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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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Plasmodium falciparum is the major human malaria agent responsible for 200 to 300 million infections and one to three million deaths annually , mainly among African infants . The origin and evolution of this pathogen within the human lineage is still unresolved . A single species , P . reichenowi , which infects chimpa... | In 2002 , the publication of the genome of Plasmodium falciparum , the most malignant agent of malaria , generated hopes in the fight against this deadly disease by the opportunities it offered to discover new drug targets . Since then results have not lived up to the expectations . The development of comparative genom... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics"
] | 2009 | A New Malaria Agent in African Hominids |
Myosins are ATP-driven linear molecular motors that work as cellular force generators , transporters , and force sensors . These functions are driven by large-scale nucleotide-dependent conformational changes , termed “strokes”; the “power stroke” is the force-generating swinging of the myosin light chain–binding “neck... | Myosin Va is a “two-legged” ATP-dependent linear molecular motor that transports cellular organelles by “stepping” along actin filaments in a processive manner analogous to human walking , the two “feet” alternating between forward and backward positions . During stepping , the lifted leg undergoes rotational Brownian ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biomacromolecule-ligand",
"interactions",
"biochemistry",
"enzyme",
"structure",
"cell",
"motility",
"actin",
"filaments",
"enzymes",
"biology",
"enzyme",
"kinetics",
"biophysics"
] | 2011 | Direct Observation of the Myosin Va Recovery Stroke That Contributes
to Unidirectional Stepping along Actin |
Apicomplexa tick-borne hemoparasites , including Babesia bovis , Babesia microti , and Theileria equi are responsible for bovine and human babesiosis and equine theileriosis , respectively . These parasites of vast medical , epidemiological , and economic impact have complex life cycles in their vertebrate and tick hos... | The tick-borne apicomplexan parasites Babesia and Theileria are responsible for costly and devastating diseases globally . Improved control is needed , but the biology of these parasites remains poorly understood . Significant gaps include better understanding of the mechanisms involved in control of gene expression an... | [
"Abstract",
"Introduction",
"Concluding",
"Remarks"
] | [
"sequencing",
"techniques",
"parasite",
"groups",
"plasmodium",
"gene",
"regulation",
"regulatory",
"proteins",
"dna-binding",
"proteins",
"parasitic",
"protozoans",
"parasitology",
"developmental",
"biology",
"apicomplexa",
"review",
"protozoans",
"transcription",
"factors",... | 2016 | Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi |
Little is known about the genetic basis of ecologically important morphological variation such as the diverse color patterns of mammals . Here we identify genetic changes contributing to an adaptive difference in color pattern between two subspecies of oldfield mice ( Peromyscus polionotus ) . One mainland subspecies h... | The tremendous amount of variation in color patterns among organisms helps individuals survive and reproduce in the wild , yet we know surprisingly little about the genes that produce these adaptive patterns . Here we used a genomic analysis to uncover the molecular basis of a pale color pattern that camouflages beach ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"evolutionary",
"biology",
"mus",
"(mouse)"
] | 2007 | Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes |
In the context of an ageing population , understanding the transmission of infectious diseases such as scabies through well-connected sub-units of the population , such as residential care homes , is particularly important for the design of efficient interventions to mitigate against the effects of those diseases . Her... | Our work makes five main contributions . ( 1 ) We study a previously under-modelled scenario—transmission of scabies in residential care homes—that is of significant and growing public health importance in the context of an ageing population . ( 2 ) We develop a Markov-chain-based modelling framework that accurately ca... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death",
"rates",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"markov",
"models",
"dose",
"prediction",
"methods",
"applied",
"mathematics",
"tropical",
"diseases",
"social",
"sciences",
"parasitic",
"diseases",
"animals",
"health",
"care",
"simulation",
... | 2018 | Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units |
In many sensory systems , transmembrane receptors are spatially organized in large clusters . Such arrangement may facilitate signal amplification and the integration of multiple stimuli . However , this organization likely also affects the kinetics of signaling since the cytoplasmic enzymes that modulate the activity ... | To navigate their environments , organisms must remain sensitive to small changes in their surroundings while adapting to persistent conditions . Bacteria travel by performing a random walk biased toward nutrients and away from toxins . The decision of a bacterium to continue in a given direction or to reorient is cont... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Adaptation Dynamics in Densely Clustered Chemoreceptors |
Repairing broken chromosomes via joint molecule ( JM ) intermediates is hazardous and therefore strictly controlled in most organisms . Also in budding yeast meiosis , where production of enough crossovers via JMs is imperative , only a subset of DNA breaks are repaired via JMs , closely regulated by the ZMM pathway . ... | Homologous recombination allows repair of DNA breaks from intact templates of identical sequence by a “copy-and-paste” like mechanism . However , the double Holliday Junction ( dHJ ) is a hazardous intermediate that can form during homologous recombination , if single stranded DNA from both ends of a lesion pair with t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Smc5/6-Mms21 Prevents and Eliminates Inappropriate Recombination Intermediates in Meiosis |
An open problem in the field of computational neuroscience is how to link synaptic plasticity to system-level learning . A promising framework in this context is temporal-difference ( TD ) learning . Experimental evidence that supports the hypothesis that the mammalian brain performs temporal-difference learning includ... | What are the physiological changes that take place in the brain when we solve a problem or learn a new skill ? It is commonly assumed that behavior adaptations are realized on the microscopic level by changes in synaptic efficacies . However , this is hard to verify experimentally due to the difficulties of identifying... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"neuroscience",
"neuroscience/theoretical",
"neuroscience"
] | 2011 | An Imperfect Dopaminergic Error Signal Can Drive Temporal-Difference Learning |
Annual mass drug administration ( MDA ) over five years is the WHO's recommended strategy to eliminate lymphatic filariasis ( LF ) . Some experts , however , consider that longer periods of treatment might be necessary in certain high prevalence and transmission environments based upon past unsuccessful field experienc... | Large-scale intervention programmes to control filariasis are currently underway worldwide . However , a major unresolved question remains: what is the appropriate duration for these programmes ? Recent theoretical work and clinical field experience has highlighted how the ecological diversity between different endemic... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"neglected",
"tropical",
"diseases",
"lymphatic",
"filariasis"
] | 2011 | The Impact of a Filariasis Control Program on Lihir Island, Papua New Guinea |
Photosynthesis is the final determinator for crop yield . To gain insight into genes controlling photosynthetic capacity , we selected from our large T-DNA mutant population a rice stunted growth mutant with decreased carbon assimilate and yield production named photoassimilate defective1 ( phd1 ) . Molecular and bioch... | Photosynthesis is carried out in chloroplast , a plant-specific organelle . Photosynthetic membranes in chloroplasts contain high levels of glycolipids , and UDP-galactose is a dominating donor for glycolipid biosynthesis . Although glycolipid assembly of photosynthetic membranes has been characterized at the genetic a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"agriculture",
"biology"
] | 2011 | A Rice Plastidial Nucleotide Sugar Epimerase Is Involved in Galactolipid Biosynthesis and Improves Photosynthetic Efficiency |
We investigated the relationship of treatment regimens for visceral leishmaniasis ( VL ) with post-kala-azar dermal leishmaniasis ( PKDL ) and visceral leishmaniasis relapse ( VLR ) development . Study subjects included cohorts of patients cured of VL since treatment with monotherapy by sodium stibogluconate ( SSG ) , ... | Post-kala-azar Dermal Leishmaniasis ( PKDL ) , a sequale of visceral leishmaniasis ( VL ) , and reappearance VL ( visceral leishmaniasis relapse , VLR ) are intra-epidemic reservoirs of VL and threats control of VL in long run . Currently there is no strategy for prevention of PKDL and VLR . If a relationship between t... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"kala-azar",
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"drugs",
"tropical",
"diseases",
"microbiology",
"geographical",
"locations",
"antifungals",
"parasitic",
"diseases",
"data",
"management",
"pharmaceutics",
"neglected",
"tropical",
"diseases",
"pharmac... | 2019 | Relationship between treatment regimens for visceral leishmaniasis and development of post-kala-azar dermal leishmaniasis and visceral leishmaniasis relapse: A cohort study from Bangladesh |
Broadly neutralizing antibodies ( bnAbs ) are thought to be a critical component of a protective HIV vaccine . However , designing vaccines immunogens able to elicit bnAbs has proven unsuccessful to date . Understanding the correlates and immunological mechanisms leading to the development of bnAb responses during natu... | Understanding how HIV-1-broadly neutralizing antibodies ( bnAbs ) develop during natural infection is essential to the design of an efficient HIV vaccine . We studied kinetics and correlates of neutralization breadth in a large sub-Saharan African longitudinal cohort of 439 participants with primary HIV-1 infection . B... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort |
Plasmodium vivax remains an important cause of malaria in South America and the Asia-Pacific . Naturally acquired antibody responses against multiple P . vivax proteins have been described in numerous countries , however , direct comparison of these responses has been difficult with different methodologies employed . W... | In the pursuit of eliminating all species of malaria , Plasmodium vivax presents one of the most substantial challenges , particularly in countries in Asia , the Western-Pacific and South America . This is primarily due to the ability of P . vivax to cause relapse infections months to years after the initial infectious... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"plasmodium",
"immunology",
"geographical",
"locations",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitology",
"apicomplexa",
"regional",
"geography",
"antibodies",
"antibody",... | 2017 | Naturally acquired antibody responses to more than 300 Plasmodium vivax proteins in three geographic regions |
