) . Environmental enteropathy ( EE ) is an acquired inflammatory di... | Environmental enteropathy ( EE ) is a disease found in children living in low- and middle-income countries , involving gut inflammation similar to that seen in Crohn’s disease or celiac disease . The inflammation leads to poor absorption of nutrients that these children would normally get in their diets , and this mala... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"enteropathies",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"biopsy",
"immunology",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"protein",
"expression",
"endoscopy",
"signs",
"and",
"symptoms",
"gastroenterology",
... | 2018 | High SMAD7 and p-SMAD2,3 expression is associated with environmental enteropathy in children |
Snakebite envenomation is a serious medical problem in many tropical developing countries and was considered by WHO as a neglected tropical disease . Antivenom ( AV ) , the rational and most effective treatment modality , is either unaffordable and/or unavailable in many affected countries . Moreover , each AV is speci... | Antivenom is the most effective treatment modality for snake envenoming . However , they are specific and effective against only one or a few snake venoms . Production of antivenom against many snake species covering a wide geographic area of some countries or regions e . g . , Asia and Africa , is not yet possible . T... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"serum",
"medicine",
"and",
"health",
"sciences",
"toxins",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"immune",
"physiology",
"enzyme-linked",
"immunoassays",
"immunology",
"vertebrates",
"animals",
"mammals",
"toxicology",
"toxic",
"agent... | 2016 | A Simple and Novel Strategy for the Production of a Pan-specific Antiserum against Elapid Snakes of Asia |
Although cell polarity is an essential feature of living cells , it is far from being well-understood . Using a combination of computational modeling and biological experiments we closely examine an important prototype of cell polarity: the pheromone-induced formation of the yeast polarisome . Focusing on the role of n... | Cell polarity is the fundamental process of breaking symmetry to create asymmetric cellular structures . It is an open question how randomness ( stochasticity ) in the cell hinders or helps cell polarity . In this work , we focus on the ability of yeast cells to sense a spatial gradient of mating pheromone and respond ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"developmental",
"biology",
"computer",
"science",
"model",
"organisms",
"computer",
"modeling",
"yeast",
"and",
"fungal",
"models",
"biology",
"computational",
"biology",
"saccharomyces",
"cerevisiae",
"computerized",
"simulations"
] | 2013 | Spatial Stochastic Dynamics Enable Robust Cell Polarization |
NLRC3 , a member of the NLR family , has been reported as a negative regulator of inflammatory signaling pathways in innate immune cells . However , the direct role of NLRC3 in modulation of CD4+ T-cell responses in infectious diseases has not been studied . In the present study , we showed that NLRC3 plays an intrinsi... | Accumulating evidence that NLRs play an intrinsic roles in regulating T cell responses in lungs and lymphoid tissues , however , to our known , contribution for NLRs modulation of T-cell responses directly in infectious diseases has not been studied . NLRC3 , a member of the NLR family , has been reported as a negative... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"immunology",
"immune",
"receptor",
"signaling",
"developmental",
"biology",
"membrane",
"receptor",
"signaling",
"molecular"... | 2018 | NLRC3 negatively regulates CD4+ T cells and impacts protective immunity during Mycobacterium tuberculosis infection |
Age-associated telomere shortening is a well documented feature of peripheral blood cells in human population studies , but it is not known to what extent these data can be transferred to the individual level . Telomere length ( TL ) in two blood samples taken at ∼10 years interval from 959 individuals was investigated... | An age-dependent telomere shortening has been frequently observed in cross-sectional studies on human blood cells . Telomerase is an enzyme capable of lengthening telomeres , and it is activated in most tumor cells in order for them to become immortalized . This is one of the first longitudinal studies on telomere leng... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and",
"genomics/chromosome",
"biology"
] | 2009 | The Individual Blood Cell Telomere Attrition Rate Is Telomere Length Dependent |
The inflammatory response is prominent in the pathogenesis of dermal leishmaniasis . We hypothesized that regulatory T cells ( Tregs ) may be diminished in chronic dermal leishmaniasis ( CDL ) and contribute to healing during treatment . The frequency and functional capacity of Tregs were evaluated at diagnosis and fol... | The immune inflammatory response is a double edged sword . During infectious diseases , regulatory T cells can prevent eradication of the pathogen but can also limit inflammation and tissue damage . We investigated the role of regulatory T cells in chronic dermal leishmaniasis caused by species of the parasite Leishman... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"immune",
"cells",
"leishmaniasis",
"t",
"cells",
"immunology",
"biology",
"microbiology",
"parasitic",
"diseases",
"parasitology"
] | 2012 | Regulatory T Cells in the Pathogenesis and Healing of Chronic Human Dermal Leishmaniasis Caused by Leishmania (Viannia) Species |
During Ebola virus ( EBOV ) infection a significant amount of surface glycoprotein GP is shed from infected cells in a soluble form due to cleavage by cellular metalloprotease TACE . Shed GP and non-structural secreted glycoprotein sGP , both expressed from the same GP gene , have been detected in the blood of human pa... | Ebola virus , a member of the Filoviridae family , causes lethal hemorrhagic fever in man and primates , displaying up to 90% mortality rates . Viral infection is typified by an excessive systemic inflammatory response resembling septic shock . It also damages endothelial cells and creates difficulty in coagulation , u... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"inflammatory",
"diseases",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"cell",
"biology",
"virology",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"molecular",
"biology"
] | 2014 | Shed GP of Ebola Virus Triggers Immune Activation and Increased Vascular Permeability |
High-throughput studies of the 6 , 200 genes of Saccharomyces cerevisiae have provided valuable data resources . However , these resources require a return to experimental analysis to test predictions . An in-silico screen , mining existing interaction , expression , localization , and phenotype datasets was developed ... | Since the genome of S . cerevisiae was sequenced in 1996 , a major objective has been to characterize its 6 , 200 genes . Important contributions to this have been made using high-throughput screens . These have provided a vast quantity of information , but many genes remain minimally characterized , and the high-throu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"cell",
"biology",
"yeast",
"and",
"fungi",
"eukaryotes",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"saccharomyces"
] | 2007 | Novel Roles for Selected Genes in Meiotic DNA Processing |
RfaH is a virulence factor from Escherichia coli whose C-terminal domain ( CTD ) undergoes a dramatic α-to-β conformational transformation . The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain ( NTD ) , masking an RNA polymerase binding site until a specific recruitment site is encoun... | To carry out their biological functions , proteins must fold into defined three-dimensional structures . In most proteins , a single fold determined by the amino acid sequence , and sometimes influenced by environmental conditions , is believed to be suited for each protein’s dedicated task . However , some proteins ch... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [] | 2015 | Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape |
Poliovirus ( PV ) is a well-characterized RNA virus , and the RNA-dependent RNA polymerase ( RdRp ) from PV ( 3Dpol ) has been widely employed as an important model for understanding the structure-function relationships of RNA and DNA polymerases . Many experimental studies of the kinetics of nucleotide incorporation b... | The missing link between dynamics and structure or between dynamics and function of a protein has recently been paid much attention by many scientists since it has been recognized that a folded protein should be considered as an ensemble of conformations fluctuating in the neighborhood of its native state , instead of ... | [
"Abstract",
"Introduction",
"Methods",
"Results/Discussion"
] | [
"chemistry",
"biology",
"computational",
"chemistry",
"biophysics"
] | 2012 | What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus? |
Andes virus ( ANDV ) is the etiological agent of hantavirus cardiopulmonary syndrome in Chile . In this study , we evaluated the profile of the pro-inflammatory cytokines IL-1β , IL-12p70 , IL-21 , TNF-α , IFN-γ , IL-10 and IL-6 in serum samples of ANDV-infected patients at the time of hospitalization . The mean levels... | Andes virus ( ANDV ) causes hantavirus cardiopulmonary syndrome ( HCPS ) that is characterized by the development of vascular leakage syndrome , eventually leading to massive pulmonary edema , shock and , in many cases , death . To date , no FDA-approved immunotherapeutics , specific antivirals , or vaccines are availa... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"respiratory",
"infections",
"chile",
"(country)",
"pathogens",
"immunology",
"geographical",
"locations",
"microbiolo... | 2017 | Serum levels of interleukin-6 are linked to the severity of the disease caused by Andes Virus |
Characterizing the distribution of effects from genome-wide genotyping data is crucial for understanding important aspects of the genetic architecture of complex traits , such as number or proportion of non-null loci , average proportion of phenotypic variance explained per non-null effect , power for discovery , and p... | We describe in detail the implications of a particular mixture model ( a scale mixture of two normals ) for effect size distributions from genome-wide genotyping data . Parameters from this model can be used for estimation of the non-null proportion , the probability of replication in de novo samples , the local false ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [] | 2015 | An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies |
Many morphogenetic processes involve mechanical rearrangements of epithelial tissues that are driven by precisely regulated cytoskeletal forces and cell adhesion . The mechanical state of the cell and intercellular adhesion are not only the targets of regulation , but are themselves the likely signals that coordinate d... | Mechanical forces play many important roles in cell biology and animal and plant development . In contrast to inanimate matter , forces in living matter are generated by active and highly regulated processes within and between cells . The ability to directly measure forces and mechanical stress on the cellular scale wi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"physics",
"biology",
"biophysics"
] | 2012 | Mechanical Stress Inference for Two Dimensional Cell Arrays |
