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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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We have obtained precatalytic ( enzyme–substrate complex ) and postcatalytic ( enzyme–product complex ) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal . Using the natural satellite tobacco ringspot virus hammerhead RNA sequence , the self-cleavage reaction was modulated by substi... | Enzymes use variations of a few standard approaches to catalyze reactions . One of these approaches , acid–base catalysis , is of such fundamental importance that it is common to both protein enzymes and RNA-based enzymes , or ribozymes . The hammerhead ribozyme is one such ribozyme that uses an invariant guanine resid... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"biochemistry"
] | 2008 | Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis |
A20 negatively regulates multiple inflammatory signalling pathways . We here addressed the role of A20 in club cells ( also known as Clara cells ) of the bronchial epithelium in their response to influenza A virus infection . Club cells provide a niche for influenza virus replication , but little is known about the fun... | Influenza viruses are a major public health threat . Each year , the typical seasonal flu epidemic affects millions of people with sometimes fatal outcomes , especially in high risk groups such as young children and elderly . The sporadic pandemic outbreaks can have even more disastrous consequences . The protein A20 i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"respiratory",
"infections",
"influenza",
"pathogens",
"immunology",
"microbiology",
"orthomyxoviruses",
"pulmonology",
"epithelial",
"cells",
"viru... | 2016 | A20 Deficiency in Lung Epithelial Cells Protects against Influenza A Virus Infection |
Hippocampal damage results in profound retrograde , but no anterograde amnesia in contextual fear conditioning ( CFC ) . Although the content learned in the latter have been discussed , alternative regions supporting CFC learning were seldom proposed and never empirically addressed . Here , we employed network analysis... | When determined cognitive performances are not affected by brain lesions of regions generally involved in that performance , the interpretation is that the remaining regions can promote function despite of ( or compensate ) the damaged one . In contextual fear conditioning , a memory model largely used in laboratory ro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"learning",
"cognitive",
"neurology",
"medicine",
"and",
"health",
"sciences",
"neural",
"networks",
"brain",
"damage",
"brain",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"cognitive",
"neuroscience",
"cognitive",
"psychology",
"cognition",
"netw... | 2018 | Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex |
Urbanization is increasing across the globe , and diseases once considered rural can now be found in urban areas due to the migration of populations from rural endemic areas , local transmission within the city , or a combination of factors . We investigated the epidemiologic characteristics of urban immigrants and nat... | Urban transmission of schistosomiasis is becoming more recognized as rural disease is becoming less common and urbanization increases . Characteristics of infection of the immigrant population to cities and genetic characteristics of the parasite population itself indicate local transmission is the most important facto... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | The Relative Contribution of Immigration or Local Increase for Persistence of Urban Schistosomiasis in Salvador, Bahia, Brazil |
Cells reliably sense environmental changes despite internal and external fluctuations , but the mechanisms underlying robustness remain unclear . We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simul... | Cells sense their surroundings and respond to soluble factors in the extracellular space . Extracellular factors frequently induce heterogeneous responses , thereby restricting the biological outcome to a fraction of the cell population . However , the question arises how such cell-to-cell variability can be controlled... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Determinants of Cell-to-Cell Variability in Protein Kinase Signaling |
In the early spring of 2013 , Chinese health authorities reported several cases of H7N9 influenza virus infections in humans . Since then the virus has established itself at the human-animal interface in Eastern China and continues to cause several hundred infections annually . In order to characterize the antibody res... | Several hundred human avian H7N9 virus infections with a case fatality rate of approximately 37% have occurred in China since 2013 . The emergence of this virus has raised concerns about its pandemic potential and has triggered the development of H7N9 vaccines . Using the traditional correlate of protection for influen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"h7n9",
"medicine",
"and",
"health",
"sciences",
"viral",
"vaccines",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"split-decomposition",
"method",
"immunology",
"microbiology",
"orthomyxoviruses",
"viru... | 2016 | Broadly-Reactive Neutralizing and Non-neutralizing Antibodies Directed against the H7 Influenza Virus Hemagglutinin Reveal Divergent Mechanisms of Protection |
Saccharomyces cerevisiae Rad9 is required for an effective DNA damage response throughout the cell cycle . Assembly of Rad9 on chromatin after DNA damage is promoted by histone modifications that create docking sites for Rad9 recruitment , allowing checkpoint activation . Rad53 phosphorylation is also dependent upon BR... | In response to DNA damage all eukaryotic cells activate a surveillance mechanism , known as the DNA damage checkpoint , which delays cell cycle progression and modulates DNA repair . Yeast RAD9 was the first DNA damage checkpoint gene identified . The genetic tools available in this model system allow to address releva... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/histone",
"modification",
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics/cancer",
"genetics",
"molecular",
"biology/chromatin",
"structure",
"molecular",
"biology/dna",
"repair"
] | 2010 | Dynamics of Rad9 Chromatin Binding and Checkpoint Function Are Mediated by Its Dimerization and Are Cell Cycle–Regulated by CDK1 Activity |
The set of regulatory interactions between genes , mediated by transcription factors , forms a species' transcriptional regulatory network ( TRN ) . By comparing this network with measured gene expression data , one can identify functional properties of the TRN and gain general insight into transcriptional control . We... | Bacterial cells can adapt to various genomic mutations and intriguingly many environmental changes . They do this by adjusting their gene expression profile to meet the requirements of a new condition . In this work , we study the interplay of different mechanisms of gene regulatory control driving this adaptation in t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"computational",
"biology/transcriptional",
"regulation"
] | 2010 | Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli |
microRNAs ( miRs ) are small RNAs that regulate gene expression at the posttranscriptional level . It is anticipated that , in combination with transcription factors ( TFs ) , they span a regulatory network that controls thousands of mammalian genes . Here we set out to uncover local and global architectural features o... | It is becoming increasingly appreciated that a new type of gene which does not code for proteins , the regulatory RNAs , constitutes a considerable portion of mammalian genomes , and these genes serve as key players in the regulatory network of living cells . Among these regulatory RNAs are the microRNAs ( miRs ) , sma... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"homo",
"(human)",
"genetics",
"and",
"genomics",
"computational",
"biology"
] | 2007 | Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network |
Dynamic regulation of chromatin structure is of fundamental importance for modulating genomic activities in higher eukaryotes . The opposing activities of Polycomb group ( PcG ) and trithorax group ( trxG ) proteins are part of a chromatin-based cellular memory system ensuring the correct expression of specific transcr... | In higher eukaryotes only a small proportion of genomic information is required in any specific cell type at a given developmental stage . The intricate decision whether a gene should be active or repressed is made by the counteractive activities of trithorax group ( trxG ) and Polycomb group ( PcG ) proteins that form... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/cell",
"differentiation",
"genetics",
"and",
"genomics/epigenetics",
"developmental",
"biology/plant",
"growth",
"and",
"development",
"genetics",
"and",
"genomics/plant",
"genetics",
"and",
"gene",
"expression"
] | 2009 | CHD3 Proteins and Polycomb Group Proteins Antagonistically Determine Cell Identity in Arabidopsis |
Studies of sequential decision-making in humans frequently find suboptimal performance relative to an ideal actor that has perfect knowledge of the model of how rewards and events are generated in the environment . Rather than being suboptimal , we argue that the learning problem humans face is more complex , in that i... | Every decision-making experiment has a structure that specifies how rewards are obtained , which is usually explained to the subject at the beginning of the experiment . Participants frequently fail to act as if they understand the experimental structure , even in tasks as simple as determining which of two biased coin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/psychology",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Structure Learning in Human Sequential Decision-Making |
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences . These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants , microbes , and insects . Multilocus sequence a... | We sequenced the genomes of seven strains of the Pseudomonas fluorescens group that colonize plant surfaces and function as biological control agents , protecting plants from disease . In this study , we demonstrated the genomic diversity of the group by comparing these strains to each other and to three other strains ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"genome-wide",
"association",
"studies",
"microbial",
"metabolism",
"plant",
"biology",
"microbiology",
"chemical",
"biology",
"gene",
"function",
"genome",
"sequencing",
"plant",
"science",
"plant",
"pathology",
"plant",
"microbiology",
"chemistry",
"comp... | 2012 | Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions |
Experimental infections with visceral Leishmania spp . are frequently performed referring to stationary parasite cultures that are comprised of a mixture of metacyclic and non-metacyclic parasites often with little regard to time of culture and metacyclic purification . This may lead to misleading or irreproducible exp... | Protozoan of the genus Leishmania undergo several developmental transitions during its life cycle . Leishmania alternates between two morphologically distinct forms , promastigotes ( insect stage ) and amastigotes ( vertebrate stage ) . Most of the available information about Leishmania spp . has been obtained from stu... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"protozoology",
"biology",
"microbiology",
"parasitology"
] | 2012 | Impact of Continuous Axenic Cultivation in Leishmania infantum Virulence |