CD1d-mediated presentation of glycolipid antigens to T cells is capable of initiating powerful immune responses that can have a beneficial impact on many diseases . Molecular analyses have recently detailed the lipid antigen recognition strategies utilized by the invariant Vα24-Jα18 TCR rearrangements of iNKT cells , w... | Certain lineages of T cells can recognize lipids as stimulatory antigens when presented in the context of CD1 molecules . We know how most Natural Killer T ( NKT ) cells react with this unusual ligand because they use a single invariant T cell receptor ( TCR ) alpha chain to do the job . NKT cells place particular emph... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology",
"biology"
] | 2012 | The Molecular Basis for Recognition of CD1d/α-Galactosylceramide by a Human Non-Vα24 T Cell Receptor |
The metabolic symbiosis with photosynthetic algae allows corals to thrive in the oligotrophic environments of tropical seas . Different aspects of this relationship have been investigated using the emerging model organism Aiptasia . However , many fundamental questions , such as the nature of the symbiotic relationship... | The symbiotic relationship with photosynthetic algae is key to the success of reef building corals in the nutrient poor environment of tropical waters . Extensive insight has been obtained from both physiological and “omics” level studies , yet , there are still gaps in our knowledge with respect to the metabolic inter... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"carbohydrate",
"metabolism",
"chemical",
"compounds",
"symbiosis",
"statistics",
"metaanalysis",
"carbohydrates",
"glucose",
"metabolism",
"animals",
"organic",
"compounds",
"glucose",
"organisms",
"mathematics",
"research",
"and",
"analysis",
"methods",
"... | 2019 | Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia |
Characterising the spatio-temporal dynamics of pathogens in natura is key to ensuring their efficient prevention and control . However , it is notoriously difficult to estimate dispersal parameters at scales that are relevant to real epidemics . Epidemiological surveys can provide informative data , but parameter estim... | In spatial epidemiology , dispersal kernels quantify how the probability of pathogen dissemination varies with distance from an infection source . Spatial models of pathogen spread are sensitive to kernel parameters; yet these parameters have rarely been estimated using field data gathered at relevant scales . Robust e... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"orchards",
"medicine",
"and",
"health",
"sciences",
"infectious",
"disease",
"epidemiology",
"kernel",
"functions",
"plant",
"science",
"farms",
"probability",
"distribution",
"mathematics",
"plant",
"pathology",
"infectious",
"disease",
"control",
"infectious",
"disease... | 2018 | Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape |
Oxidative stress is a common etiological feature of neurological disorders , although the pathways that govern defence against reactive oxygen species ( ROS ) in neurodegeneration remain unclear . We have identified the role of oxidation resistance 1 ( Oxr1 ) as a vital protein that controls the sensitivity of neuronal... | Oxygen is vital for life , but it can also cause damage to cells . Consequently , protective proteins ( antioxidants ) are utilised to maintain the fine balance between oxygen metabolism and the production of potentially toxic reactive oxygen species ( ROS ) . If this balance is not maintained , oxidative stress occurs... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"medicine",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"model",
"organisms",
"neurological",
"disorders",
"neurology",
"neurodegenerative",
"diseases",
"biology",
"neuroscience",
"cerebellar",
"disorders"
] | 2011 | Oxr1 Is Essential for Protection against Oxidative Stress-Induced Neurodegeneration |
The dynamic nature of technological developments invites us to rethink the learning spaces . In this context , science education can be enriched by the contribution of new computational resources , making the educational process more up-to-date , challenging , and attractive . Bioinformatics is a key interdisciplinary ... | Bioinformatics is an interdisciplinary activity that complements and connects several fields with biology and can also be used as an educational tool for science . During 2017 , the Structural Bioinformatics Group at National University of Quilmes in Buenos Aires , Argentina , worked together with public and private sc... | [
"Abstract",
"Background",
"and",
"motivation",
"Discussion"
] | [
"learning",
"education",
"engineering",
"and",
"technology",
"sociology",
"social",
"sciences",
"teachers",
"neuroscience",
"learning",
"and",
"memory",
"cell",
"phones",
"computers",
"cognitive",
"psychology",
"research",
"and",
"analysis",
"methods",
"computer",
"and"... | 2019 | Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools |
The Ebola virus disease epidemic between 2013 and 2016 in West Africa was unprecedented . It resulted in approximately 28 . 000 cases and 10 . 000 Ebola survivors . Many survivors face social , economic and health-related predicaments and media reporting is crucially important in infectious disease outbreaks . However ... | The largest Ebola epidemic occurred in West Africa between 2013 and 2016 . Liberia was one of the most affected countries with more than 1500 survivors registered . In the height of the Ebola outbreak survivors were increasingly included in the treatment and care of patients and in health sensitizing and social mobilis... | [
"Abstract",
"Introduction",
"Material",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"sociology",
"tropical",
"diseases",
"microbiology",
"geographical",
"locations",
"ebola",
"hemorrhagic",
"fever",
"social",
"sciences",
"health",
"care... | 2017 | "We are survivors and not a virus:" Content analysis of media reporting on Ebola survivors in Liberia |
Self-renewing organs often experience a decline in function in the course of aging . It is unclear whether chronological age or external factors control this decline , or whether it is driven by stem cell self-renewal—for example , because cycling cells exhaust their replicative capacity and become senescent . Here we ... | Stem cell cycling is expected to be beneficial because it helps delay aging , by ensuring organ self-renewal . Yet stem cell cycling is best used sparingly: cycling likely causes mutation accumulation—increasing the likelihood of cancer—and may eventually cause stem cells to senesce and thus stop contributing to organ ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"physiology",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"senescence",
"gonads",
"caenorhabditis",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"animals",
"germ",
"cells",
"animal",
"models",
"physio... | 2016 | Intermittent Stem Cell Cycling Balances Self-Renewal and Senescence of the C. elegans Germ Line |
The advent of two-photon microscopy now reveals unprecedented , detailed spatio-temporal data on cellular motility and interactions in vivo . Understanding cellular motility patterns is key to gaining insight into the development and possible manipulation of the immune response . Computational simulation has become an ... | Advances in imaging technology allow investigators to monitor the movements and interactions of immune cells in a live animal , processes essential to understanding and manipulating how an immune response is generated . T cells in the brains of Toxoplasma gondii-infected mice have previously been described as performin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"classical",
"mechanics",
"fluid",
"mechanics",
"immunology",
"mathematical",
"models",
"simulation",
"and",
"modeling",
"mathematics",
"brownian",
"motion",
"statistics",
... | 2016 | Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection |
Subtelomeres are duplication-rich , structurally variable regions of the human genome situated just proximal of telomeres . We report here that the most terminally located human subtelomeric genes encode a previously unrecognized third subclass of the Wiskott-Aldrich Syndrome Protein family , whose known members reorga... | Human subtelomeres are rearrangement-prone regions near chromosome ends . They are concentrations of large , recent interchromosomal duplications . Over half of subtelomeric sequences changed copy number or location since humans and chimpanzee diverged , and subtelomeric content varies greatly among humans . Despite th... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Supporting",
"Information"
] | [
"primates",
"developmental",
"biology",
"infectious",
"diseases",
"cell",
"biology",
"entamoeba",
"caenorhabditis",
"human",
"computational",
"biology",
"evolutionary",
"biology",
"drosophila",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | Human Subtelomeric WASH Genes Encode a New Subclass of the WASP Family |
Accurate diagnosis of Loa loa infection is essential to the success of mass drug administration efforts to eliminate onchocerciasis and lymphatic filariasis , due to the risk of fatal encephalopathic reactions to ivermectin occurring among highly microfilaremic Loa-infected individuals living in areas co-endemic for mu... | Loa loa is a filarial nematode that infects over 10 million people in Africa . Most infections cause no symptoms , but individuals with large numbers of blood-stage microfilariae are at risk for fatal reactions to ivermectin , an antiparasitic agent used to treat and prevent infections with Onchocerca volvulus , a rela... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"diagnostic",
"medicine",
"global",
"health",
"neglected",
"tropical",
"diseases",
"loiasis"
] | 2011 | Rapid Molecular Assays for Specific Detection and Quantitation of Loa loa Microfilaremia |
Persistent bacteremia caused by Staphylococcus aureus ( SA ) , especially methicillin-resistant SA ( MRSA ) , is a significant cause of morbidity and mortality . Despite susceptibility phenotypes in vitro , persistent MRSA strains fail to clear with appropriate anti-MRSA therapy during bacteremia in vivo . Thus , ident... | Staphylococcus aureus causes potentially lethal infections of the bloodstream and target organs when able to enter the body , often via skin trauma or catheterization . Methicillin-resistant Staphylococcus aureus ( MRSA ) resist common antibiotics , but are often successfully treated with vancomycin . However , in some... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"antimicrobials",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"drugs",
"immunology",
"cell",
"processes",
"microbiology",
"mathematical",
"models",
"vancomycin",
"staphylococcus",
... | 2019 | Identifying determinants of persistent MRSA bacteremia using mathematical modeling |
Mayaro virus ( MAYV ) of the genus alphavirus is a mosquito-transmitted emerging infectious disease that causes an acute febrile illness , rash , headaches , and nausea that may turn into incapacitating , persistent arthralgias in some victims . Since its discovery in Trinidad in 1954 , cases of MAYV infection have lar... | Mayaro virus ( MAYV ) is a mosquito-transmitted virus that causes fever , headache , chills , nausea and joint pain that can last for months after infection . The rising number of cases , due to increased mosquito circulation , and the threat of an epidemic emphasize its importance as an emerging virus , but there are ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"humoral",
"immunity",
"blood",
"serum",
"medicine",
"and",
"health",
"sciences",
"enzyme-linked",
"immunoassays",
"immune",
"physiology",
"body",
"fluids",
"immune",
"cells",
"immunology",
"vaccines",
"animal",
"models",
"model",
"organisms",
"exper... | 2019 | Protective immunity by an engineered DNA vaccine for Mayaro virus |
