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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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|---|---|---|---|---|---|
Transcriptome dynamics is governed by two opposing processes , mRNA production and degradation . Recent studies found that changes in these processes are frequently coordinated and that the relationship between them shapes transcriptome kinetics . Specifically , when transcription changes are counter-acted with changes... | Organisms alter genes expression programs in response to changes in their environment . Such programs can specify fast induction , slow relaxation , oscillations , etc . Conceivably these kinetic outputs may depend on proper orchestration of the various phases of gene expression , including transcription , translation ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"genomics",
"theoretical",
"biology",
"biology",
"computational",
"biology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2011 | Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II |
The spliceosome is a molecular machine that performs the excision of introns from eukaryotic pre-mRNAs . This macromolecular complex comprises in human cells five RNAs and over one hundred proteins . In recent years , many spliceosomal proteins have been found to exhibit intrinsic disorder , that is to lack stable nati... | In eukaryotic cells , introns are spliced out of proteincoding mRNAs by a highly dynamic and extraordinarily plastic molecular machine called the spliceosome . In recent years , multiple regions of intrinsic structural disorder were found in spliceosomal proteins . Intrinsically disordered regions lack stable native th... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"macromolecular",
"complex",
"analysis",
"sequence",
"analysis",
"protein",
"structure",
"biology",
"computational",
"biology",
"macromolecular",
"structure",
"analysis"
] | 2012 | Intrinsic Disorder in the Human Spliceosomal Proteome |
Salt is a major threat to plant growth and crop productivity . Calmodulin ( CaM ) , the most important multifunctional Ca2+ sensor protein in plants , mediates reactions against environmental stresses through target proteins; however , direct proof of the participation of CaM in salt tolerance and its corresponding sig... | Calmodulins ( CaMs ) are a highly conserved protein family in eukaryotes . They are known to be important for plant tolerance against external stimuli . Here we described a new molecular function of the Arabidopsis thaliana CaMs in response to salinity . We reported that two CaM isoforms AtCaM1 and AtCaM4 , which encod... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"ecology",
"and",
"environmental",
"sciences",
"neurochemistry",
"brassica",
"plant",
"physiology",
"neuroscience",
"plant",
"biotechnology",
"plant",
"science",
"model",
"organisms",
"luminescent",
"proteins",
"genetically",
"modified",
"plants",
"yellow",... | 2016 | Arabidopsis CaM1 and CaM4 Promote Nitric Oxide Production and Salt Resistance by Inhibiting S-Nitrosoglutathione Reductase via Direct Binding |
Dengue virus ( DENV ) transmission is ubiquitous throughout the tropics . More than 70% of the current global dengue disease burden is borne by people who live in the Asia-Pacific region . We sequenced the E gene of DENV isolated from travellers entering Western Australia between 2010–2012 , most of whom visited Indone... | Dengue is currently the most rapidly spreading mosquito-borne viral disease of humans , and is endemic in most tropical and sub-tropical countries . An estimated 390 million infections occur annually , and over 70% of the current global dengue disease burden is borne by people who live in Southeast Asia and the Western... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Emergence of a New Lineage of Dengue Virus Type 2 Identified in Travelers Entering Western Australia from Indonesia, 2010-2012 |
Biological functions typically involve complex interacting molecular networks , with numerous feedback and regulation loops . How the properties of the system are affected when one , or several of its parts are modified is a question of fundamental interest , with numerous implications for the way we study and understa... | Heritable phenotypic properties are often defined by complex pathways and therefore dependent on multiple polymorphisms affecting different genes . Mapping phenotypic consequences of such genetic variation is central to our understanding of disease susceptibility and is fundamental to understanding evolutionary dynamic... | [
"Abstract",
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/signaling",
"networks",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2011 | Epistasis in a Model of Molecular Signal Transduction |
The function of adult neurogenesis in the rodent brain remains unclear . Ablation of adult born neurons has yielded conflicting results about emotional and cognitive impairments . One hypothesis is that adult neurogenesis in the hippocampus enables spatial pattern separation , allowing animals to distinguish between si... | Adult neurogenesis occurs in the rodent brain , but its function remains unclear . Current theories support the view that adult neurogenesis in the hippocampus supports pattern separation in the hippocampus , thereby allowing animals to distinguish between similar , overlapping inputs . However the effects of pharmacol... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Ablating Adult Neurogenesis in the Rat Has No Effect on Spatial Processing: Evidence from a Novel Pharmacogenetic Model |
The Fragile X-related disorders ( FXDs ) are Repeat Expansion Diseases resulting from an expansion of a CGG-repeat tract at the 5’ end of the FMR1 gene . The mechanism responsible for this unusual mutation is not fully understood . We have previously shown that mismatch repair ( MMR ) complexes , MSH2/MSH3 ( MutSβ ) an... | The Fragile X-related disorders arise from expansion of a tandem repeat or microsatellite consisting of CGG-repeat units . The expansion mutation is not well understood , but our previous data suggests that MutSα and MutSβ , mismatch repair ( MMR ) proteins that normally protect the genome against microsatellite instab... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"liver",
"nucleases",
"cardiovascular",
"anatomy",
"enzymes",
"dna-binding",
"proteins",
"enzymology",
"animal",
"models",
"mutation",
"model",
"organisms",
"heart",
"experimental",
"organism",
"systems",
... | 2018 | MutLγ promotes repeat expansion in a Fragile X mouse model while EXO1 is protective |
Entamoeba histolytica infection may have various clinical manifestations . Nine out of ten E . histolytica infections remain asymptomatic , while the remainder become invasive and cause disease . The most common form of invasive infection is amebic diarrhea and colitis , whereas the most common extra-intestinal disease... | The parasite Entamoeba histolytica can cause serious disease by invading the lining of the large intestine and spreading to other organs of the body . However , most infected individuals never develop symptoms , and it is not clear what determines the different outcomes of infection . Factors that might be having an ef... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/protozoal",
"infections",
"molecular",
"biology/recombination",
"infectious",
"diseases/gastrointestinal",
"infections"
] | 2008 | Tissue Invasion by Entamoeba histolytica: Evidence of Genetic Selection and/or DNA Reorganization Events in Organ Tropism |
Buruli Ulcer ( BU ) is a necrotizing skin disease caused by Mycobacterium ulcerans infection . BU is characterized by a wide range of clinical forms , including non-ulcerative cutaneous lesions that can evolve into severe ulcers if left untreated . Nevertheless , spontaneous healing has been reported to occur , althoug... | Buruli Ulcer ( BU ) is a devastating skin disease caused by Mycobacterium ulcerans . BU usually starts off as a non-ulcerative lesion , but if lesions are left untreated they can evolve into ulcers or may even affect the bone . Nevertheless , spontaneous healing of active lesions has been reported in some patients , al... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Spontaneous Healing of Mycobacterium ulcerans Lesions in the Guinea Pig Model |
Improving the ability to reverse engineer biochemical networks is a major goal of systems biology . Lesions in signaling networks lead to alterations in gene expression , which in principle should allow network reconstruction . However , the information about the activity levels of signaling proteins conveyed in overal... | Elucidating the biochemical interactions in living cells is essential to understanding their behavior under various external conditions . Some of these interactions occur between signaling components with many active states , and their activity levels may be difficult to measure directly . However , most methods to rev... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/signaling",
"networks"
] | 2010 | Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows |
The IFN-inducible antiviral protein tetherin ( or BST-2/CD317/HM1 . 24 ) impairs release of mature HIV-1 particles from infected cells . HIV-1 Vpu antagonizes the effect of tetherin . The fate of virions trapped at the cell surface remains poorly understood . Here , we asked whether tetherin impairs HIV cell-to-cell tr... | Tetherin is a cell surface “restriction factor” that acts as an innate antiviral defense . Tetherin prevents newly produced particles of HIV-1 and other enveloped viruses from escaping the surface of infected cells . HIV-1 encodes the protein Vpu to counteract this host defense . We have studied here if HIV-1 particles... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/immunodeficiency",
"viruses",
"virology",
"infectious",
"diseases/hiv",
"infection",
"and",
"aids",
"virology/host",
"antiviral",
"responses",
"virology/host",
"invasion",
"and",
"cell",
"entry"
] | 2010 | Tetherin Restricts Productive HIV-1 Cell-to-Cell Transmission |
The Fungal Genome Initiative of the Broad Institute , in partnership with the Paracoccidioides research community , has recently sequenced the genome of representative isolates of this human-pathogen dimorphic fungus: Pb18 ( S1 ) , Pb03 ( PS2 ) and Pb01 . The accomplishment of future high-throughput , genome-wide , fun... | Diverse eukaryotes , including various fungi , utilize RNA interference ( RNAi ) pathways to regulate genome-wide gene expression . Since the initial characterization of these pathways and the demonstration of its artificial induction in the filamentous ascomycete Neurospora crassa , RNAi has emerged as the most robust... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"molecular",
"probe",
"techniques",
"marker",
"genes",
"cloning",
"codons",
"dna",
"sequences",
"complementary",
"rna",
"dna",
"construction",
"dna",
"molecular",
"biology",
"techniques",
"genetic",
"engineering",
"promoter",
"regions",
"plasmid",
"vect... | 2014 | New Developments of RNAi in Paracoccidioides brasiliensis: Prospects for High-Throughput, Genome-Wide, Functional Genomics |
The herpesviruses , like most other DNA viruses , replicate in the host cell nucleus . Subnuclear domains known as promyelocytic leukemia protein nuclear bodies ( PML-NBs ) , or ND10 bodies , have been implicated in restricting early herpesviral gene expression . These viruses have evolved countermeasures to disperse P... | Many DNA viruses , including varicella-zoster virus ( VZV ) , a herpesvirus that causes varicella ( chickenpox ) and zoster ( shingles ) , replicate in the host cell nucleus . Here , we have identified an intrinsic antiviral mechanism that specifically targets newly assembled VZV capsids and contains these essential vi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/infectious",
