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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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Bcl-w belongs to the prosurvival group of the Bcl-2 family , while the glutamate receptor δ2 ( Grid2 ) is an excitatory receptor that is specifically expressed in Purkinje cells , and required for Purkinje cell synapse formation . A recently published result as well as our own findings have shown that Bcl-w can physica... | A neuron cell is composed of cell body , axons , and dendrites . Dendritic spines on dendrites form synapses with axons of other neurons , establishing communication between neuron cells . Dendrite development and synapse formation are therefore important for neuronal function . Although many genes have been previously... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"neuroscience/motor",
"systems",
"neuroscience/neurodevelopment",
"neuroscience/neuronal",
"signaling",
"mechanisms",
"neuroscience"
] | 2008 | Mitochondrial Morphogenesis, Dendrite Development, and Synapse Formation in Cerebellum Require both Bcl-w and the Glutamate Receptor δ2 |
Central regulators of cell fate , or selector genes , establish the identity of cells by direct regulation of large cohorts of genes . In Caenorhabditis elegans , foregut ( or pharynx ) identity relies on the FoxA transcription factor PHA-4 , which activates different sets of target genes at various times and in divers... | Central regulators of cell fate establish the identity of cells by direct regulation of large cohorts of genes . In Caenorhabditis elegans , foregut ( or pharynx ) identity relies on the FoxA transcription factor PHA-4 , which activates different target genes in different cellular environments . An outstanding question... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/embryology",
"developmental",
"biology",
"molecular",
"biology/transcription",
"initiation",
"and",
"activation",
"developmental",
"biology/cell",
"differentiation",
"developmental",
"biology/organogenesis"
] | 2010 | Dynamic Chromatin Organization during Foregut Development Mediated by the Organ Selector Gene PHA-4/FoxA |
Members of the APOBEC3 family of deoxycytidine deaminases counteract a broad range of retroviruses in vitro through an indirect mechanism that requires virion incorporation and inhibition of reverse transcription and/or hypermutation of minus strand transcripts in the next target cell . The selective advantage to the h... | Members of the APOBEC3 gene family can potently inhibit a broad range of retroviruses , including HIV-1 . In cell culture , APOBEC3 counteracts retroviruses by: ( 1 ) reducing the infectivity of virions; and ( 2 ) inducing lethal G-to-A hypermutation in the next target cell . The selective advantage to the host of an ‘... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"humoral",
"immunity",
"animal",
"models",
"of",
"infection",
"viral",
"vaccines",
"mechanisms",
"of",
"resistance",
"and",
"susceptibility",
"immunity",
"virology",
"innate",
"immunity",
"immune",
"defense",
"biology",
"microbiology",
"viral",
"evolution",
"pathogenesi... | 2011 | Noninfectious Retrovirus Particles Drive the Apobec3/Rfv3 Dependent Neutralizing Antibody Response |
Endosymbiotic Wolbachia bacteria are potent modulators of pathogen infection and transmission in multiple naturally and artificially infected insect species , including important vectors of human pathogens . Anopheles mosquitoes are naturally uninfected with Wolbachia , and stable artificial infections have not yet suc... | Infection with Wolbachia bacteria has been shown to reduce pathogen levels in multiple mosquito species . Anopheles mosquitoes ( the obligate vectors of human malaria ) are naturally uninfected with Wolbachia , and stable artificial infections have not yet succeeded in this genus; however somatic infections can be esta... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"medicine",
"biochemistry",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"ecology",
"global",
"health",
"genetics",
"immunology",
"biology",
"microbiology",
"molecular",
"cell",
"biology",
"public",
"health",
"genetics",
"and",
"... | 2011 | Wolbachia Infections Are Virulent and Inhibit the Human Malaria Parasite Plasmodium Falciparum in Anopheles Gambiae |
The role of secondary metabolites in the determination of cell identity has been an area of particular interest over recent years , and studies strongly indicate a connection between cell fate and the regulation of enzymes involved in secondary metabolism . In Arabidopsis thaliana , the maternally derived seed coat pla... | Plant secondary metabolites accumulate in seeds to protect the developing embryo . Using an RNA sequencing approach in conjunction with enrichment analyses we identified the homeotic MADS-domain gene SEEDSTICK ( STK ) as a regulator of metabolic processes during seed development . We analyzed the role of STK as a key r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"plant",
"science",
"cell",
"biology",
"plant",
"development",
"plant",
"growth",
"and",
"development",
"plant",
"cell",
"biology",
"biology",
"and",
"life",
"sciences",
"molecular",
"cell",
"biology",
"molecular",
"biology"
] | 2014 | SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat |
There is an intense debate concerning whether selection or demographics has been most important in shaping the sequence variation observed in modern human mitochondrial DNA ( mtDNA ) . Purifying selection is thought to be important in shaping mtDNA sequence evolution , but the strength of this selection has been debate... | Mammalian mitochondrial DNA ( mtDNA ) is maternally transmitted and does not undergo bi-parental recombination in the germ line . This asexual mode of transmission , together with a high rate of mutation , should eventually lead to the accumulation of numerous deleterious mtDNA mutations and a “mutational meltdown” ( a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"evolutionary",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2008 | Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA |
Reversion and spread of vaccine-derived poliovirus ( VDPV ) to cause outbreaks of poliomyelitis is a rare outcome resulting from immunisation with the live-attenuated oral poliovirus vaccines ( OPVs ) . Global withdrawal of all three OPV serotypes is therefore a key objective of the polio endgame strategic plan , start... | Global , coordinated withdrawal of serotype-2 OPV ( OPV2 ) is planned for April 2016 and will mark a major milestone for the Global Polio Eradication Initiative ( GPEI ) . Because OPV2 withdrawal will leave cohorts of young children susceptible to serotype-2 poliovirus , minimising the risk of new serotype-2 vaccine-de... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"children",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"geographical",
"locations",
"microbiology",
"mathematical",
"models",
"viruses",
"preventive",
"medicine",
"vaccines",
"age",
"groups",
"rna",
... | 2016 | Preventing Vaccine-Derived Poliovirus Emergence during the Polio Endgame |
Cellular heterogeneity , which plays an essential role in biological phenomena , such as drug resistance and migration , is considered to arise from intrinsic ( i . e . , reaction kinetics ) and extrinsic ( i . e . , protein variability ) noise in the cell . However , the mechanistic effects of these types of noise to ... | Individual cell behaviors are controlled by a variety of noise , such as fluctuations in biochemical reactions , protein variability , molecular diffusion , transcriptional noise , cell-to-cell contact , temperature , and pH . Such cellular noise often interferes with signal responses from external stimuli , and such h... | [
"Abstract",
"Introduction",
"Model",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"phosphorylation",
"egfr",
"signaling",
"mathematical",
"models",
"simulation",
"and",
"modeling",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
"methods",
"erk",
"signaling",
"cascade",
"proteins",
"mathematical",
"and",
"statistical",
"... | 2016 | Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway |
Association testing of multiple correlated phenotypes offers better power than univariate analysis of single traits . We analyzed 6 , 600 individuals from two population-based cohorts with both genome-wide SNP data and serum metabolomic profiles . From the observed correlation structure of 130 metabolites measured by n... | In this study , we aim to identify novel genetic variants for metabolism , characterize their effects on nearby genes , and show that the nearby genes are associated with metabolism and atherosclerosis . To discover new genetic variants , we use an alternative approach to traditional genome-wide association studies: we... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"systems",
"biology",
"medicine",
"gene",
"expression",
"genetics",
"atherosclerosis",
"biology",
"genetics",
"and",
"genomics",
"cardiovascular"
] | 2012 | Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis |
Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways , and represent potential vulnerabilities that can be therapeutically exploited . Here we describe an RNA interference ( RNAi ) –based synthetic interaction screen to identify genes preferenti... | The conversion of a normal cell into a cancer cell involves activating genes that promote cancer growth ( oncogenes ) and/or inactivating genes that normally act to inhibit cancer growth ( tumor suppressor genes ) . The tumor suppressor gene p53 is the most frequently mutated gene in human cancers , being inactivated i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"functional",
"genomics",
"rna",
"interference",
"protein",
"interactions",
"dna-binding",
"proteins",
"dna",
"transcription",
"gene",
"function",
"animal",
"models",
"mitosis",
"model",
"organisms",
"cell",
"division",
"proteins",
"gene",
"expression",
"biology",
"mous... | 2012 | A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells |
Human T-cell leukemia virus type 1 ( HTLV-1 ) causes adult T-cell leukemia-lymphoma ( ATL ) and inflammatory diseases . To enhance cell-to-cell transmission of HTLV-1 , the virus increases the number of infected cells in vivo . HTLV-1 bZIP factor ( HBZ ) is constitutively expressed in HTLV-1 infected cells and ATL cell... | Since HTLV-1 infects only through cell-to-cell transmission , increasing the number of infected cells is critical for transmission of HTLV-1 . Proliferation of HTLV-1 infected cells is critical for development of leukemia and inflammatory diseases . In this study , we showed that HBZ promotes the proliferation of infec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"cd",
"coreceptors",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"rna",
"... | 2017 | HTLV-1 bZIP Factor Enhances T-Cell Proliferation by Impeding the Suppressive Signaling of Co-inhibitory Receptors |
HSPB7 is a member of the small heat-shock protein ( HSPB ) family and is expressed in the cardiomyocytes from cardiogenesis onwards . A dramatic increase in HSPB7 is detected in the heart and blood plasma immediately after myocardial infarction . Additionally , several single-nucleotide polymorphisms of HSPB7 have been... | The intercalated disc is an indispensable structure that connects neighboring cardiomyocytes . It is also considered to be a single functional unit for cellular electric , mechanical , and signaling communication to maintain cardiomyocyte rigidity and synchrony . Mutation or defect in intercalated disc components usual... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"myofibrils",
"muscle",
"tissue",
"cardiovascular",
"anatomy",
"nervous",
"system",
"molecular",
"probe",
"techniques",
"junctional",
"complexes",
"electrophysiology",
"cloning",
"neuroscience",
"animal",
"mod... | 2017 | HSPB7 prevents cardiac conduction system defect through maintaining intercalated disc integrity |