Neuronal ceroid lipofuscinosis ( NCL ) is a progressive neurodegenerative disease characterized by brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin in neurons and other cells . Tibetan terriers show a late-onset lethal form of NCL manifesting... | The neuronal ceroid lipofuscinosis ( NCL ) is a neurodegenerative storage diseases characterized by psychomotor retardation , blindness , and premature death . NCL has been reported in several dog breeds . NCL is characterized by progressive brain and retinal atrophy and the intracellular accumulation of autofluorescen... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"genetics",
"veterinary",
"neurology",
"animal",
"management",
"animal",
"breeding",
"neuroscience",
"genetics",
"and",
"genomics",
"veterinary",
"science",
"veterinary",
"medicine"
] | 2011 | A One Base Pair Deletion in the Canine ATP13A2 Gene Causes Exon Skipping and Late-Onset Neuronal Ceroid Lipofuscinosis in the Tibetan Terrier |
Accumulating evidence suggests that IL-9-mediated immunity plays a fundamental role in control of intestinal nematode infection . Here we report a different impact of Foxp3+ regulatory T cells ( Treg ) in nematode-induced evasion of IL-9-mediated immunity in BALB/c and C57BL/6 mice . Infection with Strongyloides ratti ... | Parasitic worms are large multicellular organisms that manage completion of their life cycles despite exposure to their host's immune system . To avoid expulsion , parasitic worms actively suppress their host's immune response . Here we show that the pathogenic nematode Strongyloides ratti induces the expansion of a sp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immune",
"cells",
"immunity",
"immunity",
"to",
"infections",
"immunology",
"immunoregulation",
"biology",
"zoology",
"immunomodulation",
"parasitology",
"helminthology"
] | 2014 | Foxp3+ Regulatory T Cells Delay Expulsion of Intestinal Nematodes by Suppression of IL-9-Driven Mast Cell Activation in BALB/c but Not in C57BL/6 Mice |
Muscle fatigue is a temporary decline in the force and power capacity of skeletal muscle resulting from muscle activity . Because control of muscle is realized at the level of the motor unit ( MU ) , it seems important to consider the physiological properties of motor units when attempting to understand and predict mus... | Skeletal muscle fatigue reduces strength during work and play and profoundly impairs motor function in many neuromuscular disorders . Muscle is composed of groupings of fibres called motor units and these have an extensive range of characteristics from small , weak , and fatigue-resistant to large , strong , and highly... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"material",
"fatigue",
"medicine",
"and",
"health",
"sciences",
"legs",
"classical",
"mechanics",
"pathology",
"and",
"laboratory",
"medicine",
"fatigue",
"skeletal",
"muscles",
"limbs",
"(anatomy)",
"neuroscience",
"biomechanics",
"muscle",
"contraction",
"motor",
"neu... | 2017 | A motor unit-based model of muscle fatigue |
DNA methylation is pervasive across all domains of life . In bacteria , the presence of N6-methyladenosine ( m6A ) has been detected among diverse species , yet the contribution of m6A to the regulation of gene expression is unclear in many organisms . Here we investigated the impact of DNA methylation on gene expressi... | DNA methylation is common among many bacterial species , yet the contribution of DNA methylation to the regulation of gene expression is unclear outside of a limited number of gram-negative species . We characterized sites of DNA methylation throughout the genome of the gram-positive pathogen Streptococcus pyogenes or ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blood",
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"gene",
"regulation",
"pathogens",
"immunology",
"microbiology",
"streptococcus",
"pyogenes",
"signs",
"and",
"symptoms",
"sequence",
"motif",
"... | 2019 | DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes |
Memory-like CD8+ T cells expressing eomesodermin are a subset of innate T cells initially identified in a number of genetically modified mice , and also exist in wild mice and human . The acquisition of memory phenotype and function by these T cells is dependent on IL–4 produced by PLZF+ innate T cells; however , their... | Over the course of viral infection there may be a limited time period during which the host system can eliminate the virus . When viruses are not eliminated within this period of time , virus can establish persistent infection . Here , we show that IL-4-induced innate CD8+ T cells are able to effectively control chroni... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | IL-4 Induced Innate CD8+ T Cells Control Persistent Viral Infection |
Viruses within a family often vary in their cellular tropism and pathogenicity . In many cases , these variations are due to viruses switching their specificity from one cell surface receptor to another . The structural requirements that underlie such receptor switching are not well understood especially for carbohydra... | Viruses need to bind to receptors on host cells for viral entry and infection , and the type of receptor bound determines the range of hosts and tissues the virus can infect . Viruses within a family often vary in their tissue distribution and pathogenicity because changes in receptor specificity can produce a virus wi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus |
Evolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system , with effects ( masculinization or feminization of the X ) depending on the dominance of mutations . Organisms with alternative modes of inheritan... | Males and females differ in their optimal values for most phenotypic traits , which makes intra-locus genetic conflicts among sexes common . Sex chromosomes have a sex-biased transmission , a pattern which might create favourable conditions for the spread of sexually antagonistic alleles ( i . e . alleles beneficial fo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome",
"expression",
"analysis",
"mutation",
"sexual",
"selection",
"chromosomal",
"inheritance",
"chromosome",
"biology",
"natural",
"selection",
"sexual",
"conflict",
"heredity",
"gene",
"expression",
"genetics",
"genome",
"evolution",
"biology",
"genomics",
"evoluti... | 2013 | Masculinization of the X Chromosome in the Pea Aphid |
While high-frequency deep brain stimulation is a well established treatment for Parkinson’s disease , its underlying mechanisms remain elusive . Here , we show that two competing hypotheses , desynchronization and entrainment in a population of model neurons , may not be mutually exclusive . We find that in a noisy gro... | While high-frequency deep brain stimulation ( DBS ) is a decades old treatment for alleviating the motor symptoms Parkinsons disease , the way in which it alleviates these symptoms is not well understood . Making matters more complicated , some experimental results suggest that DBS works by making neurons fire more reg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Clustered Desynchronization from High-Frequency Deep Brain Stimulation |
Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes . While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells , rigorous exp... | Selection is a ubiquitous process in biological populations in which individuals are endowed with heterogeneous reproductive abilities , and it occurs even among genetically homogeneous cells due to the existence of phenotypic noise . Unlike genotypes , which can remain stable for many generations , phenotypic fluctuat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"antimicrobials",
"medicine",
"and",
"health",
"sciences",
"cell",
"division",
"analysis",
"cell",
"cycle",
"and",
"cell",
"division",
"drugs",
"cell",
"processes",
"microbiology",
"streptomycin",
"protein",
"expression",
"probability",
"distribution",
"mathematics",
"a... | 2017 | Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data |
In order to maintain genome information accurately and relevantly , original genome annotations need to be updated and evaluated regularly . Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research . For this rea... | Entamoeba histolytica is an anaerobic parasitic protozoan that causes amoebic dysentery . The parasites colonize the large intestine , but under some circumstances may invade the intestinal mucosa , enter the bloodstream and lead to the formation of abscesses such amoebic liver abscesses . The draft genome of E . histo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"and",
"Discussion"
] | [
"genetics",
"and",
"genomics/genome",
"projects",
"genetics",
"and",
"genomics/bioinformatics",
"genetics",
"and",
"genomics/genomics"
] | 2010 | New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information |
Pattern classification of human brain activity provides unique insight into the neural underpinnings of diverse mental states . These multivariate tools have recently been used within the field of affective neuroscience to classify distributed patterns of brain activation evoked during emotion induction procedures . He... | Functional brain imaging techniques provide a window into neural activity underpinning diverse cognitive processes , including visual perception , decision-making , and memory , among many others . By treating functional imaging data as a pattern-recognition problem , similar to face- or character-recognition , researc... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"functional",
"magnetic",
"resonance",
"imaging",
"personality",
"traits",
"social",
"sciences",
"biomarkers",
"neuroscience",
"magnetic",
"resonance",
"imaging",
"fear",
"anxiety",
"cognition",
"brain",
... | 2016 | Decoding Spontaneous Emotional States in the Human Brain |
Calorie restriction ( CR ) , the only non-genetic intervention known to slow aging and extend life span in organisms ranging from yeast to mice , has been linked to the down-regulation of Tor , Akt , and Ras signaling . In this study , we demonstrate that the serine/threonine kinase Rim15 is required for yeast chronolo... | Reduction in calorie intake is a well-established intervention that extends the life span of a variety of biological model organisms studied . Calorie restriction also delays and attenuates age-related changes in primates , although its longevity-promoting effect has not been demonstrated . Here , we utilized a single ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Supporting",
"Information"
] | [
"genetics",
"and",
"genomics",
"cell",
"biology",
"developmental",
"biology",
"saccharomyces"
] | 2008 | Life Span Extension by Calorie Restriction Depends on Rim15 and Transcription Factors Downstream of Ras/PKA, Tor, and Sch9 |
In sub-Saharan Africa , systematic surveillance of young children with suspected invasive bacterial disease ( e . g . , septicemia , meningitis ) has revealed non-typhoidal Salmonella ( NTS ) to be a major pathogen exhibiting high case fatality ( ~20% ) . Where infant vaccination against Haemophilus influenzae type b (... | A surveillance program at Gabriel Touré Hospital in Mali observed a high burden of invasive disease caused by non-typhoidal Salmonella ( iNTS ) . This surveillance program was originally instituted to measure the amount of invasive disease ( e . g . , septicemia , meningitis ) caused by two bacteria that invade the res... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"mali",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"geographical",
"locations",
"microbiology",
"pediatrics",
"vaccines",
"preventive",
"medicine",
"bacterial",
"diseases",
"enterobacteriaceae",
"vaccina... | 2017 | Modeling the Potential for Vaccination to Diminish the Burden of Invasive Non-typhoidal Salmonella Disease in Young Children in Mali, West Africa |
