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Pseudomonas aeruginosa is a common environmental bacterium that is also a significant opportunistic pathogen , particularly of the human lung . We must understand how P . aeruginosa responds to the lung environment in order to identify the regulatory changes that bacteria use to establish and maintain infections . The ...	Many opportunistic pathogens transition from an environmental niche into the host . To establish an infection , these bacteria must rapidly adapt their transcriptional profile to the conditions at the site of infection . We used the response of Pseudomonas aeruginosa to lung surfactant as a model to discover genes impo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "microbial", "metabolism", "lipids", "gram", "negative", "sphingolipids", "gene", "expression", "genetics", "gene", "regulation", "molecular", "genetics", "host-pathogen", "interaction", "biology", "microbiology", "bacterial", "pathogens", "dna", "transcript...	2014	Detection of Host-Derived Sphingosine by Pseudomonas aeruginosa Is Important for Survival in the Murine Lung
Entamoeba histolytica is an obligate protozoan parasite of humans , and amebiasis , an infectious disease which targets the intestine and/or liver , is the second most common cause of human death due to a protozoan after malaria . Although amebiasis is usually asymptomatic , E . histolytica has potent pathogenic potent...	Reactive oxygen species are the most studied of environmental stresses generated by the host immune defense against pathogens . Although most of the studies that have investigated the effect of oxidative stress on an organism have focused on changes which occur at the protein level , only a few studies have investigate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Proteomic Identification of Oxidized Proteins in Entamoeba histolytica by Resin-Assisted Capture: Insights into the Role of Arginase in Resistance to Oxidative Stress
Parasitological cure for Chagas disease is considered extremely difficult to achieve because of the lack of effective chemotherapeutic agents against Trypanosoma cruzi at different stages of infection . There are currently only two drugs available . These have several limitations and can produce serious side effects . ...	Chagas disease is a neglected tropical parasitic infection . An estimated 10 million people are infected worldwide , and more than 25 million people are at risk of acquiring the disease . The therapeutic agents used to treat the disease may not be effective in all cases and also produce considerable side effects . Ther...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "molecular", "cell", "biology", "protozoology", "biology", "microbiology", "pathogenesis", "parasitology" ]	2014	A Cytoplasmic New Catalytic Subunit of Calcineurin in Trypanosoma cruzi and Its Molecular and Functional Characterization
Electrical synapses between neurons , also known as gap junctions , are direct cell membrane channels between adjacent neurons . Gap junctions play a role in the synchronization of neuronal network activity; however , their involvement in cognition has not been well characterized . Three-hour olfactory associative memo...	One of the most important questions in the neuroscience is how the brain process memory . Memory formation requires neuronal communication in the brain via synaptic transmissions , which include chemical and electrical synapses . Unlike the chemical synapses , the biological functions of electrical synapses in memory f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "plant", "anatomy", "medicine", "and", "health", "sciences", "nervous", "system", "membrane", "potential", "junctional", "complexes", "electrophysiology", "neuroscience", "learning", "and", "memory", "animals", "gap", "junctions", ...	2019	Electrical synapses between mushroom body neurons are critical for consolidated memory retrieval in Drosophila
One of the three most frequently documented copy number variations associated with autism spectrum disorder ( ASD ) is a 1q21 . 1 duplication that encompasses sequences encoding DUF1220 protein domains , the dosage of which we previously implicated in increased human brain size . Further , individuals with ASD frequent...	Autism Spectrum Disorder ( ASD ) is a common behaviorally defined condition noted by impairments in social reciprocity and communicative abilities and exaggerated repetitive behaviors and stereotyped interests . Individuals with ASD frequently have a larger and more rapidly growing brain than their typically developing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "behavioral", "neuroscience", "functional", "genomics", "developmental", "and", "pediatric", "neurology", "biology", "genomics", "neuroscience", "pediatrics" ]	2014	DUF1220 Dosage Is Linearly Associated with Increasing Severity of the Three Primary Symptoms of Autism
Bistable epigenetic switches are fundamental for cell fate determination in unicellular and multicellular organisms . Regulatory proteins associated with bistable switches are often present in low numbers and subject to molecular noise . It is becoming clear that noise in gene expression can influence cell fate . Altho...	Errors in information transfer from DNA to RNA to protein are inevitable and ubiquitous . When errors that occur in DNA are not repaired and become fixed as permanent mutations , they can have heritable phenotypic consequences for cells . In contrast , errors that occur during RNA transcription are considered transient...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "microbiology", "molecular", "biology", "genetics", "and", "genomics" ]	2009	Transcriptional Infidelity Promotes Heritable Phenotypic Change in a Bistable Gene Network
Immunologically intact BALB/c mice infected with Leishmania mexicana develop non-healing progressively growing lesions associated with a biased Th2 response while similarly infected IL-4Rα-deficient mice fail to develop lesions and develop a robust Th1 response . In order to determine the functional target ( s ) for IL...	Leishmania species are parasites , transmitted by sandflies which are of extensive public health importance in the tropical and subtropical regions of the world . A large number of distinct Leishmania species cause cutaneous disease and the vast majority of studies utilize the caustive agent of Old World cutaneous leis...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunity", "to", "infections" ]	2011	BALB/c Mice Deficient in CD4+ T Cell IL-4Rα Expression Control Leishmania mexicana Load although Female but Not Male Mice Develop a Healer Phenotype
A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes , e . g . by duplication or horizontal transfer . In contrast , many viruses generate protein-coding genes de novo , via the overprinting of a new reading frame onto an existing ( “ancestral” ) frame . This ...	How does novelty originate in nature ? It is commonly thought that new genes are generated mainly by modifications of existing genes ( the “tinkering” model ) . In contrast , we have shown recently that in viruses , numerous genes are generated entirely de novo ( “from scratch” ) . The role of these genes remains under...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "virulence", "factors", "and", "mechanisms", "virology", "molecular", "genetics", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "microbiology", "computational", "biology", "viral", "evolution" ]	2013	Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses
Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain ( CasSD ) of p130Cas ( or BCAR1 ) has eluded an experimentally validated structural understanding . Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility , sen...	Mechanical stretching of cells causes the substrate domain of p130Cas ( CasSD ) to be phosphorylated on 15 tyrosine residues embedded along its length . CasSD is rich in proline and surprisingly well conserved in placental mammals . Stretching of CasSD by atomic force microscopy has identified that it requires far less...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "biology", "and", "life", "sciences", "computational", "biology", "molecular", "cell", "biology", "biophysics" ]	2014	Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain — Implication in Mechanosensing
Copper toxicity and copper limitation can both be effective host defense mechanisms against pathogens . Tolerance of high copper by fungi makes toxicity as a defense mechanism largely ineffective against fungal pathogens . A forward genetic screen for Histoplasma capsulatum mutant yeasts unable to replicate within macr...	Control of primary pathogens that infect phagocytes often requires adaptive immunity , but the mechanisms that convert host cells from permissive to antimicrobial states are only partially understood . The intracellular fungal pathogen Histoplasma capsulatum resides and proliferates within the macrophage phagosome . Du...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "yeast", "infections", "immune", "cells", "pathology", "and", "laboratory", "medicine", "vesicles", "markov", "models", "pathogens", "immunology", "microbiology", "organisms", "fungi", "mathematics", "phagosomes...	2018	Macrophage activation by IFN-γ triggers restriction of phagosomal copper from intracellular pathogens
Gene expression dynamics have provided foundational insight into almost all biological processes . Here , we analyze expression of environmentally responsive genes and transcription factor genes to infer signals and pathways that drive pathogen gene regulation during invasive Candida albicans infection of a mammalian h...	We have a limited understanding of how the expression of pathogens’ genes changes during infection of humans or other animal hosts , in contrast to in vitro models of infection . Here we profile the alteration in gene expression over time as a predictor of functional consequences during invasive growth of Candida in th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Activation and Alliance of Regulatory Pathways in C. albicans during Mammalian Infection
Shuni virus ( SHUV ) is an orthobunyavirus that belongs to the Simbu serogroup . SHUV was isolated from diverse species of domesticated animals and wildlife , and is associated with neurological disease , abortions , and congenital malformations . Recently , SHUV caused outbreaks among ruminants in Israel , representin...	Arthropod-borne ( arbo ) viruses are notorious for causing unpredictable and large-scale epidemics and epizootics . Apart from viruses such as West Nile virus and Rift Valley fever virus that are well known to have a significant impact on human and animal health , many arboviruses remain neglected . Shuni virus ( SHUV ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "culicoides", "microbiology", "saliva", "animals", "viruses", "rna", "viruses", "insect", "vector...	2019	Vector competence of biting midges and mosquitoes for Shuni virus
The regulation of intracellular levels of reactive oxygen species ( ROS ) is critical for developmental differentiation and virulence of many pathogenic fungi . In this report we demonstrate that a novel transmembrane protein , TmpL , is necessary for regulation of intracellular ROS levels and tolerance to external ROS...	The critical roles of reactive oxygen species ( ROS ) in fungal development and virulence have been well established over the past half a century since the first experimental detection of hydrogen peroxide in fungal cells by Bach ( 1950 ) . In the cell , ROS act as signaling molecules regulating physiological responses...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "plant", "biology/plant-biotic", "interactions", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "respiratory", "medicine/respiratory", "infections", "cell", "biology/cellular", "death", ...	2009	TmpL, a Transmembrane Protein Required for Intracellular Redox Homeostasis and Virulence in a Plant and an Animal Fungal Pathogen