Streptococcus pneumoniae accounts for more deaths worldwide than any other single pathogen through diverse disease manifestations including pneumonia , sepsis and meningitis . Life-threatening acute cardiac complications are more common in pneumococcal infection compared to other bacterial infections . Distinctively , ... | Cardiac complications frequently accompany invasive disease caused by the pathogen Streptococcus pneumoniae and are associated with significant increases in mortality , however the underlying mechanisms remain elusive . Here , we describe a new mechanism by which pneumococci in the blood stream induce elevation of circ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Circulating Pneumolysin Is a Potent Inducer of Cardiac Injury during Pneumococcal Infection |
Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis . Because this response involves coordinate regulation of hundreds of genes , it provides a powerful biological system to elucidate the molecular strategies that underlie signal-... | The innate immune response is a complex biological program that is configured to allow host cells to rapidly respond to infection and tissue injury . An essential feature of this response is the sequential activation of large numbers of genes that play roles in amplification of the initial inflammatory response , exert... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"processing",
"molecular",
"biology",
"gene",
"expression",
"immunology",
"biology",
"molecular",
"cell",
"biology",
"chromatin",
"dna",
"transcription",
"histone",
"modification"
] | 2011 | Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes |
Exogenous Interleukin-7 ( IL-7 ) , in supplement to antiretroviral therapy , leads to a substantial increase of all CD4+ T cell subsets in HIV-1 infected patients . However , the quantitative contribution of the several potential mechanisms of action of IL-7 is unknown . We have performed a mathematical analysis of rep... | HIV infection is characterized by a decrease of CD4+ T-lymphocytes in the blood . Whereas antiretroviral treatment succeeds to control viral replication , some patients fail to reconstitute their CD4+ T cell count to normal value . IL-7 is a promising cytokine under evaluation for its use in HIV infection , in suppleme... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"computer",
"and",
"information",
"sciences",
"medicine",
"and",
"health",
"sciences",
"systems",
"science",
"mathematics",
"sexually",
"transmitted",
"diseases",
"population",
"modeling",
"aids",
"biology",
"and",
"life",
"sciences",
"infectio... | 2014 | Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+T Cells in HIV-1 Infection |
Adaptation in extended populations often occurs through multiple independent mutations responding in parallel to a common selection pressure . As the mutations spread concurrently through the population , they leave behind characteristic patterns of polymorphism near selected loci—so-called soft sweeps—which remain vis... | When a species is spread out over a large geographic range , different regions may adapt to the same selection pressure by acquiring distinct beneficial mutations . The resulting pattern of genetic variation in the population is called a soft sweep . Dispersal strongly influences soft sweep patterns , as it determines ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"parasite",
"evolution",
"population",
"genetics",
"social",
"sciences",
"cloning",
"parasitology",
"kernel",
"functions",
"mutation",
"probability",
"distribution",
"mathematics",
"animal",
"behavior",
"molecular",
"biology",
"techniques",
"population",
"biology",
"zoology... | 2019 | Spatial soft sweeps: Patterns of adaptation in populations with long-range dispersal |
Cross-referencing experimental data with our current knowledge of signaling network topologies is one central goal of mathematical modeling of cellular signal transduction networks . We present a new methodology for data-driven interrogation and training of signaling networks . While most published methods for signalin... | Cellular signal transduction is orchestrated by communication networks of signaling proteins commonly depicted on signaling pathway maps . However , each cell type may have distinct variants of signaling pathways , and wiring diagrams are often altered in disease states . The identification of truly active signaling to... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs |
We present a simple physically based quantitative model of blood platelet shape and its evolution during agonist-induced activation . The model is based on the consideration of two major cytoskeletal elements: the marginal band of microtubules and the submembrane cortex . Mathematically , we consider the problem of min... | Blood platelets are the second most numerous component of blood after red blood cells . Their main function is to stop bleeding upon vessel wall injury . Contact with foreign substances , normally absent inside the bloodstream , leads to platelet activation . After this , platelets adhere to the damaged surface and to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"microtubules",
"radii",
"platelet",
"activation",
"light",
"geometry",
"electromagnetic",
"radiation",
"light",
"scattering",
"mathematics",
"platelets",
"cellular",
"structures",
"and",
"orga... | 2018 | Method for the simulation of blood platelet shape and its evolution during activation |
Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks , offering a promising approach towards the biological interpretation of phenotype differentiating genes . Early pathway analysis methodologies , named as gene set analysis ( GSA )... | It is generally recognized that using different sources of information and knowledge is better than just using a single source . This is most profound in the post-genomics era . On one hand , the advent of genomic high-throughput technologies realized by DNA microarray and next generation RNAseq technologies enabled a ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"genetic",
"networks",
"gene",
"regulation",
"cell",
"processes",
"network",
"analysis",
"genome",
"analysis",
"bioassays",
"and",
"physiological",
"analysis",
"mapk",
"signaling",
"cascades",
"research",
"and",
"analysis",
"methods",
"computer",
"and... | 2016 | MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways |
The survival of animals depends critically on prioritizing responses to motivationally salient stimuli . While it is generally believed that motivational salience increases decision speed , the quantitative relationship between motivational salience and decision speed , measured by reaction time ( RT ) , remains unclea... | Humans and animals face the constant challenge of identifying the subset of incoming sensory stimuli that are most behaviorally relevant and prioritizing behavioral responses accordingly . Critical to this decision is the ability to determine whether a stimulus is motivationally salient—that is , whether the stimulus p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cognitive",
"science",
"specimen",
"preparation",
"and",
"treatment",
"mechanical",
"treatment",
"of",
"specimens",
"cognitive",
"neuroscience",
"specimen",
"disruption",
"cognition",
"decision",
"making",
"biology",
"and",
"life",
"sciences",
"electroporation",
"neurosc... | 2014 | Motivational Salience Signal in the Basal Forebrain Is Coupled with Faster and More Precise Decision Speed |
There is increasing interest in employing shotgun sequencing , rather than amplicon sequencing , to analyze microbiome samples . Typical projects may involve hundreds of samples and billions of sequencing reads . The comparison of such samples against a protein reference database generates billions of alignments and th... | Microbiome sequencing projects continue to grow rapidly , both in the number of samples considered and sequencing reads collected . With MEGAN Community Edition ( CE ) , we provide a highly efficient program for interactive analysis and comparison of such data , allowing one to explore hundreds of samples and billions ... | [
"Abstract",
"Introduction",
"Design",
"and",
"Implementation",
"Results",
"Availability",
"and",
"Future",
"Directions"
] | [
"sequencing",
"techniques",
"taxonomy",
"microbiome",
"microbiology",
"cloning",
"data",
"management",
"metagenomics",
"shotgun",
"sequencing",
"molecular",
"biology",
"techniques",
"dna",
"cloning",
"microbial",
"genomics",
"research",
"and",
"analysis",
"methods",
"sequ... | 2016 | MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data |
The HIV-1 pandemic has disproportionately affected individuals in resource-constrained settings . It is important to determine if other prevalent infections affect the progression of HIV-1 in co-infected individuals in these settings . Some observational studies suggest that helminth infection may adversely affect HIV-... | Many people living in areas of the world most affected by the HIV/AIDS pandemic are also exposed to other common infections . Parasitic infections with helminths ( intestinal worms ) are common in Africa and affect over half of the population in some areas . There are plausible biological reasons why treating helminth ... | [
"Abstract",
"Introduction",
"Methods",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2007 | Treatment of Helminth Co-Infection in Individuals with HIV-1: A Systematic Review of the Literature |
The asymmetric cell division cycle of Caulobacter crescentus is orchestrated by an elaborate gene-protein regulatory network , centered on three major control proteins , DnaA , GcrA and CtrA . The regulatory network is cast into a quantitative computational model to investigate in a systematic fashion how these three p... | Because of its small genome size and the ease by which it can be manipulated genetically and biochemically , Caulobacter crescentus provides unique opportunities to study the molecular circuitry controlling the asymmetric cell division cycle of bacteria . A large amount of experimental data accumulated on this model or... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"computational",
"biology/signaling",
"networks"
] | 2009 | Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus |
Complement C3 and C4 play key roles in the main physiological activities of complement system , and their deficiencies or over-expression are associated with many clinical infectious or immunity diseases . A two-stage genome-wide association study ( GWAS ) was performed for serum levels of C3 and C4 . The first stage w... | The complement system plays important roles in the innate and adaptive immune functions . C3 and C4 participate in almost all physiological activities and activated pathways as key complement members and host defense proteins . Identifying the genes that influence serum levels of C3 and C4 may help to elucidate the fac... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"of",
"the",
"immune",
"system",
"immunology",
"biology",
"genomics",
"genetics",
"and",
"genomics"
] | 2012 | Genome-Wide Association Study for Serum Complement C3 and C4 Levels in Healthy Chinese Subjects |
Genome-wide interaction-based association ( GWIBA ) analysis has the potential to identify novel susceptibility loci . These interaction effects could be missed with the prevailing approaches in genome-wide association studies ( GWAS ) . However , no convincing loci have been discovered exclusively from GWIBA methods ,... | Recent studies on the genetic basis of common diseases have identified many loci that confer disease susceptibility . However , much of the heritability of these diseases remains unexplained . Loci involved in gene–gene interactions are considered cryptic , because they confer susceptibility , but may not generate a de... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/bioinformatics",
