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article stringlengths 4.36k 149k | summary stringlengths 32 3.35k | section_headings listlengths 1 91 | keywords listlengths 0 141 | year stringclasses 13
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Computational procedures for predicting metabolic interventions leading to the overproduction of biochemicals in microbial strains are widely in use . However , these methods rely on surrogate biological objectives ( e . g . , maximize growth rate or minimize metabolic adjustments ) and do not make use of flux measurem... | Over the past few years , there has been an unprecedented increase in the use of microorganisms for the production of biofuels , industrial chemicals and pharmaceutical precursors . In this regard , biotechnologists are confronted with the challenge to efficiently convert biomass and other renewable resources into usef... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/systems",
"biology",
"biochemistry/bioinformatics",
"computational",
"biology/metabolic",
"networks",
"biotechnology/bioengineering"
] | 2010 | OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions |
Rotavirus ( RV ) is the major cause of severe gastroenteritis in young children . A virus-encoded enterotoxin , NSP4 is proposed to play a major role in causing RV diarrhoea but how RV can induce emesis , a hallmark of the illness , remains unresolved . In this study we have addressed the hypothesis that RV-induced sec... | Rotavirus ( RV ) can cause severe dehydration and is a leading cause of childhood deaths worldwide . While most deaths occur due to excessive loss of fluids and electrolytes through vomiting and diarrhoea , the pathophysiological mechanisms that underlie this life-threatening disease remain to be clarified . Our previo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"virology",
"biology",
"microbiology",
"viral",
"diseases"
] | 2011 | Rotavirus Stimulates Release of Serotonin (5-HT) from Human Enterochromaffin Cells and Activates Brain Structures Involved in Nausea and Vomiting |
PKR is well characterized for its function in antiviral immunity . Using Toxoplasma gondii , we examined if PKR promotes resistance to disease caused by a non-viral pathogen . PKR−/− mice infected with T . gondii exhibited higher parasite load and worsened histopathology in the eye and brain compared to wild-type contr... | PKR was identified more than 30 years ago as an inhibitor of viral replication . It is unknown if PKR promotes protection against disease caused by non-viral pathogens . We addressed this question using Toxoplasma gondii , a major parasitic pathogen . T . gondii can cause cerebral and/or eye disease primarily in immuno... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"parastic",
"protozoans",
"protein",
"kinase",
"signaling",
"cascade",
"signal",
"transduction",
"toxoplasma",
"gondii",
"protozoology",
"immunology",
"biology",
"microbiology",
"molecular",
"cell",
"biology",
"immune",
"response",
"signaling",
"cascades"
] | 2013 | The Protein Kinase Double-Stranded RNA-Dependent (PKR) Enhances Protection against Disease Cause by a Non-Viral Pathogen |
Histidine kinase QseE and response regulator QseF compose a two-component system in Enterobacteriaceae . In Escherichia coli K-12 QseF activates transcription of glmY and of rpoE from Sigma 54-dependent promoters by binding to upstream activating sequences . Small RNA GlmY and RpoE ( Sigma 24 ) are important regulators... | Bacteria use two-component systems , composed of a membrane-bound histidine kinase and a cytoplasmic response regulator , to sense environmental cues and adapt gene expression accordingly . The enterobacterial two-component system QseE/QseF controls functions related to the cell envelope . In pathogens , QseE/QseF were... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"cell",
"physiology",
"blood",
"serum",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"body",
"fluids",
"chemical",
"compounds",
"neuroscience",
"organic",
"compounds",
"plasmid",
"construction",
"hormones",
"membrane",
"proteins",
"regulat... | 2018 | Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli |
For a rapid induction and efficient resolution of the inflammatory response , gene expression in cells of the immune system is tightly regulated at the transcriptional and post-transcriptional level . The control of mRNA translation has emerged as an important determinant of protein levels , yet its role in macrophage ... | When macrophages encounter pathogens , they initiate inflammation by secreting pro-inflammatory factors such as the cytokine TNF . Because a prolonged or overshooting release of these factors is harmful for the organism , their production needs to be tightly controlled and shut off in due time . To ensure a rapid but t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"protein",
"translation",
"gene",
"expression",
"genetics",
"biology",
"and",
"life",
"sciences",
"immunology",
"molecular",
"cell",
"biology",
"immune",
"response"
] | 2014 | Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation |
Chagas disease is a trypanosomiasis whose agent is the protozoan parasite Trypanosoma cruzi , which is transmitted to humans by hematophagous bugs known as triatomines . Even though insecticide treatments allow effective control of these bugs in most Latin American countries where Chagas disease is endemic , the diseas... | Chagas disease is one of the most important endemic diseases of South and Central America . Its causative agent is the protozoan Trypanosoma cruzi , which is transmitted to humans by blood-feeding insects known as triatomine bugs . These vectors mainly belong to Rhodnius , Triatoma and Panstrongylus genera of Reduviida... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"microbiology"
] | 2012 | Cultivation-Independent Methods Reveal Differences among Bacterial Gut Microbiota in Triatomine Vectors of Chagas Disease |
Open source drug discovery offers potential for developing new and inexpensive drugs to combat diseases that disproportionally affect the poor . The concept borrows two principle aspects from open source computing ( i . e . , collaboration and open access ) and applies them to pharmaceutical innovation . By opening a p... | Open source drug discovery can be an influential model for discovering and developing new medicines and diagnostics for neglected diseases . It offers the opportunity to accelerate the discovery progress while keeping expenditures to a minimum by encouraging incremental contributions from volunteer scientists . Publish... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"medical",
"devices",
"drug",
"research",
"and",
"development",
"drugs",
"and",
"devices",
"global",
"health",
"pharmacology",
"drug",
"discovery"
] | 2012 | Open Source Drug Discovery in Practice: A Case Study |
Inverted repeats ( IRs ) can facilitate structural variation as crucibles of genomic rearrangement . Complex duplication—inverted triplication—duplication ( DUP-TRP/INV-DUP ) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome ( MIM#300260 ) and... | Genomic architecture , such as direct or inverted repeats , can facilitate structural variation ( SV ) of the human genome . SV can consist of deletion , duplication , or inversion of a genomic segment , or combinations thereof , the latter referred to as complex genomic rearrangements ( CGR ) . CGR are defined as requ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication |
A critical feature of Mycobacterium tuberculosis , the causative agent of human tuberculosis ( TB ) , is its ability to survive and multiply within macrophages , making these host cells an ideal niche for persisting microbes . Killing the intracellular tubercle bacilli is a key requirement for efficient tuberculosis tr... | Tuberculosis is still a major threat to global health . The disease in humans is caused by a bacterium , Mycobacterium tuberculosis , and treatment of an infected individual requires more than six months of chemotherapy . Because such a long course of treatment is required , compliance is low , which can result in the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"chemical",
"biology/small",
"molecule",
"chemistry",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"infectious",
"diseases/antimicrobials",
"and",
"drug",
"resistance"
] | 2009 | High Content Screening Identifies Decaprenyl-Phosphoribose 2′ Epimerase as a Target for Intracellular Antimycobacterial Inhibitors |
Exome sequencing coupled with homozygosity mapping was used to identify a transition mutation ( c . 794T>C; p . Leu265Ser ) in ELMOD3 at the DFNB88 locus that is associated with nonsyndromic deafness in a large Pakistani family , PKDF468 . The affected individuals of this family exhibited pre-lingual , severe-to-profou... | Autosomal recessive nonsyndromic hearing loss is a genetically heterogeneous disorder . Here , we report a severe-to-profound mixed hearing loss locus , DFNB88 on chromosome 2p12-p11 . 2 . Exome enrichment followed by massive parallel sequencing revealed a c . 794T>C transition mutation in ELMOD3 that segregated with D... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | An Alteration in ELMOD3, an Arl2 GTPase-Activating Protein, Is Associated with Hearing Impairment in Humans |
During embryogenesis , the neural stem cells ( NSC ) of the developing cerebral cortex are located in the ventricular zone ( VZ ) lining the cerebral ventricles . They exhibit apical and basal processes that contact the ventricular surface and the pial basement membrane , respectively . This unique architecture is impo... | The developing cerebral cortex contains bipolar neural stem cells that span the cortical layers between the inner ventricular surface and the outer pial surface of the embryonic brain . The nuclei of these cells remain near the ventricular cavity , a microenvironment or niche thought to provide vital signals . It is no... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/neuronal",
"and",
"glial",
"cell",
"biology",
"developmental",
"biology/stem",
"cells",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"neuroscience/neurodevelopment",
"developmental",
"biology/neurodevelopment",
"cell",
"biology/extra-cellular",
"m... | 2009 | β1 Integrin Maintains Integrity of the Embryonic Neocortical Stem Cell Niche |
The worldwide neglect of immunotherapeutic products for the treatment of snakebite has resulted in a critical paucity of effective , safe and affordable therapy in many Third World countries , particularly in Africa . Snakebite ranks high among the most neglected global health problems , with thousands of untreated vic... | Antivenom is the only specific treatment for systemic envenoming from snakebite , but remains unavailable to thousands of snakebite victims around the world . A cycle of inconsistent and low market demand , sub-optimal utilisation , rising costs and reduced output of antivenoms have resulted from long term under-invest... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"drugs",
"and",
"devices",
"toxicology",
"occupational",
"and",
"industrial",
"health",
"global",
"health",
"neglected",
"tropical",
"diseases",
"pharmacology",
"infectious",
"diseases",
"toxin",
"binding",
"public"... | 2012 | Consequences of Neglect: Analysis of the Sub-Saharan African Snake Antivenom Market and the Global Context |
Certain pathogens deliver effectors into plant cells to modify host protein targets and thereby suppress immunity . These target modifications can be detected by intracellular immune receptors , or Resistance ( R ) proteins , that trigger strong immune responses including localized host cell death . The accelerated cel... | Plants defend themselves against pathogens via immune receptors that trigger responses including the suicide of infected cells to limit pathogen growth . The accelerated cell death 11 ( acd11 ) knockout mutant of the model plant Arabidopsis thaliana kills itself in the absence of invading pathogens . By screening for s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology/plant",
