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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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Evaluating the importance of higher-order correlations of neural spike counts has been notoriously hard . A large number of samples are typically required in order to estimate higher-order correlations and resulting information theoretic quantities . In typical electrophysiology data sets with many experimental conditi... | Populations of neurons signal information by their joint activity . Dependencies between the activity of multiple neurons are typically described by the linear correlation coefficient . However , this description of the dependencies is not complete . Dependencies beyond the linear correlation coefficient , so-called hi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"visual",
"system",
"probability",
"distribution",
"mathematics",
"computational",
"neuroscience",
"statistics",
"biology",
"sensory",
"systems",
"neuroscience",
"statistical",
"methods",
"probability",
"theory",
"coding",
"mechanisms"
] | 2012 | A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts |
An increasing number of biological machines have been revealed to have more than two macroscopic states . Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions . However , the present models seem to be insufficient to describe such multiple-state systems . To meet... | A central goal of biology is to understand the function of the organism and its constituent parts at each of its scales of complexity . Function at the molecular level is often realized by changes in conformation . Unfortunately , experimental explorations of global motions critical for functional conformational change... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"computational",
"biology",
"biophysics",
"simulations",
"biophysics"
] | 2012 | Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein |
Extracellular matrix ( ECM ) assembly and remodelling is critical during development and organ morphogenesis . Dysregulation of ECM is implicated in many pathogenic conditions , including cancer . The type II transmembrane serine protease matriptase and the serine protease prostasin are key factors in a proteolytic cas... | Epithelial tissue covers the outside of the animal body and lines internal organs . Its disorganization is the source of approximately 90% of all human cancers . Elaboration of the basic epithelial characteristics has led to an understanding of how complex structures such as the branched tubular networks of vertebrate ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"chitin",
"invertebrates",
"zymogens",
"enzymes",
"enzymology",
"vertebrates",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"materials",
"science",
"experimental",
"organism",
"systems",
"embryos",
"macromole... | 2019 | Conserved function of the matriptase-prostasin proteolytic cascade during epithelial morphogenesis |
The present study aims to identify antigens in protein extracts of promastigote and amastigote-like Leishmania ( Leishmania ) chagasi syn . L . ( L . ) infantum recognized by antibodies present in the sera of dogs with asymptomatic and symptomatic visceral leishmaniasis ( VL ) . Proteins recognized by sera samples were... | Canine visceral leishmaniasis ( CVL ) is an important emerging zoonosis caused by Leishmania ( Leishmania ) infantum in the Mediterranean and Middle East and L . ( L . ) chagasi ( syn . L . ( L . ) infantum ) in Latin America . Due to their genotypic relationships , these species are considered identical . The present ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"clinical",
"laboratory",
"sciences",
"immunology",
"neglected",
"tropical",
"diseases",
"veterinary",
"science",
"veterinary",
"medicine",
"infectious",
"diseases",
"veterinary",
"diseases",
"proteins",
"zoonotic",
"diseases",
"biology",
"proteomics",
"biochemi... | 2012 | Identification of Proteins in Promastigote and Amastigote-like Leishmania Using an Immunoproteomic Approach |
Cationic antimicrobial peptides are ancient and ubiquitous immune effectors that multicellular organisms use to kill and police microbes whereas antibiotics are mostly employed by microorganisms . As antimicrobial peptides ( AMPs ) mostly target the cell wall , a microbial ‘Achilles heel’ , it has been proposed that ba... | Cationic antimicrobial peptides are ancient and ubiquitous immune effectors that multicellular organisms use to kill and police microbes , whilst antibiotics are mostly employed by microorganisms . Here we provide a new hypothesis to explain this widespread adoption of antimicrobial peptides . We show that cationic ant... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"immunology",
"species",
"interactions",
"microbiology",
"evolutionary",
"biology"
] | 2014 | Antimicrobials, Stress and Mutagenesis |
We previously reported the presence of memory CD4+ T cells that express low levels of SAMHD1 ( SAMHD1low ) in peripheral blood and lymph nodes from both HIV-1 infected and uninfected individuals . These cells are enriched in Th17 and Tfh subsets , two populations known to be preferentially targeted by HIV-1 . Here we i... | In our previous results we reported that memory CD4+ T cells expressing low levels of SAMHD1 ( SAMHD1low ) are present in peripheral blood and lymph nodes from HIV-1 infected and uninfected individuals . These cells were enriched in Th17 and Tfh , two populations targeted by HIV-1 . Here we used purified memory CD4+CD4... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"evolutionary",
"biology",
"pathogens",
"immunology",
"microbiology",
"neuroscience",
"learning",
"and",
"memory",
... | 2019 | Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations |
After internalization , ubiquitinated signaling receptors are delivered to early endosomes . There , they are sorted and incorporated into the intralumenal invaginations of nascent multivesicular bodies , which function as transport intermediates to late endosomes . Receptor sorting is achieved by Hrs—an adaptor-like p... | The cell's genetic program is modulated by extracellular signals that activate cell surface receptors and , in turn , intracellular effectors , to regulate transcription . For cells to function normally , these signals must be turned off to avoid permanent activation—a situation often associated with cancer . For many ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"cell",
"biology"
] | 2008 | Hrs and SNX3 Functions in Sorting and Membrane Invagination within Multivesicular Bodies |
Zoonotic pathogens that cause leprosy ( Mycobacterium leprae ) and tuberculosis ( Mycobacterium tuberculosis complex , MTBC ) continue to impact modern human populations . Therefore , methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats .... | Mycobacterial pathogens that cause tuberculosis and leprosy can be detected in wild animal populations using non-invasive cheek swab samples and quantitative polymerase chain reaction assays that target specific portions of mycobacterial genomes . A preliminary study in armadillos confirms that using multiple assays in... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [] | 2015 | Validation of qPCR Methods for the Detection of Mycobacterium in New World Animal Reservoirs |
The olfactory systems of insects are fundamental to all aspects of their behaviour , and insect olfactory receptor neurons ( ORNs ) exhibit exquisite specificity and sensitivity to a wide range of environmental cues . In Drosophila melanogaster , ORN responses are determined by three different receptor families , the o... | The olfactory systems of insects are fundamental to critical behaviours such as finding mates , food and host plants . Insects can detect a wide range of environmental cues using three different families of olfactory receptor proteins . Why insects have three different families of receptor genes , and how they function... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"biochemistry",
"signal",
"transduction",
"lipids",
"cellular",
"neuroscience",
"model",
"organisms",
"genetic",
"mutation",
"molecular",
"neuroscience",
"genetic",
"screens",
"genetics",
"membranes",
"and",
"sorting",
"sensory",
"systems",
"biology",
... | 2014 | The Drosophila melanogaster Phospholipid Flippase dATP8B Is Required for Odorant Receptor Function |
Approximately 2 billion people currently suffer from intestinal helminth infections , which are typically chronic in nature and result in growth retardation , vitamin A deficiency , anemia and poor cognitive function . Such chronicity results from co-evolution between helminths and their mammalian hosts; however , the ... | Parasitic soil-transmitted helminths ( STH ) live , feed and mate within the intestine of their mammalian hosts . Infection is caused by ingestion of eggs and larvae or by active penetration of the skin by larvae from contaminated soil in poverty stricken areas lacking adequate sanitation . Infection with soil-transmit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology",
"biology"
] | 2013 | IL-1β Suppresses Innate IL-25 and IL-33 Production and Maintains Helminth Chronicity |
Repair of DNA breaks by single-strand annealing ( SSA ) is a major mechanism for the maintenance of genomic integrity . SSA is promoted by proteins ( single-strand-annealing proteins [SSAPs] ) , such as eukaryotic RAD52 and λ phage Redβ . These proteins use a short single-stranded region to find sequence identity and i... | High-fidelity repair of DNA breaks begins with accurate annealing of the complementary DNA strands . How sequence homology is efficiently detected—error-free—and eventually secured together on the molecular level is a fundamental , unsolved question . In this study , we show that the single-strand annealing protein Red... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology |
Hepatitis C virus ( HCV ) is hepatotropic and only infects humans and chimpanzees . Consequently , an immunocompetent small animal model is lacking . The restricted tropism of HCV likely reflects specific host factor requirements . We investigated if dominant restriction factors expressed in non-liver or non-human cell... | The barriers preventing viral transmission across species are only incompletely understood . On one hand , narrow tropism reflects dependence of viruses on host cell factors and their species-specific utilization . On the other hand , host cellular antiviral factors can preclude virus replication . These may be constit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"microbiology",
"host-pathogen",
"interaction",
"mechanisms",
"of",
"resistance",
"and",
"susceptibility",
"hepatitis",
"hepatitis",
"c",
"animal",
"models",
"of",
"infection",
"infectious",
"diseases",
"medical",
"microbiology",
"microbial",
"pathogens",
"bio... | 2011 | Completion of Hepatitis C Virus Replication Cycle in Heterokaryons Excludes Dominant Restrictions in Human Non-liver and Mouse Liver Cell Lines |
Sex chromosomes originated from ordinary autosomes , and their evolution is characterized by continuous gene loss from the ancestral Y chromosome . Here , we document a new feature of sex chromosome evolution: bursts of adaptive fixations on a newly formed X chromosome . Taking advantage of the recently formed neo-X ch... | Sex chromosomes have evolved independently many times in both animals and plants from ordinary chromosomes . Much research on sex chromosome evolution has focused on the degeneration and loss of genes from the Y chromosome . Here , we describe another principle of sex chromosome evolution: bursts of adaptive fixations ... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology"
] | 2009 | Accelerated Adaptive Evolution on a Newly Formed X Chromosome |