Gammaherpesviruses encode proteins with homology to the cellular purine metabolic enzyme formyl-glycinamide-phosphoribosyl-amidotransferase ( FGARAT ) , but the role of these viral FGARATs ( vFGARATs ) in the pathogenesis of a natural host has not been investigated . We report a novel role for the ORF75A vFGARAT of mur... | Gammaherpesviruses are infectious agents that cause cancer . The study of viral genes unique to this subfamily may offer insight into the strategies that these viruses use to persist in the host and drive disease . The vFGARATs are a family of viral proteins found only in gammaherpesviruses , and are critical for repli... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"spleen",
"microbiology",
"viral",
"structure",
"fibroblasts",
"viral",
"genome",
"connective",
"tissue",
"cells",
"mammalian",
"genomics",
"microbial",
"genomics",
"viral",
"genomics",
"animal",
"cells",
... | 2018 | Viral FGARAT ORF75A promotes early events in lytic infection and gammaherpesvirus pathogenesis in mice |
Strongyloides stercoralis is a neglected soil-transmitted helminth that occurs worldwide , though it is particularly endemic in tropical and subtropical areas . It can cause long-lasting and potentially fatal infections due to its ability to replicate within its host . S . stercoralis causes gastrointestinal and dermat... | The threadworm , Strongyloides stercoralis , is a highly neglected worm infection , transmitted through infective larvae in the soil . Threadworms occur worldwide , particularly in tropical climates . It may cause long-lasting and potentially fatal infections due to the parasite’s ability to replicate within its host .... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"statistics",
"geographical",
"locations",
"parasitic",
"diseases",
"animals",
"urine",
"developmental",
"biology",
"mathematics",
"forecasting",
"medical",
"risk",
"factors",
"strongyloides",
"st... | 2019 | Strongyloides stercoralis: Spatial distribution of a highly prevalent and ubiquitous soil-transmitted helminth in Cambodia |
Hybrid genotypes have been repeatedly described among natural isolates of Leishmania , and the recovery of experimental hybrids from sand flies co-infected with different strains or species of Leishmania has formally demonstrated that members of the genus possess the machinery for genetic exchange . As neither gamete s... | Leishmania promastigotes are able to undergo genetic exchange during their growth and development in the sand fly vector , however , it is still not known if they have a true sexual cycle involving meiosis . Here , we used whole genome sequencing to follow the chromosomal inheritance patterns of 44 experimental hybrids... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"sequencing",
"techniques",
"meiosis",
"trisomics",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"cloning",
"departures",
"from",
"diploidy",
"parasitic",
"protozoans",
"organisms",
"genome",
"sequencing",
"protozoans",
"leishmania",
"dna",
"molecula... | 2019 | Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania |
Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans infection , is a debilitating disease of the skin and underlying tissue . The first phase of a BU prevention and treatment programme ( BUPaT ) was initiated from 2005–2008 , in the Ga-West and Ga-South municipalities in Ghana to increase access to BU treatment and ... | Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans infection , is a debilitating disease of the skin and underlying tissue which starts as a painless nodule , oedema or plaque and could develop into painful and massive ulcers if left untreated . Using a combination of quantitative and qualitative methods , the stud... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"public",
"health"
] | 2011 | Health Services for Buruli Ulcer Control: Lessons from a Field Study in Ghana |
LSH/DDM1 enzymes are required for DNA methylation in higher eukaryotes and have poorly defined roles in genome maintenance in yeast , plants , and animals . The filamentous fungus Neurospora crassa is a tractable system that encodes a single LSH/DDM1 homolog ( NCU06306 ) . We report that the Neurospora LSH/DDM1 enzyme ... | Inside cells , eukaryotic DNA exists in a highly packaged structure called chromatin . Chromatin packaging often inhibits enzymes that need to access the genetic information . It is therefore important for cells to regulate chromatin structure so that the genome can function properly . Mammalian LSH ( Lymphoid-specific... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa |
The prevalence of skin disease in low and middle income countries is high and communicable skin diseases are a significant public health problem . Tungiasis is an ectoparasite infestation caused by the flea Tunga penetrans , which has a widespread geographical distribution . Tungiasis causes painful skin lesions and ma... | Skin disorders are very common in all geographical locations and especially so in low and middle income countries . In these settings many of the commonest skin disorders are communicable . Human ectoparasites such as lice and scabies mites live on the skin and Tunga penetrans fleas enter the skin to shed their eggs an... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"schoolchildren",
"medicine",
"and",
"health",
"sciences",
"education",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"health",
"care",
"skin",
"infections",
"ectoparasitic",
"infections",
"... | 2017 | The prevalence and association with health-related quality of life of tungiasis and scabies in schoolchildren in southern Ethiopia |
Bacterial cell division predominantly occurs by a highly conserved process , termed binary fission , that requires the bacterial homologue of tubulin , FtsZ . Other mechanisms of bacterial cell division that are independent of FtsZ are rare . Although the obligate intracellular human pathogen Chlamydia trachomatis , th... | The obligate intracellular human pathogen Chlamydia trachomatis is the leading bacterial cause of sexually transmitted infections . C . trachomatis does not express FtsZ , which is necessary for the highly conserved process of binary fission that most bacteria utilize to divide . Nonetheless , it has been assumed that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"cell",
"division",
"analysis",
"hela",
"cells",
"asses",
"cell",
"cycle",
"and",
"cell",
"division",
"chlamydia",
"trachomatis",
"cell",
"processes",
"patho... | 2016 | Polarized Cell Division of Chlamydia trachomatis |
Short insertions and deletions ( InDels ) comprise an important part of the natural mutational repertoire . InDels are , however , highly deleterious , primarily because two-thirds result in frame-shifts . Bypass through slippage over homonucleotide repeats by transcriptional and/or translational infidelity is known to... | Homonucleotide repeats are exceptionally prone to insertions and/or deletions of bases ( InDels ) . However , unless they occur in a multiplicity of 3 bases , InDels disrupt the reading frame and are thus expected to be purged from coding regions . Homonucleotide repeats , however , are also vulnerable to slippage by R... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins |
Spike timing is precise in the auditory system and it has been argued that it conveys information about auditory stimuli , in particular about the location of a sound source . However , beyond simple time differences , the way in which neurons might extract this information is unclear and the potential computational ad... | There is growing evidence that the temporal coordination of spikes is important for neural computation , especially in auditory perception . Yet it is unclear what computational advantage it might provide , if any . We investigated this issue in the context of a difficult auditory task which must be performed quickly b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/theoretical",
"neuroscience",
"neuroscience/sensory",
"systems",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Spike-Timing-Based Computation in Sound Localization |
Fly lobula plate tangential cells are known to perform wide-field motion integration . It is assumed that the shape of these neurons , and in particular the shape of the subclass of VS cells , is responsible for this type of computation . We employed an inverse approach to investigate the morphology-function relationsh... | It is well established that neuronal morphology influences the computation performed by a single neuron . However , it remains largely unknown how these computations emerge from the interaction between dendritic morphology , the distribution of ion-channels and synaptic inputs . To investigate this neuronal morphology-... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Wide-Field Motion Integration in Fly VS Cells: Insights from an Inverse Approach |
Two eukaryotic pathways for processing double-strand breaks ( DSBs ) as crossovers have been described , one dependent on the MutL homologs Mlh1 and Mlh3 , and the other on the structure-specific endonuclease Mus81 . Mammalian MUS81 has been implicated in maintenance of genomic stability in somatic cells; however , lit... | Failure to undergo faithful meiotic chromosome segregation during mammalian meiosis can result in aneuploidy in the offspring and is a major cause of pregnancy loss and birth defects in humans . One essential component of meiotic prophase I is the exchange of genetic information between maternal and paternal chromosome... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/gene",
"function"
] | 2008 | MUS81 Generates a Subset of MLH1-MLH3–Independent Crossovers in Mammalian Meiosis |
Hybridization has recently gained considerable interest both as a unique opportunity for observing speciation mechanisms and as a potential engine for speciation . The latter remains a controversial topic . It was recently hypothesized that the reciprocal sorting of genetic incompatibilities from parental species could... | Hybridization is observed ubiquitously in nature . Its outcome can range from extinction to the creation of new species . With respect to the latter , the probability of homoploid hybrid speciation , i . e . the formation of a new species as a result of a hybridization event without changes in the ploidy of the organis... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion",
"Conclusion"
] | [
"epistasis",
"population",
"metrics",
"haplotypes",
"population",
"size",
"natural",
"selection",
"speciation",
"heredity",
"alleles",
"genetics",
"biology",
"and",
"life",
"sciences",
"population",
"biology",
"population",
"genetics",
"evolutionary",
"biology",
"hybrid",... | 2018 | In search of the Goldilocks zone for hybrid speciation |
X linked lymphoproliferative disease ( XLP ) is an inherited immunodeficiency resulting from mutations in the gene encoding the slam associated protein ( SAP ) . One of the defining characteristics of XLP is extreme susceptibility to infection with Epstein-Barr virus ( EBV ) , a gammaherpesvirus belonging to the genus ... | During an immune response , B cells respond to invading pathogens by undergoing massive expansion during the germinal center reaction . This proliferation requires signals from CD4 T cells , with some B cells then maturing into antibody secreting plasma cells , while others mature into memory B cells that may persist f... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viral",
"persistence",
"and",
"latency",
"biology",
"and",
"life",
"sciences",
"microbiology",
"virology"