"genetics",
"and",
"gene",
"expression",
"plant",
"biology/plant-biotic",
"interactions",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses",
"immunology/inna... | 2010 | Autoimmunity in Arabidopsis acd11 Is Mediated by Epigenetic Regulation of an Immune Receptor |
Hepatitis E Virus ( HEV ) is the leading cause of acute viral hepatitis globally . Symptomatic infection is associated with case fatality rates of ~20% in pregnant women and it is estimated to account for ~10 , 000 annual pregnancy-related deaths in southern Asia alone . Recently , large and well-documented outbreaks w... | Hepatitis E virus is a leading cause of acute viral hepatitis in developing countries . About 20% of those infected develop clinical symptoms; of those , about 2% of non-pregnant cases and 20% of pregnant cases die . There is a safe and effective HEV vaccine that is licensed in China for those aged 16–65 years who are ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"liver",
"diseases",
"health",
"care",
"viruses",
"preventive",
"medicine",
"vaccines",
"gastroenterology",
"and",
"hepato... | 2018 | Reactive and pre-emptive vaccination strategies to control hepatitis E infection in emergency and refugee settings: A modelling study |
More than 5% of alternatively spliced internal exons in the human genome are derived from Alu elements in a process termed exonization . Alus are comprised of two homologous arms separated by an internal polypyrimidine tract ( PPT ) . In most exonizations , splice sites are selected from within the same arm . We hypoth... | Human genes are composed of functional regions , termed exons , separated by non-functional regions , termed introns . Intronic sequences may gradually accumulate mutations and subsequently become recognized by the splicing machinery as exons , a process termed exonization . Alu elements are prone to undergo exonizatio... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/alternative",
"splicing",
"molecular",
"biology/rna",
"splicing",
"computational",
"biology/genomics",
"computational",
"biology/protein",
"homology",
"detection"
] | 2009 | The Pivotal Roles of TIA Proteins in 5′ Splice-Site Selection of Alu Exons and Across Evolution |
Members of the highly conserved class of BEACH domain containing proteins ( BDCPs ) have been established as broad facilitators of protein–protein interactions and membrane dynamics in the context of human diseases like albinism , bleeding diathesis , impaired cellular immunity , cancer predisposition , and neurologica... | BEACH ( beige and Chediak Higashi ) domain containing proteins ( BDCPs ) are a highly conserved protein family in eukaryotes . BDCPs are known to be important for membrane dynamics such as vesicle transport , membrane fission and fusion events , and autophagy . Here we describe a new , membrane-independent molecular fu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The BEACH Domain Protein SPIRRIG Is Essential for Arabidopsis Salt Stress Tolerance and Functions as a Regulator of Transcript Stabilization and Localization |
Disruption of the blood-brain barrier ( BBB ) is a hallmark event in the pathophysiology of bacterial meningitis . Several inflammatory mediators , such as tumor necrosis factor alpha ( TNF-α ) , nitric oxide and matrix metalloproteinases ( MMPs ) , contribute to this disruption . Here we show that infection of human b... | A crucial step in the pathogenesis of bacterial meningitis is the disturbance of cerebral microvascular endothelial function , resulting in blood-brain barrier ( BBB ) breakdown . Matrix metalloproteinases ( MMPs ) have been implicated in BBB damage in bacterial meningitis in several studies . MMPs are a family of zinc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"microbiology"
] | 2010 | Neisseria meningitidis Induces Brain Microvascular Endothelial Cell Detachment from the Matrix and Cleavage of Occludin: A Role for MMP-8 |
Our earlier genome-wide expression study revealed up-regulation of a tryptophan-catabolizing enzyme , indoleamine 2 , 3-dioxygenase ( IDO1 ) , in patients with scrub typhus . This gene has been previously reported to have anti-microbial activity in a variety of infectious diseases; therefore , we aimed to prove whether... | Scrub typhus is a potentially life-threatening infectious disease that is a major cause of acute undifferentiated fever in Asia-Pacific region . It is caused by Orientia tsutsugamushi ( OT ) , an obligatory intracellular gram-negative bacterium in family rickettsiaceae . Earlier studies have shown that IFN-γ is essenti... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"zoonoses",
"clinical",
"immunology",
"immunity",
"immunity",
"to",
"infections",
"immunology",
"biology",
"scrub",
"typhus"
] | 2012 | Activation of Indoleamine 2,3-Dioxygenase in Patients with Scrub Typhus and Its Role in Growth Restriction of Orientia tsutsugamushi |
Myosin VI , found in organisms from Caenorhabditis elegans to humans , is essential for auditory and vestibular function in mammals , since genetic mutations lead to hearing impairment and vestibular dysfunction in both humans and mice . Here , we show that a missense mutation in this molecular motor in an ENU-generate... | Human deafness is extremely heterogeneous , with mutations in over 50 genes known to be associated with this common form of sensory loss . Among them , mutations in five myosins are associated with human hereditary hearing impairment , demonstrating that this family of proteins is essential for the proper function of t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/gene",
"discovery",
"neuroscience/sensory",
"systems",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"computational",
"biology/evolutionary",
"modeling",
"genetics",
"and",
"genomics/d... | 2008 | A Myo6 Mutation Destroys Coordination between the Myosin Heads, Revealing New Functions of Myosin VI in the Stereocilia of Mammalian Inner Ear Hair Cells |
Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions . To reliably characterize such condition-specific regulatory binding we introduce MultiGPS , an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments . MultiGPS is based on a g... | Many proteins that regulate the activity of other genes do so by attaching to the genome at specific binding sites . The locations that a given regulatory protein will bind , and the strength or frequency of such binding at an individual location , can vary depending on the cell type . We can profile the locations that... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"gene",
"regulation",
"molecular",
"genetics",
"biology",
"computational",
"biology"
] | 2014 | An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding |
The concept of "protein-based inheritance" defines prions as epigenetic determinants that cause several heritable traits in eukaryotic microorganisms , such as Saccharomyces cerevisiae and Podospora anserina . Previously , we discovered a non-chromosomal factor , [NSI+] , which possesses the main features of yeast prio... | The data presented in the paper deepens and enriches the concept of protein-based inheritance . According to this concept , prion conformational switches change protein functional activity , and such changes are inherited . Here , for the first time , we demonstrate that heritable traits may appear not only due to a co... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chemical",
"compounds",
"prions",
"light",
"microscopy",
"carbohydrates",
"galactose",
"organic",
"compounds",
"plasmid",
"construction",
"fungi",
"model",
"organisms",
"microscopy",
"materials",
"science",
"experimental",
"organism",
"systems",
"dna",
"construction",
"m... | 2016 | Interaction of Prions Causes Heritable Traits in Saccharomyces cerevisiae |
Schistosomiasis , caused by parasitic flatworms of the genus Schistosoma , is a neglected tropical disease affecting hundreds of millions globally . Praziquantel ( PZQ ) , the only drug currently available for treatment and control , is largely ineffective against juvenile worms , and reports of PZQ resistance lend add... | Schistosomes , infect hundreds of millions of people worldwide , causing schistosomiasis , a disease with devastating effects on human health and economic development . Despite the prevalence of this disease , there is only a single drug , praziquantel , available for treatment and control . Praziquantel is effective ,... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Evidence for Novel Pharmacological Sensitivities of Transient Receptor Potential (TRP) Channels in Schistosoma mansoni |
Uncoupling protein 2 ( UCP2 ) is a mitochondrial transporter that has been shown to lower the production of reactive oxygen species ( ROS ) . Intracellular pathogens such as Leishmania upregulate UCP2 and thereby suppress ROS production in infected host tissues , allowing the multiplication of parasites within murine p... | The leishmaniases comprise a group of diseases caused by infection by several species of intracellular protozoan parasites of the genus Leishmania , which are transmitted by the bite of an infected sandfly . The leishmaniases represent a global public health problem , affecting an estimated 12 million people around the... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"immunology",
"microbiology",
"host-pathogen",
"interaction",
"parasitic",
"diseases",
"parasitology",
"animal",
"models",
"model",
"organisms",
"neglected",
"tropical",
"diseases",
"veterinary",
"science",
"infectious",
"diseases",
"zoonoses",
"microbial",
"pat... | 2013 | UCP2 Deficiency Helps to Restrict the Pathogenesis of Experimental Cutaneous and Visceral Leishmaniosis in Mice |
Dengue is a reportable disease in Brazil; however , pregnancy has been included in the application form of the Brazilian notification information system only after 2006 . To estimate the severity of maternal dengue infection , the available data that were compiled from January 2007 to December 2008 by the official surv... | Dengue represents a major worldwide public health problem . According to the WHO , up to 50 million dengue infections occur each year . The occurrence of dengue fever and dengue hemorrhagic fever has increased in Brazil , in part due to the simultaneous circulation of DENV-1 , DENV-2 and DENV-3 . Although a primary inf... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine"
] | 2013 | Is Pregnancy Associated with Severe Dengue? A Review of Data from the Rio de Janeiro Surveillance Information System |
Bcl-2 family proteins control a decisive apoptotic event: mitochondrial outer membrane permeabilization ( MOMP ) . To discover MOMP-regulating proteins , we expressed a library of intracellular single-chain variable fragments ( scFvs ) ( “intrabodies” ) and selected for those rescuing cells from apoptosis induced by Bi... | Proteins belonging to the Bcl-2 family regulate a common form of cell death known as apoptosis . Typically , these proteins function in apoptosis by controlling the formation of large pores in the mitochondrial outer membrane ( MOM ) . While many proteins that regulate apoptosis have been identified over the years , so... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"death",
"chemical",
"compounds",
"293t",
"cells",
"gene",
"regulation",
"ketones",
"cell",
"processes",
"biological",
"cultures",
"pyruvate",
"plasmid",
"construction",
"membrane",
"proteins",
"outer",
"membrane",
"proteins",
"mitochondria",
"molecular",
"biolo... | 2019 | Phenotypic selection with an intrabody library reveals an anti-apoptotic function of PKM2 requiring Mitofusin-1 |