"genetics",
"and",
"genomics/medical",
"genetics"
] | 2011 | Genome-Wide Interaction-Based Association Analysis Identified Multiple New Susceptibility Loci for Common Diseases |
Neuronal specification is often seen as a multistep process: earlier regulators confer broad neuronal identity and are followed by combinatorial codes specifying neuronal properties unique to specific subtypes . However , it is still unclear whether early regulators are re-deployed in subtype-specific combinatorial cod... | The nervous system contains a daunting number of different cell types , perhaps as many as 10 , 000 in mammals , far outnumbering regulatory genes in many animal species . Studies of the determinants of cell fate in many systems during the last decade have supported the conclusion that cell fate is not determined by an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"developmental",
"biology",
"neuroscience",
"drosophila",
"genetics",
"and",
"genomics"
] | 2007 | Specification of Neuronal Identities by Feedforward Combinatorial Coding |
Staphylococcus aureus is a leading cause of skin and soft-tissue infections worldwide . Mice are the most commonly used animals for modeling human staphylococcal infections . However a supra-physiologic S . aureus inoculum is required to establish gross murine skin pathology . Moreover , many staphylococcal factors , i... | S . aureus infection has emerged in the past decade as a major burden to public health and is responsible for a surge in preclinical research . Mice are the most commonly studied animals for modeling of human S . aureus infection . However , it is increasingly evident that available murine models poorly mimic human S .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Increased Susceptibility of Humanized NSG Mice to Panton-Valentine Leukocidin and Staphylococcus aureus Skin Infection |
The TRAIL ( TNF-related apoptosis inducing ligand ) death receptors ( DRs ) of the tumor necrosis factor receptor superfamily ( TNFRSF ) can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection . In turn , human cytomegalovirus ( HCMV ) expresses immunomodulatory proteins... | Natural killer ( NK ) cells are critical to the innate immune system along with their ability to detect and destroy cells infected by viruses . To avoid discovery by cytotoxic lymphocytes and to allow for longtime persistence in the host , human cytomegalovirus ( HCMV ) evolved a number of genes to evade or inhibit imm... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"cell",
"death",
"immune",
"cells",
"immunology",
"signaling",
"networks",
"protein",
"structure",
"signaling",
"pathways",
"apoptotic",
"signaling",
"glycoproteins",
"immunomodulation",
"signaling",
"in",
"cellular",
"processes",
... | 2013 | Structure of Human Cytomegalovirus UL141 Binding to TRAIL-R2 Reveals Novel, Non-canonical Death Receptor Interactions |
Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information . Among those are principal component analysis ( PCA ) , which identifies the most correlated groups of residues , and direct coupling analysis ( DCA ) , a... | Extracting functional and structural information about protein families from the covariation of residues in multiple sequence alignments is an important challenge in computational biology . Here we propose a statistical-physics inspired framework to analyze those covariations , which naturally unifies existing methods ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physics",
"sequence",
"analysis",
"forms",
"of",
"evolution",
"statistical",
"mechanics",
"coevolution",
"evolutionary",
"modeling",
"protein",
"structure",
"biology",
"computational",
"biology",
"evolutionary",
"biology",
"proteomics",
"evolutionary",
"processes",
"macrom... | 2013 | From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction |
Eukaryotic genomes are partitioned into active and inactive domains called euchromatin and heterochromatin , respectively . In Neurospora crassa , heterochromatin formation requires methylation of histone H3 at lysine 9 ( H3K9 ) by the SET domain protein DIM-5 . Heterochromatin protein 1 ( HP1 ) reads this mark and dir... | DNA methylation is a common feature of eukaryotic genomes . Methylation is typically associated with silenced chromosomal domains and is essential for development of plants and animals . Although the control of DNA methylation is not well understood , recent findings with model organisms , including the fungus Neurospo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2011 | Substitutions in the Amino-Terminal Tail of Neurospora Histone H3 Have Varied Effects on DNA Methylation |
The difference in epilepsy burden existing among populations in tropical regions has been attributed to many factors , including the distribution of infectious diseases with neurologic sequels . To define the burden of epilepsy in Latin American Countries ( LAC ) and to investigate the strength of association with neur... | Epilepsy affects approximately 70 million people worldwide and at least five million people in Latin America . Many researchers have pointed out a different distribution of epilepsy in Latin American countries , with some regions presenting higher frequencies and others presenting lower frequencies . This difference in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Epilepsy and Neurocysticercosis in Latin America: A Systematic Review and Meta-analysis |
Tsetse flies ( Glossina spp . ) transmit parasitic African trypanosomes ( Trypanosoma spp . ) , including Trypanosoma congolense , which causes animal African trypanosomiasis ( AAT ) . AAT detrimentally affects agricultural activities in sub-Saharan Africa and has negative impacts on the livelihood and nutrient availab... | Tsetse flies are economically important insects responsible for transmitting African trypanosomes , which cause debilitating and fatal diseases in humans and animals in sub-Saharan Africa . In the tsetse vector , trypanosomes undergo complex developmental processes in the midgut , culminating with the generation of mam... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"trypanosoma",
"congolense",
"social",
"sciences",
"neuroscience",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"genome",
"analysis",
"mechanoreceptors",
"gene",
"expression",
"sensory",
"rece... | 2017 | Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection |
Sexually transmitted Entamoeba histolytica infection ( EHI ) has been increasingly recognized among men who have sex with men ( MSM ) . We used the National Disease Surveillance Systems ( NDSS ) to identify prevalent and incident HIV diagnoses among adults with EHI and to determine the associated factors . The NDSS col... | Although sexually transmitted Entamoeba histolytica infection has been increasingly recognized among men who have sex with men ( MSM ) in Australia , Japan , Korea , and Taiwan , particularly those with HIV infection , no studies have examined E . histolytica infection in relation to HIV and attribution of sexual trans... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"hiv",
"epidemiology",
"infectious",
"disease",
"surveillance",
"infectious",
"diseases",
"hiv",
"infections",
"plant",
"science",
"medicine",
"and",
"health",
"sciences",
"amebiasis",
"epidemiology",
"disease",
"surveillance",
"plant",
"pathology",
"biology",
"and",
"l... | 2014 | Prevalent and Incident HIV Diagnoses among Entamoeba histolytica-Infected Adult Males: A Changing Epidemiology Associated with Sexual Transmission — Taiwan, 2006–2013 |
Adeno-associated viruses are members of the genus dependoviruses of the parvoviridae family . AAV vectors are considered promising vectors for gene therapy and genetic vaccination as they can be easily produced , are highly stable and non-pathogenic . Nevertheless , transduction of cells in vitro and in vivo by AAV in ... | SUMOylation is a post-translational modification in which a small protein ( SUMO ) is covalently attached to target proteins . Three key enzymes are controlling this modification: The E1 activating complex composed of the heterodimer Sae1/Sae2 , the E2 conjugation enzyme Ubc9 and one of many E3 enzymes which specifical... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | The SUMOylation Pathway Restricts Gene Transduction by Adeno-Associated Viruses |
Phylodynamic modelling , which studies the joint dynamics of epidemiological and evolutionary processes , has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling . These advances have greatly improved our understanding of transmission dynamics of ma... | Integrated modelling of conventional epidemiological data and modern genomic data ( i . e . phylodynamics ) has made significant progress in recent years , due to the ever-increasing availability of genomic data and development of statistical methods . However , there is a lack of tools for carrying out effective diagn... | [
"Abstract",
"Introduction",
"Models",
"and",
"methods",
"Results",
"Discussion"
] | [
"epidemiological",
"statistics",
"medicine",
"and",
"health",
"sciences",
"epidemiological",
"methods",
"and",
"statistics",
"mathematics",
"diagnostic",
"medicine",
"pathology",
"and",
"laboratory",
"medicine",
"simulation",
"and",
"modeling",
"epidemiology",
"statistics",... | 2019 | Model diagnostics and refinement for phylodynamic models |
The nuclear pore complex ( NPC ) forms a gateway for nucleocytoplasmic transport . The outer ring protein complex of the NPC ( the Nup107-160 subcomplex in humans ) is a key component for building the NPC . Nup107-160 subcomplexes are believed to be symmetrically localized on the nuclear and cytoplasmic sides of the NP... | The nuclear pore complexes ( NPCs ) form gateways to transport intracellular molecules between the nucleus and the cytoplasm across the nuclear envelope . The Nup107-160 subcomplex , that forms nuclear and cytoplasmic outer rings , is a key complex responsible for building the NPC by symmetrical localization on the nuc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"meiosis",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"light",
"microscopy",
"fungi",
"model",
"organisms",
"microscopy",
"experimental",
"organism",
"systems",
"cell",
"nucleus",
"cellular",
"structures",
"and",
"organelles... | 2019 | Asymmetrical localization of Nup107-160 subcomplex components within the nuclear pore complex in fission yeast |
The identification of rare coding or splice site variants remains the most straightforward strategy to link genes with human phenotypes . Here , we analyzed the association between 137 , 086 rare ( minor allele frequency ( MAF ) <1% ) coding or splice site variants and 15 hematological traits in up to 308 , 572 partici... | Genome-wide association studies ( GWAS ) have identified thousand of genetic associations between common DNA sequence variants ( e . g . single nucleotide polymorphisms ( SNPs ) ) and complex human diseases or traits . In most cases , these associations highlight non-coding variants , and thus fall short of identifying... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"quantitative",
"trait",
"loci",
"blood",
"counts",
"alleles",
"genome",
"analysis",
"platelets",
"hemoglobin",
"animal",
"cells",
"proteins",
"geneti... | 2017 | Rare coding variants pinpoint genes that control human hematological traits |
Lymphatic filariasis can be associated with development of serious pathology in the form of lymphedema , hydrocele , and elephantiasis in a subset of infected patients . To elucidate the role of CD4+ T cell subsets in the development of lymphatic pathology , we examined specific sets of cytokines in individuals with fi... | Lymphatic filariasis afflicts over 120 million people worldwide . While the infection is mostly clinically asymptomatic , approximately 40 million people suffer from overt , morbid clinical pathology , characterized by swelling of the scrotal area and lower limbs ( hydrocele and lymphedema ) . Host immunologic factors ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immunology/immunomodulation",