"diseases",
"of",
"the",
"nervous",
"system",
"pathology/neuropathology",
"molecular",
"biology/nucleolus",
"and",
"nuclear",
"bodies",
"virology/virion",
"structure,",
"assembly,",
"and",
"egress",
"neurological",
"disorders/infectious",
... | 2011 | Entrapment of Viral Capsids in Nuclear PML Cages Is an Intrinsic Antiviral Host Defense against Varicella-Zoster Virus |
Despite recent advances in our understanding of the pathogenesis of attaching and effacing ( A/E ) Escherichia coli infections , the mechanisms by which the host defends against these microbes are unclear . The goal of this study was to determine the role of goblet cell-derived Muc2 , the major intestinal secretory muc... | Enteropathogenic E . coli ( EPEC ) and Enterohemorrhagic E . coli ( EHEC ) are important causes of diarrheal disease and other serious complications worldwide . Despite many studies addressing the pathogenic strategies used by these microbes , how the host protects itself from these pathogens is poorly understood . A c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"gastroenterology",
"and",
"hepatology/colon",
"and",
"rectum",
"infectious",
"diseases/gastrointestinal",
"infections",
"immunology/innate",
"immunity"
] | 2010 | Muc2 Protects against Lethal Infectious Colitis by Disassociating Pathogenic and Commensal Bacteria from the Colonic Mucosa |
Travel across multiple time zones results in desynchronization of environmental time cues and the sleep–wake schedule from their normal phase relationships with the endogenous circadian system . Circadian misalignment can result in poor neurobehavioral performance , decreased sleep efficiency , and inappropriately time... | Traveling across several times zones can cause an individual to experience “jet lag , ” which includes trouble sleeping at night and trouble remaining awake during the day . A major cause of these effects is the desynchronization between the body's internal circadian clock and local environmental cues . A well-known in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"computer",
"science",
"computational",
"biology"
] | 2009 | Taking the Lag out of Jet Lag through Model-Based Schedule Design |
The majority of human genes are conserved among mammals , but some gene families have undergone extensive expansion in particular lineages . Here , we present an evolutionary analysis of one such gene family , the poly–zinc-finger ( poly-ZF ) genes . The human genome encodes approximately 700 members of the poly-ZF fam... | Gene families , arising by the repeated duplication and diversification of existing genes , are a pervasive feature of the genomes of higher organisms . In this study , we analyze the evolutionary history of one of the largest gene families in humans , the poly–zinc-finger genes . Each poly–zinc-finger gene is thought ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology/human",
"evolution",
"evolutionary",
"biology/genomics",
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics"
] | 2009 | Adaptive Evolution in Zinc Finger Transcription Factors |
The third variable loop ( V3 ) of the human immunodeficiency virus type 1 ( HIV-1 ) envelope is a principal determinant of antibody neutralization and progression to AIDS . Although it is undoubtedly an important target for vaccine research , extensive genetic variation in V3 remains an obstacle to the development of a... | The third variable loop ( V3 ) of the human immunodeficiency virus type 1 ( HIV-1 ) envelope is a principal determinant of viral growth characteristics and an important target for the immune system . Interactions between residues of V3 allow the virus to shift between combinations of residues to escape the immune syste... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Supporting",
"Information"
] | [
"evolutionary",
"biology",
"viruses",
"virology",
"computational",
"biology"
] | 2007 | An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope |
Olfactory receptor neurons ( ORNs ) convey odor information to the central brain , but like other sensory neurons were thought to play a passive role in memory formation and storage . Here we show that Notch , part of an evolutionarily conserved intercellular signaling pathway , is required in adult Drosophila ORNs for... | Appropriate behavioral responses to changing environmental signals , such as odors , are essential for an organism’s survival . In Drosophila odors are detected by olfactory receptor neurons ( ORNs ) that synapse with second order projection neurons ( PNs ) and local interneurons in morphologically identifiable neuropi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Notch Is Required in Adult Drosophila Sensory Neurons for Morphological and Functional Plasticity of the Olfactory Circuit |
Hospitalization of patients during outbreaks of chikungunya virus has been reported to be uncommon ( 0 . 5–8 . 7% ) , but more frequent among infants and the elderly . CHIKV was first detected in Puerto Rico in May 2014 . We enrolled patients with acute febrile illness ( AFI ) presenting to two hospital emergency depar... | Chikungunya is an emerging infectious disease caused by a virus ( chikungunya virus , CHIKV ) transmitted through the bite of infected mosquitos; typical symptoms are fever and joint pain . After CHIKV was first detected in Puerto Rico in 2014 , an epidemic quickly spread across the island . Because previous reports id... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"hospitalizations",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"togaviruses",
"chikungunya",
"infection",
"respiratory",
"infections",
"pathogens",
"tropical",
"diseases",
"microbiology",
"geographical",
"locations",
"alphaviruses",... | 2019 | Risk factors for hospitalization of patients with chikungunya virus infection at sentinel hospitals in Puerto Rico |
Endocytic sorting is achieved through the formation of morphologically and functionally distinct sub-domains within early endosomes . Cargoes destined for recycling are sorted to and transported through newly-formed tubular membranes , but the processes that regulate membrane tubulation are poorly understood . Here , w... | The process by which cells take up nutrients and other large molecules from the extracellular environment is known as endocytosis . At the cell surface , external molecules become enclosed in membrane spheres called endosomes . Early endosomes serve as a sorting station , directing the contents ( cargo molecules ) to t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/membranes",
"and",
"sorting"
] | 2010 | Endocytic Sorting and Recycling Require Membrane Phosphatidylserine Asymmetry Maintained by TAT-1/CHAT-1 |
Host signal-transduction pathways are intimately involved in the switch between latency and productive infection of herpes viruses . As with other herpes viruses , infection by Kaposi's sarcoma herpesvirus ( KSHV ) displays these two phases . During latency only few viral genes are expressed , while in the productive i... | The switch from latency to productive viral replication ( reactivation ) is a crucial decision in the viral life cycle , and recent clinico-epidemiological studies support the importance of lytic replication in the development and progression of Kaposi's sarcoma . Hence , cellular signaling pathways operative during vi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/persistence",
"and",
"latency",
"virology/viruses",
"and",
"cancer",
"cell",
"biology/cell",
"signaling"
] | 2009 | KSHV Reactivation from Latency Requires Pim-1 and Pim-3 Kinases to Inactivate the Latency-Associated Nuclear Antigen LANA |
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities . When matched metagenomic and/or metatranscriptomic data of the microbial communities are available , metaproteomic data analyses often employ a me... | In recent years , meta-omic ( including metatranscriptomic and metaproteomic ) techniques have been adopted as complementary approaches to metagenomic sequencing to study functional characteristics and dynamics of microbial communities , aiming at a holistic understanding of a community to respond to the changes in the... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"database",
"searching",
"sequence",
"assembly",
"tools",
"plant",
"science",
"metagenomics",
"genome",
"analysis",
"molecular",
"biology",
"techniques",
"photosynthesis",
"ribulose-1,5-bisphosphate",
"carboxylase",
"oxygenase",
"sequence",
"simila... | 2016 | A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics |
Among millions of people who suffer from schistosomiasis in China , adolescents are at increased risk to be infected . However , there is a lack of theory-guided behavioral prevention intervention programs to protect these adolescents . This study attempted to apply the Protection Motivation Theory ( PMT ) in predictin... | In China , millions of population suffer from schistosomiasis infection and adolescents tend to have higher infection rates than adults . The Knowledge-Attitude-Practice ( KAP ) Theory has traditionally been used as guidance to schistosomiasis prevention in China . However , despite increases in knowledge among residen... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"plant",
"science",
"infectious",
"disease",
"epidemiology",
"epidemiology",
"plant",
"pathology",
"biology",
"and",
"life",
"sciences"
] | 2014 | Protection Motivation Theory in Predicting Intention to Engage in Protective Behaviors against Schistosomiasis among Middle School Students in Rural China |
Aging is associated with highly reproducible DNA methylation ( DNAm ) changes , which may contribute to higher prevalence of malignant diseases in the elderly . In this study , we analyzed epigenetic aging signatures in 5 , 621 DNAm profiles of 25 cancer types from The Cancer Genome Atlas ( TCGA ) . Overall , age-assoc... | Our genome harbors epigenetic marks , such as DNA methylation ( DNAm ) at cytosine residues , which govern cellular differentiation . Some epigenetic modifications accumulate throughout life in a highly reproducible manner–they may contribute to the aging process and facilitate reliable age-predictions . So far , littl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Epigenetic Aging Signatures Are Coherently Modified in Cancer |
The correct organization of single subunits of multi-protein machines in a three dimensional context is critical for their functionality . Type III secretion systems ( T3SS ) are molecular machines with the capacity to deliver bacterial effector proteins into host cells and are fundamental for the biology of many patho... | Many Gram negative pathogens such as Salmonella , Yersinia , or Shigella use the type III secretion system ( T3SS ) to initiate infection in eukaryotic cells , resulting in well known clinical symptoms ranging from mild headaches and diarrhea to life-threatening diseases such as typhoid fever or bubonic plague . The T3... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"infectious",
"diseases",
"biochemistry/macromolecular",
"assemblies",
"and",
"machines",
"microbiology"
] | 2010 | Topology and Organization of the Salmonella typhimurium Type III Secretion Needle Complex Components |
