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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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The cell envelope of mycobacteria is a highly unique and complex structure that is functionally equivalent to that of Gram-negative bacteria to protect the bacterial cell . Defects in the integrity or assembly of this cell envelope must be sensed to allow the induction of stress response systems . The promoter that is ... | The mycobacterial cell wall is a complex and unique structure that protects extremely well against harmful compounds . Understanding the biogenesis and functioning of this cell envelope is essential to be able to effectively target mycobacteria . One way to uncover cell envelope functionality is to study stress mechani... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"disaccharides",
"drugs",
"microbiology",
"operons",
"carbohydrates",
"organic",
"compounds",
"regulator",
"genes",
"antibiotics",
"genetic",
"elements",
"gene",
"types",
"dna",
"pharmacol... | 2017 | Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose |
Variable numbers of tandem repeats ( VNTR ) typing is widely used for studying the bacterial cause of tuberculosis . Knowledge of the rate of mutation of VNTR loci facilitates the study of the evolution and epidemiology of Mycobacterium tuberculosis . Previous studies have applied population genetic models to estimate ... | Genetically typing the bacterium responsible for tuberculosis is useful for understanding the evolutionary and epidemiological characteristics of the disease . Typing methods based on variable number tandem repeat ( VNTR ) loci are increasingly being used . These loci , which are composed of repeated units , mutate by ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"microbial",
"evolution",
"statistics",
"biology",
"microbiology",
"biostatistics"
] | 2012 | A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis |
Upon reactivation from latency and during lytic infections in neurons , alphaherpesviruses assemble cytosolic capsids , capsids associated with enveloping membranes , and transport vesicles harboring fully enveloped capsids . It is debated whether capsid envelopment of herpes simplex virus ( HSV ) is completed in the s... | Human and animal alphaherpesviruses establish lifelong latent infections in neurons of the peripheral nervous system and cause many diseases upon primary infection as well as following reactivation from latency . The highly prevalent human herpes simplex viruses HSV-1 and HSV-2 are responsible for facial and genital he... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"vesicles",
"microtubules",
"cell",
"processes",
"microbiology",
"viral",
"structure",
"neuroscience",
"nerve",
"fibers",
"cellular",
"structures",
"and",
"organelles",
"cytoskeleton",
"animal",
"cells",
"axons",
"viral",
"packaging",
"viral",
"replication",
"virions",
... | 2017 | Inner tegument proteins of Herpes Simplex Virus are sufficient for intracellular capsid motility in neurons but not for axonal targeting |
It has recently been estimated that a single HIV-1 infected cell produces between and more than viral particles over its life span . Since body-wide estimates of the ratio of free virus to productively infected cells are smaller than and much smaller than , individual virions must be cleared rapidly . This seems diffic... | A human cell that is infected with the AIDS virus HIV-1 may produce more than new viral particles over its short life span . In patients chronically infected with HIV-1 , one can estimate that on average there are much less than free viral particles per productively infected cell . This suggests that the rate at which ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"mathematics",
"virology/immunodeficiency",
"viruses"
] | 2010 | Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues |
Tuberculosis ( TB ) treatment is hampered by the long duration of antibiotic therapy required to achieve cure . This indolent response has been partly attributed to the ability of subpopulations of less metabolically active Mycobacterium tuberculosis ( Mtb ) to withstand killing by current anti-TB drugs . We have used ... | Tuberculosis ( TB ) caused by Mycobacterium tuberculosis ( Mtb ) is a leading infectious cause of morbidity and mortality . Although current antibiotic regimens can cure TB , treatment requires at least six months for completion . Recent studies indicate that bacteria in a less metabolically active state are less respo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bacteriology",
"medicine",
"microbial",
"metabolism",
"cellular",
"stress",
"responses",
"functional",
"genomics",
"medicinal",
"chemistry",
"immune",
"cells",
"pathology",
"immunologic",
"subspecialties",
"drugs",
"and",
"devices",
"immunology",
"microbiology",
"host-path... | 2011 | Phosphodiesterase-4 Inhibition Alters Gene Expression and Improves Isoniazid – Mediated Clearance of Mycobacterium tuberculosis in Rabbit Lungs |
The NALCN/NCA ion channel is a cation channel related to voltage-gated sodium and calcium channels . NALCN has been reported to be a sodium leak channel with a conserved role in establishing neuronal resting membrane potential , but its precise cellular role and regulation are unclear . The Caenorhabditis elegans ortho... | Dopamine is a neurotransmitter that acts in the brain by binding seven transmembrane receptors that are coupled to heterotrimeric GTP-binding proteins ( G proteins ) . Neuronal G proteins often function by modulating ion channels that control membrane excitability . Here we identify a molecular cascade downstream of do... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"acetylcholine",
"chemical",
"compounds",
"neuroscience",
"organic",
"compounds",
"biological",
"locomotion",
"hormones",
"motor",
"neurons",
"amines",
"neurotransmitters",
"interneurons",
"catecholamines",
"g",
"pr... | 2017 | Dopamine negatively modulates the NCA ion channels in C. elegans |
The Pneumococcal serine-rich repeat protein ( PsrP ) is a pathogenicity island encoded adhesin that has been positively correlated with the ability of Streptococcus pneumoniae to cause invasive disease . Previous studies have shown that PsrP mediates bacterial attachment to Keratin 10 ( K10 ) on the surface of lung cel... | Serine-rich repeat proteins ( SRRPs ) are a family of surface-expressed proteins found in numerous Gram-positive pathogens , including Staphylococcus aureus , Streptococcus pneumoniae , Group B streptococci , and the oral streptococci that cause infective endocarditis . For all of these bacteria , SRRPs have been demon... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology",
"infectious",
"diseases/respiratory",
"infections"
] | 2010 | The Pneumococcal Serine-Rich Repeat Protein Is an Intra-Species Bacterial Adhesin That Promotes Bacterial Aggregation In Vivo and in Biofilms |
The proto-oncoprotein Raf is pivotal for mitogen-activated protein kinase ( MAPK ) signaling , and its aberrant activation has been implicated in multiple human cancers . However , the precise molecular mechanism of Raf activation , especially for B-Raf , remains unresolved . By genetic and biochemical studies , we dem... | Receptor tyrosine kinase ( RTK ) /Ras signaling pathways control many different biological processes during metazoan development . Mutations that disrupt this signaling pathway cause many human diseases , including cancer . The proto-oncoprotein Raf functions downstream of Ras in transducing signals from RTK . Activati... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"cell",
"biology"
] | 2008 | Raf Activation Is Regulated by Tyrosine 510 Phosphorylation in Drosophila |
Sexual dimorphism in body weight , fat distribution , and metabolic disease has been attributed largely to differential effects of male and female gonadal hormones . Here , we report that the number of X chromosomes within cells also contributes to these sex differences . We employed a unique mouse model , known as the... | Differences exist between men and women in the development of obesity and related metabolic diseases such as type 2 diabetes and cardiovascular disease . Previous studies have focused on the sex-biasing role of hormones produced by male and female gonads , but these cannot account fully for the sex differences in metab... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"medicine",
"animal",
"genetics",
"model",
"organisms",
"genetics",
"genetics",
"and",
"genomics",
"biology",
"mouse",
"metabolic",
"disorders"
] | 2012 | The Number of X Chromosomes Causes Sex Differences in Adiposity in Mice |
The regulation of alternative splicing involves interactions between RNA-binding proteins and pre-mRNA positions close to the splice sites . T-cell intracellular antigen 1 ( TIA1 ) and TIA1-like 1 ( TIAL1 ) locally enhance exon inclusion by recruiting U1 snRNP to 5′ splice sites . However , effects of TIA proteins on s... | Studies of splicing regulation have generally focused on RNA elements located close to alternative exons . Recently , it has been suggested that splicing of alternative exons can also be regulated by distal regulatory sites , but the underlying mechanism is not clear . The TIA proteins are key splicing regulators that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular",
"biology/rna-protein",
"interactions",
"computational",
"biology/sequence",
"motif",
"analysis",
"computational",
"biology/alternative",
"splicing",
"molecular",
"biology/rna",
"splicing",
"biochemistry/bioinformatics",
"biochemistry/transcription",
"and",
"translation"
... | 2010 | iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions |
Dengue is a mosquito-borne disease that is common in many tropical and subtropical areas . Dengue infections can occur at any age and time in the lifespan , including during pregnancy . Few large scale studies have been conducted to determine the risk of preterm birth ( PTB ) and low birthweight ( LBW ) for infants bor... | Previous studies have reported that dengue fever during pregnancy may be related to preterm birth and low birthweight among infants . However , few studies have used an appropriate control group to compare the risk of these outcomes for infants whose mothers had dengue fever to infants whose mothers did not . We design... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"plant",
"science",
"pediatric",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"plant",
"pathology",
"biology",
"and",
"life",
"sciences"
] | 2014 | Symptomatic Dengue Infection during Pregnancy and Infant Outcomes: A Retrospective Cohort Study |
Genome-wide association studies ( GWAS ) have identified >300 loci associated with measures of adiposity including body mass index ( BMI ) and waist-to-hip ratio ( adjusted for BMI , WHRadjBMI ) , but few have been identified through screening of the African ancestry genomes . We performed large scale meta-analyses and... | Genome-wide association studies ( GWAS ) have identified >300 genetic regions that influence body size and shape as measured by body mass index ( BMI ) and waist-to-hip ratio ( WHR ) , respectively , but few have been identified in populations of African ancestry . We conducted large scale high coverage GWAS and replic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"genome-wide",
"association",
"studies",
"africans",
"alleles",
"ethnicities",
"mathematics",
"statistics",
"(mathematics)",
"genome",
"analysis",
"trait",
"locus",
"analysis",
"research",
"and",
"analysis",
"methods",
"genomic",
"signal",
"processing",
"mathematical",
"a... | 2017 | Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium |
In present-day eukaryotes , the cell division cycle is controlled by a complex network of interacting proteins , including members of the cyclin and cyclin-dependent protein kinase ( Cdk ) families , and the Anaphase Promoting Complex ( APC ) . Successful progression through the cell cycle depends on precise , temporal... | The eukaryotic cell division cycle is driven by fluctuating activities of cyclin-dependent kinases ( Cdk ) , which are activated and inactivated by several mechanisms , including cyclin synthesis and degradation . Although the cell cycle is driven by many different Cdk-cyclin complexes in present-day eukaryotes , exper... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Cell Cycle Control by a Minimal Cdk Network |
It is generally believed that associative memory in the brain depends on multistable synaptic dynamics , which enable the synapses to maintain their value for extended periods of time . However , multistable dynamics are not restricted to synapses . In particular , the dynamics of some genetic regulatory networks are m... | It has been known since the pioneering studies of Ivan Petrovich Pavlov that changes in the nervous system enable animals to associate neutral stimuli with stimuli of ecological significance . The goal of this paper is to study whether genetic regulatory networks that govern the production and degradation of proteins i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"neural",
"networks",
"computational",
"neuroscience",
"regulatory",
"networks",
"biology",
"computational",
"biology",
"neuroscience"
] | 2013 | Stochasticity, Bistability and the Wisdom of Crowds: A Model for Associative Learning in Genetic Regulatory Networks |
Although vitamin D deficiency is a common feature among patients presenting with active tuberculosis , the full scope of vitamin D action during Mycobacterium tuberculosis ( Mtb ) infection is poorly understood . As macrophages are the primary site of Mtb infection and are sites of vitamin D signaling , we have used th... | In 2010 there were ∼9 million cases of tuberculosis and 1 . 4 million deaths , representing the second largest cause of death worldwide and the leading cause of death from a curable disease . M . tuberculosis ( Mtb ) replicates within cells of the immune system called macrophages over an approximate 72 hour period , ul... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"mycobacterium",
"immune",
"cells",
"cytokines",
"monocytes",
"tuberculosis",
"immunology",
"biology",
"immune",
"response",
"immune",
"system"
] | 2013 | Vitamin D Induces Interleukin-1β Expression: Paracrine Macrophage Epithelial Signaling Controls M. tuberculosis Infection |
Existing methods to ascertain small sets of markers for the identification of human population structure require prior knowledge of individual ancestry . Based on Principal Components Analysis ( PCA ) , and recent results in theoretical computer science , we present a novel algorithm that , applied on genomewide data ,... | Genetic markers can be used to infer population structure , a task that remains a central challenge in many areas of genetics such as population genetics , and the search for susceptibility genes for common disorders . In such settings , it is often desirable to reduce the number of markers needed for structure identif... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"homo",
"(human)",
"genetics",
"and",
"genomics",
"computer",
"science"
] | 2007 | PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations |
Ribonuclease P ( RNase P ) is an essential enzyme required for 5′-maturation of tRNA . While an RNA-free , protein-based form of RNase P exists in eukaryotes , the ribonucleoprotein ( RNP ) form is found in all domains of life . The catalytic component of the RNP is an RNA known as RNase P RNA ( RPR ) . Eukaryotic RPR ... | The processing of the 5′ end of nascent tRNAs is catalyzed by ribonuclease P ( RNase P ) , an essential enzyme . In the ribonucleoprotein form of this enzyme , the RNase P RNA ( RPR ) functions as a ribozyme aided by protein cofactors . All previously examined eukaryotic RPR genes are transcribed from their own promote... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"rna",
"enzymes",
"biology",
"and",
"life",
"sciences",
"molecular",
"evolution",
"enzymology",
"evolutionary",
"biology",
"ribozymes"
] | 2015 | Transcriptional Control of an Essential Ribozyme in Drosophila Reveals an Ancient Evolutionary Divide in Animals |
Early diagnosis of dengue can assist patient triage and management and prevent unnecessary treatments and interventions . Commercially available assays that detect the dengue virus protein NS1 in the plasma/serum of patients offers the possibility of early and rapid diagnosis . The sensitivity and specificity of the Pa... | Dengue is the most important mosquito-borne viral disease of humans and an enormous public health burden in affected countries . Early , sensitive and specific diagnosis of dengue is needed for appropriate patient management as well as for early epidemic detection . Commercially available assays that detect the dengue ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"virology/diagnosis",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"virology/emerging",
"viral",
"diseases",
"infectious",
"diseases/viral",
"infections",
"infectious",
"diseases/tropical",
"and",
"travel-associated",
"diseases"
] | 2010 | Multi-Country Evaluation of the Sensitivity and Specificity of Two Commercially-Available NS1 ELISA Assays for Dengue Diagnosis |
Nucleoproteins ( NPs ) encapsidate the Phlebovirus genomic ( - ) RNA . Upon recombinant expression , NPs tend to form heterogeneous oligomers impeding characterization of the encapsidation process through crystallographic studies . To overcome this problem , we set up a standard protocol in which production under both ... | Phleboviruses have a worldwide distribution and are usually represented by their prototype Rift Valley fever virus that can have a great impact on health and economy in Africa . The genome of phleboviruses is a segmented negative strand RNA that is encapsidated by the nucleoprotein . The structure of the monomeric nucl... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"molecular",
"biology/rna-protein",
"interactions",
"biophysics/protein",
"folding",
"virology/virion",
"structure,",
"assembly,",
"and",
"egress",
"biotechnology/protein",
"chemistry",
"and",
"proteomics"
] | 2011 | Comparative Production Analysis of Three Phlebovirus Nucleoproteins under Denaturing or Non-Denaturing Conditions for Crystallographic Studies |
Molecular research in cancer is one of the largest areas of bioinformatic investigation , but it remains a challenge to understand biomolecular mechanisms in cancer-related pathways from high-throughput genomic data . This includes the Nuclear-factor-kappa-B ( NFκB ) pathway , which is central to the inflammatory respo... | In molecular research in cancer it remains challenging to uncover biomolecular mechanisms in cancer-related pathways from high-throughput genomic data , including the Nuclear-factor-kappa-B ( NFκB ) pathway . Despite close scrutiny and a deep understanding of many of the NFκB pathway members’ biomolecular activities , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"urology",
"medicine",
"and",
"health",
"sciences",
"genetic",
"networks",
"protein",
"interactions",
"gene",
"regulation",
"regulatory",
"proteins",
"protein",
"interaction",
"networks",
"genitourinary",
"tract",
"tumors",
"cancers",
"and",
"neoplasms",
"dna-binding",
... | 2016 | Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer |
Mycobacterium tuberculosis ( Mtb ) requires the ESX1 specialized protein secretion system for virulence , for triggering cytosolic immune surveillance pathways , and for priming an optimal CD8+ T cell response . This suggests that ESX1 might act primarily by destabilizing the phagosomal membrane that surrounds the bact... | From studies of BCG , the tuberculosis vaccine , we know that Mycobacterium tuberculosis requires a specialized protein secretion system , ESX1 , to cause disease in people . ESX1 is required for Mtb to co-opt the host cells in which the bacterium resides and it is thought that this explains its central role in virulen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology"
] | 2010 | EspA Acts as a Critical Mediator of ESX1-Dependent Virulence in Mycobacterium tuberculosis by Affecting Bacterial Cell Wall Integrity |
Human Cytomegalovirus ( HCMV ) is a widespread pathogen , infection with which can cause severe disease for immunocompromised individuals . The complex changes wrought on the host’s immune system during both productive and latent HCMV infection are well known . Infected cells are masked and manipulated and uninfected i... | Human cytomegalovirus ( HCMV ) infects from 45% to 100% of people worldwide , depending on local socio-economic factors . Although usually harmless in healthy individuals , infection with HCMV can cause severe disease in people with weakened or immature immune systems such as transplant recipients and newborns . The es... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"phosphorylation",
"t",
"helper",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"cytomegalovirus",
"infection... | 2017 | The human cytomegalovirus glycoprotein pUL11 acts via CD45 to induce T cell IL-10 secretion |
Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer’s and Parkinson's . The goal of this work is to provide insights into the structural changes that characterize the kinetic... | Understanding the mechanisms of protein folding and aggregation is of fundamental importance in elucidating the biological function of proteins and their complex . Many advances have been made in our ability to describe protein folding based both on ideas from biophysics and improvements in supercomputing power , yet r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways |
We investigated changes in the spatial distribution of schistosomiasis in Mali following a decade of donor-funded control and a further 12 years without control . National pre-intervention cross-sectional schistosomiasis surveys were conducted in Mali in 1984–1989 ( in communities ) and again in 2004–2006 ( in schools ... | Geostatistical maps are increasingly being used to plan neglected tropical disease control programmes . We investigated the spatial distribution of schistosomiasis in Mali prior to implementation of national donor-funded mass chemotherapy programmes using data from 1984–1989 and 2004–2006 . The 2004–2006 dataset was co... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology/epidemiology",
"infectious",
"diseases/helminth",
"infections",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"infectious",
"diseases/epidemiology",
"and",
"... | 2009 | A Comparative Study of the Spatial Distribution of Schistosomiasis in Mali in 1984–1989 and 2004–2006 |
Adaptor protein ( AP ) complexes regulate clathrin-coated vesicle assembly , protein cargo sorting , and vesicular trafficking between organelles in eukaryotic cells . Because disruption of the various subunits of the AP complexes is embryonic lethal in the majority of cases , characterization of their function in vivo... | We describe a novel genetic syndrome that we named MEDNIK , to designate a disease characterized by mental retardation , enteropathy , deafness , peripheral neuropathy , ichthyosis and keratodermia . This syndrome was found in four French-Canadian families with a common ancestor and is caused by a mutation in the AP1S1... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"dermatology/pediatric",
"skin",
"diseases,",
"including",
"genetic",
"diseases",
"neurological",
"disorders/spinal",
