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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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|---|---|---|---|---|---|
Nasal colonization by both gram-positive and gram-negative pathogens induces expression of the innate immune protein lipocalin 2 ( Lcn2 ) . Lcn2 binds and sequesters the iron-scavenging siderophore enterobactin ( Ent ) , preventing bacterial iron acquisition . In addition , Lcn2 bound to Ent induces release of IL-8 fro... | Bacterial pathogens such as Klebsiella pneumoniae require iron and use secreted molecules called siderophores to strip iron from mammalian proteins . When bacteria colonize the upper respiratory tract , the mucosa secretes the protein lipocalin 2 ( Lcn2 ) that binds to the siderophore enterobactin ( Ent ) and disrupts ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/innate",
"immunity",
"microbiology/immunity",
"to",
"infections",
"microbiology"
] | 2009 | Mucosal Lipocalin 2 Has Pro-Inflammatory and Iron-Sequestering Effects in Response to Bacterial Enterobactin |
The pilus 2a backbone protein ( BP-2a ) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus . It is characterized by six main immunologically distinct allelic variants , each inducing variant-specific protection . To investigate the ... | Group B Streptococcus ( GBS ) is the leading cause of neonatal invasive diseases and pili , as long filamentous fibers protruding from the bacterial surface , have been discovered as important virulence factors and potential vaccine candidates . The bacterial surface is the main interface between host and pathogen , an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequence",
"analysis",
"computer",
"science",
"computer",
"modeling",
"antigen",
"processing",
"and",
"recognition",
"streptococci",
"protein",
"structure",
"immunology",
"host-pathogen",
"interaction",
"biology",
"computational",
"biology",
"microbiology",
"computerized",
... | 2013 | Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus |
Genetic transformation , in which cells internalize exogenous DNA and integrate it into their chromosome , is widespread in the bacterial kingdom . It involves a specialized membrane-associated machinery for binding double-stranded ( ds ) DNA and uptake of single-stranded ( ss ) fragments . In the human pathogen Strept... | Natural genetic transformation , a programmed mechanism for horizontal gene transfer , permits the passage of environmental double-stranded ( ds ) DNA through the bacterial membrane and its subsequent integration into the recipient chromosome by homology . In the human pathogen Streptococcus pneumoniae , it requires de... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"streptococci",
"genetics",
"microbial",
"pathogens",
"molecular",
"genetics",
"biology",
"microbiology",
"molecular",
"cell",
"biology",
"bacterial",
"pathogens",
"gram",
"positive"
] | 2013 | Midcell Recruitment of the DNA Uptake and Virulence Nuclease, EndA, for Pneumococcal Transformation |
Aedes aegypti is the major vector of yellow and dengue fevers . After 10 generations of adult selection , an A . aegypti strain ( SP ) developed 1650-fold resistance to permethrin , which is one of the most widely used pyrethroid insecticides for mosquito control . SP larvae also developed 8790-fold resistance followin... | Aedes aegypti inhabits tropical and subtropical regions worldwide and is the major vector of dengue and yellow fevers , and a secondary vector of chikungunya fever . Dengue fever is epidemic in more than 110 countries and causes up to 100 million infections annually . As there is no efficient vaccine or medicine curren... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"entomology",
"enzyme",
"metabolism",
"enzymes",
"biology",
"and",
"life",
"sciences",
"enzymology",
"zoology",
"enzyme",
"chemistry",
"genetic",
"toxicology",
"toxicology",
"neurotoxicology"
] | 2014 | Mechanisms of Pyrethroid Resistance in the Dengue Mosquito Vector, Aedes aegypti: Target Site Insensitivity, Penetration, and Metabolism |
Wing pattern evolution in Heliconius butterflies provides some of the most striking examples of adaptation by natural selection . The genes controlling pattern variation are classic examples of Mendelian loci of large effect , where allelic variation causes large and discrete phenotypic changes and is responsible for b... | Identifying the genetic changes responsible for beneficial variation is essential for understanding how organisms adapt . Here , we use a combination of mapping , population genetic analysis , and gene expression studies to identify the genomic regions responsible for phenotypic evolution in the Neotropical butterfly H... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"evolutionary",
"biology/genomics",
"evolutionary",
"biology/pattern",
"formation",
"evolutionary",
"biology",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2010 | Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato |
orb is a founding member of the CPEB family of translational regulators and is required at multiple steps during Drosophila oogenesis . Previous studies showed that orb is required during mid-oogenesis for the translation of the posterior/germline determinant oskar mRNA and the dorsal-ventral determinant gurken mRNA . ... | The specification of polarity axes in the Drosophila egg and embryo depends on the proper organization of the microtubule ( MT ) and actin cytoskeleton during mid-oogenesis . During this period , the MT organizing center at the posterior of the oocyte is disassembled and a MT network is established at the anterior and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"rna",
"interference",
"messenger",
"rna",
"reproductive",
"physiology",
"cell",
"polarity",
"germ",
"cells",
"oocytes",
"epigenetics",
"cellular",
"structures",
"and",
"organelles"... | 2019 | The CPEB translational regulator, Orb, functions together with Par proteins to polarize the Drosophila oocyte |
Predators of all kinds , be they lions hunting in the Serengeti or fishermen searching for their catch , display various collective strategies . A common strategy is to share information about the location of prey . However , depending on the spatial characteristics and mobility of predators and prey , information shar... | When should we work together and when should we work alone ? This question is central to our efforts to understand social and ecological systems alike , from lions hunting in the Serengeti to fishermen searching for their catch . Here , we develop a mathematical modeling framework to identify the essential spatial fact... | [
"Abstract",
"Introduction",
"Behavioral",
"Modeling",
"of",
"Predators",
"Agent-Based",
"Model",
"Simulation",
"Experiments",
"Results",
"Discussion"
] | [
"ecology",
"and",
"environmental",
"sciences",
"predator-prey",
"dynamics",
"population",
"dynamics",
"mathematical",
"models",
"animal",
"signaling",
"and",
"communication",
"simulation",
"and",
"modeling",
"systems",
"science",
"mathematics",
"animal",
"behavior",
"popu... | 2016 | The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information |
As a major component of ideal plant architecture , leaf angle especially flag leaf angle ( FLA ) makes a large contribution to grain yield in rice . We utilized a worldwide germplasm collection to elucidate the genetic basis of FLA that would be helpful for molecular design breeding in rice . Genome-wide association st... | Rice leaf angle is a major component of ideal plant architecture that determines plant density . Many leaf angle-related genes have been characterized based on mutants , but natural variations of these genes and potential values in genetic improvement have not been evaluated . Here we explore the genetic basis of rice ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"genome-wide",
"association",
"studies",
"plant",
"anatomy",
"ecology",
"and",
"environmental",
"sciences",
"quantitative",
"trait",
"loci",
"conservation",
"genetics",
"genetic",
"mapping",
"plant",
"science",
"rice",
"genetically",
"modified",
"plants",... | 2018 | Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa) |
Inside individual cells , expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers . Since proteins half-lives can be comparable to the cell-cycle length , randomness in cell-division times generates additional intercellular variability in protein levels . ... | Inside individual cells , gene products often occur at low molecular counts and are subject to considerable stochastic fluctuations ( noise ) in copy numbers over time . An important consequence of noisy expression is that the level of a protein can vary considerably even among genetically identical cells exposed to th... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"engineering",
"and",
"technology",
"cell",
"cycle",
"and",
"cell",
"division",
"signal",
"processing",
"cell",
"processes",
"binomials",
"random",
"variables",
"noise",
"reduction",
"dna",
"transcription",
"probability",
"distribution",
"mathematics",
"algebra",
"polyn... | 2016 | Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes |
Kinetochores are multi-protein complexes that mediate the physical coupling of sister chromatids to spindle microtubule bundles ( called kinetochore ( K ) -fibres ) from respective poles . These kinetochore-attached K-fibres generate pushing and pulling forces , which combine with polar ejection forces ( PEF ) and elas... | To achieve proper cell division , newly duplicated chromosomes must be segregated into daughter cells with high fidelity . This occurs in mitosis where during the crucial metaphase stage chromosomes are aligned on an imaginary plate , called the metaphase plate . Chromosomes are attached to a structural scaffold—the mi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics |
The potential of broadly neutralizing antibodies targeting the HIV-1 envelope trimer to prevent HIV-1 transmission has opened new avenues for therapies and vaccines . However , their implementation remains challenging and would profit from a deepened mechanistic understanding of HIV-antibody interactions and the mucosa... | Successful solicitation of the potential of neutralizing antibodies for HIV-1 prevention will require a deepened understanding of HIV-1 transmission and antibody neutralization . In this study , we experimentally determined molecular parameters of the HIV-1-antibody interaction , and subsequently used this knowledge to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"viral",
"structure",
"animals",
"mamm... | 2017 | Predicting HIV-1 transmission and antibody neutralization efficacy in vivo from stoichiometric parameters |
Interaction between the hepatitis C virus ( HCV ) envelope protein E2 and the host receptor CD81 is essential for HCV entry into target cells . The number of E2-CD81 complexes necessary for HCV entry has remained difficult to estimate experimentally . Using the recently developed cell culture systems that allow persist... | The interaction between the hepatitis C virus ( HCV ) envelope protein E2 and the host cell surface receptor CD81 is critical for HCV entry into hepatocytes and presents a promising drug and vaccine target . Yet , the number of E2-CD81 complexes that must be formed between a virus and a target cell to enable viral entr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"theoretical",
"biology",
"gastroenterology",
"and",
"hepatology",
"biology",
"computational",
"biology"
] | 2011 | Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry |
Asymmetric cell division and apoptosis ( programmed cell death ) are two fundamental processes that are important for the development and function of multicellular organisms . We have found that the processes of asymmetric cell division and apoptosis can be functionally linked . Specifically , we show that asymmetric c... | Asymmetric cell division and apoptosis ( programmed cell death ) are two fundamental processes that are important for the development and function of multicellular organisms . Asymmetric cell division creates daughter cells of different fates , and this is critical for the generation of cellular diversity . Apoptosis e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"developmental",
"biology",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2008 | Control of Apoptosis by Asymmetric Cell Division |
Cytokines such as TNF and FASL can trigger death or survival depending on cell lines and cellular conditions . The mechanistic details of how a cell chooses among these cell fates are still unclear . The understanding of these processes is important since they are altered in many diseases , including cancer and AIDS . ... | Activation of death receptors ( TNFR and Fas ) can trigger either survival or cell death according to the cell type and the cellular conditions . In other words , the same signal can have antagonist responses . On one hand , the cell can survive by activating the NFκB signalling pathway . On the other hand , it can die... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
"computational",
"biology/signaling",
"networks",
"computational",
"biology/systems",
"biology",
"cell",
"biology/cell",
"signaling"
] | 2010 | Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement |
Cellular toxicity introduced by protein misfolding threatens cell fitness and viability . Failure to eliminate these polypeptides is associated with various aggregation diseases . In eukaryotes , the ubiquitin proteasome system ( UPS ) plays a vital role in protein quality control ( PQC ) , by selectively targeting mis... | The accumulation of misfolded proteins threatens cell fitness and viability and their aggregation is commonly associated with numerous neurodegenerative disorders . Cells therefore rely on a number of protein quality control ( PQC ) pathways to prevent protein aggregation . In eukaryotes , the ubiquitin proteasome syst... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The Protein Quality Control Machinery Regulates Its Misassembled Proteasome Subunits |
Iron sequestration by host iron-binding proteins is an important mechanism of resistance to microbial infections . Inside oral epithelial cells , iron is stored within ferritin , and is therefore not usually accessible to pathogenic microbes . We observed that the ferritin concentration within oral epithelial cells was... | Iron is an essential nutrient for all microbes . Many human pathogenic microbes have developed sophisticated strategies to acquire iron from the host as most compartments in the body contain little free iron . For example , in oral epithelial cells intracellular iron is bound to ferritin , a protein that is highly resi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/fungal",
"infections",
"genetics",
"and",
"genomics/gene",
"function",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2008 | The Hyphal-Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin |
Glycosyltransferases are a class of enzymes that catalyse the posttranslational modification of proteins to produce a large number of glycoconjugate acceptors from a limited number of nucleotide-sugar donors . The products of one glycosyltransferase can be the substrates of several other enzymes , causing a combinatori... | While enzymes tend to have a narrow substrate specificity , there are a number of enzymes that are promiscuous , acting on a wide range of substrates . In this article we derive expressions for general multi-substrate competitive inhibition for the class of transferases , with particular emphasis on glycosylation . By ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"competitive",
"inhibitors",
"post-translational",
"modification",
"proteins",
"enzyme",
"metabolism",
"enzymes",
"transferases",
"biology",
"and",
"life",
"sciences",
"glycosylation",
"enzymology",
"enzyme",
"kinetics",
"enzyme",
"inhibitors",
"enzyme",
"ch... | 2018 | A mechanism for bistability in glycosylation |
Human T lymphotropic virus type I ( HTLV-I ) infection is largely latent in infected persons . How HTLV-1 establishes latency and reactivates is unclear . Here we show that most HTLV-1-infected HeLa cells become senescent . By contrast , when NF-κB activity is blocked , senescence is averted , and infected cells contin... | Most HTLV-1-infected individuals are asymptomatic . It is thought that the proviral DNA is transcriptionally inert and HTLV-1 replicates through mitotic expansion of host cells . The evolving provirus integration patterns in HTLV-1 carriers , however , suggest new infection occurs continuously . Whether or how HTLV-1 e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"hiv",
"immunopathogenesis",
"clinical",
"immunology",
"virology",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"viral",
"diseases"
] | 2014 | Regulation of Human T-Lymphotropic Virus Type I Latency and Reactivation by HBZ and Rex |
Nipah virus ( NiV ) is an emerging disease that causes severe encephalitis and respiratory illness in humans . Pigs were identified as an intermediate host for NiV transmission in Malaysia . In Bangladesh , NiV has caused recognized human outbreaks since 2001 and three outbreak investigations identified an epidemiologi... | Nipah virus ( NiV ) , is an emerging disease that causes severe encephalitis and respiratory illness in humans . Pigs were identified as an intermediate host for NiV transmission in Malaysia , and in Bangladesh three NiV outbreak investigations since 2001 identified an epidemiological association between close contact ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"public",
"and",
"occupational",
"health",
"research",
"design",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"animal",
"studies",
"epidemiology",
"tropical",
"diseases",
"research",
"and",
"analysis",
"methods"
] | 2014 | Serological Evidence of Henipavirus Exposure in Cattle, Goats and Pigs in Bangladesh |
Echinococcosis is a neglected zoonotic disease affecting over 1 million people worldwide at any given time . It is the leading cause of hospital admissions for parasitic diseases in Chile . We conducted a retrospective investigation of hospitalized cases to describe the epidemiological trends of echinococcosis in Chile... | Humans are infected by many types of parasites that originate from animals . Cystic echinococcosis ( CE ) is a tapeworm infection that affects over 1 million people over the world at any given time , with symptoms such as abdominal pain , chest pain , vomiting , and allergic reactions . The lifecycle of this parasite i... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"hospitalizations",
"livestock",
"medicine",
"and",
"health",
"sciences",
"chile",
"(country)",
"ruminants",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"health",
"care",
"neglected",
"tropical",
"dise... | 2017 | Trends and correlates of cystic echinococcosis in Chile: 2001–2012 |
Lytic herpes simplex virus 1 ( HSV-1 ) infection triggers disruption of transcription termination ( DoTT ) of most cellular genes , resulting in extensive intergenic transcription . Similarly , cellular stress responses lead to gene-specific transcription downstream of genes ( DoG ) . In this study , we performed a det... | Recently , we reported that productive herpes simplex virus 1 ( HSV-1 ) infection leads to disruption of transcription termination ( DoTT ) of most but not all cellular genes . This results in extensive transcription beyond poly ( A ) sites and into downstream genes . Subsequently , cellular stress responses were found... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cellular",
"stress",
"responses",
"classical",
"mechanics",
"gene",
"regulation",
"cell",
"processes",
"dna-binding",
"proteins",
"vertebrates",
"mechanical",
"stress",
"dogs",
"animals",
"mammals",
"dna",
"transcription",
"epigenetics",
"chromatin",
"chromosome",
"biolo... | 2018 | HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes |
In the current study , we used a mouse model and human blood samples to determine the effects of chronic alcohol consumption on immune responses during Mycobacterium tuberculosis ( Mtb ) infection . Alcohol increased the mortality of young mice but not old mice with Mtb infection . CD11b+Ly6G+ cells are the major sourc... | Chronic alcohol consumption modulates the host immune defense mechanism ( s ) and makes the host susceptible to various fungal , viral and bacterial infections , including Mycobacterium tuberculosis ( Mtb ) . However , limited information is available about the mechanisms involved in alcohol-mediated host susceptibilit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"death",
"rates",
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"chemical",
"compounds",
"immunology",
"social",
"sciences",
"diet",
"light",
"microscopy",
"organic",
"compounds",
"nutrition",
"microscopy",
"confocal",
"microscopy",
"po... | 2018 | Alcohol enhances type 1 interferon-α production and mortality in young mice infected with Mycobacterium tuberculosis |
In a living cell , the antiparallel double-stranded helix of DNA is a dynamically changing structure . The structure relates to interactions between and within the DNA strands , and the array of other macromolecules that constitutes functional chromatin . It is only through its changing conformations that DNA can organ... | In a living cell , DNA both is an information carrier and carries out important structural tasks , such as organizing its replication and distributing the chromosomes to the daughter cells . DNA is frequently depicted as an antiparallel double-stranded helix , but DNA may rather be viewed as having a dynamically changi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"molecular",
"biology",
"genetics",
"and",
"genomics",
"homo",
"(human)",
"computational",
"biology"
] | 2007 | The Human Genomic Melting Map |
Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale . However , the relation of these models to the properties of single neurons is unclear . Here we derive an equation for several interacting populations at the mesoscopic scale starting from a micros... | Understanding the brain requires mathematical models on different spatial scales . On the “microscopic” level of nerve cells , neural spike trains can be well predicted by phenomenological spiking neuron models . On a coarse scale , neural activity can be modeled by phenomenological equations that summarize the total a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"population",
"dynamics",
"membrane",
"potential",
"condensed",
"matter",
"physics",
"computational",
"biology",
"electrophysiology",
"neuroscience",
"computational",
"neuroscience",
"pop... | 2017 | Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size |