] | 2014 | Expansion of Murine Gammaherpesvirus Latently Infected B Cells Requires T Follicular Help |
Molecular methods have great potential for sensitive parasite detection in the diagnosis of human African trypanosomiasis ( HAT ) , but the requirements in terms of laboratory infrastructure limit their use to reference centres . A recently developed assay detects the Trypanozoon repetitive insertion mobile element ( R... | Diagnosis and effective treatment are cornerstones in the control of human African trypanosomiasis ( HAT ) . Molecular tools such as the polymerase chain reaction ( PCR ) detect the parasite's DNA and are generally very sensitive and specific . However , PCR is not applicable in field settings because it requires a lab... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Diagnostic Accuracy of Loopamp Trypanosoma brucei Detection Kit for Diagnosis of Human African Trypanosomiasis in Clinical Samples |
Small non-coding RNAs ( sRNAs ) that act as regulators of gene expression have been identified in all kingdoms of life , including microRNA ( miRNA ) and small interfering RNA ( siRNA ) in eukaryotic cells . Numerous sRNAs identified in Salmonella are encoded by genes located at Salmonella pathogenicity islands ( SPIs ... | Regulated expression of virulence factors is essential for infection by human pathogens such as Salmonella . Small non-coding RNAs ( sRNAs ) that act as regulators of gene expression have been identified in all kingdoms of life , and many sRNAs in Salmonella are encoded by genes located at Salmonella pathogenicity isla... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology",
"veterinary",
"science",
"agriculture"
] | 2011 | A Salmonella Small Non-Coding RNA Facilitates Bacterial Invasion and Intracellular Replication by Modulating the Expression of Virulence Factors |
The kinetics of arthropod-borne virus ( arbovirus ) transmission by their vectors have long been recognized as a powerful determinant of arbovirus epidemiology . The time interval between virus acquisition and transmission by the vector , termed extrinsic incubation period ( EIP ) , combines with vector mortality rate ... | Transmission of arboviruses by mosquitoes is a time-dependent process because dissemination of the virus from the insect’s digestive tract , where the infection is initially established , to the salivary glands , where it can be transmitted to the next host , typically takes several days . The duration of this time int... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"invertebrates",
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"animals",
"simulation",
"and",
"modeling",
"viruses",
"systems",
"science",
"mathematics",
"rna",
... | 2018 | Epidemiological significance of dengue virus genetic variation in mosquito infection dynamics |
Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology . Despite this , much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities . By pairing auxo... | Many basic characteristics underlying the establishment of cooperative growth in bacterial communities have not been studied in detail . The presented work sought to understand the adaptation of syntrophic communities by first employing a new computational method to generate a comprehensive catalog of E . coli auxotrop... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"carbohydrate",
"metabolism",
"protein",
"metabolism",
"enzymology",
"cloning",
"glucose",
"metabolism",
"mutation",
"metabolites",
"enzyme",
"metabolism",
"molecular",
"biology",
"techniques",
"evolutionary",
"adaptation",
"enzyme",
"chemistry",
"research",
"and",
"analysi... | 2019 | The genetic basis for adaptation of model-designed syntrophic co-cultures |
We propose a network representation of electrically coupled beta cells in islets of Langerhans . Beta cells are functionally connected on the basis of correlations between calcium dynamics of individual cells , obtained by means of confocal laser-scanning calcium imaging in islets from acute mouse pancreas tissue slice... | Complex network theory has provided new tools for studying the structure and function of complex systems . A particularly attractive avenue in this context is the analysis of biological systems , since structural principles of complex networks have been identified at all scales of functioning of living organisms . In t... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"complex",
"systems",
"medicine",
"physiological",
"processes",
"mathematics",
"homeostasis",
"endocrinology",
"applied",
"mathematics",
"endocrine",
"system",
"topology",
"diabetes",
"and",
"endocrinology",
"anatomy",
"and",
"physiology",
"physiology",
"endocrine",
"physio... | 2013 | Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices |
The central event in prion diseases is the conformational conversion of the cellular prion protein ( PrPC ) into PrPSc , a partially protease-resistant and infectious conformer . However , the mechanism by which PrPSc causes neuronal dysfunction remains poorly understood . Levels of Shadoo ( Sho ) , a protein that rese... | Shadoo is a protein that resembles the prion protein , which causes prion diseases such as Creutzfeldt-Jakob disease in humans and “mad cow” disease . In this paper , we demonstrate that during prion disease in animals , levels of Shadoo were reduced in the brain and correlated with levels of infectious prions . This p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonotic",
"diseases",
"veterinary",
"science",
"prion",
"diseases"
] | 2011 | Protease-Resistant Prions Selectively Decrease Shadoo Protein |
Fabry disease ( FD ) is an X-linked hereditary defect of glycosphingolipid storage caused by mutations in the gene encoding the lysosomal hydrolase α-galactosidase A ( GLA , α-gal A ) . To date , over 400 mutations causing amino acid substitutions have been described . Most of these mutations are related to the classic... | Fabry disease is caused by a single gene deficiency . It is the second most common lysosomal storage disorder and the result is a build-up of glycosphingolipids in different areas of the body ( kidneys , intestine , etc ) . It is an important consideration for clinicians in the diagnosing of stroke , kidney and cardiov... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"computer",
"science",
"biology"
] | 2013 | Functional Characterisation of Alpha-Galactosidase A Mutations as a Basis for a New Classification System in Fabry Disease |
Meiotic recombination generates reciprocal exchanges between homologous chromosomes ( also called crossovers , COs ) that are essential for proper chromosome segregation during meiosis and are a major source of genome diversity by generating new allele combinations . COs have two striking properties: they occur at spec... | Meiosis is the process of cell division that reduces the number of chromosome sets from two to one , so producing gametes for sexual reproduction . During meiosis in many organisms , there is reciprocal exchange of genetic material between homologous chromosomes by the formation of “crossovers , ” which promote genetic... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"meiosis",
"histone",
"modification",
"epigenetics",
"dna",
"chromatin",
"chromosome",
"biology",
"biology",
"molecular",
"biology",
"cell",
"biology",
"nucleic",
"acids",
"genetics",
"dna",
"recombination",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
... | 2011 | Mouse PRDM9 DNA-Binding Specificity Determines Sites of Histone H3 Lysine 4 Trimethylation for Initiation of Meiotic Recombination |
The parasitic protozoan Trypanosoma brucei causes Human African Trypanosomiasis and Nagana in other mammals . These diseases present a major socio-economic burden to large areas of sub-Saharan Africa . Current therapies involve complex and toxic regimens , which can lead to fatal side-effects . In addition , there is e... | Human African Trypanosomiasis ( HAT ) is a neglected tropical disease affecting mostly rural communities of sub-Saharan Africa . New drugs for this parasitic disease have been slow to develop , but one new class of drug , the benzoxaboroles , has proven to be highly effective in preclinical models and holds promise for... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"enzymes",
"enzymology",
"cell",
"metabolism",
"parasitic",
"protozoans",
"metabolomics",
"methylation",
"protozoans",
"metabolites",
"pharmacology",
"molecular",
"biology",
"techniques",
"drug",
"metabolism",
... | 2018 | Benzoxaborole treatment perturbs S-adenosyl-L-methionine metabolism in Trypanosoma brucei |
Rhinovirus ( RV ) is the most prevalent human respiratory virus and is responsible for at least half of all common colds . RV infections may result in a broad spectrum of effects that range from asymptomatic infections to severe lower respiratory illnesses . The basis for inter-individual variation in the response to R... | Rhinovirus ( RV ) is the predominant cause of the common cold . However , infections with RV result in a broad spectrum of effects ranging from asymptomatic infections to severe lower respiratory illnesses . We hypothesized that diversity in response to RV-infections is , at least in part , due to variation in the host... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection |
Tumor suppressor protein p53 is regulated by two structurally homologous proteins , Mdm2 and MdmX . In contrast to Mdm2 , MdmX lacks ubiquitin ligase activity . Although the essential interactions of MdmX are known , it is not clear how they function to regulate p53 . The regulation of tumor suppressor p53 by Mdm2 and ... | A Molecular Interaction Map ( MIM ) akin to a circuit diagram of an electric device can give a comprehensive view of cellular processes and help understand complex protein functions in cells . To this end , we generated a MIM focused on the p53-Mdm2-MdmX network proteins and performed computer simulations to help under... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/molecular",
"dynamics",
"computational",
"biology/systems",
"biology",
"computational",
"biology/signaling",
"networks"
] | 2010 | Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage |
Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex ( ORC ) binds chromosomal positions and triggers molecular events culminating in the initiation of DNA replication ( a . k . a . origin firing ) during S-phase . Each chromosome uses multiple origins for its duplication , an... | Cell division requires the duplication of chromosomes , protein-DNA complexes harboring genetic information . Specific chromosomal positions , origins , initiate this duplication . Multiple origins are required for accurate , efficient duplication—an insufficient number leads to mistakes in the genetic material and pat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | A Link between ORC-Origin Binding Mechanisms and Origin Activation Time Revealed in Budding Yeast |
SAMHD1 is a host restriction factor that blocks the ability of lentiviruses such as HIV-1 to undergo reverse transcription in myeloid cells and resting T-cells . This restriction is alleviated by expression of the lentiviral accessory proteins Vpx and Vpr ( Vpx/Vpr ) , which target SAMHD1 for proteasome-mediated degrad... | At least 40 primate species in the wild are infected with their own lentivirus . Many of these infections arose from cross-species transmission followed by adaptation to a new host . Host antiviral proteins , called restriction factors , work to defend against both known and novel viruses and are thus engaged in a cons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"immunodeficiency",