"disorders",
"cell",
"biology",
"neurological",
"disorders",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",
"genomics/gene",
"f... | 2008 | Disruption of AP1S1, Causing a Novel Neurocutaneous Syndrome, Perturbs Development of the Skin and Spinal Cord |
Pseudogenes are usually considered to be completely neutral sequences whose evolution is shaped by random mutations and chance events . It is possible , however , for disrupted genes to generate products that are deleterious due either to the energetic costs of their transcription and translation or to the formation of... | Pseudogenes have traditionally been viewed as evolving in a strictly neutral manner . In bacteria , however , pseudogenes are deleted rapidly from genomes , suggesting that their presence is somehow deleterious . The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"evolutionary",
"biology/genomics",
"genetics",
"and",
"geno... | 2010 | The Extinction Dynamics of Bacterial Pseudogenes |
Alveolar echinococcosis ( AE ) is a life-threatening disease caused by larvae of the fox-tapeworm Echinococcus multilocularis . Crucial to AE pathology is continuous infiltrative growth of the parasite's metacestode stage , which is driven by a population of somatic stem cells , called germinative cells . Current anti-... | The lethal disease AE is characterized by continuous and infiltrative growth of the metacestode larva of the tapeworm E . multilocularis within host organs . This cancer-like progression is exclusively driven by a population of parasite stem cells ( germinative cells ) that have to be eliminated for an effective cure o... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitology",
"developmental",
"biology",
"clinical",
"medicine",
"neglected",
"tropical",
"diseases",
"pharmacol... | 2014 | Targeting Echinococcus multilocularis Stem Cells by Inhibition of the Polo-Like Kinase EmPlk1 |
The gaseous hormone ethylene is one of the master regulators of development and physiology throughout the plant life cycle . Ethylene biosynthesis is stringently regulated to permit maintenance of low levels during most phases of vegetative growth but to allow for rapid peaks of high production at developmental transit... | Like animals , plants produce a number of substances that regulate growth and coordinate developmental transitions and responses to environmental signals . Ethylene gas is one such regulator of the plant life cycle , playing important roles in fruit ripening , pathogen defenses , and the regulation of cell expansion . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology/plant",
"growth",
"and",
"development",
"plant",
"biology/plant",
"biochemistry",
"and",
"physiology",
"genetics",
"and",
"genomics/plant",
"genetics",
"and",
"gene",
"expression"
] | 2011 | Protein Phosphatase 2A Controls Ethylene Biosynthesis by Differentially Regulating the Turnover of ACC Synthase Isoforms |
Human cytomegalovirus ( HCMV ) enters host by glycoprotein B ( gB ) -mediated membrane fusion upon receptor-binding to gH/gL-related complexes , causing devastating diseases such as birth defects . Although an X-ray crystal structure of the recombinant gB ectodomain at postfusion conformation is available , the structu... | Infection by herpesviruses leads to many human diseases , ranging from mild cold sores to devastating cancers . Human cytomegalovirus ( HCMV ) is among the most medically significant herpesviruses and causes birth defects and life-threatening complications in immuno-suppressed individuals . HCMV infection begins with c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"crystal",
"structure",
"viral",
"transmission",
"and",
"infection",
"condensed",
"matter",
"physics",
"microbiology",
"viral",
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"membrane",
"fusion",
"protein",
"structure",
"crystallography",
"cellular",
"structures",
"and",
"organelles",
"viral",
"entry",
... | 2018 | Different functional states of fusion protein gB revealed on human cytomegalovirus by cryo electron tomography with Volta phase plate |
Ubiquitination of the replication clamp proliferating cell nuclear antigen ( PCNA ) at the conserved residue lysine ( K ) 164 triggers postreplicative repair ( PRR ) to fill single-stranded gaps that result from stalled DNA polymerases . However , it has remained elusive as to whether cells engage PRR in response to re... | Genome duplication via the process of DNA replication is a prerequisite for cell division and underlies the propagation of all living organisms . This fundamentally important mechanism has been highly conserved throughout eukaryotic evolution , allowing us to use the relatively simple and genetically tractable Saccharo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Genetic Interactions Implicating Postreplicative Repair in Okazaki Fragment Processing |
Components of promyelocytic leukaemia ( PML ) nuclear bodies ( ND10 ) are recruited to sites associated with herpes simplex virus type 1 ( HSV-1 ) genomes soon after they enter the nucleus . This cellular response is linked to intrinsic antiviral resistance and is counteracted by viral regulatory protein ICP0 . We repo... | Viruses encounter several different defences that impede infection , including acquired immunity mediated by the immune system and innate immunity that includes the synthesis of antiviral proteins through the interferon pathway . In recent years , a third arm of antiviral defence has been described , named intrinsic im... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cellular",
"structures",
"mechanisms",
"of",
"resistance",
"and",
"susceptibility",
"molecular",
"cell",
"biology",
"cell",
"biology",
"virology",
"biology",
"microbiology",
"viral",
"replication",
"cell",
"nucleus"
] | 2011 | SUMO Pathway Dependent Recruitment of Cellular Repressors to Herpes Simplex Virus Type 1 Genomes |
Discovering genetic mechanisms driving complex diseases is a hard problem . Existing methods often lack power to identify the set of responsible genes . Protein-protein interaction networks have been shown to boost power when detecting gene-disease associations . We introduce a Bayesian framework , Conflux , to find di... | Networks and pathway-based methods are commonly used to improve the power of gene detection in associations with complex human diseases . Network diffusion approaches have shown their effectiveness and superior performance in cancer studies . Still , there are many problems such as noise and missingness with currently ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"genetic",
"networks",
"protein",
"interactions",
"protein",
"interaction",
"networks",
"cancers",
"and",
"neoplasms",
"oncology",
"mutation",
"network",
"analysis",
"genome",
"analysis",
"epilepsy",
"computer",
"and",
"informati... | 2017 | Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases |
Alternative splicing is an evolutionary innovation to create functionally diverse proteins from a limited number of genes . SNAP-25 plays a central role in neuroexocytosis by bridging synaptic vesicles to the plasma membrane during regulated exocytosis . The SNAP-25 polypeptide is encoded by a single copy gene , but in... | In evolution , duplication of genes or gene segments appears to be an efficient way to add diverse functions in more complex organisms . The SNAP-25 protein plays an important role in mediating the release of neurotransmitters and hormones . SNAP-25 exists as two variants: SNAP-25a , which is present in early developme... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"cell",
"biology/cell",
"signaling",
"developmental",
"biology/developmental",
"evolution",
"cell",
"biology/neuronal",
"signaling",
"mechanisms",
"cell",
"biology/membranes",
"and",
"sorting",
"physiology/cell",
"signaling",
"neuroscien... | 2008 | An Ancient Duplication of Exon 5 in the Snap25 Gene Is Required for Complex Neuronal Development/Function |
Characterizing the fitness landscape , a representation of fitness for a large set of genotypes , is key to understanding how genetic information is interpreted to create functional organisms . Here we determined the evolutionarily-relevant segment of the fitness landscape of His3 , a gene coding for an enzyme in the h... | An intuitive understanding of protein evolution dictates that , with the exception of adaptive substitutions , amino acid states should be freely exchangeable between the same gene from different species . However , the extent to which this assertion holds true has not been tested in a controlled experiment . Here , we... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [] | 2019 | An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape |
The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation . However , with the exception of hybrid inviability and sterility factors , little is known about the extent of other , more subtle genetic incompatibilities between inc... | Determining the extent of genomic incompatibilities is a pivotal issue in understanding the process of speciation . A controversial topic that has recently sparked debate is whether there are few isolated genetic regions ( so-called “genomic islands of speciation” ) or extensive genetic regions ( “genomic continents of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"processes",
"population",
"genetics",
"biology",
"evolutionary",
"biology",
"genomic",
"evolution",
"evolutionary",
"genetics",
"evolutionary",
"theory"
] | 2012 | Incompatibility and Competitive Exclusion of Genomic Segments between Sibling Drosophila Species |
A major goal of evolutionary developmental biology ( evo-devo ) is to understand how multicellular body plans of increasing complexity have evolved , and how the corresponding developmental programs are genetically encoded . It has been repeatedly argued that key to the evolution of increased body plan complexity is th... | An important question in evolutionary developmental biology is how the complex organisms we see around us have evolved , and how this complexity is encoded in their DNA . An often heard statement is that the gene regulatory networks underlying developmental processes are modular; that is , different functions are carri... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"evolutionary",
"biology",
"computerized",
"simulations",
"developmental",
"biology",
"mathematical",
"computing",
"mathematics",
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"biology",
"biology",
"nonlinear",
"dynamics",
"biophysics",
"physics",
"systems",
"biology",
"computer",
"science",
"computer",
... | 2011 | Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability |
Negative regulation of receptor signaling is essential for controlling cell activation and differentiation . In B-lymphocytes , the down-regulation of B-cell antigen receptor ( BCR ) signaling is critical for suppressing the activation of self-reactive B cells; however , the mechanism underlying the negative regulation... | Mechanisms to shut down B-cell activation are necessary to ensure termination of an immune response when an infection has been cleared . When this negative regulation goes wrong , it can also lead to autoimmunity . To understand how this inhibitory process is regulated , here we utilized knockout mice containing B cell... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | N-WASP Is Essential for the Negative Regulation of B Cell Receptor Signaling |
