headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell death",
"invertebrates",
"vesicles",
"rna interference",
"caenorhabditis",
"enzymes",
"cell processes",
"enzymology",
"animals",
"animal models",
"developmental biology",
"caenorhabditis elegans",
"guanine nucleotide exchange factors",
"model organisms",
"phagosomes",
"experiment... | The small GTPase RAB-35 defines a third pathway that is required for the recognition and degradation of apoptotic cells | journal.pgen.1007558 | null | [
[
"During the development of metazoans , cells that undergo apoptosis are internalized and degraded by other cells that are referred to as engulfing cells or phagocytes [1–3] .",
"The phagocytic removal of apoptotic cells is an evolutionarily conserved event that supports normal tissue turnover and homeosta... | [
"In metazoans , apoptotic cells are swiftly engulfed by phagocytes and degraded inside phagosomes .",
"Multiple small GTPases in the Rab family are known to function in phagosome maturation by regulating vesicle trafficking .",
"We discovered rab-35 as a new gene important for apoptotic cell clearance from a ge... | [
"After apoptosis , cell corpses must be promptly recognized and phagocytosed by engulfing cells .",
"These nascent phagosomes then undergo a maturation process that results in the degradation of the apoptotic cell corpse .",
"Phagosome maturation is enabled and coordinated through Rabs , small GTPases that recr... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"biology",
"microbiology"
] | A Large-Scale Complex Haploinsufficiency-Based Genetic Interaction
Screen in Candida albicans: Analysis of the RAM Network during
Morphogenesis | journal.pgen.1002058 | null | [
[
"Candida albicans is a member of the resident flora of the",
"gastrointestinal tract and is the most common fungal pathogen in humans .",
"The most",
"severe manifestations of candidiasis occur in immunocompromised patients and include",
"debilitating mucosal disease such as oropharyngeal cand... | [
"The morphogenetic transition between yeast and filamentous forms of the human",
"fungal pathogen Candida albicans is regulated by a variety of",
"signaling pathways .",
"How these pathways interact to orchestrate morphogenesis ,",
"however , has not been as well characterized .",
"To address this questio... | [
"Candida albicans is the most common cause of fungal infections",
"in humans .",
"As a diploid yeast without a classical sexual cycle , many genetic",
"approaches developed for large-scale genetic interaction studies in the model",
"yeast Saccharomyces cerevisiae cannot be applied to C .",
"albicans .",
... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"vertebrates",
"parasitic diseases",
"parasitic protozoans",
"animals",
"mammals",
"primates",
"physiological processes",
"protozoans",
"old world monkeys",
"infectious diseases",
"tissue repair",
"zoonoses",
"monkeys",
"baboons",
"proteins",
"recombin... | A Primate APOL1 Variant That Kills Trypanosoma brucei gambiense | journal.pntd.0004903 | null | [
[
"African trypanosomes continue to exert a significant barrier to agricultural production and rural development across sub-Saharan Africa [1] .",
"Due to a primate-specific innate trypanolytic mechanism , the majority of trypanosome species are unable to infect man .",
"However , two sub-species of Try... | [
"Humans are protected against infection from most African trypanosomes by lipoprotein complexes present in serum that contain the trypanolytic pore-forming protein , Apolipoprotein L1 ( APOL1 ) .",
"The human-infective trypanosomes , Trypanosoma brucei rhodesiense in East Africa and T . b .",
"gambiense in West... | [
"African trypanosomes are protozoan parasites that affect both humans and animals in poor rural areas of sub-Saharan Africa , and are a major constraint on health and agricultural development .",
"Disease control is principally dependent on the administration of drugs , which are old and largely unsatisfactory ."... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/dna repair",
"molecular biology/recombination",
"molecular biology/dna replication",
"genetics and genomics/chromosome biology"
] | The C-Terminal Domain of the Bacterial SSB Protein Acts as a DNA Maintenance Hub at Active Chromosome Replication Forks | journal.pgen.1001238 | null | [
[
"Maintaining genome integrity is a permanent challenge for all organisms , particularly during genome duplication , when accidental replication fork arrests expose the genome to damage .",
"Numerous mechanisms have evolved to counteract the deleterious consequences of fork arrest ( reviewed in [1] , [2] )... | [
"We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein ( SSBCter ) as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries .",
"We probed this SSBCter interactome using GFP fusions and... | [