The hippocampal formation is a key structure for memory function in the brain . The functional anatomy of the brain suggests that the hippocampus may be a convergence zone , as it receives polysensory input from distributed association areas throughout the neocortex . However , recent quantitative graph-theoretic analy... | The hippocampus is a key structure in the brain , particularly for memory function . The functional anatomy of brain networks suggests that the hippocampus should be a hub in the large-scale connectome , yet so far quantitative network analyses have failed to find any evidence of such a role . Here we show that when co... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"connectomics",
"neuroanatomy",
"anatomy",
"computational",
"neuroscience",
"nervous",
"system",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"neuroscience"
] | 2014 | A Network Convergence Zone in the Hippocampus |
The mitochondrial ribosome , which translates all mitochondrial DNA ( mtDNA ) -encoded proteins , should be tightly regulated pre- and post-transcriptionally . Recently , we found RNA-DNA differences ( RDDs ) at human mitochondrial 16S ( large ) rRNA position 947 that were indicative of post-transcriptional modificatio... | RNA modifications constitute an important layer of information , with functional implications that are not written in the underlying DNA sequence . Recently , we observed an apparent RNA-DNA difference ( RDD ) at position 947 of the human mitochondrial 16S ribosomal RNA ( rRNA ) , but its nature and mechanism were uncl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"transfer",
"rna",
"mitochondrial",
"dna",
"gene",
"regulation",
"rna",
"extraction",
"vertebrates",
"nucleotides",
"animals",
"forms",
"of",
"dna",
"mitochondria",
"dna",
"bioenergetics",
"cellular",
"structures",
"and",
"organelles",
"extraction",
"techniques",
"resea... | 2016 | Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates |
The effective size of populations ( Ne ) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution . Despite their high mutation rate and rapid evolution , this parameter is poorly documented experimentally in viruses , particularly plant viruses . All availabl... | Whether selection or stochastic genetic drift is the major force driving the evolution of a virus depends largely on the size of the viral population , with the former being predominant in large populations and the latter taking over when population sizes are transiently or durably reduced . This question has been inte... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"microbiology/plant-biotic",
"interactions",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"virology/virus",
"evolution",
"and",
"symbiosis",
"virology",
"plant",
"biology",
"evolutionary",
"biology",
"virology/host",
"invasion",
"and",
"cell",
"entry"
... | 2008 | Large Bottleneck Size in Cauliflower Mosaic Virus Populations during Host Plant Colonization |
Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a non-bridging oxygen with a sulfur atom at specific sequences . The biological implications of this DNA S-modification ( phosphorothioation ) were unknown . We observed that simultaneous expression of the dndA-E gene cluster from Strept... | Bacteria frequently exchange genetic information among themselves . DNA from one species can be transferred efficiently to unrelated microbes . Bacteria have developed systems that restrict gene transfer . Many restriction systems recognize and destroy foreign DNA entering the cells , but there are also enzymes inducin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chemical",
"biology",
"microbiology/applied",
"microbiology"
] | 2010 | Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA |
The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology . Constraint-based models in particular play a key role in the attempt to obtain a quantitative understanding of cellular metabolism at genome scale . In ... | The operation of biological systems is constrained under all circumstances by the laws of physics . Thermodynamics , in particular , dictates preferential directions in which biochemical reactions should flow at stationarity . When applied to cellular reaction systems ( like metabolic networks ) , it favors the emergen... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"systems",
"biology",
"biophysics",
"theory",
"biology",
"computational",
"biology",
"metabolic",
"networks",
"biophysics"
] | 2012 | A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks |
Human lymphatic filariasis is a major tropical disease transmitted through mosquito vectors which take up microfilarial larvae from the blood of infected subjects . Microfilariae are produced by long-lived adult parasites , which also release a suite of excretory-secretory products that have recently been subject to in... | Triose phosphate isomerase ( TPI ) is a ubiquitous and highly conserved enzyme in intracellular glucose metabolism . Surprisingly , the human lymphatic filariai nematode parasite Brugia malayi , releases TPI into the extracellular environment , suggesting a role in helminth survival in the mammalian host . We first est... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"enzymes",
"parasitology",
"immunology",
"host-pathogen",
"interaction",
"biology",
"microbiology",
"immune",
"response",
"immunoglobulins"
] | 2014 | The Secreted Triose Phosphate Isomerase of Brugia malayi Is Required to Sustain Microfilaria Production In Vivo |
Canine leishmaniasis is an important zoonotic disease of dogs . The clinical outcome of infection is variable , with the efficiency of the immune response being the key determining factor . There is now a general consensus that a predominant Th1 immune profile in an overall mixed Th1/Th2 response is associated with res... | The dog is the principle reservoir of Leishmania infantum , a parasite spread from dog to dog by a sandfly vector . The reduction of canine leishmaniasis is therefore a key factor in the overall management of the epidemiology of this parasite . There is also a need for effective prevention on welfare grounds because of... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"veterinary",
"immunology",
"veterinary",
"diseases",
"veterinary",
"parasitology",
"zoonotic",
"diseases",
"leishmaniasis",
"immunology",
"veterinary",
"science",
"veterinary",
"medicine"
] | 2012 | Use of a LiESP/QA-21 Vaccine (CaniLeish) Stimulates an Appropriate Th1-Dominated Cell-Mediated Immune Response in Dogs |
Hepatitis C virus ( HCV ) is a positive-strand RNA virus of the Flaviviridae family and a major cause of liver disease worldwide . HCV replicates in the cytoplasm , and the synthesis of viral proteins induces extensive rearrangements of host cell membranes producing structures , collectively termed the membranous web (... | Hepatitis C virus ( HCV ) is a positive-strand RNA virus and it is a major cause of liver disease worldwide affecting more than 170 million individuals . Infection of cells with HCV leads to rearrangement of cytoplasmic host cell membranes and the formation of the membranous web ( MW ) containing viral replication and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"fluorescence",
"imaging",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"immunology",
"microbiology",
"viral",
"structure",
"membrane",
"proteins",
"viruses",
"rna",
"viruses",
"antibodies",
"cellular",
"structures",
"and",
"organelles",
"research",
... | 2016 | The Hepatitis C Virus-Induced Membranous Web and Associated Nuclear Transport Machinery Limit Access of Pattern Recognition Receptors to Viral Replication Sites |
The digestive tract is the first organ affected by the ingestion of foodborne bacteria . While commensal bacteria become resident , opportunistic or virulent bacteria are eliminated from the gut by the local innate immune system . Here we characterize a new mechanism of defense , independent of the immune system , in D... | The intestine is the first barrier to fight non-commensal bacteria ingested along with the food . The innate immune system is the main mean mounted by the gut lining in response to ill-causing bacteria to avoid detrimental impact . Intestinal cells produce chlorine bleach and antimicrobial peptides that destroy exogeno... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"disaccharides",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"carbohydrates",
"animals",
"organic",
"compounds",
"muscle",
"contraction",
"animal",
"models",
"physiological",
... | 2018 | The DH31/CGRP enteroendocrine peptide triggers intestinal contractions favoring the elimination of opportunistic bacteria |
Two large-scale efficacy studies with the recombinant yellow fever-17D–dengue virus , live-attenuated , tetravalent dengue vaccine ( CYD-TDV ) candidate undertaken in Asia ( NCT01373281 ) and Latin America ( NCT01374516 ) demonstrated significant protection against dengue disease during two years’ active surveillance (... | A live-attenuated , tetravalent dengue vaccine ( CYD-TDV ) has been shown to provide protection against dengue disease in two large-scale , placebo-controlled , phase III efficacy studies . Continued surveillance of study participants was subsequently undertaken to better define longer term vaccine efficacy and safety ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"viral",
"vaccines",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"tropical",
"diseases",
"microbiology",
"vaccines",
"preventive",
"medicine",
"ph... | 2016 | Cytokine Profile of Children Hospitalized with Virologically-Confirmed Dengue during Two Phase III Vaccine Efficacy Trials |
Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation . Here , we investigate the influence of rare and common genetic variants on gene expression patterns , using variants identified from sequencing data from t... | The recent availability of almost fully sequenced human genomes by the 1000 genomes project allows the direct study of genetic variants that influence levels of gene expression in the cell . In this study , we explore the effect of rare and common variants on levels of gene expression . We show that the availability of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"genome",
"analysis",
"tools",
"gene",
"expression",
"genetics",
"biology",
"genomics",
"genetics",
"and",
"genomics",
"genetic",
"maps"
] | 2011 | Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes |
In the vertebrate retina , horizontal cells generate the inhibitory surround of bipolar cells , an essential step in contrast enhancement . For the last decades , the mechanism involved in this inhibitory synaptic pathway has been a major controversy in retinal research . One hypothesis suggests that connexin hemichann... | Contrast enhancement is a fundamental feature of our visual system , initiated at the first synaptic connections in the retina . These are the synapses between photoreceptors ( rods and cones ) and their targets , horizontal cells and bipolar cells . Horizontal cells receive input from many cones and subsequently send ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"visual",
"system",
"biology",
"sensory",
"systems",
"neuroscience"
] | 2011 | Synaptic Transmission from Horizontal Cells to Cones Is Impaired by Loss of Connexin Hemichannels |
Legionella pneumophila and L . longbeachae are two species of a large genus of bacteria that are ubiquitous in nature . L . pneumophila is mainly found in natural and artificial water circuits while L . longbeachae is mainly present in soil . Under the appropriate conditions both species are human pathogens , capable o... | Legionella longbeachae , found in potting soil , and L . pneumophila , present in aquatic environments , are opportunistic human pathogens that cause Legionnaires' disease , a severe and often fatal pneumonia . The analysis and comparison of the genome sequences of four L . longbeachae genomes together with the study o... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"infectious",