Dengue is the most important mosquito-borne viral disease affecting humans . The only prevention measure currently available is the control of its vectors , primarily Aedes aegypti . Recent advances in genetic engineering have opened the possibility for a new range of control strategies based on genetically modified mo... | Dengue is a viral disease that affects approximately 50 million people annually , and is estimated to result in 12 , 500 fatalities . Dengue viruses are vectored by mosquitoes , predominantly by the species Aedes aegypti . Because there is currently no vaccine or specific treatment , the only available strategy to redu... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"ecology/population",
"ecology",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2009 | Skeeter Buster: A Stochastic, Spatially Explicit Modeling Tool for Studying Aedes aegypti Population Replacement and Population Suppression Strategies |
The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein ( NP ) . Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA , and prior work has compared human and avian viral strains to identify amino-acid differences in NP that af... | During viral infection , human cells express proteins that can restrict virus replication . However , in many cases it remains unclear what determines the sensitivity of a given viral strain to a particular restriction factor . Here we use a high-throughput approach to measure how all amino-acid mutations to the nucleo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"microbial",
"mutation",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"influenza",
"pathogens",
"microbiology",
"dna-binding",
"proteins",
"vertebrates",
"orthomyxoviruses",
"animals",
"viruses",
"polymerases",
"rna",
"viruses",
"... | 2017 | Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA |
The European & Developing Countries Clinical Trials Partnership ( EDCTP ) is a partnership of European and sub-Saharan African countries that aims to accelerate the development of medical interventions against poverty-related diseases ( PRDs ) . A bibliometric analysis was conducted to 1 ) measure research output from ... | The European & Developing Countries Clinical Trials Partnership ( EDCTP ) was created in 2003 as a European response to the global health crisis caused by the three main poverty-related diseases ( PRDs ) of HIV/AIDS , tuberculosis and malaria . EDCTP funds research focusing on clinical trials for diagnosing , preventin... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Bibliometric Assessment of European and Sub-Saharan African Research Output on Poverty-Related and Neglected Infectious Diseases from 2003 to 2011 |
Calorie restriction ( CR ) robustly extends the lifespan of numerous species . In the yeast Saccharomyces cerevisiae , CR has been proposed to extend lifespan by boosting the activity of sirtuin deacetylases , thereby suppressing the formation of toxic repetitive ribosomal DNA ( rDNA ) circles . An alternative theory i... | There are only a few techniques that reliably promote longevity in multiple , distantly related species . Perhaps the best known , caloric restriction ( CR ) , was first shown to promote lifespan in rodents in the 1930s and has since been shown to work in most species it has been tested on . We and others have previous... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"microbiology",
"molecular",
"biology",
"genetics",
"and",
"genomics",
"saccharomyces"
] | 2007 | MSN2 and MSN4 Link Calorie Restriction and TOR to Sirtuin-Mediated Lifespan Extension in Saccharomyces cerevisiae |
AGGF1 is an angiogenic factor with therapeutic potential to treat coronary artery disease ( CAD ) and myocardial infarction ( MI ) . However , the underlying mechanism for AGGF1-mediated therapeutic angiogenesis is unknown . Here , we show for the first time that AGGF1 activates autophagy , a housekeeping catabolic cel... | Coronary artery disease is the number one killer disease worldwide . Recently , therapeutic angiogenesis has been proposed as an attractive new strategy for treating this and other ischemic diseases . This study establishes the angiogenic factor AGGF1 as a novel target and agent that can successfully treat coronary art... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"autophagic",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"ultrasound",
"imaging",
"cardiovascular",
"physiology",
"cardiovascular",
"anatomy",
"gene",
"regulation",
"cell",
"processes",
"echocardiography",
"angiog... | 2016 | Angiogenic Factor AGGF1 Activates Autophagy with an Essential Role in Therapeutic Angiogenesis for Heart Disease |
The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear . Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes . RIP-Seq analysis of these two yeast proteins identified overlapping ... | All organisms must respond to changes in their external environment such as exposure to different stresses . The availability of genome sequences and post-genomic technologies has enabled the analysis of these adaptive responses at the molecular level in terms of altered gene expression profiles . However , relatively ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"rna",
"cell",
"biology",
"oxidative",
"stress",
"gene",
"expression",
"genetics",
"biology",
"and",
"life",
"sciences",
"proteomics",
"molecular",
"cell",
"biology",
"oxidative",
"damage",
"antioxidants",
"ribosomes"
] | 2015 | The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response |
Arf4 is proposed to be a critical regulator of membrane protein trafficking in early secretory pathway . More recently , Arf4 was also implicated in regulating ciliary trafficking , however , this has not been comprehensively tested in vivo . To directly address Arf4’s role in ciliary transport , we deleted Arf4 specif... | Primary cilia are sensory organelles found on most cells and contain specific receptors that detect extracellular stimuli . Defects in trafficking receptors to cilia cause a diverse set of diseases called ciliopathies , which include polycystic kidney disease , obesity , cerebral anomalies and retinal degeneration . Ba... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"zymogens",
"enzymology",
"social",
"sciences",
"neuroscience",
"animal",
"models",
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"organisms",
"experimental",
"organism",
"systems",
"sequence",
"motif",
"analysis",
"kidneys",
"cellular",
"structures",
"and",
"organe... | 2017 | Loss of Arf4 causes severe degeneration of the exocrine pancreas but not cystic kidney disease or retinal degeneration |
The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target , rather antibiotic induced stress seems to resonate through the bacterium , creating selective pressures that drive the emergence of adaptive mutations not only in the direct target , but in genes involved in... | While antibiotic resistant bacterial pathogens cause millions of deaths each year it remains largely unclear how a bacterium deals with antibiotic-induced stress and how this leads to the emergence of resistance . Moreover , many bacterial species are composed of strains whose genomes vary considerably , and while this... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [
"bacteriology",
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"genetic",
"networks",
"pathology",
"and",
"laboratory",
"medicine",
"pneumococcus",
"gene",
"regulation",
"pathogens",
"drugs",
"microbiology",
"antibiotic",
"resistance",
"regulator",
"genes",
"a... | 2016 | Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome |
A major bottleneck in understanding zoonotic pathogens has been the analysis of pathogen co-infection dynamics . We have addressed this challenge using a novel direct sequencing approach for pathogen quantification in mixed infections . The major zoonotic food-borne pathogen Campylobacter jejuni , with an important res... | Pathogenic bacteria that can be transferred from animals to humans represent a highly potent human health hazard . Understanding the ecology of these pathogens in the animal host is of fundamental importance . A major analytical challenge , however , is the fact that individual animal hosts can be colonised by multiple... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"chicken",
"ecology",
"public",
"health",
"and",
"epidemiology"
] | 2007 | Co-Infection Dynamics of a Major Food-Borne Zoonotic Pathogen in Chicken |
Autocrine priming of cells by small quantities of constitutively produced type I interferon ( IFN ) is a well-known phenomenon . In the absence of type I IFN priming , cells display attenuated responses to other cytokines , such as anti-viral protection in response to IFNγ . This phenomenon was proposed to be because I... | Cells of the immune system release interferons ( IFNs ) in response to pathogens or tumor cells; these proteins signal to other immune cells to initiate the body's defense mechanisms . The two classes of IFNs—types I and II—have different receptors and distinct effects on the cells; however , there is “crosstalk” betwe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/cell",
"signaling",
"biochemistry/chemical",
"biology",
"of",
"the",
"cell",
"immunology/immune",
"response",
"infectious",
"diseases/viral",
"infections",
"immunology/immunity",
"to",
"infections",
"cell",
"biology/gene",
"expression"
] | 2010 | Functional Crosstalk between Type I and II Interferon through the Regulated Expression of STAT1 |
Clonorchiasis , caused by the infection of Clonorchis sinensis ( C . sinensis ) , is a kind of neglected tropical disease , but it is highly related to cholangiocarcinoma and hepatocellular carcinoma ( HCC ) . It has been well known that the excretory/secretory products of C . sinensis ( CsESPs ) play key roles in clon... | Clonorchis sinensis ( C . sinensis ) has afflicted more than 35 million people in world and approximately 15 million in China , creating a socio-economic burden in epidemic regions . The infection of C . sinensis is highly related to cholangiocarcinoma and hepatocellular carcinoma ( HCC ) . It has been documented that ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Molecular Characterization of Severin from Clonorchis sinensis Excretory/Secretory Products and Its Potential Anti-apoptotic Role in Hepatocarcinoma PLC Cells |
Despite the wealth of knowledge regarding the mechanisms of action and the mechanisms of resistance to azole antifungals , very little is known about how the azoles are imported into pathogenic fungal cells . Here the in-vitro accumulation and import of Fluconazole ( FLC ) was examined in the pathogenic fungus , Candid... | Azole antifungals are used to treat a wide variety of fungal infections of humans , animals and plants . A great deal is known about how the azoles interact with their target enzyme within fungal cells and how the azoles are exported from the fungal cell through various efflux pumps . Altered interactions with the targ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/fungal",
"infections",
"microbiology/medical",
"microbiology",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance"
] | 2010 | Azole Drugs Are Imported By Facilitated Diffusion in Candida albicans and Other Pathogenic Fungi |
Fluoroquinolones are antibacterial drugs that inhibit DNA Gyrase and Topoisomerase IV . These essential enzymes facilitate chromosome replication and RNA transcription by regulating chromosome supercoiling . High-level resistance to fluoroquinolones in E . coli requires the accumulation of multiple mutations , includin... | The increasing frequency of human pathogens resistant to important classes of antibiotics poses a serious and growing challenge for medicine and society . We need improved strategies to reduce the rate of resistance development , for established and novel drugs , based on knowledge of the factors that drive the increas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance",