"infectious",
"diseases/helminth",
"infections",
"immunology/immunity",
"to",
"infections"
] | 2009 | Filarial Lymphedema Is Characterized by Antigen-Specific Th1 and Th17 Proinflammatory Responses and a Lack of Regulatory T Cells |
Scabies is a major public health problem in the Pacific and is associated with an increased risk of bacterial skin infections , glomerulonephritis and rheumatic fever . Mass drug administration with ivermectin is a promising strategy for the control of scabies . Mass treatment with ivermectin followed by active case fi... | Scabies is a parasitic infection caused by the mite Sarcoptes scabiei . Scabies is a risk factor for bacterial skin infections and as a result of these secondary infections , individuals with scabies are also at risk of kidney disease and possibly rheumatic heart disease . Traditionally the management of scabies has in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Long Term Control of Scabies Fifteen Years after an Intensive Treatment Programme |
Chikungunya Virus ( CHIKV ) , a re-emerging arbovirus that may cause severe disease , constitutes an important public health problem . Herein we describe a novel CHIKV infection model in zebrafish , where viral spread was live-imaged in the whole body up to cellular resolution . Infected cells emerged in various organs... | Chikungunya , a re-emerging disease caused by a mosquito-transmitted virus , is an important public health problem . We developed a zebrafish model for chikungunya virus infection . For the first time , rise and death of virus-infected cells could be live imaged in the entire body of a vertebrate . We observed a widesp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"animal",
"models",
"of",
"infection",
"zebrafish",
"viral",
"clearance",
"model",
"organisms",
"host",
"cells",
"neuroinvasiveness",
"immunity",
"viral",
"transmission",
"and",
"infection",
"virology",
"innate",
"immunity",
"immunity",
"to",
"infe... | 2013 | Real-Time Whole-Body Visualization of Chikungunya Virus Infection and Host Interferon Response in Zebrafish |
Environmental factors such as temperature can alter mosquito vector competence for arboviruses . Results from recent studies indicate that daily fluctuations around an intermediate mean temperature ( 26°C ) reduce vector competence of Aedes aeygpti for dengue viruses ( DENV ) . Theoretical predictions suggest that the ... | Mosquitoes in the wild are exposed to daily fluctuations in temperature , but in the laboratory , the effect of temperature on vector competence is generally assessed using constant temperatures . Recent studies demonstrate that realistic fluctuations in temperature around an intermediate mean ( 26°C ) can alter life-h... | [
"Abstract",
"Introduction",
"Methods",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"mosquitoes",
"entomology",
"vector",
"biology",
"neglected",
"tropical",
"diseases",
"dengue",
"biology",
"microbiology",
"viral",
"diseases",
"zoology"
] | 2013 | Fluctuations at a Low Mean Temperature Accelerate Dengue Virus Transmission by Aedes aegypti |
Resection of the bulk of a tumour often cannot eliminate all cancer cells , due to their infiltration into the surrounding healthy tissue . This may lead to recurrence of the tumour at a later time . We use a reaction-diffusion equation based model of tumour growth to investigate how the invasion front is delayed by re... | Mathematical models of propagating fronts have been used to represent a wide variety of biological phenomena from action potentials in neural cells to invasive species in ecology and epidemic spreading . Here we show that when such models are used to predict the effects of external perturbations the results can be very... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"cancer",
"treatment",
"clinical",
"oncology",
"biological",
"cultures",
"cancers",
"and",
"neoplasms",
"blastomas",
"cell",
"processes",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"oncology",
"... | 2017 | The role of Allee effect in modelling post resection recurrence of glioblastoma |
Neurons and other cells display a large variation in size in an organism . Thus , a fundamental question is how growth of individual cells and their organelles is regulated . Is size scaling of individual neurons regulated post-mitotically , independent of growth of the entire CNS ? Although the role of insulin/IGF-sig... | Nerve cells display a large variation in size in an organism . Thus , a fundamental question is how growth of individual cells and their organelles is regulated . We ask if there is a regulatory mechanism for scaling the size of individual nerve cells , independent of the growth of the entire central nervous system ( C... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Insulin/IGF-Regulated Size Scaling of Neuroendocrine Cells Expressing the bHLH Transcription Factor Dimmed in Drosophila |
Vaccines that elicit protective cytotoxic T lymphocytes ( CTL ) may improve on or augment those designed primarily to elicit antibody responses . However , we have little basis for estimating the numbers of CTL required for sterilising immunity at an infection site . To address this we begin with a theoretical estimate... | In the search for vaccines that provide reliable protection against major diseases such as HIV-AIDS , TB and Malaria , there is now a focus on generating populations of antigen-specific cytotoxic T lymphocytes ( CTL ) , immune cells that recognise and kill infected cells . However , we have little idea of the number or... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"immune",
"cells",
"t",
"cells",
"immunology",
"biology",
"computational",
"biology",
"immune",
"response"
] | 2011 | Virus Replication Strategies and the Critical CTL Numbers Required for the Control of Infection |
The non-homologous end joining of a DNA double strand break is initiated by the MRE11-NBS1-RAD50 complex whose subunits are the first three proteins to arrive to the breakage site thereby making the recruitment time of MRE11 , NBS1 and RAD50 essential for cell survival . In the present investigation , the nature of MRE... | The DNA repair mechanism is crucial for a cell to avoid apoptosis , and is a complicated process involving many different repair proteins . The mean of transportation of these repair proteins is largely unknown as their transportation mechanisms need clarification . We have focused on the transportation of some of the ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"dna",
"damage",
"mathematics",
"statistics",
"(mathematics)",
"dna",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
"methods",
"mathematical",
"and",
"statistical",
"techniques",
"chemistry",
"monte",
"carlo",
"method",
"biophysics",
"rib... | 2018 | Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion |
Patterning of functional blood vessel networks is achieved by pruning of superfluous connections . The cellular and molecular principles of vessel regression are poorly understood . Here we show that regression is mediated by dynamic and polarized migration of endothelial cells , representing anastomosis in reverse . E... | The question of how blood vessel networks achieve their branching patterns is key to our understanding of organ formation as well as diseases that involve vascular anomalies . Regression ( or pruning ) of blood vessel segments is required for functional vascular branching patterns; however , the molecular basis for thi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Dynamic Endothelial Cell Rearrangements Drive Developmental Vessel Regression |
While T cell immunity initially limits Mycobacterium tuberculosis infection , why T cell immunity fails to sterilize the infection and allows recrudescence is not clear . One hypothesis is that T cell exhaustion impairs immunity and is detrimental to the outcome of M . tuberculosis infection . Here we provide functiona... | Tuberculosis is a leading cause of morbidity and mortality across the globe . Fortunately , most people infected with M . tuberculosis mount a protective immune response and only a small fraction develops active disease . Impairment of immunity late during the course of disease can lead to bacterial recrudescence; howe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"cd",
"coreceptors",
"immunology",
"tropical",
"diseases",
"cell-mediated",
"immunity",
"bacterial",
"diseases",
"development... | 2016 | TIM3 Mediates T Cell Exhaustion during Mycobacterium tuberculosis Infection |
The variation in weight within a shared environment is largely attributable to genetic factors . Whilst many genes/loci confer susceptibility to obesity , little is known about the genetic architecture of healthy thinness . Here , we characterise the heritability of thinness which we found was comparable to that of sev... | Obesity-associated disorders are amongst the leading causes of morbidity and mortality worldwide . Most genome-wide association studies ( GWAS ) have focused on body mass index ( BMI = weight in Kg divided by height squared ( m2 ) ) and obesity , but to date no genetic association study testing thin and healthy individ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"statistics",
"metaanalysis",
"physiological",
"parameters",
"mathematics",
"obesity",
"genome",
"analysis",
"research",
"and",
"analysis",
"methods",
"genomic",
"signal",
... | 2019 | Genetic architecture of human thinness compared to severe obesity |
Vibrio cholerae is a diarrheal pathogen that induces accumulation of lipid droplets in enterocytes , leading to lethal infection of the model host Drosophila melanogaster . Through untargeted lipidomics , we provide evidence that this process is the product of a host phospholipid degradation cascade that induces lipid ... | The virulence program of intestinal pathogens such as Vibrio cholerae depends on the continued function of target host proteins . If these proteins are inactivated by methionine oxidation , virulence may also depend on repair of these proteins by host methionine sulfoxide reductases such as MsrA . Dietary methionine su... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"aliphatic",
"amino",
"acids",
"pathogens",
"vibrio",
"microbiology",
"organic",
"compounds",
"animals",
"animal",
"models",
"vibrio",
"chole... | 2017 | Vibrio cholerae ensures function of host proteins required for virulence through consumption of luminal methionine sulfoxide |
Retrotransposons are major components of plant and animal genomes . They amplify by reverse transcription and reintegration into the host genome but their activity is usually epigenetically silenced . In plants , genomic copies of retrotransposons are typically associated with repressive chromatin modifications install... | Transposons are programmed to amplify within their host genomes . In defense , hosts have evolved mechanisms to impede transposon activation , often by epigenetic transcriptional silencing . A constant and likely unending arms race between host and invader has brought about different strategies to mutually counteract t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"gene",
"expression",
"genetics",
"plant",
"genetics",
"epigenetics",
"molecular",
"genetics",
"biology",
"dna",
"modification",
"dna",
"transcription"
] | 2014 | How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation |
Cerebral malaria ( CM ) is associated with a high mortality rate and long-term neurocognitive impairment in survivors . The murine model of experimental cerebral malaria ( ECM ) induced by Plasmodium berghei ANKA ( PbA ) -infection reproduces several of these features . We reported recently increased levels of IL-33 pr... | The cerebral complication of malaria caused by Plasmodium falciparum infection , is associated with long-term neurological sequelae in survivors . The mechanisms involved in neurocognitive impairments during cerebral malaria development are still unknown . We reported recently the essential role of IL-33/ST2 pathway in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cognitive",
"neurology",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"astrocytes",
"tropical",
"diseases",
"brain",
"parasitic",
"diseases",
"neuroscience",
"macroglial",
"cells",
"microglial",
"cells",
"animal",
"models",
"cognitive",
"neuroscience",
... | 2017 | IL-33 receptor ST2 regulates the cognitive impairments associated with experimental cerebral malaria |
Globally , about 1 . 5 billion people are infected with at least one species of soil-transmitted helminth ( STH ) . Soil is a critical environmental reservoir of STH , yet there is no standard method for detecting STH eggs in soil . We developed a field method for enumerating STH eggs in soil and tested the method in B... | Intestinal worm infections are common in populations living in tropical , low-income countries . People primarily become infected when they consume intestinal worm eggs from contaminated water , hands , and food . Intestinal worm eggs are transmitted from infected people and spread through the environment , particularl... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"specific",
"gravity",
"helminths",
"tropical",
"diseases",
"hookworms",
"parasitic",
"diseases",
"animals",
"developmental",
"biology",
"ascaris",
"materials",
"science",
"neglected",
"tropical",
"diseases",
"surf... | 2017 | Detecting and enumerating soil-transmitted helminth eggs in soil: New method development and results from field testing in Kenya and Bangladesh |
Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes . In mice , Intracisternal A Particles ( IAPs ) are a frequent source of both new mutations and polymorphism across laboratory strains . Intronic IAPs can induce alternative RNA processing choices , including alternat... | Transposable elements , including endogenous retroviruses , have long been hypothesized as a substrate for creating or modulating gene regulatory networks , particularly through effects on transcription . However , several classes of elements are also known to affect alternative RNA processing events . We previously sh... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Nxf1 Natural Variant E610G Is a Semi-dominant Suppressor of IAP-Induced RNA Processing Defects |
Serological tests have been used for the diagnosis of Taenia solium infection in pigs . However , those serological results do not necessarily correlate with the actual infection burden after performing pig necropsy . This study aimed to evaluate the Electro Immuno Transfer Blot ( EITB ) seropositivity with infection b... | Taenia solium is a parasite that infects humans . The parasite eggs are released into the environment with human feces in villages with inadequate sanitation . Pigs might ingest the parasite eggs and develop the larval stage named cysticercosis ( cysts ) , mainly in the muscles and heart . If a human accidentally inges... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taeniasis",
"medicine",
"infectious",
"diseases",
"zoonoses",
"veterinary",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"cysticercosis",
"neglected",
"tropical",
"diseases",
"parasitic",
"diseases",
"veterinary",
"science"
] | 2013 | Relationship between Serum Antibodies and Taenia solium Larvae Burden in Pigs Raised in Field Conditions |
Ribosome-binding proteins function broadly in protein synthesis , gene regulation , and cellular homeostasis , but the complete complement of functional ribosome-bound proteins remains unknown . Using quantitative mass spectrometry , we identified late-annotated short open reading frame 2 ( Lso2 ) as a ribosome-associa... | Translation , or the production of protein from messenger RNA ( mRNA ) , is catalyzed by a universally conserved macromolecular machine known as the ribosome . Ribosome-binding factors are also required for all substeps of translation , from initial recruitment of mRNA to peptide chain elongation to release of the matu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cdna",
"libraries",
"transfer",
"rna",
"nucleases",
"enzymes",
"dna-binding",
"proteins",
"enzymology",
"fungi",
"forms",
"of",
"dna",
"dna",
"libraries",
"molecular",
"biology",
"techniques",
"dna",
"cellular",
"structures",
"and",
"organelles",
"genetic",
"footprin... | 2018 | Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast |
Schistosomiasis is a neglected disease affecting hundreds of millions worldwide . Of the three main species affecting humans , Schistosoma haematobium is the most common , and is the leading cause of urogenital schistosomiasis . S . haematobium infection can cause different urogenital clinical complications , particula... | Schistosomiasis is a neglected tropical disease affecting millions of people worldwide . Of the main three species affecting humans , Schistosoma haematobium is the most common , and is the leading cause of urogenital schistosomiasis . This parasite can cause a range of clinical complications associated with bladder pa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"immune",
"physiology",
"helminths",
"immunology",
"microbiology",
"viral",
"structure",
"parasitic",
"diseases",
"animals",
"urine",
"antibodies",
"immune... | 2019 | In-depth proteomic characterization of Schistosoma haematobium: Towards the development of new tools for elimination |
The evolution of an obligate parasitic lifestyle is often associated with genomic reduction , in particular with the loss of functions associated with increasing host-dependence . This is evident in many parasites , but perhaps the most extreme transitions are from free-living autotrophic algae to obligate parasites . ... | Helicosporidium is a highly-adapted obligate parasite of animals . Its evolutionary origins were unclear for almost a century , but molecular analysis ultimately and surprisingly showed that it is a green alga , which means it has undergone an evolutionary transition from autotrophy to parasitism comparable to that of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"organismal",
"evolution",
"computer",
"and",
"information",
"sciences",
"genome",
"complexity",
"genomics",
"genome",
"evolution",
"network",
"analysis",
"eukaryotic",
"evolution",
"genetics",
"biology",
"and",
"life",
"sciences",
"metabolic",
"networks",
"comparative",
... | 2014 | A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium |
Gene duplication is a powerful driver of evolution . Newly duplicated genes acquire new roles that are relevant to fitness , or they will be lost over time . A potential path to functional relevance is mutation of the coding sequence leading to the acquisition of novel biochemical properties , as analyzed here for the ... | The duplication of a gene from a common ancestor , resulting in two copies known as paralogs , plays an important role in evolution . Newly duplicated genes must acquire new functions in order to remain relevant , otherwise they are lost via mutation over time . We have performed genome-wide location analysis ( ChIP–Se... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"genetics",
"biology",
"genomics",
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2 |
Transcription and replication of the influenza A virus ( IAV ) genome occur in the nucleus of infected cells and are carried out by the viral ribonucleoprotein complex ( vRNP ) . As a major component of the vRNP complex , the viral nucleoprotein ( NP ) mediates the nuclear import of the vRNP complex via its nuclear loc... | Influenza viral RNA is encapsidated by three polymerase proteins and the NP protein to form the vRNP complex , which is transported to the nucleus of infected cells for viral transcription and replication . The active nuclear import of the vRNP complex is mediated by the interaction between NP and importin α through th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"nuclear",
"import",
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"gene",
"regulation",
"pathogens",
"cell",
"processes",
"signaling",
"networks",
"microbiology",
"orthomyxoviruses",
"viruses",
"wireless",
"sens... | 2018 | Phospholipid scramblase 1 interacts with influenza A virus NP, impairing its nuclear import and thereby suppressing virus replication |
Although genome-wide association studies ( GWASs ) have discovered numerous novel genetic variants associated with many complex traits and diseases , those genetic variants typically explain only a small fraction of phenotypic variance . Factors that account for phenotypic variance include environmental factors and gen... | Although genome-wide association studies ( GWASs ) have discovered numerous novel genetic variants associated with many complex traits and diseases , those genetic variants typically explain only a small fraction of phenotypic variance . Factors that account for phenotypic variance include environmental factors and gen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"population",
"genetics",
"mathematics",
"statistics",
"(mathematics)",
"test",
"statistics",
"genome",
"analysis",
"population",
"biology",
"research",
"and",
"analysis",
"methods",
"statistical",
"distributions",
"lipids",
"fats",
... | 2016 | Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models |
Several nucleoporins in the nuclear pore complex ( NPC ) have been reported to be involved in abiotic stress responses in plants . However , the molecular mechanism of how NPC regulates abiotic stress responses , especially the expression of stress responsive genes remains poorly understood . From a forward genetics sc... | Nuclear pore complex ( NPC ) mediates the traffic between nucleus and cytoplasm . This work identified NUCLEOPORIN 85 ( NUP85 ) as an important factor for the expression of stress-responsive luciferase reporter gene RD29A-LUC in response to ABA and salt stress from a forward genetics screen . Mutation in NUP85 and othe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"ecology",
"and",
"environmental",
"sciences",
"gene",
"regulation",
"brassica",
"rna",
"extraction",
"plant",
"physiology",
"suppressor",
"genes",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"gene",
"types",
"plant",
"pathology",
... | 2017 | An Arabidopsis Nucleoporin NUP85 modulates plant responses to ABA and salt stress |
EBV latent antigen 3C ( EBNA3C ) is essential for EBV-induced primary B-cell transformation . Infection by EBV induces hypermethylation of a number of tumor suppressor genes , which contributes to the development of human cancers . The Ras association domain family isoform 1A ( RASSF1A ) is a cellular tumor suppressor ... | Epstein-Barr virus ( EBV ) which is associated with multiple lymphoid and epithelial malignancies was the first recognized oncogenic virus in humans . EBNA3C , an essential latent antigen encoded by EBV interacts with numerous host transcription factors and plays an important role in the transformation of primary B-cel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"microtubules",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"immunology",
"immunoprecipitation",
"epigenetics",
"dna",
"molecular",
"biology",
"techniqu... | 2019 | EBNA3C facilitates RASSF1A downregulation through ubiquitin-mediated degradation and promoter hypermethylation to drive B-cell proliferation |