The mammalian suprachiasmatic nuclei ( SCN ) contain thousands of neurons capable of generating near 24-h rhythms . When isolated from their network , SCN neurons exhibit a range of oscillatory phenotypes: sustained or damping oscillations , or arrhythmic patterns . The implications of this variability are unknown . Ex... | Circadian rhythms are daily , near 24-h oscillations in biological processes that nearly all organisms on Earth experience . Single cells contain a molecular clock that drives circadian rhythms in physiology and , when many cells synchronize in a population , daily behaviors . We hypothesized that small differences in ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biophysic",
"al",
"simulations",
"biology",
"computational",
"biology",
"neuroscience",
"neurophysiology"
] | 2012 | Weakly Circadian Cells Improve Resynchrony |
Mosquito-borne viral diseases cause significant burden in much of the developing world . Although host-virus interactions have been studied extensively in the vertebrate host , little is known about mosquito responses to viral infection . In contrast to mosquitoes of the Aedes and Culex genera , Anopheles gambiae , the... | Mosquito-borne viral diseases are found across the globe and are responsible for numerous severe human infections . In order to develop novel methods for prevention and treatment of these diseases , detailed understanding of the biology of viral infection and transmission is required . Little is known about invertebrat... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"virology",
"immunology",
"biology",
"microbiology"
] | 2012 | Anopheles gambiae Antiviral Immune Response to Systemic O'nyong-nyong Infection |
Taenia solium is a zoonotic cestode parasite which causes human neurocysticercosis . Pigs transmit the parasite by acting as the intermediate host . An intervention was implemented to control transmission of T . solium by pigs in Dalit communities of Banke District , Nepal . Every 3 months , pigs were vaccinated with t... | Neurocysticercosis is a disease caused by a parasitic infection of the brain . The parasite responsible , Taenia solium , is transmitted by pigs where human sanitation is poor and pigs roam freely . Neurocysticercosis is responsible for many cases of epilepsy in people living in poor , developing countries . The feasib... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"neurocysticercosis",
"immunology",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"animal",
"slaughter",
"preventive",
"medicine",
"pharmaceutics",
"neglected",
"tr... | 2019 | Implementation of a practical and effective pilot intervention against transmission of Taenia solium by pigs in the Banke district of Nepal |
The envelope glycoproteins of primate lentiviruses , including human and simian immunodeficiency viruses ( HIV and SIV ) , are heterodimers of a transmembrane glycoprotein ( usually gp41 ) , and a surface glycoprotein ( gp120 ) , which binds CD4 on target cells to initiate viral entry . We have used electron tomography... | Retroviruses such as simian immunodeficiency virus and HIV-1 enter target cells by exploiting the interaction between their surface glycoproteins and cell surface receptors . Knowledge of the structures of these glycoproteins and of the molecular details of their interaction with cell surface receptors is of fundamenta... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"viruses",
"biophysics",
"biochemistry",
"virology"
] | 2007 | Electron Tomography of the Contact between T Cells and SIV/HIV-1: Implications for Viral Entry |
CD8+ cytotoxic T lymphocytes ( CTLs ) are critical for clearing many viral infections , and protective CTL memory can be induced by vaccination with attenuated viruses and vectors . Non-replicating vaccines are typically potentiated by the addition of adjuvants that enhance humoral responses , however few are capable o... | Current respiratory-virus vaccines typically employ non-replicating antigens and rely solely on the generation of humoral responses for protection . Viruses such as influenza can mutate and escape these responses , thereby limiting immunity and necessitating revaccination . Cell-mediated immunity ( CMI ) could provide ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"spleen",
"immunology",
"neuroscience",
"learning",
"and",
"memory",
"vaccines",
"preventive",
"med... | 2016 | Effective Respiratory CD8 T-Cell Immunity to Influenza Virus Induced by Intranasal Carbomer-Lecithin-Adjuvanted Non-replicating Vaccines |
The contribution of regulatory versus protein change to adaptive evolution has long been controversial . In principle , the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or fr... | We present an analysis of the genome sequences of multiple wild house mice . Wild house mice are about ten times more genetically diverse than humans , reflecting the large effective population size of the species . This manifests itself as more effective natural selection acting against deleterious mutations and favou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents |
Norepinephrine , a neuromodulator that activates β-adrenergic receptors ( βARs ) , facilitates learning and memory as well as the induction of synaptic plasticity in the hippocampus . Several forms of long-term potentiation ( LTP ) at the Schaffer collateral CA1 synapse require stimulation of both βARs and N-methyl-D-a... | Noradrenaline is a stress related molecule that facilitates learning and memory when released in the hippocampus . The facilitation of memory is related to modulation of synaptic plasticity , but the mechanisms underlying this modulation are not well understood . We utilize a combination of live cell imaging and comput... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"phosphorylation",
"medicine",
"and",
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"sciences",
"enzymes",
"drugs",
"enzymology",
"neurites",
"simulation",
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"fluorophotometry",
"lyases",
"pharmacology",
"cellular",
"structures",
"and",
"organelles",
"neuronal",
"dendrites",
"research",
"an... | 2016 | Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons |
Influenza Virus ( IV ) pneumonia is associated with severe damage of the lung epithelium and respiratory failure . Apart from efficient host defense , structural repair of the injured epithelium is crucial for survival of severe pneumonia . The molecular mechanisms underlying stem/progenitor cell mediated regenerative ... | Influenza Virus ( IV ) pneumonia causes disruption of the alveolar epithelial barrier , leading to edema formation which severely affects gas exchange . Recovery after IV-induced acute lung injury includes not only innate immune responses to clear virus infection , but also tissue renewal processes to restore the alveo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"flow",
"cytometry",
"organoids",
"medicine",
"and",
"health",
"sciences",
"organ",
"transplantation",
"biological",
"cultures",
"cloning",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"epithelial",
"cells",
"endocrine",
"physiology",
"developmental",
"biology"... | 2016 | Influenza Virus Infects Epithelial Stem/Progenitor Cells of the Distal Lung: Impact on Fgfr2b-Driven Epithelial Repair |
Optimal management of eumycetoma , a severely debilitating chronic progressive fungal infection of skin , disseminating to bone and viscera , remains challenging . Especially , optimal antifungal treatment and duration are ill defined . We conducted a monocentric retrospective study of 11 imported cases of eumycetoma t... | Eumycetoma is a severe chronic progressive fungal infection of skin and ultimately bone or viscera that affect mainly people with low economic status . Optimal treatment of this condition relies on medical and often surgical therapy and remains challenging because of lack of gold standard therapy and high rate of relap... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"subcutaneous",
"mycoses",
"medicine",
"and",
"health",
"sciences",
"mycetoma",
"fungal",
"diseases",
"soft",
"tissue",
"infections"
] | 2014 | Last Generation Triazoles for Imported Eumycetoma in Eleven Consecutive Adults |
A common challenge in systems biology is quantifying the effects of unknown parameters and estimating parameter values from data . For many systems , this task is computationally intractable due to expensive model evaluations and large numbers of parameters . In this work , we investigate a new method for performing se... | Mathematical models in systems biology often have many parameters , such as biochemical reaction rates , whose true values are unknown . When the number of parameters is large , it becomes computationally difficult to analyze their effects and to estimate parameter values from experimental data . This is especially cha... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"markov",
"models",
"simulation",
"and",
"modeling",
"fungi",
"model",
"organisms",
"probability",
"distribution",
"mathematics",
"statistics",
"(mathematics)",
"algebra",
"experimental",
"organism",
"systems",
"cellular",
"structures",
"and",
"organelles",
"polynomials",
... | 2018 | Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization |
Given current neglect for Chagas disease in public health programs in Mexico , future healthcare and economic development policies will need a more robust model to analyze costs and impacts of timely clinical attention of infected populations . A Markov decision model was constructed to simulate the natural history of ... | Chagas disease is caused by the flagellated protozoan parasite Trypanosoma cruzi , vectored in Mexico in both rural and urban areas via one of 18 triatomine bug species . Despite ample morbidity and mortality evidence , however , health policy managers in Mexico have continued to neglect prevention , control and clinic... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"health",
"economics",
"social",
"sciences",
"economics",
"health",
"care"
] | 2014 | Opportunity Cost for Early Treatment of Chagas Disease in Mexico |
Humans and dogs are both affected by the allergic skin disease atopic dermatitis ( AD ) , caused by an interaction between genetic and environmental factors . The German shepherd dog ( GSD ) is a high-risk breed for canine AD ( CAD ) . In this study , we used a Swedish cohort of GSDs as a model for human AD . Serum IgA... | Humans and dogs are both affected by the allergic skin disease atopic dermatitis ( AD ) , caused by an interaction between genetic and environmental factors . The German shepherd dog ( GSD ) is a high-risk breed for canine AD ( CAD ) , also affected by low serum IgA levels . A Swedish cohort of GSDs was used as a model... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genome",
"analysis",
"tools",
"veterinary",
"immunology",
"animal",
"genetics",
"veterinary",
"diagnostics",
"genetics",
"biology",
"genomics",
"genetics",
"of",
"disease",
"computational",
"biology",
"small",
"animal",
"care",
... | 2013 | Genome-Wide Analysis in German Shepherd Dogs Reveals Association of a Locus on CFA 27 with Atopic Dermatitis |
The Toxoplasma gondii genome contains two aromatic amino acid hydroxylase genes , AAH1 and AAH2 encode proteins that produce L-DOPA , which can serve as a precursor of catecholamine neurotransmitters . It has been suggested that this pathway elevates host dopamine levels thus making infected rodents less fearful of the... | Toxoplasma gondii is an intracellular parasite that infects up to one-quarter of humans worldwide . Although it can infect virtually any warm-blooded animal , its definitive host is the cat where the sexual cycle occurs in enterocytes of the small intestine , producing microscopic , durable oocysts that are shed in fec... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"oocysts",
"pathology",
"and",
"laboratory",
"medicine",
"toxoplasma",
"gondii",
"vertebrates",
"cloning",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"animals",