Lifelong persistence of Epstein-Barr virus ( EBV ) in infected hosts is mainly owed to the virus' pronounced abilities to evade immune responses of its human host . Active immune evasion mechanisms reduce the immunogenicity of infected cells and are known to be of major importance during lytic infection . The EBV genes... | Despite strong cellular and humoral immune responses , herpesviruses persist in their hosts for a lifetime . Epstein-Barr virus ( EBV ) is a herpesvirus that infects human B cells . This results in a latent infection where only a minimal set of viral proteins is expressed and infected cells cannot be eradicated by immu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"medicine",
"immune",
"evasion",
"basic",
"cancer",
"research",
"virology",
"biology",
"microbiology"
] | 2012 | The EBV Immunoevasins vIL-10 and BNLF2a Protect Newly Infected B Cells from Immune Recognition and Elimination |
Zika virus ( ZIKV ) is a mosquito-borne positive sense RNA virus . Recently , ZIKV emerged into the Western hemisphere as a human health threat , with severe disease associated with developmental and neurological complications . The structural envelope protein of ZIKV and other neurotropic flaviviruses contains an exte... | Zika virus ( ZIKV ) is a mosquito-transmitted virus that was recently introduced in Brazil and subsequently spread throughout the Americas . ZIKV is highly similar to the related dengue virus but causes unique disease outcomes including neurological disease in adults and fetal developmental complications . The ZIKV env... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"microbial",
"mutation",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"nervous",
"system",
"pathogens",
"immunology",
"microbiology",
"viruses",
"mutation",
"substitution",
... | 2019 | Shortening of Zika virus CD-loop reduces neurovirulence while preserving antigenicity |
Infection with Plasmodium vivax results in strong activation of monocytes , which are important components of both the systemic inflammatory response and parasite control . The overall goal of this study was to define the role of monocytes during P . vivax malaria . Here , we demonstrate that P . vivax–infected patient... | Malaria , caused by a protozoa parasite , Plasmodium , affects more than 200 million people per year . The infection triggers an acute febrile illness , the paroxysms , occurring every 48 or 72 hours depending on the species . Plasmodium vivax , in most cases , does not cause severe malaria , but it is the most geograp... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immune",
"response",
"biology",
"and",
"life",
"sciences",
"immunology"
] | 2014 | The CD14+CD16+ Inflammatory Monocyte Subset Displays Increased Mitochondrial Activity and Effector Function During Acute Plasmodium vivax Malaria |
An epidemiological study of leishmaniasis was performed in Amazonian areas of Ecuador since little information on the prevalent Leishmania and sand fly species responsible for the transmission is available . Of 33 clinical specimens from patients with cutaneous leishmaniasis ( CL ) , causative parasites were identified... | In Ecuador , leishmaniasis is endemic in Pacific coast subtropical , Amazonian , and Andean highland areas . Seven Leishmania species , Leishmania ( Leishmania ) mexicana , L . ( L . ) amazonensis , L . ( L . ) major-like , Leishmania ( Viannia ) guyanensis , L . ( V . ) panamensis , L . ( V . ) braziliensis , and L . ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"ecuador",
"tropical",
"diseases",
"geographical",
"locations",
"sand",
"flies",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"leishmania",
"phylogenetic",
"analysis",
"neglected",
"... | 2016 | First Human Cases of Leishmania (Viannia) lainsoni Infection and a Search for the Vector Sand Flies in Ecuador |
Yersinia pseudotuberculosis binds to β1 integrin receptors , and uses the type III secretion proteins YopB and YopD to introduce pores and to translocate Yop effectors directly into host cells . Y . pseudotuberculosis lacking effectors that inhibit Rho GTPases , YopE and YopT , have high pore forming activity . Here , ... | The type III secretion system ( TTSS ) is essential for the virulence of a number of Gram-negative human pathogens of enormous clinical significance . The molecular mechanisms by which TTSS effector proteins are translocated into the host cell are not well understood . The work presented here proposes a new model in wh... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"microbiology",
"homo",
"(human)",
"eubacteria"
] | 2008 | Yersinia Controls Type III Effector Delivery into Host Cells by Modulating Rho Activity |
Hydrophobins , produced by filamentous fungi , are small amphipathic proteins whose biological functions rely on their unique surface-activity properties . Understanding the mechanistic details of the multimerization process is of primary importance to clarify the interfacial activity of hydrophobins . We used free ene... | Fungi proliferate by creating a complex hyphal network growing within a wet environment . However , for most fungi to colonize new territories , they must produce spores carried by aerial hyphae and spread them into the air . Aerial structures need to overcome the surface tension of the surrounding water in order to gr... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"dimers",
"(chemical",
"physics)",
"chemical",
"bonding",
"crystal",
"structure",
"electricity",
"condensed",
"matter",
"physics",
"fungal",
"structure",
"electrostatics",
"crystallography",
"thermodynamics",
"hydrogen",
"bonding",
"physical",
"chemistry",
"mycology",
"soli... | 2016 | Induced Fit in Protein Multimerization: The HFBI Case |
Two-component signal transduction pathways comprising histidine protein kinases ( HPKs ) and their response regulators ( RRs ) are widely used to control bacterial responses to environmental challenges . Some bacteria have over 150 different two-component pathways , and the specificity of the phosphotransfer reactions ... | The ability to respond to environmental stimuli is a universal feature of living cells . Evolution has created a vast array of signalling mechanisms that enable cells to react in many ways to extracellular changes . In bacteria , two-component signalling mechanisms , comprising a sensor protein kinase paired with its a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry/cell",
"signaling",
"and",
"trafficking",
"structures",
"cell",
"biology/cell",
"signaling"
] | 2010 | Using Structural Information to Change the Phosphotransfer Specificity of a Two-Component Chemotaxis Signalling Complex |
During infection by invasive bacteria , epithelial cells contribute to innate immunity via the local secretion of inflammatory cytokines . These are directly produced by infected cells or by uninfected bystanders via connexin-dependent cell-cell communication . However , the cellular pathways underlying this process re... | Epithelial cells line internal body cavities of multicellular organisms . They represent the first line of defense against various pathogens including bacteria and viruses . They can sense the presence of invasive pathogens and initiate the recruitment of immune cells to infected tissues via the local secretion of solu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"hela",
"cells",
"gene",
"regulation",
"pathogens",
"biological",
"cultures",
"immunology",
"microbiology",
"shigell... | 2017 | ALPK1 controls TIFA/TRAF6-dependent innate immunity against heptose-1,7-bisphosphate of gram-negative bacteria |
Several infrequent genetic polymorphisms in the SERPINA1 gene are known to substantially reduce concentration of alpha1-antitrypsin ( AAT ) in the blood . Since low AAT serum levels fail to protect pulmonary tissue from enzymatic degradation , these polymorphisms also increase the risk for early onset chronic obstructi... | Low levels of alpha1-antitrypsin ( AAT ) in the blood are a well-established risk factor for accelerated loss in lung function and chronic obstructive pulmonary disease . While a few infrequent genetic polymorphisms are known to influence the serum levels of this enzyme , the role of common genetic variants has not bee... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"epidemiology",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"of",
"disease",
"pulmonology",
"genetic",
"epidemiology"
] | 2013 | Causal and Synthetic Associations of Variants in the SERPINA Gene Cluster with Alpha1-antitrypsin Serum Levels |
Leishmania parasites , the causative agent of leishmaniasis , are transmitted through the bite of an infected sand fly . Leishmania parasites present two basic forms known as promastigote and amastigote which , respectively , parasitizes the vector and the mammalian hosts . Infection of the vertebrate host is dependent... | Leishmania parasites are the causative agent of a spectrum of diseases characterized by severe lesions in skin or life threatening visceral infections . In the parasite life cycle , a range of morphological transitions can be found such as amastigotes ( hosted in humans and others mammals ) and promastigotes ( located ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion"
] | [
"parastic",
"protozoans",
"leishmania",
"parasitology",
"protozoology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"microbial",
"growth",
"and",
"development"
] | 2012 | Leishmania Metacyclogenesis Is Promoted in the Absence of Purines |
Gene loci are found in nuclear subcompartments that are related to their expression status . For instance , silent genes are often localized to heterochromatin and the nuclear periphery , whereas active genes tend to be found in the nuclear center . Evidence also suggests that chromosomes may be specifically positioned... | How are genomes—and the chromosomes that comprise them—organized in the eukaryotic nucleus ? This long-standing question in cell biology has gained renewed interest due to observations that gene regulation is correlated with the nonrandom distribution of gene loci linearly along chromosomes and spatially within the nuc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"cell",
"biology",
"molecular",
"biology",
"hematology"
] | 2007 | Coordinate Gene Regulation during Hematopoiesis Is Related to Genomic Organization |
Listeria monocytogenes ( Lm ) infection induces rapid and robust activation of host natural killer ( NK ) cells . Here we define a region of the abundantly secreted Lm endopeptidase , p60 , that potently but indirectly stimulates NK cell activation in vitro and in vivo . Lm expression of p60 resulted in increased IFNγ ... | Pathogens have evolved diverse strategies to influence host immune responses . By studying these strategies , we may learn how to therapeutically intervene to manipulate immune responses during infectious and other diseases . In this study , we investigated how the bacterial pathogen Listeria monocytogenes ( Lm ) stimu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"gram",
"negative",
"immune",
"cells",
"nk",
"cells",
"immunity",
"immune",
"activation",
"innate",
"immunity",
"immunology",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"bacterial",
"pathogens",
"gram",
"positive"
] | 2011 | A LysM and SH3-Domain Containing Region of the Listeria monocytogenes p60 Protein Stimulates Accessory Cells to Promote Activation of Host NK Cells |
Staphylococcus aureus is a major human pathogen that causes a range of infections from acute invasive to chronic and difficult-to-treat . Infection strategies associated with persisting S . aureus infections are bacterial host cell invasion and the bacterial ability to dynamically change phenotypes from the aggressive ... | Staphylococcus aureus is a frequent pathogen of severe invasive infections that can develop into chronicity and become extremely difficult to eradicate . Chronic infections have been highly associated with altered bacterial phenotypes , i . e . , the small colony variants ( SCVs ) that dynamically appear after bacteria... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Sigma Factor SigB Is Crucial to Mediate Staphylococcus aureus Adaptation during Chronic Infections |