Variation in the branching of plant inflorescences determines flower number and , consequently , reproductive success and crop yield . Nightshade ( Solanaceae ) species are models for a widespread , yet poorly understood , program of eudicot growth , where short side branches are initiated upon floral termination . Thi... | Among the most distinguishing features of plants are the flower-bearing shoots , called inflorescences . Despite a solid understanding of flower development , the molecular mechanisms that control inflorescence architecture remain obscure . We have explored this question in tomato , where mutations in two genes , ANANT... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"plant",
"biology"
] | 2008 | The Making of a Compound Inflorescence in Tomato and Related Nightshades |
The differentiation of discrete and continuous movement is one of the pillars of motor behavior classification . Discrete movements have a definite beginning and end , whereas continuous movements do not have such discriminable end points . In the past decade there has been vigorous debate whether this classification i... | A fundamental question in motor control research is whether distinct movement classes exist . Candidate classes are discrete and continuous movement . Discrete movements have a definite beginning and end , whereas continuous movements do not have such discriminable end points . In the past decade there has been vigorou... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neuroscience/behavioral",
"neuroscience",
"neuroscience/motor",
"systems",
"neuroscience/theoretical",
"neuroscience",
"computational",
"biology/computational",
"neuroscience"
] | 2008 | Distinct Timing Mechanisms Produce Discrete and Continuous Movements |
Field-applicable tests detecting asymptomatic Mycobacterium leprae ( M . leprae ) infection or predicting progression to leprosy , are urgently required . Since the outcome of M . leprae infection is determined by cellular- and humoral immunity , we aim to develop diagnostic tests detecting pro-/anti-inflammatory and r... | Leprosy is one of the six diseases considered by WHO as a major threat in developing countries and often results in severe , life-long disabilities and deformities due to delayed diagnosis . Early detection of Mycobacterium leprae ( M . leprae ) infection , followed by effective interventions , is considered vital to i... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"humoral",
"immunity",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"clinical",
"laboratory",
"sciences",
"immune",
"cells",
"diagnostic",
"medicine",
"cell",
"biology",
"animal",
"cells",
"immunity",
"clinical",
"immunology",
"immunity",
"to",
"... | 2014 | Field-Evaluation of a New Lateral Flow Assay for Detection of Cellular and Humoral Immunity against Mycobacterium leprae |
Vanillyl alcohol oxidase ( VAO ) is a homo-octameric flavoenzyme belonging to the VAO/PCMH family . Each VAO subunit consists of two domains , the FAD-binding and the cap domain . VAO catalyses , among other reactions , the two-step conversion of p-creosol ( 2-methoxy-4-methylphenol ) to vanillin ( 4-hydroxy-3-methoxyb... | Enzymes are bionanomachines , which speed up chemical reactions in organisms . To understand how they achieve that , we need to study their mechanisms . Computational enzymology can show us what happens in the enzyme’s active site during a reaction . But molecules need first to reach the active site before a reaction c... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"crystal",
"structure",
"chemical",
"compounds",
"oxides",
"split-decomposition",
"method",
"condensed",
"matter",
"physics",
"enzymology",
"organic",
"compounds",
"multiple",
"alignment",
"calculation",
"flavin",
"crystallography",
"hydrogen",
"peroxide",
"alcohols",
"enzy... | 2017 | The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths |
Mutations causing replication stress can lead to genomic instability ( GIN ) . In vitro studies have shown that drastic depletion of the MCM2-7 DNA replication licensing factors , which form the replicative helicase , can cause GIN and cell proliferation defects that are exacerbated under conditions of replication stre... | Proper replication of the genome is essential for maintenance of the genetic material and normal cell proliferation . DNA replication can be compromised by exogenous factors and genetic disruptions . Such compromise can lead to disease such as cancer , which is characterized by genomic instability ( an elevated mutatio... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry/replication",
"and",
"repair",
"genetics",
"and",
"genomics/cancer",
"genetics",
"genetics",
"and",
"genomics/animal",
"genetics",
"genetics",
"and",
"genomics/chromosome",
"biology"
] | 2010 | Incremental Genetic Perturbations to MCM2-7 Expression and Subcellular Distribution Reveal Exquisite Sensitivity of Mice to DNA Replication Stress |
Network motifs have been identified as building blocks of regulatory networks , including gene regulatory networks ( GRNs ) . The most basic motif , autoregulation , has been associated with bistability ( when positive ) and with homeostasis and robustness to noise ( when negative ) , but its general importance in netw... | Multicellular organisms show an incredible diversity of cell types in their different tissues . Functional classes of cells can be attributed to the activation and repression of genes , which enable each cell type to support different functions within the organism . These patterns of activity have been studied by means... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"developmental",
"biology",
"theoretical",
"biology",
"gene",
"regulatory",
"networks",
"natural",
"selection",
"neutral",
"theory",
"biology",
"and",
"life",
"sciences",
"population",
"genetics",
"computational",
"biology",
"evolutionary",
"biology",
"evolutionary",
"pro... | 2014 | Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks |
Seemingly minor details of mathematical and computational models of evolution are known to change the effect of population structure on the outcome of evolutionary processes . For example , birth-death dynamics often result in amplification of selection , while death-birth processes have been associated with suppressio... | Whether a mutation spreads in a population or not is one of the most important questions in biology . The evolution of cancer and antibiotic resistance , for example , are mediated by invading mutants . Recent work has shown that population structure can have important consequences for the outcome of evolution . For in... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"bacteriology",
"infographics",
"organismal",
"evolution",
"interaction",
"networks",
"population",
"dynamics",
"microbiology",
"fungal",
"evolution",
"microbial",
"evolution",
"population",
"biology",
"computer",
"and",
"information",
"sciences",
"mycology",
"molecular",
"... | 2019 | Motion, fixation probability and the choice of an evolutionary process |
Grade of membership models , also known as “admixture models” , “topic models” or “Latent Dirichlet Allocation” , are a generalization of cluster models that allow each sample to have membership in multiple clusters . These models are widely used in population genetics to model admixed individuals who have ancestry fro... | Gene expression profile of a biological sample ( either from single cells or pooled cells ) results from a complex interplay of multiple related biological processes . Consequently , for example , distal tissue samples may share a similar gene expression profile through some common underlying biological processes . Our... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"blastocysts",
"sequencing",
"techniques",
"population",
"genetics",
"neuronal",
"differentiation",
"neuroscience",
"cell",
"differentiation",
"developmental",
"biology",
"molecular",
"biology",
"techniques",
"population",
"biology",
"embryos",
"rna",
"sequencing",
"research"... | 2017 | Visualizing the structure of RNA-seq expression data using grade of membership models |
The intestinal epithelium plays a critical role in host-microbe homeostasis by sensing gut microbes and subsequently initiating proper immune responses . During the neonatal stage , the intestinal epithelium is under immune repression , allowing the transition for newborns from a relatively sterile intra-uterine enviro... | Precisely controlled host-microbe interactions in the gastrointestinal tract are crucial for human overall health and well-being . Dysregulated host responses to gut microbiota are the major cause of autoimmune diseases , inflammatory disorders and cancers . The intestinal epithelium lines the gastrointestinal tract an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"immunofluorescence",
"staining",
"immunology",
"epithelial",
"cells",
"animal",
"models",
"developmental",
"biology",
"model",
"organisms",
"signs",
"and",
"symptoms",
"experimental",
... | 2017 | hnRNP I regulates neonatal immune adaptation and prevents colitis and colorectal cancer |
Many biological and clinical outcomes are based not on single proteins , but on modules of proteins embedded in protein networks . A fundamental question is how the proteins within each module contribute to the overall module activity . Here , we study the modules underlying three representative biological programs rel... | Biological outcomes are often determined by modules of proteins working in combination . In classic biological studies , these modules have been shown to encode a diverse repertoire of logic functions which provide the means to express complex regulatory programs using a limited number of proteins . Here , we integrate... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cancer",
"detection",
"and",
"diagnosis",
"medicine",
"breast",
"tumors",
"cancers",
"and",
"neoplasms",
"basic",
"cancer",
"research",
"algorithms",
"oncology",
"neurological",
"tumors",
"developmental",
"biology",
"organism",
"development",
"regulatory",
"networks",
... | 2011 | Protein Networks as Logic Functions in Development and Cancer |
Praziquantel ( PZQ ) is the drug compound of choice in the control and treatment of schistosomiasis . PZQ is administered as a racemate , i . e . 1∶1 mixture of enantiomers . The schistosomicidal activity arises from one PZQ-enantiomer , whereas the other enantiomer does not contribute to the activity . The WHO's Speci... | Schistosomiasis , or Bilharzia , is a parasitic disease caused by flatworms , which affects about 200 million people worldwide . Praziquantel ( PZQ ) is the drug compound of choice in the control and treatment of this disease . Only half of the drug dose currently administered actually has activity against schistosomia... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"pediatrics",
"and",
"child",
"health",
"chemistry/organic",
"chemistry",
"infectious",
"diseases/neglected",
"tropical",
"diseases"
] | 2009 | Taste, A New Incentive to Switch to (R)-Praziquantel in Schistosomiasis Treatment |
Recent advances in experimental techniques have allowed the simultaneous recordings of populations of hundreds of neurons , fostering a debate about the nature of the collective structure of population neural activity . Much of this debate has focused on the empirical findings of a phase transition in the parameter spa... | Neurons encoding the natural world are correlated in their activities . The structure of this correlation fundamentally changes the population code , and these effects increase in larger neural populations . We experimentally recorded from populations of 100+ retinal ganglion cells and probed the structure of their joi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"membrane",
"potential",
"ocular",
"anatomy",
"electrophysiology",
"neuroscience",
"probability",
"distribution",
"mathematics",
"ganglion",
"cells",
"systems",
"science",
"neuronal",
"tuning",
"computer",
"... | 2017 | The structured ‘low temperature’ phase of the retinal population code |