The analysis of the mutational landscape of cancer , including mutual exclusivity and co-occurrence of mutations , has been instrumental in studying the disease . We hypothesized that exploring the interplay between co-occurrence , mutual exclusivity , and functional interactions between genes will further improve our ... | The genomic landscape of cancer obtained from large scale studies revealed mutational patterns such as mutual exclusivity and co-occurrences . Despite significant efforts , the understanding of the patterns harbored by specific genes and their interplay with functional interactions are still limited . Both mutual exclu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"breast",
"tumors",
"cancer",
"risk",
"factors",
"cancers",
"and",
"neoplasms",
"oncology",
"dna",
"damage",
"mutation",
"dna",
"proteins",
"breast",
"cancer",
"somatic",
"mutation",
"genetic",
"causes",
"of",
"cancer",
"bi... | 2017 | BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions |
Modern functional genomics uncovered numerous functional elements in metazoan genomes . Nevertheless , only a small fraction of the typical non-exonic genome contains elements that code for function directly . On the other hand , a much larger fraction of the genome is associated with significant evolutionary constrain... | A key challenge in functional genomics is to predict evolutionary dynamics from functional annotation of the genome and vice versa . Modern epigenomic studies helped assign function to numerous new sequence elements , but left most of the genome essentially uncharacterized . Evolutionary genomics , on the other hand , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genomics",
"functional",
"genomics",
"genome",
"evolution",
"evolutionary",
"modeling",
"comparative",
"genomics",
"biology",
"epigenomics",
"computational",
"biology"
] | 2013 | Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences |
Neurotransmitter: sodium symporters ( NSSs ) regulate neuronal signal transmission by clearing excess neurotransmitters from the synapse , assisted by the co-transport of sodium ions . Extensive structural data have been collected in recent years for several members of the NSS family , which opened the way to structure... | Bacterial leucine transporter ( LeuT ) belongs to neurotransmitter:sodium symporter ( NSS ) family . Its human orthologs include dopamine transporter and serotonin transporter . Malfunction of NSS members has been implicated in neurological diseases , hence the significance of elucidating their mechanism of function as... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology",
"and",
"life",
"sciences"
] | 2014 | Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle |
Adaptor protein ( AP ) complexes sort cargo into vesicles for transport from one membrane compartment of the cell to another . Four distinct AP complexes have been identified , which are present in most eukaryotes . We report the existence of a fifth AP complex , AP-5 . Tagged AP-5 localises to a late endosomal compart... | Adaptor protein ( AP ) complexes facilitate the trafficking of cargo from one membrane compartment of the cell to another by recruiting other proteins to particular types of vesicles . For over 10 years , it has been assumed that there are four , and only four , distinct AP complexes in eukaryotic cells . We report the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2011 | The Fifth Adaptor Protein Complex |
Multicellular tumour spheroids capture many characteristics of human tumour microenvironments , including hypoxia , and represent an experimentally tractable in vitro model for studying interactions between radiotherapy and anticancer drugs . However , interpreting spheroid data is challenging because of limited abilit... | Studies in 3D cultures , notably multicellular tumour spheroids that mimic many features of solid tumours , have great potential for speeding up anticancer drug development . However the increased complexity of 3D cultures makes interpretation of experiments more difficult . We have developed a hybrid continuum/agent-b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods",
"and",
"materials"
] | [
"cell",
"physiology",
"carbohydrate",
"metabolism",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"oxygen",
"cell",
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"and",
"cell",
"division",
"cell",
"processes",
"carbohydrates",
"glucose",
"metabolism",
"organic",
"compounds",
"glucose",
... | 2018 | An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids |
African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development . Trypanosoma brucei rhodesiense , which infects humans and livestock in East and Southern Africa , has classicall... | Trypanosomes are single-celled organisms transmitted by the biting tsetse fly , which cause sleeping sickness in humans in sub-Saharan Africa , but also infect livestock and other mammals . Most trypanosomes cannot infect humans as they die in human serum , but two mutants of Trypanosoma brucei have evolved the ability... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Population Genetics of Trypanosoma brucei rhodesiense: Clonality and Diversity within and between Foci |
Elucidating the precise molecular events altered by disease-causing genetic variants represents a major challenge in translational bioinformatics . To this end , many studies have investigated the structural and functional impact of amino acid substitutions . Most of these studies were however limited in scope to eithe... | Identifying the molecular changes caused by mutations is a major challenge in understanding and treating human genetic disease . To address this problem , we have developed a wide range of profiling tools designed to predict specific types of functional site from protein 3D structures . We then apply these tools to dat... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infographics",
"chemical",
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"organic",
"compounds",
"mutation",
"substitution",
"mutation",
"amino",
"acid",
"substitution",
"protein",
"structure",
"prediction",
"amino",
"acids",
"protein",
"structure",
"protein",
"structure",
"databases",
"mutation",
"data... | 2016 | The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease |
Japanese encephalitis ( JE ) virus infection can cause severe disease in humans , resulting in death or permanent neurologic deficits among survivors . Studies indicate that the incidence of JE is high in northwestern Bangladesh . Pigs are amplifying hosts for JE virus ( JEV ) and a potentially important source of viru... | Japanese encephalitis ( JE ) virus infection can cause severe neurological disease in man . More JE cases are seen in northwestern districts in Bangladesh . Pigs are the most common amplifying host of the virus and can act as a potential environmental source . We conducted a comprehensive census of pigs in three JE end... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"humoral",
"immunity",
"medicine",
"and",
"health",
"sciences",
"infectious",
"disease",
"epidemiology",
"immunology",
"spatial",
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"vector-borne",
"diseases",
"tropical",
"diseases",
"epidemiological",
"methods",
"and",
"statistics",
"encephalitis",
"plant",
... | 2014 | Dynamics of Japanese Encephalitis Virus Transmission among Pigs in Northwest Bangladesh and the Potential Impact of Pig Vaccination |
Biological systems use a variety of mechanisms to deal with the uncertain nature of their external and internal environments . Two of the most common motifs employed for this purpose are the incoherent feedforward ( IFF ) and feedback ( FB ) topologies . Many theoretical and experimental studies suggest that these circ... | Essential to the survival of biological organisms is their ability to decipher and respond accordingly to stress scenarios presented by a changing and often unpredictable environment . Cellular noise , present due to the inherently random nature of both the external and internal environments , can obfuscate and corrupt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
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] | [
"control",
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"transduction",
"gene",
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"signal",
"processing",
"noise",
"reduction",
"control",
"engineering",
"micrornas",
"systems",
"... | 2016 | Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits |
Knowing how hosts respond to parasite infection is paramount in understanding the effects of parasites on host populations and hence host–parasite co-evolution . Modification of life-history traits in response to parasitism has received less attention than other defence strategies . Life-history theory predicts that pa... | Hosts have developed a variety of mechanisms to compensate for the negative impact of parasite infection . Modification of life-history traits in response to parasitism has received less attention than other defence strategies . Life-history theory assumes trade-offs between resource allocation to different fitness com... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
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] | [
"plant",
"biology/plant-biotic",
"interactions",
"ecology/evolutionary",
"ecology",
"virology/virus",
"evolution",
"and",
"symbiosis",
"evolutionary",
"biology/evolutionary",
"ecology",
"infectious",
"diseases/viral",
"infections",
"evolutionary",
"biology/developmental",
"evolutio... | 2008 | Host Responses in Life-History Traits and Tolerance to Virus Infection in Arabidopsis thaliana |
The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription , translation , ligand-substrate binding , and host immunity . In order to accurately identify motifs and other genome-scale patterns of interest ,... | The generation of random sequences is instrumental to the accurate identification of non-random motifs within genomes , yet there are currently no tools available that allow users to simultaneously specify amino acid and GC composition to create random coding sequences . Here , we develop an algorithm based on maximum ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing",
"techniques",
"computational",
"biology",
"amino",
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"analysis",
"genome",
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"motif",
"analysis",
"molecular",
"biology",
"techniques",
"thermodynamics",
"structural",
"genomics",
"research",
"and",
"analysis",
"method... | 2016 | NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents |
Although thousands of long non-coding RNAs ( lncRNA ) have been identified in the genomes of higher eukaryotes , the precise function of most of them is still unclear . Here , we show that a >65 kb , male-specific , lncRNA , called male-specific abdominal ( msa ) is required for the development of the secondary cells o... | In many animals , the male seminal fluid induces physiology changes in the mated female that increase a male’s reproductive success . These changes are often referred to as the post-mating response ( PMR ) . In Drosophila , the seminal fluid proteins responsible for generating the PMR are made in a specialized gland , ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
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] | [
"invertebrates",
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"cells",
"animals",
"long",
"non-coding",
"rnas",
"animal",
"models",
"micrornas",
"model",
"organisms",
"drosophila... | 2018 | The lncRNA male-specific abdominal plays a critical role in Drosophila accessory gland development and male fertility |
Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology . In the liver of mammals , these rhythms are controlled by transcription–translation feedback loops of the core circadian clock and by feeding–fasting cycles . To better understand the regulatory interplay between the c... | The molecular circadian clock is conserved from cyanobacteria to mammals and is believed to align behavioral and biochemical processes with the day’s 24-h diurnal cycle . How the circadian clock and feeding rhythm transcriptionally interact and what the contribution is of cis-regulatory modules to this interconnection ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Materials",