To eliminate Lymphatic filariasis ( LF ) as a public health problem , the World Health Organization ( WHO ) recommends that any area with infection prevalence greater than or equal to 1% ( denoted by presence of microfilaremia or antigenemia ) should receive mass drug administration ( MDA ) of antifilarial drugs for at... | Lymphatic filariasis ( LF ) is among the leading causes of disability among tropical diseases and is caused by a mosquito-transmitted parasite but can be prevented using mass drug therapy and vector-control . In recent years , an international effort has been mounted to eliminate LF . In order to focus limited resource... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"global",
"health",
"neglected",
"tropical",
"diseases",
"spatial",
"epidemiology",
"parasitic",
"diseases",
"lymp... | 2012 | Secondary Mapping of Lymphatic Filariasis in Haiti-Definition of Transmission Foci in Low-Prevalence Settings |
Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies . Recently , genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include ... | Structural systems pharmacology is an emerging field of computational biology research that aims to merge network and molecular views of biology . Genome-scale models are in silico , network models of metabolism , and by integrating the detailed knowledge we can gain from molecular simulations with these models , we ca... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"protein",
"metabolism",
"enzymology",
"red",
"blood",
"cells",
"enzyme",
"metabolism",
"protein",
"structure",
"protein",
"structure",
"databases",
"pharmacology",
"drug",
"metabolism",
"enzyme",
"chemistry",
... | 2016 | A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism |
The characterization of mutational spectra is usually carried out in one of three ways–by direct observation through mutation accumulation ( MA ) experiments , through parent-offspring sequencing , or by indirect inference from sequence data . Direct observations of spontaneous mutations with MA experiments are limited... | The mutational spectrum is central to our understanding of molecular evolution . However , mutational spectra are difficult to study because spontaneous mutations are rare , difficult to observe , and a large number of events is required to detect subtle differences between mutational bias , selection and selection lik... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"fungal",
"genetics",
"invertebrate",
"genomics",
"mutation",
"fungi",
"plant",
"science",
"model",
"organisms",
"substitution",
"mutation",
"experimental",
"organism",
"systems",
"plant",
"genomics",
"saccharomyces",
"research",
"and",
"analysis",
"metho... | 2017 | Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum |
Innate immunity is regulated by cholinergic signalling through nicotinic acetylcholine receptors . We show here that signalling through the M3 muscarinic acetylcholine receptor ( M3R ) plays an important role in adaptive immunity to both Nippostrongylus brasiliensis and Salmonella enterica serovar Typhimurium , as M3R-... | Recent data indicate that acetylcholine ( ACh ) , a neurotransmitter which regulates a variety of physiological functions , also influences the immune system , and that lymphocytes have the capacity to synthesise and release ACh , controlling local innate immune responses and suppressing inflammation . Thus far however... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The M3 Muscarinic Receptor Is Required for Optimal Adaptive Immunity to Helminth and Bacterial Infection |
Transcriptional activation in response to hypoxia in plants is orchestrated by ethylene-responsive factor group VII ( ERF-VII ) transcription factors , which are stable during hypoxia but destabilized during normoxia through their targeting to the N-end rule pathway of selective proteolysis . Whereas the conditionally ... | Respiratory metabolism in land plants requires oxygen availability to be able to generate ATP , which is essential for biosynthetic processes . Cellular hypoxia can be triggered as a consequence of environmental events ( mainly floods ) , anatomical constraints ( low tissue permeability to gases ) , or elevated cellula... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"cellular",
"stress",
"responses",
"plant",
"growth",
"and",
"development",
"cell",
"processes",
"brassica",
"developmental",
"biology",
"plant",
"science",
"model",
"organisms",
"genetically",
"modified",
"plants",
"plants",
"arabidopsis",
"thaliana",
... | 2014 | A Trihelix DNA Binding Protein Counterbalances Hypoxia-Responsive Transcriptional Activation in Arabidopsis |
Hox genes that determine anteroposterior body axis formation in all bilaterians are often found to have partially overlapping expression pattern . Since posterior genes dominate over anterior Hox genes in the region of co-expression , the anterior Hox genes are thought to have no function in such regions . In this stud... | The spatially non-overlapping function of Hox genes is known to determine Antero-posterior body axis in all the bilaterians . The expression of Hox genes is found to be overlapping in several cases . According to the posterior prevalence rule , posterior Hox genes suppress the function of anterior Hox genes in the over... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"organism",
"development",
"biology",
"and",
"life",
"sciences",
"organogenesis",
"morphogenesis",
"pattern",
"formation"
] | 2014 | Role of abd-A and Abd-B in Development of Abdominal Epithelia Breaks Posterior Prevalence Rule |
An unrealized potential to understand the genetic basis of aging in humans , is to consider the immense survival advantage of the rare individuals who live 100 years or more . The Longevity Gene Study was initiated in 1998 at the Albert Einstein College of Medicine to investigate longevity genes in a selected populatio... | Previous research showed that the frequency of deleterious genotype of some age-related disease decreases its prevalence as the population ages , as expected , since subjects with deleterious genotype are weeded out due to mortality . There exists , however , a set of age-related genes whose deleterious genotype indeed... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"buffering",
"systems",
"biology",
"longevity",
"computational",
"biology",
"evolutionary",
"biology",
"gene",
"networks",
"genetics",
"and",
"genomics",
"evolution"
] | 2007 | Buffering Mechanisms in Aging: A Systems Approach Toward Uncovering the Genetic Component of Aging |
Astroglia from the postnatal cerebral cortex can be reprogrammed in vitro to generate neurons following forced expression of neurogenic transcription factors , thus opening new avenues towards a potential use of endogenous astroglia for brain repair . However , in previous attempts astroglia-derived neurons failed to e... | The brain consists of two major cell types: neurons , which transmit information , and glial cells , which support and protect neurons . Interestingly , evidence suggests that some glial cells , including astroglia , can be directly converted into neurons by specific proteins , a transformation that may aid in the func... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology/cell",
"differentiation",
"neuroscience/neurobiology",
"of",
"disease",
"and",
"regeneration",
"neuroscience/neuronal",
"and",
"glial",
"cell",
"biology",
"developmental",
"biology/stem",
"cells"
] | 2010 | Directing Astroglia from the Cerebral Cortex into Subtype Specific Functional Neurons |
We previously reported interferon gamma secretion by human CD4+ and CD8+ T cells in response to recombinant E . coli-expressed Rv1860 protein of Mycobacterium tuberculosis ( MTB ) as well as protection of guinea pigs against a challenge with virulent MTB following prime-boost immunization with DNA vaccine and poxvirus ... | Tuberculosis ( TB ) , although recognized as an infectious disease for centuries , is still the leading cause of human deaths , claiming a million lives annually . Successful control of TB , either through drugs or effective preventive vaccines has not been achieved despite decades of research . We have studied the rol... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"host-pathogen",
"interactions",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"pathogenesis",
"bacterial",
"p... | 2014 | The Glycosylated Rv1860 Protein of Mycobacterium tuberculosis Inhibits Dendritic Cell Mediated TH1 and TH17 Polarization of T Cells and Abrogates Protective Immunity Conferred by BCG |
Negative frequency-dependent selection ( NFDS ) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci , such as the vertebrate MHC and R-genes in plants . Matching-allele interactions of hosts and parasites that prevent the emergence ... | Negative frequency-dependent selection , whereby common genotypes are disfavored , resulting in cyclic change of gene frequencies and maintenance of genetic diversity in host and parasite populations , is one the mechanisms predicted to drive host-parasite coevolution . Specific matching-allele interactions between hos... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"quantitative",
"trait",
"loci",
"cloning",
"parasitic",
"diseases",
"alleles",
"animals",
"genetic",
"mapping",
"molecular",
"biology",
"techniques",
"research",
"an... | 2017 | The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model |
Electronic patient records remain a rather unexplored , but potentially rich data source for discovering correlations between diseases . We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner . By extracting phenotype informa... | Text mining and information extraction can be seen as the challenge of converting information hidden in text into manageable data . We have used text mining to automatically extract clinically relevant terms from 5543 psychiatric patient records and map these to disease codes in the International Classification of Dise... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"medicine",
"text",
"mining",
"computer",
"science",
"diagnostic",
"medicine",
"mental",
"health",
"biology",
"computational",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts |
The human whipworm Trichuris trichiura is a parasite that infects around 500 million people globally , with consequences including damage to physical growth and educational performance . Current drugs such as mebendazole have a notable lack of efficacy against whipworm , compared to other soil-transmitted helminths . M... | The human whipworm , Trichuris trichiura , infects around 500 million people globally , impacting on their physical growth and educational performance . There are currently huge mass drug administration ( MDA ) programs aiming to control whipworm , along with the other major soil transmitted helminths , Ascaris and hoo... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion",
"Conclusions"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"caenorhabditis",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"toxicology",
"animal",
"models",
"developmental",
"biology",
"caenorhabditis",
"elegans",
... | 2018 | 2,4-Diaminothieno[3,2-d]pyrimidines, a new class of anthelmintic with activity against adult and egg stages of whipworm |
The assembly of ribosomal subunits in eukaryotes is a complex , multistep process so far mostly studied in yeast . In S . cerevisiae , more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits . To date , only few human homologs o... | Ribosomes are molecular machines that synthesize proteins and are found in every cell . Each ribosome has a small and a large subunit , each of which is in turn composed of ribosomal RNA and many ribosomal proteins . In eukaryotic cells , the generation of these ribosomal subunits is a complex process requiring the par... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Material",
"and",
"Methods"
] | [
"biochemistry",
"cell",
"biology/nuclear",
"structure",
"and",
"function",
"cell",
"biology",
"biochemistry/macromolecular",
"assemblies",
"and",
"machines",
"computational",
"biology"
] | 2010 | A Protein Inventory of Human Ribosome Biogenesis Reveals an Essential Function of Exportin 5 in 60S Subunit Export |