"diseases/respiratory",
"infections",
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2010 | Analysis of the Legionella longbeachae Genome and Transcriptome Uncovers Unique Strategies to Cause Legionnaires' Disease |
Viruses have to encapsidate their own genomes during the assembly process . For most RNA viruses , there are sequences within the viral RNA and virion proteins needed for high efficiency of genome encapsidation . However , the roles of host proteins in this process are not understood . Here we find that the cellular DE... | Foamy viruses are complex retroviruses that infect non-human primates , cats , cows , and horses . Humans are not natural hosts but can acquire primate foamy viruses as zoonotic infections . During foamy virus assembly process , viral RNAs and Gag capsid proteins are targeted to a discrete intra-cytoplasmic site where ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"microbiology"
] | 2011 | The DEAD-box RNA Helicase DDX6 is Required for Efficient Encapsidation of a Retroviral Genome |
Globally , regions at the highest risk for emerging infectious diseases are often the ones with the fewest resources . As a result , implementing sustainable infectious disease surveillance systems in these regions is challenging . The cost of these programs and difficulties associated with collecting , storing and tra... | The emergence of infectious diseases can have devastating public health and economic consequences . Being able to identify such events at early stages could significantly mitigate some of these outcomes . In many resource poor regions of the world , current surveillance methods are hindered by the costs associated with... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Xenosurveillance: A Novel Mosquito-Based Approach for Examining the Human-Pathogen Landscape |
Reproductive senescence is a hallmark of aging . The molecular mechanisms regulating reproductive senescence and its association with the aging of somatic cells remain poorly understood . From a full genome RNA interference ( RNAi ) screen , we identified 32 Caenorhabditis elegans gene inactivations that delay reproduc... | Female reproductive senescence is one hallmark of human aging , and as the germline ages , there is increased incidence of chromosome non-dysjunction and DNA damage . Delayed childbearing is a general feature in modern society , resulting in high risk of infertility , miscarriage and birth defects . Thus , understandin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"aging",
"developmental",
"biology",
"animal",
"genetics",
"invertebrate",
"genetics",
"organism",
"development",
"genetics",
"biology",
"and",
"life",
"sciences"
] | 2014 | Gene Pathways That Delay Caenorhabditis elegans Reproductive Senescence |
Snakebite accidents are an important health problem in rural areas of tropical countries worldwide , including Costa Rica , where most bites are caused by the pit-viper Bothrops asper . The treatment of these potentially fatal accidents is based on the timely administration of specific antivenom . In many regions of th... | Snakebite accidents are a neglected cause of much death and suffering worldwide . The situation is especially severe in rural areas of low income tropical countries , where long distances to well-equipped health care facilities mean that the time needed to reach antivenom treatment is often long . Delays in receiving a... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"geography",
"social",
"and",
"behavioral",
"sciences",
"epidemiology",
"global",
"health",
"public",
"health",
"toxicology"
] | 2013 | Using Geographical Information Systems to Identify Populations in Need of Improved Accessibility to Antivenom Treatment for Snakebite Envenoming in Costa Rica |
African Pygmy groups show a distinctive pattern of phenotypic variation , including short stature , which is thought to reflect past adaptation to a tropical environment . Here , we analyze Illumina 1M SNP array data in three Western Pygmy populations from Cameroon and three neighboring Bantu-speaking agricultural popu... | Africa is thought to be the location of origin of modern humans within the past 200 , 000 years and the source of our dispersion across the globe within the past 100 , 000 years . Africa is also a region of extreme environmental , cultural , linguistic , and phenotypic diversity , and human populations living there sho... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"biology",
"genomics",
"evolutionary",
"biology",
"population",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies |
In prion diseases , the cellular form of the prion protein , PrPC , undergoes a conformational conversion to the infectious isoform , PrPSc . PrPC associates with lipid rafts through its glycosyl-phosphatidylinositol ( GPI ) anchor and a region in its N-terminal domain which also binds to heparan sulfate proteoglycans ... | The prion diseases are unique in that their infectious nature is not dependent on nucleic acid but is instead attributed to a misfolded protein , the prion protein . This misfolded prion protein is capable of inducing the misfolding of the normal form of the prion protein that is present on the surface of neurons and o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurological",
"disorders/alzheimer",
"disease",
"biochemistry",
"infectious",
"diseases/prion",
"diseases",
"cell",
"biology/membranes",
"and",
"sorting",
"neurological",
"disorders/prion",
"diseases"
] | 2009 | Glypican-1 Mediates Both Prion Protein Lipid Raft Association and Disease Isoform Formation |
Antenatal exposure to Zika virus ( ZIKV ) is related to severe neurological manifestations . A previous study in Brazil reported an increased incidence of non-severe congenital heart defects in infants with diagnosis of congenital Zika syndrome but without laboratory confirmation of ZIKV infection in the mother or infa... | We performed cardiologic assessment of 120 infants born between November 2015 and January 2017 with confirmed vertical exposure to Zika virus ( ZIKV ) . The diagnosis of ZIKV exposure was confirmed by PCR in maternal blood specimens and/or amniotic fluid during pregnancy and/or infant specimens including PCR of the cer... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"children",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"maternal",
"health",
"obstetrics",
"and",
"gynecology",
"cardiovascular",
"anatomy",
"nervous",
"system",
"pathogens",
"geographical",
"locations",
"microbiology",
"viruses... | 2018 | Cardiac findings in infants with in utero exposure to Zika virus- a cross sectional study |
Mycobacterium tuberculosis ( Mtb ) is thought to preferentially rely on fatty acid metabolism to both establish and maintain chronic infections . Its metabolic network , however , allows efficient co-catabolism of multiple carbon substrates . To gain insight into the importance of carbohydrate substrates for Mtb pathog... | The development of new drugs targeting Mycobacterium tuberculosis ( Mtb ) will benefit from a better understanding of the mechanisms by which this pathogen establishes and maintains chronic infections . Mtb has to adapt its metabolic needs to the nutritional environment in the host . We investigated the role of glucose... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbial",
"metabolism",
"microbial",
"physiology",
"microbial",
"pathogens",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"pathogenesis"
] | 2013 | Glucose Phosphorylation Is Required for Mycobacterium tuberculosis Persistence in Mice |
We address here the issue of prioritizing non-coding mutations in the tumoral genome . To this aim , we created two independent computational models . The first ( germline ) model estimates purifying selection based on population SNP data . The second ( somatic ) model estimates tumor mutation density based on whole ge... | Cancer cells undergo a mutation/selection process that resembles that of any living cell . Most mutations in cancer cell DNA occur in the so-called "non-coding" regions that represent 98 . 5% of the genome length . Pinning down which of these mutations contribute to the fitness of cancer cells would be important for id... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events |
The sensitivity of a neuron to its input can be modulated in several ways . Changes in the slope of the neuronal input-output curve depend on factors such as shunting inhibition , background noise , frequency-dependent synaptic excitation , and balanced excitation and inhibition . However , in early development GABAerg... | Computation in a single neuron is regulated by gain control – the change in the sensitivity of a neuron to different patterns of stimulation . Hence , it is important to understand the different mechanisms underlying gain modulation . Earlier work focused on gain modulation in mature networks with functional connectivi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/neurodevelopment",
"biophysics/theory",
"and",
"simulation",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Shunting Inhibition Controls the Gain Modulation Mediated by Asynchronous Neurotransmitter Release in Early Development |
The modulation of the sensitivity , or gain , of neural responses to input is an important component of neural computation . It has been shown that divisive gain modulation of neural responses can result from a stochastic shunting from balanced ( mixed excitation and inhibition ) background activity . This gain control... | Many neural computations , including sensory and motor processing , require neurons to control their sensitivity ( often termed ‘gain’ ) to stimuli . One common form of gain manipulation is divisive gain control , where the neural response to a specific stimulus is simply scaled by a constant . Most previous theoretica... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational",
"biology/computational",
"neuroscience"
] | 2009 | Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons |
Visceral leishmaniasis is the most severe form of leishmaniasis . Approximately 20% of zoonotic human visceral leishmaniasis worldwide is caused by Leishmania infantum , which is also known as Leishmania chagasi in Latin America , and disease incidence is increasing in urban and peri-urban areas of the tropics . In thi... | Globally , the number of new human cases of visceral leishmaniasis ( VL ) is estimated to be approximately 500 , 000 per year . This is the most severe of all forms of leishmaniasis , and the zoonotic form of VL , caused by Leishmania infantum ( also known as Leishmania chagasi ) , represents 20% of human visceral leis... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"veterinary",
"diseases",
"veterinary",
"parasitology",
"zoonotic",
"diseases",
"immunology",
"biology",
"veterinary",
"science",
"immunoglobulins"
] | 2011 | High-Throughput Analysis of Synthetic Peptides for the Immunodiagnosis of Canine Visceral Leishmaniasis |
Rabies virus kills tens of thousands of people globally each year , especially in resource-limited countries . Yet , there are genetically- and antigenically-related lyssaviruses , all capable of causing the disease rabies , circulating globally among bats without causing conspicuous disease outbreaks . The species ric... | Rabies virus kills tens of thousands of people globally each year and causes indescribable misery and family disturbance , especially in developing countries . Yet in much of the world there are related viruses , called lyssaviruses , which circulate among bats without causing conspicuous outbreaks . The greater divers... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biogeography",