Genotype imputation methods are now being widely used in the analysis of genome-wide association studies . Most imputation analyses to date have used the HapMap as a reference dataset , but new reference panels ( such as controls genotyped on multiple SNP chips and densely typed samples from the 1 , 000 Genomes Project... | Large association studies have proven to be effective tools for identifying parts of the genome that influence disease risk and other heritable traits . So-called “genotype imputation” methods form a cornerstone of modern association studies: by extrapolating genetic correlations from a densely characterized reference ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/bioinformatics"
] | 2009 | A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies |
Mixed intestinal infections with Entamoeba histolytica , Entamoeba dispar and bacteria with exacerbated manifestations of disease are common in regions where amoebiasis is endemic . However , amoeba–bacteria interactions remain largely unexamined . Trophozoites of E . histolytica and E . dispar were co-cultured with en... | In amoebiasis , a human disease that is a serious health problem in many developing countries , efforts have been made to identify responsible factors for the tissue damage inflicted by the parasite Entamoeba histolytica . This amoeba lives in the lumen of the colon without causing damage to the intestinal mucosa , but... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/bacterial",
"infections",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/tropical",
"and",
"travel-associated",
"diseases",
"infectious",
"diseases/protozoal",
"infections"
] | 2008 | The Interplay between Entamoeba and Enteropathogenic Bacteria Modulates Epithelial Cell Damage |
The global burden of cholera is largely unknown because the majority of cases are not reported . The low reporting can be attributed to limited capacity of epidemiological surveillance and laboratories , as well as social , political , and economic disincentives for reporting . We previously estimated 2 . 8 million cas... | The global burden of cholera is largely unknown because the majority of cases are not reported . The low reporting can be attributed to limited capacity of epidemiological surveillance and laboratories , as well as social , political , and economic disincentives for reporting . We previously estimated 2 . 8 million cas... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Updated Global Burden of Cholera in Endemic Countries |
Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions . Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity , computational modeling could play an im... | An N-glycan is a carbohydrate chain covalently linked to the side chain of asparagine . Due to the flexibility of carbohydrate chains , it is believed that the N-glycan chains would not have a well-defined structure . However , our survey of N-glycan structures in the PDB shows that the N-glycan structures found on the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology",
"computational",
"biology"
] | 2013 | Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling |
The innate immune system is the first line of host defense against invading organisms . Thus , pathogens have developed virulence mechanisms to evade the innate immune system . Here , we report a novel means for inhibition of neutrophil recruitment by Group A Streptococcus ( GAS ) . Deletion of the secreted esterase ge... | GAS is a major human pathogen causing a variety of infections , including pharyngitis and necrotizing fasciitis . GAS pathogenesis is mediated by a large array of secreted and cell-surface virulence factors . However , the functions of many GAS virulence factors are poorly understood . Recently , we reported that the e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"infectious",
"diseases",
"bacterial",
"diseases",
"immunity",
"enzymes",
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2012 | Group A Streptococcus Secreted Esterase Hydrolyzes Platelet-Activating Factor to Impede Neutrophil Recruitment and Facilitate Innate Immune Evasion |
Paragonimiasis is a food-borne trematode infection acquired by eating raw or undercooked crustaceans . It is a major public health problem in the far East , but it also occurs in South Asia , Africa , and in the Americas . Paragonimus worms cause chronic lung disease with cough , fever and hemoptysis that can be confus... | Paragonimiasis is a food-borne trematode infection that people acquire when they eat raw or undercooked crustaceans . Disease symptoms ( including cough , fever , blood in sputum , etc . ) can be similar to those observed in patients with tuberculosis or bacterial pneumonia , frequently resulting in misdiagnosis . Alth... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results/Discussion"
] | [
"next-generation",
"sequencing",
"genome",
"expression",
"analysis",
"infectious",
"diseases",
"helminth",
"infections",
"medicine",
"and",
"health",
"sciences",
"genomics",
"foodborne",
"trematodiases",
"diagnostic",
"medicine",
"paragonimiasis",
"genome",
"analysis",
"ser... | 2014 | Systems Biology Studies of Adult Paragonimus Lung Flukes Facilitate the Identification of Immunodominant Parasite Antigens |
Epigenetic modifications influence gene expression and provide a unique mechanism for fine-tuning cellular differentiation and development in multicellular organisms . Here we report on the biological functions of UTX-1 , the Caenorhabditis elegans homologue of mammalian UTX , a histone demethylase specific for H3K27me... | Chromatin organization influences gene expression , and its regulation is crucial to achieve correct cellular differentiation and development in multicellular organisms . Histone demethylases are among several factors responsible for regulating chromatin dynamics . Here we report on the biological functions of UTX-1 , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"biochemistry",
"developmental",
"biology",
"caenorhabditis",
"elegans",
"model",
"organisms",
"organism",
"development",
"protein",
"interactions",
"genetics",
"epigenetics",
"biology",
"proteomics",
"genetics",
"and",
"genomics",
"histone",
"modificati... | 2012 | The C. elegans H3K27 Demethylase UTX-1 Is Essential for Normal Development, Independent of Its Enzymatic Activity |
The Bck2 protein is a potent genetic regulator of cell-cycle-dependent gene expression in budding yeast . To date , most experiments have focused on assessing a potential role for Bck2 in activation of the G1/S-specific transcription factors SBF ( Swi4 , Swi6 ) and MBF ( Mbp1 , Swi6 ) , yet the mechanism of gene activa... | Cell-cycle-dependent gene expression is a universal feature of cell cycles , with clear transcriptional programs in yeast , bacteria , and metazoans . At the M/G1 transition , many of the up-regulated genes encode key regulators of DNA replication ( CDC6 ) and cyclins that initiate the events of cell cycle commitment (... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"division",
"gene",
"regulation",
"genetics",
"gene",
"expression",
"molecular",
"genetics",
"biology",
"cyclins",
"molecular",
"cell",
"biology",
"chromatin",
"dna",
"transcription",
"gene",
"function"
] | 2013 | Bck2 Acts through the MADS Box Protein Mcm1 to Activate Cell-Cycle-Regulated Genes in Budding Yeast |
Pathway analyses of genome-wide association studies aggregate information over sets of related genes , such as genes in common pathways , to identify gene sets that are enriched for variants associated with disease . We develop a model-based approach to pathway analysis , and apply this approach to data from the Wellco... | Genome-wide association studies have helped locate gene variants that affect our susceptibility to diseases . The analysis of these studies is typically straightforward: test each genetic variant whether it is correlated with predisposition to disease . This approach often works well for identifying commonly occurring ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease |
The phytohormone abscisic acid ( ABA ) is critical to plant development and stress responses . Abiotic stress triggers an ABA signal transduction cascade , which is comprised of the core components PYL/RCAR ABA receptors , PP2C-type protein phosphatases , and protein kinases . Small GTPases of the ROP/RAC family act as... | The plant hormone abscisic acid ( ABA ) is critical to plant development and stress responses . The ABA signaling cascade is comprised of ABA receptors , negatively regulating PP2C protein phosphatases and transducing protein kinases . Biochemical assays have indicated that certain ABA receptors constitutively bind to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"anatomy",
"plant",
"growth",
"and",
"development",
"enzymes",
"lateral",
"roots",
"enzymology",
"phosphatases",
"developmental",
"biology",
"guanine",
"nucleotide",
"exchange",
"factors",
"plant",
"science",
"seedlings",
"plants",
"cellular",
"structures",
"an... | 2016 | Release of GTP Exchange Factor Mediated Down-Regulation of Abscisic Acid Signal Transduction through ABA-Induced Rapid Degradation of RopGEFs |
BK polyomavirus ( BKV or BKPyV ) associated nephropathy affects up to 10% of kidney transplant recipients ( KTRs ) . BKV isolates are categorized into four genotypes . It is currently unclear whether the four genotypes are also serotypes . To address this issue , we developed high-throughput serological assays based on... | Serological studies have shown that nearly all humans are chronically infected with BK polyomavirus ( BKV ) . The infection isn't usually associated with noticeable symptoms . However , opportunistic replication of BKV in therapeutically immunosuppressed kidney transplant recipients ( KTRs ) can lead to dysfunction or ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"renal",
"transplantation",
"virology",
"biology",
"microbiology",
"nephrology"
] | 2012 | Neutralization Serotyping of BK Polyomavirus Infection in Kidney Transplant Recipients |
The beneficial contribution of commensal bacteria to host health and homeostasis led to the concept that exogenous non-pathogenic bacteria called probiotics could be used to limit disease caused by pathogens . However , despite recent progress using gnotobiotic mammal and invertebrate models , mechanisms underlying pro... | The beneficial contribution of commensal bacteria to host health led to the concept that exogenous and non-pathogenic bacteria ( probiotics ) could be used to prevent infectious disease . However , the absence of relevant experimentally tractable in vivo models severely limits our understanding of the molecular process... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"microbiology",
"host-pathogen",
"interaction",
"escherichia",
"coli",
"animal",
"models",
"model",
"organisms",
"bacterial",
"pathogens",
"biology",
"zebrafish",
"bacterial",
"biofilms",
"gram",
"negative",
"immunity",
"innate",
"immunity",
"microbial",
"... | 2012 | A New Zebrafish Model of Oro-Intestinal Pathogen Colonization Reveals a Key Role for Adhesion in Protection by Probiotic Bacteria |
Skeletal muscle contraction is initiated when an action potential triggers the release of Ca2+ into the sarcomere in a process referred to as excitation-contraction coupling . The speed and scale of this process makes direct observation very challenging and invasive . To determine how the concentration of Ca2+ changes ... | In this study we develop a structural stochastic diffusion model , to study how calcium ions diffuse and interact within a skeletal muscle sarcomere following a simulated muscle activation . This type of model allows us to explore how structural elements , namely the actin and myosin filaments , within the sarcomere af... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methodology"
