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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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Plant tissue architecture and organ morphogenesis rely on the proper orientation of cell divisions . Previous attempts to predict division planes from cell geometry in plants mostly focused on 2D symmetric divisions . Using the stereotyped division patterns of Arabidopsis thaliana early embryogenesis , we investigated ... | The proper positioning of division planes is key for correct development and morphogenesis of organs , in particular in plants were cellular walls prevent cell rearrangements . Elucidating how division planes are selected is therefore essential to decipher the cellular bases of plant morphogenesis . Previous attempts t... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"plant",
"anatomy",
"cell",
"division",
"analysis",
"cell",
"cycle",
"and",
"cell",
"division",
"plant",
"cell",
"biology",
"cell",
"processes",
"brassica",
"simulation",
"and",
"modeling",
"developmental",
"biology",
"plant",
"science",
"model",
"organisms",
"exper... | 2019 | Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos |
Influenza virus produces a protein , NS1 , that inhibits infected cells from releasing type I interferon ( IFN ) and blocks maturation of conventional dendritic cells ( DCs ) . As a result , influenza virus is a poor activator of both mouse and human DCs in vitro . However , in vivo a strong immune response to virus in... | Influenza infection leads to a serious respiratory infection of the lung epithelium . Lying directly below the epithelial cells are immune system sentinels known as dendritic cells . These cells interact with the virus and carry parts of the virus to draining lymph nodes to activate killer T cells . In order to effecti... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/immune",
"response",
"immunology/innate",
"immunity",
"virology/effects",
"of",
"virus",
"infection",
"on",
"host",
"gene",
"expression",
"immunology/immunity",
"to",
"infections",
"virology/host",
"antiviral",
"responses"
] | 2008 | Interferon-β Pretreatment of Conventional and Plasmacytoid Human Dendritic Cells Enhances Their Activation by Influenza Virus |
Leishmania infantum is an etiological agent of the life-threatening visceral form of leishmaniasis . Liposomal amphotericin B ( AmB ) followed by a short administration of miltefosine ( MF ) is a drug combination effective for treating visceral leishmaniasis in endemic regions of India . Resistance to MF can be due to ... | Miltefosine and amphotericin B are two leading molecules in the fight against the vector-borne disease Leishmaniasis . We demonstrate here that different point mutations in a P-type ATPase could play an important role in resistance , not only to miltefosine , but also to amphotericin B . Furthermore , macrophage-infect... | [
"Abstract",
"Introduction",
"Material",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"mutation",
"protozoans",
"leishmania",
"cellular",
"structures",
"and",
"organelles",
"lipids",
"sterols",
"cell",
"membranes",
"biochemistry",
"leishmania",
"infantum",
"point",... | 2016 | Different Mutations in a P-type ATPase Transporter in Leishmania Parasites are Associated with Cross-resistance to Two Leading Drugs by Distinct Mechanisms |
The gut microbiome is a dynamic system that changes with host development , health , behavior , diet , and microbe-microbe interactions . Prior work on gut microbial time series has largely focused on autoregressive models ( e . g . Lotka-Volterra ) . However , we show that most of the variance in microbial time series... | Dynamics reveal crucial information about how a system functions . In this study , we develop an approach for disentangling two types of dynamics within the human gut microbiome . We find that autoregressive dynamics involve recovery from large deviations in community structure . These recovery processes appear to invo... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion"
] | [
"taxonomy",
"ecology",
"and",
"environmental",
"sciences",
"microbiome",
"community",
"structure",
"microbiology",
"phylogenetics",
"data",
"management",
"information",
"technology",
"data",
"processing",
"microbial",
"genomics",
"computer",
"and",
"information",
"sciences"... | 2017 | Two dynamic regimes in the human gut microbiome |
Germ granules , termed P granules in nematode C . elegans , are the germline-specific cytoplasmic structures widely observed from worms to humans . P granules are known to have critical functions for postembryonic germline development likely through regulating RNA metabolism . They are localized at the perinuclear regi... | C . elegans provides a prime model for studying evolutionarily conserved biological mechanisms that control development and physiology . One of the conserved features of germ cells is the presence of germ granules , the germline-specific cytoplasmic structures observed in various organisms from worms to humans . P gran... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"cell",
"physiology",
"cell",
"death",
"invertebrates",
"autophagic",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"rna",
"interference",
"gonads",
"caenorhabditis",
"cell",
"processes",
"animals",
"germ",
"cells",
"dna",
"damage... | 2019 | Autophagy of germ-granule components, PGL-1 and PGL-3, contributes to DNA damage-induced germ cell apoptosis in C. elegans |
Rapid colour change is a remarkable natural phenomenon that has evolved in several vertebrate and invertebrate lineages . The two principal explanations for the evolution of this adaptive strategy are ( 1 ) natural selection for crypsis ( camouflage ) against a range of different backgrounds and ( 2 ) selection for con... | The ability to change colour has evolved in numerous vertebrate and invertebrate groups , the most well-known of which are chameleons and cephalopods ( octopuses and their relatives ) . There is great variation among species , however , in the apparent capacity for colour change , ranging from limited changes in bright... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology",
"evolutionary",
"biology",
"neuroscience"
] | 2008 | Selection for Social Signalling Drives the Evolution of Chameleon Colour Change |
Driven by clinical needs and progress in neurotechnology , targeted interaction with neuronal networks is of increasing importance . Yet , the dynamics of interaction between intrinsic ongoing activity in neuronal networks and their response to stimulation is unknown . Nonetheless , electrical stimulation of the brain ... | Electrical stimulation of the brain is increasingly used to alleviate the symptoms of a range of neurological disorders and as a means to artificially inject information into neural circuits in neuroprosthetic applications . Machine learning has been proposed to find optimal stimulation settings autonomously . However ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"learning",
"medicine",
"and",
"health",
"sciences",
"action",
"potentials",
"neural",
"networks",
"membrane",
"potential",
"social",
"sciences",
"electrophysiology",
"neuroscience",
"learning",
"and",
"memory",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"o... | 2016 | Autonomous Optimization of Targeted Stimulation of Neuronal Networks |
Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries , with major public health and economic implications in West Africa . Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circulating level... | Buruli ulcer is a skin disease caused by inoculation of Mycobacterium ulcerans bacteria , which is emerging in tropical countries . Lesions typically start as nodules , which eventually open to form progressive , non-healing wounds . Although anti-mycobacterial antibiotics are efficient at stopping the infection , ulce... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease |
Pseudohyphal growth is a nutrient-regulated program in which budding yeast form multicellular filaments of elongated and connected cells . Filamentous growth is required for virulence in pathogenic fungi and provides an informative model of stress-responsive signaling . The genetics and regulatory networks modulating p... | Changes in metabolite levels underlie important biological processes , including cellular responses to nutrient stress . One such response encompasses the nitrogen stress-induced transition of budding yeast cells into multicellular filaments , relevant as a model of directional growth and fungal pathogenesis . We repor... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"chemical",
"compounds",
"enzymes",
"salts",
"enzymology",
"phosphatases",
"fungi",
"model",
"organisms",
"experimental",
"organism",
"systems",
"molecular",
"biology",
"techniques",
"mapk",
"signaling",
"cascades",
"saccharomyces",
"research",
"and",
"analysis",
"methods... | 2018 | Inositol polyphosphates regulate and predict yeast pseudohyphal growth phenotypes |
Despite very small genomes , mycoplasmas retain large multigene families encoding variable antigens whose exact role in pathogenesis needs to be proven . To understand their in vivo significance , we used Mycoplasma agalactiae as a model exhibiting high-frequency variations of a family of immunodominant Vpma lipoprotei... | Though implicated to play important roles in mycoplasma pathogenicity , the biological significance of large multigene families causing phase variation of immunodominant surface antigens has never been directly proven . Using M . agalactiae and its Xer1-mediated high-frequency variation system of Vpma surface lipoprote... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"milk",
"body",
"fluids",
"immune",
"physiology",
"ruminants",
"immunology",
"antigenic",
"variation",
"diet",
"vertebrates",
"cloning",
"animals",
"mammals",
"nutrition",
"animal",
"behavior",
"mycoplasma",
"molecular",
"biology... | 2017 | Vpma phase variation is important for survival and persistence of Mycoplasma agalactiae in the immunocompetent host |
Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen . Such differential response can influence the spread of infectious disease , indicating why such diseases impact some populations more than others . Here , we study the impact of population-level genetic ... | Levels of immunity to strains of H1N1 influenza can vary , depending on the individual . This strongly influences how the disease spreads in a population . Accounting for such variations is a major challenge for the epidemiology of infectious diseases . We study the effect of population-level genetic heterogeneity on t... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"animal",
"diseases",
"pathology",
"and",
"laboratory",
"medicine",
"infectious",
"disease",
"epidemiology",
"influenza",
"pathogens",
"swine",
"influenza",
"microbiology",
"orthomyxoviruses",
"epidemiological",
"methods",
"and",
"... | 2018 | Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza |
Gonorrhea is one of the most prevalent sexually transmitted diseases in the world . A naturally occurring variation of the terminal carbohydrates on the lipooligosaccharide ( LOS ) molecule correlates with altered disease states . Here , we investigated the interaction of different stable gonoccocal LOS phenotypes with... | Neisseria gonorrhoeae is a species of Gram-negative bacteria responsible for the sexually transmitted disease gonorrhea . Although effective antibiotic treatments are available , little is known about the host immune response to this pathogen . Here , we analyzed three well-characterized gonococcal variants that only d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunology/cellular",
"microbiology",
"and",
"pathogenesis",
"immunology/immunomodulation",
"cell",
"biology",
"immunology/immune",
"response",
"microbiology/innate",
"immunity",
"infectious",
"diseases/bacterial",