"mammals",
"parasitology",
"apicomplexa... | 2017 | The aromatic amino acid hydroxylase genes AAH1 and AAH2 in Toxoplasma gondii contribute to transmission in the cat |
Release factors ( RFs ) govern the termination phase of protein synthesis . Human mitochondria harbor four different members of the class 1 RF family: RF1Lmt/mtRF1a , RF1mt , C12orf65 and ICT1 . The homolog of the essential ICT1 factor is widely distributed in bacteria and organelles and has the peculiar feature in hum... | Mammalian mitochondrial ICT1 , a bacterial ArfB homolog , is interestingly an integral component of the mitoribosome ( MRPL58 ) . The mechanism of ribosome rescue by this factor was obscure and is addressed here . Utilizing a homologous mitochondria system of purified components we demonstrate that the integrated ICT1 ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"cell",
"biology",
"biochemistry",
"biology",
"and",
"life",
"sciences",
"cell",
"biology"
] | 2014 | Ribosome Rescue and Translation Termination at Non-Standard Stop Codons by ICT1 in Mammalian Mitochondria |
Enhancers and promoters often contain multiple binding sites for the same transcription factor , suggesting that homotypic clustering of binding sites may serve a role in transcription regulation . Here we show that clustering of binding sites for the transcription termination factor TTF-I downstream of the pre-rRNA co... | The sequence-specific binding of proteins to regulatory regions controls gene expression . Binding sites for transcription factors are rather short and present several million times in large genomes . However , only a small number of these binding sites are functionally important . How proteins can discriminate and sel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites |
Transcription factor binding site ( s ) ( TFBS ) gain and loss ( i . e . , turnover ) is a well-documented feature of cis-regulatory module ( CRM ) evolution , yet little attention has been paid to the evolutionary force ( s ) driving this turnover process . The predominant view , motivated by its widespread occurrence... | Transcription factor binding sites ( TFBS ) turnover ( i . e . lineage-specific gain and loss ) is a well-documented phenomenon in eukaryote cis-regulatory modules ( CRM ) . The wide spread of the phenomenon and the appearance of conserved expression patterns for diverged orthologous CRM led to the standing view that t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"natural",
"selection",
"neutral",
"theory",
"population",
"genetics",
"biology",
"evolutionary",
"biology"
] | 2011 | Does Positive Selection Drive Transcription Factor Binding Site
Turnover? A Test with Drosophila Cis-Regulatory Modules |
Merkel cell carcinoma ( MCC ) is an aggressive skin cancer with a high propensity for recurrence and metastasis . Merkel cell polyomavirus ( MCPyV ) is recognised as the causative factor in the majority of MCC cases . The MCPyV small tumour antigen ( ST ) is considered to be the main viral transforming factor , however... | The majority of cancer-related deaths occur due to metastatic disease . Therefore , understanding the molecular and cellular mechanisms underlying the process of metastasis is essential to developing new therapeutic interventions to improve cancer patient survival . Merkel cell carcinoma ( MCC ) is an aggressive and hi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"motility",
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"and",
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"probe",
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"hek",
"293",
"cells",
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"cultures",
"immunoblotting",
"basic",
"cancer",
"research",
"membrane",
"proteins",
"oncology",
"developmental",
"biology",
"molecular"... | 2018 | Cellular sheddases are induced by Merkel cell polyomavirus small tumour antigen to mediate cell dissociation and invasiveness |
Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide , including syphilis , leptospirosis , relapsing fever , and Lyme borreliosis . They navigate efficiently through dense extracellular matrix and cross the blood–brain barrier by unknown mechanisms . Due to their slend... | Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide , including syphilis , leptospirosis , relapsing fever , and Lyme disease . They exhibit an unusual form of motility and can infect many different tissues; however , the mechanism by which they disseminate from the bl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology"
] | 2008 | Real-Time High Resolution 3D Imaging of the Lyme Disease Spirochete Adhering to and Escaping from the Vasculature of a Living Host |
The molecular mechanisms that underlie asymmetric PTEN distribution at the posterior of polarized motile cells and regulate anterior pseudopod formation were addressed by novel single-molecule tracking analysis . Heterogeneity in the lateral mobility of PTEN on a membrane indicated the existence of three membrane-bindi... | Signaling molecules can adopt multiple states that are characterized by intermolecular interactions and chemical modifications , and can thus describe a mechanistic basis for signal transduction . To understand the molecular mechanisms driving signaling reactions , the kinetics and spatial regulation of the state trans... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology",
"phosphoinositide",
"signal",
"transduction",
"model",
"organisms",
"cell",
"movement",
"signaling",
"signaling",
"pathways",
"biophysics",
"simulations",
"dictyostelium",
"discoideum",
"signaling",
"in",
"cellular",
"processes",
"biophysics",
"theory",
"pro... | 2013 | Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions |
Both type I interferon ( IFN-I ) and CD40 play a significant role in various infectious diseases , including malaria and autoimmune disorders . CD40 is mostly known to function in adaptive immunity , but previous observations of elevated CD40 levels early after malaria infection of mice led us to investigate its roles ... | Malaria parasites infect millions of people and can cause severe disease with diverse symptoms . No highly effective vaccine is available to prevent malaria infection , largely due to the lack of understanding of the molecular mechanisms of host-parasite interactions . Here we investigated the interaction of two import... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
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"luciferase",
"pathology",
"and",
"laboratory",
"medicine",
"enzymes",
"293t",
"cells",
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"tropical",
"diseases",
"enzymology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"immune",
"receptor",
"si... | 2016 | Increased CD40 Expression Enhances Early STING-Mediated Type I Interferon Response and Host Survival in a Rodent Malaria Model |
The bacterial flagellar type III export apparatus utilizes ATP and proton motive force ( PMF ) to transport flagellar proteins to the distal end of the growing flagellar structure for self-assembly . The transmembrane export gate complex is a H+–protein antiporter , of which activity is greatly augmented by an associat... | For construction of the bacterial flagellum beyond the inner and outer membranes , the flagellar type III export apparatus transports fourteen flagellar proteins with their copy numbers ranging from a few to tens of thousands to the distal growing end of the flagellar structure . The export apparatus consists of a tran... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"protein",
"transport",
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"immunoblotting",
"microbiology",
... | 2016 | The Bacterial Flagellar Type III Export Gate Complex Is a Dual Fuel Engine That Can Use Both H+ and Na+ for Flagellar Protein Export |
Despite the current debate about the computational role of experimentally observed precise spike patterns it is still theoretically unclear under which conditions and how they may emerge in neural circuits . Here , we study spiking neural networks with non-additive dendritic interactions that were recently uncovered in... | Most nerve cells in neural circuits communicate by sending and receiving short stereotyped electrical pulses called action potentials or spikes . Recent neurophysiological experiments found that under certain conditions the neuronal dendrites ( branched projections of the neuron that transmit inputs from other neurons ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"neuroscience",
"biology",
"neuroscience"
] | 2012 | Non-Additive Coupling Enables Propagation of Synchronous Spiking Activity in Purely Random Networks |
Microglia are the immune cells of the brain . In the absence of pathological insult , their highly motile processes continually survey the brain parenchyma and transiently contact synaptic elements . Aside from monitoring , their physiological roles at synapses are not known . To gain insight into possible roles of mic... | Microglia are important players in immune responses to brain injury . In the event of pathological insults , microglia rapidly become activated and acquire the ability to release various inflammatory molecules that influence neuronal survival as well as synaptic function and plasticity . Similarly to macrophages in oth... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/neuronal",
"and",
"glial",
"cell",
"biology",
"neuroscience/sensory",
"systems",
"immunology/immune",
"response",
"neuroscience/neurodevelopment",
"cell",
"biology/extra-cellular",
"matrix",
"neuroscience/neuronal",
"and",
"glial",
"cell",
"biology",
"neuroscie... | 2010 | Microglial Interactions with Synapses Are Modulated by Visual Experience |
We undertook a population genetics analysis of the tsetse fly Glossina palpalis gambiensis , a major vector of sleeping sickness in West Africa , using microsatellite and mitochondrial DNA markers . Our aims were to estimate effective population size and the degree of isolation between coastal sites on the mainland of ... | Guinea is the country with the highest prevalence of sleeping sickness in West Africa , and we undertook a population genetics analysis there of the most dangerous tsetse fly species of West Africa , Glossina palpalis gambiensis . Our aims were to estimate effective population size and the degree of isolation between c... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"public",
"health",
"and",
"epidemiology",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2009 | The Population Structure of Glossina palpalis gambiensis from Island and Continental Locations in Coastal Guinea |
Individuals living in areas endemic for helminths are commonly infected with multiple species . Despite increasing emphasis given to the potential health impacts of polyparasitism , few studies have investigated the relative importance of household and environmental factors on the risk of helminth co-infection . Here ,... | Helminth species such as Necator americanus and Schistosoma mansoni are among the most prevalent of chronic human infections in the developing world . Individuals living in endemic areas are commonly infected with both species . Although the implications of being co-infected with helminths are increasingly recognized ,... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases"
] | 2008 | Human Helminth Co-Infection: Analysis of Spatial Patterns and Risk Factors in a Brazilian Community |