"and",
"methods"
] | [
"nucleases",
"deoxyribonucleases",
"enzymes",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"enzymology",
"dna",
"footprinting",
"circadian",
"oscillators",
"transcription",
"factors",
"chronobiology",
"molecular",
"biology",
"techniques",
"geneti... | 2017 | Transcriptional regulatory logic of the diurnal cycle in the mouse liver |
Helminth infection may affect vaccine immunogenicity and efficacy . Adolescents , a target population for tuberculosis booster vaccines , often have a high helminth burden . We investigated effects of Schistosoma mansoni ( Sm ) on the immunogenicity and safety of MVA85A , a model candidate tuberculosis vaccine , in BCG... | There is an urgent global need for an improved TB vaccine strategy . Adolescents are an important target population for a TB vaccine . In field settings where the need for a vaccine is greatest , co-infection with other pathogens including malaria , HIV and helminths , may interfere with the impact of such strategies .... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"clinical",
"research",
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"immunology",
"tropical",
"diseases",
"parasitic",
"diseases",
"animals",
"vaccines",
"bacterial",
"diseases",
... | 2017 | The effect of current Schistosoma mansoni infection on the immunogenicity of a candidate TB vaccine, MVA85A, in BCG-vaccinated adolescents: An open-label trial |
Leishmania infantum ( syn . L . chagasi ) is the causative agent of visceral leishmaniasis ( VL ) in the New World ( NW ) with endemic regions extending from southern USA to northern Argentina . The two hypotheses about the origin of VL in the NW suggest ( 1 ) recent importation of L . infantum from the Old World ( OW ... | Leishmaniasis is a vector borne disease with a broad spectrum of clinical forms caused by protozoan parasites of the genus Leishmania . Visceral leishmaniasis is the most severe , systemic form of the disease . It is caused by parasites belonging to the Leishmania donovani complex , which includes L . infantum and L . ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
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"and",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"population",
"genetics",
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"population",
"modeling",
"neglected",
"tropical",
"diseases",
"population",
"biology",
"infectious",
"disease",
"control",
"... | 2011 | Comparative Microsatellite Typing of New World Leishmania infantum Reveals Low Heterogeneity among Populations and Its Recent Old World Origin |
Genome engineering is a powerful approach to study how chromosomal architecture impacts phenotypes . However , quantifying the fitness impact of translocations independently from the confounding effect of base substitutions has so far remained challenging . We report a novel application of the CRISPR/Cas9 technology al... | Chromosomes are highly dynamic objects that often undergo large structural variations such as reciprocal translocations . Such rearrangements can have dramatic functional consequences , as they can disrupt genes , change their regulation or create novel fusion genes at their breakpoints . For instance , 90–95% of patie... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biotechnology",
"chemical",
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"genome",
"analysis",
"karyotypes",
"dna",
"genetic",
"engineering",
"bioengineering",
"genomic",
"libraries",
"genomics",
"chromosome",
"biology",
"chromosomal",
"aberrations",
"guide... | 2019 | Reshuffling yeast chromosomes with CRISPR/Cas9 |
Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution , disease genetics and the maintenance of variation genome-wide . Here , we develop an approximation to the distribution of fitness effects ( DFE ) of segregating single-nuc... | The relative frequencies of polymorphic mutations that are deleterious , nearly neutral and neutral is traditionally called the distribution of fitness effects ( DFE ) . Obtaining an accurate approximation to this distribution in humans can help us understand the nature of disease and the mechanisms by which variation ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"genetic",
"polymorphism",
"genome",
"evolution",
"natural",
"selection",
"genome",
"analysis",
"genetics",
"biology",
"and",
"life",
"sciences",
"population",
"genetics",
"computational",
"biology",
"evolutionary",
"biology",
"gen... | 2014 | Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms |
Isolations of sylvatic dengue-2 virus from mosquitoes , humans and non-human primates in Senegal show synchronized multi-annual dynamics over the past 50 years . Host demography has been shown to directly affect the period between epidemics in other pathogen systems , therefore , one might expect unsynchronized multi-a... | Dengue virus has been isolated from mosquitoes , non-human primates and humans in Senegalese jungles for the past 50 years . This sylvatic cycle shows unique transmission dynamics that are unexpected given previous theory and observation: First , the isolations appear to be synchronized across several host and vector s... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"mosquitoes",
"mathematics",
"ecology",
"dengue",
"fever",
"neglected",
"tropical",
"diseases",
"theoretical",
"ecology",
"biology",
"population",
"ecology",
"vectors",
"and",
"hosts",
"nonlinear",
"dynamics"
] | 2012 | Synchrony of Sylvatic Dengue Isolations: A Multi-Host, Multi-Vector SIR Model of Dengue Virus Transmission in Senegal |
Behavioral plasticity is the most striking trait in locust phase transition . However , the genetic basis for behavioral plasticity in locusts is largely unknown . To unravel the molecular mechanisms underlying the behavioral phase change in the migratory locust Locusta migratoria , the gene expression patterns over th... | The migratory locust , Locusta migratoria , is a worldwide agricultural pest whose outbreaks can result in plagues during which locusts mass migrate in marching bands and flying swarms . They exhibit striking phenotypic plasticity depending on the population density . They can transform between the barely-visible solit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics/gene",
"expression"
] | 2011 | CSP and Takeout Genes Modulate the Switch between Attraction and Repulsion during Behavioral Phase Change in the Migratory Locust |
Activating transcription factor 3 ( Atf3 ) is rapidly and transiently upregulated in numerous systems , and is associated with various disease states . Atf3 is required for negative feedback regulation of other genes , but is itself subject to negative feedback regulation possibly by autorepression . In cardiomyocytes ... | Activating transcription factor 3 ( Atf3 ) is an important regulatory transcription factor which is associated with inflammation , restraint of the immune response and cancer . In this work , we develop a series of mathematical models to understand how Atf3 may be regulated . Informed with data from the literature and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"mathematics",
"cell",
"biology",
"calculus",
"applied",
"mathematics",
"biology",
"and",
"life",
"sciences",
"physical",
"sciences",
"molecular",
"cell",
"biology",
"differential",
"equations"
] | 2014 | Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation |
Control of soil-transmitted helminth ( STH ) infections relies on the periodic and long-term administration of anthelmintic drugs to high-risk groups , particularly school-age children living in endemic areas . There is limited data on the effectiveness of long-term periodic anthelmintic treatment on the prevalence of ... | Soil-transmitted helminth ( intestinal worm ) infections are very common in developing countries and are an important cause of illness . Mass de-worming treatments of school children are an important strategy to reduce illness caused by these infections in communities without access to clean water and sanitation . Few ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/epidemiology",
"infectious",
"diseases/helminth",
"infections",
"public",
"health",
"and",
"epidemiology/global",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2008 | Impact of Long-Term Treatment with Ivermectin on the Prevalence and Intensity of Soil-Transmitted Helminth Infections |
A pioneering strategy developed by the World Health Organization ( WHO ) for the control of schistosomiasis was the concept of a height-based dose pole to determine praziquantel ( PZQ ) dosing in large-scale treatment campaigns . However , some recent studies have shown variable accuracy for the dose pole in terms of p... | Schistosomiasis control is currently based on large-scale , preventive chemotherapy treatment with praziquantel ( PZQ ) , and this has resulted in a significant reduction in its prevalence and associated morbidity worldwide . Recommended PZQ dosing is 40–60 mg/Kg body weight , but to facilitate large-scale drug adminis... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"body",
"weight",
"medicine",
"and",
"health",
"sciences",
"tropical",
"diseases",
"geographical",
"locations",
"parasitic",
"diseases",
"health",
"care",
"age",
"groups",
"physiological",
"parameters",
"pharmaceutics",
"obesity",
"neglected",
"tropical",
"diseases",
"a... | 2018 | Accuracy of the WHO praziquantel dose pole for large-scale community treatment of urogenital schistosomiasis in northern Mozambique: Is it time for an update? |
Endocycle is a commonly observed cell cycle variant through which cells undergo repeated rounds of genome DNA replication without mitosis . Endocycling cells arise from mitotic cells through a switch of the cell cycle mode , called the mitotic-to-endocycle switch ( MES ) , to initiate cell growth and terminal different... | Endocycle , a cell cycle variant consisting of DNA replication and Gap phases without a mitotic phase , is widespread in nature . Endocycling cells arise from proliferating cells through a switch of the cell cycle mode called mitotic-to-endocycle switching ( MES ) . While the molecular mechanisms regulating progression... | [
"Abstract",
"Introduction",
"Result",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"rna",
"interference",
"gene",
"regulation",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"animals",
"animal",
"models",
"developmental",
"biology",
"regulator",
"genes",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimen... | 2019 | Chaperonin TRiC/CCT supports mitotic exit and entry into endocycle in Drosophila |
Gamma interferon ( IFN-γ ) is known to negatively regulate murine gammaherpesvirus-68 ( MHV-68 or γHV-68 ) replication . This process involves the suppression of the viral gene replication and transcription activator ( RTA ) promoter , as well as activation of signal transducers and activators of transcription ( STAT1 ... | While viruses have developed various mechanisms to evade immune responses , hosts also have mechanisms to negatively regulate the antiviral signaling pathways to minimize potential damage . In this study , we show that MHV-68 , a gamma-herpesvirus , is able to stimulate macrophages to produce the cellular protein SOCS1... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"phosphorylation",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"rna",
"extraction",
"microbiology",
"immune",
"receptor",
"signaling",
"membrane",
"receptor",
"signaling",
"extraction",
"techniques",
"research",
"and",
"an... | 2018 | Inhibition of murine herpesvirus-68 replication by IFN-gamma in macrophages is counteracted by the induction of SOCS1 expression |