Ivermectin is the only drug currently recommended for the treatment of onchocerciasis , the second leading infectious cause of blindness in the world . This drug kills only the first stage larvae—microfilariae ( mf ) of Onchocerca volvulus and is to be used cautiously in areas where Loa loa is prevalent because of seve...	Onchocerciasis is a chronic disease of humans that affects mainly the skin and eyes . It is an insect-borne disease , caused by a nematode worm , Onchocerca volvulus . It is a public health problem and an obstacle to socio-economic development in affected communities . There is currently no vaccine , and no adult worm ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "onchocerca", "volvulus", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "helminths", "methylenes", "hexanes", "tropical", "diseases", "parasitic", "diseases", "animals", "onchocerca", "toxi...	2018	Filaricidal properties of Lantana camara and Tamarindus indica extracts, and Lantadene A from L. camara against Onchocerca ochengi and Loa loa
Hearing and vestibular function depend on mechanosensory staircase collections of hair cell stereocilia , which are produced from microvillus-like precursors as their parallel actin bundle scaffolds increase in diameter and elongate or shorten . Hair cell stereocilia contain multiple classes of actin-bundling protein ,...	Stereocilia are the fingerlike projections of inner ear hair cells that detect sound and motion . Stereocilia grow to specific lengths and diameters and form staircase-like arrays . The changes in size appear to be driven by matching alterations in the dimensions of an underlying molecular scaffold consisting of a bund...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cellular", "structures", "neurobiology", "of", "disease", "and", "regeneration", "animal", "genetics", "neuroscience", "cell", "differentiation", "animal", "models", "developmental", "biology", "otology", "model", "organisms", "hearing", "disorders", "cytoske...	2011	Roles of the Espin Actin-Bundling Proteins in the Morphogenesis and Stabilization of Hair Cell Stereocilia Revealed in CBA/CaJ Congenic Jerker Mice
Vertebrate dentitions originated in the posterior pharynx of jawless fishes more than half a billion years ago . As gnathostomes ( jawed vertebrates ) evolved , teeth developed on oral jaws and helped to establish the dominance of this lineage on land and in the sea . The advent of oral jaws was facilitated , in part ,...	During evolution , teeth originated deep in the pharynx of ancient and extinct jawless fishes . Later , with the evolution of bony fish , teeth appeared in the mouth , as in most current vertebrates , although some living fishes retain teeth in the posterior pharynx . We integrate comparative morphology , paleontology ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "developmental", "biology" ]	2009	An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws
Mutations in the retinoblastoma tumor suppressor gene ( rb1 ) cause both sporadic and familial forms of childhood retinoblastoma . Despite its clinical relevance , the roles of rb1 during normal retinotectal development and function are not well understood . We have identified mutations in the zebrafish space cadet loc...	Before an organism can execute necessary behavioral responses to environmental stimuli , the underlying neural circuits that regulate these behaviors must be precisely wired during embryonic development . A properly wired neural circuit is the product of a sophisticated collaboration of multiple genetic pathways that o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	The Tumor Suppressor Gene Retinoblastoma-1 Is Required for Retinotectal Development and Visual Function in Zebrafish
Differential equation models that describe the dynamic changes of biochemical signaling states are important tools to understand cellular behavior . An essential task in building such representations is to infer the affinities , rate constants , and other parameters of a model from actual measurement data . However , i...	Differential equation models of signaling processes are useful to gain a molecular and quantitative understanding of cellular information flow . Although these models are typically based on simple kinetic rules , they can often qualitatively describe the behavior of biological systems . However , in the quest to transf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "computational", "biology/synthetic", "biology", "cell", "biology/cell", "signaling", "mathematics", "computer", "science/systems", "and", "control", "theory", "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "diabetes", "and", "en...	2009	Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model
The steady states of cells affect their response to perturbation . Indeed , diagnostic markers for predicting the response to therapeutic perturbation are often based on steady state measurements . In spite of this , no method exists to systematically characterize the relationship between steady state and response . Ma...	Diagnostic markers are derived from steady state measurements , but are used to predict the cellular response to therapy . To develop new and better diagnostics , we would like to systematically characterize the relationship between steady state and the response to a given therapeutic . Mathematical models have powerfu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "biochemical", "simulations", "mathematics", "theoretical", "biology", "biochemistry", "simulations", "algebra", "linear", "algebra", "biology", "computational", "biology", "algebraic", "equations" ]	2013	Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models
Unrepaired or inaccurately repaired DNA damage can lead to a range of cell fates , such as apoptosis , cellular senescence or cancer , depending on the efficiency and accuracy of DNA damage repair and on the downstream DNA damage signalling . DNA damage repair and signalling have been studied and modelled in detail sep...	All cells are subject to damage and DNA is the most important molecule to protect . Cells communicate DNA damage through p53—‘the guardian of the genome’—and the dynamics of p53 signalling is one the main mechanisms that determine the outcome for the cell . On detection of DNA damage , p53 is activated and cell cycle a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling
Influenza virus has the ability to evade host immune surveillance through rapid viral genetic drift and reassortment; therefore , it remains a continuous public health threat . The development of vaccines producing broadly reactive antibodies , as well as therapeutic strategies using human neutralizing monoclonal antib...	Influenza virus is classified into types A , B and C . Influenza A virus is further divided into many subtypes , all of which exist in animals , indicating pandemic potential . By contrast , influenza B virus circulates almost exclusively in humans and , as there is no evidence for reassortment with influenza A virus ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "viruses", "virology", "viral", "classification", "biology", "microbiology" ]	2013	Human Monoclonal Antibodies Broadly Neutralizing against Influenza B Virus
DNA demethylation mediated by the DNA glycosylase ROS1 helps determine genomic DNA methylation patterns and protects active genes from being silenced . However , little is known about the mechanism of regulation of ROS1 enzymatic activity . Using a forward genetic screen , we identified an anti-silencing ( ASI ) factor...	DNA cytosine methylation is a major epigenetic mark that confers transcriptional regulation . Active removal of DNA methylation is important for plants and mammals during development and in responses to various stress conditions . In the model plant species Arabidopsis thaliana , active DNA demethylation depends on a f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	MET18 Connects the Cytosolic Iron-Sulfur Cluster Assembly Pathway to Active DNA Demethylation in Arabidopsis
The mouse organ of Corti , housed inside the cochlea , contains hair cells and supporting cells that transduce sound into electrical signals . These cells develop in two main steps: progenitor specification followed by differentiation . Fibroblast Growth Factor ( FGF ) signaling is important in this developmental pathw...	The mammalian cochlea contains the organ of Corti , a specialized sensory epithelium populated by hair cells and supporting cells that detect sound . Hair cells are susceptible to injury by noise , toxins , and other insults . In mammals , hair cells cannot be regenerated after injury , resulting in permanent hearing l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ears", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cell", "differentiation", "endocrine", "physiology", "developmental", "biology", "organ", "of", "corti", "inner", "ear", "growth", "factors", "fibrobla...	2019	Sox2 and FGF20 interact to regulate organ of Corti hair cell and supporting cell development in a spatially-graded manner
Campylobacter jejuni is a leading cause of food-borne illness . Although a natural reservoir of the pathogen is domestic poultry , the degree of genomic diversity exhibited by the species limits the application of epidemiological methods to trace specific infection sources . Bacteriophage predation is a common burden p...	Campylobacter jejuni is the major cause of bacterial food-borne illness worldwide . Predation of C . jejuni by virulent bacteriophage offers the prospect of controlling bacterial populations at source in poultry . We report that in chickens , bacteriophage resistance is infrequent because the mutants that escape bacter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "infectious", "diseases", "chicken", "in", "vitro", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	Genome Dynamics of Campylobacter jejuni in Response to Bacteriophage Predation
The functional interpretation of high throughput metabolomics by mass spectrometry is hindered by the identification of metabolites , a tedious and challenging task . We present a set of computational algorithms which , by leveraging the collective power of metabolic pathways and networks , predict functional activity ...	Mass spectrometry based untargeted metabolomics can now profile several thousand of metabolites simultaneously . However , these metabolites have to be identified before any biological meaning can be drawn from the data . Metabolite identification is a challenging and low throughput process , therefore becomes the bott...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "metabolic", "networks", "biology", "computational", "biology" ]	2013	Predicting Network Activity from High Throughput Metabolomics