Intercellular signaling plays an important role in controlling cellular behavior in apical meristems and developing organs in plants . One prominent example in Arabidopsis is the regulation of floral organ shape , ovule integument morphogenesis , the cell division plane , and root hair patterning by the leucine-rich re... | Plant organs , such as flowers or leaves , are made up of distinct cell layers . Although communication across these cell layers is essential for organ development , we have only recently gained some insight into the underlying mechanisms . Receptor-like kinases are cell-surface receptors that perceive and relay interc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology/plant-biotic",
"interactions",
"cell",
"biology/cell",
"signaling",
"cell",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology/cell",
"growth",
"and",
"division",
"plant",
"biology/plant",
"cell",
"biology",
"cell",
"biology/developmental"... | 2009 | DETORQUEO, QUIRKY, and ZERZAUST Represent Novel Components Involved in Organ Development Mediated by the Receptor-Like Kinase STRUBBELIG in Arabidopsis thaliana |
We report the identification and characterization of a previously unknown suppressor of myopathy caused by expansion of CUG repeats , the mutation that triggers Myotonic Dystrophy Type 1 ( DM1 ) . We screened a collection of genes encoding RNA–binding proteins as candidates to modify DM1 pathogenesis using a well estab... | Myotonic dystrophy type 1 ( DM1 ) is the most common among the muscular dystrophies causing muscle weakness and wasting in adults , and it is triggered by expansion of an untranslated CUG repeat . To identify potential therapeutic approaches , we used a Drosophila DM1 model to screen for genes capable of suppressing CU... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"genetic",
"screens",
"genetics",
"biology",
"human",
"genetics",
"molecular",
"cell",
"biology",
"autosomal",
"dominant"
] | 2013 | Smaug/SAMD4A Restores Translational Activity of CUGBP1 and Suppresses CUG-Induced Myopathy |
Attachment proteins from the surface of eukaryotic cells , bacteria and viruses are critical receptors in cell adhesion or signaling and are primary targets for the development of vaccines and therapeutic antibodies . It is proposed that the ligand-binding pocket in receptor proteins can shift between inactive and acti... | A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive ( orthosteric ) mechanism . However , using monoclona... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Inhibition and Reversal of Microbial Attachment by an Antibody with Parasteric Activity against the FimH Adhesin of Uropathogenic E. coli |
Large experimental efforts are characterizing the regulatory genome , yet we are still missing a systematic definition of functional and silent genetic variants in non-coding regions . Here , we integrated DNaseI footprinting data with sequence-based transcription factor ( TF ) motif models to predict the impact of a g... | A large fraction of genetic variants that have been associated with complex traits are found outside of protein coding genes and likely affect gene regulation . Many experimental efforts have been dedicated to mapping regulatory regions in the genome but there are not many systematic methods that integrate functional d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"genome-wide",
"association",
"studies",
"functional",
"genomics",
"gene",
"regulation",
"population",
"genetics",
"dna",
"footprinting",
"genome",
"analysis",
"sequence",
"motif",
"analysis",
"molecular",
"biology",
"techniques",
"population",
... | 2016 | Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? |
Of the Orthomyxoviridae family of viruses , only influenza A viruses are thought to exist as multiple subtypes and has non-human maintenance hosts . In April 2011 , nasal swabs were collected for virus isolation from pigs exhibiting influenza-like illness . Subsequent electron microscopic , biochemical , and genetic st... | Influenza C viruses infect most humans during childhood . Unlike influenza A viruses , influenza C viruses exhibit little genetic variability and evolve at a comparably slower rate . Influenza A viruses exist as multiple subtypes and cause disease in numerous mammals . In contrast , influenza C viruses are comprised of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"emerging",
"infectious",
"diseases",
"viral",
"transmission",
"and",
"infection",
"virology",
"viral",
"classification",
"biology",
"microbiology",
"viral",
"evolution"
] | 2013 | Isolation of a Novel Swine Influenza Virus from Oklahoma in 2011 Which Is Distantly Related to Human Influenza C Viruses |
Swarming , a collective motion of many thousands of cells , produces colonies that rapidly spread over surfaces . In this paper , we introduce a cell-based model to study how interactions between neighboring cells facilitate swarming . We chose to study Myxococcus xanthus , a species of myxobacteria , because it swarms... | Many bacteria are able to spread rapidly over the surface using a strategy called swarming . When the cells cover a surface at high density and compete with each other for nutrients , swarming permits them to maintain rapid growth at the swarm edge . Swarming with flagella has been investigated for many years , and muc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious",
"diseases",
"developmental",
"biology",
"eubacteria",
"computational",
"biology"
] | 2007 | Social Interactions in Myxobacterial Swarming |
Complex phenotypes such as the transformation of a normal population of cells into cancerous tissue result from a series of molecular triggers gone awry . We describe a method that searches for a genetic network consistent with expression changes observed under the knock-down of a set of genes that share a common role ... | Biological processes are the result of the actions and interactions of many genes and the proteins that they encode . Our knowledge of interactions for many biological processes is limited , especially for cancer where genomic alterations may create entirely novel pathways not present in normal tissue . Perturbing gene... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/systems",
"biology",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and",
"genomics/bioinformatics"
] | 2009 | A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations |
Parasitic infections are still of considerable public health relevance , notably among children in low- and middle-income countries . Measures to assess the magnitude of ill-health in infected individuals , however , are debated and patient-based proxies through generic health-related quality of life ( HrQoL ) instrume... | Infectious diseases like malaria and parasitic worms affect hundreds of millions of people , and impact physical and cognitive development of children in Africa , Asia , and the Americas . Over the past 20 years , it was debated how the magnitude of ill-health due to these conditions should be assessed . One proposed s... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"helminth",
"infections",
"medicine",
"and",
"health",
"sciences",
"plant",
"science",
"schistosomiasis",
"parasitic",
"intestinal",
"diseases",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"plant",
"pathology",
"biology",
"and",
"lif... | 2014 | Health-Related Quality of Life among School Children with Parasitic Infections: Findings from a National Cross-Sectional Survey in Côte d'Ivoire |
Dietary restriction ( DR ) is a dietary regimen that extends lifespan in many organisms . One mechanism contributing to the conserved effect of DR on longevity is the cellular recycling process autophagy , which is induced in response to nutrient scarcity and increases sequestration of cytosolic material into double-me... | Dietary restriction ( DR ) without inducing malnutrition has robust beneficial effects on lifespan in many species , including humans . The cellular recycling process of autophagy contributes to DR-mediated longevity . Autophagy is triggered by nutrient scarcity and increases the degradation of cytosolic molecules and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"autophagic",
"cell",
"death",
"lysosomes",
"rna",
"interference",
"pathology",
"and",
"laboratory",
"medicine",
"caenorhabditis",
"pathogens",
"cell",
"processes",
"cloning",
"animals",
"animal"... | 2016 | Intestinal Autophagy Improves Healthspan and Longevity in C. elegans during Dietary Restriction |
Single-cell variability in gene expression is important for generating distinct cell types , but it is unclear how cells use the same set of regulatory molecules to specifically control similarly regulated genes . While combinatorial binding of transcription factors at promoters has been proposed as a solution for cell... | DNA is the blueprint of life . Yet the order in which a cell follows these instructions makes it capable of generating thousands of different fates . How this information is extracted from underlying gene regulatory networks is unclear , especially given that biological networks are highly interconnected , and that the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"phosphorylation",
"sequencing",
"techniques",
"gene",
"regulation",
"neuroscience",
"regulator",
"genes",
"gene",
"types",
"epigenetics",
"molecular",
"biology",
"techniques",
"chromatin",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"chromosome",
"b... | 2016 | Noncommutative Biology: Sequential Regulation of Complex Networks |
This paper introduces a time- and state-dependent measure of integrated information , φ , which captures the repertoire of causal states available to a system as a whole . Specifically , φ quantifies how much information is generated ( uncertainty is reduced ) when a system enters a particular state through causal inte... | We have suggested that consciousness has to do with a system's capacity to generate integrated information . This suggestion stems from considering two basic properties of consciousness: ( i ) each conscious experience generates a large amount of information , by ruling out alternative experiences; and ( ii ) the infor... | [
"Abstract",
"Models",
"Results",
"Discussion"
] | [
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience",
"computational",
"biology"
] | 2008 | Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework |
Closed-loop neurotechnologies often need to adaptively learn an encoding model that relates the neural activity to the brain state , and is used for brain state decoding . The speed and accuracy of adaptive learning algorithms are critically affected by the learning rate , which dictates how fast model parameters are u... | Closed-loop neurotechnologies for treatment of neurological disorders often require adaptively learning an encoding model to relate the neural activity to the brain state and decode this state . Fast and accurate adaptive learning is critically affected by the learning rate , a key variable in any adaptive algorithm . ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"learning",
"action",
"potentials",
"medicine",
"and",
"health",
"sciences",
"classical",
"mechanics",
"engineering",
"and",
"technology",
"electronics",
"applied",
"mathematics",
"membrane",
"potential",
"social",
"sciences",
"random",
"variables",
"electrophysiology",
"... | 2018 | Optimizing the learning rate for adaptive estimation of neural encoding models |
The ability of human immunodeficiency virus type 1 ( HIV-1 ) to develop high levels of genetic diversity , and thereby acquire mutations to escape immune pressures , contributes to the difficulties in producing a vaccine . Possibly no single HIV-1 sequence can induce sufficiently broad immunity to protect against a wid... | The ability of human immunodeficiency virus type 1 ( HIV-1 ) to acquire mutations that preserve virus viability yet evade immune responses contributes to the current failure in producing a vaccine . We describe the generation of candidate HIV-1 immunogens that include multiple forms of variable elements of the virus in... | [