"Cell multiplication relies primarily on the complete and accurate duplication of the genome .",
"Thus , all organisms have evolved multiple mechanisms to protect , repair , and re-activate the DNA replication forks .",
"A large body of research is currently aimed at deciphering the mechanisms that precisely di... | 2010 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"systems biology",
"biochemistry",
"biochemical simulations",
"medicine and health sciences",
"clinical medicine",
"pharmacodynamics",
"biology and life sciences",
"pharmacology",
"computational biology",
"pharmacokinetics"
] | The Pharmacodynamics of the p53-Mdm2 Targeting Drug Nutlin: The Role of Gene-Switching Noise | journal.pcbi.1003991 | null | [
[
"The p53 gene is an important oncosuppressor gene , and its product is heavily involved in the control of both cell proliferation and cell differentiation .",
"It is well known that p53 triggers cell cycle arrest and even apoptotic pathways in response to moderate and , respectively , strong stress signal... | [
"In this work we investigate , by means of a computational stochastic model , how tumor cells with wild-type p53 gene respond to the drug Nutlin , an agent that interferes with the Mdm2-mediated p53 regulation .",
"In particular , we show how the stochastic gene-switching controlled by p53 can explain experimenta... | [
"P53 is an antitumor gene regulating vital cellular functions such as repair of DNA damage , cellular suicide , and cell proliferation: in many tumors p53 is lowly expressed and/or mutated .",
"Drugs targeting the biomolecular network of p53 are becoming important .",
"The network includes the key proteins Mdm2... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"drugs and devices",
"african trypanosomiasis",
"host-pathogen interaction",
"microbiology",
"parasitic diseases",
"parasitology",
"parastic protozoans",
"neglected tropical diseases",
"infectious disease control",
"infectious diseases",
"infectious diseases of the nervous system",... | In Vivo Imaging of Trypanosome-Brain Interactions and Development of a Rapid Screening Test for Drugs against CNS Stage Trypanosomiasis | journal.pntd.0002384 | null | [
[
"Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , is endemic to sub-Saharan Africa [1] , [2] and is almost always fatal if untreated .",
"Although its prevalence fell to a position of near control in the 1960s , a breakdown of surveillance and treatment allowed its re-emergence , ... | [
"Human African trypanosomiasis ( HAT ) manifests in two stages of disease: firstly , haemolymphatic , and secondly , an encephalitic phase involving the central nervous system ( CNS ) .",
"New drugs to treat the second-stage disease are urgently needed , yet testing of novel drug candidates is a slow process beca... | [
"Trypanosoma brucei , a parasite transmitted by the bite of tsetse fly , is responsible for the disease human African trypanosomiasis ( HAT ) .",
"In advanced stages of HAT , trypanosomes invade the central nervous system ( CNS ) , resulting in an array of neurological symptoms , and eventually death .",
"Exist... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/population genetics",
"evolutionary biology/animal genetics",
"ecology/evolutionary ecology",
"evolutionary biology/evolutionary ecology",
"ecology",
"evolutionary biology",
"computational biology/evolutionary modeling",
"evolutionary biology/plant genetics and gene expression",... | Red Queen Dynamics with Non-Standard Fitness Interactions | journal.pcbi.1000469 | null | [
[
"Host-parasite interactions have the potential to produce rapid co-evolutionary dynamics .",
"If host genotypes are favoured that resist infection by the most common parasites and parasite genotypes are favoured that thrive on frequent hosts , this will produce selection against common genotypes and hence... | [
"Antagonistic coevolution between hosts and parasites can involve rapid fluctuations of genotype frequencies that are known as Red Queen dynamics .",
"Under such dynamics , recombination in the hosts may be advantageous because genetic shuffling can quickly produce disproportionately fit offspring ( the Red Queen... | [
"The Red Queen has become an eponym for rapid and perpetual evolutionary arms races between hosts and parasites .",
"The Red Queen also lends her name to the idea that such arms races are at the core of the question of why sexual reproduction is so widespread among higher-level organisms .",
"According to this ... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"chickenpox",
"clinical immunology",
"immunology",
"viral diseases",
"infectious disease control",
"immunomodulation",
"immune response"
] | CD4 T Cell Immunity Is Critical for the Control of Simian Varicella Virus Infection in a Nonhuman Primate Model of VZV Infection | journal.ppat.1002367 | null | [
[