"infections"
] | 2009 | Variation of Neisseria gonorrhoeae Lipooligosaccharide Directs Dendritic Cell–Induced T Helper Responses |
Toxoplasma gondii is a natural intracellular protozoal pathogen of mice and other small mammals . After infection , the parasite replicates freely in many cell types ( tachyzoite stage ) before undergoing a phase transition and encysting in brain and muscle ( bradyzoite stage ) . In the mouse , early immune resistance ... | Toxoplasma gondii infects many warm-blooded animals , including approximately one quarter of the world's human population , residing life-long , usually asymptomatically , in cysts in the brain . If , however , the immune system is weakened for any reason , T . gondii can break out and cause life-threatening disease . ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/membranes",
"and",
"sorting",
"infectious",
"diseases/protozoal",
"infections",
"immunology/innate",
"immunity",
"cell",
"biology/cellular",
"death",
"and",
"stress",
"responses"
] | 2009 | Disruption of the Toxoplasma gondii Parasitophorous Vacuole by IFNγ-Inducible Immunity-Related GTPases (IRG Proteins) Triggers Necrotic Cell Death |
Impairment of the autophagy pathway has been observed during the pathogenesis of Alzheimer’s disease ( AD ) , a neurodegenerative disorder characterized by abnormal deposition of extracellular and intracellular amyloid β ( Aβ ) peptides . Yet the role of autophagy in Aβ production and AD progression is complex . To stu... | Accumulation of amyloid β peptides ( Aβ ) is a major cause of Alzheimer’s disease ( AD ) . Although many efforts have been made , no effective therapies are available to cure AD . Autophagy is a stress-induced pathway nerve cells use to dispose damaged structures , and may be a strategy to eliminate Aβ aggregation . Ho... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell",
"death",
"cognitive",
"neurology",
"autophagic",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"neurodegenerative",
"diseases",
"cell",
"processes",
"sports",
"and",
"exercise",
"medicine",
"physical",
"activity",
"neuroscience",
"biological",
"locom... | 2017 | A Becn1 mutation mediates hyperactive autophagic sequestration of amyloid oligomers and improved cognition in Alzheimer's disease |
Based on large genomic sequence polymorphisms , several haplotypes belonging to two major lineages of the human pathogen Mycobacterium ulcerans could be distinguished among patient isolates from various geographic origins . However , the biological relevance of insertional/deletional diversity is not understood . Using... | The emerging human disease Buruli ulcer , caused by Mycobacterium ulcerans , is of increasing challenge for public health systems in many countries , mainly in West and Central sub-Saharan Africa . Genetic differentiation of patient isolates , a prerequisite for scientific studies on and intervention of disease transmi... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"microbiology/microbial",
"evolution",
"and",
"genomics",
"immunology/i... | 2008 | Differential Gene Repertoire in Mycobacterium ulcerans Identifies Candidate Genes for Patho-Adaptation |
The primary cilium is a sensory organelle , defects in which cause a wide range of human diseases including retinal degeneration , polycystic kidney disease and birth defects . The sensory functions of cilia require specific receptors to be targeted to the ciliary subdomain of the plasma membrane . Arf4 has been propos... | Primary cilia are ubiquitous sensory organelles that play vital roles in an ever-growing class of human diseases termed ciliopathies including obesity , retinal degeneration and polycystic kidney disease . The proper function of the primary cilium relies on a cell's ability to target and concentrate specific receptors ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"embryology",
"developmental",
"biology",
"genetics",
"biology",
"gene",
"function"
] | 2014 | Arf4 Is Required for Mammalian Development but Dispensable for Ciliary Assembly |
Trehalose 6 , 6′-dimycolate ( TDM ) , a cord factor of Mycobacterium tuberculosis ( Mtb ) , is an important regulator of immune responses during Mtb infections . Macrophages recognize TDM through the Mincle receptor and initiate TDM-induced inflammatory responses , leading to lung granuloma formation . Although various... | Tuberculosis is one of the world's most pernicious diseases . Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis , has a lipid-rich cell wall that contains immunostimulatory properties . One of the lipid cell wall components , trehalose 6 , 6′-dimycolate ( TDM ) , is a Mincle ligand and an immunog... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunity",
"immunology",
"biology",
"microbiology",
"immune",
"system"
] | 2012 | Neutrophils Promote Mycobacterial Trehalose Dimycolate-Induced Lung Inflammation via the Mincle Pathway |
With the development of high-throughput sequencing and genotyping technologies , the number of markers collected in genetic association studies is growing rapidly , increasing the importance of methods for correcting for multiple hypothesis testing . The permutation test is widely considered the gold standard for accur... | In genome-wide association studies , it is important to account for the fact that a large number of genetic variants are tested in order to adequately control for false positives . The simplest way to correct for multiple hypothesis testing is the Bonferroni correction , which multiplies the p-values by the number of m... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"computer",
"science/applications",
"genetics",
"and",
"genomics/complex",
"traits",
"computational",
"biology",
"mathematics/statistics",
"genetics",
"and",
"genomics/bioinformatics",
"genetics",
"and",
"genomics/population",
"genetics"
] | 2009 | Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers |
The World Health Organization has targeted elimination of visceral leishmaniasis ( VL ) in the Indian subcontinent ( ISC ) by 2020 . Despite distinctive decline seen in the number of VL cases in ISC , there is still a quest for development of a diagnostic test which has the utility for detection of active infection and... | Definitive diagnosis of visceral leishmaniasis ( VL ) by demonstration of amastigotes by microscopy is invasive and risky . Serology based diagnosis using rK39 rapid diagnostic test ( RDT ) has excellent sensitivity of~97% when combined with clinical symptoms but is inconclusive for detection of active infection and re... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"tropical",
"diseases",
"geographical",
"locations",
"india",
"parasitic",
"diseases",
"neglected",
"tropical",
"diseases",
"molecular",
"biology",
"techniques",
"extraction",
"techniques",
"research",
"and",
"a... | 2018 | Validation of SYBR green I based closed tube loop mediated isothermal amplification (LAMP) assay and simplified direct-blood-lysis (DBL)-LAMP assay for diagnosis of visceral leishmaniasis (VL) |
The mechanisms that cells use to monitor telomere integrity , and the array of responses that may be induced , are not fully defined . To date there have been no studies in animals describing the ability of cells to survive and contribute to adult organs following telomere loss . We developed assays to monitor the abil... | In this work , we describe two simple assays for examining the fate of cells that lose a telomere . We applied these assays to examine the role of DNA damage response genes in controlling the fate of such cells . The checkpoint kinase Chk2 is known to activate the p53 tumor suppressor to promote apoptosis of cells with... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"cellular",
"stress",
"responses",
"animal",
"genetics",
"cancer",
"genetics",
"gene",
"function",
"animal",
"models",
"mitosis",
"telomeres",
"drosophila",
"melanogaster",
"model",
"organisms",
"cell",
"division",
"cell",
"growth",
"chromosome",
"bio... | 2011 | Chk2 and p53 Are Haploinsufficient with Dependent and Independent Functions to Eliminate Cells after Telomere Loss |
Improving knowledge on local determinants of visceral leishmaniasis ( VL ) is crucial to guide the development of relevant control strategies . This study aimed to identify individual and household level determinants of primary VL in 24 highly endemic villages of Tabarak Allah hospital’s catchment area , Gedaref State ... | Visceral leishmaniasis ( VL ) , a fatal disease without treatment , is caused by a parasite ( Leishmania ) transmitted to humans through sandflies . Its epidemiology and the vectors involved in its transmission differ importantly between endemic zones . Preventive measures aim at reducing the parasite reservoirs and at... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Determinants of Visceral Leishmaniasis: A Case-Control Study in Gedaref State, Sudan |
Pyrethroids are increasingly used to block the transmission of diseases spread by Aedes aegypti such as dengue and yellow fever . However , insecticide resistance poses a serious threat , thus there is an urgent need to identify the genes and proteins associated with pyrethroid resistance in order to produce effective ... | Dengue fever , transmitted by Aedes mosquito vectors , is a major public health problem in over 100 countries . Prevention of the disease relies heavily on the use of insecticides such as pyrethroids . Unfortunately , mosquitoes are becoming resistant to these insecticides so it is urgent to identify the genes involved... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"medicine",
"public",
"health",
"and",
"epidemiology",
"enzymes",
"pest",
"control",
"global",
"health",
"neglected",
"tropical",
"diseases",
"infectious",
"diseases",
"enzyme",
"classes",
"proteins",
"biology",
"public",
"health",
"agriculture",
"bioch... | 2012 | Pinpointing P450s Associated with Pyrethroid Metabolism in the Dengue Vector, Aedes aegypti: Developing New Tools to Combat Insecticide Resistance |
Translation is a regulated process and is pivotal to proper cell growth and homeostasis . All retroviruses rely on the host translational machinery for viral protein synthesis and thus may be susceptible to its perturbation in response to stress , co-infection , and/or cell cycle arrest . HIV-1 infection arrests the ce... | Retroviruses are intracellular parasites that utilize the host translation machinery to catalyze viral protein synthesis . The activity of the translation machinery fluctuates during cell cycle progression and is reduced in the G2/M phase . HIV-1 infection causes the cells to arrest in the G2/M phase , which has the po... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"biology"
] | 2012 | Thriving under Stress: Selective Translation of HIV-1 Structural Protein mRNA during Vpr-Mediated Impairment of eIF4E Translation Activity |
Digestive damage due to Chagas disease ( CD ) occurs in 15–20% of patients diagnosed as a result of peristaltic dysfunction in some endemic areas . The symptoms of chronic digestive CD are non-specific , and there are numerous confounders . Diagnosis of CD may easily be missed if symptoms are not evaluated by a well tr... | Digestive damage due to Chagas disease ( CD ) , which symptoms are non-specific , occurs in 15–20% of patients as a result of peristaltic dysfunction . The results of this study with 71 individuals with T . cruzi infection and 18 without it coming from Latin American countries and performed in a non endemic setting sho... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"enteropathies",
"infectious",
"diseases",
"medicine",
"and",
"health",
"sciences",
"radiology",
"and",
"imaging",
"chagas",
"disease",
"diagnostic",
"medicine",
"diagnostic",
"radiology",
"emerging",
"infectious",
"diseases",
"gastrointestinal",
"motility",
"disorders",
... | 2014 | Characterization of Digestive Involvement in Patients with Chronic T. cruzi Infection in Barcelona, Spain |