"Abstract",
"Introduction",
"Methods",
"Known",
"Epitope",
"Coverage",
"Results",
"Discussion"
] | [
"viruses",
"infectious",
"diseases",
"virology",
"immunology",
"microbiology"
] | 2007 | Coping with Viral Diversity in HIV Vaccine Design |
Syncytins are envelope genes of retroviral origin that have been co-opted for a role in placentation . They promote cell–cell fusion and are involved in the formation of a syncytium layer—the syncytiotrophoblast—at the materno-fetal interface . They were captured independently in eutherian mammals , and knockout mice d... | Syncytins are “new” genes encoding the envelope protein of captured endogenous retroviral elements . Their unambiguous status of “cellular gene” was recently demonstrated by knocking them out in genetically modified mice , showing their absolute requirement for placenta formation and embryo survival , via formation by ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"molecular",
"cell",
"biology",
"virology",
"genetics",
"biology",
"genomics",
"evolutionary",
"biology",
"microbiology",
"genetics",
"and",
"genomics"
] | 2013 | Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation |
The accurate segregation of chromosomes during cell division is achieved by attachment of chromosomes to the mitotic spindle via the kinetochore , a large multi-protein complex that assembles on centromeres . The budding yeast kinetochore comprises more than 60 different proteins . Although the structure and function o... | As cells divide , their replicated chromosomes must be correctly allocated to the two nascent daughter cells . This is achieved by the kinetochore , which provides a physical link between the chromosomes and the microtubules that drive their movement . If chromosome separation fails , the resulting cells have an abnorm... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microtubules",
"chromosome",
"structure",
"and",
"function",
"centromeres",
"enzymes",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"enzymology",
"ubiquitin",
"ligases",
"molecular",
"biology",
"techniques",
"cellular",
"structures",
"and",
"organel... | 2016 | Synergistic Control of Kinetochore Protein Levels by Psh1 and Ubr2 |
Dominant mutations in CACNA1A , encoding the α-1A subunit of the neuronal P/Q type voltage-dependent Ca2+ channel , can cause diverse neurological phenotypes . Rare cases of markedly severe early onset developmental delay and congenital ataxia can be due to de novo CACNA1A missense alleles , with variants affecting the... | Calcium channels control the levels of calcium within cells and are important in human health . Indeed , groups of patients with disorders of balance known as ataxia have been found to have mutations in a calcium channel gene in the human genome called CACNA1A . CACNA1A mutations have also been observed in patients wit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"neurodegenerative",
"diseases",
"social",
"sciences",
"cloning",
"neuroscience",
"animals",
"invertebrate",
"genomics",
"alleles",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"microscopy"... | 2017 | Clinically severe CACNA1A alleles affect synaptic function and neurodegeneration differentially |
Horizontal gene transfer ( HGT ) can promote evolutionary adaptation by transforming a species’ relationship to the environment . In most well-understood cases of HGT , acquired and donor functions appear to remain closely related . Thus , the degree to which HGT can lead to evolutionary novelties remains unclear . Muc... | A central question in evolutionary biology is how novel traits arise . Gravitropism—the orientation of growth based on gravity—evolved independently in different groups of plants and fungi . Dense bodies formed within distinct organelles play a key role by sedimenting under the influence of gravity to activate signalin... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Methods"
] | [
"taxonomy",
"horizontal",
"gene",
"transfer",
"crystal",
"structure",
"chemical",
"compounds",
"plant",
"growth",
"and",
"development",
"condensed",
"matter",
"physics",
"crystal",
"lattices",
"plant",
"physiology",
"organic",
"compounds",
"gene",
"transfer",
"developme... | 2018 | Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly |
Triosephosphate isomerase ( TPI ) deficiency is a poorly understood disease characterized by hemolytic anemia , cardiomyopathy , neurologic dysfunction , and early death . TPI deficiency is one of a group of diseases known as glycolytic enzymopathies , but is unique for its severe patient neuropathology and early morta... | Glycolysis is the metabolic pathway that cells use to break down the sugar glucose , and mutations in the genes that control the glycolytic pathway elicit a collection of diseases known as glycolytic enzymopathies . Glycolytic enzymopathies are rare genetic diseases that lead to the degeneration of patient red blood ce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"dimers",
"(chemical",
"physics)",
"invertebrates",
"vesicles",
"classical",
"mechanics",
"crystal",
"structure",
"enzymes",
"isomerases",
"condensed",
"matter",
"physics",
"enzymology",
"mechanical",
"stress",
"animals",
"animal",
"models",
"drosophila",
"melanogaster",
... | 2016 | Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics |
Hedgehog ( Hh ) signaling regulates multiple aspects of metazoan development and tissue homeostasis , and is constitutively active in numerous cancers . We identified Ubr3 , an E3 ubiquitin ligase , as a novel , positive regulator of Hh signaling in Drosophila and vertebrates . Hh signaling regulates the Ubr3-mediated ... | Hedgehog signaling regulates many important biological processes and has been linked to developmental disorders , wound healing , and cancer . Although the major components in the pathway have been well studied in Drosophila and vertebrates , how the signaling is regulated by different modulators is not well understood... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"gene",
"regulation",
"vertebrates",
"cloning",
"animals",
"animal",
"models",
"osteichthyes",
"drosophila",
"melanogaster",
"model",
"organisms",
"immunoprecipitation",
"molecular",
"biology",
"techniques",
"eyes",
... | 2016 | Ubr3, a Novel Modulator of Hh Signaling Affects the Degradation of Costal-2 and Kif7 through Poly-ubiquitination |
Human rhinoviruses ( HRV ) cause the majority of common colds and acute exacerbations of asthma and chronic obstructive pulmonary disease ( COPD ) . Effective therapies are urgently needed , but no licensed treatments or vaccines currently exist . Of the 100 identified serotypes , ∼90% bind domain 1 of human intercellu... | Viruses exploit receptors on the host cell to cause infection . Therapies aimed at blocking virus-receptor interactions have the potential to prevent viral disease . Cellular receptors are also important for normal host cell function . Therefore , new therapies targeting these receptors to block viral infection may als... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immune",
"cells",
"cytokines",
"viral",
"transmission",
"and",
"infection",
"immune",
"activation",
"immunity",
"to",
"infections",
"immunology",
"host-pathogen",
"interaction",
"microbiology",
"animal",
"models",
"viral",
"attachment",
"model",
"organisms",
"immune",
... | 2013 | An Anti-Human ICAM-1 Antibody Inhibits Rhinovirus-Induced Exacerbations of Lung Inflammation |
Multiple recent outbreaks of Rift Valley Fever ( RVF ) in Africa , Madagascar , and the Arabian Peninsula have resulted in significant morbidity , mortality , and financial loss due to related livestock epizootics . Presentation of human RVF varies from mild febrile illness to meningoencephalitis , hemorrhagic diathesi... | The underlying risk factors that lead to severe human Rift Valley Fever disease are unknown , but are likely multi-factorial . Host factors , such as innate immune genetic makeup , are likely important determinants of disease phenotype . This study investigated the association of 46 single nucleotide polymorphisms ( SN... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Association of Symptoms and Severity of Rift Valley Fever with Genetic Polymorphisms in Human Innate Immune Pathways |
Dengue is a disease of great complexity , due to interactions between humans , mosquitoes and various virus serotypes as well as efficient vector survival strategies . Thus , understanding the factors influencing the persistence of the disease has been a challenge for scientists and policy makers . The aim of this stud... | Dengue is the most rapidly spreading mosquito-borne viral disease in the world and approximately 2 . 5 billion people live in dengue endemic countries . In Brazil it is mainly transmitted by Aedes aegypti mosquitoes . The wide clinical spectrum ranges from asymptomatic infections or mild illness , to the more severe fo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/epidemiology",
"computer",
"science/applications",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases"
] | 2011 | Modeling the Dynamic Transmission of Dengue Fever: Investigating Disease Persistence |
Integrating data from multiple regulatory layers across cancer types could elucidate additional mechanisms of oncogenesis . Using antibody-based protein profiling of 736 cancer cell lines , along with matching transcriptomic data , we show that pan-cancer bimodality in the amounts of mRNA , protein , and protein phosph... | Profiling molecular and phenotypic characteristics of large collections of cancer cell lines can be used to identify distinct and common oncogenic pathways across cancer types . So far , most large-scale data obtained from cancer cell lines have been at the genomic , transcriptomic , and phenotypic levels . Recently , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biotechnology",
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"small",
"molecules",
"gene",
"regulation",
"messenger",
"rna",
"organic",
"compounds",
"oncology",
"protein",
"expression",
"genome",
"analysis",
"molecular",
"biology",... | 2018 | Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition |
Relay cells are prevalent throughout sensory systems and receive two types of inputs: driving and modulating . The driving input contains receptive field properties that must be transmitted while the modulating input alters the specifics of transmission . For example , the visual thalamus contains relay neurons that re... | In cellular biology , it is important to characterize the electrophysiological dynamics of a cell as a function of the cell type and its inputs . Typically , these dynamics are modeled as a set of parametric nonlinear ordinary differential equations which are not always easy to analyze . Previous studies performed phas... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"bioengineering",
"biomedical",
"engineering",
"biotechnology",
"biological",
"systems",
"engineering",
"control",
"engineering",
"control",
"systems",
"computational",
"neuroscience",
"single",
"neuron",
"function",
"biology",
"computational",
"biology",
"engineering"
] | 2012 | Performance Limitations of Relay Neurons |
Dengue is a potentially fatal acute febrile illness ( AFI ) caused by four mosquito-transmitted dengue viruses ( DENV-1–4 ) that are endemic in Puerto Rico . In January 2010 , the number of suspected dengue cases reported to the passive dengue surveillance system exceeded the epidemic threshold and an epidemic was decl... | Dengue is a potentially fatal acute febrile illness that is endemic throughout the tropics and sub-tropics . Dengue has been endemic in Puerto Rico for several decades and recent epidemics occurred in 1994–5 , 1998 and 2007 . In January 2010 , dengue surveillance indicated that an epidemic had begun . The epidemic peak... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"emerging",