Over the past ten years the incidence of pertussis in the United States ( U . S . ) has risen steadily , with 2012 seeing the highest case number since 1955 . There has also been a shift over the same time period in the age group reporting the largest number of cases ( aside from infants ) , from adolescents to 7–11 ye... | Over the past ten years the incidence of pertussis in the United States ( U . S . ) has risen steadily , with 2012 seeing the highest case number since 1955 . There has also been a shift over the same time period in the age group reporting the largest number of cases ( aside from infants ) , from adolescents to 7–11 ye... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States |
Mathematical models that integrate multi-scale physiological data can offer insight into physiological and pathophysiological function , and may eventually assist in individualized predictive medicine . We present a methodology for performing systematic analyses of multi-parameter interactions in such complex , multi-s... | As our understanding of the human body at all scales increases , the construction of a “Virtual Physiological Human” is becoming more feasible and will be an important step towards individualized diagnosis and treatment . As computational models increase in complexity to reflect this growth in understanding , analysis ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"systems",
"biology",
"physiological",
"processes",
"homeostasis",
"theoretical",
"biology",
"physiology",
"integrative",
"physiology",
"biology",
"anatomy",
"and",
"physiology",
"cardiovascular",
"system",
"computational",
"biology",
"circulatory",
"physiology"
] | 2012 | Virtual Patients and Sensitivity Analysis of the Guyton Model of Blood Pressure Regulation: Towards Individualized Models of Whole-Body Physiology |
Chikungunya virus ( CHIKV ) is a positive sense , single stranded RNA virus in the genus Alphavirus , and the etiologic agent of epidemics of severe arthralgia in Africa , Asia , Europe and , most recently , the Americas . CHIKV causes chikungunya fever ( CHIK ) , a syndrome characterized by rash , fever , and debilita... | Chikungunya virus ( CHIKV ) , the etiologic agent of chikungunya fever ( CHIK ) , is a positive sense , single-stranded RNA virus in the genus Alphavirus . Chikungunya fever begins as a flu-like illness , which progresses to severe arthralgia and debilitating arthritis . This syndrome is often self-limited and rarely f... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | A Rodent Model of Chikungunya Virus Infection in RAG1 -/- Mice, with Features of Persistence, for Vaccine Safety Evaluation |
African trypanosomes are devastating human and animal pathogens that cause significant human mortality and limit economic development in sub-Saharan Africa . Studies of trypanosome biology generally consider these protozoan parasites as individual cells in suspension cultures or in animal models of infection . Here we ... | African trypanosomes , e . g . Trypanosoma brucei , and related kinetoplastid parasites cause morbidity and mortality in several million people worldwide . Trypanosomes are protists and are thus generally considered to behave as single-celled microorganisms . In other microorganisms , social interactions among individu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"cell",
"biology",
"microbiology/parasitology"
] | 2010 | Social Motility in African Trypanosomes |
Skeletal muscles provide metazoans with the ability to feed , reproduce and avoid predators . In humans , a heterogeneous group of genetic diseases , termed muscular dystrophies ( MD ) , lead to skeletal muscle dysfunction . Mutations in the gene encoding Caveolin-3 , a principal component of the membrane micro-domains... | Membrane structures are critical to skeletal muscle excitation-contraction coupling , and disruptions in key membrane proteins can lead to muscular dystrophy . Caveolae , micro-domains in the cell membrane , are known to be important in forming muscle-specific membrane structures such as the T-tubule network and play a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"swimming",
"skeletal",
"muscles",
"vertebrates",
"animals",
"biomechanics",
"biological",
"locomotion",
"animal",
"models",
"osteichthyes",
"developmental",
"biology",
"muscle",
"proteins",
"model",
"organisms",
"skeletal",
"muscl... | 2016 | Cavin4b/Murcb Is Required for Skeletal Muscle Development and Function in Zebrafish |
Traction forces exerted by adherent cells on their microenvironment can mediate many critical cellular functions . Accurate quantification of these forces is essential for mechanistic understanding of mechanotransduction . However , most existing methods of quantifying cellular forces are limited to single cells in iso... | Adherent cells sense , transduce and respond to their microenvironment by generating traction forces on their surroundings . To accurately understand these mechanotransduction processes , it is critical to have a robust and reliable method for traction force visualization and quantification . However , most cell tracti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"physics",
"mechanical",
"engineering",
"nanoengineering",
"classical",
"mechanics",
"materials",
"science",
"engineering",
"and",
"technology",
"biology",
"and",
"life",
"sciences",
"biomaterials",
"computational",
"biology",
"physical",
"sciences",
"bioph... | 2014 | A Novel Cell Traction Force Microscopy to Study Multi-Cellular System |
CD4 T cells harboring HIV-1/SIV represent a formidable hurdle to eradicating infection , and yet their detailed phenotype remains unknown . Here we integrate two single-cell technologies , flow cytometry and highly multiplexed quantitative RT-PCR , to characterize SIV-infected CD4 T cells directly ex vivo . Within indi... | HIV-1 , and its simian counterpart , SIV , infect and kill CD4 T cells , resulting in their massive depletion that ultimately leads to AIDS in the absence of antiretroviral therapy . With effective therapy , these cells are largely preserved , but a subset harbors latent virus that can persist for decades and reemerge ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"t",
"helper",
"cells",
"mhc",
"class",
"i",
"genes",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency",
... | 2017 | Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells |
Innate immune responses in general , and type I interferons ( T1IFNs ) in particular , play an important and often essential role during primary viral infections , by directly combatting the virus and by maximizing the primary adaptive immune response . Several studies have suggested that T1IFNs also contribute very su... | Type I interferons ( T1IFNs ) are key pleiotropic anti-viral cytokines , necessary to effectively promote and coordinate immune responses and control a number of primary viral infections . In their absence , the expansion and later memory formation of anti-viral T cells is severely curtailed . T1IFNs are also thought t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"cytokines",
"viral",
"transmission",
"and",
"infection",
"spleen",
"immunology",
"microbiology",
"neuroscience",
"learning",
"and",
"me... | 2016 | Type I IFN Signaling Is Dispensable during Secondary Viral Infection |
Within an isogenic population , even in the same extracellular environment , individual cells can exhibit various phenotypic states . The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood , especially in the presence of positiv... | Identifying the mechanism underlying the coexistence of multiple stable phenotypic states has been a challenging scientific problem for more than half a century , and an appropriate mathematical model at the single-cell level is also in high demand . Single-cell measurements conducted in the past ten years have shown t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"chemical",
"compounds",
"disaccharides",
"gene",
"regulation",
"enzymology",
"operons",
"carbohydrates",
"organic",
"compounds",
"dna",
"transcription",
"probability",
"distribution",
"mathematics",
"dna",
"enzyme",
"kinetics",
"chemical",
"dissociation",
"lac",
"operon",
... | 2018 | Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state |
The Sigatoka disease complex , caused by the closely-related Dothideomycete fungi Pseudocercospora musae ( yellow sigatoka ) , Pseudocercospora eumusae ( eumusae leaf spot ) , and Pseudocercospora fijiensis ( black sigatoka ) , is currently the most devastating disease on banana worldwide . The three species emerged on... | Understanding the evolutionary and genomic changes involved in the emergence of new pathogens and shifts in virulence spectra is vital for deciphering the biological process of disease emergence and for designing new and effective disease control methods . In this study , we employed comparative genomics in order to ex... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"bananas",
"genome",
"evolution",
"fungal",
"genetics",
"plant",
"science",
"phylogenetic",
"analysis",
"crops",
"plant",
"pathology",
"molecular",
"biology",
"techniques",
"plants",
"research",
"and",
"analysis",
"methods",
"mycology",
"genome",
"complexity",
"crop",
... | 2016 | Comparative Genomics of the Sigatoka Disease Complex on Banana Suggests a Link between Parallel Evolutionary Changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and Increased Virulence on the Banana Host |
The chiasma is a structure that forms between a pair of homologous chromosomes by crossover recombination and physically links the homologous chromosomes during meiosis . Chiasmata are essential for the attachment of the homologous chromosomes to opposite spindle poles ( bipolar attachment ) and their subsequent segreg... | Gametes form through a special type of cell division called meiosis . During meiosis , two nuclear divisions take place successively; the first division is specific only to meiosis , in that homologous chromosomes segregate from each other . Homologous chromosome segregation requires physical association of the homolog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology/centromeres",
"genetics",
"and",
"genomics/chromosome",
"biology",
"cell",
"biology/cytoskeleton"
] | 2011 | Chiasmata Promote Monopolar Attachment of Sister Chromatids and Their Co-Segregation toward the Proper Pole during Meiosis I |
Little is known about the presence/absence and prevalence of Rickettsia spp , Bartonella spp . and Yersinia pestis in domestic and urban flea populations in tropical and subtropical African countries . Fleas collected in Benin , the United Republic of Tanzania and the Democratic Republic of the Congo were investigated ... | Fleas are associated with many bacterial diseases such as rickettsioses , bartonelloses and plague . These diseases may be severe , and little is known about their prevalence . Accordingly , we believe that our data shed light on the problem of unexplained fevers in tropical and subtropical African areas . Using molecu... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"disease",
"surveillance",
"plant",
"science",
"medicine",
"and",
"health",
"sciences",
"clinical",
"epidemiology",
"disease",
"dynamics",
"epidemiology",
"vector",
"biology",
"disease",
"surveillance",
"plant",
"pathology",
"biology",
"and",
"life",
"scie... | 2014 | Detection of Rickettsia felis, Rickettsia typhi, Bartonella Species and Yersinia pestis in Fleas (Siphonaptera) from Africa |
Despite major attempts to prevent cholera transmission , millions of people worldwide still must address this devastating disease . Cholera research has so far mainly focused on the causative agent , the bacterium Vibrio cholerae , or on disease treatment , but rarely were results from both fields interconnected . Inde... | Cholera research has so far mainly focused on the causative agent , the bacterium Vibrio cholerae , or on disease treatment , but rarely were results from both fields interconnected . Indeed , the treatment of this severe diarrheal disease is mostly accomplished by oral rehydration therapy ( ORT ) . ORT aims at rehydra... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"bacterial",