"organismal",
"evolution",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"population",
"genetics",
"geographical",
"locations",
"microbiology",
"vertebrates"... | 2016 | The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis |
Viruses use a limited set of host pathways for infection . These pathways represent bona fide antiviral targets with low likelihood of viral resistance . We identified the salicylanilide niclosamide as a broad range antiviral agent targeting acidified endosomes . Niclosamide is approved for human use against helminthic... | Current antiviral approaches are directed against specific viral targets but are limited in their broad-spectrum potential . Targeting host pathways , on the other hand can have broad antiviral effects , albeit with possible side effects . Here , we report the mode of antiviral action of a small chemical compound , nic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"influenza",
"amides",
"organic",
"compounds",
"aromatic",
"hydrocarbons",
"rhinovirus",
"infection",
"infectious",
"disease",
"control",
"infectious",
"diseases",
"enterovirus",
"infection",
"membranes",
"and",
"sorting",
"chemistry",
"biology",
"organic",
"c... | 2012 | Niclosamide Is a Proton Carrier and Targets Acidic Endosomes with Broad Antiviral Effects |
Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology . Here , we adapt concepts of spatial statistics to assess the functional content of molecular networks . Based on the guilt-by-association principle , our approach ( called SANTA ) quantifies the strength o... | Molecular networks are maps of the tens of thousands of interactions that occur between the components of biological systems . Types of interactions include physical , genetic and functional interactions between genes , gene products and metabolites . Network-based approaches to molecular biology are increasingly being... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biology",
"and",
"life",
"sciences",
"computational",
"biology"
] | 2014 | SANTA: Quantifying the Functional Content of Molecular Networks |
Despite provision of preventive measures against schistosomiasis such as mass drug administration ( MDA ) , the prevalence of Schistosoma mansoni remains high in communities living near Lake Victoria . This study aimed to analyse the status of schistosomiasis , including its prevalence , health education , knowledge , ... | According to WHO , it is estimated that at least 206 million people required preventive treatment for schistosomiasis in 2016 and of those at least 90% live in Africa . Moreover , school-age children are most affected by this worm . In Kenya , despite preventive measures against schistosomiasis such as mass drug admini... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"textbooks",
"schistosoma",
"invertebrates",
"schistosoma",
"mansoni",
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"surface",
"water",
"body",
"fluids",
"education",
"helminths",
"sociology",
"tropical",
"diseases",
"social",
... | 2019 | Is there a gap between health education content and practice toward schistosomiasis prevention among schoolchildren along the shores of Lake Victoria in Kenya? |
Lysosomes are membrane-bound organelles that contain acid hydrolases that degrade cellular proteins , lipids , nucleic acids , and oligosaccharides , and are important for cellular maintenance and protection against age-related decline . Lysosome related organelles ( LROs ) are specialized lysosomes found in organisms ... | Lysosome related organelles ( LROs ) are specialized , membrane-bound organelles that share many common features of canonical lysosomes . Mutations in critical components of LRO biogenesis lead to human diseases of immunity , blood clotting , and pigmentation . In Caenorhabditis elegans , LROs are the site of accumulat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Genetic Regulation of Caenorhabditis elegans Lysosome Related Organelle Function |
Sand fly saliva compounds are able to elicit specific immune responses that have a significant role in Leishmania parasite establishment and disease outcome . Characterizing anti-saliva immune responses in individuals living in well defined leishmaniasis endemic areas would provide valuable insights regarding their eff... | During murine experimental leishmaniasis sand fly saliva components modulate the host immune response and facilitate infection while pre-exposition to uninfected sand fly bites is associated with a protective cellular response against subsequent infection . Human anti-saliva immune responses are not well defined in lei... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"enzyme-linked",
"immunoassays",
"immunology",
"tropical",
"diseases",
"sand",
"flies",
"parasitic",
"diseases",
"saliva",
"neglected",
"tropical",
"diseases",
"immunologic",
"techniques",
"insect",
"vectors",
"... | 2017 | Human cellular and humoral immune responses to Phlebotomus papatasi salivary gland antigens in endemic areas differing in prevalence of Leishmania major infection |
Translesion synthesis ( TLS ) helps cells to accomplish chromosomal replication in the presence of unrepaired DNA lesions . In eukaryotes , the bypass of most lesions involves a nucleotide insertion opposite the lesion by either a replicative or a specialized DNA polymerase , followed by extension of the resulting dist... | Genomic instability is associated with multiple genetic diseases . Endogenous and exogenous DNA-damaging factors constitute a major source of genomic instability . Mutations occur when DNA lesions are bypassed by specialized translesion synthesis ( TLS ) DNA polymerases that are less accurate than the normal replicativ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | DNA Polymerase ζ-Dependent Lesion Bypass in Saccharomyces cerevisiae Is Accompanied by Error-Prone Copying of Long Stretches of Adjacent DNA |
Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation . This initial step may be untangled by analyzing appropriate ancestral molecules , but it is a daunting task to recapitulate the evolution of non-additive ( epistatic ) interactions of amino acids and... | Mapping the genotype-phenotype relationship is necessary to understand how variable phenotypes have evolved in nature . The blue-sensitive visual pigment in human ( human S1 ) evolved from the UV-sensitive pigment in the Boreoeutherian ( or Boreotherian ) ancestor ( AncBoreotheria S1 ) by seven mutations . Mutagenesis ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"physical",
"sciences"
] | 2014 | Epistatic Adaptive Evolution of Human Color Vision |
One of the hallmarks of opportunistic pathogens is their ability to adjust and respond to a wide range of environmental and host-associated conditions . The human pathogen Pseudomonas aeruginosa has an ability to thrive in a variety of hosts and cause a range of acute and chronic infections in individuals with impaired... | Identifying coordinately regulated genes and their control by environmentally-initiated signal transduction pathways is important for understanding bacterial virulence mechanisms . The work reported here provides a comprehensive , high resolution , transcriptome map of the opportunistic pathogen Pseudomonas aeruginosa ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"biology",
"microbiology"
] | 2012 | The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature |
Numerous instances of presence/absence variations for introns have been documented in eukaryotes , and some cases of recurrent loss of the same intron have been suggested . However , there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss . Of 883 cases of intron presence/absence vari... | The spliceosomal introns are nucleotide sequences that interrupt coding regions of eukaryotic genes and are removed by RNA splicing after transcription . Recent studies have reported several examples of possible recurrent intron loss or gain , i . e . , introns that are independently removed from or inserted into the i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"organismal",
"evolution",
"plant",
"science",
"genomics",
"genome",
"evolution",
"plant",
"evolution",
"genetics",
"biology",
"and",
"life",
"sciences",
"comparative",
"genomics",
"computational",
"biology",
"evolutionary",
"biology"
] | 2014 | Recurrent Loss of Specific Introns during Angiosperm Evolution |
Bacterial biofilms are associated with numerous human infections . The predominant protein expressed in enteric biofilms is the amyloid curli , which forms highly immunogenic complexes with DNA . Infection with curli-expressing bacteria or systemic exposure to purified curli-DNA complexes triggers autoimmunity via the ... | Bacterial amyloids are conserved proteins expressed by many bacteria in biofilms . Bacterial amyloid curli and DNA form highly immunogenic complexes that stimulate autoimmunity and accelerate the progression of systemic lupus erythematosus . Here , we show that the innate immune receptors TLR2 and TLR9 are critical for... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"bacteriology",
"biofilms",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"cellulose",
"pathogens",
"immunology",
"microbiology",
"organic",
"c... | 2017 | Bacterial amyloid curli acts as a carrier for DNA to elicit an autoimmune response via TLR2 and TLR9 |
Q fever is a worldwide zoonotic disease caused by Coxiella burnetii . Epidemiologically , animals are considered reservoirs and humans incidental hosts . We investigated Q fever in rural Senegal . Human samples ( e . g . , sera , saliva , breast milk , feces ) were screened in the generally healthy population of two vi... | Q fever is a zoonotic disease known since 1937 . The disease may be severe , causing pneumonia , hepatitis and endocarditis . Q fever agent has been described as a possible biological weapon . Animals—especially domestic cows , goats and sheep—are considered reservoirs for this infection . They are capable of sustainin... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"microbiology/environmental",
"microbiology",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"ecology/environmental",
"microbiology",
"infectious",
"diseases/bacterial",
"infections",
"microbiology/applied",
"microbiology",
"infectious",
"diseases/tropical",
"and",
"trav... | 2010 | Coxiella burnetii in Humans and Ticks in Rural Senegal |
Plant pathogen effectors can recruit the host post-translational machinery to mediate their post-translational modification ( PTM ) and regulate their activity to facilitate parasitism , but few studies have focused on this phenomenon in the field of plant-parasitic nematodes . In this study , we show that the plant-pa... | Post-translational modification ( PTM ) is a tool used by prokaryotic and eukaryotic cells to regulate protein activity , and many unique and important functions of proteins depend on appropriate PTMs . Evidence is emerging that plant pathogen effectors can utilize the host post-translational machinery to mediate their... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"pathology",
"and",
"laboratory",
"medicine",
"plant",
"science",
"rice",
"genetically",
"modified",
"plants",
"experimental",
"organism",
"sy... | 2017 | A novel Meloidogyne graminicola effector, MgGPP, is secreted into host cells and undergoes glycosylation in concert with proteolysis to suppress plant defenses and promote parasitism |