"viral",
"diseases",
"dengue",
"microbiology",
"neglected",
"tropical",
"diseases",
"infectious",
"diseases",
"molecular",
"epidemiology",
"dengue",
"fever",
"epide... | 2013 | Virus-Specific Differences in Rates of Disease during the 2010 Dengue Epidemic in Puerto Rico |
The response of a neuron to repeated somatic fluctuating current injections in vitro can elicit a reliable and precisely timed sequence of action potentials . The set of responses obtained across trials can also be interpreted as the response of an ensemble of similar neurons receiving the same input , with the precise... | Neurons respond with precise spike times to fluctuating current injections , leading to peaks in ensemble firing rate . The structure of these peaks , or spike events , provides a compact description of the neural response . We explore the consequences of precise spike times for neural coding in vivo , by investigating... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"information",
"science",
"social",
"and",
"behavioral",
"sciences",
"neural",
"networks",
"neuroscience",
"mathematics",
"computational",
"neuroscience",
"biophysics",
"simulations",
"biophysics",
"theory",
"biology",
"nonlinear",
"dynamics",
"biophysics",
"physics",
"cent... | 2012 | Multiple Spike Time Patterns Occur at Bifurcation Points of Membrane Potential Dynamics |
In Neurospora crassa , the transcription factor COL-26 functions as a regulator of glucose signaling and metabolism . Its loss leads to resistance to carbon catabolite repression . Here , we report that COL-26 is necessary for the expression of amylolytic genes in N . crassa and is required for the utilization of malto... | In nature , filamentous fungi sense nutrient availability in the surrounding environment and adjust their metabolism for optimal utilization , growth and reproduction . Carbon and nitrogen are two of major elements required for life . Within cells , signals from carbon and nitrogen catabolism are integrated , resulting... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"carbohydrate",
"metabolism",
"chemical",
"compounds",
"gene",
"regulation",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
"fungi",
"model",
"organisms",
"experimental",
"organism",
"systems",
"acidic",
"amino",
"acids",
"amino",
"acids",
... | 2017 | A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism |
We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum . RbdB is a nuclear protein that accumulates , together with Dicer B , in nucleolar foci reminiscent of plant dicing bodies . Disruption of rbdB results in loss of miRNAs and accumulation of primary mi... | miRNAs are essential regulators in eukaryotic cells and serve to control translation and stability of mRNAs . Processing of primary miRNA transcripts is carried out in two steps by evolutionary conserved machineries consisting mainly of double-strand specific RNases of the Dicer family and accessory double-strand RNA b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"interference",
"molecular",
"probe",
"techniques",
"gene",
"regulation",
"dictyosteliomycota",
"cloning",
"dictyostelium",
"plasmid",
"construction",
"northern",
"blot",
"micrornas",
"model",
"organisms",
"dna",
"construction",
"molecular",
"biology",
"techniques",
... | 2016 | Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein |
Although homologous recombination is an important pathway for the repair of double-stranded DNA breaks in mitotically dividing eukaryotic cells , these events can also have negative consequences , such as loss of heterozygosity ( LOH ) of deleterious mutations . We mapped about 140 spontaneous reciprocal crossovers on ... | Double-strand breaks ( DSBs ) are DNA lesions that can be fatal to a cell if left unrepaired . They can be caused by exogenous sources , such as gamma radiation , or endogenous stresses , such as high levels of transcription . Yeast cells primarily repair DSBs that are initiated outside of meiosis by mitotic recombinat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"nucleic",
"acids",
"genetics",
"dna",
"biology",
"dna",
"recombination"
] | 2013 | High-Resolution Mapping of Spontaneous Mitotic Recombination Hotspots on the 1.1 Mb Arm of Yeast Chromosome IV |
Eukaryotic release factors 1 and 3 , encoded by SUP45 and SUP35 , respectively , in Saccharomyces cerevisiae , are required for translation termination . Recent studies have shown that , besides these two key factors , several genetic and epigenetic mechanisms modulate the efficiency of translation termination . These ... | Proper termination is an important step in a successful mRNA translation event . Many factors , employing genetic and epigenetic mechanisms , are involved in modifying translation termination efficiency in the budding yeast , Saccharomyces cerevisiae . [PSI+] , the prion conformation of Sup35p , one of the translation ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology"
] | 2012 | Genetic Basis of Hidden Phenotypic Variation Revealed by Increased Translational Readthrough in Yeast |
RNA viruses induce specialized membranous structures for use in genome replication . These structures are often referred to as replication organelles ( ROs ) . ROs exhibit distinct lipid composition relative to other cellular membranes . In many picornaviruses , phosphatidylinositol-4-phosphate ( PI4P ) is a marker of ... | Picornaviruses replicate their genomes in association with host membranes . Early during infection , existing membranes are used but remodeled to contain a repertoire of lipids best suited for virus multiplication . Later , new membrane synthesis occurs , which requires biosynthesis of phosphatidylcholine in addition t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"transfection",
"nuclear",
"staining",
"hela",
"cells",
"biological",
"cultures",
"microbiology",
"cell",
"cultures",
"molecular",
"biology",
"techniques",
"research",
"and",
"analysis",
"methods",
"specimen",
"preparation",
"and",
"treatment",
"staining",
"lipids",
"vi... | 2018 | Hijacking of multiple phospholipid biosynthetic pathways and induction of membrane biogenesis by a picornaviral 3CD protein |
Peptide recognition domains ( PRDs ) are ubiquitous protein domains which mediate large numbers of protein interactions in the cell . How these PRDs are able to recognize peptide sequences in a rapid and specific manner is incompletely understood . We explore the peptide binding process of PDZ domains , a large PRD fam... | The complex biological processes occurring in living organisms are enabled by numerous networks of interacting proteins . It is therefore of great interest to understand the physical interplay between proteins and , in particular , how this process gives rise to highly specific network connectivities . For a long time ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"physics",
"biomacromolecule-ligand",
"interactions",
"biophysic",
"al",
"simulations",
"biology",
"computational",
"biology",
"biophysics",
"simulations",
"biophysics"
] | 2011 | Binding Free Energy Landscape of Domain-Peptide Interactions |
Genetic engineering with luciferase reporter genes allows monitoring Trypanosoma brucei ( T . b . ) infections in mice by in vivo bioluminescence imaging ( BLI ) . Until recently , luminescent T . b . models were based on Renilla luciferase ( RLuc ) activity . Our study aimed at evaluating red-shifted luciferases for i... | Research on African trypanosomes heavily relies on rodent infection models . One way to reduce the number of laboratory rodents used in each experiment and effectively follow the progression of the infection in the same animals is to use genetically modified trypanosomes that allow monitoring of the infection over time... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"medicine",
"and",
"health",
"sciences",
"african",
"trypanosomiasis",
"neglected",
"tropical",
"diseases",
"biology",
"and",
"life",
"sciences",
"vector-borne",
"diseases",
"tropical",
"diseases",
"trypanoso... | 2014 | A Panel of Trypanosoma brucei Strains Tagged with Blue and Red-Shifted Luciferases for Bioluminescent Imaging in Murine Infection Models |
The role of environmental factors in driving adaptive trajectories of living organisms is still being debated . This is even more important to understand when dealing with important neglected diseases and their vectors . In this paper , we analysed genetic divergence , computed from seven microsatellite loci , of 614 t... | The role of environmental factors in driving adaptive trajectories of living organisms is still being debated . This is even more important to understand when dealing with important and /or neglected diseases and their vectors . In this paper , we analysed genetic divergence , computed from several genetic markers , of... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Ecotype Evolution in Glossina palpalis Subspecies, Major Vectors of Sleeping Sickness |
Rabies is a major public health problem with a fatality rate close to 100%; however , complete prevention can be achieved through pre- or post-exposure prophylaxis . The rapid fluorescent focus inhibition test ( RFFIT ) is one of the recommended testing methods to determine the production of neutralizing antibodies aft... | Rabies represents a significant cause of fatality upon presentation of symptoms; however , pre- or timely post-exposure prophylaxis can provide complete protection to a population . The current reagents available for laboratory tests to determine the level of Rabies virus ( RABV ) neutralizing antibodies are not readil... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"post-exposure",
"prophylaxis",
"immunology",
"tropical",
"diseases",
"microbiology",
"light",
"microscopy",
"geographical",
"locations",
"viruses",
... | 2017 | Development and evaluation of an anti-rabies virus phosphoprotein-specific monoclonal antibody for detection of rabies neutralizing antibodies using RFFIT |
Plasmodium and dengue virus , the causative agents of the two most devastating vector-borne diseases , malaria and dengue , are transmitted by the two most important mosquito vectors , Anopheles gambiae and Aedes aegypti , respectively . Insect-bacteria associations have been shown to influence vector competence for hu... | The infectious agents that cause malaria and dengue are transmitted by Anopheles and Aedes mosquitoes , respectively . Bacteria found in the mosquito midgut have the potential to dramatically affect the susceptibility of the mosquito vector to the malaria parasite and dengue virus . In this work , we investigate one su... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"bacteriology",
"antimicrobials",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"emerging",
"viral",
"diseases",
"microbiology",
"animals",
"parasitology",
"viral",
"vec... | 2014 | Chromobacterium Csp_P Reduces Malaria and Dengue Infection in Vector Mosquitoes and Has Entomopathogenic and In Vitro Anti-pathogen Activities |
Animals’ exchanges are considered the most effective route of between-farm infectious disease transmission . However , despite being often overlooked , the infection spread due to contaminated equipment , vehicles , or personnel proved to be important for several livestock epidemics . This study investigated the role o... | Farm-to-farm contacts due to shared operators and vehicles–such as veterinarians , hoof-trimmers , milk and rendering trucks–are generally considered important for the spread of many infectious diseases in livestock systems . These contacts are usually defined as indirect , as opposed to animal movements which are defi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"livestock",
"medicine",
"and",
"health",
"sciences",
"animal",
"diseases",
"ruminants",
"infectious",
"disease",
"epidemiology",
"vertebrates",
"animals",
"mammals",
"paratuberculosis",
"farms",