Cholera is an acute voluminous dehydrating diarrheal disease caused by toxigenic strains of Vibrio cholerae O1 and occasionally O139 . A growing body of evidence indicates that immune responses targeting the O-specific polysaccharide ( OSP ) of V . cholerae are involved in mediating protection against cholera . We ther... | Cholera is a severe watery diarrheal disease , caused by pathogenic strains of V . cholerae . Protective immunity against cholera is serogroup specific , and serogroup specificity is determined by the O-specific polysaccharide ( OSP ) of V . cholerae lipopolysaccharide ( LPS ) . Despite this , no previous work has dire... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"vibrio",
"immunology",
"tropical",
"diseases",
"microbiology",
"vaccines",
"diarrhea",
"bacterial",
"diseases",
"v... | 2018 | Anti-O-specific polysaccharide (OSP) immune responses following vaccination with oral cholera vaccine CVD 103-HgR correlate with protection against cholera after infection with wild-type Vibrio cholerae O1 El Tor Inaba in North American volunteers |
The Dot/Icm system of the intracellular pathogen Legionella pneumophila has the capacity to deliver over 270 effector proteins into host cells during infection . Important questions remain as to spatial and temporal mechanisms used to regulate such a large array of virulence determinants after they have been delivered ... | The intracellular pathogen Legionella pneumophila encodes at least 270 effectors that modulate trafficking of the pathogen-occupied vacuole . The mechanisms by which effectors are controlled in host cells are of key interest . Spatial and temporal regulation of effector function has been proposed to involve effector bi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"host-pathogen",
"interactions",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"pathogenesis",
"bacterial",
"pathogens"
] | 2014 | The Machinery at Endoplasmic Reticulum-Plasma Membrane Contact Sites Contributes to Spatial Regulation of Multiple Legionella Effector Proteins |
Un-physiological activation of hypoxia inducible factor ( HIF ) is an early event in most renal cell cancers ( RCC ) following inactivation of the von Hippel-Lindau tumor suppressor . Despite intense study , how this impinges on cancer development is incompletely understood . To test for the impact of genetic signals o... | Though numerous DNA polymorphisms that modulate the risk of developing cancer have been identified , understanding the functional role of extra-genic variation has so far proved difficult , in part because it is difficult to link such variation to a functional framework . To address this , we aligned extragenic renal c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"gene",
"regulation",
"computational",
"biology",
"renal",
"cancer",
"alleles",
"genetic",
"mapping",
"genome",
"analysis",
"epigenetics",
"chromatin",
"small",
"interfering",
"rnas",
"chr... | 2017 | Multiple renal cancer susceptibility polymorphisms modulate the HIF pathway |
Increasing evidence suggests that dysregulation of lipid metabolism is associated with neurodegeneration in retinal diseases such as age-related macular degeneration and in brain disorders such as Alzheimer’s and Parkinson’s diseases . Lipid storage organelles ( lipid droplets , LDs ) , accumulate in many cell types in... | Lipids are major cell constituents and are present in the membranes , as free lipids in the cytoplasm , or stored in vesicles called lipid droplets ( LDs ) . Under conditions of stress , lipids stored in LDs can be released to serve as substrates for energy metabolism by mitochondria . However , lipid storage is dysreg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"ocular",
"anatomy",
"social",
"sciences",
"neuroscience",
"animals",
"pigments",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"materials",
"science",
"experimental",
"organis... | 2018 | Physiological and pathological roles of FATP-mediated lipid droplets in Drosophila and mice retina |
Tetherin , also known as BST2 , CD317 or HM1 . 24 , was recently identified as an interferon-inducible host–cell factor that interferes with the detachment of virus particles from infected cells . HIV-1 overcomes this restriction by expressing an accessory protein , Vpu , which counteracts tetherin . Since lentiviruses... | Tetherin was recently identified as a host–cell factor that interferes with the detachment of virus particles from infected cells . HIV-1 overcomes the antiviral effects of tetherin by expressing Vpu , which mediates the degradation of tetherin . While tetherin has broad activity against diverse types of viruses , only... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/virus",
"evolution",
"and",
"symbiosis",
"virology/immunodeficiency",
"viruses",
"virology/animal",
"models",
"of",
"infection",
"virology/mechanisms",
"of",
"resistance",
"and",
"susceptibility,",
"including",
"host",
"genetics",
"virology/immune",
"evasion"
] | 2009 | Species-Specific Activity of SIV Nef and HIV-1 Vpu in Overcoming Restriction by Tetherin/BST2 |
Genetic mutations disrupting the structure and function of primary cilia cause various inherited retinal diseases in humans . Bardet-Biedl syndrome ( BBS ) is a genetically heterogeneous , pleiotropic ciliopathy characterized by retinal degeneration , obesity , postaxial polydactyly , intellectual disability , and geni... | The BBSome is a protein complex that regulates ciliary trafficking in primary cilia , and mutations that impair BBSome function cause Bardet-Biedl Syndrome ( BBS ) . BBS patients have retinal degeneration leading to blindness , but the disease pathophysiology has not been fully elucidated . In this study , we found tha... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"ocular",
"anatomy",
"social",
"sciences",
"neuroscience",
"animal",
"models",
"retinal",
"disorders",
"age",
"groups",
"developmental",
"biology",
"adults",
"model",
"organisms",
"experimental",
"organism",
"systems",
"eyes",
... | 2017 | BBSome function is required for both the morphogenesis and maintenance of the photoreceptor outer segment |
We propose a novel method and software tool , Strawberry , for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation . Strawberry consists of two modules: assembly and quantification . The novelty of Strawberry is that the two modules us... | Transcript assembly and quantification are important bioinformatics applications of RNA-Seq . The difficulty of solving these problem arises from the ambiguity of reads assignment to isoforms uniquely . This challenge is twofold: statistically , it requires a high-dimensional mixture model , and computationally , it ne... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"applied",
"mathematics",
"brassica",
"sequence",
"assembly",
"tools",
"simulation",
"and",
"modeling",
"algorithms",
"alternative",
"splicing",
"optimization",
"model",
"organisms",
"mathematics",
"experimental",
"organism",
"systems",
"genome",
"analysis",
"plants",
"re... | 2017 | Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq |
Cervical carcinomas result from cellular transformation by the human papillomavirus ( HPV ) E6 and E7 oncogenes which are constitutively expressed in cancer cells . The E6 oncogene degrades p53 thereby modulating a large set of p53 target genes as shown previously in the cervical carcinoma cell line HeLa . Here we show... | High-risk human papillomavirus infection can cause cancer of the uterine cervix . The viral proteins leading to transformation of the infected keratinocytes are the E6 and E7 oncogenes which interact with and induce degradation of the cell cycle regulators p53 and pRB . In cervical carcinoma cells , repression of E6/E7... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"cell",
"biology",
"cell",
"adhesion",
"virology",
"gene",
"expression",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"molecular",
"biology",
"dna",
"transcription"
] | 2011 | The Human Papillomavirus E6 Oncogene Represses a Cell Adhesion Pathway and Disrupts Focal Adhesion through Degradation of TAp63β upon Transformation |
We aimed to evaluate the relationships between climate variability , animal reservoirs and scrub typhus incidence in Southern China . We obtained data on scrub typhus cases in Guangzhou every month from 2006 to 2014 from the Chinese communicable disease network . Time-series Poisson regression models and distributed la... | Scrub typhus has been endemic in southern China for several decades . In recent years , it has been increasingly reported and has become a significant health concern in China . The incidence of scrub typhus , a vector-borne disease , is influenced by the density of rats and changes in climate . Several studies have foc... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"typhus",
"medicine",
"and",
"health",
"sciences",
"china",
"atmospheric",
"science",
"geographical",
"locations",
"vertebrates",
"animals",
"mammals",
"bacterial",
"diseases",
"materials",
"science",
"surface",
"properties",
"humidity",
"surface",
"tempe... | 2017 | Climate variability, animal reservoir and transmission of scrub typhus in Southern China |
Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions , caused by parasitic flatworms of the genus Schistosoma ( subclass Digenea ) . Following major water development schemes in the 1980s , schistosomiasis has become an important parasitic disease of children livin... | Schistosome blood flukes cause significant disease in humans and their livestock in tropical and subtropical regions of the world . They have a two host-life cycle with a sexual stage within the mammalian host and are transmitted through water contact . Understanding the biology of these dioecious parasites is essentia... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/helminth",
"infections",
"ecology/evolutionary",
"ecology",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases",
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2009 | Bidirectional Introgressive Hybridization between a Cattle and Human Schistosome Species |
Pathogenicity differences among laboratory isolates of the dominant clonal North American and European lineages of Toxoplasma gondii are largely controlled by polymorphisms and expression differences in rhoptry secretory proteins ( ROPs ) . However , the extent to which such differences control virulence in natural iso... | The determinants of virulence are rarely defined for eukaryotic parasites such as T . gondii , a widespread parasite of mammals that also infects humans , sometimes with serious consequences . Recent laboratory studies have established that variation in a single secreted protein , a serine/threonine kinase known as ROP... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"molecular",
"biology/molecular",
"evolution",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2009 | Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice |
The mechanism underlying persistent hepatitis B virus ( HBV ) infection remains unclear . We investigated the role of innate immune responses to persistent HBV infection in 154 HBV-infected patients and 95 healthy controls . The expression of NKG2D- and 2B4-activating receptors on NK cells was significantly decreased ,... | NK cells have been viewed as the most important effectors of the initial antiviral innate immune response . Their activation depends on the integration of signals from “co-activation” receptors , and the cytotoxic effects of NK cells on target cells are tempered by a need for combined signals from multiple activating r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"immune",
"cells",
"clinical",
"immunology",
"immunology",
"biology"
] | 2012 | TGF-β1 Down-Regulation of NKG2D/DAP10 and 2B4/SAP Expression on Human NK Cells Contributes to HBV Persistence |