"microbiology"
] | 2009 | Interplay in the Selection of Fluoroquinolone Resistance and Bacterial Fitness |
Understanding how genetic variation interacts with the environment is essential for understanding adaptation . In particular , the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation ( G x E ) . The mechanistic basis for G x E is almost co... | Many traits are influenced by genetic variation in interaction with the environment , so called G x E variation . In agriculture , for example , different varieties are optimal in different environments . In evolution , G x E is also crucial for local adaptation . Identifying the genes underlying G x E has proven extre... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | "Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana |
Between October 2013 and April 2014 , more than 30 , 000 cases of Zika virus ( ZIKV ) disease were estimated to have attended healthcare facilities in French Polynesia . ZIKV has also been reported in Africa and Asia , and in 2015 the virus spread to South America and the Caribbean . Infection with ZIKV has been associ... | Since the first reported major outbreak of Zika virus disease in Micronesia in 2007 , the virus has caused outbreaks throughout the Pacific and South America . Transmitted by the Aedes genus of mosquitoes , the virus has been linked to possible neurological complications including Guillain-Barré Syndrome and microcepha... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"microcephaly",
"pathology",
"and",
"laboratory",
"medicine",
"demography",
"pathogens",
"geographical",
"locations",
"microbiology",
"vector-borne",
"diseases",
"mathematical",
"models",
"animals"... | 2016 | Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013–14 French Polynesia Outbreak |
Fish-borne zoonotic trematodes ( FZT ) infections including liver- and minute intestinal flukes are common in Southeast Asia in both humans and domestic animals eating raw fish and since 2010 , the liver flukes are recognised as neglected tropical diseases by WHO . Mass drug treatment with praziquantel is advised for h... | Fish-borne zoonotic trematodes ( FZT ) including liver and small intestinal flukes in humans and domestic animals are a growing problem in Southeast Asia . WHO has recently recognized the problem , listed the liver flukes as neglected tropical diseases and recommends mass drug treatment of humans to overcome the diseas... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2014 | Reinfection of Dogs with Fish-Borne Zoonotic Trematodes in Northern Vietnam following a Single Treatment with Praziquantel |
Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales . Structurally characterizing these exchanges is challenging , both experimentally and computationally . Large , diffusional motions are often on timescales that are difficul... | Multi-cellular physiology is an emergent property , which depends critically on inter-cellular signaling pathways . Transmembrane G protein-coupled receptors ( GPCRs ) mediate a large variety of physiological events throughout the body , such as vision or cardiovascular regulation . It is thus no surprise that GPCRs ar... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs |
Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation . Increasingly , the capacity for high-throughput experimentation provided by new imaging modalities , cont... | New technologies have increased the size and content-richness of biological imaging datasets . As a result , automated image processing is increasingly necessary to extract relevant data in an objective , consistent and time-efficient manner . While image processing tools have been developed for general problems that a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans |
Large-scale protein interaction networks ( PINs ) have typically been discerned using affinity purification followed by mass spectrometry ( AP/MS ) and yeast two-hybrid ( Y2H ) techniques . It is generally recognized that Y2H screens detect direct binary interactions while the AP/MS method captures co-complex associati... | To understand and model cellular processes , we require accurate descriptions of the interactions occurring between constituent proteins . Large-scale protein interaction maps have typically been measured in two distinct ways . The first detects direct pair-wise associations by testing only two proteins at a time for a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/bioinformatics",
"computational",
"biology/systems",
"biology"
] | 2009 | A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity |
A structure-based model of myosin motor is built in the same spirit of our early work for kinesin-1 and Ncd towards physical understanding of its mechanochemical cycle . We find a structural adaptation of the motor head domain in post-powerstroke state that signals faster ADP release from it compared to the same from t... | Molecular motors are perhaps the most important proteins present in the cell . The importance specifically lies with the fact that these proteins use the chemical energy source ( such as ATP ) of the cell to generate mechanical work and perform a wide range of functionalities . In this article , we generalize the idea ... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [
"cell",
"motility",
"kinesins",
"crystal",
"structure",
"actin",
"filaments",
"engineering",
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"technology",
"condensed",
"matter",
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"engines",
"molecular",
"motors",
"actin",
"motors",
"crystallography",
"motor",
"proteins",
"contractile",
"proteins",
"s... | 2016 | Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity |
The aim of this study was to determine , through a genome-wide association study ( GWAS ) , the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis ( SSc ) . We considered limited ( lcSSc ) and diffuse ( dcSSc ) cutaneous involvement , and the relationships with presence of the SS... | Scleroderma or systemic sclerosis is a complex autoimmune disease affecting one individual of every 100 , 000 in Caucasian populations . Even though current genetic studies have led to better understanding of the pathogenesis of the disease , much remains unknown . Scleroderma is a heterogeneous disease , which can be ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"clinical",
"immunology",
"genetics",
"immunology",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Identification of Novel Genetic Markers Associated with Clinical Phenotypes of Systemic Sclerosis through a Genome-Wide Association Strategy |
Tripartite Motif ( TRIM ) ubiquitin ligases act in the innate immune response against viruses . One of the best characterized members of this family , TRIM5α , serves as a potent retroviral restriction factor with activity against HIV . Here , we characterize what are likely to be the youngest TRIM genes in the human g... | A fundamental question in biology is how the immune system is able to inactivate the enormous number of pathogens that it faces . The vast majority of pathogens are quickly neutralized by the innate immune system , a large network of defenses to which approximately 1/30 of the human genome is devoted . Because pathogen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"biology",
"genomics",
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Identification of a Genomic Reservoir for New TRIM Genes in Primate Genomes |
Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family . Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in t... | Plasmodium falciparum is a protist parasite that causes malaria and kills more than 800 , 000 people per year . The parasite escapes from the human immune response by antigenic variation through switching between expression of different var genes . These encode different variant antigens that are expressed on the surfa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/protozoal",
"infections",
"genetics",
"and",
"genomics/epigenetics",
"cell",
"biology/gene",
"expression"
] | 2011 | Expression of P. falciparum var Genes Involves Exchange of the Histone Variant H2A.Z at the Promoter |
Middle East respiratory syndrome coronavirus ( MERS-CoV ) remains a threat to public health worldwide; however , effective vaccine or drug against CoVs remains unavailable . CoV helicase is one of the three evolutionary most conserved proteins in nidoviruses , thus making it an important target for drug development . W... | Severe acute respiratory syndrome coronavirus ( SARS-CoV ) and Middle East respiratory syndrome coronavirus ( MERS-CoV ) caused global pandemics in 2003 and 2012 with the fatality rates of 10–35% . Outbreak of MERS-CoV in the Republic of Korea in 2015 highlighted that the newly emerged CoVs remain a concern for the pub... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"coronaviruses",
"crystal",
"structure",
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"and",
"laboratory",
"medicine",
"enzymes",
"pathogens",
"split-decomposition",
"method",
"condensed",
"matter",
"physics",
"microbiology",
"enzymology",
"phosphatases",
"viruses"... | 2017 | Crystal structure of Middle East respiratory syndrome coronavirus helicase |
Learning in biologically relevant neural-network models usually relies on Hebb learning rules . The typical implementations of these rules change the synaptic strength on the basis of the co-occurrence of the neural events taking place at a certain time in the pre- and post-synaptic neurons . Differential Hebbian learn... | Which learning rules can be used to capture the temporal relations between activation events involving pairs of neurons in artificial neural networks ? Previous computational research proposed various differential Hebbian learning ( DHL ) rules that rely on the activation of neurons and time derivatives of their activa... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"learning",
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"and",
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"action",
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"engineering",
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"nervous",
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"signal",
"processing",
"membrane",
"potential",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
... | 2018 | General differential Hebbian learning: Capturing temporal relations between events in neural networks and the brain |
Filamentous fungi produce a diverse array of secondary metabolites ( SMs ) critical for defense , virulence , and communication . The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes , an atypical arrangement for metabolic pathways in other eukaryotes . Comparative studies of ... | All organisms produce metabolites , which are small molecules important for growth , reproduction , and other essential functions . Some organisms , including fungi , plants , and bacteria , make specialized forms of metabolites known as “secondary” metabolites that are ecologically important and improve their producer... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"taxonomy",
"aspergillus",
"fumigatus",
"medicine",
"and",
"health",
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"pathology",
"and",
"laboratory",
"medicine",
"aspergillus",
"fungal",
"genetics",
"pathogens",
"microbiology",
"fungi",
"phylogenetics",