"viruses",
"immunity",
"virology",
"innate",
"immunity",
"host-pathogen",
"interaction",
"biology",
"microbiology",
"evolutionary",
"biology",
"viral",
"evolution"
] | 2013 | Evolutionary Toggling of Vpx/Vpr Specificity Results in Divergent Recognition of the Restriction Factor SAMHD1 |
Collaboration plays an increasingly important role in promoting research productivity and impact . What remains unclear is whether female and male researchers in science , technology , engineering , and mathematical ( STEM ) disciplines differ in their collaboration propensity . Here , we report on an empirical analysi... | Collaboration plays an increasingly important role in promoting research productivity and impact . What remains unclear is whether female and male researchers differ in their collaboration practices . In our study , we report on an empirical analysis of the complete publication records of 3 , 980 faculty members in six... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"employment",
"ecology",
"and",
"environmental",
"sciences",
"engineering",
"and",
"technology",
"social",
"sciences",
"careers",
"chemical",
"ecology",
"scientists",
"mathematics",
"statistics",
"(mathematics)",
"genome",
"analysis",
"research",
"and",
"analysis",
"metho... | 2016 | Differences in Collaboration Patterns across Discipline, Career Stage, and Gender |
Neuronal physiology is particularly sensitive to acute stressors that affect excitability , many of which can trigger seizures and epilepsies . Although intrinsic neuronal homeostasis plays an important role in maintaining overall nervous system robustness and its resistance to stressors , the specific genetic and mole... | Neurons are extremely sensitive to diverse environmental stressors , including rapid changes in the ambient temperature . To buffer environmental stress , many animals have evolved diverse physiological mechanisms to protect neuronal activity from acute and chronic stressors . Failures of these safeguards often lead to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"voltage-gated",
"ion",
"channels",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"classical",
"mechanics",
"nervous",
"system",
"membrane",
"potential",
"mechanical",
"stress",
"electrophysiology",
"neuroscience",
"animals",
"animal",
... | 2019 | The Drosophila ERG channel seizure plays a role in the neuronal homeostatic stress response |
Elucidation of the mechanism of biomacromolecular recognition events has been a topic of intense interest over the past century . The inherent dynamic nature of both protein and ligand molecules along with the continuous reshaping of the energy landscape during the binding process renders it difficult to characterize t... | Molecular recognition plays a central role in many biological processes , ensuring specific and efficient interaction between binding partners . Various models for describing the mechanisms of molecular recognition have been proposed , but the validation of these models has been traditionally difficult due to the trans... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"biology",
"computational",
"biology",
"biophysics"
] | 2011 | In Silico Elucidation of the Recognition Dynamics of Ubiquitin |
Mitochondrial fatty-acid beta-oxidation ( mFAO ) plays a central role in mammalian energy metabolism . Multiple severe diseases are associated with defects in this pathway . Its kinetic structure is characterized by a complex wiring of which the functional implications have hardly been explored . Repetitive cycles of r... | Burning of fat is essential to provide energy to our bodies . However , fat metabolism is also involved in well-known diseases , such as metabolic syndrome and type 2 diabetes . In severe , inherited deficiencies of enzymes in the fatty-acid oxidation pathway , children run the risk of life-threatening low glucose leve... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biotechnology",
"chemical",
"compounds",
"enzymes",
"enzymology",
"microbiology",
"esters",
"metabolites",
"biocatalysis",
"enzyme",
"metabolism",
"mitochondria",
"bioenergetics",
"enzyme",
"inhibitors",
"cellular",
"structures",
"and",
"organelles",
"enzyme",
"chemistry",
... | 2017 | The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation |
A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010 . Nasopharyngeal swabs were collected monthly , from birth to 24 months of age , with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria ... | The nasopharynx hosts a community of microbes that first colonise us during infancy and that changes as we grow . Colonisation with certain species is a risk factor for developing respiratory infections such as pneumonia , while other species can have a protective influence . In this study we use molecular methods to i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"antimicrobials",
"children",
"medicine",
"and",
"health",
"sciences",
"microbiome",
"pathology",
"and",
"laboratory",
"medicine",
"pneumococcus",
"pathogens",
"drugs",
"microbiology",
"pulmonology",
"pneumonia",
"age",
"groups",
"antibiotics",
"corynebacteria",
"infants",
... | 2017 | A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children |
Several antimalarial drugs exist , but differences between life cycle stages among malaria species pose challenges for developing more effective therapies . To understand the diversity among stages and species , we reconstructed genome-scale metabolic models ( GeMMs ) of metabolism for five life cycle stages and five s... | Malaria kills nearly one-half million people a year and over 1 billion people are at risk of becoming infected by the parasite . Plasmodial infections are difficult to treat for a myriad of reasons , but the ability of the organism to remain latent in hosts and the complex life cycles greatly contributed to the difficu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"plasmodium",
"gametocytes",
"tropical",
"diseases",
"vertebrates",
"plasmodium",
"falciparum",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"animals",
"parasitology",
"mammals",
"germ",
"cells",
"devel... | 2018 | Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting |
Leishmania infantum causes a chronic infectious disease named visceral leishmaniasis ( VL ) . We employed a non-human primate model to monitor immune parameters over time and gain new insights into the disease . Rhesus macaques were infected with L . infantum and the T helper and B cell immunological profiles character... | We introduced a non-human primate model for visceral leishmaniasis by intravenous injection of L . infantum promastigotes in rhesus macaques and followed the animals for a period of eight months . In this model , parasites dock to the liver and spleen shortly after inoculation and remain in these visceral compartments ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"humoral",
"immunity",
"immune",
"cells",
"cytokines",
"immune",
"activation",
"immunology",
"microbiology",
"lymphoid",
"organs",
"parasitic",
"protozoans",
"developmental",
"biology",
"protozoans",
"leishmania",
"lymphatic",
"system",
"molecular",
"dev... | 2014 | Abortive T Follicular Helper Development Is Associated with a Defective Humoral Response in Leishmania infantum-Infected Macaques |
Chagas’ disease is responsible for significant mortality and morbidity in Latin America . Current treatments display variable efficacy and have adverse side effects , hence more effective , better tolerated drugs are needed . However , recent efforts have proved unsuccessful with failure of the ergosterol biosynthesis ... | Chagas’ disease is caused by the protozoan parasite Trypanosoma cruzi , and is a major health problem in Latin America . There is an urgent need for new treatments as the few currently used drugs have many serious drawbacks . New potential drugs inhibiting parasite ergosterol biosynthesis have recently failed in the cl... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"biological",
"cultures",
"tropical",
"diseases",
"microbiology",
"cloning",
"parasitic",
"diseases",
"protozoan",
"life",
"cycles",
"parasitic",
"protozoans",
"developmental",
"biology",
"trypomastigotes",
"protoz... | 2018 | Development of Trypanosoma cruzi in vitro assays to identify compounds suitable for progression in Chagas’ disease drug discovery |
We present and develop the theory of 3-way networks , a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models . We explore approaches of how to prune these 3-way networks , illustrate their utility in comparative genomics... | Genomes contain the information underlying the molecular functions of an organism . One way to compare the entire genomes of different organisms is to compare their gene-family content profiles which is effectively a comparison of their functional potential . Standard networks , when used to model phylogenomic similari... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics |
The coordinated activities at centromeres of two key cell cycle kinases , Polo and Aurora B , are critical for ensuring that the two sister kinetochores of each chromosome are attached to microtubules from opposite spindle poles prior to chromosome segregation at anaphase . Initial attachments of chromosomes to the spi... | When cells divide , their chromosomes segregate to the two daughter cells on the mitotic spindle , a dynamic macromolecular scaffold composed of microtubules . Each chromosome consists of two sister chromatids . Microtubules attach to the chromatids at structures called kinetochores , which assemble at the surface of t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"biochemistry",
"model",
"organisms",
"molecular",
"cell",
"biology",
"cell",
"division",
"cell",
"biology",
"chromosome",
"biology",
"genetics",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | The Chromosomal Passenger Complex Activates Polo Kinase at Centromeres |
Cell fate determination is usually described as the result of the stochastic dynamics of gene regulatory networks ( GRNs ) reaching one of multiple steady-states each of which corresponds to a specific decision . However , the fate of a cell is determined in finite time suggesting the importance of transient dynamics i... | Multicellular organisms , single-celled organisms , and even viruses can exhibit alternative responses to various internal and environmental conditions . At the cellular level , alternative fate determination is usually described as the result of the inherent bistability of gene regulatory networks ( GRNs ) . However ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"systems",
"biology",
"viral",
"persistence",
"and",
"latency",
"virology",
"regulatory",
"networks",
"co-infections",
"biology",
"computational",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"genetics",
"and",
"genomics"
] | 2011 | To Lyse or Not to Lyse: Transient-Mediated Stochastic Fate Determination in Cells Infected by Bacteriophages |
Venezuelan equine encephalitis ( VEE ) complex alphaviruses are important re-emerging arboviruses that cause life-threatening disease in equids during epizootics as well as spillover human infections . We conducted a comprehensive analysis of VEE complex alphaviruses by sequencing the genomes of 94 strains and performi... | The Venezuelan equine encephalitis ( VEE ) complex comprises a broadly distributed group of alphaviruses in the Americas that have the potential to emerge and cause severe disease . Historically , VEE complex viruses have caused recurring outbreaks of human and equine encephalitis in Central and South America as well a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"taxonomy",