"Varicella zoster virus ( VZV ) , a neurotropic alphaherpesvirus , is the causative agent of varicella ( chickenpox ) .",
"Following resolution of the acute infection , VZV establishes latency in sensory ganglia , and can reactivate years later , manifesting as dermatomal vesicular lesions known as herpes... | [
"Primary infection with varicella zoster virus ( VZV ) results in varicella ( more commonly known as chickenpox ) after which VZV establishes latency in sensory ganglia .",
"VZV can reactivate to cause herpes zoster ( shingles ) , a debilitating disease that affects one million individuals in the US alone annuall... | [
"Varicella zoster virus ( VZV ) causes chickenpox and establishes a life-long latent infection in humans .",
"VZV can reactivate years later to cause shingles , a debilitating and painful disease .",
"Vaccines against both chickenpox and shingles are available but not 100% efficacious .",
"Two doses of the ch... | 2011 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"salaries",
"disabilities",
"tropical diseases",
"geographical locations",
"india",
"social sciences",
"health care",
"bacterial diseases",
"health care providers",
"neglected tropical diseases",
"medical risk factors",
"public and occupational health",
"inf... | Risk of disability among adult leprosy cases and determinants of delay in diagnosis in five states of India: A case-control study | journal.pntd.0007495 | null | [
[
"Leprosy is an infectious disease caused by the Mycobacterium leprae and is one of the important causes of preventable disability [1] .",
"Early diagnosis and prompt treatment of all new cases of leprosy with World Health Organization ( WHO ) recommended multidrug therapy ( MDT ) remain the key strategies... | [
"A high proportion of grade 2 disability ( visible deformity ) is indicative of delay in detection of leprosy and leprosy is one of the major causes of preventable disability .",
"We conducted this study to determine the risk factors associated with disability ( G2D and G1D ) among adult new leprosy cases and to ... | [
"Leprosy is an infectious disease caused by the Mycobacterium leprae and is one of the major causes of preventable disability .",
"In the recent years there has been an increase in the number of new leprosy patients with disability in India .",
"People affected by leprosy often experience severe stigmatization ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"rna interference",
"gene regulation",
"dna transcription",
"gene function",
"molecular genetics",
"personalized medicine",
"gene expression",
"gene splicing",
"biology",
"molecular biology",
"genotypes",
"phenotypes",
"heredity",
"gene identification and analysis",
"genetics",
"human ... | RHOA Is a Modulator of the Cholesterol-Lowering Effects of Statin | journal.pgen.1003058 | null | [
[
"Genome-wide association studies ( GWAS ) have been used to identify genetic contributors to a number of common diseases and traits [1] .",
"However , a major problem with this approach is that very large sample sizes are generally required to detect statistically significant associations [2] .",
"Thi... | [
"Although statin drugs are generally efficacious for lowering plasma LDL-cholesterol levels , there is considerable variability in response .",
"To identify candidate genes that may contribute to this variation , we used an unbiased genome-wide filter approach that was applied to 10 , 149 genes expressed in immor... | [
"Statins , or HMG CoA reductase inhibitors , are widely used to lower plasma LDL-cholesterol levels as a means of reducing risk for cardiovascular disease .",
"We performed an unbiased genome-wide survey to identify novel candidate genes that may be involved in statin response using genome-wide mRNA expression an... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"gene regulation",
"immunology",
"notch signaling",
"cell differentiation",
"developmental biology",
"mathematics",
"network analysis",
"computer and information sciences",
"white blood cells",
"transcriptional control",
"netwo... | An enriched network motif family regulates multistep cell fate transitions with restricted reversibility | journal.pcbi.1006855 | null | [
[
"Cell fate transition , including differentiation , de-differentiation and trans-differentiation , is a fundamental biological process in which the function of a cell gets specialized , reprogrammed or altered .",
"The process often involves significant changes of multiple cellular properties , including ... | [
"Multistep cell fate transitions with stepwise changes of transcriptional profiles are common to many developmental , regenerative and pathological processes .",
"The multiple intermediate cell lineage states can serve as differentiation checkpoints or branching points for channeling cells to more than one lineag... | [