Like other arthropod-borne viruses ( arboviruses ) , mosquito-borne dengue virus ( DENV ) is maintained in an alternating cycle of replication in arthropod and vertebrate hosts . The trade-off hypothesis suggests that this alternation constrains DENV evolution because a fitness increase in one host usually diminishes f... | Dengue virus ( DENV ) is an arthropod-borne virus of immense public health concern . Recent studies suggest that the rate of DENV evolution has accelerated , as well as the disease severity ( virulence ) , most likely driven by the increased transmission and selection by the vector , Aedes aegypti , over the last 50 ye... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"virology/virus",
"evolution",
"and",
"symbiosis",
"evolutionary",
"biology/genomics",
"infectious",
"diseases/viral",
"infections",
"... | 2009 | Mosquitoes Put the Brake on Arbovirus Evolution: Experimental Evolution Reveals Slower Mutation Accumulation in Mosquito Than Vertebrate Cells |
MicroProteins are short , single domain proteins that act by sequestering larger , multi-domain proteins into non-functional complexes . MicroProteins have been identified in plants and animals , where they are mostly involved in the regulation of developmental processes . Here we show that two Arabidopsis thaliana mic... | MicroProteins are short single-domain proteins that possess the ability to interfere with larger multi-domain proteins . These protein species can be identified in plants and animals where they evolved from large proteins by successive domain-loss . MicroProteins often act as decoys thus interaction with their targets ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"sequencing",
"techniques",
"plant",
"anatomy",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"plant",
"science",
"genetically",
"modified",
"plants",
"transcription",
"factors",
"sequence",
"motif",
"analysis",
"molecular",
"... | 2016 | MicroProtein-Mediated Recruitment of CONSTANS into a TOPLESS Trimeric Complex Represses Flowering in Arabidopsis |
Action potential ( AP ) generation in inhibitory interneurons is critical for cortical excitation-inhibition balance and information processing . However , it remains unclear what determines AP initiation in different interneurons . We focused on two predominant interneuron types in neocortex: parvalbumin ( PV ) - and ... | Inhibitory interneurons in the cerebral cortex are diverse in many respects . Here , we examine whether this diversity extends to the composition of ion channels along the axon , which might determine the neurons' excitability . We performed patch-clamp recordings from cortical interneuron axons in brain slices obtaine... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"epilepsy",
"medicine",
"and",
"health",
"sciences",
"physiology",
"neurology",
"biology",
"and",
"life",
"sciences",
"electrophysiology",
"neuroscience"
] | 2014 | Action Potential Initiation in Neocortical Inhibitory Interneurons |
The ability of intracellular pathogens to manipulate host-cell viability is critical to successful infection . Some pathogens promote host-cell survival to protect their replicative niche , whereas others trigger host-cell death to facilitate release and dissemination of the pathogen after intracellular replication has... | Histoplasma capsulatum is the causative agent of histoplasmosis , a fungal infection that can be fatal in a wide range of mammalian hosts , including otherwise healthy , immunocompetent individuals . Histoplasma cells replicate to very high levels within host macrophages , eventually causing macrophage death and the re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"yeast",
"infections",
"pathology",
"and",
"laboratory",
"medicine",
"intracellular",
"pathogens",
"gene",
"regulation",
"pathogens",
"regulatory",
"proteins",
"immunology",
... | 2017 | The transcription factor CHOP, an effector of the integrated stress response, is required for host sensitivity to the fungal intracellular pathogen Histoplasma capsulatum |
KtrAB belongs to the Trk/Ktr/HKT superfamily of monovalent cation ( K+ and Na+ ) transport proteins that closely resemble K+ channels . These proteins underlie a plethora of cellular functions that are crucial for environmental adaptation in plants , fungi , archaea , and bacteria . The activation mechanism of the Trk/... | Animals have organs that regulate the balance of water and ions in the fluids bathing their cells . In contrast , the cells of plants , bacteria , and fungi have little or no control over those fluids and , thus , they have to cope with changes in the local environment . These cells have therefore evolved specific mole... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"vesicles",
"crystal",
"structure",
"chemical",
"compounds",
"built",
"structures",
"engineering",
"and",
"technology",
"condensed",
"matter",
"physics",
"electrophysiology",
"neuroscience",
"organic",
"compounds",
"membrane",
"pro... | 2016 | Dissecting the Molecular Mechanism of Nucleotide-Dependent Activation of the KtrAB K+ Transporter |
Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure . Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use , from maximum likelihood and pa... | Phylogenetic networks are used to represent reticulate evolution , that is , cases in which the tree-of-life metaphor for evolution breaks down , because some of its branches have merged at one or several points in the past . This may occur , for example , when some organisms in the phylogeny are hybrids . In this pape... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"horizontal",
"gene",
"transfer",
"organismal",
"evolution",
"microbiology",
"gene",
"transfer",
"optimization",
"phylogenetics",
"data",
"management",
"mathematics",
"phylogenetic",
"analysis",
"network",
"analysis",
"microbial",
"evolution",
"computer",
"and",... | 2017 | Rearrangement moves on rooted phylogenetic networks |
Cryptosporidium is an important zoonotic parasite globally . Few studies have examined the ecology and epidemiology of this pathogen in rural tropical systems characterized by high rates of overlap among humans , domesticated animals , and wildlife . We investigated risk factors for Cryptosporidium infection and assess... | Cryptosporidium is a common zoonotic gastrointestinal parasite . In a cross-sectional survey of humans , non-human primates ( chimpanzees and baboons ) and livestock in the Greater Gombe Ecosystem , Tanzania , Cryptosporidium infection rate was 4 . 3% , 16 . 0% and 9 . 6% respectively . Infection was not associated wit... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Epidemiology and Molecular Characterization of Cryptosporidium spp. in Humans, Wild Primates, and Domesticated Animals in the Greater Gombe Ecosystem, Tanzania |
Tissue shape is often established early in development and needs to be scaled isotropically during growth . However , the cellular contributors and ways by which cells interact tissue-wide to enable coordinated isotropic tissue scaling are not yet understood . Here , we follow cell and tissue shape changes in the zebra... | As the shape of a tissue or organ is usually important for its function , it is critical to understand both how tissues form with the correct size and how their shape is maintained during development . However , so far , most studies have focused on how the shape of tissues changes during morphogenesis , while little i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"fish",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"ocular",
"anatomy",
"vertebrates",
"geometry",
"animals",
"aspect",
"ratio",
"animal",
"models",
"osteichthyes",
"developmental",
"biology",
"model",
"... | 2018 | A non-cell-autonomous actin redistribution enables isotropic retinal growth |
Cofilin is an essential actin remodeling protein promoting depolymerization and severing of actin filaments . To address the relevance of cofilin for the development and function of T cells in vivo , we generated knock-in mice in which T-cell–specific nonfunctional ( nf ) cofilin was expressed instead of wild-type ( WT... | T cells are produced in the thymus and are critical to fighting infections and combating cancer . To move through the body and to fulfill their specific functions , T cells need to dynamically reshape their cell body . This requires remodeling the actin cytoskeleton using a plethora of actin-binding proteins , includin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"animal",
"models",
"model",
"organisms",
"stem",
"cells",
"experimental",
"organism",
"systems",
"research",
"and",
"analysis",
"method... | 2018 | The actin remodeling protein cofilin is crucial for thymic αβ but not γδ T-cell development |
Chikungunya virus ( CHIKV ) is a re-emerging global pathogen with pandemic potential , which causes fever , rash and debilitating arthralgia . Older adults over 65 years are particularly susceptible to severe and chronic CHIKV disease ( CHIKVD ) , accounting for >90% of all CHIKV-related deaths . There are currently no... | Chikungunya virus ( CHIKV ) causes an acute febrile syndrome and severe acute and chronic joint disease that , for unknown reasons , especially affects older adults . CHIKV has recently reached the Americas and is threatening the Southeastern USA . At the present there is no approved vaccine or antiviral treatments aga... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"togaviruses",
"chikungunya",
"infection",
"immune",
"cells",
"enzyme-linked",
"immunoassays",
"pa... | 2016 | Dysregulated TGF-β Production Underlies the Age-Related Vulnerability to Chikungunya Virus |
To date , no large scale , systematic description of the blood serum proteome has been performed in inflammatory bowel disease ( IBD ) patients . By using microarray technology , a more complete description of the blood proteome of IBD patients is feasible . It may help to achieve a better understanding of the disease ... | GWAS have resulted in greater than one hundred susceptibility loci for inflammatory bowel disease ( Crohn’s Disease and Ulcerative Colitis ) . However , the molecular etiology of these diseases is not completely understood . In this study we profiled serum protein levels in IBD and control subjects and demonstrated an ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"serum",
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"ulcerative",
"colitis",
"colitis",
"physiological",
"processes",
"developmental",
"biology",
"organism",
"development",
"gastroenterology",
"and",
"hepat... | 2017 | High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors |
Altered cellular metabolism is an important characteristic and driver of cancer . Surprisingly , however , we find here that aggregating individual gene expression using canonical metabolic pathways fails to enhance the classification of noncancerous vs . cancerous tissues and the prediction of cancer patient survival ... | Cancer proliferating cells adapt their metabolism to support the conversion of available nutrients into biomass , which often involves an increased rate of specific metabolic pathways , such as glycolysis . Surprisingly , however , we observe that aggregating individual gene expression using canonical human metabolic p... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"metabolic",
"networks",
"cancers",
"and",
"neoplasms",
"cell",
"metabolism",
"neuroscience",
"oncology",
"metabolites",
"artificial",
"intelligence",
"network",
"analysis",
"computer",
"... | 2016 | Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction |
Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies . This work presents a simulation method to directly study the equilibrium of multiple states . This method constructs a virtual mixture of multi... | Computer simulation plays an important role to understand molecular systems and has been applied to problems of increasing complexity . Multistate equilibrium is a fundamental concept behind the structure and function of biological systems . Due to the limit in computing resources and lack of good alternative methods ,... | [
"Abstract",
"Introduction",
"Results",
"Discussions",
"Methods"
] | [] | 2015 | A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water |
As many as 59% of the transcription factors in Escherichia coli regulate the transcription rate of their own genes . This suggests that auto-regulation has one or more important functions . Here , one possible function is studied . Often the transcription rate of an auto-regulator is also controlled by additional trans... | Bacteria adjust which proteins they make , and how many copies of each kind , depending on their environment . The production rate of each regulated protein is controlled by a special class of proteins called transcription factors . The rate at which a certain protein is produced usually depends on the cellular concent... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biophysics/transcription",
"and",
"translation",
"genetics",
"and",
"genomics/gene",
"expression",
"computational",
"biology/transcriptional",
"regulation"
] | 2010 | Combinatorial Gene Regulation Using Auto-Regulation |
Facultative bacterial endosymbionts are associated with many arthropods and are primarily transmitted vertically from mother to offspring . However , phylogenetic affiliations suggest that horizontal transmission must also occur . Such horizontal transfer can have important biological and agricultural consequences when... | Vertically-transmitted facultative bacterial endosymbionts are common in invertebrates , and affect traits as diverse as the mode of sexual reproduction , speciation , and susceptibility to pathogens . Horizontal transmission of endosymbionts is thought to be infrequent in most species , and not to contribute to their ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The Intracellular Bacterium Wolbachia Uses Parasitoid Wasps as Phoretic Vectors for Efficient Horizontal Transmission |
Respiratory syncytial virus ( RSV ) is an important cause of acute respiratory disease in infants , immunocompromised subjects and the elderly . However , it is unclear why most primary RSV infections are associated with relatively mild symptoms , whereas some result in severe lower respiratory tract infections and bro... | Respiratory syncytial virus ( RSV ) infections are an important cause of hospitalization of infants during the winter season . However , RSV is often not the only detectable pathogen , but co-infections with respiratory bacteria are common . It has been hypothesized that this results from epithelial damage caused by th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/virulence",
"factors",
"and",
"mechanisms",
"respiratory",
"medicine/respiratory",
"infections",
"virology/vaccines",
"infectious",
"diseases/viral",
"infections",
"infectious",
"diseases/respiratory",
"infections",
"respiratory",
"medicine/respiratory",
"pediatrics",
"mi... | 2010 | The Synthetic Bacterial Lipopeptide Pam3CSK4 Modulates Respiratory Syncytial Virus Infection Independent of TLR Activation |
TANK-binding kinase-1 ( TBK1 ) is an integral component of Type I interferon induction by microbial infection . The importance of TBK1 and Type I interferon in antiviral immunity is well established , but the function of TBK1 in bacterial infection is unclear . Upon infection of murine embryonic fibroblasts with Salmon... | Early control of invading microbial pathogens is an essential function of the host response to infection . Previous studies have shown that upon viral infection , a protein called TANK-binding kinase-1 ( TBK1 ) signals the induction of a program of protection that results in inhibition of viral replication . During inf... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion",
"Supporting",
"Information"
] | [
"infectious",
"diseases",
"homo",
"(human)",
"immunology",
"microbiology",
"mus",
"(mouse)",
"molecular",
"biology",
"eubacteria"
] | 2007 | TBK1 Protects Vacuolar Integrity during Intracellular Bacterial Infection |
Burkholderia pseudomallei is the causative agent of melioidosis , a severe infectious disease in tropical regions . It is necessary to understand the risk of acquiring this infection from the environment . The prevalence , concentration and genetic diversity of B . pseudomallei isolates collected from two sites in Buri... | Burkholderia pseudomallei , an environmental bacterium , causes melioidosis , a serious but neglected infectious disease that is endemic in many tropical regions . Infection routes include inoculation , ingestion and inhalation . Several environmental sources serve as niches for persistence , providing a mechanism for ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"water",
"resources",
"body",
"fluids",
"melioidosis",
"geographical",
"locations",
"ponds",
"bacterial",
"diseases",
"plant",
"science",
"rice",
"experimental",
"organism",
"systems... | 2019 | Prevalence and genetic diversity of Burkholderia pseudomallei isolates in the environment near a patient’s residence in Northeast Thailand |
The genus Neisseria includes both commensal and pathogenic species which are genetically closely related . However , only meningococcus and gonococcus are important human pathogens . Very few toxins are known to be secreted by pathogenic Neisseria species . Recently , toxins secreted via type V secretion system and bel... | Many bacteria are able to secrete toxins targeted against neighboring cells . In order to protect themselves against their own toxin , they also express an “immunity” protein . In silico analysis of bacterial genomes predicts that numerous genes could encode potential new toxin-immunity systems . The recently described... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"molecular",
"biology",
"biology",
"and",
"life",
"sciences",
"microbiology"
] | 2015 | A New Family of Secreted Toxins in Pathogenic Neisseria Species |
We report here the ~670 Mb genome assembly of the Asian seabass ( Lates calcarifer ) , a tropical marine teleost . We used long-read sequencing augmented by transcriptomics , optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 s... | We describe the genome assembly of Asian seabass ( Lates calcarifer ) , a marine teleost with aquaculture relevance . Though >500 eukaryotic genome sequences are available in public repositories , the majority are highly fragmented with incomplete assemblies , which explains why considerable effort and resources are of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"genomic",
"library",
"construction",
"sequence",
"assembly",
"tools",
"genome",
"analysis",
"dna",
"construction",
"molecular",
"biology",
"techniques",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"genomic",
"libraries",
... | 2016 | Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding |
There is much interest in the mechanisms that regulate adult tissue homeostasis and their relationship to processes governing foetal development . Mice deleted for the Wilms' tumour gene , Wt1 , lack kidneys , gonads , and spleen and die at mid-gestation due to defective coronary vasculature . Wt1 is vital for maintain... | It is important to understand the cellular and molecular pathways that regulate the maintenance and turnover of adult tissues . These processes often go awry in diseases and are likely to deteriorate with ageing . Here we show that removal of a single gene , the Wilms' Tumour gene , Wt1 , in the adult mouse leads to th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"developmental",
"biology",
"histology",
"model",
"organisms",
"physiology",
"genetics",
"immunology",
"biology",
"anatomy",
"and",
"physiology",
"molecular",
"cell",
"biology",
"proteomics",
"genetics",
"and",
"genomics"
] | 2011 | Acute Multiple Organ Failure in Adult Mice Deleted for the Developmental Regulator Wt1 |
An increased prevalence of epilepsy has been reported in many onchocerciasis endemic areas . The objective of this study was to determine the prevalence of epilepsy in onchocerciasis endemic areas in the Democratic Republic of the Congo ( DRC ) and investigate whether a higher annual intake of Ivermectin was associated... | An increased prevalence of epilepsy has been reported in many onchocerciasis endemic areas . Between July 2014 and February 2016 , house-to-house epilepsy prevalence surveys were carried out in the Bas-Uele , Tshopo and Ituri province of the Democratic Republic of the Congo , in areas with a high level of onchocerciasi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"rivers",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"age",
"gro... | 2017 | High prevalence of epilepsy in onchocerciasis endemic regions in the Democratic Republic of the Congo |
Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes . The traditional view of these elements is that of local RNA structures . This perspective , however , is changing due to increasing discoveries of functional viral RNA elements that are formed by lo... | Plus-strand ( i . e . messenger-sensed ) RNA viruses are responsible for significant diseases in plants and animals . The single-stranded RNA genomes of these viruses serve as templates for translation of viral proteins and perform other essential functions that generally involve local RNA structures , such as RNA hair... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry/molecular",
"evolution",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"biochemistry/rna",
"structure",
"virology/viral",
"replication",
"and",
"gene",
"regulation",
"evolutionary",
"biology/genomics",
"virology",
"biochemistry/structural",
"g... | 2009 | A Discontinuous RNA Platform Mediates RNA Virus Replication: Building an Integrated Model for RNA–based Regulation of Viral Processes |
Clostridium difficile spore germination is critical for the transmission of disease . C . difficile spores germinate in response to cholic acid derivatives , such as taurocholate ( TA ) , and amino acids , such as glycine or alanine . Although the receptor with which bile acids are recognized ( germinant receptor ) is ... | Germination by C . difficile spores is one of the very first steps in the pathogenesis of this organism . The transition from the metabolically dormant spore form to the actively-growing , toxin-producing vegetative form is initiated by certain host-derived bile acids and amino acid signals . Despite near universal con... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"bacteriology",
"medicine",
"and",
"health",
"sciences",
"gut",
"bacteria",
"body",
"fluids",
"chemical",
"compounds",
"pathology",
"and",
"laboratory",
"medicine",
"aliphatic",
"amino",
"acids",
"pathogens",
"bacillus",
"microbiology",
"bile",
"organic",
"compounds",
... | 2019 | The requirement for co-germinants during Clostridium difficile spore germination is influenced by mutations in yabG and cspA |
Horizontal gene transfer ( HGT ) , the transfer of genetic material between organisms , is crucial for genetic innovation and the evolution of genome architecture . Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral ( vertically derived ) genes ... | The transfer of genetic material between organisms , usually denoted as horizontal ( or lateral ) gene transfer ( HGT or LGT ) , is a prime mechanism in microbial evolution and responsible for genetic innovation and the evolution of genome architecture . Detecting HGT between closely related species or strains is imper... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [] | 2015 | Detecting Horizontal Gene Transfer between Closely Related Taxa |