Klotho acts as a co-receptor for and dictates tissue specificity of circulating FGF23 . FGF23 inhibits PTH secretion , and reduced Klotho abundance is considered a pathogenic factor in renal secondary hyperparathyroidism . To dissect the role of parathyroid gland resident Klotho in health and disease , we generated mic... | Inorganic calcium is a critical element for a diverse range of cellular processes ranging from cell signaling to energy metabolism , and its extracellular concentration is controlled by parathyroid hormone ( PTH ) . Klotho is expressed in parathyroid chief cells and reported to facilitate PTH secretion during hypocalce... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Parathyroid-Specific Deletion of Klotho Unravels a Novel Calcineurin-Dependent FGF23 Signaling Pathway That Regulates PTH Secretion |
Osteoporotic fracture is a major cause of morbidity and mortality worldwide . Low bone mineral density ( BMD ) is a major predisposing factor to fracture and is known to be highly heritable . Site- , gender- , and age-specific genetic effects on BMD are thought to be significant , but have largely not been considered i... | Osteoporotic fracture is a major cause of early mortality and morbidity in the community . To identify genes associated with osteoporosis , we have performed a genome-wide association study . In order to improve study power and to address the demographic group of highest risk from osteoporotic fracture , we have used a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"diabetes",
"and",
"endocrinology/bone",
"and",
"mineral",
"metabolism",
"rheumatology/bone",
"and",
"mineral",
"metabolism"
] | 2011 | Genome-Wide Association Study Using Extreme Truncate Selection
Identifies Novel Genes Affecting Bone Mineral Density and Fracture
Risk |
Genome-wide association studies ( GWAS ) have recently identified KIF1B as susceptibility locus for hepatitis B virus ( HBV ) –related hepatocellular carcinoma ( HCC ) . To further identify novel susceptibility loci associated with HBV–related HCC and replicate the previously reported association , we performed a large... | Previous studies strongly suggest the importance of genetic susceptibility for hepatocellular carcinoma ( HCC ) . However , the studies about genetic etiology on HBV–related HCC were limited . Our genome-wide association study included 523 , 663 autosomal SNPs in 1 , 538 HBV–positive HCC patients and 1 , 465 chronic HB... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"cancer",
"genetics",
"genetics",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | GWAS Identifies Novel Susceptibility Loci on 6p21.32 and 21q21.3 for Hepatocellular Carcinoma in Chronic Hepatitis B Virus Carriers |
Quantifying heterogeneity in gene expression among single cells can reveal information inaccessible to cell-population averaged measurements . However , the expression level of many genes in single cells fall below the detection limit of even the most sensitive technologies currently available . One proposed approach t... | Different cells can make different amounts of biomolecules such as RNA transcripts of genes . New technologies are emerging to measure the transcript level of many genes in single cells . However , accurate quantification of the biological variation from cell to cell can be challenging due to the low transcript level o... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"engineering",
"and",
"technology",
"signal",
"processing",
"immunology",
"population",
"genetics",
"gene",
"pool",
"simulation",
"and",
"modeli... | 2016 | Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling |
The proper temporal and spatial expression of genes during plant development is governed , in part , by the regulatory activities of various types of small RNAs produced by the different RNAi pathways . Here we report that transgenic Arabidopsis plants constitutively expressing the rapeseed SB1 SINE retroposon exhibit ... | Short interspersed elements ( SINEs ) are transposable elements in eukaryotic genomes that mobilize through an RNA intermediate . Recently , mammalian SINE RNAs were shown to have roles as noncoding riboregulators in stress situations or in specific tissues . Mammalian SINE RNAs modulate the level of mRNAs and proteins... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/epigenetics",
"genetics",
"and",
"genomics",
"biochemistry/rna",
"structure",
"molecular",
"biology/rna-protein",
"interactions"
] | 2008 | SINE RNA Induces Severe Developmental Defects in Arabidopsis thaliana and Interacts with HYL1 (DRB1), a Key Member of the DCL1 Complex |
Geophysical models of climate change are becoming increasingly sophisticated , yet less effort is devoted to modelling the human systems causing climate change and how the two systems are coupled . Here , we develop a simple socio-climate model by coupling an Earth system model to a social dynamics model . We treat soc... | The importance of anthropogenic CO2 emissions on climate change trajectories is widely acknowledged . However , geophysical climate models rarely account for dynamic human behaviour , which determines the emissions trajectory , and is itself affected by the climate system . Here , using a coupled socio-climate model , ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"learning",
"anthropogenic",
"climate",
"change",
"ecology",
"and",
"environmental",
"sciences",
"chemical",
"compounds",
"atmospheric",
"science",
"social",
"sciences",
"neuroscience",
"learning",
"and",
"memory",
"physical",
"geography",
"simulation",
"and",
"modeling",... | 2019 | Charting pathways to climate change mitigation in a coupled socio-climate model |
Lassa virus ( LASV ) , the causative agent of Lassa fever ( LF ) , is endemic in West Africa , accounting for substantial morbidity and mortality . In spite of ongoing research efforts , LF pathogenesis and mechanisms of LASV immune control remain poorly understood . While normal laboratory mice are resistant to LASV ,... | Lassa virus ( LASV ) is the causative agent of Lassa fever ( LF ) , accounting for substantial morbidity and mortality in West Africa . Yet the mechanisms leading to disease remain poorly understood . Here we propose a concept whereby the body's immune defense either defeats LASV rapidly or , if unsuccessful , becomes ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/viral",
"infections",
"immunology/immunity",
"to",
"infections",
"immunology/immune",
"response",
"immunology/innate",
"immunity"
] | 2010 | T Cell-Dependence of Lassa Fever Pathogenesis |
TLR2 is a cell surface receptor which elicits an immediate response to a wide repertoire of bacteria and viruses . Its response is usually thought to be proinflammatory rather than an antiviral . In monocytic cells TLR2 cooperates with coreceptors , e . g . CD14 , CD36 and αMβ2-integrin . In an earlier work we showed t... | In an earlier work we showed that a relevant contribution to the overall IFN-based antiviral response of the cell to herpes simplex virus is exerted by αvβ3-integrin which acts in concert with TLR2 in eliciting this response . Major characteristics of this branch of the innate response are the secretion of IFN-α and -β... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences"
] | 2014 | The Epithelial αvβ3-Integrin Boosts the MYD88-Dependent TLR2 Signaling in Response to Viral and Bacterial Components |
Mucosal mononuclear ( MMC ) CCR5+CD4+ T cells of the gastrointestinal ( GI ) tract are selectively infected and depleted during acute HIV-1 infection . Despite early initiation of combination antiretroviral therapy ( cART ) , gut-associated lymphoid tissue ( GALT ) CD4+ T cell depletion and activation persist in the ma... | This study was undertaken to determine if the gastrointestinal tract is a site of ongoing viral replication during suppressive combination antiretroviral therapy ( cART ) ( defined by plasma HIV-1 RNA levels below 50 copies/ml ) . We found no evidence of substantial viral evolution in HIV-1 envelope sequences derived f... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"gastroenterology",
"and",
"hepatology",
"hiv",
"biology",
"genomics",
"viral",
"diseases",
"genetics",
"and",
"genomics"
] | 2012 | Absence of HIV-1 Evolution in the Gut-Associated Lymphoid Tissue from Patients on Combination Antiviral Therapy Initiated during Primary Infection |
The single glycoprotein ( G ) of rabies virus ( RABV ) dictates all viral entry steps from receptor engagement to membrane fusion . To study the uptake of RABV into primary neuronal cells in culture , we generated a recombinant vesicular stomatitis virus in which the G protein was replaced with that of the neurotropic ... | Rabies virus is the causative agent of a generally fatal and incurable disease of the central nervous system ( CNS ) . Rabies lethality requires that the virus invade the brain , a feat accomplished by neuronal transmission from the site of infection to the CNS . Using cultures of peripheral neurons and chemicals that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"cell",
"processes",
"microbiology",
"viral",
"structure",
"neurites",
"neuroscience",
"motor",
"neurons",
"viruses",
"rna",
"viruses",
... | 2016 | Rabies Internalizes into Primary Peripheral Neurons via Clathrin Coated Pits and Requires Fusion at the Cell Body |
HIV-1 can disseminate between susceptible cells by two mechanisms: cell-free infection following fluid-phase diffusion of virions and by highly-efficient direct cell-to-cell transmission at immune cell contacts . The contribution of this hybrid spreading mechanism , which is also a characteristic of some important comp... | The ability to spread using more than once mechanism , named hybrid spreading , is a ubiquitous feature of many real world epidemics including HIV and Hepatitis C virus infection in vivo , and computer worms spreading on the Internet . Hybrid spreading of HIV is well documented experimentally but its importance to HIV ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection |
The Toxin Complex ( TC ) is a large multi-subunit toxin first characterized in the insect pathogens Photorhabdus and Xenorhabdus , but now seen in a range of pathogens , including those of humans . These complexes comprise three protein subunits , A , B and C which in the Xenorhabdus toxin are found in a 4∶1∶1 stoichio... | Bacterial pathogens of insects deploy a range of toxins to combat the innate immune system and kill the host . There is significant interest in developing these toxins as candidates for crop protection strategies . To date , transgenic crops expressing Bacillus thuringiensis Cry toxins have been used to resist predatio... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"gram",
"negative",
"microbial",
"pathogens",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"bacterial",
"pathogens",
"pathogenesis"
] | 2012 | Pdl1 Is a Putative Lipase that Enhances Photorhabdus Toxin Complex Secretion |
Phylogenetically distinct Mycobacterium tuberculosis lineages differ in their phenotypes and pathogenicity . Consequently , understanding mycobacterial population structures phylogeographically is essential for design , interpretation and generalizability of clinical trials . Comprehensive efforts are lacking to date t... | Tuberculosis is caused by bacteria belonging to the Mycobacterium tuberculosis complex ( MTBc ) , which consists of seven major , phylogenetically distinct lineages and their families . West Africa is the only region in the world where , besides the common M . tuberculosis lineages , the two M . africanum lineages are ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biogeography",
"taxonomy",
"ecology",
"and",
"environmental",
"sciences",
"medicine",
"and",
"health",
"sciences",
"population",
"dynamics",
"population",
"genetics",
"geographical",
"locations",
"tropical",
"diseases",
"bacterial",
"diseases",
"phylogenetics",
"data",
"... | 2016 | A Mycobacterial Perspective on Tuberculosis in West Africa: Significant Geographical Variation of M. africanum and Other M. tuberculosis Complex Lineages |