"diseases",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"cholera",
"population",
"modeling",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"and",
"life",
"sciences",
"microbiology",
"infectious",
"disease",
"modeling",... | 2014 | Glucose- but Not Rice-Based Oral Rehydration Therapy Enhances the Production of Virulence Determinants in the Human Pathogen Vibrio cholerae |
The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand , thus avoiding accumulating somatic mutations . However , quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo . Here we show tha... | Cairn proposed in 1975 that upon proliferation , cells might not segregate DNA strands randomly into daughter cells , but preferentially keep the ancestral ( blue print ) template strand in stem cells . This mechanism would allow to drastically reduce the rate of mutation accumulation in human tissues . Testing the hyp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"small",
"intestine",
"medicine",
"and",
"health",
"sciences",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"neuroscience",
"cell",
"differentiation",
"oncology",
"mutation",
"developmental",
"biology",
"stem",
"cells",
"digestive",
"system",
"anim... | 2018 | Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates |
Protein modifications regulate both DNA repair levels and pathway choice . How each modification achieves regulatory effects and how different modifications collaborate with each other are important questions to be answered . Here , we show that sumoylation regulates double-strand break repair partly by modifying the e... | Proper repair of DNA lesions is crucial for cell growth and organism development . Both the choice and capacity of DNA repair pathways are tightly regulated in response to environmental cues and cell cycle phase . Recent work has uncovered the importance of protein modifications , such as phosphorylation and sumoylatio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences"
] | 2015 | Sumoylation Influences DNA Break Repair Partly by Increasing the Solubility of a Conserved End Resection Protein |
Timing of cell division is coordinated by the Septation Initiation Network ( SIN ) in fission yeast . SIN activation is initiated at the two spindle pole bodies ( SPB ) of the cell in metaphase , but only one of these SPBs contains an active SIN in anaphase , while SIN is inactivated in the other by the Cdc16-Byr4 GAP ... | Rod shaped fission yeast cells , as the name suggests , divide by medial fission . The proper timing of this cytokinesis and septation event is controlled by a signaling pathway called the Septum Initiation Network , or SIN . The SIN is activated only after chromosomes start to separate in anaphase . At this stage , th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"model",
"organisms",
"cell",
"division",
"cytokinesis",
"yeast",
"and",
"fungal",
"models",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology"
] | 2013 | Dynamics of SIN Asymmetry Establishment |
The cortex processes stimuli through a distributed network of specialized brain areas . This processing requires mechanisms that can route neuronal activity across weakly connected cortical regions . Routing models proposed thus far are either limited to propagation of spiking activity across strongly connected network... | The cortex is a highly modular structure with a large number of functionally specialized areas that communicate with each other through long-range cortical connections . It is has been suggested that communication between spiking neuronal networks ( SNNs ) requires synchronization of spiking activity which is either pr... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"neuroscience",
"biology",
"and",
"life",
"sciences",
"computational",
"biology"
] | 2014 | Communication through Resonance in Spiking Neuronal Networks |
Interleukin 18 ( IL18 ) is a cytokine that plays an important role in inflammation as well as host defense against microbes . Mammals encode a soluble inhibitor of IL18 termed IL18 binding protein ( IL18BP ) that modulates IL18 activity through a negative feedback mechanism . Many poxviruses encode homologous IL18BPs ,... | Interleukin 18 ( IL18 ) is an important cytokine in inflammation and immunity . Mammals and poxviruses encode homologous inhibitory proteins of IL18 , named IL18BPs , which regulate IL18 activity and , in the case of the viral proteins , contribute to virulence . Previous structural and functional studies revealed resi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"protein",
"chemistry",
"macromolecular",
"assemblies",
"biology",
"computational",
"biology",
"biophysics",
"macromolecular",
"structure",
"analysis"
] | 2012 | A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein |
Molecular interactions between killer immunoglobulin-like receptors ( KIRs ) and their MHC class I ligands play a central role in the regulation of natural killer ( NK ) cell responses to viral pathogens and tumors . Here we identify Mamu-A1*00201 ( Mamu-A*02 ) , a common MHC class I molecule in the rhesus macaque with... | NK cells provide an important first line of defense against infectious diseases and tumors by virtue of their ability to kill infected or malignant cells without prior sensitization . NK cell activation is regulated in part through interactions between KIRs expressed on the surface of NK cells and their MHC class I lig... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/immunodeficiency",
"viruses",
"immunology/immune",
"response",
"microbiology/innate",
"immunity",
"immunology/innate",
"immunity",
"virology/animal",
"models",
"of",
"infection",
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"infectious",
"diseases/viral",
... | 2011 | KIR Polymorphisms Modulate Peptide-Dependent Binding to an MHC Class I Ligand with a Bw6 Motif |
Chromosomal organization in 3D plays a central role in regulating cell-type specific transcriptional and DNA replication timing programs . Yet it remains unclear to what extent the resulting long-range contacts depend on specific molecular drivers . Here we propose a model that comprehensively assesses the influence on... | Chromosomal DNA is tightly packed in three dimensions ( 3D ) such that a 2-meter long human genome can fit into a microscopic nucleus . Recent studies have revealed that such packing of DNA is not random but instead structured into functional DNA loops . Those loops are essential to numerous key processes in the cell ,... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"protein",
"interactions",
"dna-binding",
"proteins",
"enzymology",
"animals",
"invertebrate",
"genomics",
"animal",
"models",
"insulators",
"drosophila",
"melanogaster",
"model",
"organisms",
"materials",
"science",
"experimental",
"organism",
"systems",
"... | 2017 | Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach |
The Kaposi's sarcoma-associated herpesvirus ( KSHV ) genome encodes a G protein-coupled receptor ( vGPCR ) . vGPCR is a ligand-independent , constitutively active signaling molecule that promotes cell growth and proliferation; however , it is not clear how vGPCR is negatively regulated . We report here that the KSHV K7... | Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma . KSHV is also found in primary effusion lymphoma and multicentric Castleman's disease , rare lymphoproliferative diorders associated with immuno-suppression . The KSHV genome encodes a G protein-coupled receptor ( vGPCR ) tha... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis"
] | 2008 | Kaposi's Sarcoma-Associated Herpesvirus K7 Induces Viral G Protein-Coupled Receptor Degradation and Reduces Its Tumorigenicity |
St . Louis encephalitis virus ( SLEV ) is a causative agent of encephalitis in humans in the Western hemisphere . SLEV is a positive-sense RNA virus that belongs to the Flavivirus genus , which includes West Nile encephalitis virus , Japanese encephalitis virus , Dengue virus and other medically important viruses . Rec... | St . Louis encephalitis virus ( SLEV ) , a member of the Flavivirus genus , which includes West Nile encephalitis virus , Japanese encephalitis virus , Dengue virus , and other medically important viruses , is a cause of encephalitis in humans and animals . SLEV is considered endemic in the Americas , and currently the... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Isolation of Saint Louis Encephalitis Virus from a Horse with Neurological Disease in Brazil |
Typhoid fever is endemic in many developing countries . In the early 20th century , newly industrializing countries including the United States successfully controlled typhoid as water treatment ( chlorination/sand filtration ) and improved sanitation became widespread . Enigmatically , typhoid remained endemic through... | Typhoid fever was successfully controlled in Santiago , Chile , after a series of interventions including vaccination with a live oral vaccine ( Ty21a ) , and an environmental sanitation improvement , when a ban was put on the irrigation of salad vegetable crops with untreated sewage . Data collected during this period... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"age",
"distribution",
"immunology",
"microbiology",
"salmonella",
"typhi",
"health",
"care",
"vaccines",
"preventive",
"medicine",
"bacterial",
"diseases",
"signs",
"and... | 2018 | Typhoid fever in Santiago, Chile: Insights from a mathematical model utilizing venerable archived data from a successful disease control program |
The extent of epigenetic variation is currently well documented , but the number of natural epialleles described so far remains very limited . Determining the relevance of epigenetic changes for natural variation is an important question of research that we investigate by isolating natural epialleles segregating in Ara... | Epialleles are gene variants based on epigenetic marks stably transmitted between generations . Most of the known epialleles existing in the wild were described in plant populations but very few are associated with phenotypes or agronomical traits . In this study , we isolated a new natural epiallele resulting from the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chromosome",
"5",
"biotechnology",
"brassica",
"chromosome",
"1",
"plant",
"science",
"model",
"organisms",
"experimental",
"organism",
"systems",
"plant",
"genomics",
"epigenetics",
"dna",
"molecular",
"biology",
"techniques",
"plants",
"dna",
"methylation",
"chromati... | 2017 | An Arabidopsis Natural Epiallele Maintained by a Feed-Forward Silencing Loop between Histone and DNA |
In Tunisia , almost 77% of clinically and bacteriologically diagnosed cases of extrapulmonary tuberculosis ( EPTB ) are zoonotic TB , caused by M . bovis . Although several studies have analyzed bovine TB in cattle in Tunisia , no study has evaluated the risk of transmission to humans in such an endemic country . We ai... | In South Tunisia , the prevalence of bovine TB is high with Mycobacterium bovis as causative agent and cattle as reservoir of the bacteria . However as previously mentioned in several studies , M . bovis is also responsible for human extrapulmonary tuberculosis ( EPTB ) cases in South Tunisia . Despite the veterinary a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"livestock",
"medicine",
"and",
"health",
"sciences",
"milk",
"body",
"fluids",
"population",
"genetics",
"geographical",
"locations",
"tropical",
"diseases",
"diet",
"bacterial",
"diseases",
"nutrition",
"population",
"biology",
"bacteria",
"africa",