Tubular protrusions are a common feature of living cells , arising from polymerization of stiff protein filaments against a comparably soft membrane . Although this process involves many accessory proteins in cells , in vitro experiments indicate that similar tube-like structures can emerge without them , through spont...	The necessary biophysical conditions for the formation of tubular membrane protrusions by polymerizing actin filament bundles have not yet been fully understood . For this reason we introduce a novel grand canonical simulation model that describes stochastic polymerization of filaments against a fluctuating fluid membr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "classical", "mechanics", "simulation", "and", "modeling", "damage", "mechanics", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "bending", "polymer", "chemistry", "contractile", "proteins", "actins", "lipids", "proteins", "defo...	2016	The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation
Among human RNA viruses , hepatitis C virus ( HCV ) is unusual in that it causes persistent infection in the majority of infected people . To establish persistence , HCV evades host innate and adaptive immune responses by multiple mechanisms . Recent studies identified virus genome-derived small RNAs ( vsRNAs ) in HCV-...	The mechanism by which hepatitis C virus ( HCV ) establishes persistent human infection is complex and incompletely understood . Recent studies identified virus-derived small RNAs ( vsRNAs ) in HCV-infected cells; however , their biological significance is unclear . One HCV vsRNA arising from the E2 coding region reduc...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "transfection", "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "immunology", "microbiology", "fibrosis", "viruses", "...	2017	Hepatitis C virus infection inhibits a Src-kinase regulatory phosphatase and reduces T cell activation in vivo
Nodal and Activin are morphogens of the TGFbeta superfamily of signaling molecules that direct differential cell fate decisions in a dose- and distance-dependent manner . During early embryonic development the Nodal/Activin pathway is responsible for the specification of mesoderm , endoderm , node , and mesendoderm . I...	Nodal and Activin are extracellular signaling molecules that diffuse from the source of secretion and induce recipient stem cells to become new cell types according to a concentration gradient . In the early embryo , they are important for the specification of tissues at the correct place and time , but paradoxically t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "signaling", "networks", "signaling", "in", "selected", "disciplines", "sequence", "assembly", "tools", "cell", "differentiation", "dna", "transcription", "genome", "sequencing", "developmental", "biology", "genome", "analysis", "tools"...	2011	Graded Nodal/Activin Signaling Titrates Conversion of Quantitative Phospho-Smad2 Levels into Qualitative Embryonic Stem Cell Fate Decisions
Soil-transmitted helminths ( STHs ) are a major health concern in tropical and sub-tropical countries . Oesophagostomum infection is considered endemic to West Africa but has also been identified in Uganda , East Africa , among primates ( including humans ) . However , the taxonomy and ecology of Oesophagostomum in Uga...	Nodule worms infect the gastrointestinal tracts of a number of mammalian species , including humans and other primates . This study sought to identify the species of nodule worms causing infections within and around an East African national park in Uganda where monkeys and apes co-occur and overlap with people . Some p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "social", "and", "behavioral", "sciences", "medicine", "veterinary", "science", "biology" ]	2014	Nodule Worm Infection in Humans and Wild Primates in Uganda: Cryptic Species in a Newly Identified Region of Human Transmission
Organismal development and many cell biological processes are organized in a modular fashion , where regulatory molecules form groups with many interactions within a group and few interactions between groups . Thus , the activity of elements within a module depends little on elements outside of it . Modularity facilita...	Throughout life's history , organisms have produced evolutionary innovations , features that are useful when facing new ecological and environmental challenges . A property that aids in the production of such innovations is modularity . Modular systems consist of groups of molecules with many interactions within a grou...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "developmental", "biology/developmental", "evolution", "evolutionary", "biology/developmental", "evolution" ]	2010	Specialization Can Drive the Evolution of Modularity
Human networks of sexual contacts are dynamic by nature , with partnerships forming and breaking continuously over time . Sexual behaviours are also highly heterogeneous , so that the number of partners reported by individuals over a given period of time is typically distributed as a power-law . Both the dynamism and h...	The formation and dissolution of sexual relationships in human populations constitute an ever-changing network of links between individuals through which sexually transmitted diseases spread . To study this phenomenon , we developed a dynamic simulation algorithm that can reproduce the same distribution of sexual conta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "immunology", "microbiology", "vaccines", "preventive", "medicine", "antibiotic", "resistance", "probability", "distribution", "mathematics", "sexually", "transmitted", "diseases", "network", "analysis", "pharmacology", "infectious", ...	2019	A dynamic power-law sexual network model of gonorrhoea outbreaks
Dengue , an arboviral disease , is a public health problem in tropical and subtropical regions worldwide . In Brazil , epidemics have become increasingly important , with increases in the number of hospitalizations and the costs associated with the disease . This study aimed to describe the direct costs of hospitalized...	The costs of dengue outbreaks and hospitalizations have recently increased . Endemic in many tropical and subtropical parts of the world , dengue outbreaks occur each year and require appropriate economic studies to determine the potential financial and public health impacts of dengue management policies . Economic lit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "socioeconomic", "aspects", "of", "health", "medicine", "and", "health", "sciences", "health", "economics", "dengue", "fever", "neglected", "tropical", "diseases", "tropical", "diseases", "viral", "d...	2014	Direct Costs of Dengue Hospitalization in Brazil: Public and Private Health Care Systems and Use of WHO Guidelines
Dilated cardiomyopathy ( DCM ) is a structural heart disease with strong genetic background . Monogenic forms of DCM are observed in families with mutations located mostly in genes encoding structural and sarcomeric proteins . However , strong evidence suggests that genetic factors also affect the susceptibility to idi...	Dilated cardiomyopathy is a severe disease of the heart muscle and often leads to chronic heart failure , eventually with the consequence of cardiac transplantation . Identification of genetic disease markers in at-risk persons could play an important role in preventive health care . Several mutations in familial forms...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cardiovascular", "disorders/myopathies", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "disease", "cardiovascular", "disorders/heart", "failure" ]	2010	Genetic Association Study Identifies HSPB7 as a Risk Gene for Idiopathic Dilated Cardiomyopathy
The rate of meiotic recombination varies markedly between species and among individuals . Classical genetic experiments demonstrated a heritable component to population variation in recombination rate , and specific sequence variants that contribute to recombination rate differences between individuals have recently be...	Homologous recombination is an indispensable feature of the mammalian meiotic program and an important mechanism for creating genetic diversity . Despite its central significance , recombination rates vary markedly between species and among individuals . Although recent studies have begun to unravel the genetic basis o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "linkage", "(genetics)", "trait", "locus", "phenotypes", "heredity", "genetics", "biology", "evolutionary", "biology", "quantitative", "traits", "cytogenetics", "evolutionary", "genetics", "genetics", "and", "genomics", "complex", "traits", "genotypes" ]	2011	Genetic Analysis of Genome-Scale Recombination Rate Evolution in House Mice
Buruli ulcer is a stigmatising disease treated with antibiotics and wound care , and sometimes surgical intervention is necessary . Permanent limitations in daily activities are a common long term consequence . It is unknown to what extent patients perceive problems in participation in social activities . The psychomet...	Buruli ulcer is a stigmatising condition caused by infection with Mycobacterium ulcerans . Besides the long term medical consequences , Buruli ulcer may lead to participation restrictions in social life . The Participation Scale intends to assess perceived participation restrictions; however , this instrument has been ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "sociology", "social", "sciences", "physiotherapy", "health", "care" ]	2014	Psychometric Properties of the Participation Scale among Former Buruli Ulcer Patients in Ghana and Benin
A vaccine to prevent infection and disease caused by Plasmodium vivax is needed both to reduce the morbidity caused by this parasite and as a key component in efforts to eradicate malaria worldwide . Vivax malaria protein 1 ( VMP001 ) , a novel chimeric protein that incorporates the amino- and carboxy- terminal regions...	Plasmodium vivax malaria has several unique features . Two of the main features are the inability to culture this parasite in vitro and its propensity to form dormant stages within the liver , which can only be treated with a single class of drugs that are contraindicated for a proportion of the population . Therefore ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "physiology", "enzyme-linked", "immunoassays", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "animals", "parasitology", "vaccines", "preventive", "medici...	2016	Phase 1/2a Trial of Plasmodium vivax Malaria Vaccine Candidate VMP001/AS01B in Malaria-Naive Adults: Safety, Immunogenicity, and Efficacy
Zika virus ( ZIKV ) and dengue virus ( DENV ) are genetically and antigenically related flaviviruses that now co-circulate in much of the tropical and subtropical world . The rapid emergence of ZIKV in the Americas in 2015 and 2016 , and its recent associations with Guillain-Barré syndrome , birth defects , and fetal l...	Pre-existing immunity to one of the four DENV serotypes is known to increase the risk of severe disease upon secondary infection with a different serotype . Due to the antigenic similarities between ZIKV and DENV , it has been proposed that these viruses could interact in a similar fashion . Data from in vitro experime...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "methods" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "enzyme-linked", "immunoassays", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "...	2019	Primary infection with dengue or Zika virus does not affect the severity of heterologous secondary infection in macaques