] | [
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"actin",
"filaments",
"myofibrils",
"muscle",
"tissue",
"simulation",
"and",
"modeling",
"molecular",
"motors",
"actin",
"motors",
"myofilaments",
"motor",
"proteins",
"research",
"and",
"analysis",
"methods... | 2019 | A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell |
Laboratory confirmation of Zika virus ( ZIKV ) infection during pregnancy is challenging due to cross-reactivity with dengue virus ( DENV ) and limited knowledge about the kinetics of anti-Zika antibody responses during pregnancy . We described ZIKV and DENV serological markers and the maternal-fetal transfer of antibo... | The epicenter of the ZIKV epidemic was located in Northeast Brazil ( 2015/16 ) and was followed by a space and time cluster of congenital microcephaly cases . This region is also a dengue hyperendemic setting . Laboratory confirmation of ZIKV infection during pregnancy is challenging due to cross-reactivity with other ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"microcephaly",
"pathology",
"and",
"laboratory",
"medicine",
"enzyme-linked",
"immunoassays",
"pathogens",
"immunology",
"microbiology",
"viruses",
"research",
"design",
"developmental",
... | 2019 | Perinatal analyses of Zika- and dengue virus-specific neutralizing antibodies: A microcephaly case-control study in an area of high dengue endemicity in Brazil |
Sporadic evidence suggests Notch is involved in cell adhesion . However , the underlying mechanism is unknown . Here I have investigated an epithelial remodeling process in the Drosophila eye in which two primary pigment cells ( PPCs ) with a characteristic ‘kidney’ shape enwrap and eventually isolate a group of cone c... | In developing tissues , one way to isolate a group of cells from the rest of the tissue is to induce a few neighboring cells to surround them . How centrally localized cells communicate with neighboring cells and how neighboring cells respond to signaling is not well understood . This work describes a mechanism underly... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"genetics",
"developmental",
"biology",
"biology"
] | 2014 | Notch Controls Cell Adhesion in the Drosophila Eye |
According to the Centers for Disease Control and Prevention ( CDC ) , one in twenty five hospital patients are infected with at least one healthcare acquired infection ( HAI ) on any given day . Early detection of possible HAI outbreaks help practitioners implement countermeasures before the infection spreads extensive... | Healthcare acquired infections ( HAIs ) lead to significant losses of lives and result in heavy economic burden on healthcare providers worldwide . Timely detection of HAI outbreaks will have a significant impact on the health infrastructure . Here , we propose an efficient and effective approach to detect HAI outbreak... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"gut",
"bacteria",
"medical",
"personnel",
"sociology",
"social",
"sciences",
"health",
"care",
"simulation",
"and",
"modeling",
"health",
"care",
"providers",
"systems",
"science",
"mathematics",
"network",
"analysis",
"social... | 2019 | Fast and near-optimal monitoring for healthcare acquired infection outbreaks |
The aetiological diagnostic of fevers in Laos remains difficult due to limited laboratory diagnostic facilities . However , it has recently become apparent that both scrub and murine typhus are common causes of previous undiagnosed fever . Epidemiological data suggests that scrub typhus would be more common in rural ar... | Scrub typhus and murine typhus are neglected but important treatable causes of fever , morbidity and mortality in South-East Asia . Epidemiological data suggests that scrub typhus would be more common in rural areas and murine typhus in urban areas but there are very few comparative data from places where both diseases... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology/epidemiology",
"public",
"health",
"and",
"epidemiology/social",
"and",
"behavioral",
"determinants",
"of",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"... | 2010 | Contrasting Spatial Distribution and Risk Factors for Past Infection with Scrub Typhus and Murine Typhus in Vientiane City, Lao PDR |
Asymmetrical dimethylarginine ( ADMA ) , an endogenous inhibitor of nitric oxide synthase ( NOS ) , is a predictor of mortality in critical illness . Severe malaria ( SM ) is associated with decreased NO bioavailability , but the contribution of ADMA to the pathogenesis of impaired NO bioavailability and adverse outcom... | Severe falciparum malaria is associated with impaired microvascular perfusion , lung injury and decreased bioavailability of nitric oxide ( NO ) , but the causes of these processes are not fully understood . Asymmetrical dimethylarginine ( ADMA ) , a competitive endogenous inhibitor of nitric oxide synthase ( NOS ) , i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"infectious",
"diseases/protozoal",
"infections"
] | 2010 | Increased Asymmetric Dimethylarginine in Severe Falciparum Malaria: Association with Impaired Nitric Oxide Bioavailability and Fatal Outcome |
Coxiella burnetii is an intracellular bacterium that replicates within an expansive phagolysosome-like vacuole . Fusion between the Coxiella-containing vacuole ( CCV ) and late endosomes/multivesicular bodies requires Rab7 , the HOPS tethering complex , and SNARE proteins , with actin also speculated to play a role . H... | Coxiella burnetii , the human Q fever bacterium , replicates in a harsh , lysosome-like compartment termed the Coxiella-containing vacuole ( CCV ) . Here , the pathogen directs formation of the CCV through the activities of secreted type 4B ( T4B ) effector proteins . Questions remain concerning how the host cytoskelet... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"biological",
"cultures",
"microbiology",
"membrane",
"fusion",
"cellular",
"structures",
"and",
"organelles",
"bacterial",
"pathogens",
"end... | 2018 | Actin polymerization in the endosomal pathway, but not on the Coxiella-containing vacuole, is essential for pathogen growth |
Lymphatic endothelial cells ( LECs ) are differentiated from blood vascular endothelial cells ( BECs ) during embryogenesis and this physiological cell fate specification is controlled by PROX1 , the master regulator for lymphatic development . When Kaposi sarcoma herpes virus ( KSHV ) infects host cells , it activates... | Kaposi's sarcoma ( KS ) is one of the most common neoplasms in HIV-positive individuals and organ transplant recipients . KS-associated herpes virus ( KSHV ) , also known as human herpes virus ( HHV ) -8 , has been identified as the causative agent and infects endothelial cells to form KS . Importantly , we and others ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"mechanisms",
"of",
"signal",
"transduction",
"endothelial",
"cells",
"microbiology",
"host-pathogen",
"interaction",
"cancers",
"and",
"neoplasms",
"feeback",
"regulation",
"dna",
"transcription",
"oncology",
"bone",
"and",
"soft",
"tissue",
"sarcomas",
"ge... | 2012 | Opposing Regulation of PROX1 by Interleukin-3 Receptor and NOTCH Directs Differential Host Cell Fate Reprogramming by Kaposi Sarcoma Herpes Virus |
As model organism-based research shifts from forward to reverse genetics approaches , largely due to the ease of genome editing technology , a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein . In zebrafish , this low frequenc... | The recent rise of reverse genetic , gene targeting methods has allowed researchers to readily generate mutations in any gene of interest with relative ease . Should these mutations have the predicted effect on the mRNA and encoded protein , we would expect many more abnormal phenotypes than are typically being seen in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"fish",
"vertebrates",
"animals",
"animal",
"models",
"osteichthyes",
"mutation",
"developmental",
"biology",
"model",
"organisms",
"nonsense",
"mutation",
"experimental",
"organism",
"systems",
"sequence",
"motif",
"analysis",
"molecular",
"biology",
"techniques",
"resea... | 2017 | mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay |
The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known . It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments . Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by intervening sequenc... | Deinococcus radiodurans is known for its exceptional ability to tolerate exposure to DNA damaging agents and , in particular , to very high doses of ionizing radiation . This exceptional radioresistance results from many features including efficient DNA double strand break repair . Here , we examine genome stability in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium |
The four dengue viruses , the agents of dengue fever and dengue hemorrhagic fever in humans , are transmitted predominantly by the mosquito Aedes aegypti . The abundance and the transmission potential of Ae . aegypti are influenced by temperature and precipitation . While there is strong biological evidence for these e... | Dengue viruses are a major health problem throughout the tropical and subtropical regions of the world . Because they are transmitted by mosquitoes that are sensitive to changes in rainfall and temperature , transmission intensity may be regulated by weather and climate . Laboratory studies have shown this to be biolog... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology/epidemiology",
"infectious",
"diseases/viral",
"infections",
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
... | 2009 | Local and Global Effects of Climate on Dengue Transmission in Puerto Rico |
Glossina ( G . ) spp . ( Diptera: Glossinidae ) , known as tsetse flies , are vectors of African trypanosomes that cause sleeping sickness in humans and nagana in domestic livestock . Knowledge on tsetse distribution and accurate species identification help identify potential vector intervention sites . Morphological s... | Tsetse flies are confined to tropical Africa and are carriers for trypanosomes , single-celled blood parasites . Through the bite of an infective tsetse , people and animals may contract trypanosomiasis , a degenerative disease leading to death if left untreated . Tsetse control proved effective for disease containment... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"veterinary",
"diseases",
"clinical",
"laboratory",
"sciences",
"diagnostic",
"medicine",
"veterinary",
"parasitology",
"veterinary",
"diagnostics",
"zoonotic",
"diseases",
"livestock",
"care",
"proteomics",
"biology",
"trypanosomiasis",
"veterinary",
"science",
... | 2013 | Identification of Tsetse (Glossina spp.) Using Matrix-Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry |
Although the transcription factors IRF-3 and IRF-7 are considered master regulators of type I interferon ( IFN ) induction and IFN stimulated gene ( ISG ) expression , Irf3−/−×Irf7−/− double knockout ( DKO ) myeloid dendritic cells ( mDC ) produce relatively normal levels of IFN-β after viral infection . We generated I... | Host pathogen sensors , including those of the Toll-like receptor and RIG-I like receptor ( RLR ) families , detect viral infection in cells . Signaling through these receptors triggers expression of type I interferon ( IFN ) and IFN-stimulated genes ( ISGs ) , in part through the IRF family of transcription factors . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"immunity",
"to",
"infections",
"immunology",
"microbiology",
"immune",
"defense",
"infectious",
"disease",
"control",
"animal",
"models",
"of",
"infection",
"infectious",
"diseases",
"biology",
"immune",
"response",
"west",