Point mutations resulting in the substitution of a single amino acid can cause severe functional consequences , but can also be completely harmless . Understanding what determines the phenotypical impact is important both for planning targeted mutation experiments in the laboratory and for analyzing naturally occurring... | Point mutations ( i . e . , changes of a single sequence element ) can have a severe impact on protein function . Many diseases are caused by such minute defects . On the other hand , the majority of such mutations does not lead to noticeable effects . Although previous research has revealed important aspects that infl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/disease",
"models",
"computational",
"biology/macromolecular",
"sequence",
"analysis",
"genetics",
"and",
"genomics/bioinformatics"
] | 2010 | Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions |
We have developed genetically modified Ae . aegypti mosquitoes that activate the conserved antiviral JAK/STAT pathway in the fat body tissue , by overexpressing either the receptor Dome or the Janus kinase Hop by the blood feeding-induced vitellogenin ( Vg ) promoter . Transgene expression inhibits infection with sever... | Dengue has represented a significant public health burden for a number of decades , and given the lack of dengue-specific drugs and limited availability of licensed vaccine , new methods for prevention and control are urgently needed . Here , we investigated whether genetic manipulation of the mosquitoes’ native JAK/ST... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"chikungunya",
"infection",
"gene",
"regulation",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"tropical",
"diseases",
"animals",
"genome",
"analysis",
"neglected",
"tropic... | 2017 | Engineered Aedes aegypti JAK/STAT Pathway-Mediated Immunity to Dengue Virus |
We describe a method to predict protein-protein interactions ( PPIs ) formed between structured domains and short peptide motifs . We take an integrative approach based on consensus patterns of known motifs in databases , structures of domain-motif complexes from the PDB and various sources of non-structural evidence .... | Complexes formed between a structured domain on one protein and an unstructured peptide on another are ubiquitous . However , they are often quite difficult to detect experimentally . The development of computational approaches to predict domain-motif interactions is therefore an important goal . We report a method to ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Predicting Peptide-Mediated Interactions on a Genome-Wide Scale |
Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane . The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial , plant-specific mechanism mediating multiple self-organizing deve... | The plant hormone auxin belongs to the major plant-specific developmental regulators . It mediates or modifies almost all aspects of plant life . One of the fascinating features of the auxin action is its directional movement between cells , whose direction can be regulated by auxin signaling itself . This plant-specif... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"plant",
"anatomy",
"gene",
"regulation",
"brassica",
"hormones",
"cell",
"polarity",
"plant",
"science",
"model",
"organisms",
"plant",
"hormones",
"experimental",
"organism",
"systems",
"bioassays",
"and",
"physiological",
"analysis",
"seedlings"... | 2018 | WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity |
Among immigrants of sub-Saharan origin , parasitic infection is the leading cause of eosinophilia , which is generally interpreted as a defense mechanism . A side effect of the inflammatory mediators released by eosinophils is damage to host organs , especially the heart . The main objectives of this study were to i ) ... | Endomyocardial fibrosis is characterized by fibrosis of the apical endocardium of the right ventricle , left ventricle , or both . Epidemiological studies of endomyocardial fibrosis indicate a predominance in tropical regions , with young people and men being affected predominantly . Little is known about the natural h... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"diagnostic",
"radiology",
"ultrasound",
"imaging",
"cardiovascular",
"anatomy",
"cardiac",
"ventricles",
"immunology",
"fibrosis",
"parasitic",
"diseases",
"echocardiography",
"developmental",
... | 2017 | Endomyocardial involvement in asymptomatic sub-Saharan immigrants with helminth-related eosinophilia |
Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes . Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level , this is still possible only in especially favorable cases . Therefor... | Unraveling the lower-level ( microscopic ) processes underlying the overall ( macroscopic ) cell response to a given stimulus is a challenging problem in cell physiology . This has been a classic problem in biophysics , where the ability to record the activity of single ion channels that generate a macroscopic ion curr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"statistical",
"noise",
"electrophysiology",
"neuroscience",
"g-protein",
"signaling",
"optimization",
"ion",
"channels",
"mathematics",
"statistics",
"(mathematics)",
"neurotransmitters",
"research",
"and",
"analysis... | 2017 | Elucidation of molecular kinetic schemes from macroscopic traces using system identification |
Extensive use of praziquantel for treatment and control of schistosomiasis requires a comprehensive understanding of efficacy and safety of various doses for different Schistosoma species . A systematic review and meta-analysis of comparative and non-comparative trials of praziquantel at any dose for any Schistosoma sp... | Praziquantel is the drug used worldwide to treat intestinal and urinary schistosomiasis , diseases caused by the infection with different species of the parasitic worm Schistosoma . Summarizing findings of different studies is important in order to characterize how the parasite responds to treatment and to what extent ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"research",
"design",
"medicine",
"and",
"health",
"sciences",
"clinical",
"medicine",
"mathematics",
"statistics",
"(mathematics)",
"clinical",
"research",
"design",
"epidemiology",
"clinical",
"trials",
"meta-analysis",
"systematic",
"reviews",
"adverse",
"reactions",
"... | 2014 | Clinical Efficacy and Tolerability of Praziquantel for Intestinal and Urinary Schistosomiasis—A Meta-analysis of Comparative and Non-comparative Clinical Trials |
Paracoccidioidomycosis ( PCM ) , an endemic systemic mycosis caused by the fungus Paracoccidioides brasiliensis ( Pb ) , usually results in severe lung damage in patients . Considering the difficulties to sequentially study the infection in humans , this work was done in mice inoculated intranasally with infective Pb-c... | Paracoccidioidomycosis ( PCM ) , an endemic fungal infection of pulmonary origin resulting in severe disseminated disease , occurs in rural areas of most South American countries and presents several clinical forms . The infection is acquired by inhalation of specific fungal propagules , called conidia . Considering th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"histology",
"infectious",
"diseases",
"model",
"organisms",
"neglected",
"tropical",
"diseases",
"immunology",
"biology",
"microbiology",
"fungal",
"diseases",
"infectious",
"disease",
"modeling",
"respiratory",
"medicine",
"pulmonology"
] | 2011 | Structural and Topographic Dynamics of Pulmonary Histopathology and Local Cytokine Profiles in Paracoccidioides brasiliensis Conidia-Infected Mice |
Staphylococcus aureus and other bacterial pathogens affix wall teichoic acids ( WTAs ) to their surface . These highly abundant anionic glycopolymers have critical functions in bacterial physiology and their susceptibility to β-lactam antibiotics . The membrane-associated TagA glycosyltransferase ( GT ) catalyzes the f... | Gram-positive bacteria cause thousands of deaths in the United States each year and are a growing health concern because many bacterial strains have become resistant to commonly used antibiotics . One of the most abundant polymers displayed on the surface of Gram-positive bacteria is wall teichoic acid ( WTA ) , a nega... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"crystal",
"structure",
"enzymes",
"condensed",
"matter",
"physics",
"enzymology",
"materials",
"science",
"crystallography",
"oligomers",
"cellular",
"structures",
"and",
"organelles",
"macromolecules",
"polymers",
"polymer",
"chemistry",
"lipids",
"solid",
"state",
"phy... | 2019 | Structure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteria |
As the demand for rabies post-exposure prophylaxis ( PEP ) treatments has increased exponentially in recent years , the limited supply of human and equine rabies immunoglobulin ( HRIG and ERIG ) has failed to provide the required passive immune component in PEP in countries where canine rabies is endemic . Replacement ... | Human mortality from endemic canine rabies is estimated to be 55 , 000 deaths per year in Africa and Asia , yet rabies remains a neglected disease throughout most of these countries . More than 99% of human rabies cases are caused by infections resulting from a dog-bite injury . In the vast majority of human exposures ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/viral",
"infections",
"virology/animal",
"models",
"of",
"infection",
"virology/new",
"therapies,",
"including",
"antivirals",
"and",
"immunotherapy",
"infectious",
"diseases/epidemiology",
"and",
"control",
"of",
"infectious",
"diseases"
] | 2009 | Development of a Mouse Monoclonal Antibody Cocktail for Post-exposure Rabies Prophylaxis in Humans |
Telomerase activity is restricted in humans . Consequentially , telomeres shorten in most cells throughout our lives . Telomere dysfunction in vertebrates has been primarily studied in inbred mice strains with very long telomeres that fail to deplete telomeric repeats during their lifetime . It is , therefore , unclear... | Telomerase mutations in humans give rise to premature ageing syndromes . In animals , the wealth of knowledge in telomere biology has been biased by the almost exclusive analysis of long-telomere mice . The role of telomere shortening requires investigation in organisms that , much like humans , have evolved telomere l... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"aging",
"physiological",
"processes",
"developmental",
"biology",
"telomeres",
"molecular",
"cell",
"biology",
"organism",
"development",
"cell",
"biology",
"chromosome",
"biology",
"physiology",
"biology",
"anatomy",
"and",
"physiology"
] | 2013 | Telomerase Is Required for Zebrafish Lifespan |
The rapidly evolving field of metabolomics aims at a comprehensive measurement of ideally all endogenous metabolites in a cell or body fluid . It thereby provides a functional readout of the physiological state of the human body . Genetic variants that associate with changes in the homeostasis of key lipids , carbohydr... | This paper reports what is , to the best of our knowledge , the first genome-wide association ( GWA ) study with metabolic traits as phenotypic traits . By simultaneous measurements of single nucleotide polymorphisms ( SNPs ) and serum concentrations of endogenous organic compounds in a human population , we identify g... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/functional",
"genomics",
"public",
"health",
"and",
"epidemiology/epidemiology",
"diabetes",
"and",
"endocrinology/type",
"2",
"diabetes",
"cardiovascular",
"disorders/coronary",
"artery",
"disease",
"genetics",
"and",
"genomics/population",
"gene... | 2008 | Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum |
Determining the molecular events induced in the spleen during schistosome infection is an essential step in better understanding the immunopathogenesis of schistosomiasis and the mechanisms by which schistosomes modulate the host immune response . The present study defines the transcriptional and cellular events occurr... | Schistosomiasis is a significant cause of illness and death in the developing world . Inflammation and scarring in the liver and enlargement of the spleen ( splenomegaly ) are common features of the disease . Changes occurring in the spleen have the potential to influence the way in which the body deals with infection ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"microbiology/immunity",
"to",
"infections",
"immunology/immune",
"response",
"immunology/immunity",
"to",
"infections",
"infectious",
"diseases/helminth",
"infections",
"microbiology/parasitology",
"pathology/immunology",... | 2010 | Co-ordinated Gene Expression in the Liver and Spleen during Schistosoma japonicum Infection Regulates Cell Migration |
Bacterial morphology is a complex trait that is highly sensitive to changes in the environment . For heterotrophic organisms , such as Escherichia coli , increases in nutrient levels are frequently accompanied by several-fold increases in both size and growth rate . Despite the dramatic nature of these changes , how al... | Often taken for granted , the shape of bacterial cells is a complex trait that is highly sensitive to environmental perturbations . Nutrients in particular , strongly impact bacterial morphology together with growth rate . The ubiquitous , rod-shaped bacteria Escherichia coli increases both length and width several fol... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"carbohydrate",
"metabolism",
"chemical",
"compounds",
"cell",
"cycle",
"and",
"cell",
"division",
"metabolic",
"processes",
"cell",
"processes",
"carbohydrates",
"cell",
"metabolism",
"organic",
"compounds",
"glucose",
"glucose",
"metabolism",
"gl... | 2018 | Comprehensive analysis of central carbon metabolism illuminates connections between nutrient availability, growth rate, and cell morphology in Escherichia coli |
Dietary restriction ( DR; sometimes called calorie restriction ) has profound beneficial effects on physiological , psychological , and behavioral outcomes in animals and in humans . We have explored the molecular mechanism of DR-induced memory enhancement and demonstrate that dietary tryptophan—a precursor amino acid ... | Optimized dietary intake is crucial for maintaining cognitive performance . A mild reduction ( between 20% and 40% ) in food intake—called dietary restriction ( DR ) or calorie restriction—has been shown to extend life span and to improve cognitive ability in various species through a mechanism that is not fully unders... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neurochemistry",
"brain",
"vertebrates",
"diet",
"mice",
"neuroscience",
"learning",
"and",
"memory",
"animals",
"mammals",
"serotonin",
"nutrition",
"cognition",
"memory",
"neurotransmitters",
"animal",
"management",
"animal",
... | 2019 | Serotonin receptor HTR6-mediated mTORC1 signaling regulates dietary restriction–induced memory enhancement |
Human zinc deficiency increases susceptibility to bacterial infection . Although zinc supplementation therapies can reduce the impact of disease , the molecular basis for protection remains unclear . Streptococcus pneumoniae is a major cause of bacterial pneumonia , which is prevalent in regions of zinc deficiency . We... | Zinc deficiency affects one-third of the world’s population and is associated with an increased susceptibility to bacterial infection . Despite this , the molecular basis for how zinc deficiency compromises host control of infection remains to be understood . We show that dietary zinc deficiency impacts host tissue zin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pneumococcus",
"respiratory",
"infections",
"statistics",
"pathogens",
"immunology",
"microbiology",
"pulmonology",
"analysis",
... | 2019 | Dietary zinc and the control of Streptococcus pneumoniae infection |
Hexavalent chromium [Cr ( VI ) ] damages DNA and causes cancer , but it is unclear which DNA damage responses ( DDRs ) most critically protect cells from chromate toxicity . Here , genome-wide quantitative functional profiling , DDR measurements and genetic interaction assays in Schizosaccharomyces pombe reveal a chrom... | Hexavalent chromium is a carcinogen that is found at toxic waste sites and in some groundwater supplies . Cellular metabolism converts chromium into DNA-damaging chromate , but it is unclear which types of chromate-DNA lesions are most dangerous , and which cellular mechanisms most critically prevent chromium toxicity ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"phosphorylation",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"dna",
"damage",
"fungi",
"model",
"organisms",
"dna",
"replication",
"experimental",
"organism",
"systems",
"dna",
"synthesis",
"phase",
"schizosaccharomyces",
"research",
"and",
"ana... | 2018 | Tdp1 processes chromate-induced single-strand DNA breaks that collapse replication forks |
In Drosophila oocytes achiasmate homologs are faithfully segregated to opposite poles at meiosis I via a process referred to as achiasmate homologous segregation . We observed that achiasmate homologs display dynamic movements on the meiotic spindle during mid-prometaphase . An analysis of living prometaphase oocytes r... | Proper chromosome segregation is essential during the production of eggs and sperm . Chromosome missegregation during meiosis results in the lethality of the offspring or in children carrying extra copies of a given chromosome ( for example , Down syndrome ) . Recombination results in homologous chromosomes becoming ph... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/chromosome",
"biology"
] | 2009 | Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes |
Seizures occur in a recurrent manner with intermittent states of interictal and ictal discharges ( IIDs and IDs ) . The transitions to and from IDs are determined by a set of processes , including synaptic interaction and ionic dynamics . Although mathematical models of separate types of epileptic discharges have been ... | In pathological conditions of epilepsy , the functioning of the neural network crucially depends on the ionic concentrations inside and outside neurons . A number of factors that affect neuronal activity is large . That is why the development of a minimal model that reproduces typical seizures could structure further e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"chemical",
"compounds",
"depolarization",
"membrane",
"potential",
"electrophysiology",
"neuroscience",
"systems",
"science",
"mathematics",
"interneurons",
"potassium",
"computer",
"and",
"information",
"sci... | 2018 | Minimal model of interictal and ictal discharges “Epileptor-2” |
Globally , more than 10 million people are infected with Trypanosoma cruzi , which causes about 20 000 annual deaths . Although Chagas disease is endemic to certain regions of Latin America , migratory flows have enabled its expansion into areas where it was previously unknown . Economic , social and cultural factors p... | Social and cultural factors are increasingly recognized as relevant to the likelihood of infection with Chagas disease as well as the health seeking practices of those affected . In response , qualitative methods have been used more often to study such factors . This is the first systematic review to focus on the socio... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Socio-Cultural Aspects of Chagas Disease: A Systematic Review of Qualitative Research |
How cells acquiring mutations in tumor suppressor genes outcompete neighboring wild-type cells is poorly understood . The phosphatidylinositol 3-kinase ( PI3K ) –phosphatase with tensin homology ( PTEN ) and tuberous sclerosis complex ( TSC ) -target of rapamycin ( TOR ) pathways are frequently activated in human cance... | The final size of a developing organ is finely modulated by nutrient conditions through the activity of nutrient sensing pathways , and deregulation of these pathways is often causative of tumorigenesis . Besides the well-known roles of these pathways in inducing tissue and cell growth , here we identify a nonautonomou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Dally Proteoglycan Mediates the Autonomous and Nonautonomous Effects on Tissue Growth Caused by Activation of the PI3K and TOR Pathways |
Canine rabies is endemic in Cameroon , but human rabies exposures and cases are likely underreported because of inadequate surveillance . In 2014 , the surveillance network in the West region of Cameroon was reinforced by introducing a new anti-rabies center , a framework for data collection and evaluation , provisions... | Dog-mediated human rabies causes tens of thousands of human deaths annually in economically disadvantaged countries . The disease is almost invariably fatal once symptoms appear but can be prevented if post-exposure prophylaxis is received within a few days after the exposure . Canine rabies is endemic in Cameroon but ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"post-exposure",
"prophylaxis",
"tropical",
"diseases",
"geographical",
"locations",
"vertebrates",
"animals",
"mammals",
"dogs",
"preventive",
"medicine",
"rabies",
"neglected",
"tropical",
"diseases",
"veterinarians",
"africa",
"... | 2018 | Improving systematic rabies surveillance in Cameroon: A pilot initiative and results for 2014-2016 |
Diploid hybrids of Saccharomyces cerevisiae and its closest relative , Saccharomyces paradoxus , are viable , but the sexual gametes they produce are not . One of several possible causes of this gamete inviability is incompatibility between genes from different species—such incompatible genes are usually called “specia... | A species is usually defined as such because it cannot exchange its genes with other species . Closely related species may attempt to breed but be unsuccessful . A common example of this occurs when a donkey mates with a horse . The offspring of this mating is a hybrid called a mule . Mules are sterile and cannot repro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics",
"saccharomyces"
] | 2007 | A Screen for Recessive Speciation Genes Expressed in the Gametes of F1 Hybrid Yeast |
Purifying selection during dengue viral infection has been suggested as the driving force of viral evolution and the higher complexity of the intra-host quasi-species is thought to offer an adaptive advantage for arboviruses as they cycle between arthropod and vertebrate hosts . However , very few studies have been per... | Virus genomes can show changes due to transmission between hosts . In evolutionary scale , replacements with new viral lineages are usually associated with alternating clinical burdens or epidemic potentials , but few studies have integrated viral dynamics from intra-host viral variations to macro-level clade ( a monop... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"sequencing",
"techniques",
"taxonomy",
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"population",
"genetics",
"geographical",
"locations",
"microbiology",
"tropical",
"diseases",
"viruses",
"phylog... | 2018 | Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan |
Modified vaccinia virus Ankara ( MVA ) is an attenuated poxvirus that has been engineered as a vaccine against infectious agents and cancers . Our goal is to understand how MVA modulates innate immunity in dendritic cells ( DCs ) , which can provide insights to vaccine design . In this study , using murine bone marrow-... | Modified vaccinia virus Ankara ( MVA ) is an attenuated vaccinia strain with large deletions of the parental genome that render it non-replicative in mammalian cells . MVA is a safe and effective vaccine against both smallpox and monkeypox . MVA has been investigated as a vaccine vector for infectious diseases and canc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Modified Vaccinia Virus Ankara Triggers Type I IFN Production in Murine Conventional Dendritic Cells via a cGAS/STING-Mediated Cytosolic DNA-Sensing Pathway |