Leishmania ( L . ) species are the causative agent of leishmaniasis . Due to the lack of efficient vaccine candidates , drug therapies are the only option to deal with cutaneous leishmaniasis . Unfortunately , chemotherapeutic interventions show high toxicity in addition to an increased risk of dissemination of drug-re...	As many as 12 million people suffer from Leishmania ( L . ) infection worldwide with about one to two million newly infected people every year . Due to the lack of vaccine strategies , the only option is chemotherapeutic intervention which can cause serious side effects . Therefore , new prevention or treatment strateg...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "leishmania", "immunology", "biology", "microbiology", "protozoology", "host-pathogen", "interaction", "immune", "response" ]	2012	Leishmania major Infection in Humanized Mice Induces Systemic Infection and Provokes a Nonprotective Human Immune Response
Human immunodeficiency virus ( HIV ) infection is often accompanied by infection with other pathogens , in particular herpes simplex virus type 2 ( HSV-2 ) . The resulting coinfection is involved in a vicious circle of mutual facilitations . Therefore , an important task is to develop a compound that is highly potent a...	To contain the HIV-1 epidemic , it is necessary to develop antivirals that prevent HIV-1 transmission . It is well known that HIV infection might be accompanied by other pathogens , which often are engaged with HIV-1 in a vicious circle of mutual facilitation . One of the most common of these pathogens is herpes simple...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "drug", "research", "and", "development", "herpes", "simplex", "drugs", "and", "devices", "hiv", "viral", "diseases", "drug", "discovery" ]	2013	A Multi-targeted Drug Candidate with Dual Anti-HIV and Anti-HSV Activity
Due to the recent advances in high-throughput sequencing technologies , it becomes possible to directly analyze microbial communities in human body and environment . To understand how microbial communities adapt , develop , and interact with the human body and the surrounding environment , one of the fundamental challe...	Microbial communities exhibit rich dynamics including the way they adapt , develop , and interact with the human body and the surrounding environment . The associations among microbes can provide a solid foundation to model the interplay between the ( host ) human body and the microbial populations . However , due to t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "microbiome", "applied", "mathematics", "microbiology", "cloning", "random", "variables", "covariance", "simulation", "and", "modeling", "algorithms", "non-coding", "rna", "mathematics", "statistics", "(mathematics)", "network", "analysis", "shot...	2017	MPLasso: Inferring microbial association networks using prior microbial knowledge
Dengue is a mosquito-borne disease caused by one of four serotypes of Dengue virus ( DENV-1–4 ) . Severe dengue infection in humans is characterized by thrombocytopenia , increased vascular permeability , hemorrhage and shock . However , there is little information about host response to DENV infection . Here , mechani...	Dengue fever and its severe forms , dengue hemorrhagic fever and dengue shock syndrome , are the most prevalent mosquito-borne diseases on Earth . It is caused by one of four serotypes of Dengue virus ( DENV-1–4 ) . At present , there are no vaccines or specific therapies for dengue and treatment is supportive . Host r...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "models", "model", "organisms", "emerging", "infectious", "diseases", "immunity", "virology", "microbial", "pathogens", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "immune", "response" ]	2011	IFN-γ Production Depends on IL-12 and IL-18 Combined Action and Mediates Host Resistance to Dengue Virus Infection in a Nitric Oxide-Dependent Manner
Most common methods for inferring transposable element ( TE ) evolutionary relationships are based on dividing TEs into subfamilies using shared diagnostic nucleotides . Although originally justified based on the “master gene” model of TE evolution , computational and experimental work indicates that many of the subfam...	The most common entities in vertebrate genomes are transposable elements ( TEs ) , DNA sequences that have been repeatedly copied and inserted into new locations throughout the genome . Some TEs have been replicated hundreds of thousands of times , and their ecology and evolutionary history within a genome is thus crit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "genome", "evolution", "genome", "analysis", "evolutionary", "processes", "evolutionary", "modeling", "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "molecular", "genetics", "computational", "biology", "evolutionary", "biology", "...	2014	Inference of Transposable Element Ancestry
In understanding the etiology of breast cancer , the contributions of both genetic and environmental risk factors are further complicated by the impact of breast developmental stage . Specifically , the time period ranging from childhood to young adulthood represents a critical developmental window in a woman’s life wh...	A woman’s lifetime risk of developing breast cancer is affected by both genetic and environmental risk factors that can be further exacerbated by breast developmental stage . Time periods conferring increased risk are referred to as Windows of Susceptibility ( WOS ) and , generally speaking , the molecular mechanisms r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "genome", "engineering", "medicine", "and", "health", "sciences", "breast", "tumors", "reproductive", "system", "engineering", "and", "technology", "synthetic", "biology", "carcinomas", "cancers", "and", "neoplasms", "cloning", "synthetic", "bioengineerin...	2016	The Non-coding Mammary Carcinoma Susceptibility Locus, Mcs5c, Regulates Pappa Expression via Age-Specific Chromatin Folding and Allele-Dependent DNA Methylation
Pathogenic and commensal Neisseria species produce an Adhesin Complex Protein , which was first characterised in Neisseria meningitidis ( Nm ) as a novel surface-exposed adhesin with vaccine potential . In the current study , the crystal structure of a recombinant ( r ) Nm-ACP Type I protein was determined to 1 . 4 Å r...	The genus Neisseria contains two major human pathogens: N . meningitidis ( Nm ) causes meningitis and sepsis , and N . gonorrhoeae ( Ng ) causes the sexually transmitted disease gonorrhoea . In addition , the genus contains a larger number of commensal organisms , including N . lactamica ( Nl ) . Common to all of these...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "condensed", "matter", "physics", "microbiology", "neisseria", "gonorrhoeae", "physiological", "processes", "sequence", "motif", "analysis", "crysta...	2017	Structure of the Neisseria Adhesin Complex Protein (ACP) and its role as a novel lysozyme inhibitor
Land plants rely mainly on gravitropism and phototropism to control their posture and spatial orientation . In natural conditions , these two major tropisms act concurrently to create a photogravitropic equilibrium in the responsive organ . Recently , a parsimonious model was developed that accurately predicted the com...	Although plants are mostly seen as static , they are constantly moving to adapt to changes in their stature and to their environment . Gravity and light , among others , are major factors that sculpt the shapes of plants . Plants tend to grow in the direction of the light to get access to their energy resource . At the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception
Recently , a number of Global Health Initiatives ( GHI ) have been created to address single disease issues in low-income countries , such as poliomyelitis , trachoma , neonatal tetanus , etc . . Empirical evidence on the effects of such GHIs on local health systems remains scarce . This paper explores positive and neg...	Prevention of neglected tropical diseases was recently significantly scaled up in sub-Saharan Africa , protecting entire populations with mass distribution of drugs: five different diseases are now addressed simultaneously with a package of four drugs . Some argue however that , similarly to other major control program...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/preventive", "medicine", "public", "health", "and", "epidemiology/global", "health" ]	2010	Interactions between Global Health Initiatives and Country Health Systems: The Case of a Neglected Tropical Diseases Control Program in Mali
Trypanosoma brucei , the agents of African trypanosomiasis , undergo density-dependent differentiation in the mammalian bloodstream to prepare for transmission by tsetse flies . This involves the generation of cell-cycle arrested , quiescent , stumpy forms from proliferative slender forms . The signalling pathway respo...	African trypanosome parasites respond to density sensing information in the bloodstream of their mammalian hosts to generate their transmission stage , the stumpy form . Components of this ‘quorum sensing’ signalling cascade are known but their interactions and ordering are not . Here we have dissected the dependency r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "rna", "interference", "parasitic", "cell", "cycles", "cell", "cycle", "and", "cell", "division", "cell", "processes", "parasitic", "diseases", "parasitic", "protozoans", "cell", "differentiation", "parasitolog...	2018	Non-linear hierarchy of the quorum sensing signalling pathway in bloodstream form African trypanosomes
Accurate and reliable forecasts of seasonal epidemics of infectious disease can assist in the design of countermeasures and increase public awareness and preparedness . This article describes two main contributions we made recently toward this goal: a novel approach to probabilistic modeling of surveillance time series...	Seasonal influenza is associated with 250 000 to 500 000 deaths worldwide each year ( WHO estimates ) . In the United States and other temperate regions , seasonal influenza epidemics occur annually , but their timing and intensity varies significantly; accurate and reliable forecasts that quantify their uncertainty ca...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "density", "influenza", "applied", "mathematics", "simulation", "and", "modeling", "algorithms", "seasons", "probability", "distribution", "mathematics", "forecasting", "statistics", "(mathematics)", "materials", "science", "material...	2018	Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions
Zinc finger nucleases ( ZFNs ) have been used successfully to create genome-specific double-strand breaks and thereby stimulate gene targeting by several thousand fold . ZFNs are chimeric proteins composed of a specific DNA-binding domain linked to a non-specific DNA-cleavage domain . By changing key residues in the re...	Zinc finger nucleases ( ZFNs ) are a powerful tool to create site-specific genomic modifications in a wide variety of cell types and organisms and are about to enter human gene therapy clinical trials . An important aspect of using ZFNs for use in gene therapy is to minimize off-target effects . We made ZFNs that conta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "genetics", "and", "genomics/gene", "therapy", "genetics", "and", "genomics", "genetics", "and", "genomics/gene", "expression" ]	2009	Attenuation of Zinc Finger Nuclease Toxicity by Small-Molecule Regulation of Protein Levels