Process-based models have been used to simulate and forecast a number of nonlinear dynamical systems , including influenza and other infectious diseases . In this work , we evaluate the effects of model initial condition error and stochastic fluctuation on forecast accuracy in a compartmental model of influenza transmi... | Mathematical models are now used to forecast infectious disease incidence at the population scale . By better understanding how errors in prediction systems are introduced , grow and impact the predictability of infectious disease , forecast accuracy could be improved . Here we explore the growth pattern of errors intr... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"respiratory",
"infections",
"influenza",
"atmospheric",
"science",
"pulmonology",
"systems",
"science",
"mathematics",
"humidity",
"infectious",
"diseases",
"computer",
"and",
"inform... | 2019 | Predictability in process-based ensemble forecast of influenza |
The PhoQ/PhoP signaling system responds to low magnesium and the presence of certain cationic antimicrobial peptides . It regulates genes important for growth under these conditions , as well as additional genes important for virulence in many gram-negative pathogens . PhoQ is a sensor kinase that phosphorylates and ac... | The proteins PhoQ and PhoP comprise an environmental sensing system that has been extensively studied in numerous bacteria , including Salmonella typhimurium and Escherichia coli . The PhoQ/PhoP system is stimulated by conditions of low extracellular magnesium or the presence of certain cationic antimicrobial peptides;... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/microbial",
"physiology",
"and",
"metabolism",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis"
] | 2009 | Feedback Inhibition in the PhoQ/PhoP Signaling System by a Membrane Peptide |
An integrated strategy of intervention against tsetse flies was implemented in the Upper West Region of Ghana ( 9 . 62°–11 . 00° N , 1 . 40°–2 . 76° W ) , covering an area of ≈18 , 000 km2 within the framework of the Pan-African Tsetse and Trypanosomosis Eradication Campaign . Two species were targeted: Glossina tachin... | We document the impact of an integrated strategy of intervention against riverine tsetse flies in the Upper West Region of Ghana within the framework of the Pan-African Tsetse and Trypanosomosis Eradication Campaign , in an area of ≈18 , 000 km2 . The strategy included a sequential aerosol technique ( SAT ) component ,... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"veterinary",
"diseases",
"pest",
"control",
"african",
"trypanosomiasis",
"zoonotic",
"diseases",
"neglected",
"tropical",
"diseases",
"veterinary",
"science",
"integrated",
"control",
"agriculture",
"trypanosomiasis"
] | 2013 | The Sequential Aerosol Technique: A Major Component in an Integrated Strategy of Intervention against Riverine Tsetse in Ghana |
For a quantitative understanding of the process of adaptation , we need to understand its “raw material , ” that is , the frequency and fitness effects of beneficial mutations . At present , most empirical evidence suggests an exponential distribution of fitness effects of beneficial mutations , as predicted for Gumbel... | Although mutations with positive effect on fitness are rare , they contribute disproportionally to evolution , because they are favored by natural selection . Because they are rare and hard to study experimentally , little is known about the frequency and variation in fitness effects of beneficial mutations , and it is... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"parallel",
"evolution",
"mutation",
"forms",
"of",
"evolution",
"adaptation",
"medical",
"microbiology",
"microbial",
"evolution",
"biology",
"evolutionary",
"biology",
"microbiology",
"evolutionary",
"processes",
"evolutionary",
"genetics",
"evolutionary",
"theory"
] | 2012 | Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme |
The exosome and its nuclear specific subunit Rrp6 form a 3’-5’ exonuclease complex that regulates diverse aspects of RNA biology including 3’ end processing and degradation of a variety of noncoding RNAs ( ncRNAs ) and unstable transcripts . Known targets of the nuclear exosome include short ( <1000 bp ) RNAPII transcr... | RNAPII is responsible for transcription of protein-coding genes and short , regulatory RNAs . In Saccharomyces cerevisiae , termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex ( comprised of Nrd1 , Nab3 , and Sen1 ) , processing by the exosome , and the nuclear specific catalytic subunit , Rrp6 ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | The Exosome Component Rrp6 Is Required for RNA Polymerase II Termination at Specific Targets of the Nrd1-Nab3 Pathway |
Dengue virus is endemic in tropical and sub-tropical resource-poor countries . Dengue illness can range from a nonspecific febrile illness to a severe disease , Dengue Shock Syndrome ( DSS ) , in which patients develop circulatory failure . Earlier diagnosis of severe dengue illnesses would have a substantial impact on... | Patients with severe dengue illness typically develop complications in the later stages of illness , making early clinical management of all patients with suspected dengue infection difficult . An early prediction tool to identify which patients will have a severe dengue illness will improve the utilization of limited ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/viral",
"infections"
] | 2010 | Prediction of Dengue Disease Severity among Pediatric Thai Patients Using Early Clinical Laboratory Indicators |
Telomeres are chromosome end structures and are essential for maintenance of genome stability . Highly repetitive telomere sequences appear to be susceptible to oxidative stress-induced damage . Oxidation may therefore have a severe impact on telomere integrity and function . A wide spectrum of oxidative pyrimidine-der... | Oxidative stress causes DNA base damage that is mainly repaired by base excision repair pathway , where a DNA glycosylase initiates the recognition and removal of specific base damage . Mammalian telomeres are composed of repetitive purine and pyrimidine bases , TTAGGG , which are prone to damage by oxidation . Though ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"biology"
] | 2013 | Defective Repair of Oxidative Base Lesions by the DNA Glycosylase Nth1 Associates with Multiple Telomere Defects |
Subtelomeric DNA in budding yeasts , like metazoan heterochromatin , is gene poor , repetitive , transiently silenced , and highly dynamic . The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements . However , we found evid... | Many plants , fungi , pathogens , and animals have chromosome regions that are silenced . Special proteins change the chromosome structure in these domains , turning genes off or lowering their expression levels . We found an increased frequency of DNA mutations in these silenced regions of closely related yeasts . Thi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"evolutionary",
"biology/evolutionary",
"and",
"comparative",
"genetics",
"computational",
"biology/comparative",
"sequence",
"analysis",
"genetics",
"and",
"genomics/chromosome",
"biology",
"evolutionary",
"biology/genomics"... | 2008 | Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts |
Cranial neural crest cells ( CNCCs ) have the remarkable capacity to generate both the non-ectomesenchyme derivatives of the peripheral nervous system and the ectomesenchyme precursors of the vertebrate head skeleton , yet how these divergent lineages are specified is not well understood . Whereas studies in mouse have... | A fascinating question of vertebrate development is how a single cell population—the cranial neural crest—creates such different types of structures as the peripheral nervous system and head skeleton . To date , the molecular signals that instruct neural crest cells to develop into head skeleton at the expense of nervo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"model",
"organisms",
"genetics",
"biology",
"genetics",
"and",
"genomics"
] | 2012 | Bmps and Id2a Act Upstream of Twist1 To Restrict Ectomesenchyme Potential of the Cranial Neural Crest |
Derived large-mouthed snakes ( macrostomatans ) possess numerous specializations in their skull and lower jaws that allow them to consume large vertebrate prey . In contrast , basal snakes lack these adaptations and feed primarily on small prey items . The sequence of osteological and behavioral modifications involved ... | Snakes first appear in the fossil record towards the end of the dinosaur era , approximately 98 million years ago . Snake fossils from that time are fragmentary , usually consisting of parts of the backbone . Relatively complete snake fossils preserving skulls and occasionally hindlimbs are quite rare and have only bee... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Methods"
] | [
"evolutionary",
"biology",
"evolutionary",
"biology/paleontology"
] | 2010 | Predation upon Hatchling Dinosaurs by a New Snake from the Late Cretaceous of India |
In areas where the prevalence of soil-transmitted helminthiasis ( STH ) is >20% , the World Health Organization ( WHO ) recommends that deworming medication be given periodically to preschool-age children . To reduce risk of choking-related deaths in children <3 years old , WHO recommends that deworming tablets be crus... | To improve the health of young children with intestinal worm infections , the World Health Organization recommends that they periodically receive deworming medication . The medicines are safe and effective but young children occasionally choke on the chewable tablets . Rarely , this results in death . Consequently , th... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"children",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"swallowing",
"tropical",
"diseases",
"parasitic",
"diseases",
"organic",
"compounds",
"pediatrics",
"physiological",
"processes",
"age",
"groups",
"pharmaceutics",
"drug",
"administration",
"ne... | 2018 | Risk of adverse swallowing events and choking during deworming for preschool-aged children |
Nonstructural protein 4B ( NS4B ) is a key organizer of hepatitis C virus ( HCV ) replication complex formation . In concert with other nonstructural proteins , it induces a specific membrane rearrangement , designated as membranous web , which serves as a scaffold for the HCV replicase . The N-terminal part of NS4B co... | With an estimated 180 million chronically infected individuals , hepatitis C virus ( HCV ) is a leading cause of chronic hepatitis , liver cirrhosis and hepatocellular carcinoma worldwide . HCV is a positive-strand RNA virus that builds its replication complex on rearranged intracellular membranes , designated as membr... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"microbiology",
"virology"
] | 2014 | Aminoterminal Amphipathic α-Helix AH1 of Hepatitis C Virus Nonstructural Protein 4B Possesses a Dual Role in RNA Replication and Virus Production |
In many bacteria , there is a genome-wide bias towards co-orientation of replication and transcription , with essential and/or highly-expressed genes further enriched co-directionally . We previously found that reversing this bias in the bacterium Bacillus subtilis slows replication elongation , and we proposed that th... | An important feature of genome organization is that transcription and replication are selectively co-oriented . This feature helps to avoid conflicts between head-on replication and transcription . The precise consequences of the conflict and how it affects genome organization remain to be understood . We previously fo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"genetics",
"and",
"genomics",
"microbiology"
] | 2010 | Co-Orientation of Replication and Transcription Preserves Genome Integrity |