The ability to detect a chemical gradient is fundamental to many cellular processes . In multicellular organisms gradient sensing plays an important role in many physiological processes such as wound healing and development . Unicellular organisms use gradient sensing to move ( chemotaxis ) or grow ( chemotropism ) tow... | In order to survive , many organisms must not only be able to detect the presence of a chemical compound , but also in which direction that compound increases or decreases in concentration . For example , bacteria cells prefer to move towards areas with high sugar concentrations . The process by which cells determine t... | [
"Abstract",
"Introduction",
"Discussion",
"Methods"
] | [
"engineering",
"and",
"technology",
"signal",
"processing",
"cell",
"processes",
"noise",
"reduction",
"simulation",
"and",
"modeling",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
"methods",
"pheromone",
"receptors",
"biophysics",
"cell... | 2017 | Testing the limits of gradient sensing |
Similar multicellular structures can evolve within the same organism that may have different evolutionary histories , be controlled by different regulatory pathways , and play similar but nonidentical roles . In the human fungal pathogen Candida albicans , a quite extraordinary example of this has occurred . Depending ... | Single-celled microbes can form biofilms , or aggregates of cells that adhere to one another on a surface , in response to many environmental factors . Like many microbial pathogens , the yeast Candida albicans can form biofilms that normally provide protective environments against antifungals , antibodies , and white ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2011 | Alternative Mating Type Configurations (a/α versus a/a or α/α) of Candida albicans Result in Alternative Biofilms Regulated by Different Pathways |
Despite the presence of significant levels of systemic Interferon gamma ( IFNγ ) , the host protective cytokine , Kala-azar patients display high parasite load with downregulated IFNγ signaling in Leishmania donovani ( LD ) infected macrophages ( LD-MØs ) ; the cause of such aberrant phenomenon is unknown . Here we rev... | The disease Visceral Leishmaniasis or Kala-azar is extending its base in the Indian subcontinent and elsewhere . The emergence of drug resistant cases is aggravating the problem further . The kala-azar patients do not respond to the host-protective cytokine IFNγ at the active stage of the disease , the cause of which i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immune",
"cells",
"cytokines",
"immunity",
"antigen-presenting",
"cells",
"immunity",
"to",
"infections",
"immunology",
"biology",
"immunoregulation",
"immunomodulation",
"immune",
"response",
"immune",
"system"
] | 2011 | Restoration of IFNγR Subunit Assembly, IFNγ Signaling and Parasite Clearance in Leishmania donovani Infected Macrophages: Role of Membrane Cholesterol |
The basidiomycete Ustilago maydis causes smut disease in maize , with large plant tumors being formed as the most prominent disease symptoms . During all steps of infection , U . maydis depends on a biotrophic interaction , which requires an efficient suppression of plant immunity . In a previous study , we identified ... | Biotrophic plant-pathogen interactions depend on the suppression of the host immune system . In the compatible Ustilago maydis–maize interaction , living host cells are colonized without inducing defense responses . Thereby , host metabolism and gene expression are widely reprogrammed , resulting in the formation of la... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"science",
"model",
"organisms",
"ustilago",
"maydis",
"plant",
"biology",
"plant",
"pathogens",
"plant",
"pathology",
"yeast",
"and",
"fungal",
"models",
"biology",
"microbiology"
] | 2013 | Compatibility in the Ustilago maydis–Maize Interaction Requires Inhibition of Host Cysteine Proteases by the Fungal Effector Pit2 |
Differentiating dengue patients from other acute febrile illness patients is a great challenge among physicians . Several dengue diagnosis methods are recommended by WHO . The application of specific laboratory tests is still limited due to high cost , lack of equipment , and uncertain validity . Therefore , clinical d... | In many parts of the world , dengue diagnosis still relies on clinical manifestation and basic laboratory tests . However , clinical manifestation of dengue patients is usually unspecific especially during the early stage , which makes accurate dengue diagnosis a challenge for physicians . Recently , the World Health O... | [
"Abstract",
"Introduction",
"Method",
"Result",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"physicians",
"medical",
"doctors",
"clinical",
"laboratory",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"medical",
"personnel",
"influenza",
"tropical",
"diseases",
"health",
"care",
"bacterial",
"diseases",
"heal... | 2018 | Accuracy of dengue clinical diagnosis with and without NS1 antigen rapid test: Comparison between human and Bayesian network model decision |
In complement to an effective vaccine , development of potent anti-HIV microbicides remains an important priority . We have previously shown that the miniCD4 M48U1 , a functional mimetic of sCD4 presented on a 27 amino-acid stable scaffold , inhibits a broad range of HIV-1 isolates at sub-nanomolar concentrations in ce... | This report describes the protective effect of a CD4 peptide mimetic against HIV infection on human mucosal explants and further on , when used in a microbicide gel , against a SHIV challenge in cynomolgus macaques . Evidence is given that our “miniprotein engineering” strategy , which corresponds to miniaturizing a bi... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"hiv",
"prevention",
"sexually",
"transmitted",
"diseases",
"aids",
"hiv",
"viral",
"diseases"
] | 2012 | MiniCD4 Microbicide Prevents HIV Infection of Human Mucosal Explants and Vaginal Transmission of SHIV162P3 in Cynomolgus Macaques |
This study investigates the inter-trial variability of saccade trajectories observed in five rhesus macaques ( Macaca mulatta ) . For each time point during a saccade , the inter-trial variance of eye position and its covariance with eye end position were evaluated . Data were modeled by a superposition of three noise ... | In movement control , online feedback compensation of internal noise directly affects the statistics of the movement trajectory , namely the development of the variance during the movement and the correlation of the effectors position during the movement and its end position . We used here the statistics of the movemen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"statistical",
"noise",
"engineering",
"and",
"technology",
"signal",
"processing",
"vertebrates",
"random",
"variables",
"neuroscience",
"animals",
"mammals",
"covariance",
"noise",
"reduction",
"motor",
"neurons",
"primates",
"... | 2016 | Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus |
Noise driven exploration of a brain network’s dynamic repertoire has been hypothesized to be causally involved in cognitive function , aging and neurodegeneration . The dynamic repertoire crucially depends on the network’s capacity to store patterns , as well as their stability . Here we systematically explore the capa... | Recent developments in non-invasive brain imaging allow reconstructing axonal tracts in the human brain and building realistic network models of the human brain . These models resemble brain systems in their network character and allow deciphering how different regions share signals and process information . Inspired b... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Multistability in Large Scale Models of Brain Activity |
Multilocus sequence typing ( MLST ) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology . Trypanosoma cruzi , the protozoan agent of American trypanosomiasis ( Chagas disease ) , has remarkable genetic and ecological diversity . A standardised MLST protocol that i... | The single-celled parasite Trypanosoma cruzi occurs in animals and insect vectors in the Americas . When transmitted to humans it causes a major public health problem , Chagas disease ( American trypanosomiasis ) . T . cruzi is genetically diverse and currently split into six groups , known as TcI to TcVI . Multilocus ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"ecology/evolutionary",
"ecology",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"molecular",
"biology/molecular",
"evolution",
"molecular",
"biology/recombination",
"infectious",
"diseases/protozoal",
"infections",
"molecular",
"biology"
] | 2011 | Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi |
Although many of the core components of the embryonic cell-cycle network have been elucidated , the question of how embryos achieve robust , synchronous cellular divisions post-fertilization remains unexplored . What are the different schemes that could be implemented by the embryo to achieve synchronization ? By exten... | Cell divisions across an embryo occur in rapid synchrony - like clockwork - starting within minutes of fertilization . How does an embryo achieve this remarkable uniformity ? Simple diffusion is too slow: typical proteins diffuse with a rate of 10 µm2/s , requiring nearly 14 hours to traverse a 1 mm embryo . An excitin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"developmental",
"biology",
"biology",
"computational",
"biology",
"biophysics",
"genetics",
"and",
"genomics"
] | 2011 | Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator? |
Drechmeria coniospora is an obligate fungal pathogen that infects nematodes via the adhesion of specialized spores to the host cuticle . D . coniospora is frequently found associated with Caenorhabditis elegans in environmental samples . It is used in the study of the nematode’s response to fungal infection . Full unde... | Some soil-living fungi can kill nematodes and are used as biocontrol agents against plant parasitic nematodes . Certain species trap their prey using adhesive knobs or nets . For others , like Drechmeria coniospora , infection starts with the adhesion of specialized non-motile spores to the nematode cuticle . We have s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"fungal",
"genetics",
"caenorhabditis",
"pathogens",
"computational",
"biology",
"microbiology",
"parasitic",
"diseases",
"animals",
"nematode",
"infections",
"animal",
... | 2016 | Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes |
The cholesterol-dependent cytolysins ( CDCs ) constitute a family of pore-forming toxins that contribute to the pathogenesis of a large number of Gram-positive bacterial pathogens . The most highly conserved region in the primary structure of the CDCs is the signature undecapeptide sequence ( ECTGLAWEWWR ) . The CDC po... | The CDCs are a large family of pathogenesis-associated pore-forming toxins that are expressed by many Gram-positive pathogens . The conserved undecapeptide motif of the CDCs has been regarded as the signature peptide sequence for these toxins , yet its function has remained obscure . The studies herein show that the un... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"infectious",
"diseases",
"biology",
"microbiology"
] | 2012 | The Cholesterol-Dependent Cytolysin Signature Motif: A Critical Element in the Allosteric Pathway that Couples Membrane Binding to Pore Assembly |
Dengue is a mosquito-borne viral disease that has become more prevalent in the last few decades . Most patients are viremic when they present with symptoms , and early diagnosis of dengue is important in preventing severe clinical complications associated with this disease and also represents a key factor in differenti... | Dengue is the most common mosquito-borne viral disease affecting humans , with an estimated 100 million cases annually . Being able to achieve early and correct detection of all four serotypes of dengue virus can have an impact on the diagnosis of individual patients , such as febrile travelers returning home , but can... | [