Evolution is shaping the world around us . At the core of every evolutionary process is a population of reproducing individuals . The outcome of an evolutionary process depends on population structure . Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations . T... | At the center of any evolutionary process is a population of reproducing individuals . The structure of this population can greatly affect the outcome of evolution . If the fitness of an individual is determined by its interactions with others , then we are in the world of evolutionary game theory . The population stru... | [
"Abstract",
"Introduction",
"Results",
"Discussion"
] | [
"evolutionary",
"biology/evolutionary",
"ecology",
"evolutionary",
"biology/human",
"evolution",
"mathematics",
"computational",
"biology/evolutionary",
"modeling",
"evolutionary",
"biology"
] | 2009 | Calculating Evolutionary Dynamics in Structured Populations |
At the Drosophila NMJ , BMP signaling is critical for synapse growth and homeostasis . Signaling by the BMP7 homolog , Gbb , in motor neurons triggers a canonical pathway—which modulates transcription of BMP target genes , and a noncanonical pathway—which connects local BMP/BMP receptor complexes with the cytoskeleton ... | Synaptic activity and synapse development are intimately linked , but our understanding of the coupling mechanisms remains limited . Anterograde and retrograde signals together with trans-synaptic complexes enable intercellular communications . How synapse activity status is monitored and relayed across the synaptic cl... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"phosphorylation",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"electrophysiology",
"neuroscience",
"animals",
"motor",
"neurons",
"animal",
"models",
"organisms",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organis... | 2016 | A Novel, Noncanonical BMP Pathway Modulates Synapse Maturation at the Drosophila Neuromuscular Junction |
Loops in proteins are flexible regions connecting regular secondary structures . They are often involved in protein functions through interacting with other molecules . The irregularity and flexibility of loops make their structures difficult to determine experimentally and challenging to model computationally . Confor... | Loops in proteins are flexible regions connecting regular secondary structures . They are often involved in protein functions through interacting with other molecules . The irregularity and flexibility of loops make their structures difficult to determine experimentally and challenging to model computationally . Despit... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"proteins",
"protein",
"folding",
"protein",
"structure",
"biology",
"and",
"life",
"sciences",
"computational",
"biology",
"biophysics"
] | 2014 | Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method |
Viruses impose diverse and dynamic challenges on host defenses . Diversifying selection of codons and gene copy number variation are two hallmarks of genetic innovation in antiviral genes engaged in host-virus genetic conflicts . The myxovirus resistance ( Mx ) genes encode interferon-inducible GTPases that constitute ... | Evolutionary analyses have the potential to reveal not only biochemical details about host-virus arms-races but also the nature of the pathogens that drove them . Primate MxB was recently shown to restrict the replication of primate lentiviruses , including HIV-1 . However , we find that positive selection in primate M... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction |
Changes of synaptic connections between neurons are thought to be the physiological basis of learning . These changes can be gated by neuromodulators that encode the presence of reward . We study a family of reward-modulated synaptic learning rules for spiking neurons on a learning task in continuous space inspired by ... | Humans and animals learn if they receive reward . Such reward is likely to be communicated throughout the brain by neuromodulatory signals . In this paper we present a network of model neurons , which communicate by short electrical pulses ( spikes ) . Learning is achieved by modifying the input connections depending o... | [
"Abstract",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/theoretical",
"neuroscience"
] | 2009 | Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail |
The upper respiratory tract mucosa is the location for commensal Streptococcus ( S . ) pneumoniae colonization and therefore represents a major site of contact between host and bacteria . The CD4+ T cell response to pneumococcus is increasingly recognised as an important mediator of immunity that protects against invas... | The S . pneumoniae bacteria is a major cause of disease ( e . g . pneumonia and meningitis ) particularly affecting infants . In most cases bacteria can colonise the nose without causing harm , however colonisation is thought to be a prerequisite of disease . With increasing age colonization and disease , rates gradual... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"adaptive",
"immunity",
"immune",
"cells",
"aging",
"and",
"immunity",
"streptococci",
"immunity",
"t",
"cells",
"immunology",
"biology",
"microbiology",
"immunoregulation",
"bacterial",
"pathogens",
"immune",
"response"
] | 2011 | Acquisition of Pneumococci Specific Effector and Regulatory Cd4+ T Cells Localising within Human Upper Respiratory-Tract Mucosal Lymphoid Tissue |
De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population . These orphan proteins need to , at the bare minimum , not cause serious harm to the organism , meaning that they should for instance not aggregate . Theref... | We show that the GC content of a genome is of great importance for the properties of an orphan protein . GC content affects the frequency of the codons and this affects the probability for each amino acid to be included in a de novo created protein . The codons encoding for Ala , Pro and Gly contain 80% GC , while codo... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"invertebrate",
"genomics",
"animals",
"animal",
"models",
"age",
"groups",
"fungi",
"drosophila",
"melanogaster",
"model",
"organisms",
... | 2017 | High GC content causes orphan proteins to be intrinsically disordered |
Plasmodium parasites , along with their Piroplasm relatives , have caused malaria-like illnesses in terrestrial mammals for millions of years . Several Plasmodium-protective alleles have recently evolved in human populations , but little is known about host adaptation to blood parasites over deeper evolutionary timesca... | Malaria caused by the parasite Plasmodium falciparum remains the third-most deadly infectious disease of humans . Over the last 75 , 000 years , partial genetic resistance to malaria has evolved several times , earning malaria the title of "one of the strongest selective forces on the human genome . " Yet , these human... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"plasmodium",
"parasite",
"evolution",
"tropical",
"diseases",
"vertebrates",
"parasitic",
"diseases",
"animals",
"mammals",
"parasitology",
"parasitic",
"protozoa... | 2017 | High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites |
The molecular triggers for axon degeneration remain unknown . We identify endogenous Nmnat2 as a labile axon survival factor whose constant replenishment by anterograde axonal transport is a limiting factor for axon survival . Specific depletion of Nmnat2 is sufficient to induce Wallerian-like degeneration of uninjured... | In a normally functioning neuron , the cell body supplies the axon with materials needed to keep it healthy . This complex logistical activity breaks down completely after injury and often becomes compromised in neurodegenerative diseases , leading to degeneration of the isolated axon . Whilst there are probably many i... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurological",
"disorders/peripheral",
"neuropathies",
"neuroscience/neuronal",
"signaling",
"mechanisms",
"neuroscience/neurobiology",
"of",
"disease",
"and",
"regeneration",
"neurological",
"disorders/spinal",
"disorders"
] | 2010 | Endogenous Nmnat2 Is an Essential Survival Factor for Maintenance of Healthy Axons |
Arthropod vectors have multiple physical and immunological barriers that impede the development and transmission of parasites to new vertebrate hosts . These barriers include the peritrophic matrix ( PM ) , a chitinous barrier that separates the blood bolus from the midgut epithelia and modulates vector-pathogens inter... | Insects are responsible for transmission of parasites that cause deadly diseases in humans and animals . Understanding the key factors that enhance or interfere with parasite transmission processes can result in new control strategies . Here , we report that a proportion of tsetse flies with African trypanosome infecti... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Conclusion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoans",
"mitochondria",
"bioenergetics",
"infectious",
"disease",
"control",
"cellular",
"structures",
"and",
"organelles",
"cardia",
"digestive",
"system"... | 2018 | A fine-tuned vector-parasite dialogue in tsetse's cardia determines peritrophic matrix integrity and trypanosome transmission success |
Immunotherapy using regulatory T cells ( Treg ) has been proposed , yet cellular and molecular mechanisms of human Tregs remain incompletely characterized . Here , we demonstrate that human Tregs promote the generation of myeloid dendritic cells ( DC ) with reduced capacity to stimulate effector T cell responses . In a... | Graft-versus-host disease ( GVHD ) is the most serious complication of bone marrow transplants between individuals ( so-called allogenic transplants ) . The class of suppressor immune cells called regulatory T cells ( Tregs ) inhibit GVHD by dampening the effects of donor immune cells in the grafted tissue . The cellul... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/immunomodulation",
"hematology/bone",
"marrow",
"and",
"stem",
"cell",
"transplantation",
"immunology/immune",
"response"
] | 2010 | Regulatory T Cells and Human Myeloid Dendritic Cells Promote Tolerance via Programmed Death Ligand-1 |
The earliest immune responses activated in acute human immunodeficiency virus type 1 infection ( AHI ) exert a critical influence on subsequent virus spread or containment . During this time frame , components of the innate immune system such as macrophages and DCs , NK cells , β-defensins , complement and other anti-m... | Acquired immune deficiency syndrome ( AIDS ) remains a major health problem worldwide , affecting predominantly the adult population in the western world and in developing countries in particular . Despite a tremendous effort to develop a cure or a vaccine that confers protection against human immunodeficiency virus ( ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"cell",
"biology/cell",
"signaling",
"cell",
"biology",
"biochemistry/chemical",
"biology",
"of",
"the",
"cell",
"chemical",
"biology/protein",
"chemistry",
"and",
"proteomics",
"chemical",
"biology/chemical",
"biology",
"of",
"the",
"cell"
] | 2010 | Elevation of Intact and Proteolytic Fragments of Acute Phase Proteins Constitutes the Earliest Systemic Antiviral Response in HIV-1 Infection |
Thymus is crucial for generation of a diverse repertoire of T cells essential for adaptive immunity . Although thymic epithelial cells ( TECs ) are crucial for thymopoiesis and T cell generation , how TEC development and function are controlled is poorly understood . We report here that mTOR complex 1 ( mTORC1 ) in TEC... | The thymus is the primary organ for T cell generation . Abnormal thymus function profoundly affects host immunity and numerous diseases . Thymopoiesis and thymus function rely on orchestrated interaction between multiple cell types representing different origins . Among them , thymic epithelial cells ( TECs ) are cruci... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"atrophy",