"infectious",
"dis... | 2019 | A first insight into genetic diversity of Mycobacterium bovis isolated from extrapulmonary tuberculosis patients in South Tunisia assessed by spoligotyping and MIRU VNTR |
The molecular complexity within a cell may be seen as an evolutionary response to the external complexity of the cell’s environment . This suggests that the external environment may be harnessed to interrogate the cell’s internal molecular architecture . Cells , however , are not only nonlinear and non-stationary , but... | We have developed a cellular interrogation methodology that combines programmable microfluidics , fluorescence microscopy and mathematical analysis and have used it to discriminate between models of repetitive Ca2+ spiking in HeLa cells . Our approach exploits the natural variability in response of individual cells in ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurochemistry",
"classical",
"mechanics",
"chemical",
"compounds",
"fluid",
"mechanics",
"engineering",
"and",
"technology",
"hela",
"cells",
"signal",
"processing",
"biological",
"cultures",
"mathematical",
"models",
"neuroscience",
"organic",
"compounds",
"simulation",
... | 2016 | Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling |
Total internal reflection fluorescence microscopy ( TIR-FM ) has become a powerful tool for studying clathrin-mediated endocytosis . However , due to difficulties in tracking and quantifying their heterogeneous dynamic behavior , detailed analyses have been restricted to a limited number of selected clathrin-coated pit... | Clathrin-mediated endocytosis is the major pathway for the uptake of molecules into eukaryotic cells and is regulated by the GTPase dynamin . Adaptor proteins recruit clathrin to the plasma membrane , where clathrin-coated pits capture transmembrane cargo molecules , again via adaptors . The pits invaginate and pinch o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology"
] | 2009 | Cargo and Dynamin Regulate Clathrin-Coated Pit Maturation |
During various inflammatory processes circulating cytokines including IL-6 , IL-1β , and TNFα elicit a broad and clinically relevant impairment of hepatic detoxification that is based on the simultaneous downregulation of many drug metabolizing enzymes and transporter genes . To address the question whether a common me... | During inflammation , circulating proinflammatory cytokines such as TNFα , IL-1ß , and IL-6 , which are produced by , e . g . , Kupffer cells , macrophages , or tumor cells , play important roles in hepatocellular signaling pathways and in the regulation of cellular homeostasis . In particular , these cytokines are res... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling |
The parasite Giardia lamblia must remain attached to the host small intestine in order to proliferate and subsequently cause disease . However , little is known about the factors that may cause detachment in vivo , such as changes in the aqueous environment . Osmolality within the proximal small intestine can vary by n... | The single-celled organism Giardia lamblia colonizes the small intestine of a wide variety of hosts , including humans . Giardiasis infections can cause severe gastrointestinal symptoms and pose a major health concern in the developing world . Giardia are known to attach robustly to a variety of surfaces , but the cond... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/protozoal",
"infections",
"gastroenterology",
"and",
"hepatology/gastrointestinal",
"infections",
"microbiology/parasitology"
] | 2008 | Tonic Shock Induces Detachment of Giardia lamblia |
The development of primordial germ cells ( PGCs ) involves several waves of epigenetic reprogramming . A major step is following specification and involves the transition from the stably suppressive histone modification H3K9me2 to the more flexible , still repressive H3K27me3 , while PGCs are arrested in G2 phase of th... | Primordial germ cells ( PGCs ) are the origin of sperm and oocytes , and are responsible for transferring genetic information to the next generation faithfully . PGCs are first specified from pluripotent epiblast cells early in embryonic development . Second , they reprogram their epigenetic signature by changing histo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | A Critical Function of Mad2l2 in Primordial Germ Cell Development of Mice |
Human genetic factors such as blood group antigens may affect the severity of infectious diseases . Presence of specific ABO and Lewis blood group antigens has been shown previously to be associated with the risk of different enteric infections . The aim of this study was to determine the relationship of the Lewis bloo... | Cholera remains a severe diarrheal disease , capable of causing extensive outbreaks and high mortality . Blood group is one of the genetic factors determining predisposition to disease , including infectious diseases . Expression of different Lewis or ABO blood group types has been shown to be associated with risk of d... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"immunology",
"biology"
] | 2011 | Individuals with Le(a+b−) Blood Group Have Increased Susceptibility to Symptomatic Vibrio cholerae O1 Infection |
Recognition of single-stranded DNA ( ssDNA ) or single-stranded RNA ( ssRNA ) is important for many fundamental cellular functions . A variety of single-stranded DNA-binding proteins ( ssDBPs ) and single-stranded RNA-binding proteins ( ssRBPs ) have evolved that bind ssDNA and ssRNA , respectively , with varying degre... | Quantifying bimolecular self-assembly is pivotal to understanding cellular function . In recent years , a large progress has been made in understanding the structure and biophysics of protein-protein interactions . Particularly , various computational tools are available for predicting these structures and to estimate ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2019 | Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins |
Mucosal-Associated Invariant T ( MAIT ) cells , present in high frequency in airway and other mucosal tissues , have Th1 effector capacity positioning them to play a critical role in the early immune response to intracellular pathogens , including Mycobacterium tuberculosis ( Mtb ) . MR1 is a highly conserved Class I-l... | Tuberculosis , caused by the bacterium Mycobacterium tuberculosis ( Mtb ) , remains a global health concern , with an estimated 9 million new cases and 1 . 5 million deaths each year . Mucosal-associated invariant T ( MAIT ) cells were recently identified as a non-classical CD8+ T cell subset that responds to intracell... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"antigen",
"presentation",
"immune",
"cells",
"enzyme-linked",
"immunoassays",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"gene",
"regulation",
"ant... | 2016 | Endosomal MR1 Trafficking Plays a Key Role in Presentation of Mycobacterium tuberculosis Ligands to MAIT Cells |
Free-living amoebae are present worldwide . They can survive in different environment causing human diseases in some instances . Acanthamoeba sp . is known for causing sight-threatening keratitis in humans . Free-living amoeba keratitis is more common in developing countries . Amoebae of family Vahlkampfiidae are rarel... | Free-living amoebae are present worldwide . Some species are known to cause chronic keratitis in human . Amoebic chronic keratitis is sight-threatening disease occurring in both developing and well-developed countries . Allovahlkampfia spelaea is a newly discovered free-living amoeba . We report the first human case of... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [
"trophozoites",
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"keratitis",
"rabbits",
"vertebrates",
"parasitic",
"protozoans",
"animals",
"mammals",
"parasitology",
"acanthamoeba",
"animal",
"models",
"apicomplexa",
"model",
"organisms",
"protozoans",
"a... | 2016 | Allovahlkampfia spelaea Causing Keratitis in Humans |
The RNA-dependent RNA polymerase VP1 of infectious pancreatic necrosis virus ( IPNV ) is a single polypeptide responsible for both viral RNA transcription and genome replication . Sequence analysis identifies IPNV VP1 as having an unusual active site topology . We have purified , crystallized and solved the structure o... | Infectious pancreatic necrosis virus ( IPNV ) is highly contagious and causes severe disease in fish . As a result of intensive rearing conditions it has become a serious problem for the salmon and trout farming industries . IPNV , like many other viruses , replicates its genome using a protein ( a ‘polymerase’ ) that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"protein",
"interactions",
"enzymes",
"viral",
"enzymes",
"microbiology",
"fish",
"farming",
"aquaculture",
"protein",
"structure",
"dna",
"rna",
"synthesis",
"enzyme",
"kinetics",
"dna",
"synthesis",
"proteins",
"marine",
"and",... | 2011 | The N-Terminus of the RNA Polymerase from Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment |
Enterovirus 71 ( EV71 ) , a major causative agent of hand , foot , and mouth disease , occasionally causes severe neurological symptoms . We identified P-selectin glycoprotein ligand-1 ( PSGL-1 ) as an EV71 receptor and found that an amino acid residue 145 in the capsid protein VP1 ( VP1-145 ) defined PSGL-1-binding ( ... | Recently , large outbreaks of hand , foot , and mouth disease , including fatal neurological cases in young children primarily because of enterovirus 71 ( EV71 ) have been reported , particularly in the Asia Pacific regions where the disease poses a serious threat to public health . Based on mutational and structural a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | The Role of VP1 Amino Acid Residue 145 of Enterovirus 71 in Viral Fitness and Pathogenesis in a Cynomolgus Monkey Model |
Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes . However , retrieving biological insights from large-scale protein dynamics data remains a challenging task . Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and develop... | A systematic characterization of the proteomic changes during the process of cell differentiation is critical for understanding the underlying molecular mechanisms . However , protein expression can be largely affected by changes in cell physiological state , which hampers the detection of regulatory interactions . Her... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cellular",
"stress",
"responses",
"gene",
"regulation",
"cell",
"processes",
"protein",
"abundance",
"protein",
"expression",
"protein",
"synthesis",
"molecular",
"biology",
"techniques",
"chemical",
"synthesis",
"research",
"and",
"analysis",
"methods",
"proteins",
"g... | 2017 | Reconstructing the regulatory circuit of cell fate determination in yeast mating response |
To develop more detailed models of EBV persistence we have studied the dynamics of virus shedding in healthy carriers . We demonstrate that EBV shedding into saliva is continuous and rapid such that the virus level is replaced in ≤2 minutes , the average time that a normal individual swallows . Thus , the mouth is not ... | Epstein-Barr virus is a human pathogen associated with several human cancers that nevertheless persists benignly as a latent infection in the majority of adults . EBV persistence is characterized by the presence of latently infected cells in the blood and the shedding of virus into saliva . We present the first systema... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/persistence",
"and",
"latency"
] | 2009 | The Dynamics of EBV Shedding Implicate a Central Role for Epithelial Cells in Amplifying Viral Output |
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