"invertebrates",
"organismal",
"evolution",
"medicine",
"and",
"health",
"sciences",
"animal",
"diseases",
"microbiology",
"animals",
"sequence",
"assembly",
"tools",
"phylogenetics",
"data",
"management",
"phylogenetic",
"analysis",
"microbial",
"evolution",
... | 2017 | Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas |
Regular preventive chemotherapy ( PCT ) targeting high-risk populations is an effective way to control STH in the short term , but sustainable long-term STH control is expected to require improved access to water , sanitation , and hygiene ( WASH ) . However , experimental studies have not been able to conclusively dem... | Soil-transmitted helminths ( STH ) , which are transmitted via faecal contamination of the environment , still infect over 1 billion people in developing countries because of absence or poor access to improved sources of water , sanitation , and hygiene ( WASH ) . In this study , we use a mathematical model for transmi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"helminths",
"tropical",
"diseases",
"hookworms",
"parasitic",
"diseases",
"animals",
"health",
"care",
"ascaris",
"ascaris",
"lumbricoides",
"sanitation",
"neglected",
"tropical",
"diseases",
"public",
"and",
"o... | 2018 | Predicted short and long-term impact of deworming and water, hygiene, and sanitation on transmission of soil-transmitted helminths |
Dorsal closure is an epithelial remodeling process taking place during Drosophila embryogenesis . JNK signaling coordinates dorsal closure . We identify and characterize acal as a novel negative dorsal closure regulator . acal represents a new level of JNK regulation . The acal locus codes for a conserved , long , non-... | Changes in cell shape affect many critical cellular and bodily processes , like wound healing and developmental events , and when gone awry , metastatic processes in cancer . Evolutionarily conserved signaling pathways govern regulation of these cellular changes . The Jun-N-terminal kinase pathway regulates cell stretc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | acal is a Long Non-coding RNA in JNK Signaling in Epithelial Shape Changes during Drosophila Dorsal Closure |
Post-translational modifications ( PTMs ) regulate protein activity , stability and interaction profiles and are critical for cellular functioning . Further regulation is gained through PTM interplay whereby modifications modulate the occurrence of other PTMs or act in combination . Integration of global acetylation , ... | Normal cellular functioning is maintained by a vast array of macro-molecular machines that control both core and specialised molecular tasks . These machines are in large part multi-subunit protein complexes that undergo regulation at multiple levels , from expression of requisite components to a vast array of post tra... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"systems",
"biology",
"signal",
"transduction",
"signaling",
"in",
"cellular",
"processes",
"molecular",
"cell",
"biology",
"biology",
"computational",
"biology",
"signaling",
"networks"
] | 2013 | Dual Coordination of Post Translational Modifications in Human Protein Networks |
Within influenza virus infected cells , viral genomic RNA are selectively packed into progeny virions , which predominantly contain a single copy of 8 viral RNA segments . Intersegmental RNA-RNA interactions are thought to mediate selective packaging of each viral ribonucleoprotein complex ( vRNP ) . Clear evidence of ... | Influenza virus consists of eight viral ribonucleoproteins ( vRNPs ) that are assembled by infected cells to produce new virions . The process by which all eight vRNPs are assembled is not yet understood . We therefore used images from a previous study in which up to four vRNPs had been visualized in the same cell to c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"fluorescence",
"imaging",
"interaction",
"networks",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"molecular",
"probe",
"techniques",
"statistics",
"pathogens",
"microbiology",
"viral",
"structure",
"orthomyxoviruses",
"viruses",
... | 2019 | Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization |
Mammalian gene expression patterns , and their variability across populations of cells , are regulated by factors specific to each gene in concert with its surrounding cellular and genomic environment . Lentiviruses such as HIV integrate their genomes into semi-random genomic locations in the cells they infect , and th... | Cellular gene expression is a fundamentally stochastic process due to the intrinsic randomness of the underlying biochemical reactions involved . The resulting stochastically generated expression heterogeneities have important biological consequences and also encode information about the underlying dynamics that genera... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/viral",
"replication",
"and",
"gene",
"regulation",
"genetics",
"and",
"genomics/gene",
"expression",
"computational",
"biology/transcriptional",
"regulation",
"virology/mechanisms",
"of",
"resistance",
"and",
"susceptibility,",
"including",
"host",
"genetics",
"inf... | 2010 | HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency |
Protein phosphatase 2A ( PP2A ) is a prime example of the multisubunit architecture of protein serine/threonine phosphatases . Until substrate-specific PP2A holoenzymes assemble , a constitutively active , but nonspecific , catalytic C subunit would constitute a risk to the cell . While it has been assumed that the sev... | Multisubunit enzymes , such as protein phosphatase 2A , consist of a catalytic subunit and one of several regulatory subunits that are responsible for substrate specificity . Whereas this molecular architecture enables the assembly of a few components into many different substrate-specific enzymes , it possesses an inh... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"yeast",
"and",
"fungi",
"molecular",
"biology",
"saccharomyces"
] | 2007 | Generation of Active Protein Phosphatase 2A Is Coupled to Holoenzyme Assembly |
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families . We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6 . 12 million proteins predicted from an assem... | The rapidly emerging field of metagenomics seeks to examine the genomic content of communities of organisms to understand their roles and interactions in an ecosystem . Given the wide-ranging roles microbes play in many ecosystems , metagenomics studies of microbial communities will reveal insights into protein familie... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"viruses",
"computational",
"biology",
"evolutionary",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"eubacteria"
] | 2007 | The Sorcerer II Global Ocean Sampling Expedition: Expanding
the Universe of Protein Families |
The second parity rule states that , if there is no bias in mutation or selection , then within each strand of DNA complementary bases are present at approximately equal frequencies . In bacteria , however , there is commonly an excess of G ( over C ) and , to a lesser extent , T ( over A ) in the replicatory leading s... | When considering a single strand of DNA , it is not necessarily the case that the frequency of each base should equal its complementary partner , such that A = T and G = C . For the leading strand , it is typically the case that Gs are more common than Cs , and Ts more common than As . This bias is widely thought to ar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"microbial",
"mutation",
"genetic",
"mutation",
"evolutionary",
"selection",
"microbiology",
"mutational",
"hypotheses",
"mutation",
"mutation",
"types",
"microbial",
"evolution",
"forms",
"of",
"evolution",
"comparative",
"genomics",
"biology",
"evolutionary",
"genetics",
... | 2011 | Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation |
Stem cells rely on instructive cues from their environment . Alterations in microenvironments might contribute to tissue dysfunction and disease pathogenesis . Germline stem cells ( GSCs ) and cyst stem cells ( CySC ) in Drosophila testes are normally maintained in the apical area by the testicular hub . In this study ... | Proper differentiation of stem cell progeny is necessary for preservation of tissue homeostasis . In Drosophila testes , somatic cyst cells derived from the cyst stem cells ( CySCs ) control the differentiation of the neighboring germ cells . Disruption of CySC daughter cyst cell differentiation leads to failure in spe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"cloning",
"animals",
"cell",
"differentiation",
"germ",
"cells",
"c-jun",
"n-terminal",
"kinase",
"signaling",
"cascade",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"... | 2019 | Reproduction disrupts stem cell homeostasis in testes of aged male Drosophila via an induced microenvironment |
The combination of drug resistance , lack of an effective vaccine , and ongoing conflict and poverty means that malaria remains a major global health crisis . Understanding metabolic pathways at all parasite life stages is important in prioritising and targeting novel anti-parasitic compounds . The unusual heme synthes... | Combating , and ultimately eliminating , malaria requires drugs that hit the parasite at all stages of its life cycle . Deletions of parasite metabolism genes can expose where and when a certain metabolic pathway is essential , and hence vulnerable to drugs . However , once a parasite gene has been deleted , it is diff... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"heme",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"oocysts",
"plasmodium",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"animals",
"parasitology",
"developmental",
"biology",
"apicomplexa",
"protozoans",
"insect",
"vectors",
"i... | 2017 | A novel genetic technique in Plasmodium berghei allows liver stage analysis of genes required for mosquito stage development and demonstrates that de novo heme synthesis is essential for liver stage development in the malaria parasite |
G protein-coupled receptors ( GPCRs ) play crucial roles in cell physiology and pathophysiology . There is increasing interest in using structural information for virtual screening ( VS ) of libraries and for structure-based drug design to identify novel agonist or antagonist leads . However , the sparse availability o... | G protein-coupled receptors ( GPCRs ) are a major target for drug discovery . These receptors are highly dynamic membrane proteins , and have had limited tractability using with biophysical screens that are widely adopted for globular protein targets . Thus , structure-based virtual screening ( SBVS ) holds great promi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"ionic",
"binding",
"method",
"chemical",
"bonding",
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"inorganic",
"chemistry",
"ionic",
"bonding",
"condensed",
"matter",
"physics",
"multivariate",
"analysis",
"mathematics",
"statistics",
"(mathematics)",
... | 2017 | Improving virtual screening of G protein-coupled receptors via ligand-directed modeling |