"veterinarians",
"zoology",
"veterinary",
"science",
"infectious",
"diseases",... | 2017 | The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks |
Unlike most bacterial species , Mycobacterium tuberculosis depends on the Clp proteolysis system for survival even in in vitro conditions . We hypothesized that Clp is required for the physiologic turnover of mycobacterial proteins whose accumulation is deleterious to bacterial growth and survival . To identify cellula... | To date , studies on the regulation of physiology and virulence in Mycobacterium tuberculosis ( Mtb ) have focused on how transcriptional changes lead to adaptation . Interestingly , Mtb has numerous proteases that are essential for normal growth suggesting that protein turnover may also play an important regulatory ro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbial",
"physiology",
"microbial",
"pathogens",
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2014 | Post-Translational Regulation via Clp Protease Is Critical for Survival of Mycobacterium tuberculosis |
Lynch syndrome ( LS ) is a hereditary cancer predisposition caused by inactivating mutations in DNA mismatch repair ( MMR ) genes . Mutations in the MSH6 DNA MMR gene account for approximately 18% of LS cases . Many LS-associated sequence variants are nonsense and frameshift mutations that clearly abrogate MMR activity... | The colorectal and endometrial cancer predisposition Lynch syndrome ( LS ) is caused by an inherited heterozygous defect in one of four DNA mismatch repair ( MMR ) genes . Deleterious mutations ( e . g . , protein-deleting or -truncating ) in DNA MMR genes unambiguously allow for the clinical diagnosis LS and hence ena... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"oligonucleotide-directed",
"mutagenesis",
"alleles",
"dna",
"damage",
"mutation",
"dna",
"molecular",
"biology",
"techniques",
"mutagenesis",
"and",
"gene",
"deletion",
"techniques",
"frameshift",
"mutation",
"research",
"and",
"analysis",
"methods",
"molecular",
"biolog... | 2017 | Suspected Lynch syndrome associated MSH6 variants: A functional assay to determine their pathogenicity |
Despite the existence of safe and effective vaccines , rabies disease still causes an estimated 59 , 000 human deaths a year in the endemic areas in Asia and Africa . These numbers reflect severe drawbacks regarding the implementation of PrEP and PEP in endemic settings , such as lack of political will and low priority... | Rabies is a 100% vaccine-preventable disease but invariably fatal once symptoms occur . Annually , tens of thousands of people die after being infected with rabies virus , predominantly through bites or scratches of infected dogs . The stable mortality rates highlight the limitations of current disease specific interve... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"tropical",
"diseases",
"microbiology",
"vertebrates",
"animals",
"mammals",
"dogs",
"viruses",
"preventive",
"medicine",
"vaccines",
"rabies",
"rna",
"viru... | 2018 | A research agenda to reinforce rabies control: A qualitative and quantitative prioritization |
Plant virus movement proteins ( MPs ) localize to plasmodesmata ( PD ) to facilitate virus cell-to-cell movement . Numerous studies have suggested that MPs use a pathway either through the ER or through the plasma membrane ( PM ) . Furthermore , recent studies reported that ER-PM contact sites and PM microdomains , whi... | Intercellular trafficking of molecules through plasmodesmata ( PD ) is indispensable for plant development . Plant viruses also use the intercellular trafficking system to establish systemic infection . Virus movement proteins ( MPs ) , which have abilities to localize to PD and to move to the adjacent cells autonomous... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"fluorescence",
"imaging",
"chemical",
"compounds",
"plant",
"cell",
"biology",
"organic",
"compounds",
"luminescent",
"proteins",
"plant",
"science",
"immunoprecipitation",
"yellow",
"fluorescent",
"protein",
"chaperone",
"proteins",
"anilines",
"re... | 2017 | Dual targeting of a virus movement protein to ER and plasma membrane subdomains is essential for plasmodesmata localization |
The root knot nematode , Meloidogyne incognita , is an obligate parasite that causes significant damage to a broad range of host plants . Infection is associated with secretion of proteins surrounded by proliferating cells . Many parasites are known to secrete effectors that interfere with plant innate immunity , enabl... | Parasitic nematodes are microscopic worms that cause major diseases of plants , animals , and humans . Infection is associated with secretion of proteins by the parasite; these proteins suppress the immune system and cause other changes to host cells that are required for infection . Identification of secreted proteins... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology/plant-biotic",
"interactions",
"pathology/molecular",
"pathology"
] | 2008 | Direct Identification of the Meloidogyne incognita Secretome Reveals Proteins with Host Cell Reprogramming Potential |
In HIV-infected individuals receiving suppressive antiretroviral therapy , the virus persists indefinitely in a reservoir of latently infected cells . The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals . Because the HIV... | Although antiretroviral therapy effectively blocks HIV-1 replication , the virus persists indefinitely in a reservoir of latently infected cells . This reservoir is a major barrier to HIV-1 cure . Recent studies have identified the proliferation of latently infected cells as a mechanism that may contribute to the lifel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency",
"viruses",
"rna",
"viruses",
"viral",
"genome",
"phylogenetic",
"analysis",
"mole... | 2016 | Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality |
Cellular gene expression measurements contain regulatory information that can be used to discover novel network relationships . Here , we present a new algorithm for network reconstruction powered by the adaptive lasso , a theoretically and empirically well-behaved method for selecting the regulatory features of a netw... | Determining a unique set of regulatory relationships underlying the observed expression of genes is a challenging problem , not only because of the many possible regulatory relationships , but also because highly distinct regulatory relationships can fit data equally well . In addition , most expression data-sets have ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2010 | Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations |
Through full genome analyses of four atypical Bacillus cereus isolates , designated B . cereus biovar anthracis , we describe a distinct clade within the B . cereus group that presents with anthrax-like disease , carrying virulence plasmids similar to those of classic Bacillus anthracis . We have isolated members of th... | Anthrax has historically been attributed to a single cluster within the Bacillus cereus complex denoted as B . anthracis . Here , we demonstrate the existence of a distinct clade of B . cereus isolates causing anthrax-like disease in a range of wild and domestic mammals in tropical Africa . These strains , designated B... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"animal",
"types",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"bacillus",
"microbiology",
"vertebrates",
"animals",
"mammals",
"primates",
"phylogenetic",
"analysis",
"molecular",
"biology",
"techniques",
"mammalian... | 2016 | Bacillus cereus Biovar Anthracis Causing Anthrax in Sub-Saharan Africa—Chromosomal Monophyly and Broad Geographic Distribution |
The establishment of correct neurotransmitter characteristics is an essential step of neuronal fate specification in CNS development . However , very little is known about how a battery of genes involved in the determination of a specific type of chemical-driven neurotransmission is coordinately regulated during verteb... | Neurons utilize various chemicals to transmit signals to a target cell . Distinct types of neurons in the spinal cord and forebrain , collectively termed cholinergic neurons , utilize the same chemical , acetylcholine , for signal transmission . These neurons play critical roles in controlling locomotion and cognition ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience",
"biology",
"and",
"life",
"sciences",
"developmental",
"biology"
] | 2014 | Isl1 Directly Controls a Cholinergic Neuronal Identity in the Developing Forebrain and Spinal Cord by Forming Cell Type-Specific Complexes |
Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation ( GMEC ) . To efficiently find the GMEC , protein design algorithms must methodically reduce the conformational search space . By applying distance and energy cutoffs , the protein system... | Computational structure-based protein design algorithms have successfully redesigned proteins to fold and bind target substrates in vitro , and even in vivo . Because the complexity of a computational design increases dramatically with the number of mutable residues , many design algorithms employ cutoffs ( distance or... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"biotechnology",
"infographics",
"sequencing",
"techniques",
"chemical",
"bonding",
"protein",
"interactions",
"engineering",
"and",
"technology",
"applied",
"mathematics",
"synthetic",
"biology",
"synthetic",
"bioengineering",
"simulation",
"and",
"modeling",
"algorithms",
... | 2017 | A critical analysis of computational protein design with sparse residue interaction graphs |
Adaptation to different nutritional environments is essential for life cycle completion by all Trypanosoma brucei sub-species . In the tsetse fly vector , L-proline is among the most abundant amino acids and is mainly used by the fly for lactation and to fuel flight muscle . The procyclic ( insect ) stage of T . b . br... | Bloodsucking insects play a major role in the transmission of pathogens that cause major tropical diseases . Their capacity to transmit these diseases is directly associated with the availability and turnover of energy sources . Proline is the main readily-mobilizable fuel of the tsetse fly , which is the vector of sub... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"chemical",
"compounds",
"aliphatic",
"amino",
"acids",
"carbohydrates",
"parasitic",
"diseases",
"organic",
"compounds",
"neuroscience",
"glucose",
"glucose",
"metabolism",
"amino",
... | 2017 | Proline Metabolism is Essential for Trypanosoma brucei brucei Survival in the Tsetse Vector |
Voltage-sensitive dye imaging experiments in primary visual cortex ( V1 ) have shown that local , oriented visual stimuli elicit stable orientation-selective activation within the stimulus retinotopic footprint . The cortical activation dynamically extends far beyond the retinotopic footprint , but the peripheral sprea... | Optical imaging techniques can reveal the dynamical patterns of cortical activation that encode low-level visual features like position and orientation , which are shaped by both feed-forward projections , recurrent and long-range intra-cortical connections . Anatomical studies have characterized intra-cortical connect... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"membrane",
"potential",
"brain",
"electrophysiology",
"neuroscience",
"simulation",
"and",
"modeling",
"convolution",
"neuroimaging",
"research",
"and",
"analysis",
"methods",
"sensory",
"physiology",
"imaging... | 2017 | Neural field model to reconcile structure with function in primary visual cortex |
Members of the family Trypanosomatidae infect many organisms , including animals , plants and humans . Plant-infecting trypanosomes are grouped under the single genus Phytomonas , failing to reflect the wide biological and pathological diversity of these protists . While some Phytomonas spp . multiply in the latex of p... | Some plant trypanosomes , single-celled organisms living in phloem sap , are responsible for important palm diseases , inducing frequent expensive and toxic insecticide treatments against their insect vectors . Other trypanosomes multiply in latex tubes without detriment to their host . Despite the wide range of behavi... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"sequencing",