"Abstract",
"Introduction",
"Methods",
"Results/Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"research",
"and",
"analysis",
"methods"
] | 2014 | Universal Single-Probe RT-PCR Assay for Diagnosis of Dengue Virus Infections |
The host lymphatic network represents an important conduit for pathogen dissemination . Indeed , the lethal human pathogen group A streptococcus has a predilection to induce pathology in the lymphatic system and draining lymph nodes , however the underlying basis and subsequent consequences for disease outcome are curr... | Pathogens are known to invade the host not only via the systemic circulation but also via the lymphatic network , however the mechanisms underlying the latter route and the consequences for disease outcome have not been well studied . The important human pathogen , group A streptococcus , is responsible for a number of... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Rapid Lymphatic Dissemination of Encapsulated Group A Streptococci via Lymphatic Vessel Endothelial Receptor-1 Interaction |
Synchronized gamma frequency oscillations in neural networks are thought to be important to sensory information processing , and their effects have been intensively studied . Here we describe a mechanism by which the nervous system can readily control gamma oscillation effects , depending selectively on visual stimuli ... | In the nervous system , a network of neurons shows interesting population activities . One example is a various frequency of synchronized oscillations which are thought to be important to sensory functions . In particular , it has been reported that gamma frequency rhythms ( 30∼70Hz ) in the cortex can significantly re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/theoretical",
"neuroscience",
"biophysics/theory",
"and",
"simulation",
"computational",
"biology/systems",
"biology",
"computational",
"biology/computational",
"neuroscience"
] | 2010 | Synaptic Plasticity Controls Sensory Responses through Frequency-Dependent Gamma Oscillation Resonance |
Primary human hepatocytes isolated from patient biopsies represent the most physiologically relevant cell culture model for hepatitis C virus ( HCV ) infection , but these primary cells are not readily accessible , display individual variability , and are largely refractory to genetic manipulation . Hepatocyte-like cel... | Physiologically relevant cell-culture models for infection with hepatitis C virus ( HCV ) are scarce , and infection by viruses derived from patient serum has been inefficient . Differentiated human hepatocyte-like cells derived from pluripotent stem cells demonstrate hepatic functions but have not been explored for HC... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"oncology",
"medicine",
"developmental",
"biology",
"infectious",
"diseases",
"gastroenterology",
"and",
"hepatology",
"genetics",
"biology",
"microbiology",
"molecular",
"cell",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Productive Hepatitis C Virus Infection of Stem Cell-Derived Hepatocytes Reveals a Critical Transition to Viral Permissiveness during Differentiation |
The phenotype produced by a given genotype can be strongly modulated by environmental conditions . Therefore , natural populations continuously adapt to environment heterogeneity to maintain optimal phenotypes . It generates a high genetic variation in environment-sensitive gene networks , which is thought to facilitat... | The fruitfly Drosophila melanogaster was initially endemic to sub-Saharan Africa and started to colonize Europe and Asia around 10 , 000 years ago . Northern populations have adapted to these colder environments and differ from Sub-Saharan populations for temperature sensitive traits . Here we analyze cramped ( crm ) ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"evolutionary",
"biology/evolutionary",
"ecology",
"genetics",
"and",
"genomics/complex",
"traits",
"developmental",
"biology/developmental",
"evolution",
"genetics",
"and",
"genomics/chromosome",
"biology",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2011 | Segregating Variation in the Polycomb Group Gene cramped Alters the Effect of Temperature on Multiple Traits |
Despite recent advances in developmental biology , and the sequencing and annotation of genomes , key questions regarding the organisation of cells into embryos remain . One possibility is that uncharacterised genes having nonstandard coding arrangements and functions could provide some of the answers . Here we present... | How cells organize into embryos remains a fundamental question in developmental biology . It is likely that significant insights into embryo development will emerge from the characterisation of novel types of genes . Yet most current genome annotation methods rely heavily on comparisons with already-known gene sequence... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"developmental",
"biology",
"cell",
"biology",
"eukaryotes",
"metazoans",
"drosophila",
"genetics",
"and",
"genomics"
] | 2007 | Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family |
Entamoeba histolytica transmembrane kinases ( EhTMKs ) can be grouped into six distinct families on the basis of motifs and sequences . Analysis of the E . histolytica genome revealed the presence of 35 EhTMKB1 members on the basis of sequence identity ( ≥95% ) . Only six homologs were full length containing an extrace... | The presence of a vast array of putative transmembrane kinase genes suggests an extensive network of signaling systems in E . histolytica , particularly the ability to perceive signals from the extracellular environment and transduce these intracellularly . However , it has been very difficult to work with these molecu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/protozoal",
"infections",
"molecular",
"biology"
] | 2010 | Serum-Dependent Selective Expression of EhTMKB1-9, a Member of Entamoeba histolytica B1 Family of Transmembrane Kinases |
Pericentrin is a conserved centrosomal protein whose dysfunction has been linked to several human diseases . It has been implicated in many aspects of centrosome and cilia function , but its precise role is unclear . Here , we examine Drosophila Pericentrin-like-protein ( PLP ) function in vivo in tissues that form bot... | Centrioles are complex , microtubule ( MT ) based structures that organise two important cell organelles , the centrosome and the cilium . The centrosome is a major MT organising centre in many cell types , while the cilium functions as a cellular “antenna” responsible for regulating several cellular signalling pathway... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"centrosomes",
"spermatocytes",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"animals",
"germ",
"cells",
"mitosis",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"e... | 2018 | Drosophila PLP assembles pericentriolar clouds that promote centriole stability, cohesion and MT nucleation |
The emergence of viral respiratory pathogens with pandemic potential , such as severe acute respiratory syndrome coronavirus ( SARS-CoV ) and influenza A H5N1 , urges the need for deciphering their pathogenesis to develop new intervention strategies . SARS-CoV infection causes acute lung injury ( ALI ) that may develop... | Severe acute respiratory syndrome coronavirus ( SARS-CoV ) infection causes acute lung injury that may develop into the life-threatening acute respiratory distress syndrome ( ARDS ) in mostly elderly individuals . Although SARS-CoV infection can be fatal , most patients recover , suggesting that protective host respons... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/immunomodulation",
"cell",
"biology",
"pathology",
"immunology/immune",
"response",
"immunology/innate",
"immunity",
"virology/emerging",
"viral",
"diseases",
"virology/effects",
"of",
"virus",
"infection",
"on",
"host",
"gene",
"expression"
] | 2010 | Exacerbated Innate Host Response to SARS-CoV in Aged Non-Human Primates |
RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation . It has been implicated in various processes including adaptation , viral defence and RNA interference; however , its potential role as a mechanism in acclimatization has just recently been recog... | RNA editing is a mechanism that alters the nucleotide sequence of transcripts; edited transcripts are thus different from what is encoded in the genome . If the edits occur in coding regions , non-synonymous changes will generate additional protein diversity . Environmental stress is one of the many triggers for RNA ed... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"classical",
"mechanics",
"mechanical",
"stress",
"invertebrate",
"genomics",
"genome",
"analysis",
"sequence",
"motif",
"analysis",
"cellular",
"structures",
"and",
"organelles",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"genomic",
"libraries",
... | 2017 | Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum |
Bones at different anatomical locations vary dramatically in size . For example , human femurs are 20-fold longer than the phalanges in the fingers and toes . The mechanisms responsible for these size differences are poorly understood . Bone elongation occurs at the growth plates and advances rapidly in early life but ... | The various bones found in human extremities vary dramatically in size . For example , the femur in the thigh is approximately 20 times longer than the phalanges of the toes . The mechanisms that regulate how much a particular bone grows to attain the skeletal proportions of each animal remain mostly unknown . In this ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"growth",
"plate",
"sequencing",
"techniques",
"tibia",
"medicine",
"and",
"health",
"sciences",
"phalanges",
"chondrocytes",
"bone",
"connective",
"tissue",
"cells",
"skeleton",
"molecular",
"biology",
"techniques",
"rna",
"sequencing",
"cartilage",
"research",
"and",
... | 2018 | Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions |
The extent to which self-adopted or intervention-related changes in behaviors affect the course of epidemics remains a key issue for outbreak control . This study attempted to quantify the effect of such changes on the risk of infection in different settings , i . e . , the community and hospitals . The 2002–2003 sever... | Recent epidemics have shown that healthcare workers may be overrepresented among cases and how critical it is to protect them . For example , during the 2002–2003 severe acute respiratory syndrome ( SARS ) epidemics in Hong Kong , 27%of cases were healthcare workers when they were <1% of the population . Better means o... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/nosocomial",
"and",
"healthcare-associated",
"infections",
"public",
"health",
"and",
"epidemiology/epidemiology",
"infectious",
"diseases/viral",
"infections",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"mathematics/statistics",
"pu... | 2009 | Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong Kong |
During hematogenously disseminated disease , Candida albicans infects most organs , including the brain . We discovered that a C . albicans vps51Δ/Δ mutant had significantly increased tropism for the brain in the mouse model of disseminated disease . To investigate the mechanisms of this enhanced trafficking to the bra... | During hematogenously disseminated infection , the fungus Candida albicans is carried by the bloodstream to virtually all organs in the body , including the brain . C . albicans infection of the brain is a significant problem in premature infants with disseminated candidiasis . To infect the brain , C . albicans must a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mycology",