Breast cancer is strongly influenced by hereditary risk factors , a majority of which still remain unknown . Here , we performed a targeted next-generation sequencing of 796 genes implicated in DNA repair in 189 Finnish breast cancer cases with indication of hereditary disease susceptibility and focused the analysis on... | Although the contribution of hereditary susceptibility to breast cancer is well-established , the majority of predisposing factors still remain unidentified . Here , we have taken advantage of recent technical and methodological advances and performed a massive parallel sequencing of hundreds of DNA damage response gen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cancer",
"detection",
"and",
"diagnosis",
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"cancers",
"and",
"neoplasms",
"oncology",
"dna",
"damage",
"mutation",
"dna",
"mutation",
"databases",
"research",
"and",
"analysis",
"methods",
"ovarian",
"canc... | 2016 | Targeted Next-Generation Sequencing Identifies a Recurrent Mutation in MCPH1 Associating with Hereditary Breast Cancer Susceptibility |
Soil-transmitted helminth infections are among the most common infections in developing countries . Globally , as many as 2 billion people are considered to be at risk for soil-transmitted-helminth ( STH ) infections . Preschool children ( PSAC ) , school-age children ( SAC ) and women of reproductive age ( WRA ) are a... | Soil-transmitted helminths ( STH ) are intestinal worms that cause morbidity in many people worldwide; children and women of reproductive-age ( WRA ) are the group most at risk of these infections . The primary control strategy is the periodic anthelminthic treatment of people at risk of STH . Over the last five years ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"children",
"medicine",
"and",
"health",
"sciences",
"maternal",
"health",
"obstetrics",
"and",
"gynecology",
"helminths",
"tropical",
"diseases",
"hookworms",
"geographical",
"locations",
"parasitic",
"diseases",
"animals",
"age",
"groups",
"adults",
"... | 2018 | Estimation of the number of women of reproductive age in need of preventive chemotherapy for soil-transmitted helminth infections |
There is increasing evidence that induction of local immune responses is a key component of effective vaccines . For respiratory pathogens , for example tuberculosis and influenza , aerosol delivery is being actively explored as a method to administer vaccine antigens . Current animal models used to study respiratory p... | Influenza virus infection in pigs represents a significant problem to industry and also carries substantial risks to human health . Pigs can be infected with both bird and human forms of influenza where these viruses can mix with swine influenza viruses to generate new pandemic strains that can spread quickly and kill ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pig",
"models",
"influenza",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"cloning",
"orthomyxoviruses",
"animals",
"mammals",
"anim... | 2018 | Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig |
The relationship between population size , inbreeding , loss of genetic variation and evolutionary potential of fitness traits is still unresolved , and large-scale empirical studies testing theoretical expectations are surprisingly scarce . Here we present a highly replicated experimental evolution setup with 120 line... | Genetic variation is a prerequisite for evolution to occur . Quantifying , utilizing and understanding the role of this variation for the survival and persistence of populations is central to several research disciplines including evolutionary biology , animal and plant breeding and conservation genetics . Environments... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"ecology",
"and",
"environmental",
"sciences",
"genome",
"evolution",
"population",
"genetics",
"conservation",
"genetics",
"computational",
"biology",
"evolutionary",
"adaptation",
"population",
"biology",
"extinct",
"genomes",
"conservation",
"biology",
"genetic",
"polymo... | 2019 | Genomic variation predicts adaptive evolutionary responses better than population bottleneck history |
RNA editing ligase 1 ( TbREL1 ) is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei , the parasite responsible for the devastating tropical disease African sleeping sickness . The type of RNA editing that TbREL1 is involved in is unique to the trypanosomes , and no close human ho... | RNA editing ligase 1 ( TbREL1 ) is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei , the parasite responsible for the devastating tropical disease African sleeping sickness . The type of RNA editing that TbREL1 is involved in is unique to the trypanosomes , and no close human ho... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"and",
"Discussion"
] | [
"chemistry/biochemistry",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"biophysics/theory",
"and",
"simulation",
"computer",
"science/numerical",
"analysis",
"and",
"theoretical",
"computing",
"biophysics/protein",
"chemistry",
"and",
"proteomics",
"chemical",
"b... | 2007 | Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei |
A key step toward understanding the function of a brain circuit is to find its wiring diagram . New methods for optical stimulation and optical recording of neurons make it possible to map circuit connectivity on a very large scale . However , single synapses produce small responses that are difficult to measure on a l... | The circuitry of the brain is defined by the connections ( synapses ) between its cells . Synapses are very small , so it is difficult to identify more than a few at a time using standard methods like electron microscopy or high-precision electrical recordings from cells . This study shows that it is possible to measur... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physiology/neuronal",
"signaling",
"mechanisms",
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/computational",
"neuroscience"
] | 2008 | How To Record a Million Synaptic Weights in a Hippocampal Slice |
Bacterial pathogens that reside in membrane bound compartment manipulate the host cell machinery to establish and maintain their intracellular niche . The hijacking of inter-organelle vesicular trafficking through the targeting of small GTPases or SNARE proteins has been well established . Here , we show that intracell... | The obligate intracellular bacterial pathogen Chlamydia has developed strategies to invade , survive and replicate within the host genital , ocular and pulmonary epithelial surfaces . Chlamydia developmental cycle occurs in a membrane bound vacuole , the inclusion . The Chlamydia-dependent remodeling of the inclusion m... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"gram",
"negative",
"microbial",
"pathogens",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"microbial",
"growth",
"and",
"development",
"bacterial",
"pathogens"
] | 2011 | The Lipid Transfer Protein CERT Interacts with the Chlamydia Inclusion Protein IncD and Participates to ER-Chlamydia Inclusion Membrane Contact Sites |
The gastric lamina propria of mice that have been experimentally infected with the pathobiont Helicobacter pylori hosts a dense network of myeloid cells that includes BATF3-dependent CD103+ dendritic cells ( DCs ) . We show here that CD103+ DCs are strictly required for gastric Th1 responses to H . pylori and for H . p... | In this work , Arnold & Zhang et al report that CD103+ DCs are required for protective Th1 responses , infection control of mucosal and systemic bacterial pathogens , and anti-tumor immunity driven by CD4+ Th1 cells and CD8+ T cells . CD103+ DCs further specifically promote the recruitment of Tbet+ peripherally induced... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"cell-mediated",
"immunity",
"microbiology",
"bacterial",
"diseases",
"helicobacter",
"gastroenterolo... | 2019 | BATF3-dependent dendritic cells drive both effector and regulatory T-cell responses in bacterially infected tissues |
Trypanosomatids such as Leishmania and Trypanosoma are digenetic , single-celled , parasitic flagellates that undergo complex life cycles involving morphological and metabolic changes to fit them for survival in different environments within their mammalian and insect hosts . According to current consensus , asymmetric... | Tsetse-transmitted trypanosomes are parasitic protists that cause severe human and livestock diseases in tropical Africa . During their developmental cycle in the tsetse fly , these trypanosomes undergo complex cycles of differentiation and proliferation . Here we have investigated part of the developmental cycle of th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"trypanosoma",
"congolense",
"microbiology",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
... | 2018 | Shape-shifting trypanosomes: Flagellar shortening followed by asymmetric division in Trypanosoma congolense from the tsetse proventriculus |
During Trypanosoma cruzi infection , macrophages produce reactive oxygen species ( ROS ) in a process called respiratory burst . Several works have aimed to elucidate the role of ROS during T . cruzi infection and the results obtained are sometimes contradictory . T . cruzi has a highly efficiently regulated antioxidan... | The parasite Trypanosoma cruzi is the causative agent of Chagas’ disease , which affects 10 million people , mainly in Latin American . Macrophages are one of the first cellular actors facing the invasion of pathogens and during T . cruzi infection , produce reactive oxygen species ( ROS ) . To deal with oxidative stre... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"reactive",
"oxygen",
"species",
"immune",
"cells",
"respiratory",
"infections",
"parasite",
"replication",
"immunology",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"pulmonology",
"parasit... | 2016 | Trypanosoma cruzi Needs a Signal Provided by Reactive Oxygen Species to Infect Macrophages |
Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis , are possible and realizable on hundreds of proteins with variate structures and interfaces . We demonstrated this on the 168 proteins of t... | Protein-protein interactions ( PPI ) are at the heart of the molecular processes governing life and constitute an increasingly important target for drug design . Given their importance , it is vital to determine which protein interactions have functional relevance and to characterize the protein competition inherent to... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information |
The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation ( APP ) pathway . We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level . Results showed that 11 genes evolved adaptively in mammals . Several positively selected ... | Antigen-presenting cells digest intracellular and extracellular proteins and display the resulting antigenic repertoire on cell surface molecules for recognition by T cells . This process initiates cell-mediated immune responses and is essential to detect infections . The antigenic repertoire is generated by the antige... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"antigen",
"processing",
"and",
"recognition",
"biology",
"and",
"life",
"sciences",
"immunology",
"evolutionary",
"biology",
"evolutionary",
"genetics"
] | 2014 | An Evolutionary Analysis of Antigen Processing and Presentation across Different Timescales Reveals Pervasive Selection |
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