Even within a defined cell type , the expression level of a gene differs in individual samples . The effects of genotype , measured factors such as environmental conditions , and their interactions have been explored in recent studies . Methods have also been developed to identify unmeasured intermediate factors that c... | The first step in transmitting heritable information , expressing RNA molecules , is highly regulated and depends on activations of specific pathways and regulatory factors . The state of the cell is hard to measure , making it difficult to understand what drives the changes in the gene expression . To close this gap ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/complex",
"traits",
"genetics",
"and",
"genomics/gene",
"expression",
"computational",
"biology/transcriptional",
"regulation"
] | 2011 | Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes |
Natural transformation has significant effects on bacterial genome evolution , but the evolutionary factors maintaining this mode of bacterial sex remain uncertain . Transformation is hypothesized to have both positive and negative evolutionary effects on bacteria . It can facilitate adaptation by combining beneficial ... | Transformation of environmental DNA can provide bacteria with a means to adapt quickly to a changing environment . While this can benefit microbes by facilitating the spread of antibiotic resistance , it can also be harmful if it causes the loss of beneficial alleles from a population . Therefore , it is unclear what e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Conservative Sex and the Benefits of Transformation in Streptococcus pneumoniae |
Although the intracellular bacterium Listeria monocytogenes has an established predilection for disseminated infection during pregnancy that often results in spontaneous abortion or stillbirth , the specific host-pathogen interaction that dictates these disastrous complications remain incompletely defined . Herein , we... | Pregnant women are uniquely susceptible to the bacterium Listeria monocytogenes that preferentially lives inside infected cells . Since infection during pregnancy often triggers prematurity , abortion , or stillbirth , we propose that understanding how these complications occur represent important prerequisites for imp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"immune",
"cells",
"immunology",
"microbiology",
"host-pathogen",
"interaction",
"gynecologic",
"infections",
"bacterial",
"diseases",
"infectious",
"diseases",
"medical",
"microbiology",
"microbial",
"pathogens",
"biology",
"pathogenesis",
"immunopathology",
"lis... | 2012 | Listeria monocytogenes Cytoplasmic Entry Induces Fetal Wastage by Disrupting Maternal Foxp3+ Regulatory T Cell-Sustained Fetal Tolerance |
Rift Valley fever virus ( RVFV ) is a mosquito-borne bunyavirus of the genus Phlebovirus that is highly pathogenic to ruminants and humans . The disease is currently confined to Africa and the Arabian Peninsula , but globalization and climate change may facilitate introductions of the virus into currently unaffected ar... | The consequences of first introductions of mosquito-borne viruses into previously unaffected areas depend on environmental factors , the availability of susceptible hosts and local vector populations . We have previously demonstrated that sheep breeds native to the Netherlands are highly susceptible to Rift Valley feve... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"rift",
"valley",
"fever",
"virus",
"body",
"fluids",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"european",
"union",
"pathogens",
"immunology",
"geographical",
"location... | 2017 | Transmission of Rift Valley fever virus from European-breed lambs to Culex pipiens mosquitoes |
Members of the Ski/Sno protein family are classified as proto-oncogenes and act as negative regulators of the TGF-ß/BMP-pathways in vertebrates and invertebrates . A newly identified member of this protein family is fussel ( fuss ) , the Drosophila homologue of the human functional Smad suppressing elements ( fussel-15... | Ski/Sno proteins have been discovered as proto-oncogenes transforming chicken fibroblasts into cancer cells . They have been found to be ubiquitously expressed in embryonic and adult tissues and to interfere with TGF-ß/BMP signaling . More recently , a group of proteins has been discovered which belongs to the same pro... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"gustatory",
"system",
"nervous",
"system",
"neuronal",
"differentiation",
"social",
"sciences",
"neuroscience",
"animals",
"cell",
"differentiation",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"... | 2019 | The Drosophila fussel gene is required for bitter gustatory neuron differentiation acting within an Rpd3 dependent chromatin modifying complex |
West Nile virus ( WNV ) is a human pathogen of significant medical importance with close to 40 , 000 cases of encephalitis and more than 1 , 600 deaths reported in the US alone since its first emergence in New York in 1999 . Previous studies identified a motif in the beginning of non-structural gene NS2A of encephaliti... | Programmed ribosomal frameshift ( PRF ) is a strategy used by some viruses to regulate expression of viral genes and/or generate additional gene products for the benefit of the virus . Encephalitic flaviruses from Japanese encephalitis virus serogroup encode PRF motif in the beginning of nonstructural gene NS2A that re... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases",
"biology",
"and",
"life",
"sciences",
"microbiology",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Programmed Ribosomal Frameshift Alters Expression of West Nile Virus Genes and Facilitates Virus Replication in Birds and Mosquitoes |
The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment . However , little is known about the molecular mechanisms underlying the parasite response to environmental changes , such as nutrient availability . To elucidate nu... | Leishmania , the cause of a deadly spectrum of diseases in humans , surmounts a number of environmental challenges , including changes in the availability of salvageable nutrients , to successfully colonize its host . Adaptation to environmental stress is clearly of significance in parasite biology , but the underlying... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"systems",
"biology",
"biochemistry",
"proteomics",
"biology",
"molecular",
"cell",
"biology",
"microbiology"
] | 2014 | Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani |
The dUTPase ( Dut ) enzymes , encoded by almost all free-living organisms and some viruses , prevent the misincorporation of uracil into DNA . We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pa... | Understanding bacterial horizontal gene transfer is vital for establishing how toxins and antibiotic resistance genes are disseminated . Bacteriophage and pathogenicity islands make up key components of the wider horizontal transfer map . SaPIs are clinically relevant pathogenicity islands , residing passively in the h... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"dimers",
"(chemical",
"physics)",
"taxonomy",
"medicine",
"and",
"health",
"sciences",
"crystal",
"structure",
"pathology",
"and",
"laboratory",
"medicine",
"bacteriophages",
"pathogens",
"condensed",
"matter",
"physics",
"microbiology",
"staphylococcus",
"aureus",
"viru... | 2017 | Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization |
Trypanosoma cruzi , the protozoan that causes Chagas disease , has a complex life cycle involving several morphologically and biochemically distinct stages that establish intricate interactions with various insect and mammalian hosts . It has also a heterogeneous population structure comprising strains with distinct pr... | Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , is an infection that occurs in several Latin American countries , resulting in a mild illness or in severe damage of the heart and intestinal tract . Such a broad spectrum of clinical manifestations observed in Chagas disease patients is likely due t... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"microbiology",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"protozoan",
"life",
"cycles",
"cell",
"differentiation",
"developmental",
"biology",
"trypomastigotes",
"protozoans",
"epimastigotes",
"genomics",
"gene",
"expressi... | 2017 | Comparative transcriptome profiling of virulent and non-virulent Trypanosoma cruzi underlines the role of surface proteins during infection |
Recent sequencing of Plasmodium vivax field isolates and monkey-adapted strains enabled characterization of SNPs throughout the genome . These analyses relied on mapping short reads onto the P . vivax reference genome that was generated using DNA from the monkey-adapted strain Salvador I . Any genomic locus deleted in ... | Plasmodium vivax is responsible for most malaria cases outside Africa , but is poorly understood , as the parasite is difficult to study in vitro . Genome sequencing studies offer a novel and exciting opportunity to better understand this parasite but , so far , have directly mapped reads onto the reference genome sequ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | De Novo Assembly of a Field Isolate Genome Reveals Novel Plasmodium vivax Erythrocyte Invasion Genes |
Type III effector proteins from bacterial pathogens manipulate components of host immunity to suppress defence responses and promote pathogen development . In plants , host proteins targeted by some effectors called avirulence proteins are surveyed by plant disease resistance proteins referred to as “guards” . The Rals... | Plant and animal bacterial pathogens have evolved to produce virulence factors , called type III effectors , which are injected into host cells to suppress host defences and provide an environment beneficial for pathogen growth . Type III effectors from pathogenic bacteria display enzymatic activities , often mimicking... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/plant-biotic",
"interactions",
"plant",
"biology/plant-biotic",
"interactions"
] | 2010 | Autoacetylation of the Ralstonia solanacearum Effector PopP2 Targets a Lysine Residue Essential for RRS1-R-Mediated Immunity in Arabidopsis |
G-protein coupled receptors , the largest family of proteins in the human genome , are involved in many complex signal transduction pathways , typically activated by orthosteric ligand binding and subject to allosteric modulation . Dopaminergic receptors , belonging to the class A family of G-protein coupled receptors ... | G-protein coupled receptors represent more than 50% of the current drug targets , hence playing a crucial role in drug discovery today . A deeper understanding of G-protein coupled receptor functioning and modulation will help in the development of new drugs that are able to interact with such systems in a more subtle ... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"computational",
"biology/molecular",
"dynamics",
"biophysics",
"biochemistry",
"computational",
"biology"
] | 2010 | Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors |
Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells . Proteins of the Bin/Amphiphysin/Rvs ( BAR ) domain family , in particular , play a role in cellular morphogenesis , for example curving planar membranes into tubular membranes . However , it is still unclear h... | To generate organelles , eukaryotic cells sculpt their membranes into compartments , often employing proteins as chaperones , for example , F-BAR domains . The latter induce formation of tubular and vesicular membranes . Functional and structural studies suggest that F-BAR domains sculpt membranes through electrostatic... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"physics",
"biophysic",
"al",
"simulations",
"biology",
"computational",
"biology",