Regulation of gene expression by signaling pathways often occurs through a transcriptional switch , where the transcription factor responsible for signal-dependent gene activation represses the same targets in the absence of signaling . T-cell factors ( TCFs ) are transcription factors in the Wnt/ß-catenin pathway , wh... | The DNA of cells must be correctly “read” so that the proper genes are expressed . Transcription factors are the primary “DNA readers” , and these proteins bind to specific DNA sequences . Using nematodes as a model system , we investigated the rules of DNA binding for a particular transcription factor , called POP-1 ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"developmental",
"biology",
"animal",
"genetics",
"genetics",
"biology",
"computational",
"biology"
] | 2014 | Distinct DNA Binding Sites Contribute to the TCF Transcriptional Switch in C. elegans and Drosophila |
The DNA damage response ( DDR ) is a conglomerate of pathways designed to detect DNA damage and signal its presence to cell cycle checkpoints and to the repair machinery , allowing the cell to pause and mend the damage , or if the damage is too severe , to trigger apoptosis or senescence . Various DDR branches are regu... | The cellular DNA damage response ( DDR ) network interprets the presence of replicating viral DNA genomes as DNA damage and strives to repair it , leading to inhibition of virus replication . Many DNA viruses , including adenovirus , evolved mechanisms to inhibit the DDR , thus increasing the efficiency of virus replic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"phosphorylation",
"classical",
"mechanics",
"hela",
"cells",
"biological",
"cultures",
"microbiology",
"cloning",
"dna",
"damage",
"signal",
"inhibition",
"dna",
"replication",
"cell",
"cultures",
"damage",
"mechanics",
"dna",
"molecular",
"biology",
"techniques",
"res... | 2016 | The Adenovirus E4orf4 Protein Provides a Novel Mechanism for Inhibition of the DNA Damage Response |
Release of cell surface-bound ligands by A-Disintegrin-And-Metalloprotease ( ADAM ) transmembrane metalloproteases is essential for signalling by cytokine , cell adhesion , and tyrosine kinase receptors . For Eph receptor ligands , it provides the switch between cell-cell adhesion and repulsion . Ligand shedding is tig... | The Eph transmembrane receptors are part of the receptor tyrosine kinase family and play important roles in communication between neighbouring cells . An Eph receptor binds to its ligand , membrane-tethered ephrin , on a neighbouring cell so as to form a stable complex and activate downstream signalling events . One su... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"cell",
"biology/cell",
"signaling",
"biophysics/experimental",
"biophysical",
"methods",
"cell",
"biology",
"biochemistry/cell",
"signaling",
"and",
"trafficking",
"structures",
"biochemistry/biomacromolecule-ligand",
"interactions",
"cell",
"biology/cell",
"adhesion"
] | 2009 | Cytoplasmic Relaxation of Active Eph Controls Ephrin Shedding by ADAM10 |
In China , thirteen species of tick-borne rickettsiales bacteria pathogenic to human have been reported in ticks and host animals , and human patients caused by them also has been identified . However , investigation for rickettsiales bacteria circulating in Xi’an wasn’t performed although diseases resembling human dis... | China is severely affected by rickettsial diseases caused by rickettsiales bacteria . To date , at least 13 tick-borne rickettsiales bacteria have been reported in China . In this study , we perform molecular epidemiological investigations of rickettsiales bacteria circulating in Xi’an . Through sampling in Xi’an , we ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"taxonomy",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"ixodes",
"pathology",
"and",
"laboratory",
"medicine",
"ruminants",
"pathogens",
"microbiology",
"vertebrates",
"rickettsia",
"animals",
"mammals",
"phylogenetics",
"data",
"management",
"phylogenetic",
... | 2018 | Human-pathogenic Anaplasma spp., and Rickettsia spp. in animals in Xi’an, China |
A functioning gene drive system could fundamentally change our strategies for the control of vector-borne diseases by facilitating rapid dissemination of transgenes that prevent pathogen transmission or reduce vector capacity . CRISPR/Cas9 gene drive promises such a mechanism , which works by converting cells that are ... | Gene drive systems provide a wide array of potential applications , including new strategies for the control of vector-borne diseases . For example , a functioning gene drive system could rapidly spread a genetically modified allele designed to reduce pathogen transmission throughout a vector population . The recently ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"&",
"methods"
] | [
"biotechnology",
"genome",
"engineering",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"engineering",
"and",
"technology",
"synthetic",
"biology",
"population",
"genetics",
"microbiology",
"animals",
"alleles",
"genetic",
"mapping",
"synthetic",
"bioengineering... | 2017 | Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations |
Mass drug administration ( MDA ) of antibiotics is a key component of the so-called “SAFE” strategy for trachoma control , while MDA of anthelminthics provides the cornerstone for control of a number of other neglected tropical diseases ( NTDs ) . Simultaneous delivery of two or more of these drugs , renowned as “integ... | Trachoma is one of a group of so-called “neglected tropical diseases” ( NTDs ) for which safe and effective treatments are available . The International Trachoma Initiative oversees donation of the antibiotic azithromycin to endemic countries . Delivery of this drug to communities affected by trachoma is the responsibi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"neglected",
"tropical",
"diseases",
"infectious",
"disease",
"control",
"trachoma"
] | 2011 | The Cost of Antibiotic Mass Drug Administration for Trachoma Control in a Remote Area of South Sudan |
The kinetics of recirculation of naive lymphocytes in the body has important implications for the speed at which local infections are detected and controlled by immune responses . With a help of a novel mathematical model , we analyze experimental data on migration of 51Cr-labeled thoracic duct lymphocytes ( TDLs ) via... | It is has been well established that lymphocytes , major cells of the adaptive immune system , continuously recirculate between secondary lymphoid tissues in the body such as lymph nodes , spleen , and Peyer's patches . Yet , the kinetics of lymphocyte entrance into and more importantly , residence times in these tissu... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"anatomy",
"lymphatic",
"system",
"cell",
"biology",
"animal",
"cells",
"physiology",
"biology",
"and",
"life",
"sciences",
"cellular",
"types",
"immunology",
"lymphoid",
"organs",
"... | 2014 | Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism |
Multilocus analysis of single nucleotide polymorphism haplotypes is a promising approach to dissecting the genetic basis of complex diseases . We propose a coalescent-based model for association mapping that potentially increases the power to detect disease-susceptibility variants in genetic association studies . The a... | Genetic association studies offer great promise in dissecting the genetic contribution to complex diseases . The underlying idea of such studies is to search for genetic variants along the genome that appear to be associated with a trait of interest , e . g . , disease status for a binary trait . One then proceeds by g... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics",
"none",
"genetics",
"and",
"genomics"
] | 2007 | Genetic Association Mapping via Evolution-Based Clustering of Haplotypes |
Cholera toxin B subunit ( CTB ) is a component of an internationally licensed oral cholera vaccine . The protein induces neutralizing antibodies against the holotoxin , the virulence factor responsible for severe diarrhea . A field clinical trial has suggested that the addition of CTB to killed whole-cell bacteria prov... | Cholera sporadically causes outbreaks in regions where safe water supply and sanitation systems are not sufficient . As currently available vaccines are only effective for 2 to 3 years , reactive mass vaccination has been proposed to reduce mortality during outbreaks . Cholera toxin B subunit ( CTB ) , when combined wi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"medicine",
"plant",
"biology",
"immunology",
"plant",
"science",
"neglected",
"tropical",
"diseases",
"vaccination",
"infectious",
"diseases",
"cholera",
"proteins",
"biology",
"recombinant",
"proteins",
"biochemistry",
"clinical",
"immunology",
"immunity"... | 2013 | Rapid and Scalable Plant-based Production of a Cholera Toxin B Subunit Variant to Aid in Mass Vaccination against Cholera Outbreaks |
Translation is divided into initiation , elongation , termination and ribosome recycling . Earlier work implicated several eukaryotic initiation factors ( eIFs ) in ribosomal recycling in vitro . Here , we uncover roles for HCR1 and eIF3 in translation termination in vivo . A substantial proportion of eIF3 , HCR1 and e... | Protein synthesis ( translation ) utilizes genetic information carriers , mRNAs , as templates for the production of proteins of various cellular functions . Typically it is divided into four phases: initiation , elongation , termination and ribosomal recycling . In this article we argue that the strict mechanistic sep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Translation Initiation Factors eIF3 and HCR1 Control Translation Termination and Stop Codon Read-Through in Yeast Cells |
Interleukin-32 ( IL-32 ) is expressed in lesions of patients with American Tegumentary Leishmaniasis ( ATL ) , but its precise role in the disease remains unknown . In the present study , silencing and overexpression of IL-32 was performed in THP-1-derived macrophages infected with Leishmania ( Viannia ) braziliensis o... | Leishmania ( V . ) braziliensis and L . ( L . ) amazonensis are protozoa that infect macrophages and cause cutaneous and mucosal leishmaniasis . Here we showed that both Leishmania species induce the production of IL-32γ in human macrophages . This intracellular and pro-inflammatory cytokine mediates the production of ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"transfection",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"gene",
"regulation",
"immunology",
"messenger",
"rna",
"microbiology",
"parasitic",
"diseases",
"parasitic",... | 2017 | Cytokines and microbicidal molecules regulated by IL-32 in THP-1-derived human macrophages infected with New World Leishmania species |
Dopamine release in the striatum has been implicated in various forms of reward dependent learning . Dopamine leads to production of cAMP and activation of protein kinase A ( PKA ) , which are involved in striatal synaptic plasticity and learning . PKA and its protein targets are not diffusely located throughout the ne... | The striatum is a part of the basal ganglia which plays a role in addiction and reward learning . Its importance is underscored by pathologies such as Parkinson's disease and Huntington's disease in which degeneration of the dopamine inputs to the striatum or degeneration of neurons in the striatum , respectively , pro... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"computational",
"biology",
"neuroscience"
] | 2012 | Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites |
Intracellular proteins tagged with ubiquitin chains are targeted to the 26S proteasome for degradation . The two subunits , Rpn10 and Rpn13 , function as ubiquitin receptors of the proteasome . However , differences in roles between Rpn10 and Rpn13 in mammals remains to be understood . We analyzed mice deficient for Rp... | At least two major ubiquitin receptor subunits that directly capture ubiquitin chains have been identified in the proteasome: Rpn10 and Rpn13 . Analyses in Saccharomyces cerevisiae have suggested only a modest role of Rpn10 and Rpn13 in the recruitment of ubiquitinated proteins , as double deletion of Rpn10 and Rpn13 c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Redundant Roles of Rpn10 and Rpn13 in Recognition of Ubiquitinated Proteins and Cellular Homeostasis |
Measles virus ( MV ) is among the most infectious viruses that affect humans and is transmitted via the respiratory route . In macaques , MV primarily infects lymphocytes and dendritic cells ( DCs ) . Little is known about the initial target cell for MV infection . Since DCs bridge the peripheral mucosal tissues with l... | Despite the availability of an effective vaccine , measles virus ( MV ) is still a major cause of childhood morbidity and mortality in developing countries . Almost all non-vaccinated children catch the highly contagious virus during an MV outbreak . This suggests an efficient route for primary infection . However , th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"immunology/immunomodulation",
"immunology/antigen",
"processing",
"and",
"recognition",
"virology/host",
"invasion",
"and",
"cell",
"entry"
] | 2008 | DC-SIGN and CD150 Have Distinct Roles in Transmission of Measles Virus from Dendritic Cells to T-Lymphocytes |
A central task in the analysis of human movement behavior is to determine systematic patterns and differences across experimental conditions , participants and repetitions . This is possible because human movement is highly regular , being constrained by invariance principles . Movement timing and movement path , in pa... | When you move a cup to a new location on a table , the movement of lifting , transporting , and setting down the cup appears to be completely automatic . Although the hand could take continuously many different paths and move on any temporal trajectory , real movements are highly regular and reproducible . From repetit... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"acceleration",
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"applied",
"mathematics",
"social",
"sciences",
"random",
"variables",
"human",
"mobility",
"covariance",
"factor",
"analysis",
"simulation",
"and",
"modeling",
"algorithms",
"mathematics",... | 2016 | Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement |
The evolutionary conserved WD-40 protein PRL1 plays important roles in immunity and development . Here we show that PRL1 is required for the accumulation of microRNAs ( miRNAs ) and small interfering RNAs ( siRNAs ) . PRL1 positively influences the processing of miRNA primary transcripts ( pri-miRNAs ) and double-stran... | PRL1 , a conserved WD-40 protein , is required for plant development and immune responses . However , its functional mechanisms are not well understood . Here , we show the positive impact of PRL1 on the accumulation of miRNAs and siRNAs , which are key regulators of plant growth and immunity . PRL1 interacts with mult... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"interference",
"genetics",
"epigenetics",
"biology",
"and",
"life",
"sciences",
"plant-mediated",
"rna",
"interference"
] | 2014 | PRL1, an RNA-Binding Protein, Positively Regulates the Accumulation of miRNAs and siRNAs in Arabidopsis |
The transmission networks of Plasmodium vivax characterize how the parasite transmits from one location to another , which are informative and insightful for public health policy makers to accurately predict the patterns of its geographical spread . However , such networks are not apparent from surveillance data becaus... | The transmission of Plasmodium vivax has induced enormous public health problems at the global level . Natural transmission of P . vivax depends on interactions between anopheles mosquitoes and human beings . There are two important factors that influence its geographical spread . First , different locations may have d... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"A",
"recurrent",
"neural",
"network",
"model",
"Data",
"collection",
"and",
"parameter",
"settings",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"computer",
"science",
"computer",
"modeling",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"spatial",
"epidemiology",
"infectious",
"disease",
"modeling"
] | 2014 | Inferring Plasmodium vivax Transmission Networks from Tempo-Spatial Surveillance Data |
Human rhinovirus ( RV ) infections are the principle cause of common colds and precipitate asthma and COPD exacerbations . There is currently no RV vaccine , largely due to the existence of ∼150 strains . We aimed to define highly conserved areas of the RV proteome and test their usefulness as candidate antigens for a ... | Human rhinovirus infections cause the majority of common colds as well as asthma and chronic obstructive pulmonary disease ( COPD ) exacerbations . The disease burden attributable to rhinoviruses is therefore huge . Despite this and the fact that human rhinoviruses were discovered over 50 years ago , there are currentl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Cross-Serotype Immunity Induced by Immunization with a Conserved Rhinovirus Capsid Protein |
The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology . This is partially due to the complexity of the process , involving extensive molecular networks , multiple feedbacks between different scales of organization a... | In recent years , much research in molecular and developmental biology has been devoted to unravelling the mechanisms that govern the development of living systems . This includes the identification of key molecular networks that control shape formation and their response to hormonal regulation . However , a key challe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"tissue",
"mechanics",
"developmental",
"biology",
"computer",
"and",
"information",
"sciences",
"plant",
"development",
"floral",
"development",
"plant",
"growth",
"and",
"development",
"biology",
"and",
"life",
"sciences",
"computerized",
"simulations",
"biomechanics"
] | 2015 | A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution |
Eukaryotic genes are typically split into exons that need to be spliced together to form the mature mRNA . The splicing process depends on the dynamics and interactions among transcription by the RNA polymerase II complex ( RNAPII ) and the spliceosomal complex consisting of multiple small nuclear ribonucleo proteins (... | The DNA encoding most eukaryotic genes is interrupted by long sequences called introns . These introns need to be removed through the process of splicing to produce the mature messenger RNA . The process of splicing plays a critical role in determining the exact aminoacid content of the ensuing protein . Several molecu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"rna",
"synthesis",
"theoretical",
"biology",
"biophysics",
"theory",
"biology",
"biophysics",
"physics",
"microarrays",
"rna",
"systems",
"biology",
"rna",
"processing",
"nucleic",
"acids",
"genomics",
"computational",
"biology",
"ge... | 2012 | Theory on the Coupled Stochastic Dynamics of Transcription and Splice-Site Recognition |
During development , sensory neurons must choose identities that allow them to detect specific signals and connect with appropriate target neurons . Ultimately , these sensory neurons will successfully integrate into appropriate neural circuits to generate defined motor outputs , or behavior . This integration requires... | How do individual neurons know what type of a circuit they must integrate into ? To correctly assemble neural circuits during development , the identities of neurons must be coordinated with the identities of the circuits into which they will be integrated . How is this process regulated ? We have used the olfactory ci... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"gene",
"regulation",
"neuroscience",
"animals",
"animal",
"models",
"drosophila",
"melanogaster",
"animal",
"anatomy",
"model",
"organisms",
"antennae",
"(animal",
"physiology)",
"zoology",
... | 2016 | Chromatin Modulatory Proteins and Olfactory Receptor Signaling in the Refinement and Maintenance of Fruitless Expression in Olfactory Receptor Neurons |
Venezuelan equine encephalitis ( VEE ) is a reemerging , mosquito-borne viral disease of the neotropics that is severely debilitating and sometimes fatal to humans . Periodic epidemics mediated by equine amplification have been recognized since the 1920s , but interepidemic disease is rarely recognized . We report here... | Venezuelan equine encephalitis ( VEE ) is a mosquito-borne viral disease that has caused major epidemics in many parts of Latin America and has even spread into Texas on one occasion . These epidemics result from spillover to humans of a horse-mosquito-horse amplification cycle that has occurred periodically since the ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/infectious",
"diseases",
"of",
"the",
"nervous",
"system",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"virology/virus",
"evolution",
"and",
"symbiosis",
"neurological",
"disorders/infectious",
"diseases",
"of",
"the",
"nervo... | 2009 | Venezuelan Equine Encephalitis in Panama: Fatal Endemic Disease and Genetic Diversity of Etiologic Viral Strains |
The basal ganglia is a brain region critically involved in reinforcement learning and motor control . Synaptic plasticity in the striatum of the basal ganglia is a cellular mechanism implicated in learning and neuronal information processing . Therefore , understanding how different spatio-temporal patterns of synaptic... | Change in the strength of connections between brain cells in the basal ganglia is a mechanism implicated in learning and information processing . Learning to associate a sensory input or motor action with reward likely causes certain patterns of input to strengthen connections , a phenomenon known as long term potentia... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cellular",
"neuroscience",
"computational",
"neuroscience",
"biology",
"computational",
"biology",
"signaling",
"networks",
"neuroscience"
] | 2013 | Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity |
Advances in scientific computing have allowed the development of complex models that are being routinely applied to problems in disease epidemiology , public health and decision making . The utility of these models depends in part on how well they can reproduce empirical data . However , fitting such models to real wor... | An increasing number of scientific disciplines , and biology in particular , rely on complex computational models . The utility of these models depends on how well they are fitted to empirical data . Fitting is achieved by searching for suitable values for the models' input parameters , in a process known as calibratio... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"statistics",
"(mathematics)",
"physical",
"sciences",
"statistical",
"methods"
] | 2015 | Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda |
Knowledge of social contact patterns still represents the most critical step for understanding the spread of directly transmitted infections . Data on social contact patterns are , however , expensive to obtain . A major issue is then whether the simulation of synthetic societies might be helpful to reliably reconstruc... | Data on social contact patterns are fundamental to design adequate control policies for directly transmissible infectious diseases , ranging from a flu pandemic to tuberculosis , to recurrent epidemics of childhood diseases . Most countries in the world do not dispose of such data . We propose an approach to generate s... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/viral",