"immunology",
"cloning",
"age",
"groups",
"adults",
"signs",
"and",
"symptoms",
"stem",
"cells",
"molecular",
"biology",
"technique... | 2016 | mTORC1 in Thymic Epithelial Cells Is Critical for Thymopoiesis, T-Cell Generation, and Temporal Control of γδT17 Development and TCRγ/δ Recombination |
Establishing the sources of reinfestation after residual insecticide spraying is crucial for vector elimination programs . Triatoma infestans , traditionally considered to be limited to domestic or peridomestic ( abbreviated as D/PD ) habitats throughout most of its range , is the target of an elimination program that ... | Triatoma infestans , a highly domesticated species and historically the main vector of Trypanosoma cruzi , is the target of an insecticide-based elimination program in the southern cone countries of South America since 1991 . Only limited success has been achieved in the Gran Chaco region due to repeated reinfestations... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"spatial",
"and",
"landscape",
"ecology",
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"chagas",
"disease",
"ecology",
"epidemiology",
"genetics",
"population",
"genetics",
"biology",
"population",
"ecology",
"parasitic",
"diseases",
... | 2011 | Hidden Sylvatic Foci of the Main Vector of Chagas Disease Triatoma infestans: Threats to the Vector Elimination Campaign? |
Enteropathogenic Escherichia coli ( EPEC ) use a needle-like injection apparatus known as the type III secretion system ( T3SS ) to deliver protein effectors into host cells . Effector translocation is highly stratified in EPEC with the translocated intimin receptor ( Tir ) being the first effector delivered into the h... | Enteropathogenic Escherichia coli injects effector proteins into host cells using a type III secretion system ( T3SS ) . The translocated intimin receptor ( Tir ) is the first effector delivered into host cells and imparts efficient secretion of other effectors . However , the mechanism for Tir-dependent modulation of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"bacteriology",
"dimers",
"(chemical",
"physics)",
"complement",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"viral",
"transmission",
"and",
"infection",
"hela",
"cells",
"molecular",
"probe",
... | 2018 | Molecular basis for CesT recognition of type III secretion effectors in enteropathogenic Escherichia coli |
Treponema pallidum subsp . endemicum ( TEN ) is the causative agent of endemic syphilis ( bejel ) . An unusual human TEN 11q/j isolate was obtained from a syphilis-like primary genital lesion from a patient that returned to France from Pakistan . The TEN 11q/j isolate was characterized using nested PCR followed by Sang... | Treponema pallidum subsp . endemicum ( TEN ) is an uncultivable pathogenic treponeme that causes bejel ( endemic syphilis ) , a chronic human infection mostly affecting children under 15 years of age , occurring mainly in several African and Middle East countries . In this work , we characterized a TEN 11q/j isolate fr... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"geographical",
"locations",
"microbiology",
"sequence",
"assembly",
"tools",
"genome",
"analysis",
"molecular",
"biology",
"techniques",
"bacterial",
"pathogens",
"researc... | 2017 | Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively |
Vibrio parahaemolyticus is a leading cause of seafood-borne gastroenteritis in many parts of the world , but there is limited knowledge of the pathogenesis of V . parahaemolyticus-induced diarrhea . The absence of an oral infection-based small animal model to study V . parahaemolyticus intestinal colonization and disea... | The marine bacterium Vibrio parahaemolyticus is a leading cause worldwide of gastroenteritis linked to the consumption of contaminated seafood . Despite the prevalence of V . parahaemolyticus-induced gastroenteritis , there is limited understanding of how this pathogen causes disease in the intestine . In part , the pa... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"gastroenterology",
"and",
"hepatology",
"biology",
"microbiology",
"bacterial",
"pathogens"
] | 2012 | Inflammation and Disintegration of Intestinal Villi in an Experimental Model for Vibrio parahaemolyticus-Induced Diarrhea |
Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands . They are primarily found in bacteria . However , one riboswitch type , the thiamin pyrophosphate ( TPP ) riboswitch , has also been described in some plants , marine protists and fungi . We find that riboswitches ar... | Thiamin , or Vitamin B1 , is an essential requirement in all living organisms because it is a co-factor for many enzymes in metabolism . Unlike animals , many yeasts can synthesize thiamin , or they can import it from the environment . Expression of thiamin biosynthesis genes and of thiamin transporters is strictly reg... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"fungal",
"genetics",
"gene",
"regulation",
"pathogens",
"microbiology",
"fungi",
"model",
"organisms",
"experimental",
"organism",
"systems",
"fungal",
"pathogens",
"saccharomyces",
... | 2018 | TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida |
Temperature affects both the timing and outcome of animal development , but the detailed effects of temperature on the progress of early development have been poorly characterized . To determine the impact of temperature on the order and timing of events during Drosophila melanogaster embryogenesis , we used time-lapse... | Temperature profoundly impacts the rate of development of “cold-blooded” animals , which proceeds far faster when it is warm . There is , however , no universal relationship . Closely related species can develop at markedly different speeds at the same temperature . This creates a major challenge when comparing develop... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"growth",
"control",
"evolutionary",
"ecology",
"ecology",
"and",
"environmental",
"sciences",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"organism",
"development",
"evolutionary",
"adaptat... | 2014 | Drosophila Embryogenesis Scales Uniformly across Temperature in Developmentally Diverse Species |
Hemorrhagic fever viruses , including the filoviruses ( Ebola and Marburg ) and arenaviruses ( Lassa and Junín viruses ) , are serious human pathogens for which there are currently no FDA approved therapeutics or vaccines . Importantly , transmission of these viruses , and specifically late steps of budding , criticall... | Filoviruses ( Ebola and Marburg viruses ) and arenaviruses ( Lassa and Junín viruses ) are high-priority pathogens that hijack host proteins and pathways to complete their replication cycles and spread from cell to cell . Here we provide genetic and pharmacological evidence to demonstrate that the host calcium channel ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Calcium Regulation of Hemorrhagic Fever Virus Budding: Mechanistic Implications for Host-Oriented Therapeutic Intervention |
There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale , genome-wide epigenetic changes that are maintained over many generations . In the model plant Arabidopsis thaliana , numerous heritable DNA methylation differences have... | It continues to be hotly debated to what extent environmentally induced epigenetic change is stably inherited and thereby contributes to short-term adaptation . It has been shown before that natural Arabidopsis thaliana lines differ substantially in their methylation profiles . How much of this is independent of geneti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biogeography",
"ecology",
"and",
"environmental",
"sciences",
"plant",
"science",
"model",
"organisms",
"plant",
"genomics",
"epigenetics",
"theoretical",
"ecology",
"plant",
"ecology",
"dna",
"methylation",
"arabidopsis",
"thaliana",
"research",
"and",
"analysis",
"me... | 2015 | Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage |
Macrophages can be niches for bacterial pathogens or antibacterial effector cells depending on the pathogen and signals from the immune system . Here we show that type I and II IFNs are master regulators of gene expression during Legionella pneumophila infection , and activators of an alveolar macrophage-intrinsic immu... | Numerous intracellular bacterial pathogens replicate in specialized vacuoles within macrophages . We systematically study the molecular mechanism and the impact of macrophage-intrinsic antibacterial defense . Using L . pneumophila , an important cause of pneumonia and model organism for intracellular bacteria , we foun... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"vacuoles",
"intracellular",
"pathogens",
"pathogens",
"immunology",
"microbiology",
"animal",
"models",
"model",
"organisms",
"mitochondria",
"bi... | 2016 | IFNs Modify the Proteome of Legionella-Containing Vacuoles and Restrict Infection Via IRG1-Derived Itaconic Acid |
Although enteroparasites are common causes of diarrheal illness , few studies have been performed among children in Tanzania . This study aimed to investigate the prevalence of Cryptosporidium parvum/hominis , Entamoeba histolytica and Giardia lamblia among young children in Dar es Salaam , Tanzania , and identify risk... | Diarrheal diseases are a leading cause of disease and deaths among young children . In Africa they contribute to more than one tenth of childhood deaths . Parasites like Cryptosporidium , Entamoeba histolytica and Giardia lamblia are all common causes of diarrheal illness , but there are few studies on these enteropara... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Prevalence of Cryptosporidium parvum/hominis, Entamoeba histolytica and Giardia lamblia among Young Children with and without Diarrhea in Dar es Salaam, Tanzania |
Phosphoribosyl pyrophosphate synthetase ( PRPS ) is a rate-limiting enzyme whose function is important for the biosynthesis of purines , pyrimidines , and pyridines . Importantly , while missense mutations of PRPS1 have been identified in neurological disorders such as Arts syndrome , how they contribute to neuropathog... | Phosphoribosyl pyrophosphate synthetase ( PRPS ) is an important enzyme in nucleotide synthesis: the building blocks of DNA and RNA and other important metabolites . Importantly , while PRPS is mutated in neurological disorders such as Arts syndrome , Charcot-Marie-Tooth disease , and nonsyndromic sensorineural deafnes... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"death",
"invertebrates",
"lysosomes",
"autophagic",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"oxidative",
"stress",
"cell",
"processes",
"animals",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"experimental",
"organis... | 2019 | Pleiotropic role of Drosophila phosphoribosyl pyrophosphate synthetase in autophagy and lysosome homeostasis |
Poly ( A ) -binding proteins ( PABPs ) regulate mRNA fate by controlling stability and translation through interactions with both the poly ( A ) tail and eIF4F complex . Many organisms have several paralogs of PABPs and eIF4F complex components and it is likely that different eIF4F/PABP complex combinations regulate di... | Poly ( A ) -binding proteins ( PABPs ) bind to the poly ( A ) tails of eukaryotic mRNAs and function in regulating mRNA fate . Many eukaryotes have several PABP paralogs and the current view is that each PABP binds a specific subset of mRNAs . Trypanosoma brucei has two PABPs , and to understand the differential functi... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"rna-binding",
"proteins",
"messenger",
"rna",
"parasitic",
"protozoans",
"organisms",
"trypanosoma",
"brucei",
"fractional",
"precipitation",
"protozoans",
"translation",
"initiation",