RIG-I is a DExD/H-box RNA helicase and functions as a critical cytoplasmic sensor for RNA viruses to initiate antiviral interferon ( IFN ) responses . Here we demonstrate that another DExD/H-box RNA helicase DHX36 is a key molecule for RIG-I signaling by regulating double-stranded RNA ( dsRNA ) -dependent protein kinas... | Cellular responses to environmental stress are critical for maintaining homeostasis in living organisms . In one type of response , eukaryotic cells exhibit rapid formation of aggregates with RNA and multiple RNA-binding proteins in the cytoplasm termed stress granules ( SGs ) . Over the past decade , SGs have been sug... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"immunology",
"biology",
"microbiology"
] | 2014 | DHX36 Enhances RIG-I Signaling by Facilitating PKR-Mediated Antiviral Stress Granule Formation |
Nuclear export of mRNAs and pre-ribosomal subunits ( pre40S and pre60S ) is fundamental to all eukaryotes . While genetic approaches in budding yeast have identified bona fide export factors for mRNAs and pre60S subunits , little is known regarding nuclear export of pre40S subunits . The yeast heterodimeric transport r... | Eukaryotic pre-ribosomal subunits ( pre40S and pre60S ) are one of the largest RNA containing cargos that are transported from the nucleus through the nuclear pore complex ( NPC ) into the cytoplasm . While genetic approaches in budding yeast have identified bona fide export factors for pre60S subunits , little is know... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"transport",
"macromolecular",
"assemblies",
"microbiology",
"gene",
"function",
"model",
"organisms",
"gene",
"expression",
"biology",
"biochemistry",
"rna",
"nucleic",
"acids",
"genetic",
"screens",
"genetics",
"yeast",
"and",
"fungal",
"models",
"saccharomyces... | 2012 | Role of Mex67-Mtr2 in the Nuclear Export of 40S Pre-Ribosomes |
The success of programs to eliminate lymphatic filariasis ( LF ) depends in large part on their ability to achieve and sustain high levels of compliance with mass drug administration ( MDA ) . This paper reports results from a comprehensive review of factors that affect compliance with MDA . Papers published between 20... | Lymphatic filariasis ( LF , also known as “elephantiasis” ) is a deforming and disabling disease that is caused by roundworm parasites that are transmitted by mosquitoes . The Global Programme to Eliminate Lymphatic Filariasis is the largest public health intervention program attempted to date based on mass drug admini... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Final",
"Conclusions"
] | [] | 2013 | A Review of Factors That Influence Individual Compliance with Mass Drug Administration for Elimination of Lymphatic Filariasis |
Leishmania major infection induces robust interleukin-12 ( IL12 ) production in human dendritic cells ( hDC ) , ultimately resulting in Th1-mediated immunity and clinical resolution . The surface of Leishmania parasites is covered in a dense glycocalyx consisting of primarily lipophosphoglycan ( LPG ) and other phospho... | Leishmaniasis is a group of parasitic diseases caused by intracellular protozoa belonging to the genus Leishmania , pathological manifestations ranging from self-healing cutaneous forms to severe visceral infections that result in death . These clinical outcomes are dictated by the Leishmania species initiating the inf... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Differential Impact of LPG-and PG-Deficient Leishmania major Mutants on the Immune Response of Human Dendritic Cells |
Time-delays are common in many physical and biological systems and they give rise to complex dynamic phenomena . The elementary processes involved in template biopolymerization , such as mRNA and protein synthesis , introduce significant time delays . However , there is not currently a systematic mapping between the in... | Genetic networks display exceedingly complex and rich behavior which is modulated by multiple mechanisms , including many diverse types of interactions between DNA , mRNA and protein molecules . Mathematical models of gene networks must necessarily consider the essential mechanistic details of the processes involved in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/synthetic",
"biology",
"computational",
"biology/systems",
"biology",
"mathematics",
"computational",
"biology/metabolic",
"networks",
"biotechnology/bioengineering",
"biochemistry/theory",
"and",
"simulation",
"biochemistry/transcription",
"and",
"translati... | 2010 | The Origins of Time-Delay in Template Biopolymerization Processes |
Knowledge of the mechanisms for regulating lifespan is advancing rapidly , but lifespan is a complex phenotype and new features are likely to be identified . Here we reveal a novel approach for regulating lifespan . Using a genetic or a pharmacological strategy to lower the rate of sphingolipid synthesis , we show that... | Studies with rats in the 1930s showed a surprising increase in lifespan when the diet contained 30%–40% fewer calories than normal . This experiment has been repeated on many organisms and is the gold standard for extending lifespan . While we are beginning to understand how calorie restriction regulates lifespan , the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2012 | Down-Regulating Sphingolipid Synthesis Increases Yeast Lifespan |
We consider a world of nucleotide sequences and protocells . The sequences have the property of spontaneous self-replication . Some sequences - so-called replicases - have enzymatic activity in the sense of enhancing the replication rate of all ( or almost all ) sequences . In a well-mixed medium , natural selection wo... | The origin of life , proceeding from chemical reactions to cells , must have included a critical transitional period in which catalytically active sequences arose . A fundamental problem exists for the first catalytic sequences: their activity would not enhance their own fitness directly , and might even decrease their... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"modeling",
"biology",
"computational",
"biology"
] | 2013 | Selection for Replicases in Protocells |
Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma ( KS ) and primary effusion B-cell lymphoma . KSHV induces reactive oxygen species ( ROS ) early during infection of human dermal microvascular endothelial ( HMVEC-d ) cells that are critical for virus entry . One of the downs... | KSHV infection of endothelial cells in vivo causes Kaposi's sarcoma and understanding the steps involved in de novo KSHV infection of these cells and the consequences is important to develop therapies to counter KSHV pathogenesis . Infection of endothelial cells in vitro is preceded by the induction of a network of hos... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viruses",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"medical",
"microbiology",
"viral",
"pathogens",
"microbial",
"pathogens",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"kaposi's",
"sarcoma-associated"... | 2014 | Kaposi's Sarcoma-Associated Herpesvirus Induces Nrf2 during De Novo Infection of Endothelial Cells to Create a Microenvironment Conducive to Infection |
Major histocompatibility class I ( MHC-I ) -specific inhibitory receptors on natural killer ( NK ) cells ( iNKRs ) tolerize mature NK cell responses toward normal cells . NK cells generate cytolytic responses to virus-infected or malignant target cells with altered or decreased MHC-I surface expression due to the loss ... | A critical mechanism by which the immune system controls viruses is through destruction of infected cells . One way to avoid cytotoxic T-lymphocytes ( CTL ) is by down modulating ligands that present virus peptides , the major histocompatibility complex class I molecules ( MHC-I ) . However , MHC-I negatively regulates... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"cloning",
"retroviruses",
"viruses",
"immunodeficiency",
"viruses",
"rna",
"viru... | 2016 | A Conserved HIV-1-Derived Peptide Presented by HLA-E Renders Infected T-cells Highly Susceptible to Attack by NKG2A/CD94-Bearing Natural Killer Cells |
Protein folding dynamics is often described as diffusion on a free energy surface considered as a function of one or few reaction coordinates . However , a growing number of experiments and models show that , when projected onto a reaction coordinate , protein dynamics is sub-diffusive . This raises the question as to ... | To understand dynamics of complex systems with many degrees of freedom , one often projects it onto one or several collective variables . Protein folding , the complex , concerted motion of a protein chain towards a unique three-dimensional structure , is one example of where such reduction of complexity is useful . It... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biophysics/protein",
"folding",
"biophysics/experimental",
"biophysical",
"methods",
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/molecular",
"dynamics",
"physics/interdisciplinary",
"physics"
] | 2010 | Is Protein Folding Sub-Diffusive? |
An enhanced understanding of the hookworm genome and its resident mobile genetic elements should facilitate understanding of the genome evolution , genome organization , possibly host-parasite co-evolution and horizontal gene transfer , and from a practical perspective , development of transposon-based transgenesis for... | Because of its importance to public health , the hookworm parasite has become the focus of increased research over the past decade—research that will ultimately decipher its genetic code . We now report a gene from hookworm chromosomes known as a transposon . Transposons are genes that can move around in the genome and... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"molecular",
"biology/molecular",
"evolution"
] | 2007 | The bandit, a New DNA Transposon from a Hookworm—Possible Horizontal Genetic Transfer between Host and Parasite |
CD4 T cell-dependent antibody responses are essential for limiting Plasmodium parasite replication and the severity of malaria; however , the factors that regulate humoral immunity during highly inflammatory , Th1-biased systemic infections are poorly understood . Using genetic and biochemical approaches , we show that... | Humoral immunity is essential for host resistance to pathogens that trigger highly inflammatory immune responses , including Plasmodium parasites , the causative agents of malaria . Long-lived , secreted antibody responses depend on a specialized subset of CD4 T cells called T follicular helper ( Tfh ) cells . However ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"t",
"helper",
"cells",
"humoral",
"immunity",
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"immune",
"cells",
"immune",
"physiology",
"plasmodium",
"immunology",
"tropical",
"diseases",
"cloning",
"parasitic",
"diseases",
"parasiti... | 2016 | Type I Interferons Induce T Regulatory 1 Responses and Restrict Humoral Immunity during Experimental Malaria |
Competence for transformation is widespread among bacterial species . In the case of Gram-negative systems , a key step to transformation is the import of DNA across the outer membrane . Although multiple factors are known to affect DNA transport , little is known about the dynamics of DNA import . Here , we characteri... | Bacterial transformation is the import and inheritable integration of external DNA . As such , it is believed to be a major evolutionary force . A key step is the import of DNA through the outer membrane . Here , we have characterized the spatio-temporal dynamics of DNA during import and residence in the periplasm of t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"bacterial",
"physiology",