Prevention of viral-induced respiratory disease begins with an understanding of the factors that increase or decrease susceptibility to viral infection . The primary receptor for most adenoviruses is the coxsackievirus and adenovirus receptor ( CAR ) , a cell-cell adhesion protein normally localized at the basolateral ...	Respiratory viral infection is one of the leading causes of morbidity and mortality worldwide . Interventions that are able to limit viral infection will enhance human health and productivity . However , the mechanisms that control our susceptibility to viral infection and the factors that allow viral pathogens to brea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Adenovirus Entry From the Apical Surface of Polarized Epithelia Is Facilitated by the Host Innate Immune Response
Hantaviruses infect humans via inhalation of virus-contaminated rodent excreta . Infection can cause severe disease with up to 40% mortality depending on the viral strain . The virus primarily targets the vascular endothelium without direct cytopathic effects . Instead , exaggerated immune responses may inadvertently c...	Inhalation of hantavirus-infected rodent droppings can cause a wide range of disease ranging from mild symptoms to deaths in humans . Central to hantavirus disease is vascular leakage that can manifest in different organs , including the lungs . Although the virus can infect endothelial cells lining the blood vessels ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "biopsy", "pathogens", "immunology", "microbiology", "surgical", "and", "invasive", "medical", "procedure...	2017	Human hantavirus infection elicits pronounced redistribution of mononuclear phagocytes in peripheral blood and airways
Anopheles darlingi , the main malaria vector in the Neotropics , has been considered to be highly anthropophilic . However , many behavioral aspects of this species remain unknown , such as the range of blood-meal sources . Barrier screens were used to collect resting Anopheles darlingi mosquitoes from 2013 to 2015 in ...	Anopheles darlingi is the major malaria vector in the Amazon . This species has been commonly described as highly anthropophilic throughout its geographic range , although little is known about its feeding preferences . Scant information is available regarding the origin of An . darlingi blood-meals . In the context of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "pathology", "and", "laboratory", "medicine", "plasmodium", "atmospheric", "science", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "parasitology...	2017	Intensive trapping of blood-fed Anopheles darlingi in Amazonian Peru reveals unexpectedly high proportions of avian blood-meals
HIV-1 infection is associated with a progressive loss of T cell functional capacity and reduced responsiveness to antigenic stimuli . The mechanisms underlying T cell dysfunction in HIV-1/AIDS are not completely understood . Multiple studies have shown that binding of program death ligand 1 ( PD-L1 ) on the surface of ...	Despite 30 years of intensive research , our understanding of how HIV-1 virus undermines the ability of the immune system to fight common infections is limited . Although we know that T cells , a key cell population that normally fights invading pathogens , lose their ability to function in HIV-1-infected individuals ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology" ]	2014	Immune Suppression by Neutrophils in HIV-1 Infection: Role of PD-L1/PD-1 Pathway
Upon apoptotic stimuli , epithelial cells compensate the gaps left by dead cells by activating proliferation . This has led to the proposal that dying cells signal to surrounding living cells to maintain homeostasis . Although the nature of these signals is not clear , reactive oxygen species ( ROS ) could act as a sig...	Regenerative biology pursues to unveil the genetic networks triggered by tissue damage . Regeneration can occur after damage by cell death or by injury . We used the imaginal disc of Drosophila in which we genetically activated apoptosis or physically removed some parts and monitored the capacity to repair the damage ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	ROS-Induced JNK and p38 Signaling Is Required for Unpaired Cytokine Activation during Drosophila Regeneration
Sensing of viral RNA by RIG-I-like receptors initiates innate antiviral response , which is mediated by the central adaptor VISA . How the RIG-I-VISA-mediated antiviral response is terminated at the late phase of infection is enigmatic . Here we identified the protein kinase A catalytic ( PKAC ) subunits α and β as neg...	VISA is a central adaptor protein required for innate immune response to RNA virus . Phosphorylation of VISA by protein kinase A leads to its polyubiquitination and degradation by the E3 ligase MARCH5 at the late phase of viral infection , which provides a critical control mechanism for the host to avoid excessive and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "rna", "interference", "viral", "transmission", "and", "infection", "molecular", "probe", "techniques", "immunology", "microbiology", "plasmid", "construction", "viruses", "rna", "viruses", "dna", "construction",...	2017	PKACs attenuate innate antiviral response by phosphorylating VISA and priming it for MARCH5-mediated degradation
Seroprevalence and incidence of toxoplasmosis in women of child bearing age has remained a contentious issue in the Indian subcontinent . Different laboratories have used different patient recruitment criteria , methods and variable results , making these data difficult to compare . To map the point-prevalence and inci...	Toxoplasmosis is a protozoan parasitic disease commonly transmitted and propagated by cats as family pets . Infection acquired during pregnancy can lead to congenital abnormalities in the fetus , still birth or intrauterine death . Seroprevalence and incidence of toxoplasmosis in Indian women of child bearing age has r...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "veterinary", "diseases", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "women's", "health", "veterinary", "microbiology", "obstetrics", "and", "gynecology", "epidemiology", "biology...	2014	Serologic Prevalence of Toxoplasma gondii in Indian Women of Child Bearing Age and Effects of Social and Environmental Factors
Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited . During the course of a clinical trial of whole genomic sequencing seeking druggable targets , we examined six patients with advanced cholangiocarcinoma . Integrated genome-wide and whole transcriptome seque...	Cholangiocarcinoma is a cancer that affects the bile ducts . Unfortunately , many patients diagnosed with cholangiocarcinoma have disease that cannot be treated with surgery or has spread to other parts of the body , thus severely limiting treatment options . New advances in drug treatment have enabled treatment of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "genome", "sequencing", "medicine", "cancer", "genetics", "genetics", "cancer", "treatment", "chemotherapy", "and", "drug", "treatment", "biology", "genomics", "cancers", "and", "neoplasms", "gastrointestinal", "tumors", "genomic", "medicine", "pharmacogenomic...	2014	Integrated Genomic Characterization Reveals Novel, Therapeutically Relevant Drug Targets in FGFR and EGFR Pathways in Sporadic Intrahepatic Cholangiocarcinoma
Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA , but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation . We introduce a novel approach based on supervised machine learning that detects effects o...	Synonymous codons are not equally common in genomes . The main causes of unequal codon usage are varying nucleotide substitution patterns , as manifested in the wide range of genomic nucleotide compositions . However , since the first E . coli and yeast genes were sequenced , it became evident that there was also a bia...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "biochemistry/molecular", "evolution", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "computer", "science/applications", "genetics", "and", "genomics/comparative", "genomics", "genetics", "an...	2010	Translational Selection Is Ubiquitous in Prokaryotes
In metazoan integrin signaling is an important process of mediating extracellular and intracellular communication processes . This can be achieved by cooperation of integrins with growth factor receptors ( GFRs ) . Schistosoma mansoni is a helminth parasite inducing schistosomiasis , an infectious disease of worldwide ...	Parasites of the genus Schistosoma cause schistosomiasis , a life-threatening infectious disease for humans and animals worldwide . Among the remarkable biological features of schistosomes is the differentiation of the female gonads which is controlled by pairing with the male and a prerequisite for egg production . Eg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "cell", "death", "medicine", "and", "health", "sciences", "reproductive", "system", "helminths", "cell", "processes", "vertebrates", "animals", "xenopus", "animal", "models", "germ", "cells", "oocytes", "model", ...	2017	Evidence for Integrin – Venus Kinase Receptor 1 Alliance in the Ovary of Schistosoma mansoni Females Controlling Cell Survival
Yersinia pestis , the agent of plague , is transmitted to mammals by infected fleas . Y . pestis exhibits a distinct life stage in the flea , where it grows in the form of a cohesive biofilm that promotes transmission . After transmission , the temperature shift to 37°C induces many known virulence factors of Y . pesti...	Bubonic plague cycles depend on the ability of Yersinia pestis to alternately infect two very different hosts—a mammal and a flea . Like any arthropod-borne pathogen , Y . pestis must sense host-specific environmental cues and regulate gene expression accordingly to produce a transmissible infection in the flea after b...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "microbiology/microbial", "evolution", "and", "genomics", "microbiology/innate", "immunity", "genetics", "and", "genomics", "evolutionary", "biology", "microbiology/microbial...	2010	Transit through the Flea Vector Induces a Pretransmission Innate Immunity Resistance Phenotype in Yersinia pestis
Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site . In particular , CpG context elevates the mutation rate by an order of magnitude . Mutations also vary widely in their effect on the molecular function , ph...	Mutations occur in some sites in the genome more frequently than in others . Similarly , mutations in some sites have greater consequences than in others . The effect of mutations might not be independent of the frequency with which mutations occur . Indeed , sites where mutations happen frequently will be preserved if...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/molecular", "genetics", "evolutionary", "biology/genomics", "comput...	2008	Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection
Infections with high-risk human papillomaviruses ( HPVs ) are causally involved in the development of anogenital cancer . HPVs apparently evade the innate immune response of their host cells by dysregulating immunomodulatory factors such as cytokines and chemokines , thereby creating a microenvironment that favors mali...	Persistently high-risk HPV-infected individuals have an increased risk to develop anogenital cancer . HPV encodes the viral proteins E6 and E7 that interact with and induce the degradation of the cell cycle regulators p53 and pRb , respectively , priming immortalized keratinocytes towards malignant transformation . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "virology", "immunology", "biology", "microbiology" ]	2013	Post-Translational Control of IL-1β via the Human Papillomavirus Type 16 E6 Oncoprotein: A Novel Mechanism of Innate Immune Escape Mediated by the E3-Ubiquitin Ligase E6-AP and p53