"data",
"management",
"metabolites",
"fungal",
"patho... | 2017 | Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species |
As a result of evolution , the biology of triatomines must have been significantly adapted to accommodate trypanosome infection in a complex network of vector-vertebrate-parasite interactions . Arthropod-borne parasites have probably developed mechanisms , largely still unknown , to exploit the vector-vertebrate host i... | The control of Chagas disease , an infection that affects ca . 8 million people in Latin America , is mostly based on vector control activities . Understanding vector biology and how these insects interact with their environment , hosts and pathogens is crucial to improve vector control strategies . The behavior of tri... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Trypanosomes Modify the Behavior of Their Insect Hosts: Effects on Locomotion and on the Expression of a Related Gene |
Retroviruses and Long Terminal Repeat ( LTR ) -retrotransposons have distinct patterns of integration sites . The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters . The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe i... | Retroviruses and retrotransposons are genetic elements that propagate by integrating into chromosomes of eukaryotic cells . Genetic disorders are being treated with retrovirus-based vectors that integrate corrective genes into the chromosomes of patients . Unfortunately , the vectors can alter expression of adjacent ge... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"recombination-based",
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"molecular",
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"chromatin",
"schizosaccharomyces",
"homologous",
"recombination",
"research",
"and",
... | 2017 | Host factors that promote retrotransposon integration are similar in distantly related eukaryotes |
CD8+ T cells have been shown to play a crucial role in Trypanosoma cruzi infection . Memory CD8+ T cells can be categorised based on their distinct differentiation stages and functional activities as follows: stem cell memory ( TSCM ) , central memory ( TCM ) , transitional memory ( TTM ) , effector memory ( TEM ) and ... | Chagas disease is caused by the intracellular parasite Trypanosoma cruzi . After the onset of acute infection , all individuals enter the chronic phase and approximately 70% of them never have symptoms . However , nearly 30% of infected individuals develop symptoms , mainly of heart disease , even decades after the ini... | [
"Abstract",
"Introduction",
"Methods",
"Results",
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] | [
"medicine",
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"immunology",
"tropical",
"diseases",
"protozoan",
"infections",
"parasitic",
"diseases",
"immune",
"response"
] | 2015 | Low Frequency of Circulating CD8+ T Stem Cell Memory Cells in Chronic Chagasic Patients with Severe Forms of the Disease |
Trypanosomes show an intriguing organization of their mitochondrial DNA into a catenated network , the kinetoplast DNA ( kDNA ) . While more than 30 proteins involved in kDNA replication have been described , only few components of kDNA segregation machinery are currently known . Electron microscopy studies identified ... | Proper segregation of the mitochondrial genome during cell division is a prerequisite of healthy eukaryotic cells . However , the mechanism underlying the segregation process is only poorly understood . We use the single celled parasite Trypanosoma brucei , which , unlike most model organisms , harbors a single large m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
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"mitochondria",
"epigenetics",
"bioenergetics",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
... | 2016 | TAC102 Is a Novel Component of the Mitochondrial Genome Segregation Machinery in Trypanosomes |
Cell fate choices are tightly controlled by the interplay between intrinsic and extrinsic signals , and gene regulatory networks . In Saccharomyces cerevisiae , the decision to enter into gametogenesis or sporulation is dictated by mating type and nutrient availability . These signals regulate the expression of the mas... | The cell-fate controlling gametogenesis is essential for all sexual reproducing organisms . In Saccharomyces cerevisiae , entry into gametogenesis or sporulation is dictated by mating type and nutrient availability . These signals regulate the expression of the master regulator of entry into sporulation , IME1 . In thi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"meiosis",
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"messenger",
"rna",
"carbohydrates",
"organic",
"compounds",
"glucose",
"reproductive",
"physiology",
"glucose",
"signaling",
... | 2016 | Nutrient Control of Yeast Gametogenesis Is Mediated by TORC1, PKA and Energy Availability |
The Adenovirus ( Ad ) genome within the capsid is tightly associated with a virus-encoded , histone-like core protein—protein VII . Two other Ad core proteins , V and X/μ , also are located within the virion and are loosely associated with viral DNA . Core protein VII remains associated with the Ad genome during the ea... | The Ad major core protein VII protects the viral genome from recognition by a cellular DNA damage response during the early stages of infection and alters cellular chromatin to block innate signaling mechanisms . The packaging of the Ad genome into the capsid is thought to follow the paradigm of dsDNA bacteriophage whe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"hek",
"293",
"cells",
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"techniques",
"microbial",
"genomics",
"research",
"and",
"analysis",
"methods",
"viral",
"genomics",
"viral",
"core",
"proteins... | 2017 | The adenovirus major core protein VII is dispensable for virion assembly but is essential for lytic infection |
Trypanosoma brucei , the causative agent of Human African Trypanosomiasis ( HAT ) , expresses two proteins with homology to human glycogen synthase kinase 3β ( HsGSK-3 ) designated TbruGSK-3 short and TbruGSK-3 long . TbruGSK-3 short has previously been validated as a potential drug target and since this enzyme has als... | Over 60 million people in sub-Saharan Africa are at risk of infection with the parasite Trypanosoma brucei which causes Human African Trypanosomiasis ( HAT ) , also known as sleeping sickness . The disease results in systemic and neurological disability to its victims . At present , only four drugs are available for tr... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"medical",
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"global",
"health",
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"trypanosomiasis",
"neglected",
"tropical",
"diseases",
"biology",
"microbiology",
"parasitic",
"diseases",
"parasitology"
] | 2011 | Trypanosoma brucei Glycogen Synthase Kinase-3, A Target for Anti-Trypanosomal Drug Development: A Public-Private Partnership to Identify Novel Leads |
Src tyrosine kinases are deregulated in numerous cancers and may favor tumorigenesis and tumor progression . We previously described that Src activation in NIH-3T3 mouse fibroblasts promoted cell resistance to apoptosis . Indeed , Src was found to accelerate the degradation of the pro-apoptotic BH3-only protein Bik and... | Personalizing medicine on a molecular basis has proven its clinical benefits . The molecular study of the patient's tumor and healthy tissues allowed the identification of determinant mutations and the subsequent optimization of healthy and cancer cells specific response to treatments . Here , we propose a combined mat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"oncology",
"systems",
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"cell",
"biology",
"comp... | 2013 | Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization |
Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci , but the prevalence of such enhancer RNAs ( eRNAs ) within the transcriptome , and the association of eRNA expression with tissue-specific enhancer activity in vivo remain poorly understood . Here , we investigated the ex... | Up to 80% of mammalian genomes are actively transcribed , producing large numbers of non-coding RNAs without known functions . One particularly exciting category of such non-coding transcripts are the recently discovered enhancer RNAs ( eRNAs ) transcribed from distant-acting enhancer elements . Studies in cell-based p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"biology",
"and",
"life",
"sciences",
"developmental",
"biology"
] | 2014 | Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers |
Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments . This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life . Bacteria have evolved enormous bio... | Adaptive radiation is the rapid origination of an array of species by the divergent colonization of disparate ecological niches . In the case of pathogenic bacteria , radiations can lead to the emergence of novel human pathogens . Being divergently adapted to a range of different mammalian hosts , including humans as r... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genomics",
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"infectious",
"diseases",
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary... | 2011 | Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella |
Recent genome-wide ( GW ) scans have identified several independent loci affecting human stature , but their contribution through the different skeletal components of height is still poorly understood . We carried out a genome-wide scan in 12 , 611 participants , followed by replication in an additional 7 , 187 individ... | The first genetic association studies of adult height have confirmed a role of many common variants in influencing human height , but to date , the genetic basis of differences between different skeletal components of height have not been addressed . Here , we take advantage of recent technical and methodological advan... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/complex",
"traits",
"rheumatology/bone",
"and",
"mineral",
"metabolism",
"genetics",
"and",
"genomics",
"rheumatology/cartilage",
"biology",
"and",
"osteoarthritis"
] | 2009 | Meta-Analysis of Genome-Wide Scans for Human Adult Stature Identifies Novel Loci and Associations with Measures of Skeletal Frame Size |
Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases . The ecological niche of 28 North and Central American sand fly species , including those with epidemiological relevance... | The present study models the niche of the most abundant sand fly species in North and Central America , including all proven and incriminated vectors of Leishmaniases , an important neglected tropical disease of the region . The expansion and elevation or centroid shifts of the species' niche are modeled for extreme ( ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Current and Future Niche of North and Central American Sand Flies (Diptera: Psychodidae) in Climate Change Scenarios |
Animal heterotrimeric G proteins are activated by guanine nucleotide exchange factors ( GEF ) , typically seven transmembrane receptors that trigger GDP release and subsequent GTP binding . In contrast , the Arabidopsis thaliana G protein ( AtGPA1 ) rapidly activates itself without a GEF and is instead regulated by a s... | Extracellular signals activate intracellular changes that lead to cell behaviors . This spatial coupling is mediated by cell-surface receptor activation of the heterotrimeric G protein complex located on the cytoplasmic side of the plasma membrane . Unlike the case for metazoans , plant G proteins are constitutively ac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"signal",