"research",
"and",
"analysis",
"methods",
"proteins",
"gene",
"e... | 2018 | Comparative proteomics of the two T. brucei PABPs suggests that PABP2 controls bulk mRNA |
Severe fever with thrombocytopenia syndrome virus ( SFTSV ) , the causative agent for the fatal life-threatening infectious disease , severe fever with thrombocytopenia syndrome ( SFTS ) , was first identified in the central and eastern regions of China . Although the viral RNA was detected in free-living and parasitic... | Severe fever with thrombocytopenia syndrome virus ( SFTSV ) , a newly identified bunyavirus , has been found to circulate in mainland China , South Korea , and Japan since 2009 . This virus is the etiologic agent for an emerging fatal hemorrhagic fever , severe fever with thrombocytopenia syndrome ( SFTS ) with high fa... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Experimental and Natural Infections of Goats with Severe Fever with Thrombocytopenia Syndrome Virus: Evidence for Ticks as Viral Vector |
Hepatitis C virus ( HCV ) infection is a leading cause of liver transplantation and there is an urgent need to develop therapies to reduce rates of HCV infection of transplanted livers . Approved therapeutics for HCV are poorly tolerated and are of limited efficacy in this patient population . Human monoclonal antibody... | The majority of individuals infected with hepatitis C virus ( HCV ) become chronically infected and many go on to develop liver failure requiring liver transplantation . Unfortunately , the transplanted liver becomes infected with HCV in nearly 100% of transplant patients . Current treatments for HCV are poorly tolerat... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"animal",
"models",
"of",
"infection",
"antivirals",
"viral",
"evolution",
"mechanisms",
"of",
"resistance",
"and",
"susceptibility",
"viral",
"immune",
"evasion",
"virology",
"immunology",
"biology",
"microbiology",
"drug",
"discovery",
"immunoglobulins"... | 2012 | Human Monoclonal Antibody HCV1 Effectively Prevents and Treats HCV Infection in Chimpanzees |
Schistosome eggs must traverse tissues of the intestine or bladder to escape the human host and further the life cycle . Escape from host tissues is facilitated by secretion of immuno-reactive molecules by eggs and the formation of an intense strong granulomatous response by the host which acts to exclude the egg into ... | Adult schistosomes live within portal veins of their human hosts . Their offspring , laid as eggs within the venous system , escape by traversing the tissues between the blood vessel and the gut or bladder lumen . Eggs voided into the external environment hatch spontaneously on contact with freshwater , and the hatched... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/helminth",
"infections",
"developmental",
"biology/embryology",
"cell",
"biology/developmental",
"molecular",
"mechanisms"
] | 2008 | Correlative and Dynamic Imaging of the Hatching Biology of Schistosoma japonicum from Eggs Prepared by High Pressure Freezing |
The processing characteristics of neurons in the central auditory system are directly shaped by and reflect the statistics of natural acoustic environments , but the principles that govern the relationship between natural sound ensembles and observed responses in neurophysiological studies remain unclear . In particula... | We explore a fundamental question with regard to the representation of sound in the auditory system , namely: what are the coding strategies that underlie observed neurophysiological responses in central auditory areas ? There has been debate in recent years as to whether neural ensembles explicitly minimize their prop... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"neuroscience",
"audio",
"signal",
"processing",
"signal",
"processing",
"biology",
"computational",
"biology",
"sensory",
"systems",
"neuroscience",
"engineering",
"coding",
"mechanisms"
] | 2013 | Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds |
Several pathways control time to flowering in Arabidopsis thaliana through transcriptional and posttranscriptional gene regulation . In recent years , mRNA processing has gained interest as a critical regulator of flowering time control in plants . However , the molecular mechanisms linking RNA splicing to flowering ti... | Timing of flowering has a great effect on reproductive success and fitness . It is controlled by many external signals and internal states involving a large set of genes . Here we report that the Arabidopsis thaliana BRR2a gene is needed for normal flowering . BRR2 proteins are components of the spliceosome and highly ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"sequencing",
"techniques",
"rna",
"extraction",
"mutation",
"epigenetics",
"molecular",
"biology",
"techniques",
"plants",
"flowering",
"plants",
"extraction",
"techniques",
"chromatin",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"genome",
"complex... | 2016 | BRR2a Affects Flowering Time via FLC Splicing |
Multi-beam scanning electron microscopy ( mSEM ) enables high-throughput , nano-resolution imaging of macroscopic tissue samples , providing an unprecedented means for structure-function characterization of biological tissues and their cellular inhabitants , seamlessly across multiple length scales . Here we describe c... | Until recently , the assessment of organ and tissue health relied on site-sampling ( biopsy ) of micro-scale regions and was fraught with sampling errors . Overcoming these limitations requires a means for seamless imaging of organs , from their cellular inhabitants to whole organs , akin to charting a map of the organ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"stiffness",
"mechanical",
"properties",
"medicine",
"and",
"health",
"sciences",
"diagnostic",
"radiology",
"engineering",
"and",
"technology",
"cardiovascular",
"anatomy",
"signal",
"processing",
"osteoblasts",
"microscopy",
"pelvis",
"connective",
"tissue",
"cells",
"m... | 2016 | Creating High-Resolution Multiscale Maps of Human Tissue Using Multi-beam SEM |
Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem ( ES ) cells . The recent demonstration that 5-methylcytosine ( 5-mC ) may be further modified to 5-hydroxymethylcytosine ( 5-hmC ) in ES cells has revealed a novel regulat... | Recent studies revealed the oxygenase-catalyzed production of 5-hydroxymethylcytosine ( 5-hmC ) as a modification to mammalian DNA . 5-hmC is known to play important roles in self-renewal and cell lineage specification in embryonic stem ( ES ) cells , suggesting a potential role for 5-hmC–mediated epigenetic regulation... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"sequencing",
"genomics",
"chromosome",
"biology",
"genetics",
"epigenetics",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics"
] | 2011 | Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells |
To determine the sensitivity , specificity , and field utility of the Cepheid GeneXpert Chlamydia trachomatis ( CT ) Assay ( GeneXpert ) for ocular chlamydia infection compared to Roche Amplicor CT assay ( Amplicor ) . In a trachoma-endemic community in Kongwa Tanzania , 144 children ages 0 to 9 were surveyed to assess... | Trachoma , an eye infection caused by C . trachomatis , is the leading cause of infectious blindness worldwide , affecting the developing world . The current standard for trachoma treatment involves mass drug administration ( MDA ) of an antibiotic that is given to a community to reduce transmission . A field test for ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"neglected",
"tropical",
"diseases",
"infectious",
"diseases",
"trachoma"
] | 2013 | Field Evaluation of the Cepheid GeneXpert Chlamydia trachomatis Assay for Detection of Infection in a Trachoma Endemic Community in Tanzania |
Elg1 , the major subunit of a Replication Factor C-like complex , is critical to ensure genomic stability during DNA replication , and is implicated in controlling chromatin structure . We investigated the consequences of Elg1 loss for the dynamics of chromatin re-formation following DNA replication . Measurement of Ok... | DNA replication is the central process that duplicates the genetic information during cell multiplication . Many cellular factors play important roles in the efficient and accurate duplication of DNA , critical for faithful transmission of genetic information . One such factor is Elg1 . Elg1 acts to unload PCNA , the r... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"nucleases",
"enzymes",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"dna-binding",
"proteins",
"enzymology",
"fungi",
"dna",
"replication",
"immunoprecipitation",
"epigenetics",
"dna",
"synthesis",
"phase",
"co-immunoprecipitation",
"chromatin",
"rese... | 2018 | Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation |
Systemic lupus erythematosus ( SLE ) , a complex polygenic autoimmune disease , is associated with increased complement activation . Variants of genes encoding complement regulator factor H ( CFH ) and five CFH-related proteins ( CFHR1-CFHR5 ) within the chromosome 1q32 locus linked to SLE , have been associated with m... | Systemic lupus erythematosus ( SLE ) is a complex autoimmune disease , associated with increased complement activation . Previous studies have provided evidence for the presence of SLE susceptibility gene ( s ) in the chromosome 1q31-32 locus . Within 1q32 , genes encoding complement regulator factor H ( CFH ) and five... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"complement",
"system",
"clinical",
"immunology",
"genetic",
"association",
"studies",
"lupus",
"erythematosus",
"genetics",
"autoimmune",
"diseases",
"immunology",
"biology",
"human",
"genetics",
"genetics",
"and",
"genomics",
"immune",
"system"
] | 2011 | Association of Genetic Variants in Complement Factor H and Factor H-Related Genes with Systemic Lupus Erythematosus Susceptibility |
Leprosy , caused by Mycobacterium leprae , can lead to scarring and deformities . Human immunodeficiency virus ( HIV ) , a lymphotropic virus with high rates of replication , leads to cell death in various stages of infection . These diseases have major social and quality of life costs , and although the relevance of t... | Leprosy and HIV infections , separately , are serious modern public health problems . Many studies have been conducted on these diseases , but knowledge gaps remain . This article provides the first account of important clinical information on a significant sample of patients with leprosy , as well as patients with bot... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Leprosy Reactions in Patients Coinfected with HIV: Clinical Aspects and Outcomes in Two Comparative Cohorts in the Amazon Region, Brazil |
Chagas disease is one of the most important endemic parasitic diseases in Latin America . In its chronic phase , progression to cardiomyopathy has high morbidity and mortality . The persistence of a normal electrocardiogram ( ECG ) provides a similar prognosis to that of a non-diseased population . Benznidazole ( BNZ )... | Twenty years of follow-up of patients with Chagas disease treated with benznidazole is presented in this paper . The persistence of a normal electrocardiogram ( ECG ) provides a similar prognosis to that of a non-diseased population . Benznidazole ( BNZ ) is the only drug with trypanocidal action available in Brazil . ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"coronary",
"artery",
"disease",
"medicine",
"and",
"health",
"sciences",
"parasite",
"evolution",
"tropical",
"diseases",
"parasitic",
"diseases",
"parasitology",
"electrocardiography",
"bioassays",
"and",
"physiological",
"analysis",
"neglected",
"tropical",
"diseases",
... | 2016 | Evaluation of Parasiticide Treatment with Benznidazol in the Electrocardiographic, Clinical, and Serological Evolution of Chagas Disease |
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