"biophysics",
"simulations",
"biophysics"
] | 2013 | Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations |
Channelrhodospin-2 ( ChR2 ) , a light-sensitive ion channel , and its variants have emerged as new excitatory optogenetic tools not only in neuroscience , but also in other areas , including cardiac electrophysiology . An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optic... | Optogenetics , the use of light-sensitive ion channels for stimulation of mammalian cells and tissues , offers specificity and superior precision of control compared to traditional chemical or electrical means of stimulation . In particular , Channelrhodospin-2 ( ChR2 ) , a light-sensitive ion channel , originally deri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model |
Iron , an essential co-factor of respiratory chain proteins , is critical for mitochondrial function and maintenance of its redox balance . We previously reported a role for iron uptake in differentiation of Leishmania amazonensis into virulent amastigotes , by a mechanism that involves reactive oxygen species ( ROS ) ... | Leishmaniasis is a serious parasitic disease that affects 12 million people worldwide , with clinical manifestations ranging from self-healing cutaneous lesions to deadly visceralizing disease . A vaccine is not available , and new and less toxic drugs against this protozoan parasite are urgently needed . Following int... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2016 | A Trypanosomatid Iron Transporter that Regulates Mitochondrial Function Is Required for Leishmania amazonensis Virulence |
Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across the broad community of life scientists that circular genome-sized molecules are the primary form of plant mitochondrial DNA , despite the understanding by plant mitochondrial researchers that this is an... | Plant mitochondrial genomes are commonly depicted in research articles and textbooks as circular molecules that are the size of the genome . Although research on mitochondrial DNA ( mtDNA ) over the past few decades has revealed that genome-sized circles are exceedingly rare and that alternative forms of mtDNA are more... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"engineering",
"and",
"technology",
"mitochondrial",
"dna",
"genomic",
"library",
"construction",
"sequence",
"assembly",
"tools",
"plant",
"science",
"genome",
"analysis",
"forms",
"of",
"dna",
"plant",
"genomics",
"mitochondria",
"energy-producing",
"... | 2019 | The alternative reality of plant mitochondrial DNA: One ring does not rule them all |
Muscles must maintain cell compartmentalization when remodeled during development and use . How spatially restricted adhesions are regulated with muscle remodeling is largely unexplored . We show that the myotubularin ( mtm ) phosphoinositide phosphatase is required for integrin-mediated myofiber attachments in Drosoph... | Muscles require strong extracellular attachments to preserve cellular integrity during force-generating contractions . Integrin transmembrane receptors mediate muscle attachments at highly localized sites , but how this pattern of attachments is continuously maintained with muscle use is not understood . Human X-linked... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/animal",
"genetics",
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"cell",
"biology",
"cell",
"biology/developmental",
"molecular",
"mechanisms",
"pathology/histopathology",
"cell",
"biology/membranes",
"and",
"sorting",
"gen... | 2011 | Phosphoinositide Regulation of Integrin Trafficking Required for Muscle Attachment and Maintenance |
Effective malaria control strategies require an accurate understanding of the epidemiology of locally transmitted Plasmodium species . Compared to Plasmodium falciparum infection , Plasmodium vivax has a lower asexual parasitaemia , forms dormant liver-stages ( hypnozoites ) , and is more transmissible . Hence , treatm... | Plasmodium vivax malaria presents challenges for malaria elimination distinct from those of the other human malarias . Patients become symptomatic at lower asexual parasitaemia , making it harder to diagnose , and its dormant stages in the liver give rise to multiple clinical attacks unless treated with an 8-aminoquino... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"plasmodium",
"tropical",
"diseases",
"geographical",
"locations",
"vector-borne",
"diseases",
"database",
"searching",
"parasitic",
"diseases",
"parasitic",
"protozoans",
"parasitology",
"apicomplexa",
"plasmod... | 2019 | Growing evidence of Plasmodium vivax across malaria-endemic Africa |
Dendritic cells ( DCs ) are essential antigen-presenting cells for the induction of T cell immunity against HIV . On the other hand , due to the susceptibility of DCs to HIV infection , virus replication is strongly enhanced in DC–T cell interaction via an immunological synapse formed during the antigen presentation pr... | The cellular tropism of HIV-1 is determined by the binding of HIV-1 envelope to chemokine coreceptors , CCR5 or CXCR4 , in addition to a major entry receptor , CD4 . The mystery still now is that despite the mixed infection of CCR5-utilizing ( R5 ) and CXCR4-utilizing ( X4 ) HIV-1 in many AIDS patients , R5 is predomin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"virology/vaccines",
"virology/immunodeficiency",
"viruses",
"virology/new",
"therapies,",
"including",
"antivirals",
"and",
"immunotherapy",
"virology/mechanisms",
"of",
"resistance",
"and",
"susceptibility,",
"including",
"host",
"genetics",
"infectious",
"diseases/hiv",
"inf... | 2009 | Selective Transmission of R5 HIV-1 over X4 HIV-1 at the Dendritic Cell–T Cell Infectious Synapse Is Determined by the T Cell Activation State |
Shigella , the causative agent of bacillary dysentery , invades epithelial cells by locally reorganizing the actin cytoskeleton . Shigella invasion requires actin polymerization dependent on the Src tyrosine kinase and a functional bacterial type III secretion ( T3S ) apparatus . Using dynamic as well as immunofluoresc... | Type III secretion systems ( T3SS ) are present in a wide range of Gram-negative bacteria that are pathogenic to humans , animals , and plants . These molecular devices allow the injection of bacterial virulence factors into host cells to manipulate various cellular functions . T3SSs share similar functional features .... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"infectious",
"diseases/bacterial",
"infections",
"microbiology/cellular",
"microbiology",
"and",
"pathogenesis",
"infectious",
"diseases/gastrointestinal",
"infections",
"cell",
"biology/cytoskeleton"
] | 2009 | The IpaC Carboxyterminal Effector Domain Mediates Src-Dependent Actin Polymerization during Shigella Invasion of Epithelial Cells |
Chromatin environments differ greatly within a eukaryotic genome , depending on expression state , chromosomal location , and nuclear position . In genomic regions characterized by high repeat content and high gene density , chromatin structure must silence transposable elements but permit expression of embedded genes ... | How DNA is packaged into chromatin has profound implications for gene regulation . While certain chromatin conformations are accessible to RNA polymerase and allow expression , other chromatin structures prevent transcription . In many genomes , genes that need to be expressed and repetitive sequences that need to be s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"animal",
"models",
"genome",
"expression",
"analysis",
"drosophila",
"melanogaster",
"model",
"organisms",
"chromosome",
"biology",
"gene",
"expression",
"genetics",
"epigenetics",
"biology",
"genomics",
"genetics",
"and",
"genomics"
] | 2012 | Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain |
During the lytic phase of infection , the gamma herpesvirus Kaposi's Sarcoma-Associated Herpesvirus ( KSHV ) expresses a highly abundant , 1 . 1 kb nuclear noncoding RNA of unknown function . We observe that this polyadenylated nuclear ( PAN ) RNA avidly binds host poly ( A ) -binding protein C1 ( PABPC1 ) , which norm... | Almost all eukaryotic messenger RNAs ( mRNAs ) have a string of 150–200 adenylates at the 3′ end . This poly ( A ) tail has been implicated as important for regulating mRNA translation , stability and export . During the lytic phase of infection of Kaposi's Sarcoma-Associated Herpesvirus ( KSHV ) , a noncoding viral RN... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"rna",
"molecular",
"cell",
"biology",
"rna",
"processing",
"virulence",
"factors",
"and",
"mechanisms",
"nucleic",
"acids",
"virology",
"biology",
"microbiology",
"molecular",
"biology"
] | 2011 | A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression |
Suppression of duplication-mediated gross chromosomal rearrangements ( GCRs ) is essential to maintain genome integrity in eukaryotes . Here we report that SUMO ligase Mms21 has a strong role in suppressing GCRs in Saccharomyces cerevisiae , while Siz1 and Siz2 have weaker and partially redundant roles . Understanding ... | The human genome contains many “at-risk” sequences that are prone to mutations , including diverse repeated sequences , segmental duplications and regions of copy number variations . Such repetitive sequence elements can cause genome rearrangements through non-allelic homologous recombination ( NAHR ) and many human di... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"spectrometric",
"identification",
"of",
"proteins",
"cancer",
"genetics",
"model",
"organisms",
"proteomic",
"databases",
"enzyme",
"regulation",
"enzymes",
"genetics",
"yeast",
"and",
"fungal",
"models",
"biology",
"saccharomyces",
"cerevisiae",
"proteom... | 2013 | Distinct SUMO Ligases Cooperate with Esc2 and Slx5 to Suppress Duplication-Mediated Genome Rearrangements |
Transition metals are necessary for all forms of life including microorganisms , evidenced by the fact that 30% of all proteins are predicted to interact with a metal cofactor . Through a process termed nutritional immunity , the host actively sequesters essential nutrient metals away from invading pathogenic bacteria ... | Helicobacter pylori is a bacterium that colonizes the stomach and causes gastric diseases . Some strains of H . pylori possess a secretion system that has the capacity to inject a cancer-causing protein into host cells . The activity of this secretion system contributes to the development of inflammation and is linked ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"bacteriology",
"antimicrobials",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"immunology",
"microbiology",
"developmental",
"biology",
... | 2014 | The Host Protein Calprotectin Modulates the Helicobacter pylori cag Type IV Secretion System via Zinc Sequestration |
To better understand adaptation to harsh conditions encountered in hot arid deserts , we report the first complete genome sequence and proteome analysis of a bacterium , Deinococcus deserti VCD115 , isolated from Sahara surface sand . Its genome consists of a 2 . 8-Mb chromosome and three large plasmids of 324 kb , 314... | D . deserti belongs to the Deinococcaceae , a family of bacteria characterized by an exceptional ability to withstand the lethal effects of DNA-damaging agents , including ionizing radiation , UV light , and desiccation . It was isolated from Sahara surface sands , an extreme and nutrient-poor environment , regularly e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"microbiology/environmental",
"microbiology",
"evolutionary",
"biology/microbial",
"evolution",
"and",
"genomics",
"genetics",
"and",
"genomics/gene",
"discovery",
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression",
"molecula... | 2009 | Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti |
Genome-wide association studies ( GWAS ) have revolutionized the field of cancer genetics , but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified . Here we report the first step in such an endeavor for prostate cancer . We provide a comprehensive annotati... | In the following work we provide a complete summary annotation of functional hypotheses relating to risk identified by genome wide association studies of prostate cancer . In addition , we present new genome-wide profiles for H3K27-acetylation and TCF7L2 binding in LNCaP cells . We also introduce the concept of a risk ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Materials",
"and",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"cancer",
"genetics",
"genetic",
"mutation",
"genomics",
"genetic",
"association",
"studies",
"human",
"genetics",
"genetics",
"gene",
"regulation",
"epigenetics",
"molecular",
"genetics",
"biology",
"computational",
"biology",
"mo... | 2014 | Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci |
Papillomavirus E6 proteins bind to LXXLL peptide motifs displayed on targeted cellular proteins . Alpha genus HPV E6 proteins associate with the cellular ubiquitin ligase E6AP ( UBE3A ) , by binding to an LXXLL peptide ( ELTLQELLGEE ) displayed by E6AP , thereby stimulating E6AP ubiquitin ligase activity . Beta , Gamma... | Papillomaviruses are a large family of viruses with great medical and veterinary importance . This study explores the viral E6 oncoproteins from diverse papillomavirus genera to determine how E6 distinguishes in interaction between cellular proteins . E6 proteins have been previously found to interact with a ubiquitin ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"protein",
"interactions",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"cancers",
"and",
"neoplasms",
"notch",
"signaling",
"viruses",
"oncology",
"dna",
"viruses",
"sequence",
"motif",
"analysis",
... | 2017 | Association of papillomavirus E6 proteins with either MAML1 or E6AP clusters E6 proteins by structure, function, and evolutionary relatedness |
It is currently not known how distributed neuronal responses in early visual areas carry stimulus-related information . We made multielectrode recordings from cat primary visual cortex and applied methods from machine learning in order to analyze the temporal evolution of stimulus-related information in the spiking act... | Researchers usually assume that neuronal responses carry primarily information about the stimulus that evoked these responses . We show here that , when multiple images are shown in a fast sequence , the response to an image contains as much information about the preceding image as about the current one . Importantly ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2009 | Distributed Fading Memory for Stimulus Properties in the Primary Visual Cortex |
Expansion of the lysosomal system , including cathepsin D upregulation , is an early and prominent finding in Alzheimer's disease brain . Cell culture studies , however , have provided differing perspectives on the lysosomal connection to Alzheimer's disease , including both protective and detrimental influences . We s... | Neurodegenerative disorders , like Alzheimer's disease , are a devastating group of conditions that exact a heavy toll on patients and their families . These disorders also represent a significant and growing public health challenge as our population ages because no effective treatments are available . Research over th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"neurological",
"disorders/alzheimer",
"disease"
] | 2010 | Lysosomal Dysfunction Promotes Cleavage and Neurotoxicity of Tau In Vivo |
In endemic areas , Rift Valley fever virus ( RVFV ) is a significant threat to both human and animal health . Goals of this study were to measure human anti-RVFV seroprevalence in a high-risk area following the 2006–2007 Kenyan Rift Valley Fever ( RVF ) epidemic , to identify risk factors for interval seroconversion , ... | RVFV infection causes significant disease in both human and animal populations , resulting in significant agricultural , economic and public health consequences . We conducted a cohort study on residents of a high-risk area to measure human anti-RVFV seroprevalence , to identify risk factors , and to estimate the durab... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"rift",
"valley",
"fever",
"public",
"health",
"and",
"epidemiology",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"neglected",
"tropical",
"diseases",
"viral",
"diseases"
] | 2011 | Postepidemic Analysis of Rift Valley Fever Virus Transmission in Northeastern Kenya: A Village Cohort Study |
The protein kinase Mec1 ( ATR ortholog ) and its partner Ddc2 ( ATRIP ortholog ) play a key role in DNA damage checkpoint responses in budding yeast . Previous studies have established the model in which Ddc1 , a subunit of the checkpoint clamp , and Dpb11 , related to TopBP1 , activate Mec1 directly and control DNA da... | When DNA replication is blocked and DNA damage occurs , checkpoints arrest the cell cycle in eukaryotic cells , allowing DNA replication and repair to take place . The major regulators of the DNA damage checkpoint response are the phosphoinositide 3-kinase ( PI3K ) -related protein kinases , including ATM and ATR . In ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"nucleic",
"acids",
"dna",
"dna",
"repair",
"biology",
"molecular",
"cell",
"biology"
] | 2014 | Ddc2 Mediates Mec1 Activation through a Ddc1- or Dpb11-Independent Mechanism |
Growth and Differentiation Factor 5 ( GDF5 ) is a secreted growth factor that belongs to the Bone Morphogenetic Protein ( BMP ) family and plays a pivotal role during limb development . GDF5 is a susceptibility gene for osteoarthritis ( OA ) and mutations in GDF5 are associated with a wide variety of skeletal malformat... | Mutations can be generally classified in loss- or gain-of-function mutations depending on their specific pathomechanism . Here we report on a GDF5 mutation , p . W414R , which is associated with brachydactyly type A1 ( BDA1 ) and Multiple Synostoses Syndrome 2 ( SYNS2 ) . Interestingly , whereas shortening of phalangea... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | A GDF5 Point Mutation Strikes Twice - Causing BDA1 and SYNS2 |
Many viruses that enter cells by clathrin-dependent endocytosis are significantly larger than the dimensions of a typical clathrin-coated vesicle . The mechanisms by which viruses co-opt the clathrin machinery for efficient internalization remain uncertain . Here we examined how clathrin-coated vesicles accommodate ves... | Clathrin-dependent endocytosis accounts for the majority of uptake from the plasma membrane . However , many viruses that infect cells through an endocytic route are larger than the dimensions of a typical clathrin-coated vesicle . Working with vesicular stomatitis virus , we determined how this cargo enters cells . We... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology/host",
"invasion",
"and",
"cell",
"entry",
"cell",
"biology",
"virology"
] | 2009 | Vesicular Stomatitis Virus Enters Cells through Vesicles Incompletely Coated with Clathrin That Depend upon Actin for Internalization |
In complex diseases , various combinations of genomic perturbations often lead to the same phenotype . On a molecular level , combinations of genomic perturbations are assumed to dys-regulate the same cellular pathways . Such a pathway-centric perspective is fundamental to understanding the mechanisms of complex diseas... | It is now being recognized that complex diseases should be studied from the perspective of dys-regulated pathways and processes rather than individual genes . Indeed , various combinations of molecular perturbations might lead to the same disease . In such cases , responses to these perturbations are expected to conver... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"computational",
"biology/systems",
"biology",
"computational",
"biology"
] | 2011 | Identifying Causal Genes and Dysregulated Pathways in Complex Diseases |
Gray leaf spot ( GLS ) , caused by Cercospora zeae-maydis and Cercospora zeina , is one of the most important diseases of maize worldwide . The pathogen has a necrotrophic lifestyle and no major genes are known for GLS . Quantitative resistance , although poorly understood , is important for GLS management . We used ge... | Gray leaf spot ( GLS ) , a necrotrophic , foliar fungal disease of maize , contributes to maize yield losses worldwide . We identified and characterized regions of the maize genome that confer resistance to GLS and gained insight into the mechanisms associated with these quantitative trait loci ( QTL ) . We provide evi... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Resistance to Gray Leaf Spot of Maize: Genetic Architecture and Mechanisms Elucidated through Nested Association Mapping and Near-Isogenic Line Analysis |
Cell surface receptors for phosphatidylserine contribute to the entry of Ebola virus ( EBOV ) particles , indicating that the presence of phosphatidylserine in the envelope of EBOV is important for the internalization of EBOV particles . Phosphatidylserine is typically distributed in the inner layer of the plasma membr... | Although Ebola virus causes severe hemorrhagic fever with a high mortality rate , there are no approved therapeutics . The viral entry process is one of the targets for antiviral development . Previous studies suggest that binding of phosphatidylserine , a component of the viral envelop , to the receptors promotes the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"flow",
"cytometry",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"cell",
"processes",
"immunology",
"microbiology",
"light",
"microscopy",
"viral",
"structure",
"scanning",
... | 2018 | Ebola virus requires a host scramblase for externalization of phosphatidylserine on the surface of viral particles |
Schwann cells are integral components of vertebrate neuromuscular synapses; in their absence , pre-synaptic nerve terminals withdraw from post-synaptic muscles , leading to muscle denervation and synapse loss at the developing neuromuscular junction ( NMJ ) . Here , we report a rescue of muscle denervation and neuromus... | Nerve cells ( neurons ) communicate with each other through specialized focal connections called synapses . Synapses are commonly assembled into a tripartite structure composed of pre- and post-synaptic neurons , and a glial cell that is closely associated with both pre- and post-synaptic components . At the vertebrate... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"&",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"neuromuscular",
"junctions",
"nervous",
"system",
"skeletal",
"muscles",
"electrophysiology",
"neuroscience",
"macroglial",
"cells",
"surgical",
"and",
"invasive",
"medical",
"procedures",
"motor",
"neurons",
"respiratory",
"syste... | 2019 | Blocking skeletal muscle DHPRs/Ryr1 prevents neuromuscular synapse loss in mutant mice deficient in type III Neuregulin 1 (CRD-Nrg1) |
Pathogens often inhabit the body asymptomatically , emerging to cause disease in response to unknown triggers . In the bladder , latent intracellular Escherichia coli reservoirs are regarded as likely origins of recurrent urinary tract infection ( rUTI ) , a problem affecting millions of women worldwide . However , cli... | Millions of women suffer from recurrent urinary tract infections ( rUTI ) and the only treatment option is prophylactic antibiotics , which contributes to antibiotic resistance . In experimental models , Escherichia coli , the dominant UTI pathogen , establishes reservoirs inside the bladder lining; it is believed that... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"microbiome",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"bladder",
"microbiology",
"urine",
"animal",
"models",
"bacterial",
"diseases",
"model",
"organisms",
"experimental",
"organism",