"transduction",
"molecular",
"cell",
"biology",
"biology",
"evolutionary",
"biology",
"molecular",
"biology"
] | 2012 | G Protein Activation without a GEF in the Plant Kingdom |
Many algorithms that compare protein structures can reveal similarities that suggest related biological functions , even at great evolutionary distances . Proteins with related function often exhibit differences in binding specificity , but few algorithms identify structural variations that effect specificity . To addr... | Proteins carry out vital and specific functions by physically binding other molecules . Understanding specificity , the preferential binding of certain molecules to one another , is essential for numerous medical and industrial applications . Given the structure of a protein with unknown function , algorithms are avail... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/macromolecular",
"structure",
"analysis",
"biochemistry/bioinformatics"
] | 2010 | VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity |
The 22q11 . 2 deletion syndrome ( 22q11 . 2DS; velo-cardio-facial syndrome; DiGeorge syndrome ) is a congenital anomaly disorder in which haploinsufficiency of TBX1 , encoding a T-box transcription factor , is the major candidate for cardiac outflow tract ( OFT ) malformations . Inactivation of Tbx1 in the anterior hea... | To understand the genetic relationship between Tbx1 and canonical Wnt/β-catenin , we performed gene expression profiling and genetic rescue experiments . We found that Tbx1 and β-catenin may provide a negative feedback loop to restrict premature differentiation in the anterior heart field . This is relevant to understa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"cardiovascular",
"anatomy",
"cardiac",
"ventricles",
"ventricular",
"septal",
"defects",
"animal",
"models",
"developmental",
"biology",
"model",
"organisms",
"experimental",
"organism",
"systems",
"embryos",
"morphogenesis",
"car... | 2017 | Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome |
Mutations in Pten-induced kinase 1 ( PINK1 ) are linked to early-onset familial Parkinson's disease ( FPD ) . PINK1 has previously been implicated in mitochondrial fission/fusion dynamics , quality control , and electron transport chain function . However , it is not clear how these processes are interconnected and whe... | Parkinson's disease ( PD ) is the second most common neurodegenerative disease . It mainly affects movement in elderly people and was traditionally considered a sporadic disease with no known cause . Discoveries of genes associated with familial PD ( FPD ) have demonstrated that PD pathogenesis can be significantly inf... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"medicine",
"cellular",
"structures",
"model",
"organisms",
"molecular",
"cell",
"biology",
"cell",
"biology",
"neurological",
"disorders",
"neurology",
"biology",
"neuroscience"
] | 2012 | Parkinson's Disease–Associated Kinase PINK1 Regulates Miro Protein Level and Axonal Transport of Mitochondria |
Comprising nearly half of the human and mouse genomes , transposable elements ( TEs ) are found within most genes . Although the vast majority of TEs in introns are fixed in the species and presumably exert no significant effects on the enclosing gene , some markedly perturb transcription and result in disease or a mut... | Sequences derived from transposable elements ( TEs ) are major constituents of mammalian genomes and are found within introns of most genes . While nearly all TEs within introns appear harmless , some de novo intronic TE insertions do disrupt gene transcription and splicing and cause disease . It is unclear why some in... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"genome",
"evolution",
"evolutionary",
"biology",
"gene",
"regulation",
"molecular",
"genetics",
"biology",
"computational",
"biology",
"genomic",
"evolution"
] | 2011 | Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns |
Localization of specific mRNAs is an important mechanism through which cells achieve polarity and direct asymmetric growth . Based on a framework established in Saccharomyces cerevisiae , we describe a She3-dependent RNA transport system in Candida albicans , a fungal pathogen of humans that grows as both budding ( yea... | Generation of cellular polarity – asymmetry in shape , protein distribution , and/or sub-cellular function – is an essential feature of most eukaryotic cells and underlies such diverse processes as differentiation , mating , nutrient acquisition , and growth . Localization of specific mRNAs is one mechanism through whi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/microbial",
"physiology",
"and",
"metabolism",
"infectious",
"diseases/fungal",
"infections",
"cell",
"biology/developmental",
"molecular",
"mechanisms",
"molecular",
"biology/mrna",
"transport",
"and",
"localization",
"evolutionary",
"biology",
"genetics",
"... | 2009 | An RNA Transport System in Candida albicans Regulates Hyphal Morphology and Invasive Growth |
Phototrophic organisms such as cyanobacteria utilize the sun’s energy to convert atmospheric carbon dioxide into organic carbon , resulting in diurnal variations in the cell’s metabolism . Flux balance analysis is a widely accepted constraint-based optimization tool for analyzing growth and metabolism , but it is gener... | Phototrophic organisms such as cyanobacteria harvest the sun’s energy to convert atmospheric CO2 into organic carbon , due to which their metabolism is heavily influenced by light availability . The strongly diurnal nature of their metabolism is reflected in the presence of two distinct metabolic phases–a light-depende... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"light",
"plant",
"physiology",
"electromagnetic",
"radiation",
"plant",
"science",
"metabolites",
"genome",
"analysis",
"photosynthesis",
"bacteria",
"genomics",
"metabolic",
"pathways",
"cyanobacteria",
"physics",
"biochemistry",
"plant",
"biochemistry",
"nitrogen",
"fixa... | 2019 | A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism |
CD8 T cells are necessary for the elimination of intracellular pathogens , but during chronic viral infections , CD8 T cells become exhausted and unable to control the persistent infection . Programmed cell death-1 ( PD-1 ) blockade therapies have been shown to improve CD8 T cell responses during chronic viral infectio... | Although PD-1 therapies have revolutionized cancer treatment , these therapies have not yet been licensed to treat chronic viral infections . This is because limited benefit is seen in pre-clinical models of chronic viral infection . Interestingly , recent reports in cancer models have suggested that certain microbes c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"viral",
"transmission",
"and",
"infection",
"spleen",
"cancer",
"treatment",
"immunology",
"microbiology",
"cancer",
"immunotherapy",
"oncology",
"clinical",
"medicine... | 2019 | TLR4 signaling improves PD-1 blockade therapy during chronic viral infection |
Biological systems often detect species-specific signals in the environment . In humans , speech and language are species-specific signals of fundamental biological importance . To detect the linguistic signal , human brains must form hierarchical representations from a sequence of perceptual inputs distributed in time... | Human language is a fundamental biological signal with computational properties that differ from other perception-action systems: hierarchical relationships between sounds , words , phrases , and sentences and the unbounded ability to combine smaller units into larger ones , resulting in a "discrete infinity" of expres... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"neurolinguistics",
"linguistics",
"neural",
"networks",
"engineering",
"and",
"technology",
"signal",
"processing",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"sentence",
"processing",
"cognitive",
"psychology",
"cognition",
"memory",
... | 2017 | A mechanism for the cortical computation of hierarchical linguistic structure |
Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression . For example , cytidine deaminase ( CDA ) deficiency leads to an excess of dCTP , slowing the replication fork . We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the... | The maintenance of genome stability is essential for the accurate transmission of genetic information , to ensure the successful duplication of chromosomes and their even segregation during mitosis . Errors occurring during DNA replication may affect both the accuracy of chromosome duplication and the balance of chromo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA |
Mutations in the glucosylceramidase beta ( GBA ) gene are strongly associated with neurodegenerative diseases marked by protein aggregation . GBA encodes the lysosomal enzyme glucocerebrosidase , which breaks down glucosylceramide . A common explanation for the link between GBA mutations and protein aggregation is that... | Mutations in the GBA gene , which encodes the enzyme glucocerebrosidase , are common and increase the risk of Parkinson disease . A widely accepted explanation for the increased risk is that the fatty substance normally broken down by glucocerebrosidase builds up in the lysosome , which is the cell’s recycling center ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"death",
"invertebrates",
"autophagic",
"cell",
"death",
"lysosomes",
"vesicles",
"protein",
"aggregation",
"cell",
"processes",
"animals",
"animal",
"models",
"membrane",
"proteins",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimental",
"organism",
... | 2018 | Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles |
What does it take to convert a heap of sequencing data into a publishable result ? First , common tools are employed to reduce primary data ( sequencing reads ) to a form suitable for further analyses ( i . e . , the list of variable sites ) . The subsequent exploratory stage is much more ad hoc and requires the develo... | Galaxy users can utilize a large number of tools and workflows . What they could not previously do is run ad hoc scripts and arbitrary tools within their Galaxy instance . This was very limiting , as initial analyses of data often involve interactive exploration with tools like Jupyter or RStudio—powerful platforms tha... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results/Discussion"
] | [
"sequencing",
"techniques",
"education",
"mitochondrial",
"dna",
"astronomical",
"sciences",
"invertebrate",
"genomics",
"next-generation",
"sequencing",
"genome",
"analysis",
"forms",
"of",
"dna",
"energy-producing",
"organelles",
"molecular",
"biology",
"techniques",
"bio... | 2017 | Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers |
In order to propagate a solid tumor , cancer cells must adapt to and survive under various tumor microenvironment ( TME ) stresses , such as hypoxia or lactic acidosis . To systematically identify genes that modulate cancer cell survival under stresses , we performed genome-wide shRNA screens under hypoxia or lactic ac... | During the development of most solid tumors , there are characteristic physiological differences in the tumor that result from tumor cells outgrowing their local blood supply . Two of these physiological differences , or “stresses , ” that occur in the tumor are low oxygen levels ( hypoxia ) and an accumulation of lact... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate |
Heterozygous Twirler ( Tw ) mice develop obesity and circling behavior associated with malformations of the inner ear , whereas homozygous Tw mice have cleft palate and die shortly after birth . Zeb1 is a zinc finger protein that contributes to mesenchymal cell fate by repression of genes whose expression defines epith... | Twirler ( Tw ) mice have a combination of abnormalities that includes cleft palate , malformations of the inner ear , hearing loss , vestibular dysfunction , obesity , and lymphoid hypoplasia . In this study , we show that the underlying mutation affects the Zeb1 gene . Zeb1 was already known to encode a protein normal... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology",
"veterinary",
"science"
] | 2011 | A Noncoding Point Mutation of Zeb1 Causes Multiple Developmental Malformations and Obesity in Twirler Mice |
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is a human oncogenic virus associated with Kaposi’s sarcoma and two B-cell malignancies . The rhesus monkey rhadinovirus ( RRV ) is a virus of nonhuman primates that is closely related to KSHV . Eph family receptor tyrosine kinases ( Ephs ) are cellular receptors for the... | In immunocompromised individuals in general and in the context of HIV infection in particular , KSHV is a major cause of cancer and B-cell proliferative malignancies . We identified and mutated conserved residues in the N-terminal domain of the gH/gL glycoprotein complex of KSHV and the related monkey virus RRV that ar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"endothelial",
"cells",
"condensed",
"matter",
"physics",
"microbiology",
"fibroblasts",
"epithelial",
"cells",
"viruses",
"mutation",
"dna",
"vir... | 2018 | A conserved Eph family receptor-binding motif on the gH/gL complex of Kaposi’s sarcoma-associated herpesvirus and rhesus monkey rhadinovirus |
Proteins interact in complex protein–protein interaction ( PPI ) networks whose topological properties—such as scale-free topology , hierarchical modularity , and dissortativity—have suggested models of network evolution . Currently preferred models invoke preferential attachment or gene duplication and divergence to p... | Proteins function together forming stable protein complexes or transient interactions in various cellular processes , such as gene regulation and signaling . Here , we address the basic question of how these networks of interacting proteins evolve . This is an important problem , as the structures of such networks unde... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry/molecular",
"evolution",
"biophysics/macromolecular",
"assemblies",
"and",
"machines",
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/evolutionary",
"modeling",
"biochemistry/bioinformatics",
"biochemistry/theory",
"and",
"simulation",
"biochemistry... | 2008 | Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence |
Fusion peptides from influenza hemagglutinin act on membranes to promote membrane fusion , but the mechanism by which they do so remains unknown . Recent theoretical work has suggested that contact of protruding lipid tails may be an important feature of the transition state for membrane fusion . If this is so , then i... | Membrane fusion is a common process critical to both cellular function and infection by enveloped viruses . Influenza is a particularly useful model system for studying fusion because the fusion reaction is accomplished by a single protein , hemagglutinin . Furthermore , mutations to the membrane-inserted portion of he... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology",
"computational",
"biology"
] | 2013 | Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models |
The extent by which different cellular components generate phenotypic diversity is an ongoing debate in evolutionary biology that is yet to be addressed by quantitative comparative studies . We conducted an in vivo mass-spectrometry study of the phosphoproteomes of three yeast species ( Saccharomyces cerevisiae , Candi... | Natural selection at a population level requires phenotypic diversity , which at the molecular level arises by mutation of the genome of each individual . What kinds of changes at the level of the DNA are most important for the generation of phenotypic differences remains a fundamental question in evolutionary biology ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/signaling",
"networks",
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"cell",
"biology/cell",
"signaling"
] | 2009 | Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species |
The analysis of double-strand break ( DSB ) repair is complicated by the existence of several pathways utilizing a large number of genes . Moreover , many of these genes have been shown to have multiple roles in DSB repair . To address this complexity we used a repair reporter construct designed to measure multiple rep... | DNA is a fragile thread that often breaks . When it does , the cell must find a way to splice the broken ends back together in order to continue its cycle of replication . Cells possess an array of ways to rejoin broken DNA ends , each with advantages and disadvantages . Some are “quick and dirty , ” sacrificing accura... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology",
"genetics",
"and",
"genomics",
"drosophila",
"melanogaster"
] | 2007 | Multiple-Pathway Analysis of Double-Strand Break Repair Mutations in Drosophila |
The control of virulence regulator/sensor kinase ( CovRS ) two-component system is critical to the infectivity of group A streptococcus ( GAS ) , and CovRS inactivating mutations are frequently observed in GAS strains causing severe human infections . CovS modulates the phosphorylation status and with it the regulatory... | Group A streptococcus ( GAS ) , also known as Streptococcus pyogenes , causes a broad array of human infections of varying severity . Tight control of production of virulence factors is critical to GAS pathogenesis , and the control of virulence two-component signaling system ( CovRS ) is central to this process . The ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"pathogens",
"gene",
"regulation",
"enzymology",
"phosphatases",
"animal",
"models",
"model",
"organisms",
"experimental",
"organism",
... | 2018 | Phosphatase activity of the control of virulence sensor kinase CovS is critical for the pathogenesis of group A streptococcus |
The anthelmintic emodepside paralyses adult filarial worms , via a mode of action distinct from previous anthelmintics and has recently garnered interest as a new treatment for onchocerciasis . Whole organism data suggest its anthelmintic action is underpinned by a selective activation of the nematode isoform of an evo... | Filarial diseases affect an estimated 200 million people and the Drugs for Neglected Diseases initiative ( DNDi ) has identified development of macrofilaricidal drugs as a priority . Emodepside , currently used in companion animals , paralyses adult filarial worms and may address this unmet need for human medicine . It... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | The Cyclooctadepsipeptide Anthelmintic Emodepside Differentially Modulates Nematode, Insect and Human Calcium-Activated Potassium (SLO) Channel Alpha Subunits |
Insect molting and metamorphosis are intricately governed by two hormones , ecdysteroids and juvenile hormones ( JHs ) . JHs prevent precocious metamorphosis and allow the larva to undergo multiple rounds of molting until it attains the proper size for metamorphosis . In the silkworm , Bombyx mori , several “moltinism”... | The number of larval instars in insects varies greatly across insect taxa and can even vary at the intraspecific level . However , little is known about how the number of larval instars is fixed in each species or modified by the environment . The silkworm , Bombyx mori , provides a unique bioresource for investigating... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"developmental",
"biology",
"genetics",
"biology",
"zoology",
"genetics",
"and",
"genomics"
] | 2012 | Precocious Metamorphosis in the Juvenile Hormone–Deficient Mutant of the Silkworm, Bombyx mori |
In mammalian auditory cortex , sound source position is represented by a population of broadly tuned neurons whose firing is modulated by sounds located at all positions surrounding the animal . Peaks of their tuning curves are concentrated at lateral position , while their slopes are steepest at the interaural midline... | Ability to localize the position of a sound source is vital to many organisms , since audition provides information about areas which are not accessible visually . While its importance is undisputed , its neuronal mechanisms are not well understood . It has been observed in experimental studies that despite the crucial... | [
"Abstract",
"Introduction",
"Results",
"Properties",
"of",
"the",
"second",
"layer",
"representation",
"Discussion",
"Methods"
] | [] | 2015 | The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds |
To assess if a probabilistic model could be used to estimate the combined prevalence of infection with any species of intestinal nematode worm when only the separate prevalence of each species is reported , and to estimate the extent to which simply taking the highest individual species prevalence underestimates the co... | Mixed infections with roundworm , whipworm and hookworm are common , but survey reports often give only the separate prevalence of each type . However , the combined prevalence is important to estimate accurately the number of individuals who would benefit from control programmes and to make decisions about the frequen... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2010 | Using the Prevalence of Individual Species of Intestinal Nematode Worms to Estimate the Combined Prevalence of Any Species |
Reducing social distance between hospital staff and patients and establishing clear lines of communication is a major challenge when providing in-patient care for people afflicted by Buruli ulcer ( BU ) and chronic ulcers . Research on hospitals as therapeutic communities is virtually non-existent in Africa and is curr... | Little is known about communication patterns and social relations between health staff and long -term patients in African hospitals . An ethnography of a reference hospital treating patients afflicted with Buruli Ulcer ( BU ) and other chronic ulcers in Benin was conducted . Sources of psychosocial distress and communi... | [
"Abstract",
"Introduction",
"Methods",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"health",
"services",
"research",
"sociology",
"tropical",
"diseases",
"social",
"sciences",
"health",
"care",
"bacterial",
"diseases",
"research",
"design",
"scientists",
"signs",
... | 2016 | Steps Toward Creating A Therapeutic Community for Inpatients Suffering from Chronic Ulcers: Lessons from Allada Buruli Ulcer Treatment Hospital in Benin |
Recently , a molecular pathway linking inflammation to cell transformation has been discovered . This molecular pathway rests on a positive inflammatory feedback loop between NF-κB , Lin28 , Let-7 microRNA and IL6 , which leads to an epigenetic switch allowing cell transformation . A transient activation of an inflamma... | An increasing amount of evidence demonstrates a close relation between inflammation and cancer development , which reveals the importance of the tumor microenvironment for the development of cancers . Recently , a molecular pathway linking inflammation to cell transformation , which is a prerequisite to cancer developm... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"complex",