"nile",
"fever",
"immunity",
"v... | 2013 | IRF-3, IRF-5, and IRF-7 Coordinately Regulate the Type I IFN Response in Myeloid Dendritic Cells Downstream of MAVS Signaling |
Nicotinic acetylcholine receptors ( nAChRs ) are widely expressed throughout the central nervous system and modulate neuronal function in most mammalian brain structures . The contribution of defined nAChR subunits to a specific behavior is thus difficult to assess . Mice deleted for ß2-containing nAChRs ( ß2−/− ) have... | Understanding mechanisms underlying complex behaviors and the abnormalities that accompany most neuropathologies is a current challenge in biomedical research . A number of approaches is primarily based on the identification of genes and their associated molecular pathways implicated in complex motor or cognitive patho... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"neuroscience",
"neuroscience/animal",
"cognition"
] | 2008 | Behavioral Sequence Analysis Reveals a Novel Role for
ß2* Nicotinic Receptors in Exploration |
Bacterial operons synchronize the expression of multiple genes by placing them under the control of a shared promoter . It was previously shown that polycistronic transcripts can undergo differential RNA decay , leaving some genes within the polycistron more stable than others , but the extent of regulation by differen... | Bacteria utilize operonic transcription to synchronize the expression of multiple consecutive genes . However , this strategy lacks the ability to fine-tune the expression of specific operon members , which is often biologically important . In this report , we integrate multiple transcriptome-wide RNA-sequencing method... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"nucleases",
"enzymes",
"pathogens",
"messenger",
"rna",
"dna-binding",
"proteins",
"operons",
"enzymology",
"microbiology",
"bacterial",
"diseases",
"entero... | 2018 | Extensive reshaping of bacterial operons by programmed mRNA decay |
E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain families . Here we formally show that for “stratified” multiple hypothesis testin... | Despite decades of research , it remains a challenge to distinguish homologous relationships between proteins from sequence similarities arising due to chance alone . This is an increasingly important problem as sequence database sizes continue to grow , and even today many computational analyses require that the stati... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Beyond the E-Value: Stratified Statistics for Protein Domain Prediction |
We used the RIP1-Tag2 ( RT2 ) mouse model of islet cell carcinogenesis to profile the transcriptome of pancreatic neuroendocrine tumors ( PNET ) that were either non-invasive or highly invasive , seeking to identify pro- and anti-invasive molecules . Expression of multiple components of desmosomes , structures that hel... | The ability of a tumor to invade into the surrounding normal tissue is one hallmark of a malignant cancer . We sought to identify factors that either restrict or promote tumor invasion in a genetically engineered mouse model of pancreatic neuroendocrine cancer by characterizing the transcriptional profiles of the non-i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/gene",
"discovery",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/gene",
"function",
"geneti... | 2010 | Genetic Deletion of the Desmosomal Component Desmoplakin Promotes Tumor Microinvasion in a Mouse Model of Pancreatic Neuroendocrine Carcinogenesis |
The centromeric regions of all Saccharomyces cerevisiae chromosomes are found in early replicating domains , a property conserved among centromeres in fungi and some higher eukaryotes . Surprisingly , little is known about the biological significance or the mechanism of early centromere replication; however , the exten... | Genome duplication requires the orderly initiation of DNA synthesis at sites called origins of replication . It has long been known that different origins become active at different times in S-phase ( the period during which cells duplicate their chromosomes ) . Although such temporal regulation of replication is broad... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chromosome",
"structure",
"and",
"function",
"centromeres",
"microbiology",
"model",
"organisms",
"dna",
"replication",
"molecular",
"genetics",
"dna",
"chromosome",
"biology",
"biology",
"molecular",
"biology",
"cell",
"biology",
"nucleic",
"acids",
"genetics",
"yeast... | 2012 | Functional Centromeres Determine the Activation Time of Pericentric Origins of DNA Replication in Saccharomyces cerevisiae |
Precise patterning of morphogen molecules and their accurate reading out are of key importance in embryonic development . Recent experiments have visualized distributions of proteins in developing embryos and shown that the gradient of concentration of Bicoid morphogen in Drosophila embryos is established rapidly after... | For developing embryos , the precise , position-specific regulation of molecular processes is of fatal importance . As the mechanism of such regulation , widely accepted has been the notion of the intraembryonic distribution of regulatory molecules called “morphogens” . One of the best-studied morphogens is Bicoid in t... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"computational",
"biology/systems",
"biology",
"computational",
"biology/transcriptional",
"regulation",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"computational",
"biology/molecular",
"genetics",
"biophysics/theory",
"and",
"simulation",
"cell",
"biology/develop... | 2009 | Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo |
Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations . However , these models generally assume that individual hosts contact one another at random , ignoring the fact that many pathogens spread through highly structured contact networks . We ... | Phylodynamic models relate the branching pattern of a pathogen’s phylogenetic tree to the tree-like growth of an epidemic as it spreads through a host population . Such models are increasingly used to learn about the epidemiology of different pathogens . We extend current models to consider the structure of host contac... | [
"Abstract",
"Introduction",
"Models",
"and",
"methods",
"Results",
"Discussion"
] | [
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"infectious",
"disease",
"epidemiology",
"pathogens",
"geographical",
"locations",
"epidemiological",
"methods",
"and",
"statistics",
"simulation",
"and",
"modeling",
"phylo... | 2017 | Phylodynamics on local sexual contact networks |
The evolution of cooperation described in terms of simple two-person interactions has received considerable attention in recent years , where several key results were obtained . Among those , it is now well established that the web of social interaction networks promotes the emergence of cooperation when modeled in ter... | Humans contribute to a broad range of cooperative endeavors . In many of them , the amount or effort contributed often depends on the social context of each individual . Recent evidence has shown how modern societies are grounded in complex and heterogeneous networks of exchange and cooperation , in which some individu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology/human",
"evolution",
"mathematics"
] | 2009 | Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation |
Somatic mutations of the cohesin complex subunit STAG2 are present in diverse tumor types . We and others have shown that STAG2 inactivation can lead to loss of sister chromatid cohesion and alterations in chromosome copy number in experimental systems . However , studies of naturally occurring human tumors have demons... | Mutations of the STAG2 gene are common in several types of adult and pediatric cancers . In fact , STAG2 is one of only 12 genes known to be significantly mutated in four of more types of cancer . The STAG2 gene encodes a protein component of the “cohesin complex , ” a ring-like structure that binds chromosomes togethe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"anaphase",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"chromatids",
"mutation",
"immunoprecipitation",
"nonsense",
"mutation",
"research",
"and",
"analysis",
"methods",
"missense",
"mutation",
"chromosome",... | 2016 | Intact Cohesion, Anaphase, and Chromosome Segregation in Human Cells Harboring Tumor-Derived Mutations in STAG2 |
Cancer development is driven by series of events involving mutations , which may become fixed in a tumor via genetic drift and selection . This process usually includes a limited number of driver ( advantageous ) mutations and a greater number of passenger ( neutral or mildly deleterious ) mutations . We focus on a rea... | Cancer develops by multistep acquisition of mutations in a progenitor cell and its daughter cells . Severe congenital neutropenia ( SCN ) manifests itself through an inability to produce enough granulocytes to prevent infections . SCN commonly results from a germline ELANE mutation . Large doses of the blood growth fac... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"maternal",
"health",
"obstetrics",
"and",
"gynecology",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"immunology",
"bone",
"marrow",
"cells",
"oncology",
"physiologica... | 2019 | Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia |
DNA double-strand breaks are lesions that form during metabolism , DNA replication and exposure to mutagens . When a double-strand break occurs one of a number of repair mechanisms is recruited , all of which have differing propensities for mutational events . Despite DNA repair being of crucial importance , the relati... | DNA double-strand breaks occur during metabolism , DNA replication and by exposure to exogenous sources such as ionising radiation . When the genome is inflicted with this type of damage , DNA repair machinery is promoted to restore genome structure . The efficient interplay between DNA damage and repair is crucial to ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ionizing",
"radiation",
"dose",
"prediction",
"methods",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"dna-binding",
"proteins",
"radiation",
"simulation",
"and",
"modeling",
"dna",
"damage",
"pharmaceutics... | 2016 | Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair |
The vast majority of genome-wide association study ( GWAS ) findings reported to date are from populations with European Ancestry ( EA ) , and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry . The Population Architecture Using Genomics and Epidemiolo... | The number of known associations between human diseases and common genetic variants has grown dramatically in the past decade , most being identified in large-scale genetic studies of people of Western European origin . But because the frequencies of genetic variants can differ substantially between continental populat... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study |
Orientation preference maps ( OPMs ) are present in carnivores ( such as cats and ferrets ) and primates but are absent in rodents . In this study we investigate the possible link between astrocyte arbors and presence of OPMs . We simulate the development of orientation maps with varying hypercolumn widths using a vari... | Columns of neurons in the primary visual cortex ( V1 ) are known to be tuned to visual stimuli containing edges of a particular orientation . The arrangement of these cortical columns varies across species . In many species such as in ferrets , cats , and monkeys a topology preserving map is observed , wherein similarl... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"nervous",
"system",
"astrocytes",
"junctional",
"complexes",
"vertebrates",
"electrophysiology",
"neuroscience",
"macroglial",
"cells",
"mammals",
"animals",
"gap",
"junctions",
"synaptic",