"The functions of cells are dynamically controlled in many biological processes including development , regeneration and disease progression .",
"Cell fate transition , or the switch of cellular functions , often involves multiple steps .",
"The intermediate stages of the transition provide the biological syste... | 2019 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"developmental biology",
"model organisms",
"genetics",
"biology",
"genetics and genomics"
] | Heterochromatin Formation Promotes Longevity and Represses Ribosomal RNA Synthesis | journal.pgen.1002473 | null | [
[
"Organismal aging is accompanied by the accumulation of damage to DNA and other macromolecules , and a progressive decline in vitality and tissue function .",
"The underlying mechanisms remain unclear , and many models have been proposed to explain the aging phenomenon .",
"Prominent among these model... | [
"Organismal aging is influenced by a multitude of intrinsic and extrinsic factors , and heterochromatin loss has been proposed to be one of the causes of aging .",
"However , the role of heterochromatin in animal aging has been controversial .",
"Here we show that heterochromatin formation prolongs lifespan and... | [
"Aging is characterized by a progressive decline in vitality and tissue function , leading to the demise of the organism .",
"Many models have been proposed to explain the aging phenomenon .",
"Among the many competing and/or overlapping models is the heterochromatin loss model of aging , which posits that hete... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | Trafficking of Hepatitis C Virus Core Protein during Virus Particle Assembly | journal.ppat.1002302 | null | [
[
"Hepatitis C virus ( HCV ) is a major cause of acute and chronic hepatitis , cirrhosis , and hepatocellular carcinoma .",
"HCV is an enveloped , positive-strand RNA virus classified with the Family Flaviviridae [1] .",
"The viral genome encodes an open reading frame of ≈3011 codons that is translated ... | [
"Hepatitis C virus ( HCV ) core protein is directed to the surface of lipid droplets ( LD ) , a step that is essential for infectious virus production .",
"However , the process by which core is recruited from LD into nascent virus particles is not well understood .",
"To investigate the kinetics of core traffi... | [
"Hepatitis C virus ( HCV ) infects almost 200 million people worldwide , causing both acute and chronic liver disease .",
"Although some antiviral treatments exist , they are not fully effective against all HCV genotypes and have serious side effects .",
"In order to develop more effective treatment strategies ... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"fmri",
"biology",
"neuroscience",
"neuroimaging",
"engineering"
] | The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack | journal.pcbi.1002885 | null | [
[
"Complex systems may be represented as networks by modeling the system components as nodes and the interactions between components as links , and graph theory methods and dynamical simulations may then be applied to these networks in order to understand their structure and dynamics .",
"The human brain is... | [
"In recent years , the field of network science has enabled researchers to represent the highly complex interactions in the brain in an approachable yet quantitative manner .",
"One exciting finding since the advent of brain network research was that the brain network can withstand extensive damage , even to high... | [
"Why can the brain endure numerous micro-strokes with seemingly no detrimental impact , until one cataclysmal stroke hinders the ability to perform essential functions such as speech and mobility ?",
"Perhaps various small regions or foci of the brain are highly important to information transfer , and the loss of... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"variant genotypes",
"alleles",
"genetic mapping",
"endocrine physiology",
"coronary heart disease",
"families",
"genetic epidemiology",
"cardiology",
"epidemiology",
"endocrinology",
"genetic loci",
"people and places",
"fathers",
"heredity",
"physiolog... | Identifying genetic variants that affect viability in large cohorts | journal.pbio.2002458 | null | [
[
"A number of central questions in evolutionary genetics remain open , in particular for humans .",
"Which types of variants affect fitness ?",
"Which components of fitness do they affect ?",
"What is the relative importance of directional and balancing selection in shaping genetic variation ?",
... | [
"A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness .",
"As a step towards this goal , we developed a method to examine whether individual genetic variants , or sets of genetic variants , currently influence viability .",
"Th... | [
"Our global understanding of adaptation in humans is limited to indirect statistical inferences from patterns of genetic variation , which are sensitive to past selection pressures .",