"systems",
"systems",
"biology",
"nonlinear",
"dynamics",
"signal",
"transduction",
"stat",
"signaling",
"family",
"signaling",
"in",
"cellular",
"processes",
"mathematics",
"theoretical",
"biology",
"oncogenic",
"signaling",
"applied",
"mathematics",
"ras",
... | 2014 | A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches |
Since leprosy is both treated and controlled by multidrug therapy ( MDT ) it is important to monitor recurrent cases for drug resistance and to distinguish between relapse and reinfection as a means of assessing therapeutic efficacy . All three objectives can be reached with single nucleotide resolution using next gene... | Leprosy , one of the most ancient human infectious diseases , affects skin and nerves and is caused by Mycobacterium leprae infection . Despite the effective use of multidrug therapy/MDT since the 80´s , over 200 , 000 new cases are reported yearly , indicating active transmission , especially in India and Brazil . Alt... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"mycobacterium",
"leprae",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"biopsy",
"tropical",
"diseases",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"genome",
"sequencing",
"bacterial",
"... | 2017 | Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases |
Polycomb group ( PcG ) proteins bind to and repress genes in embryonic stem cells through lineage commitment to the terminal differentiated state . PcG repressed genes are commonly characterized by the presence of the epigenetic histone mark H3K27me3 , catalyzed by the Polycomb repressive complex 2 . Here , we present ... | In Parkinson's disease ( PD ) the motor impairment produced by the progressive death of midbrain dopaminergic neurons is commonly treated with the dopamine precursor , L-DOPA . Utilizing a mouse model of PD , we show that L-DOPA , via activation of dopamine D1 receptors , promotes the expression of genes normally repre... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Dopamine Signaling Leads to Loss of Polycomb Repression and Aberrant Gene Activation in Experimental Parkinsonism |
We performed a genome-level computational study of sequence and structure similarity , the latter using crystal structures and models , of the proteases of Homo sapiens and the human parasite Trypanosoma brucei . Using sequence and structure similarity networks to summarize the results , we constructed global views tha... | Human African trypanosomiasis ( HAT ) is caused by the protozoan parasite Trypanosoma brucei . HAT is fatal unless treated , yet the current treatment itself can cause death . New treatments are urgently needed . Our study focuses on proteases , which are enzymes that break down proteins . Because of their roles in man... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion",
"Conclusions"
] | [
"genomics",
"biology",
"computational",
"biology",
"structural",
"genomics",
"genetics",
"and",
"genomics"
] | 2012 | A Global Comparison of the Human and T. brucei Degradomes Gives Insights about Possible Parasite Drug Targets |
The burden of leptospirosis in humans and animals in Africa is higher than that reported from other parts of the world . However , the disease is not routinely diagnosed in the continent . One of major factors limiting diagnosis is the poor availability of live isolates of locally circulating Leptospira serovars for in... | Leptospirosis disease is widespread in humans and broad range of animal species in Africa . However , leptospirosis is highly neglected and not extensively taught in both medical and veterinary schools almost across Africa . Availability of live leptospires isolated from Africa for use in its diagnosis by the gold stan... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Leptospira Serovars for Diagnosis of Leptospirosis in Humans and Animals in Africa: Common Leptospira Isolates and Reservoir Hosts |
Prominent immune alterations associated with aging include the loss of naïve T-cell numbers , diversity and function . While genetic contributors and mechanistic details in the aging process have been addressed in multiple studies , the role of environmental agents in immune aging remains incompletely understood . From... | The cytomegalovirus ( CMV ) is a widespread virus of the herpesvirus family , which latently infects the majority of the adult human population worldwide . While CMV causes severe disease in AIDS patients , in recipients of organ transplants , or when infection occurs during pregnancy , this virus is considered apathog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"immune",
"cells",
"west",
"nile",
"fever",
"influenza",
"immunology",
"biology",
"viral",
"diseases",
"cytomegalovirus",
"infection",
"immunomodulation"
] | 2012 | Cytomegalovirus Infection Impairs Immune Responses and Accentuates T-cell Pool Changes Observed in Mice with Aging |
Cyclin-dependent kinase 9 ( Cdk9 ) promotes elongation by RNA polymerase II ( RNAPII ) , mRNA processing , and co-transcriptional histone modification . Cdk9 phosphorylates multiple targets , including the conserved RNAPII elongation factor Spt5 and RNAPII itself , but how these different modifications mediate Cdk9 fun... | The expression of many eukaryotic genes is regulated during the elongation phase of transcription . Cyclin-dependent kinase 9 ( CDK9 ) enzymes are key positive regulators of RNA polymerase II ( RNAPII ) elongation , and are required for co-transcriptional events such as mRNA processing and chromatin modification . Cdk9... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | The PAF Complex and Prf1/Rtf1 Delineate Distinct Cdk9-Dependent Pathways Regulating Transcription Elongation in Fission Yeast |
The developmental time of vector insects is important in population dynamics , evolutionary biology , epidemiology and in their responses to global climatic change . In the triatomines ( Triatominae , Reduviidae ) , vectors of Chagas disease , evolutionary ecology concepts , which may allow for a better understanding o... | The developmental time of vector insects is important to their population dynamics , evolutionary biology , epidemiology of the diseases they transmit , and to their responses to global climatic change . In various triatomine species vectors of Chagas disease ( Triatominae , Reduviidae ) , a delay in the molt of a smal... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"ecology/evolutionary",
"ecology",
"public",
"health",
"and",
"epidemiology",
"evolutionary",
"biology/evolutionary",
"ecology"
] | 2010 | Adaptive Developmental Delay in Chagas Disease Vectors: An Evolutionary Ecology Approach |
The insulin/IGF-1 signaling ( IIS ) pathway is a conserved regulator of longevity , development , and metabolism . In Caenorhabditis elegans IIS involves activation of DAF-2 ( insulin/IGF-1 receptor tyrosine kinase ) , AGE-1 ( PI 3-kinase ) , and additional downstream serine/threonine kinases that ultimately phosphoryl... | Cells in the body respond to a variety of on/off signals that are relayed in a defined spatial and temporal manner . These signals influence several processes such as growth , fat storage , and the repair of damaged molecules . As humans age , the onset of diseases such as Type 2 Diabetes , obesity , and cancer often r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/gene",
"discovery",
"developmental",
"biology/aging",
"diabetes",
"and",
"endocrinology",
"molecular",
"biology",
"developmental",
"biology/developmental",
"molecular",
"mechanisms"
] | 2011 | PDP-1 Links the TGF-β and IIS Pathways to Regulate Longevity, Development, and Metabolism |
For decades La Réunion has experienced a number of epidemics that have resulted in efforts to control the density of Aedes species on this Island . This study was conducted to assess household-level expenditure on protective measures against mosquito nuisance on the Island of La Réunion in 2012 . Data was collected dur... | The French Ministry of Health has , for decades , dedicated numerous resources to control mosquito density on the Island of La Réunion . These efforts were strengthened following an outbreak of chikungunya , a virus transmitted by Aedes mosquitoes , in 2005–2006 . In order to understand how public perception and behavi... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"social",
"and",
"behavioral",
"sciences",
"economics"
] | 2014 | Household-Level Expenditure on Protective Measures Against Mosquitoes on the Island of La Réunion, France |
For most of the world , human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts , factors that are captured by the concepts of biogeographic ancestry and admixture , respectively . The ancestry of non-admixed individuals can often be tr... | Admixed individuals , such as African Americans and Latinos , arise from mating between individuals from different continents . Detailed knowledge about the ancestral origin of an admixed population not only provides insight regarding the history of the population itself , but also affords opportunities to study the ev... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genomics",
"mathematics",
"evolutionary",
"biology",
"statistics",
"genetics",
"population",
"genetics",
"biology",
"computational",
"biology",
"statistical",
"methods",
"genetics",
"and",
"genomics"
] | 2011 | Ancestral Components of Admixed Genomes in a Mexican Cohort |
Mutator phenotypes accelerate the evolutionary process of neoplastic transformation . Historically , the measurement of mutation rates has relied on scoring the occurrence of rare mutations in target genes in large populations of cells . Averaging mutation rates over large cell populations assumes that new mutations ar... | Mutations fuel microbial evolution and cancer . Cells with an increased rate of mutation are said to have a “mutator phenotype” and adapt more rapidly than non-mutator cells . Our study utilizes a novel way of measuring mutation rates of individual cell divisions to show that mutator cells can adopt one of two mutation... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Volatility of Mutator Phenotypes at Single Cell Resolution |
Identifying driver mutations in cancer is notoriously difficult . To date , recurrence of a mutation in patients remains one of the most reliable markers of mutation driver status . However , some mutations are more likely to occur than others due to differences in background mutation rates arising from various forms o... | Cancer development and progression is associated with accumulation of mutations . However , only a small fraction of mutations identified in a patient is responsible for cellular transformations leading to cancer . These so-called drivers characterize molecular profiles of tumors and could be helpful in predicting clin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"mutation",
"substitution",
"mutation",
"point",
"mutation",
"cancer",
"genetics",
"nonsense",
"mutation",
"database",
"and",
"informatics",
"methods",
"silent",
"mutation",
"genetics",
"biological",
"databases",
"biology",
"and",
"life",
"sciences",
"mutation",
"databa... | 2019 | Finding driver mutations in cancer: Elucidating the role of background mutational processes |
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