"system... | 2017 | Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease |
DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabase-sized chromosome segments at specific times during S-phase . Cytogenetic studies show that these “replicon clusters” coalesce as subchromosomal units that persist through multiple cell generations , but th... | Microscopy studies have suggested that chromosomal DNA is composed of multiple , megabase-sized segments , each replicated at different times during S-phase of the cell cycle . However , a molecular definition of these coordinately replicated sequences and the stability of the boundaries between them has not been estab... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"cell",
"biology",
"computational",
"biology",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2008 | Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation |
Most ab initio gene predictors use a probabilistic sequence model , typically a hidden Markov model , to combine separately trained models of genomic signals and content . By combining separate models of relevant genomic features , such gene predictors can exploit small training sets and incomplete annotations , and ca... | We describe a new approach to statistical learning for sequence data that is broadly applicable to computational biology problems and that has experimentally demonstrated advantages over current hidden Markov model ( HMM ) -based methods for sequence analysis . The methods we describe in this paper , implemented in the... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mammals",
"computational",
"biology",
"vertebrates",
"homo",
"(human)",
"genetics",
"and",
"genomics"
] | 2007 | Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction |
Visceral leishmaniasis ( VL ) is a systemic parasitic disease that is fatal unless treated . In Kenya , national VL guidelines rely on microscopic examination of spleen aspirate to confirm diagnosis . As this procedure is invasive , it cannot be safely implemented in peripheral health structures , where non-invasive , ... | Visceral Leishmaniasis ( VL ) is potentially fatal if not treated promptly . Its diagnosis is based on the presence of parasites in spleen or bone marrow aspirates . These are invasive and risky procedures . Simple , rapid and non-invasive diagnostic tests are needed , notably in rural settings . We evaluated 2 rapid d... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Validation of Two Rapid Diagnostic Tests for Visceral Leishmaniasis in Kenya |
Swimming cells typically move along a helical path or undergo longitudinal rotation as they swim , arising from chiral asymmetry in hydrodynamic drag or propulsion bending the swimming path into a helix . Helical paths are beneficial for some forms of chemotaxis , but why asymmetric shape is so prevalent when a symmetr... | Swimming cells often follow a helical swimming path , however the advantage of helical paths over a simple straight line path is not clear . To analyse this phenomenon , I analysed the swimming of the human parasites Trypanosoma brucei ( which causes sleeping sickness/trypanosomiasis ) and Leishmania mexicana ( which c... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"cell",
"motility",
"swimming",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"microbiology",
"biological",
"locomotion",
"parasitic",
"protozoans",
"biomechanics",
"protozoan",
"... | 2017 | Use of chiral cell shape to ensure highly directional swimming in trypanosomes |
DNA polymerase V ( pol V ) of Escherichia coli is a translesion DNA polymerase responsible for most of the mutagenesis observed during the SOS response . Pol V is activated by transfer of a RecA subunit from the 3'-proximal end of a RecA nucleoprotein filament to form a functional complex called DNA polymerase V Mutaso... | DNA polymerase V from the bacterium Escherichia coli is one of a class of DNA polymerases that replicate DNA inaccurately . They thus generate mutations at elevated levels . Whereas this might seem incongruous with the goal of accurate transmission of genetic information from one generation to the next , it is actually... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | A RecA Protein Surface Required for Activation of DNA Polymerase V |
Human African trypanosomiasis ( HAT , sleeping sickness ) ranks among the most neglected tropical diseases based on limited availability of drugs that are safe and efficacious , particularly against the second stage ( central nervous system [CNS] ) of infection . In response to this largely unmet need for new treatment... | Treatment of human African trypanosomiasis ( HAT , sleeping sickness ) suffers from a shortage of medicines that are both effective , especially against the second ( late ) stage of the disease , and safe for patients . The development of new HAT medicines also has been significantly influenced by the perceived need fo... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Chemotherapy of Second Stage Human African Trypanosomiasis: Comparison between the Parenteral Diamidine DB829 and Its Oral Prodrug DB868 in Vervet Monkeys |
Paracoccidioidomycosis ( PCM ) , is a pulmonary fungal disease whose severity depends on the adequate development of T cell immunity . Although regulatory T ( Treg ) cells were shown to control immunity against PCM , deleterious or protective effects were described in different experimental settings . To clarify the fu... | Paracoccidioidomycosis ( PCM ) , the most relevant deep mycosis in Latin America , is caused by the fungus Paracoccidioides brasiliensis . The involvement of regulatory T ( Treg ) cells in the immunity against PCM has been previously demonstrated , however its underlying mechanisms are still to be elucidated . Using Fo... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Loss- and Gain-of-Function Approaches Indicate a Dual Role Exerted by Regulatory T Cells in Pulmonary Paracoccidioidomycosis |
The type II secretion system ( T2SS ) is a cell envelope-spanning macromolecular complex that is prevalent in Gram-negative bacterial species . It serves as the predominant virulence mechanism of many bacteria including those of the emerging human pathogens Vibrio vulnificus and Aeromonas hydrophila . The system is com... | Vibrio vulnificus and Aeromonas hydrophila are two bacterial species that are emerging as significant human pathogens . The major virulence mechanism utilized by these species is the Type II secretion system ( T2SS ) that functions in exporting toxic proteins produced by the bacterium into the infected individual . The... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"bacteriology",
"medicine",
"and",
"health",
"sciences",
"aeromonas",
"hydrophila",
"crystal",
"structure",
"pathology",
"and",
"laboratory",
"medicine",
"monomers",
"pathogens",
"vibrio",
"condensed",
"matter",
"physics",
"microbiology",
"electron",
"cryo-microscopy",
"h... | 2019 | Structure and assembly of pilotin-dependent and -independent secretins of the type II secretion system |
With increasing urbanization vector-borne diseases are quickly developing in cities , and urban control strategies are needed . If streets are shown to be barriers to disease vectors , city blocks could be used as a convenient and relevant spatial unit of study and control . Unfortunately , existing spatial analysis to... | Chagas disease is a major parasitic disease in Latin America . It is transmitted by Triatoma infestans an insect common in Arequipa , the second largest city in Peru . We propose a method to demonstrate that streets strongly affect the spatial distribution of infestation by this insect in Arequipa . The effect of stree... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"infectious",
"disease",
"epidemiology",
"statistics",
"microbiology",
"spatial",
"epidemiology",
"geoinformatics",
"mathematics",
"population",
"modeling",
"neglected",
"tropical",
"diseases",
"population",
"biology",
... | 2013 | The Effects of City Streets on an Urban Disease Vector |
Neurotrophism , structural plasticity , learning and long-term memory in mammals critically depend on neurotrophins binding Trk receptors to activate tyrosine kinase ( TyrK ) signaling , but Drosophila lacks full-length Trks , raising the question of how these processes occur in the fly . Paradoxically , truncated Trk ... | A long-standing paradox had been to explain how brain structural plasticity , learning and long-term memory might occur in Drosophila in the absence of canonical Trk receptors for neurotrophin ( NT ) ligands . NTs link structure and function in the brain enabling adjustments in cell number , dendritic , axonal and syna... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"nervous",
"system",
"electrophysiology",
"neuroscience",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"synaptic",
"plasticity",
"experimental",
"orga... | 2017 | Kek-6: A truncated-Trk-like receptor for Drosophila neurotrophin 2 regulates structural synaptic plasticity |
Structural features of genomes , including the three-dimensional arrangement of DNA in the nucleus , are increasingly seen as key contributors to the regulation of gene expression . However , studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model ... | How a genome folds within a nucleus can contribute to the regulation of gene expression . There is now considerable interest in understanding how the three-dimensional structure of a genome is maintained and how this structure influences biological processes . However , most studies on these phenomena focus on a few mo... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"fungal",
"genetics",
"sequence",
"assembly",
"tools",
"genome",
"analysis",
"sequence",
"motif",
"analysis",
"epigenetics",
"structural",
"genomics",
"chromatin",
"research",
"and",
"analysis",
"methods",
"sequence",
"analysis",
"genomic",
"libraries",
"mycology",
"gen... | 2018 | Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae |
Cutaneous leishmaniasis ( CL ) due to L . braziliensis infection is characterized by a strong inflammatory response with high levels of TNF and ulcer development . Less attention has been given to the role of mononuclear phagocytes to this process . Monocytes constitute a heterogeneous population subdivided into classi... | To examine the participation of MMP-9 in the pathogenesis of L . braziliensis infection , we realized a cross-sectional study with CL patients in an early phase of the disease or with a classical ulcer , and healthy controls . We evaluated the frequency of MMP-9 in monocyte subsets and its mechanism of production . Our... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonoses",
"medicine",
"and",
"health",
"sciences",
"clinical",
"immunology",
"leishmaniasis",
"neglected",
"tropical",
"diseases",
"biology",
"and",
"life",
"sciences",
"immunology",
"tropical",
"diseases",
"veterinary... | 2014 | Matrix Metalloproteinase 9 Production by Monocytes is Enhanced by TNF and Participates in the Pathology of Human Cutaneous Leishmaniasis |
Cardiac remodelling and contractile dysfunction occur during both acute and chronic disease processes including the accumulation of insoluble aggregates of misfolded amyloid proteins that are typical features of Alzheimer's , Parkinson's and Huntington's disease ( HD ) . While HD has been described mainly as a neurolog... | Huntington's disease ( HD ) is a neurodegenerative disorder for which the mutation results in an extra-long tract of glutamines that causes the huntingtin protein to aggregate . It is characterized by neurological symptoms and brain pathology that is associated with nuclear and cytoplasmic aggregates and with transcrip... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Antibodies,",
"western",
"blotting,",
"Seprion",
"ELISA",
"Immunohistochemistry",
"and",
"confocal",
"microscopy",
"TUNEL",
"assay",
"ECG",