"genome",
"analysis",
"tools",
"plant",
"science",
"plant",
"pathogens",
"plant",
"pathology",
"comparative",
"genomics",
"biology",
"genomics",
"gene",
"prediction",
"computational",
"biology"
] | 2014 | The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants |
The theory of phase oscillators is an essential tool for understanding population dynamics of pacemaking neurons . GABAergic pacemakers in the substantia nigra pars reticulata ( SNr ) , a main basal ganglia ( BG ) output nucleus , receive inputs from the direct and indirect pathways at distal and proximal regions of th... | The substantia nigra pars reticulata ( SNr ) is a main output nucleus of the basal ganglia ( BG ) , where inputs from the competing direct and indirect pathways converge onto the same neurons . Interestingly , these inputs are differentially distributed with direct and indirect pathway projections arriving at distal an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"optogenetics",
"engineering",
"and",
"technology",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"probability",
"distri... | 2019 | Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors |
We develop a unified model accounting simultaneously for the contrast invariance of the width of the orientation tuning curves ( OT ) and for the sigmoidal shape of the contrast response function ( CRF ) of neurons in the primary visual cortex ( V1 ) . We determine analytically the conditions for the structure of the a... | Both the response and membrane potential of neurons in the primary visual cortex ( V1 ) are selective to the orientation of elongated stimuli . The widths of the tuning curves , which characterize this selectivity , hardly depend on stimulus contrast whereas their amplitude does . The contrast dependence of this amplit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/natural",
"and",
"synthetic",
"vision",
"neuroscience/theoretical",
"neuroscience",
"neuroscience/sensory",
"systems"
] | 2011 | Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex |
Single-cell RNA sequencing ( scRNA-seq ) has been widely applied to discover new cell types by detecting sub-populations in a heterogeneous group of cells . Since scRNA-seq experiments have lower read coverage/tag counts and introduce more technical biases compared to bulk RNA-seq experiments , the limited number of sa... | scRNA-seq enables detailed profiling of heterogeneous cell populations and can be used to reveal lineage relationships or discover new cell types . In the literature , there has been little effort directed towards developing computational methods for cross-population transcriptome analysis of multiple single-cell popul... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"flow",
"cytometry",
"sequencing",
"techniques",
"medicine",
"and",
"health",
"sciences",
"cell",
"cycle",
"and",
"cell",
"division",
"applied",
"mathematics",
"cell",
"processes",
"marker",
"genes",
"fibroblasts",
"simulation",
"and",
"modeling",
"algorithms",
"devel... | 2018 | A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa |
The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants . Here , we describe the detailed genotypic and phenotypic analysis of a sunflower ( Helianthus annuus L . ) asso... | Selection during the evolution of crop plants has resulted in dramatic phenotypic differentiation , and these same selective pressures are expected to have had a significant impact on underlying genomic diversity . Population genomic analyses , especially when coupled with trait-based mapping approaches , thus have the... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genome-wide",
"association",
"studies",
"genomics",
"plant",
"biology",
"crops",
"genetics",
"population",
"genetics",
"biology",
"evolutionary",
"biology",
"genomic",
"evolution",
"genetics",
"and",
"genomics",
"agriculture"
] | 2013 | Association Mapping and the Genomic Consequences of Selection in Sunflower |
The Epstein-Barr virus ( EBV ) is a B lymphotropic virus that infects the majority of the human population . All EBV strains transform B lymphocytes , but some strains , such as M81 , also induce spontaneous virus replication . EBV encodes 22 microRNAs ( miRNAs ) that form a cluster within the BART region of the virus ... | The Epstein-Barr virus ( EBV ) infects more than 90% of the human adult population . Although EBV usually causes an asymptomatic infection , it is oncogenic in a small proportion of infected individuals . EBV produces a large number of microRNAs , a type of RNA that controls the production of their proteins though mult... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The Epstein-Barr Virus BART miRNA Cluster of the M81 Strain Modulates Multiple Functions in Primary B Cells |
Hookworm-related cutaneous larva migrans ( HrCLM ) is a neglected parasitic skin disease , widespread in resource-poor communities in tropical and subtropical countries . Incidence and risk factors have never been investigated in a cohort study . To understand the seasonal epidemiology of HrCLM , an open cohort of 476 ... | Hookworm-worm related cutaneous larva migrans ( HrCLM ) is a parasitic skin disease caused by hookworm larvae of cats and dogs occurring in many countries with a tropical or subtropical climate . Humans are a biological impasse for these helminths as the larvae cannot pass the basal membrane of the epidermis and hence ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"recreation",
"children",
"medicine",
"and",
"health",
"sciences",
"salaries",
"sports",
"cutaneous",
"larva",
"migrans",
"geographical",
"locations",
"tropical",
"diseases",
"social",
"sciences",
"parasitic",
"diseases",
"age",
"groups",
"seasons",
"developmental",
"bi... | 2018 | Epidemiology and morbidity of hookworm-related cutaneous larva migrans (HrCLM): Results of a cohort study over a period of six months in a resource-poor community in Manaus, Brazil |
Despite intensive efforts using linkage and candidate gene approaches , the genetic etiology for the majority of families with a multi-generational breast cancer predisposition is unknown . In this study , we used whole-exome sequencing of thirty-three individuals from 15 breast cancer families to identify potential pr... | Currently , we know that a woman who inherits a fault in one of two genes , BRCA1 or BRCA2 , has a high risk of developing both breast and ovarian cancer . However , such faults account for only half of all families with a strong family history of breast cancer . In this study , we planned to identify new genes that ma... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"cancer",
"genetics",
"genome",
"sequencing",
"genome",
"analysis",
"tools",
"genetic",
"testing",
"biology",
"trait",
"locus",
"heredity",
"genetic",
"association",
"studies",
"genetic",
"screens",
"genetics",
"genomics",
"genetics",
"of",
"disease",
"genetics",
"and... | 2012 | Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles |
The clinical spectrum of human disease caused by the roundworms Toxocara canis and Toxocara cati ranges from visceral and ocular larva migrans to covert toxocariasis . The parasite is not typically recovered in affected tissues , so detection of parasite-specific antibodies is usually necessary for establishing a diagn... | The roundworms Toxocara canis and Toxocara cati cause a broad spectrum of clinical disease in humans . Children are at particular risk of toxocariasis when they play in areas potentially contaminated with Toxocara eggs , such as playgrounds or sandboxes and ingest embryonated roundworm eggs . Currently , diagnosis for ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [] | 2015 | Development of a Luminex Bead Based Assay for Diagnosis of Toxocariasis Using Recombinant Antigens Tc-CTL-1 and Tc-TES-26 |
TDP-43 and FUS are RNA-binding proteins that form cytoplasmic inclusions in some forms of amyotrophic lateral sclerosis ( ALS ) and frontotemporal lobar degeneration ( FTLD ) . Moreover , mutations in TDP-43 and FUS are linked to ALS and FTLD . However , it is unknown whether TDP-43 and FUS aggregate and cause toxicity... | Many human neurodegenerative diseases are associated with the abnormal accumulation of protein aggregates in the neurons of affected individuals . Amyotrophic lateral sclerosis ( ALS ) , also known as Lou Gehrig's disease , is a fatal human neurodegenerative disease caused primarily by a loss of motor neurons . Recentl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurological",
"disorders/movement",
"disorders",
"neurological",
"disorders",
"genetics",
"and",
"genomics/disease",
"models",
"neuroscience/neurobiology",
"of",
"disease",
"and",
"regeneration"
] | 2011 | Molecular Determinants and Genetic Modifiers of Aggregation and
Toxicity for the ALS Disease Protein FUS/TLS |
A major challenge in developing vaccines for emerging pathogens is their continued evolution and ability to escape human immunity . Therefore , an important goal of vaccine research is to advance vaccine candidates with sufficient breadth to respond to new outbreaks of previously undetected viruses . Ebolavirus ( EBOV ... | Ebola virus causes death , fear , and economic disruption during outbreaks . It is a concern worldwide as a natural pathogen and a bioterrorism agent , and has caused death to residents and tourists of Africa where the virus circulates . A vaccine strategy to protect against all circulating Ebola viruses is complicated... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"virology/vaccines",
"immunology/immune",
"response",
"infectious",
"diseases/viral",
"infections",
"immunology/immunity",
"to",
"infections"
] | 2010 | Demonstration of Cross-Protective Vaccine Immunity against an Emerging Pathogenic Ebolavirus Species |
Positive-sense RNA virus intracellular replication is intimately associated with membrane platforms that are derived from host organelles and comprised of distinct lipid composition . For flaviviruses , such as West Nile virus strain Kunjin virus ( WNVKUN ) we have observed that these membrane platforms are derived fro... | Positive-sense RNA viruses remodel the host cytoplasmic membrane architecture to induce the formation of membranous organelles termed viral replication complexes . These complexes aid the virus in providing a more efficient microenvironment for replication but additionally shield immune-stimulatory molecules from the i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"vero",
"cells",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"biological",
"cultures",
"microbiology",
"viruses",
"rna",
"viruses",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"a... | 2018 | Phospholipase A2 activity during the replication cycle of the flavivirus West Nile virus |
Accurate modelling of biological systems requires a deeper and more complete knowledge about the molecular components and their functional associations than we currently have . Traditionally , new knowledge on protein associations generated by experiments has played a central role in systems modelling , in contrast to ... | To model accurate protein networks we need to extend our knowledge of protein associations in molecular systems much further . Biologists believe that high-throughput experiments will fill the gaps in our knowledge . However , if these approaches perform biased screenings , leaving important areas poorly characterized ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"computational",
"biology/genomics",
"computational",
"biology"
] | 2010 | Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling |
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