... | 2017 | The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective |
We report a systematic review and meta-analysis of research using animal models of chemotherapy-induced peripheral neuropathy ( CIPN ) . We systematically searched 5 online databases in September 2012 and updated the search in November 2015 using machine learning and text mining to reduce the screening for inclusion wo... | Many frequently used and effective cancer chemotherapies can cause a disabling side effect that features pain , numbness , tingling , and sensitivity to cold and heat in the extremities known as chemotherapy-induced peripheral neuropathy ( CIPN ) . There are currently no effective therapies to treat or prevent this con... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"statistics",
"metaanalysis",
"drugs",
"experimental",
"design",
"social",
"sciences",
"biological",
"locomotion",
"chemotherapeutic",
"agents",
"animal",
"models",
"oncology",
"research",
"design",
"animal",
"behavior",
"mathemati... | 2019 | Animal models of chemotherapy-induced peripheral neuropathy: A machine-assisted systematic review and meta-analysis |
Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences . The cytochrome P450 ( CYP450 ) gene superfamily is well suited to investigating this problem because it is large and well studied , and it includes both stable and unstable genes . CYP450 genes e... | Genes vary greatly in their long-term phylogenetic stability , and there exists no general explanation for these differences . Stable genes persist as a single copy over a wide range of distantly related species , whereas unstable genes undergo frequent duplication and loss in a process called birth-death evolution . T... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"teleost",
"fishes",
"chicken",
"vertebrates",
"evolutionary",
"biology",
"homo",
"(human)",
"genetics",
"and",
"genomics",
"mus",
"(mouse)"
] | 2007 | Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates |
The yeast Candida albicans is a human commensal and opportunistic pathogen . Although both commensalism and pathogenesis depend on metabolic adaptation , the regulatory pathways that mediate metabolic processes in C . albicans are incompletely defined . For example , metabolic change is a major feature that distinguish... | Metabolism is a master regulator of cell biology , including gene regulation , developmental switches and cellular life-death decisions , with the mitochondrion playing a central role in eukaryotes . For the yeast Candida albicans mitochondrial functions have been implicated in host-pathogen interactions , but the regu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans |
Rapid advances in sequencing technologies set the stage for the large-scale medical sequencing efforts to be performed in the near future , with the goal of assessing the importance of rare variants in complex diseases . The discovery of new disease susceptibility genes requires powerful statistical methods for rare va... | Risk to common diseases , such as diabetes , heart disease , etc . , is influenced by a complex interaction among genetic and environmental factors . Most of the disease-association studies conducted so far have focused on common variants , widely available on genotyping platforms . However , recent advances in sequenc... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/complex",
"traits",
"mathematics/statistics"
] | 2011 | A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease |
Understanding the relationship between genetic variation and gene expression is a central question in genetics . With the availability of data from high-throughput technologies such as ChIP-Chip , expression , and genotyping arrays , we can begin to not only identify associations but to understand how genetic variation... | One of the fundamental challenges in biology in the post-genomics era is understanding the complex regulatory mechanisms that govern how genes are turned on and off . In a single organism where the functions of individual genes in a population do not differ much , many of the differences between individuals including p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer",
"science/applications",
"computational",
"biology/systems",
"biology",
"genetics",
"and",
"genomics/gene",
"expression",
"computational",
"biology/transcriptional",
"regulation",
"genetics",
"and",
"genomics/bioinformatics"
] | 2009 | Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast |
The Middle East is a culturally and politically diverse region at the gateway between Europe , Africa and Asia . Spatial dynamics of the fatal zoonotic disease rabies among countries of the Middle East and surrounding regions is poorly understood . An improved understanding of virus distribution is necessary to direct ... | Despite being one of the oldest recognised infectious diseases , rabies continues to cause thousands of preventable human deaths per year . As a zoonotic disease , control of infection in the reservoir has been proven the most efficient route to reduction of human cases . In some regions , the epidemiology is well unde... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Complex Epidemiology of a Zoonotic Disease in a Culturally Diverse Region: Phylogeography of Rabies Virus in the Middle East |
Expression of E7 proteins encoded by carcinogenic , high-risk human papillomaviruses ( HPVs ) triggers increased expression of the histone H3 lysine 27 demethylase KDM6A . KDM6A expression is necessary for survival of high-risk HPV E7 expressing cells , including several cervical cancer lines . Here we show that increa... | High-risk human papillomaviruses ( HPVs ) are associated with approximately five percent of all human cancers , including virtually all cervical cancers as well as a large percentage of anal , vaginal , vulvar , penile , and oropharyngeal cancers . The HPV E6 and E7 proteins are the major oncogenic drivers in these tum... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"cervical",
"cancer",
"pathogens",
"cell",
"cycle",
"and",
"cell",
"division",
"carcinomas",
"cell",
"processes",
"microbiology",
"social",
"sciences",
"cancers",
"and",
"neoplasms"... | 2017 | KDM6A addiction of cervical carcinoma cell lines is triggered by E7 and mediated by p21CIP1 suppression of replication stress |
Type II secretion systems ( T2SSs ) are critical for secretion of many proteins from Gram-negative bacteria . In the T2SS , the outer membrane secretin GspD forms a multimeric pore for translocation of secreted proteins . GspD and the inner membrane protein GspC interact with each other via periplasmic domains . Three ... | Many bacterial pathogens affecting humans , animals and plants export diverse proteins across the cell membranes into the medium surrounding the bacteria . Some of these secreted proteins are involved in pathogenesis . One example is cholera toxin secreted by the bacterium Vibrio cholerae , a causative agent of cholera... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"gram",
"negative",
"transmembrane",
"proteins",
"protein",
"interactions",
"proteins",
"protein",
"structure",
"macromolecular",
"assemblies",
"microbial",
"pathogens",
"biology",
"transmembrane",
"transport",
"proteins",
"microbiology",
"bacterial",
"pathoge... | 2011 | Structural and Functional Studies on the Interaction of GspC and GspD in the Type II Secretion System |
Chagas disease , caused by the protozoan parasite Trypanosoma cruzi ( T . cruzi ) , is a life threatening global health problem with only two drugs available for treatment ( benznidazole and nifurtimox ) , both having variable efficacy in the chronic stage of the disease and high rates of adverse drug reactions . Inhib... | Chagas disease , caused by the parasite Trypanosoma cruzi ( T . cruzi ) , is endemic in Latin America and emerging in North America and Europe through human migration . It is a severe global health problem with 8–10 million people infected and an estimated 12 , 000 deaths annually . Current treatment options are poorly... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [] | 2015 | Development of a Fluorescence-based Trypanosoma cruzi CYP51 Inhibition Assay for Effective Compound Triaging in Drug Discovery Programmes for Chagas Disease |
Bangladesh is one of the endemic countries for Visceral Leishmaniasis ( VL ) . Médecins Sans Frontières ( MSF ) ran a VL treatment clinic in the most endemic district ( Fulbaria ) between 2010 and 2013 using a semi-ambulatory regimen for primary VL of 15mg/kg Liposomal Amphotericin-B ( AmBisome ) in three equal doses o... | Visceral Leishmaniasis ( VL ) is a parasitic disease which is endemic in more than 80 countries , although 90% of cases occur in India , Bangladesh , Sudan , South Sudan , Ethiopia and Brazil . Most treatments are complex , expensive and require long application periods . AmBisome is one of the newest treatments availa... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [] | 2015 | Effectiveness and Safety of Short Course Liposomal Amphotericin B (AmBisome) as First Line Treatment for Visceral Leishmaniasis in Bangladesh |
To understand whether any human-specific new genes may be associated with human brain functions , we computationally screened the genetic vulnerable factors identified through Genome-Wide Association Studies and linkage analyses of nicotine addiction and found one human-specific de novo protein-coding gene , FLJ33706 (... | For decades , gene duplication , retrotranspositions and gene fusions were believed to be major ways to increase gene number . All involve “mother” genes as the “building blocks” for new genes . However , several recently identified “motherless” genes challenged the idea in that some proteins might have emerged de novo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology/human",
"evolution",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics"
] | 2010 | A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions |
Poxviruses contain large dsDNA genomes encoding numerous open reading frames that manipulate cellular signalling pathways and interfere with the host immune response . The NF-κB signalling cascade is an important mediator of innate immunity and inflammation , and is tightly regulated by ubiquitination at several key po... | Poxviruses are large dsDNA viruses that are renowned for regulating cellular pathways and manipulating the host immune response , including the NF-κB pathway . NF-κB inhibition by poxviruses is a growing area of interest and this family of viruses has developed multiple mechanisms to manipulate the pathway . Here , we ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"of",
"infection",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"cell",
"biology",
"viral",
"immune",
"evasion",
"pathology",
"and",
"laboratory",
"medicine",
"virulence",
"factors",
"virology",
"pathogens",
"biology",
"and",
... | 2014 | EVM005: An Ectromelia-Encoded Protein with Dual Roles in NF-κB Inhibition and Virulence |
The capacity of the liver to convert the metabolic input received from the incoming portal and arterial blood into the metabolic output of the outgoing venous blood has three major determinants: The intra-hepatic blood flow , the transport of metabolites between blood vessels ( sinusoids ) and hepatocytes and the metab... | Glucose homeostasis is one of the central liver functions . The liver extracts glucose from the blood when plasma glucose levels are high and produces glucose when plasma glucose levels are low . To fulfill this function the liver is organized in smallest functional units , the sinusoidal tissue units ( STUs ) . These ... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"liver",
"body",
"fluids",
"chemical",
"compounds",
"enzymology",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
"glycobiology",
"enzyme",
"metabolism",
"enzyme",
"chemist... | 2018 | A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism |
Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging epidemic infectious disease caused by the SFTS bunyavirus ( SFTSV ) with an estimated high case-fatality rate of 12 . 7% to 32 . 6% . Currently , the disease has been reported in mainland China , Japan , Korea , and the United States . At present , the... | Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease caused by a novel SFTS bunyavirus ( SFTSV ) with an estimated high case-fatality rate . However , there is no specific antiviral therapy for SFTSV infection . Symptomatic treatment and supportive therapy are the most essential part o... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"medicine",
"and",
"health",
"sciences",
"clinical",
"laboratory",
"sciences",
"aminotransferases",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"enzymes",
"enzymology",
"microbiology",
"biomarkers",
"signs",... | 2017 | A scoring model for predicting prognosis of patients with severe fever with thrombocytopenia syndrome |
Rift Valley fever ( RVF ) is an arthropod-borne viral zoonosis . Rift Valley fever virus ( RVFV ) is an important biological threat with the potential to spread to new susceptible areas . In addition , it is a potential biowarfare agent . We developed two potential vaccines , DNA plasmids and alphavirus replicons , exp... | Rift Valley fever virus ( RVFV ) is an arthropod-borne phlebovirus associated with abortion storms , neonatal mortality in livestock and hemorrhagic fever or fatal encephalitis in a proportion of infected humans . Requirement of multiple booster immunizations to maintain the level of protective immunity with the inacti... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"virology/vaccines",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"immunology/immune",
"response",
"infectious",
"diseases/viral",
"infections"
] | 2010 | Vaccination with DNA Plasmids Expressing Gn Coupled to C3d or Alphavirus Replicons Expressing Gn Protects Mice against Rift Valley Fever Virus |
Long-term homologous and temporary heterologous protection from dengue virus ( DENV ) infection may be mediated by neutralizing antibodies . However , neutralizing antibody titers ( NTs ) have not been clearly associated with protection from infection . Data from two geographic cluster studies conducted in Kamphaeng Ph... | Dengue is caused by four different dengue virus serotypes ( DENV-1 , -2 , -3 , -4 ) . Infection induces long-term protection against the same serotype , but only short-term protection , and possible enhancement , from different serotypes . DENV neutralizing antibody titers ( NTs ) are thought to mediate protection or m... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"viral",
"hemorrhagic",
"fevers",
"infectious",
"diseases",
"infectious",
"disease",
"immunology",
"medicine",
"and",
"health",
"sciences",
"clinical",
"immunology",
"dengue",
"fever",
"biology",
"and",
"life",
"sciences",
"immunology",
"viral",
"diseases",
"vector-born... | 2014 | Dengue Virus Neutralizing Antibody Levels Associated with Protection from Infection in Thai Cluster Studies |
Gonadal failure , along with early pregnancy loss and perinatal death , may be an important filter that limits the propagation of harmful mutations in the human population . We hypothesized that men with spermatogenic impairment , a disease with unknown genetic architecture and a common cause of male infertility , are ... | Infertility is a disease that prevents the transmission of DNA from one generation to the next , and consequently it has been difficult to study the genetics of infertility using classical human genetics methods . Now , new technologies for screening entire genomes for rare and patient-specific mutations are revolution... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"aneuploidy",
"x-linked",
"chromosomal",
"disorders",
"genetics",
"biology",
"human",
"genetics",
"genetics",
"of",
"disease",
"chromosomal",
"deletions",
"and",
"duplications",
"genetics",
"and",
"genomics",
"y-linked"
] | 2013 | Human Spermatogenic Failure Purges Deleterious Mutation Load from the Autosomes and Both Sex Chromosomes, including the Gene DMRT1 |
Adults with chronic Trypanosoma cruzi exhibit a poorly functional T cell compartment , characterized by monofunctional ( IFN-γ-only secreting ) parasite-specific T cells and increased levels of terminally differentiated T cells . It is possible that persistent infection and/or sustained exposure to parasites antigens m... | Chagas disease is a neglected tropical disease affecting approximately 10 million people in the world . As a consequence of migration flows , the disease has also become established in non-endemic countries . Previous studies have demonstrated that Trypanosoma cruzi-specific T cells inversely correlates with the severi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Polyfunctional T Cell Responses in Children in Early Stages of Chronic Trypanosoma cruzi Infection Contrast with Monofunctional Responses of Long-term Infected Adults |
Modern optical imaging experiments not only measure single-cell and single-molecule dynamics with high precision , but they can also perturb the cellular environment in myriad controlled and novel settings . Techniques , such as single-molecule fluorescence in-situ hybridization , microfluidics , and optogenetics , hav... | A main objective of quantitative modeling is to predict the behaviors of complex systems under varying conditions . In a biological context , stochastic fluctuations in expression levels among isogenic cell populations have required modeling efforts to incorporate and even rely upon stochasticity . At the same time , n... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"ultraviolet",
"radiation",
"experimental",
"design",
"random",
"variables",
"light",
"covariance",
"electromagnetic",
"radiation",
"simulation",
"and",
"modeling",
"research",
"design",
"probability",
"distribution",
"mathematics",
"algebra",
"research",
"and",
"analysis",... | 2019 | The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments |
Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins . Methods predicting intrinsic disorder are based on the amino acid sequence of a protein . Therefore , there must exist an underlying difference in the sequences between eukaryotic and prokaryotic proteins causing the ( predicted ) difference ... | Intrinsic disorder is essential for various functions in eukaryotic cells and is a signature of eukaryotic proteins . Here , we try to understand the origin of the difference in disorder between eukaryotic and prokaryotic proteins . We show that eukaryotic proteins contain more extended linker regions and that these li... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"and",
"discussion"
] | [
"chemical",
"compounds",
"aliphatic",
"amino",
"acids",
"organic",
"compounds",
"serine",
"isoleucine",
"amino",
"acids",
"bacteria",
"proteins",
"prokaryotic",
"cells",
"chemistry",
"cyclic",
"amino",
"acids",
"proline",
"biochemistry",
"eukaryota",
"organic",
"chemist... | 2019 | Why do eukaryotic proteins contain more intrinsically disordered regions? |
The gene encoding a DNA/RNA binding protein FUS/TLS is frequently mutated in amyotrophic lateral sclerosis ( ALS ) . Mutations commonly affect its carboxy-terminal nuclear localization signal , resulting in varying deficiencies of FUS nuclear localization and abnormal cytoplasmic accumulation . Increasing evidence sugg... | FUS/TLS is a frequently mutated gene in amyotrophic lateral sclerosis ( ALS ) . ALS , also known as Lou Gehrig's disease , is characterized by a progressive degeneration of motor neurons . The abnormal cytoplasmic accumulation of mutant FUS protein is a characteristic pathology of ALS; however , recent evidence increas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | ALS-Associated FUS Mutations Result in Compromised FUS Alternative Splicing and Autoregulation |
Bats are a highly successful , globally dispersed order of mammals that occupy a wide array of ecological niches . They are also intensely parasitized and implicated in multiple viral , bacterial and parasitic zoonoses . Trypanosomes are thought to be especially abundant and diverse in bats . In this study , we used 18... | Bats make up a mega-diverse , intensely parasitized order of volant mammals whose unique behavioural and physiological adaptations promote infection by a vast array of microorganisms . Trypanosomes stand out as ancient protozoan parasites of bats . As cryptic morphology , low parasitaemia and selective growth in cultur... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
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"and",
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"medicine",
"geographical",
"locations",
"vertebrates",
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"diseases",
"parasitic",
"protozoans",
"animals",
"mammals",
"protozoans",
"molecular",
"biology",
"techniques",
"cellular",
"st... | 2017 | Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats |
Contemporary theory of spiking neuronal networks is based on the linear response of the integrate-and-fire neuron model derived in the diffusion limit . We find that for non-zero synaptic weights , the response to transient inputs differs qualitatively from this approximation . The response is instantaneous rather than... | Our work demonstrates a fast-firing response of nerve cells that remained unconsidered in network analysis , because it is inaccessible by the otherwise successful linear response theory . For the sake of analytic tractability , this theory assumes infinitesimally weak synaptic coupling . However , realistic synaptic i... | [
"Abstract",
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"biophysics/theory",
"and",
"simulation",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units |
Animals repeat rewarded behaviors , but the physiological basis of reward-based learning has only been partially elucidated . On one hand , experimental evidence shows that the neuromodulator dopamine carries information about rewards and affects synaptic plasticity . On the other hand , the theory of reinforcement lea... | As every dog owner knows , animals repeat behaviors that earn them rewards . But what is the brain machinery that underlies this reward-based learning ? Experimental research points to plasticity of the synaptic connections between neurons , with an important role played by the neuromodulator dopamine , but the exact w... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"computational",
"neuroscience",
"biology",
"neuroscience",
"learning",
"and",
"memory"
] | 2013 | Reinforcement Learning Using a Continuous Time Actor-Critic Framework with Spiking Neurons |
Chemical-genetic interactions–observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes–contain rich functional information linking compounds to their cellular modes of action . To systematically identify these interactions , an array of mutants is challenged with a compound and ... | Understanding how chemical compounds affect biological systems is of paramount importance as pharmaceutical companies strive to develop life-saving medicines , governments seek to regulate the safety of consumer products and agrichemicals , and basic scientists continue to study the fundamental inner workings of biolog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetic",
"networks",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"fungi",
"model",
"organisms",
"network",
"analysis",
"experimental",
"organism",
"systems",
"tubulins",
"genetic",
"interactions",
"research",
"and",
"analysis",
"methods",
"sacch... | 2018 | Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions |
Recent technologies like AGO CLIP sequencing and CLASH enable direct transcriptome-wide identification of AGO binding and miRNA target sites , but the most widely used miRNA target prediction algorithms do not exploit these data . Here we use discriminative learning on AGO CLIP and CLASH interactions to train a novel m... | MicroRNAs ( or miRNAs ) are a family of small RNA molecules that guide Argonaute ( AGO ) to specific target sites within mRNAs and regulate numerous biological processes in normal cells and in disease . Despite years of research , the principles of miRNA targeting are incompletely understood , and computational miRNA t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"sequencing",
"techniques",
"cell",
"physiology",
"cell",
"binding",
"rna-binding",
"proteins",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"gene",
"regulation",
"immunology",
"neuroscience",
"micrornas",
"mathematics",
"forecasting",
"... | 2016 | Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data |
During the last few decades , several studies have analyzed and described knowledge , attitudes , and practices ( KAP ) of populations regarding dengue . However , few studies have applied geometric data analytic techniques to generate indices from KAP domains . Results of such analyses have not been used to determine ... | Local vector control programs , as part of their routine activities , often use Knowledge Attitudes and Practices ( KAP ) surveys to guide their dengue control strategies . Usually , these questionnaires are extensive and result in a large amount of data that is difficult to analyze and summarize . This study uses an a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"decision",
"making",
"neuroscience",
"health",
"care",
"preventive",
"medicine",
"research",
"design",
"cognition",
"surveys",
"infectious",
"disease",
"control",
"questionnaires",
"research",
"and",
"a... | 2016 | KAP Surveys and Dengue Control in Colombia: Disentangling the Effect of Sociodemographic Factors Using Multiple Correspondence Analysis |
The possibility of HIV-1 eradication has been limited by the existence of latently infected cellular reservoirs . Studies to examine control of HIV latency and potential reactivation have been hindered by the small numbers of latently infected cells found in vivo . Major conceptual leaps have been facilitated by the us... | HIV establishes a state of latency in vivo and this latent reservoir , although small , is difficult to eradicate . To be able to better understand this state of latency , and to develop strategies to eliminate it , many groups have developed in vitro models of HIV latency . However , notable differences exist among ce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | An In-Depth Comparison of Latent HIV-1 Reactivation in Multiple Cell Model Systems and Resting CD4+ T Cells from Aviremic Patients |
Viruses that naturally infect cells expressing both MHC I and MHC II molecules render themselves potentially visible to both CD8+ and CD4+ T cells through the de novo expression of viral antigens . Here we use one such pathogen , the B-lymphotropic Epstein-Barr virus ( EBV ) , to examine the kinetics of these processes... | Many viruses infect cells in which both the MHC I and MHC II pathways of antigen presentation are active , and so viral proteins expressed in those cells may be presented as MHC I-peptide complexes to CD8+ T cells and as MHC II-peptide complexes to CD4+ T cells . Here we study these processes in a model system involvin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/persistence",
"and",
"latency",
"immunology/antigen",
"processing",
"and",
"recognition",
"virology/viral",
"replication",
"and",
"gene",
"regulation",
"virology/vaccines",
"immunology/immunomodulation",
"immunology/immune",
"response",
"immunology/immunity",
"to",
"inf... | 2009 | T Cell Detection of a B-Cell Tropic Virus Infection: Newly-Synthesised versus Mature Viral Proteins as Antigen Sources for CD4 and CD8 Epitope Display |
A family of secreted cathepsin L proteases with differential activities is essential for host colonization and survival in the parasitic flatworm Fasciola hepatica . While the blood feeding adult secretes predominantly FheCL1 , an enzyme with a strong preference for Leu at the S2 pocket of the active site , the infecti... | The flatworm Fasciola hepatica is responsible for fasciolosis , one of the most common parasitic diseases of livestock worldwide , with increased incidence of human cases . When contaminated plants are ingested , infective larvae are released and transverse the gut wall before migrating to the bile ducts within the liv... | [
"Abstract",
"Introduction",
"Methods",
"Results/Discussion"
] | [
"biomacromolecule-ligand",
"interactions",
"medicine",
"biochemistry",
"infectious",
"diseases",
"fasciolosis",
"enzymes",
"neglected",
"tropical",
"diseases",
"biology",
"enzyme",
"kinetics",
"parasitic",
"diseases"
] | 2013 | Dissecting the Active Site of the Collagenolytic Cathepsin L3 Protease of the Invasive Stage of Fasciola hepatica |
Incompatibilities between the nucleus and the cytoplasm of sufficiently distant species result in developmental arrest of hybrid and nucleocytoplasmic hybrid ( cybrid ) embryos . Several hypotheses have been proposed to explain their lethality , including problems in embryonic genome activation ( EGA ) and/or nucleo-mi... | When two species evolve separately for several million years , their respective genomes accumulate many small changes that together are responsible for the differences in their characters . Some of these affect the way eggs are prepared inside the germline , and/or how embryos develop , such that the egg cytoplasm of a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"embryology",
"evolutionary",
"biology",
"molecular",
"development",
"biology",
"morphogenesis",
"evolutionary",
"developmental",
"biology"
] | 2011 | Deficient Induction Response in a Xenopus Nucleocytoplasmic Hybrid |
The Asian tiger mosquito , Aedes albopictus , is a vector of dengue , Chikungunya , and Zika viruses . This mosquito inhabits a wide range of artificial water-holding containers in urban and suburban areas making it difficult to control . We tested the hypothesis that female-driven autodissemination of an insect growth... | Aedes albopictus is a highly invasive mosquito species and a competent vector of dengue , Chikungunya , Zika and other arboviruses . In the absence of therapeutics , vector control is the only means of controlling these diseases . Larvicides are important tool to limit mosquito populations . Backpack and low volume spr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"larvicides",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"togaviruses",
"pathogens",
"microbiology",
"animals",
"alphaviruses",
"reproductive",
"physiology",
"viruses",
"chikungunya",
"virus",
"rna",
"viruses",
... | 2016 | Targeting a Hidden Enemy: Pyriproxyfen Autodissemination Strategy for the Control of the Container Mosquito Aedes albopictus in Cryptic Habitats |
In budding yeast , activation of many DNA replication origins is regulated by their chromatin environment , whereas others fire in early S phase regardless of their chromosomal location . Several location-independent origins contain at least two divergently oriented binding sites for Forkhead ( Fkh ) transcription fact... | In this study , we explore the mechanisms that determine activation of DNA replication origins in early S phase . It has been shown that a subset of replication origins is regulated by Forkhead family transcription factors that ensure their firing at the beginning of S phase . However , the recruitment of Forkhead fact... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"&",
"methods"
] | [
"insertion",
"mutation",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"dna-binding",
"proteins",
"mutation",
"fungi",
"model",
"organisms",
"dna",
"replication",
"experimental",
"organism",
"systems",
"sequence",
"motif",
"analysis",
"dna",
"synthe... | 2017 | Recruitment of Fkh1 to replication origins requires precisely positioned Fkh1/2 binding sites and concurrent assembly of the pre-replicative complex |
Leptospirosis is an important cause of seasonal outbreaks in New Caledonia and the tropics . Using time series derived from high-quality laboratory-based surveillance from 2000–2012 , we evaluated whether climatic factors , including El Niño Southern Oscillation ( ENSO ) and meteorological conditions allow for the pred... | The El Niño Southern Oscillation is a major ocean – atmosphere phenomenon that strongly contributes to the timing and intensity of rainfall in the tropical Pacific islands and beyond . As a consequence , it also has a major effect on the number of cases of leptospirosis . By incorporating oceanographic parameters in mo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"atmospheric",
"science",
"tropical",
"diseases",
"social",
"sciences",
"geoinformatics",
"population",
"modeling",
"neglected",
"tropical",
"diseases",
"veterinary",
"science",
"public",
"and",
"occupational",
"health",
"infectiou... | 2014 | El Niño Southern Oscillation and Leptospirosis Outbreaks in New Caledonia |
The strengths of association mapping lie in its resolution and allelic richness , but spurious associations arising from historical relationships and selection patterns need to be accounted for in statistical analyses . Here we reanalyze one of the first generation structured association mapping studies of the Dwarf8 (... | Eleven years ago , association mapping was a cutting-edge tool used to identify regions of a genome associated with phenotypic variation . One of the first association studies performed in plants was reported in Thornsberry , et al . ( 2001 ) . Since then , researchers continued to develop new and improved genotyping ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics",
"plant",
"biology",
"crops",
"genetics",
"statistics",
"biology",
"genomics",
"genetics",
"and",
"genomics",
"agriculture"
] | 2013 | Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping |
The signaling of Toll-like receptors ( TLRs ) is the host's first line of defense against microbial invasion . The mitochondrion is emerging as a critical platform for antiviral signal transduction . The regulatory role of mitochondria for TLR signaling remains to be explored . Here , we show that the mitochondrial out... | In 2005 , MAVS was characterized as the critical adaptor protein for the signal transduction of RIG-I-like receptors ( RLRs ) . This provided the first link between mitochondria and the intracellular antiviral defense system . From then on , exploring the potential functions of novel mitochondrial proteins in microbe-h... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"immunity",
"immunology",
"biology",
"immune",
"response"
] | 2011 | Mitochondrial Ubiquitin Ligase MARCH5 Promotes TLR7 Signaling by Attenuating TANK Action |
The establishment of the germline is a critical , yet surprisingly evolutionarily labile , event in the development of sexually reproducing animals . In the fly Drosophila , germ cells acquire their fate early during development through the inheritance of the germ plasm , a specialized maternal cytoplasm localized at t... | The establishment of the germline during embryogenesis is a critical milestone for sexually reproducing organisms , but one that is surprisingly labile in evolution . For example , in the fly Drosophila , the germline is set aside early in embryogenesis due to the localized synthesis of the germ plasm at the posterior ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"transport",
"rna",
"interference",
"evolutionary",
"biology",
"germ",
"cells",
"developmental",
"biology",
"pattern",
"formation",
"gene",
"expression",
"comparative",
"genomics",
"biology",
"molecular",
"biology",
"rna",
"cell",
"biology",
"nucleic",
"acids",
... | 2011 | The Phylogenetic Origin of oskar Coincided with the
Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the
Holometabola |
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