"evaluation",
"in",
"conscious",
"mice",
"MRI... | [
"molecular",
"neuroscience",
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"genetics",
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"biology",
"and",
"life",
"sciences",
"molecular",
"genetics",
"genetic",
"diseases",
"autosomal",
"dominant",
"dise... | 2014 | Dysfunction of the CNS-Heart Axis in Mouse Models of Huntington's Disease |
RNA helicases and chaperones are the two major classes of RNA remodeling proteins , which function to remodel RNA structures and/or RNA-protein interactions , and are required for all aspects of RNA metabolism . Although some virus-encoded RNA helicases/chaperones have been predicted or identified , their RNA remodelin... | Enteroviruses contain a large number of closely related human pathogens , including poliovirus , EV71 , and coxsackie viruses , and cause ~3 billion infections annually . Among the nonstructural proteins of enteroviruses or picornaviruses , protein 2CATPase is the most conserved and complex but the least understood . O... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone |
We have developed a sparse mathematical representation of speech that minimizes the number of active model neurons needed to represent typical speech sounds . The model learns several well-known acoustic features of speech such as harmonic stacks , formants , onsets and terminations , but we also find more exotic struc... | The receptive field of a neuron can be thought of as the stimulus that most strongly causes it to be active . Scientists have long been interested in discovering the underlying principles that determine the structure of receptive fields of cells in the auditory pathway to better understand how our brains process sound ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"auditory",
"system",
"computational",
"neuroscience",
"biology",
"sensory",
"systems",
"neuroscience",
"coding",
"mechanisms"
] | 2012 | Sparse Codes for Speech Predict Spectrotemporal Receptive Fields in the Inferior Colliculus |
The early host response to viral infections involves transient activation of pattern recognition receptors leading to an induction of inflammatory cytokines such as interleukin-1β ( IL-1β ) and tumor necrosis factor α ( TNFα ) . Subsequent activation of cytokine receptors in an autocrine and paracrine manner results in... | Upon viral infection cells immediately induce an innate immune response which involves the production of inflammatory cytokines . These cytokines activate specific receptors on infected and surrounding cells leading to local signal amplification as well as signal broadcasting beyond the original site of infection . Inf... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immunity",
"virology",
"biology",
"microbiology"
] | 2012 | Viral Mediated Redirection of NEMO/IKKγ to Autophagosomes Curtails the Inflammatory Cascade |
Heterozygous mutations in p63 are associated with split hand/foot malformations ( SHFM ) , orofacial clefting , and ectodermal abnormalities . Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders . We performed genome-wide DNA–bindi... | Mammalian embryonic development requires precise control of gene expression in the right place at the right time . One level of control of gene expression is through cis-regulatory elements controlled by transcription factors . Deregulation of gene expression by mutations in such cis-regulatory elements has been descri... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"developmental",
"biology/morphogenesis",
"and",
"cell",
"biology",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/disease",
"models",
"genetics",
"and",
"genomics/genetics",
"of",
"disease",
"genetics",
"and",... | 2010 | Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus |
Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism’s complex life cycle . To better understand this regulatory machinery , we assembled a rich collection of genomic and epigenomic data sets , including in... | The parasite responsible for the most lethal form of malaria , Plasmodium falciparum , employs a variety of mechanisms to modify the expression of its genes throughout its complex life cycle . In this work , we gather a rich collection of data describing various aspects of the gene regulatory apparatus in P . falciparu... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"parasite",
"groups",
"plasmodium",
"gene",
"regulation",
"parasitology",
"dna",
"transcription",
"histone",
"modification",
"developmental",
"biology",
"apicomplexa",
"sequence",
"motif",
"analysis",
"epigenetics",
"chromatin",
"research",
"and",
"analysis",
"methods",
"... | 2019 | Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features |
Phlebotomine sand flies are blood-sucking insects that can transmit Leishmania parasites . Hosts bitten by sand flies develop an immune response against sand fly salivary antigens . Specific anti-saliva IgG indicate the exposure to the vector and may also help to estimate the risk of Leishmania spp . transmission . In ... | Leishmania infantum is the causative agent of zoonotic visceral leishmaniasis in the Mediterranean Basin and Phlebotomus perniciosus serve as the major vector . In the endemic foci , Leishmania parasites are transmitted mostly to dogs , the main reservoir host , and to humans . We studied the canine humoral immune resp... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"veterinary",
"diseases",
"zoonotic",
"diseases",
"leishmaniasis",
"biology",
"zoology",
"veterinary",
"science",
"parasitology"
] | 2011 | Canine Antibody Response to Phlebotomus perniciosus Bites Negatively Correlates with the Risk of Leishmania infantum Transmission |
An estimated 8 million persons , mainly in Latin America , are infected with Trypanosoma cruzi , the etiologic agent of Chagas disease . Existing antiparasitic drugs for Chagas disease have significant toxicities and suboptimal effectiveness , hence new therapeutic strategies need to be devised to address this neglecte... | Chronic infection with Trypanosoma cruzi causes progressive damage to the heart and other organs that is fatal in about 30% of cases . Known as Chagas disease , this is a major public health problem in Latin America . The existing medicines were developed over forty years ago and are not widely used because of toxicity... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"physical",
"sciences",
"chemistry",
"biology",
"and",
"life",
"sciences",
"medicine",
"and",
"health",
"sciences"
] | 2014 | Synergy Testing of FDA-Approved Drugs Identifies Potent Drug Combinations against Trypanosoma cruzi |
Rapid development of complex membranous replication structures is a hallmark of picornavirus infections . However , neither the mechanisms underlying such dramatic reorganization of the cellular membrane architecture , nor the specific role of these membranes in the viral life cycle are sufficiently understood . Here w... | The cellular pathways hijacked to support viral replication may provide a promising class of targets for anti-viral therapeutics , which will be effective against broad groups of viruses relying on the same cellular pathways , and will likely be refractory to the development of resistance since cellular factors are not... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"b",
"vitamins",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"hela",
"cells",
"pathogens",
"biological",
"cultures",
"microbiology",
"organic",
"compounds",
"cholines",
"viruses",
"rna",
"viruses",
"c... | 2018 | Phospholipid synthesis fueled by lipid droplets drives the structural development of poliovirus replication organelles |
Concentration-dependent transcriptional regulation and the spatial regulation of transcription factor levels are poorly studied in plant development . WUSCHEL , a stem cell-promoting homeodomain transcription factor , accumulates at a higher level in the rib meristem than in the overlying central zone , which harbors s... | Stem cell regulation is critical for the development of all organisms , and plants have particularly unique stem cell populations that are maintained throughout their lifespan at the tips of both the shoots and roots . Proper spatial and temporal regulation of gene expression by mobile proteins is essential for maintai... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"gene",
"regulation",
"cell",
"cycle",
"and",
"cell",
"division",
"membrane",
"staining",
"cell",
"processes",
"dna-binding",
"proteins",
"hormones",
"dna",
"transcription",
"membrane",
"proteins",
"plant",
"science",
"plant",
"hormones",
"cellular",
"structures",
"an... | 2018 | Cytokinin stabilizes WUSCHEL by acting on the protein domains required for nuclear enrichment and transcription |
Cells react to extracellular perturbations with complex and intertwined responses . Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data . Here we acquired time-resolved metabolomics measurem... | Phosphorylation is a broad regulatory mechanism with implications in nearly all processes of the cell . However , a global understanding of possible regulatory mechanisms remains elusive . In this study , we examined the potential regulatory role of kinases , phosphatases and transcription-factors in yeast metabolism a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"protein",
"metabolism",
"gene",
"regulation",
"regulatory",
"proteins",
"enzymology",
"dna-binding",
"proteins",
"metabolomics",
"metabolites",
"enzyme",
"metabolism",
"transcription",
"factors",
"enzyme",
"chemistry",
"proteins",
"enzyme",
"regulation",
"gene",
"expressio... | 2017 | Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast |
During the last decade , our understanding of cancer cell signaling networks has significantly improved , leading to the development of various targeted therapies that have elicited profound but , unfortunately , short-lived responses . This is , in part , due to the fact that these targeted therapies ignore context an... | A signaling pathway is a network of molecules in a cell that is typically initiated by stimuli ( e . g . , microenvironmental cues ) acting on receptors and internal signaling molecules to determine cell fate . Signaling pathways in cancer cells are different from those in normal cells , and this difference helps cance... | [
"Abstract",
"Introduction",
"Materials",
"and",
"methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"liver",
"enzymes",
"cancer",
"treatment",
"enzymology",
"signaling",
"networks",
"cancers",
"and",
"neoplasms",
"endocrine",
"physiology",
"oncology",
"network",
"analysis",
"growth",
"factors",
"epidermal",
"growth",
"factor",
... | 2018 | Cell signaling heterogeneity is modulated by both cell-intrinsic and -extrinsic mechanisms: An integrated approach to understanding targeted therapy |
Mild deficits in mitochondrial function have been shown to increase lifespan in multiple species including worms , flies and mice . Here , we study three C . elegans mitochondrial mutants ( clk-1 , isp-1 and nuo-6 ) to identify overlapping genetic pathways that contribute to their longevity . We find that genes regulat... | The use of genetic model organisms has permitted the identification of a large number of genes that influence longevity . These genes have been grouped into different pathways of lifespan extension , which have been proposed to modulate longevity by distinct mechanisms . In this work , we explore the mechanisms underly... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"deletion",
"mutation",
"reactive",
"oxygen",
"species",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"physiological",
"processes",
"mutation",
"developmental",
"biology",
"organism",
"development",
"mitochondria",
"epigenetics",
"bioenergetics",
"cellula... | 2018 | Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans |
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