Mouse apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like editing complex 3 ( mA3 ) , an intracellular antiviral factor , has 2 allelic variations that are linked with different susceptibilities to beta- and gammaretrovirus infections among various mouse strains . In virus-resistant C57BL/6 ( B6 ) mice , mA...	Susceptibility to acutely leukemogenic Friend virus ( FV ) retrovirus infection varies among different mouse strains and is governed by several genetic factors , one of which is allelic variations at the mouse Apobec3 locus . FV-resistant C57BL/6 ( B6 ) mice express higher amounts of Apobec3 transcripts than susceptibl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "viral", "transmission", "and", "infection", "virology", "genetics", "biology", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Two Genetic Determinants Acquired Late in Mus Evolution Regulate the Inclusion of Exon 5, which Alters Mouse APOBEC3 Translation Efficiency
Schistosomiasis is a disease of world-wide importance and is caused by parasitic flatworms of the genus Schistosoma . These parasites exhibit a unique reproduction biology as the female's sexual maturation depends on a constant pairing-contact to the male . Pairing leads to gonad differentiation in the female , and eve...	Schistosomiasis is an important infectious disease caused by worm parasites of the genus Schistosoma and directly affects more than 240 million people in 78 tropical and sub-tropical countries but also animals . Pathogenesis is triggered by eggs that are produced by paired females and get trapped in liver and gut causi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Combinatory Microarray and SuperSAGE Analyses Identify Pairing-Dependently Transcribed Genes in Schistosoma mansoni Males, Including Follistatin
Host-to-host transmission of a pathogen ensures its successful propagation and maintenance within a host population . A striking feature of disease transmission is the heterogeneity in host infectiousness . It has been proposed that within a host population , 20% of the infected hosts , termed super-shedders , are resp...	Bacteria belonging to the genus Salmonella are capable of causing long-term chronic systemic infections in specific hosts where they are shed in the feces . These persistently infected individuals include typhoid carriers and they serve as a reservoir for disease transmission . Despite the importance of Salmonella as a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "cytokines", "immunity", "to", "infections", "immunology", "immune", "suppression", "microbiology", "lymphoid", "organs", "host-pathogen", "interaction", "emerging", "infectious", "diseases", "immune", "defense", "immunoregulation", "immunomodulation", "b...	2013	The Systemic Immune State of Super-shedder Mice Is Characterized by a Unique Neutrophil-dependent Blunting of TH1 Responses
Axonal degeneration is a key event in the pathogenesis of neurodegenerative conditions . We show here that mec-4d triggered axonal degeneration of Caenorhabditis elegans neurons and mammalian axons share mechanistical similarities , as both are rescued by inhibition of calcium increase , mitochondrial dysfunction , and...	Axonal degeneration and neuronal loss are currently considered crucial pathological factors in neurodegenerative diseases . Therefore , delaying or blocking these procesess is key for neuroprotection . In this work , we used an in vivo approach combining invertebrate ( C . elegans ) and vertebrate ( mice ) model system...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "models", "molecular", "neuroscience", "caenorhabditis", "elegans", "cellular", "neuroscience", "model", "organisms", "neurobiology", "of", "disease", "and", "regeneration", "neuronal", "morphology", "signaling", "pathways", "biology", "mouse", "neuroscience" ]	2012	Diapause Formation and Downregulation of Insulin-Like Signaling via DAF-16/FOXO Delays Axonal Degeneration and Neuronal Loss
Chromosomal instability , which involves the deletion and duplication of chromosomes or chromosome parts , is a common feature of cancers , and deficiency screens are commonly used to detect genes involved in various biological pathways . However , despite their importance , the effects of deficiencies , duplications ,...	Although deletion heterozygotes and chromosomal aneuploidies have been used in genetic studies for decades , the relationships between chromosome doses and transcript outputs have been difficult to unravel . In other words , the effects of copy changes on the regulation of entire chromosomes or large chromosomal domain...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/chromatin", "structure", "genetics", "and", "genomics/gene", "expression", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/epigenetics...	2009	Buffering of Segmental and Chromosomal Aneuploidies in Drosophila melanogaster
The clinical syndrome associated with secondary syphilis ( SS ) reflects the propensity of Treponema pallidum ( Tp ) to escape immune recognition while simultaneously inducing inflammation . To better understand the duality of immune evasion and immune recognition in human syphilis , herein we used a combination of flo...	Syphilis , a sexually transmitted disease caused by the spirochetal bacterium Treponema pallidum , affects close to 10 million people per year worldwide . Despite the robust nature of the humoral and cellular immune responses associated with the disease , weeks to months may elapse before the host gains control of the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "syphilis" ]	2012	Immune Evasion and Recognition of the Syphilis Spirochete in Blood and Skin of Secondary Syphilis Patients: Two Immunologically Distinct Compartments
Sumoylation , the covalent attachment of SUMO ( Small Ubiquitin-Like Modifier ) to proteins , differs from other Ubl ( Ubiquitin-like ) pathways . In sumoylation , E2 ligase Ubc9 can function without E3 enzymes , albeit with lower reaction efficiency . Here , we study the mechanism through which E3 ligase RanBP2 trigge...	Post-translational modifications constitute key regulatory mechanisms in the cell . One of these modifications is the tagging of the target protein with a smaller molecule . SUMO is such a ubiquitin-like tag protein , and sumoylation is the process of tagging proteins with SUMO . The malfunctioning of sumoylation is li...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "biophysics/macromolecular", "assemblies", "and", "machines" ]	2010	A Mechanistic View of the Role of E3 in Sumoylation
The functions of several SOS regulated genes in Escherichia coli are still unknown , including dinQ . In this work we characterize dinQ and two small RNAs , agrA and agrB , with antisense complementarity to dinQ . Northern analysis revealed five dinQ transcripts , but only one transcript ( +44 ) is actively translated ...	Exposure of the bacterium Escherichia coli to DNA damaging agents induces the SOS response , which up-regulates gene functions involved in numerous cellular processes such as DNA repair , cell division , and replication . Most of the SOS regulated genes in E . coli have been characterized , but still there are several ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "cellular", "stress", "responses", "rna", "interference", "gene", "regulation", "microbiology", "gene", "function", "escherichia", "coli", "cell", "growth", "dna", "recombination", "molecular", "genetics", "dna", "microbial", "growth"...	2013	Single Transmembrane Peptide DinQ Modulates Membrane-Dependent Activities
Maternal factors initiate the zygotic developmental program in animal embryos . In embryos of the chordate , Ciona intestinalis , three maternal factors—Gata . a , β-catenin , and Zic-r . a—are required to establish three domains of gene expression at the 16-cell stage; the animal hemisphere , vegetal hemisphere , and ...	During animal development , transcription factors and signaling molecules transcriptionally regulate one another and constitute a gene regulatory network . This network is evoked by maternally provided factors . Many maternal factors are localized and thereby activate a set of genes in a specific region . In embryos of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "gene", "regulation", "reporter", "genes", "developmental", "biology", "immunoprecipitation", "gene", "types", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "embryos", "research", "and", "analysis", "methods", "sequence...	2016	A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo
Despite the formidable mutational capacity and sequence diversity of HIV-1 , evidence suggests that viral evolution in response to specific selective pressures follows generally predictable mutational pathways . Population-based analyses of clinically derived HIV sequences may be used to identify immune escape mutation...	One of the greatest challenges facing HIV-1 vaccine design today is the formidable capacity of the virus for mutation and adaptation , a characteristic that has contributed to the extensive worldwide genetic variability of HIV-1 strains observed today . On an individual basis , evolutionary selective pressures imposed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "viruses", "immunology", "virology" ]	2007	Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1
Body size is a quantitative trait that is closely associated to fitness and under the control of both genetic and environmental factors . While developmental plasticity for this and other traits is heritable and under selection , little is known about the genetic basis for variation in plasticity that can provide the r...	Environmental conditions can influence development and lead to the production of phenotypes adjusted to the conditions adults will live in . This developmental plasticity , which can help organisms cope with environmental heterogeneity , is heritable and under selection . Its evolution will depend on available genetic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "invertebrates", "medicine", "and", "health", "sciences", "abdomen", "quantitative", "trait", "loci", "population", "genetics", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "physiological", "pa...	2018	Genetic basis of thermal plasticity variation in Drosophila melanogaster body size
Drosophila segmentation is a well-established paradigm for developmental pattern formation . However , the later stages of segment patterning , regulated by the “pair-rule” genes , are still not well understood at the system level . Building on established genetic interactions , I construct a logical model of the Droso...	Segmentation in insects involves the division of the body into several repetitive units . In Drosophila embryos , all segments are patterned rapidly and simultaneously during early development , in a process known as “long-germ” embryogenesis . In contrast , many insect embryos retain an ancestral or “short-germ” mode ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "genetic", "networks", "morphogenic", "segmentation", "molecular", "probe", "techniques", "gene", "regulation", "animals", "simulation", "and", "modeling", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", ...	2017	Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation
The genetic basis of the development and variation of adult form of vertebrates is not well understood . To address this problem , we performed a mutant screen to identify genes essential for the formation of adult skeletal structures of the zebrafish . Here , we describe the phenotypic and molecular characterization o...	A major goal of the study of developmental genetics is to understand the genes and developmental mechanisms underlying the formation of organismal complexity and diversity . Here , we focus on genes controlling postembryonic development and describe mutations in genes of the ectodysplasin ( Eda ) pathway in regulating ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "genetics", "and", "genomics/animal", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "dermatology/hair", "and", "nail", "diseases", "developmental", "biology/developmental", "evolution", "genetics", "and", "genomics/disease", "models", "...	2008	Zebrafish eda and edar Mutants Reveal Conserved and Ancestral Roles of Ectodysplasin Signaling in Vertebrates
The eukaryotic XPD helicase is an essential subunit of TFIIH involved in both transcription and nucleotide excision repair ( NER ) . Mutations in human XPD are associated with several inherited diseases such as xeroderma pigmentosum , Cockayne syndrome , and trichothiodystrophy . We performed a comparative analysis of ...	The multiprotein complex TFIIH is crucially involved in two fundamental cellular processes—the transcription of genes by RNA polymerase II and the repair of UV-induced DNA damage by a mechanism called nucleotide excision repair ( NER ) . The xeroderma pigmentosum complementation group D ( XPD ) helicase , which is muta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "dna", "repair", "dna", "dna-binding", "proteins", "dna", "transcription" ]	2014	In TFIIH, XPD Helicase Is Exclusively Devoted to DNA Repair
There are no oral drugs for human African trypanosomiasis ( HAT , sleeping sickness ) . A successful oral drug would have the potential to reduce or eliminate the need for patient hospitalization , thus reducing healthcare costs of HAT . The development of oral medications is a key objective of the Consortium for Paras...	Development of orally administered medicines for human African trypanosomiasis ( HAT ) would potentially reduce the need for patient hospitalization , thus lowering healthcare costs . In this study , we investigated the potential of a novel diamidine prodrug , DB868 ( CPD-007-10 ) , as an oral treatment for first stage...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "drug", "research", "and", "development", "drugs", "and", "devices", "african", "trypanosomiasis", "neglected", "tropical", "diseases", "parasitic", "diseases", "drug", "discovery" ]	2013	Safety, Pharmacokinetic, and Efficacy Studies of Oral DB868 in a First Stage Vervet Monkey Model of Human African Trypanosomiasis
Bunyaviruses are a large family of segmented RNA viruses which , like influenza virus , use a cap-snatching mechanism for transcription whereby short capped primers derived by endonucleolytic cleavage of host mRNAs are used by the viral RNA-dependent RNA polymerase ( L-protein ) to transcribe viral mRNAs . It was recen...	Bunyaviruses are a large family of RNA viruses that include serious human , animal and plant pathogens . The viral RNA-dependent RNA polymerase ( L-protein ) is responsible for replication and transcription of the viral RNA , but apart from its central polymerase domain , it is poorly characterized . Like influenza vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/biocatalysis", "virology/viral", "replication", "and", "gene", "regulation" ]	2010	Bunyaviridae RNA Polymerases (L-Protein) Have an N-Terminal, Influenza-Like Endonuclease Domain, Essential for Viral Cap-Dependent Transcription
Glioblastomas are deadly cancers that display a functional cellular hierarchy maintained by self-renewing glioblastoma stem cells ( GSCs ) . GSCs are regulated by molecular pathways distinct from the bulk tumor that may be useful therapeutic targets . We determined that A20 ( TNFAIP3 ) , a regulator of cell survival an...	Glioblastomas are the most common and aggressive primary brain tumors in adults , with a median survival of only 12–15 months . Glioblastomas display a cellular hierarchy with a subset of cells having stem cell–like properties , including the capacity to self-renew and propagate tumors . Specific ablation of cancer ste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/neuro-oncology" ]	2010	Targeting A20 Decreases Glioma Stem Cell Survival and Tumor Growth
Ryanodine receptor type 1 ( RyR1 ) produces spatially and temporally defined Ca2+ signals in several cell types . How signals received in the cytoplasmic domain are transmitted to the ion gate and how the channel gates are unknown . We used EGTA or neuroactive PCB 95 to stabilize the full closed or open states of RyR1 ...	Maintaining a precise intracellular calcium concentration is key for cell survival . In skeletal muscle , ryanodine receptor type 1 ( RyR1 ) is an intracellular calcium-release channel that is critical for contraction . Here , we used single-channel techniques to demonstrate the presence of functionally homogenous popu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "computational", "biology", "biophysics" ]	2009	Coordinated Movement of Cytoplasmic and Transmembrane Domains of RyR1 upon Gating
The cytoplasmic polyadenylation element binding protein CPEB1 ( CPEB ) regulates germ cell development , synaptic plasticity , and cellular senescence . A microarray analysis of mRNAs regulated by CPEB unexpectedly showed that several encoded proteins are involved in insulin signaling . An investigation of Cpeb1 knocko...	One major hallmark of diabetes is insulin resistance in peripheral tissues that is controlled at the posttranslational level . For example , insulin activates a kinase cascade that leads to the phosphorylation of Akt , a centrally important molecule that regulates glucose metabolism . In this study , we define a transl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "biology", "molecular", "cell", "biology", "molecular", "biology" ]	2012	Cytoplasmic Polyadenylation Element Binding Protein Deficiency Stimulates PTEN and Stat3 mRNA Translation and Induces Hepatic Insulin Resistance
Mitochondrial DNA is a valuable taxonomic marker due to its relatively fast rate of evolution . In Trypanosoma cruzi , the causative agent of Chagas disease , the mitochondrial genome has a unique structural organization consisting of 20–50 maxicircles ( ∼20 kb ) and thousands of minicircles ( 0 . 5–10 kb ) . T . cruzi...	Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , is an important public health problem in Latin America . While molecular techniques can differentiate the major T . cruzi genetic lineages , few have sufficient resolution to describe diversity among closely related strains . The online availability ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome", "evolution", "parasite", "evolution", "biology", "genomics", "microbiology", "genetics", "and", "genomics", "parasitology" ]	2012	Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed by Maxicircle MLST and Next Generation Sequencing
Epstein Barr virus ( EBV ) infection expands CD8+ T cells specific for lytic antigens to high frequencies during symptomatic primary infection , and maintains these at significant numbers during persistence . Despite this , the protective function of these lytic EBV antigen-specific cytotoxic CD8+ T cells remains uncle...	Epstein Barr virus persistently infects more than 90% of the human adult population . While fortunately carried as an asymptomatic chronic infection in most individuals , it causes B cell lymphomas and carcinomas in some patients . Symptomatic primary EBV infection , called infectious mononucleosis , predisposes for so...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "viruses", "and", "cancer", "immunology", "microbiology", "tumor", "immunology", "epstein-barr", "virus", "infectious", "mononucleosis", "infectious", "disease", "immunology", "vaccination", "...	2014	Adoptive Transfer of EBV Specific CD8+ T Cell Clones Can Transiently Control EBV Infection in Humanized Mice
During immature capsid assembly , HIV-1 genome packaging is initiated when Gag first associates with unspliced HIV-1 RNA by a poorly understood process . Previously , we defined a pathway of sequential intracellular HIV-1 capsid assembly intermediates; here we sought to identify the intermediate in which HIV-1 Gag firs...	During HIV-1 immature capsid assembly , packaging of the viral genome is initiated when the HIV-1 capsid protein , Gag , first associates with unspliced HIV-1 RNA . Although the complex in which this association initially occurs is critical for formation of infectious virus , the identity , composition , and the mechan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "biological", "cultures", "messenger", "rna", "microbiology", "immunology", "retroviruses", "viruses", "immunodefici...	2018	Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging
Finding where transcription factors ( TFs ) bind to the DNA is of key importance to decipher gene regulation at a transcriptional level . Classically , computational prediction of TF binding sites ( TFBSs ) is based on basic position weight matrices ( PWMs ) which quantitatively score binding motifs based on the observ...	Transcription factors are critical proteins for sequence-specific control of transcriptional regulation . Finding where these proteins bind to DNA is of key importance for global efforts to decipher the complex mechanisms of gene regulation . Greater understanding of the regulation of transcription promises to improve ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Next Generation of Transcription Factor Binding Site Prediction
Dengue fever is reemerging on the island of Martinique and is a serious threat for the human population . During dengue epidemics , adult Aedes aegypti control with pyrethroid space sprays is implemented in order to rapidly reduce transmission . Unfortunately , vector control programs are facing operational challenges ...	The mosquito Aedes aegypti is the major vector of the Dengue virus in human populations and is responsible of serious outbreaks worldwide . In most countries , vector control is implemented by the use of insecticides to reduce mosquito populations . During epidemics , insecticides of the pyrethroid family ( blocking th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "mosquitoes", "pest", "control", "dengue", "fever", "neglected", "tropical", "diseases", "biology", "arboviral", "infections", "vectors", "and", "hosts", "infectious", "disease", "control", "agriculture" ]	2011	Pyrethroid Resistance Reduces the Efficacy of Space Sprays for Dengue Control on the Island of Martinique (Caribbean)
Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance . Helicobacter pylori , a human gastric pathogen , has a large number of DNA methyltransferase genes , with different strains having unique repertoires . Previous genome comparisons suggested that these methylt...	Living organisms are affected by epigenetic variation in addition to DNA sequence variation . DNA methylation is one of the most studied epigenetic modifications in both prokaryotes and eukaryotes . In prokaryotes , most DNA methylation is by DNA methyltransferases with high sequence specificity . Helicobacter pylori ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genomics", "dna", "modification", "genome", "evolution", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "dna", "comparative", "genomics", "computational", "biology", "epigenetics" ]	2014	Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity
Most tissues in metazoans undergo continuous turnover due to cell death or epithelial shedding . Since cellular replication is associated with an inherent risk of mutagenesis , tissues are maintained by a small group of stem cells ( SCs ) that replicate slowly to maintain their own population and that give rise to diff...	In multicellular organisms , tissues such as skin , the gut , and blood undergo continuous cell turnover . These tissues are maintained by a small group of tightly regulated cells known as stem cells ( SCs ) that have two defining properties: they can renew themselves and give rise to more specialized cells that perfor...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "homo", "sapiens", "oncology", "developmental", "biology", "mammals" ]	2007	(A)Symmetric Stem Cell Replication and Cancer
MicroRNAs ( miRNAs ) are thought to exert their functions by modulating the expression of hundreds of target genes and each to a small degree , but it remains unclear how small changes in hundreds of target genes are translated into the specific function of a miRNA . Here , we conducted an integrated analysis of transc...	MicroRNAs ( miRNAs ) are small RNAs encoded by our genome . Each miRNA binds hundreds of target mRNAs and performs specific functions . It is thought that miRNAs exert their function by reducing the expression of all these target genes and each to a small degree . However , these target genes often have very diverse fu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "immunology", "messenger", "rna", "micrornas", "cellular", "structures", "and", "organelles", "white", "blood", "cells", "ani...	2017	Differential Sensitivity of Target Genes to Translational Repression by miR-17~92
Chromatin regulation underlies a variety of DNA metabolism processes , including transcription , recombination , repair , and replication . To perform a quantitative genetic analysis of chromatin accessibility , we obtained open chromatin profiles across 96 genetically different yeast strains by FAIRE ( formaldehyde-as...	Quantitative trait loci ( QTL ) mapping is a genetic approach that allows the identification of genetic factors underlying a phenotype of interest . Genomic technologies such as DNA microarray and next-generation sequencing provide data that can be used for the analysis of multiple molecular phenotypes . For example , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genome", "expression", "analysis", "genomics", "genetic", "polymorphism", "gene", "expression", "genetics", "epigenetics", "biology", "population", "genetics", "chromatin", "genetics", "and", "genomics" ]	2013	Genetic Landscape of Open Chromatin in Yeast
The G protein-coupled receptor ( GPCR ) Smoothened ( Smo ) is the requisite signal transducer of the evolutionarily conserved Hedgehog ( Hh ) pathway . Although aspects of Smo signaling are conserved from Drosophila to vertebrates , significant differences have evolved . These include changes in its active sub-cellular...	N-linked glycosylation is a post-translational modification occurring on membrane proteins such as G protein-coupled receptors ( GPCR ) . Smoothened ( Smo ) is a GPCR that functions as the signal transducer of the Hedgehog ( Hh ) pathway . We used a mutagenesis approach to assess the role of N-glycans in Smo signaling ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Functional Divergence in the Role of N-Linked Glycosylation in Smoothened Signaling
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design . However , this method is not completely reliable and therefore unsatisfactory . In this study , we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular ...	Lead discovery is one of the most important processes in rational drug design . To improve the rate of the detection of lead compounds , various technologies such as high-throughput screening and combinatorial chemistry have been introduced into the pharmaceutical industry . However , since these technologies alone may...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "pharmacology/drug", "development" ]	2009	High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
Lysozymes are ancient and important components of the innate immune system of animals that hydrolyze peptidoglycan , the major bacterial cell wall polymer . Bacteria engaging in commensal or pathogenic interactions with an animal host have evolved various strategies to evade this bactericidal enzyme , one recently prop...	Lysozyme is an ancient bactericidal enzyme that is part of the antibacterial defense system of vertebrate and invertebrate animals . Bacteria colonizing or infecting an animal host have developed various ways to overcome lysozyme action , a recently proposed mechanism being the production of lysozyme inhibitors . Howev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2008	A New Family of Lysozyme Inhibitors Contributing to Lysozyme Tolerance in Gram-Negative Bacteria
Tuberculosis is a global health problem and at least one-third of the world’s population is infected with Mycobacterium tuberculosis ( MTB ) . MTB is a successful pathogen that enhances its own intracellular survival by inhibiting inflammation and arresting phago-lysosomal fusion . We previously demonstrated that Toxop...	We previously demonstrated that Toxoplasma gondii ( T . gondii ) dense granule antigen ( GRA ) 7 interacts with TRAF6 via MyD88 , enabling innate immune responses in macrophages and effective protection against T . gondii infection in vivo . However , its exact role and how it regulates host innate immune responses hav...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "phosphorylation", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "toxoplasma", "gondii", "pathogens", "immunology", "parasitic", "protozoans", "protozoans", "toxopl...	2017	Toxoplasma gondii GRA7-Targeted ASC and PLD1 Promote Antibacterial Host Defense via PKCα
West Nile virus ( WNV ) and Rift Valley fever virus ( RVFV ) are two emerging arboviruses transmitted by Culex pipiens species that includes two biotypes: pipiens and molestus . In Lebanon , human cases caused by WNV and RVFV have never been reported . However , the introduction of these viruses in the country is likel...	West Nile virus ( WNV ) and Rift Valley fever virus ( RVFV ) are two emerging mosquito-borne arboviruses mainly transmitted by Culex mosquitoes . WNV considered one of the most important causative agent of viral encephalitis has a wide distribution in many tropical and temperate countries including the Middle East . RV...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "geographical", "locations", "microbiology", "viral", ...	2018	Experimental transmission of West Nile Virus and Rift Valley Fever Virus by Culex pipiens from Lebanon
Segregation of chromosomes during the first meiotic division relies on crossovers established during prophase . Although crossovers are strictly regulated so that at least one occurs per chromosome , individual variation in crossover levels is not uncommon . In an analysis of different inbred strains of male mice , we ...	During prophase of meiosis , homologous chromosomes exchange genetic material , in a process known as crossing-over . Crossovers are thought to be essential for proper separation of chromosomes during meiosis but , surprisingly , most mammalian species exhibit substantial individual variation in the number of crossover...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "meiosis", "chromosome", "biology", "biology" ]	2014	Variation in Genome-Wide Levels of Meiotic Recombination Is Established at the Onset of Prophase in Mammalian Males
The complement cascade is crucial for clearance and control of invading pathogens , and as such is a key target for pathogen mediated host modulation . C3 is the central molecule of the complement cascade , and plays a vital role in opsonization of bacteria and recruitment of neutrophils to the site of infection . Stre...	The complement pathway is critical in the innate immune response to bacterial pathogens . It consists of a self-perpetuating proteolytic cascade initiated via three distinct pathways that converge at the central complement protein , C3 . Pathogens must evade complement-mediated immunity to cause disease , and inactivat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "body", "fluids", "pathogens", "immunology", "microbiology", "animal", "models", "bacterial", "d...	2017	Multi-functional mechanisms of immune evasion by the streptococcal complement inhibitor C5a peptidase
The IRG system of IFNγ-inducible GTPases constitutes a powerful resistance mechanism in mice against Toxoplasma gondii and two Chlamydia strains but not against many other bacteria and protozoa . Why only T . gondii and Chlamydia ? We hypothesized that unusual features of the entry mechanisms and intracellular replicat...	For some time we have studied an intracellular resistance system essential for mice to survive infection with the intracellular protozoan , Toxoplasma gondii , that is based on a family of proteins , immunity-related GTPases or IRG proteins . Immediately after the parasite enters a cell , IRG proteins accumulate on the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "disease", "immunology", "medicine", "and", "health", "sciences", "clinical", "immunology", "medical", "microbiology", "microsporidia", "microbial", "pathogens", "biology", "and", "life", "sciences", "immunology", "microbiology", "fungal", "pathogens" ]	2014	Identification of the Microsporidian Encephalitozoon cuniculi as a New Target of the IFNγ-Inducible IRG Resistance System
Copy-number variations ( CNVs ) are widespread in the human genome , but comprehensive assignments of integer locus copy-numbers ( i . e . , copy-number genotypes ) that , for example , enable discrimination of homozygous from heterozygous CNVs , have remained challenging . Here we present CopySeq , a novel computation...	Human individual genome sequencing has recently become affordable , enabling highly detailed genetic sequence comparisons . While the identification and genotyping of single-nucleotide polymorphisms has already been successfully established for different sequencing platforms , the detection , quantification and genotyp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "computational", "biology/genomics" ]	2010	Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity
Identification of the selective forces contributing to the origin and maintenance of sex is a fundamental problem in biology . The Fisher–Muller model proposes that sex is advantageous because it allows beneficial mutations that arise in different lineages to recombine , thereby reducing clonal interference and speedin...	Why have sex ? One explanation is that sex is good because it allows beneficial mutations from different lineages to recombine . This reduces competition between mutations in a population and can increase the speed with which the population can adapt to environmental change . This explanation , known as the Fisher–Mull...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "evolutionary", "biology", "eubacteria" ]	2007	Recombination Speeds Adaptation by Reducing Competition between Beneficial Mutations in Populations of Escherichia coli

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