"fungi",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"pathogenesis"
] | 2011 | Mechanisms of Candida albicans Trafficking to the Brain |
The use of networks to integrate different genetic , proteomic , and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases . Here we introduce a new phenotypic database summarizing correlations obtained from the disease history of more than 30 million patients in a Ph... | To help the understanding of physiological failures , diseases are defined as specific sets of phenotypes affecting one or several physiological systems . Yet , the complexity of biological systems implies that our working definitions of diseases are careful discretizations of a complex phenotypic space . To reconcile ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"physics/interdisciplinary",
"physics",
"public",
"health",
"and",
"epidemiology/social",
"and",
"behavioral",
"determinants",
"of",
"health",
"mathematics/statistics",
"computer",
"science/information",
"technology",
"computational",
"biology/systems",
"biology"
] | 2009 | A Dynamic Network Approach for the Study of Human Phenotypes |
Microbial pathogens exploit the clathrin endocytic machinery to enter host cells . Vesicular stomatitis virus ( VSV ) , an enveloped virus with bullet-shaped virions that measure 70×200 nm , enters cells by clathrin-dependent endocytosis . We showed previously that VSV particles exceed the capacity of typical clathrin-... | We present a detailed comparison between the clathrin-dependent entry mechanisms of a parental virus ( VSV ) and its smaller defective interfering particle ( DI-T ) . We used the difference in virion length to probe why actin assembly is required for the uptake of full-length VSV particles by nonpolarized mammalian cel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/membranes",
"and",
"sorting",
"virology/host",
"invasion",
"and",
"cell",
"entry",
"cell",
"biology/cytoskeleton"
] | 2010 | The Length of Vesicular Stomatitis Virus Particles Dictates a Need for Actin Assembly during Clathrin-Dependent Endocytosis |
The mechanistic target of rapamycin ( MTOR ) pathway regulates cell growth , energy homeostasis , apoptosis , and immune response . The regulatory associated protein of MTOR encoded by the RPTOR gene is a key component of this pathway . A previous survey of candidate genes found that RPTOR contains multiple SNPs with s... | Climate has exerted strong selective pressures in human populations during their dispersal , and signatures of these adaptations are still detectable in the geographic distribution of polymorphisms . RPTOR is a key component of the mechanistic target of rapamycin pathway , which regulates cell growth , metabolism , and... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"evolutionary",
"biology",
"genetics",
"and",
"genomics"
] | 2010 | Allele-Specific Down-Regulation of RPTOR Expression Induced by Retinoids Contributes to Climate Adaptations |
The production of aberrant RNA ( aRNA ) is the initial step in several RNAi pathways . How aRNA is produced and specifically recognized by RNA-dependent RNA polymerases ( RdRPs ) to generate double-stranded RNA ( dsRNA ) is not clear . We previously showed that in the filamentous fungus Neurospora , the RdRP QDE-1 is r... | Small RNA molecules ( 20–30 nucleotides ) play important roles in many cellular processes in eukaryotic organisms by silencing gene expression . To generate the many forms of small RNAs , DNA is first transcribed to produce single-stranded RNA ( ssRNA ) , which then is converted to double-stranded RNA ( dsRNA ) by an R... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"molecular",
"biology/mrna",
"stability",
"plant",
"biology"
] | 2010 | The DNA/RNA-Dependent RNA Polymerase QDE-1 Generates Aberrant RNA and dsRNA for RNAi in a Process Requiring Replication Protein A and a DNA Helicase |
Strong experimental evidence indicates that protein kinase and phosphatase ( KP ) cycles are critical to both the induction and maintenance of activity-dependent modifications in neurons . However , their contribution to information storage remains controversial , despite impressive modeling efforts . For instance , pl... | It is now widely recognized that learning and memory rely on activity-dependent plastic modifications of the synaptic and intrinsic properties of individual neurons . Experimental studies have identified numerous molecules that are necessary for the induction and the maintenance of plastic modifications , including act... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"computational",
"biology",
"eukaryotes",
"vertebrates",
"neuroscience",
"animals"
] | 2007 | A New Principle for Information Storage in an Enzymatic Pathway Model |
Prion Proteins ( PrP ) are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species . Here , we perform a comprehensive principle components analysis ( PCA ) on the tertiary structures of PrP globular proteins to discern PrP subdomains that ex... | Prion Proteins ( PrP ) cause a variety of incurable TSE diseases , and are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species . Here , we perform a comprehensive PCA study to assess conformational variation and discern the landscape of t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biochemistry",
"infectious",
"diseases",
"proteins",
"protein",
"structure",
"biology",
"computational",
"biology",
"macromolecular",
"structure",
"analysis",
"prion",
"diseases"
] | 2012 | The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles |
Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species . This results in the maintenance of genetic diversity at pathogen antigens ( or so-called effectors ) and host resistance genes such as the major histocompatibility complex ( MHC ) in mammals or resistance ( R ) g... | Pathogens have a negative impact on the fitness of their hosts and are responsible for drastic epidemics in humans , animals , and plants . In plants , it has been thought that natural selection acts predominantly on so-called “resistance genes , ” which recognize pathogens following a key-lock interaction . In this st... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"plant",
"biology",
"population",
"genetics",
"plant",
"science",
"plant",
"pathology",
"plant",
"genetics",
"biology",
"evolutionary",
"immunology",
"evolutionary",
"genetics",
"biochemistry",
"plant",
"biochemistry",
"plant",
"evolution",
"genetics",
"evolutionary",
"bi... | 2012 | Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense |
Listeria monocytogenes ( Lm ) is an invasive foodborne pathogen that leads to severe central nervous system and maternal-fetal infections . Lm ability to actively cross the intestinal barrier is one of its key pathogenic properties . Lm crosses the intestinal epithelium upon the interaction of its surface protein inter... | Co-evolution of microbes with their hosts can select stringently specific host-microbe interactions at the cell , tissue and species levels . Listeria monocytogenes ( Lm ) is a foodborne pathogen that causes a deadly systemic infection in humans . Lm crosses the intestinal epithelium upon the interaction of its surface... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"model",
"organisms",
"immunology",
"biology",
"microbiology"
] | 2013 | Murinization of Internalin Extends Its Receptor Repertoire, Altering Listeria monocytogenes Cell Tropism and Host Responses |
Epidemic growth rate , r , provides a more complete description of the potential for epidemics than the more commonly studied basic reproduction number , R0 , yet the former has never been described as a function of temperature for dengue virus or other pathogens with temperature-sensitive transmission . The need to un... | Recurrent , rapidly intensifying epidemics of dengue–the world’s most prevalent mosquito-borne viral disease–pose a challenge to healthcare systems throughout the tropical and subtropical world . An acute disease that tends to respond well to proper treatment , the sometimes intense nature of dengue epidemics has been ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion",
"Conclusion"
] | [
"death",
"rates",
"invertebrates",
"dengue",
"virus",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chikungunya",
"infection",
"infectious",
"disease",
"epidemiology",
"demography",
"atmospheric",
"science",
"pathogens",
"tropical... | 2017 | Temperature modulates dengue virus epidemic growth rates through its effects on reproduction numbers and generation intervals |
Identifying host immune determinants governing HIV transcription , latency and infectivity in vivo is critical to developing an HIV cure . Based on our recent finding that the host factor p21 regulates HIV transcription during antiretroviral therapy ( ART ) , and published data demonstrating that the human carbohydrate... | While antiretroviral therapy ( ART ) has significantly decreased the morbidity and mortality associated with HIV infection , a cure is not achieved due to the persistence of HIV latently-infected cells during treatment . Identifying the principal host immune determinants governing HIV transcription , latency , and infe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"hiv",
"infections",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"cloning",
"dna",
"transcription",
"retroviruses",
"viruses",
"immunodeficiency",
... | 2016 | Human Galectin-9 Is a Potent Mediator of HIV Transcription and Reactivation |
Appropriate expression of most eukaryotic genes requires the removal of introns from their pre–messenger RNAs ( pre-mRNAs ) , a process catalyzed by the spliceosome . In higher eukaryotes a large family of auxiliary factors known as SR proteins can improve the splicing efficiency of transcripts containing suboptimal sp... | The spliceosome is a large RNA-protein machine responsible for removing the noncoding ( intron ) sequences that interrupt eukaryotic genes . Nearly everything known about the behavior of this machine has been based on the analysis of only a handful of genes , despite the fact that individual introns vary greatly in bot... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"yeast",
"and",
"fungi",
"eukaryotes",
"computational",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components |
Alveolar echinococcosis ( AE ) presents a serious public health challenge within China . Mass screening ultrasound surveys can detect pre-symptomatic AE , but targeting areas identified from hospital records is inefficient regarding AE . Prediction of undetected or emerging hotspots would increase detection rates . Vol... | In humans , larvae of the fox tapeworm Echinococcus multilocularis typically infect the liver where metastasis , calcification and necrosis cause the zoonotic disease alveolar echinococcosis ( AE ) . Treatment is difficult . Early detection greatly increases patient life expectancy but under-detection is a problem . Un... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"ecology/spatial",
"and",
"landscape",
"ecology"
] | 2008 | Landscape Composition and Spatial Prediction of Alveolar Echinococcosis in Southern Ningxia, China |
Translation termination at premature termination codons ( PTCs ) triggers degradation of the aberrant mRNA , but the mechanism by which a termination event is defined as premature is still unclear . Here we show that the physical distance between the termination codon and the poly ( A ) -binding protein PABPC1 is a cru... | Correct expression of the genetic information is essential for life , and several quality control systems have evolved to ensure accurate protein synthesis . One of these processes , termed nonsense-mediated mRNA decay ( NMD ) , detects inappropriate termination of mRNA translation at premature termination codons ( PTC... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"molecular",
"biology"
] | 2008 | Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region |
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