"infections",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases",
"mathematics/statistics"
] | 2010 | Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data |
Broadly neutralizing HIV antibodies ( bnAbs ) are typically highly somatically mutated , raising doubts as to whether they can be elicited by vaccination . We used 454 sequencing and designed a novel phylogenetic method to model lineage evolution of the bnAbs PGT121–134 and found a positive correlation between the leve... | A majority of the over 30 million HIV-1 infected individuals worldwide live in poorly resourced areas where multiple boost strategies , which are likely needed to generate highly mutated antibodies , present formidable logistical challenges . Accordingly , developing new vaccination strategies that are capable of gener... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies |
Autosomal recessive mutations in the cytolinker protein plectin account for the multisystem disorders epidermolysis bullosa simplex ( EBS ) associated with muscular dystrophy ( EBS-MD ) , pyloric atresia ( EBS-PA ) , and congenital myasthenia ( EBS-CMS ) . In contrast , a dominant missense mutation leads to the disease... | Hemidesmosomes are specialized protein complexes that promote anchorage of the basal keratinocyte cell layer of the epidermis to the underlying dermis . They provide tissue integrity and resistance to mechanical forces . When hemidesmosomes do not function properly , skin blistering ensues in response to mechanical tra... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"skin",
"medicine",
"dermatology",
"cellular",
"structures",
"animal",
"genetics",
"bullous",
"disorders",
"macromolecular",
"assemblies",
"anatomy",
"and",
"physiology",
"skin",
"physiology",
"animal",
"models",
"model",
"organisms",
"integrins",
"cytoskeleton",
"protein... | 2011 | Targeted Proteolysis of Plectin Isoform 1a Accounts for Hemidesmosome Dysfunction in Mice Mimicking the Dominant Skin Blistering Disease EBS-Ogna |
Short-term synaptic depression , caused by depletion of releasable neurotransmitter , modulates the strength of neuronal connections in a history-dependent manner . Quantifying the statistics of synaptic transmission requires stochastic models that link probabilistic neurotransmitter release with presynaptic spike-trai... | Synapses between neurons transmit signals with strengths that vary with the history of their activity , over scales from milliseconds to decades . Short-term changes in synaptic strength modulate and sculpt ongoing neuronal activity , whereas long-term changes underpin memory formation . Here we focus on changes of str... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"fourier",
"analysis",
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"nervous",
"system",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"cellular",
"structures",
"and",
"organelles",
"mood",
"disorders",
"research",
"and",
... | 2018 | Transmission of temporally correlated spike trains through synapses with short-term depression |
Modern enzymes are highly optimized biocatalysts that process their substrates with extreme efficiency . Many enzymes catalyze more than one reaction; however , the persistence of such ambiguities , their consequences and evolutionary causes are largely unknown . As a paradigmatic case , we study the history of bi-func... | The term exaptation describes the process by which a trait that is initially just a by-product of another function may become important in a later evolutionary phase . For example , feathers served to insulate dinosaurs before helping birds fly . On the level of enzymes , bi-functionality can contribute to microbial ev... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"taxonomy",
"organismal",
"evolution",
"enzymes",
"enzymology",
"microbiology",
"cloning",
"phylogenetics",
"data",
"management",
"phylogenetic",
"analysis",
"enzyme",
"metabolism",
"microbial",
"evolution",
"sequence",
"motif",
"analysis",
"mole... | 2016 | Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation |
Metazoan development requires complex mechanisms to generate cells with diverse function . Alternative splicing of pre-mRNA not only expands proteomic diversity but also provides a means to regulate tissue-specific molecular expression . The N-Cadherin gene in Drosophila contains three pairs of mutually-exclusive alter... | Animal development requires complex mechanisms to generate many different types of cells . Alternative splicing is a process by which a single gene could produce several protein variants under particular circumstances . It is a useful means to generate a diversified set of proteins in different cell types . In this rep... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/rna",
"splicing",
"cell",
"biology/gene",
"expression"
] | 2009 | Conserved Alternative Splicing and Expression Patterns of Arthropod N-Cadherin |
Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities . Several bioinformatic tools can be used to functionally annotate metagenomes , allowing researchers to draw inferences about the functional potential of the community and to identi... | Microbial communities perform a wide variety of functions , from marine photosynthesis to aiding digestion in the human gut . Shotgun “metagenomic” sequencing can be used to sample millions of short DNA sequences from such communities directly , without needing to first culture its constituents in the laboratory . Usin... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes |
Upon recognition of pathogen virulence effectors , plant nucleotide-binding leucine-rich repeat ( NLR ) proteins induce defense responses including localized host cell death . In an effort to understand the molecular mechanisms leading to this response , we examined the Arabidopsis thaliana NLR protein RECOGNITION OF P... | Many plant pathogens inject proteins known as effectors into the cells of their hosts in order to suppress host immune responses and promote pathogen growth . Over time , plants have evolved receptors , described as nucleotide-binding leucine-rich repeat ( NLR ) proteins , which recognize the activity of pathogen effec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"protein",
"interactions",
"molecular",
"mass",
"cell",
"processes",
"protein",
"expression",
"plant",
"science",
"immunoprecipitation",
"co-immunoprecipitation",
"molecular",
"biology",
"techniques",
"photosynthesis",
"ribulose-1,5-bisphosphate",
"carboxylase"... | 2016 | Multiple Domain Associations within the Arabidopsis Immune Receptor RPP1 Regulate the Activation of Programmed Cell Death |
Parasitic worms alter their host's immune system to diminish the inflammatory responses directed against them , using very efficient immunomodulating molecules . We have previously shown that the helminth immunomodulator cystatin ( AvCystatin ) profoundly reduces the progression of inflammatory diseases via modulation ... | Helminths have the ability to interfere with their host's immune response , thus downregulating inflammatory responses . We previously demonstrated the role of helminth infections or isolated helminth proteins in suppressing bystander immune responses in mouse models of allergy and colitis via a macrophage and IL-10 de... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/leukocyte",
"signaling",
"and",
"gene",
"expression",
"immunology/immunomodulation",
"molecular",
"biology/bioinformatics",
"infectious",
"diseases/helminth",
"infections"
] | 2011 | A Helminth Immunomodulator Exploits Host Signaling Events to Regulate Cytokine Production in Macrophages |
MHC class Ia-restricted CD8+ T cells are important mediators of the adaptive immune response against infections caused by intracellular microorganisms . Whereas antigen-specific effector CD8+ T cells can clear infection caused by intracellular pathogens , in some circumstances , the immune response is suboptimal and th... | Killer lymphocytes are important mediators of the immunological resistance against infections caused by virus , bacteria and parasites . In some circumstances , however , these lymphocytes are unable to properly eliminate the microorganisms which survive , causing death or establishing chronic infections . The purpose ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunizations",
"adaptive",
"immunity",
"immune",
"cells",
"immunity",
"t",
"cells",
"immunology",
"biology",
"immune",
"deficiency",
"microbiology",
"immunomodulation",
"host-pathogen",
"interaction",
"pathogenesis"
] | 2012 | Pathogen-Induced Proapoptotic Phenotype and High CD95 (Fas) Expression Accompany a Suboptimal CD8+ T-Cell Response: Reversal by Adenoviral Vaccine |
Poly ( A ) Binding Protein Nuclear 1 ( PABPN1 ) is a multifunctional regulator of mRNA processing , and its expression levels specifically decline in aging muscles . An expansion mutation in PABPN1 is the genetic cause of oculopharyngeal muscle dystrophy ( OPMD ) , a late onset and rare myopathy . Moreover , reduced PA... | PABPN1 is a multifunctional regulator of mRNA processing and its levels are reduced in skeletal muscles from midlife onwards . Reduced PABPN1 levels in a mouse model causes muscle atrophy and muscle fiber switches . We show that PABPN1-regulated muscle atrophy is regulated , in part , by up regulation of Atrogin1 and r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"atrophy",
"skeletal",
"muscles",
"biological",
"cultures",
"muscle",
"proteins",
"signs",
"and",
"symptoms",
"stem",
"cells",
"cell",
"cultures",
"resear... | 2016 | PABPN1-Dependent mRNA Processing Induces Muscle Wasting |
During meiosis homologous chromosomes pair , recombine , and synapse , thus ensuring accurate chromosome segregation and the halving of ploidy necessary for gametogenesis . The processes permitting a chromosome to pair only with its homologue are not fully understood , but successful pairing of homologous chromosomes i... | Meiosis is a specialised cell division that acts to halve the chromosome complement , or ploidy , in the production of gametes for sexual reproduction in eukaryotes . To ensure that each gamete has a full complement of the genetic material , homologous chromosomes must pair and then separate in a coordinated manner dur... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"meiosis",
"genomics",
"nucleic",
"acids",
"chromosome",
"biology",
"dna",
"biology",
"dna",
"recombination",
"genetics",
"and",
"genomics"
] | 2012 | Differing Requirements for RAD51 and DMC1 in Meiotic Pairing of Centromeres and Chromosome Arms in Arabidopsis thaliana |
Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development , cell–cell signaling , and social behavior . Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes , but the nature of variation w... | Theories on the evolution of cooperation sometimes hinge on knowledge of genetic relatedness between individuals . Dictyostelium discoideum has been a model for the study of key biological phenomena , including the evolution and ecology of social cooperation , but the nature of genetic variation within this species is ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"ecology/behavioral",
"ecology"
] | 2010 | Variation, Sex, and Social Cooperation: Molecular Population Genetics of the Social Amoeba Dictyostelium discoideum |
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