"gram",
"negative",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"bacterial",
"pathogens"
] | 2014 | Concerted Spatio-Temporal Dynamics of Imported DNA and ComE DNA Uptake Protein during Gonococcal Transformation |
Transcription from the HIV-1 LTR promoter efficiently initiates but rapidly terminates because of a non-processive form of RNA polymerase II . This premature termination is overcome by assembly of an HIV-1 TAT/P-TEFb complex at the transactivation response region ( TAR ) , a structured RNA element encoded by the first ... | The human immunodeficiency virus 1 ( HIV-1 ) promoter exhibits a strong block to transcription elongation that is a critical regulator of the viral life cycle . Failure to overcome this restriction during provirus establishment results in a transcriptionally silent , latent provirus . Similarly , reactivation from this... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | ZASC1 Stimulates HIV-1 Transcription Elongation by Recruiting P-TEFb and TAT to the LTR Promoter |
Considering cells as biofactories , we aimed to optimize its internal processes by using the same engineering principles that large industries are implementing nowadays: lean manufacturing . We have applied reverse engineering computational methods to transcriptomic , metabolomic and phenomic data obtained from a colle... | Considering cells as biofactories , we aimed to optimize their internal processes by using existing design principles acquired from engineering . Herein , we present a synthetic biology approach based on experimental and computational methodology that integrates genomic , transcriptomic , metabolomic and phenomic data ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"synthetic",
"biology",
"biology",
"computational",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign |
Unraveling the evolutionary forces responsible for variations of neutral substitution patterns among taxa or along genomes is a major issue for detecting selection within sequences . Mammalian genomes show large-scale regional variations of GC-content ( the isochores ) , but the substitution processes at the origin of ... | Mammalian genomes show a very strong heterogeneity of base composition along chromosomes ( the so-called isochores ) . The functional significance of these peculiar genomic landscapes is highly debated: do isochores confer some selective advantage , or are they simply the by-product of neutral evolutionary processes ? ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary",
"biology/human",
"evolution",
"computational",
"biology/comparative",
"sequence",
"analysis",
"evolutionary",
"biology/genomics",
"computational",
"biology/evolutionary",
"modeling",
"genetics",
"and",
"genomi... | 2008 | The Impact of Recombination on Nucleotide Substitutions in the Human Genome |
Generation of reactive oxygen species and reactive nitrogen species in phagocytes is an important innate immune response mechanism to eliminate microbial pathogens . It is known that deoxynucleotides ( dNTPs ) , the precursor nucleotides to DNA synthesis , are one group of the significant targets for these oxidants and... | The cellular nucleotide pool is a significant target for oxidation by reactive oxygen species and reactive nitrogen species . Misincorporation of these oxidized non-canonical nucleotides into DNA is known to cause mutations , and may be related to carcinogenesis , aging and neurodegeneration . Cells have evolved a grou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Mycobacterial MazG Safeguards Genetic Stability via Housecleaning of 5-OH-dCTP |
Rhythmic activation and repression of the frequency ( frq ) gene are essential for normal function of the Neurospora circadian clock . WHITE COLLAR ( WC ) complex , the positive element of the Neurospora circadian system , is responsible for stimulation of frq transcription . We report that a C2H2 finger domain-contain... | Circadian clocks organize inner physiology to anticipate changes in the external environment . These clocks are controlled by the oscillation of central clock proteins which form the central oscillator . Transcriptional regulation is a critical step in the regulation of the oscillation of these core proteins . In eukar... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"luciferase",
"assay",
"chemical",
"compounds",
"carbohydrates",
"organic",
"compounds",
"glucose",
"dna",
"transcription",
"circadian",
"oscillators",
"biochemical",
"analysis",
"fungi",
"enzyme",
"assays",
"chronobiology",
"epigenetics",
"bioassays",
"and",
"physiological... | 2017 | Transcriptional repression of frequency by the IEC-1-INO80 complex is required for normal Neurospora circadian clock function |
Predicting the clinical outcome of cancer patients based on the expression of marker genes in their tumors has received increasing interest in the past decade . Accurate predictors of outcome and response to therapy could be used to personalize and thereby improve therapy . However , state of the art methods used so fa... | Why do some people with the same type of cancer die early and some live long ? Apart from influences from the environment and personal lifestyle , we believe that differences in the individual tumor genome account for different survival times . Recently , powerful methods have become available to systematically read ge... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"genome",
"expression",
"analysis",
"pathology",
"immunology",
"cancer",
"risk",
"factors",
"cancers",
"and",
"neoplasms",
"biomarkers",
"gastrointestinal",
"tumors",
"algorithms",
"oncology",
"general",
"pathology",
"genetics",
"and",
"genomics",
"immunologic... | 2012 | Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes |
Dissemination of antibiotic resistance genes occurs mostly by conjugation , which mediates DNA transfer between cells in direct contact . Conjugative plasmids of the IncA/C incompatibility group have become a substantial threat due to their broad host-range , the extended spectrum of antimicrobial resistance they confe... | Multidrug resistance is a major health concern that complicates treatments of even the most common infections caused by bacteria . In recent years , IncA/C plasmids have emerged and spread in bacteria infecting humans , food-producing animals and food products , driving at the same time the dissemination of a broad spe... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"sequencing",
"techniques",
"gram",
"negative",
"bacteria",
"horizontal",
"gene",
"transfer",
"transcription",
"activators",
"evolutionary",
"biology",
"gene",
"regulation",
"plasmids",
"nucleic",
"acid",
"sequencing",
"dna-binding",
"proteins",
"microbiolog... | 2014 | The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination |
Snakebite is a major neglected tropical health issue that affects over 5 million people worldwide resulting in around 1 . 8 million envenomations and 100 , 000 deaths each year . Snakebite envenomation also causes innumerable morbidities , specifically loss of limbs as a result of excessive tissue/muscle damage . Snake... | Snakebite is a major neglected tropical disease that affects thousands of people in the rural areas of developing countries . As well as the deaths , snakebites result in a significant number of disabilities including permanent loss of limbs that alter the lifestyle of the victims . Snake venom is a mixture of differen... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"toxins",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"metalloproteases",
"tropical",
"diseases",
"enzymology",
"toxic",
"agents",
"toxicology",
"collagens",
"muscle",
"regeneration",
"developmental",
"biology",
"muscl... | 2019 | Mechanisms underpinning the permanent muscle damage induced by snake venom metalloprotease |
Animals with rudimentary innate abilities require substantial learning to transform those abilities into useful skills , where a skill can be considered as a set of sensory–motor associations . Using linear neural network models , it is proved that if skills are stored as distributed representations , then within-lifet... | Some behaviours are purely innate ( e . g . , blinking ) , whereas other , “apparently innate , ” behaviours require a degree of learning to refine them into a useful skill ( e . g . , nest building ) . In terms of biological fitness , it matters how quickly such learning occurs , because time spent learning is time sp... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"none",
"computational",
"biology"
] | 2007 | Distributed Representations Accelerate Evolution of Adaptive Behaviours |
Chronic obstructive pulmonary disease ( COPD ) is a major global health problem . The etiology of COPD has been associated with apoptosis , oxidative stress , and inflammation . However , understanding of the molecular interactions that modulate COPD pathogenesis remains only partly resolved . We conducted an explorato... | Chronic obstructive pulmonary disease or COPD is among the most lethal of respiratory diseases . While this disease has been well characterized , more studies are needed to learn the interaction of macromolecules involved in the progression towards illness . We explored possible interactions involved in the disease pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microarrays",
"systems",
"biology",
"medicine",
"chronic",
"obstructive",
"pulmonary",
"diseases",
"genomics",
"functional",
"genomics",
"regulatory",
"networks",
"respiratory",
"medicine",
"biology",
"computational",
"biology",
"pulmonology"
] | 2012 | Suppressed Expression of T-Box Transcription Factors Is Involved in Senescence in Chronic Obstructive Pulmonary Disease |
Much of the computational power of the mammalian brain arises from its extensive top-down projections . To enable neuron-specific information processing these projections have to be precisely targeted . How such a specific connectivity emerges and what functions it supports is still poorly understood . We addressed the... | In mammalian sensory processing , extensive top-down feedback from higher brain areas reshapes the feedforward , bottom-up information processing . The structure of the top-down connectivity , the mechanisms leading to its specificity , and the functions it supports are still poorly understood . Using computational mod... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"neurogenesis",
"neural",
"networks",
"nervous",
"system",
"brain",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
"cognitive",
"psychology",
"cognition",
"network",
"analysis",
... | 2019 | Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction |
The unfolded protein response ( UPR ) is a conserved cellular response to the accumulation of proteinaceous material in endoplasmic reticulum ( ER ) , active both in health and disease to alleviate cellular stress and improve protein folding . Multiple epiphyseal dysplasia ( EDM5 ) is a genetic skeletal condition and a... | A significant proportion of genetic skeletal diseases result from misfolding of structural proteins within the endoplasmic reticulum ( ER ) of cartilage cells ( chondrocytes ) . Interestingly , these diseases often share transcriptomic changes with non-skeletal conditions such as Alzheimer’s disease and diabetes and in... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"growth",
"plate",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"chondrocytes",
"protein",
"aggregation",
"cell",
"processes",
"animal",
"models",
"model",
"organisms",
"bone",
"connective",
"tissue",
"cells",
"experimental",
"organism",
"systems",
"bioas... | 2019 | XBP1 signalling is essential for alleviating mutant protein aggregation in ER-stress related skeletal disease |
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