"We introduced a method that allowed us to directly observe ongoing selection in humans by identifying genetic variants that affe... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"biochemistry",
"in vitro",
"computational biology",
"neuroscience",
"molecular biology"
] | Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements | journal.pbio.0050040 | Alternative splicing of NMDA receptor 1 exon 21 is reversibly repressed by depolarization in a CaMK IV-dependent manner in neurons. This suggests splicing is finely tuned by dynamic activity inputs. | [
[
"N-methyl-D-aspartic acid ( NMDA ) -sensitive glutamate receptors ( NMDARs ) play important roles in modulating synaptic function in the brain [1 , 2] .",
"Functional NMDARs are heteromeric complexes assembled from one NR1 subunit and one or more NR2 subunits ( NR2A , NR2B , NR2C , and NR2D ) .",
"The... | [
"Alternative splicing controls the activity of many proteins important for neuronal excitation , but the signal-transduction pathways that affect spliced isoform expression are not well understood .",
"One particularly interesting system of alternative splicing is exon 21 ( E21 ) of the NMDA receptor 1 ( NMDAR1 E... | [
"Multiple mechanisms direct changes in neuronal activity in response to external stimuli , ranging from short-acting modifications of membrane proteins to longer-acting changes in gene expression .",
"A frequently regulated step in gene expression is the pre-mRNA splicing reaction in which the inclusion of exons ... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Ethics statement"
] | [
"animal models",
"cellular stress responses",
"model organisms",
"cancer genetics",
"gene expression",
"genetics",
"biology",
"molecular cell biology",
"mouse"
] | Cell-Cycle Dependent Expression of a Translocation-Mediated Fusion Oncogene Mediates Checkpoint Adaptation in Rhabdomyosarcoma | journal.pgen.1004107 | null | [
[
"Rhabdomyosarcoma ( RMS ) is the most common childhood soft tissue sarcoma .",
"Historically , RMS has been thought to arise from muscle because of the expression of myogenic markers .",
"Most childhood RMS falls into one of two biologically distinct subgroups: alveolar ( aRMS ) or embryonal ( eRMS ) ... | [
"Rhabdomyosarcoma is the most commonly occurring soft-tissue sarcoma in childhood .",
"Most rhabdomyosarcoma falls into one of two biologically distinct subgroups represented by alveolar or embryonal histology .",
"The alveolar subtype harbors a translocation-mediated PAX3:FOXO1A fusion gene and has an extremel... | [
"Rare childhood cancers can be paradigms from which important new principles can be discerned .",
"The childhood muscle cancer rhabdomyosarcoma is no exception , having been the focus of the original 1969 description by Drs .",
"Li and Fraumeni of a syndrome now know to be commonly caused by underlying p53 tumo... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"quantitative trait loci",
"epistasis",
"mutation",
"genome analysis",
"trait locus analysis",
"crystallographic techniques",
"research and analysis methods",
"genetic loci",
"phenotypes",
"natural selection",
"heredity",
"evolutionary processes",
"genetics",
"biology and life sciences",
... | Polygenic adaptation: From sweeps to subtle frequency shifts | journal.pgen.1008035 | null | [
[
"Rapid phenotypic adaptation of organisms to all kinds of novel environments is ubiquitous and has been described and studied for decades [1 , 2] .",
"However , while the macroscopic changes of phenotypic traits are frequently evident , their genetic and genomic underpinnings are much more difficult to re... | [
"Evolutionary theory has produced two conflicting paradigms for the adaptation of a polygenic trait .",
"While population genetics views adaptation as a sequence of selective sweeps at single loci underlying the trait , quantitative genetics posits a collective response , where phenotypic adaptation results from ... | [
"It is still an open question how complex traits adapt to new selection pressures .",
"While population genetics champions the search for selective sweeps , quantitative genetics proclaims adaptation via small concerted frequency shifts .",
"To date the empirical evidence of clear sweep signals is more scarce t... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"molecular epidemiology",
"infectious disease epidemiology",
"viruses and cancer",
"virology",
"epidemiology",
"disease surveillance",
"biology and life sciences",
"microbiology",
"viral disease diagnosis"
] | Epidemiology and Genetic Variability of HHV-8/KSHV in Pygmy and Bantu Populations in Cameroon | journal.pntd.0002851 | null | [
[
"Human herpesvirus-8 ( HHV-8 ) or Kaposi's sarcoma associated herpesvirus ( KSHV ) is a Gammaherpesvirus , first identified in a tumor biopsy from an AIDS-related Kaposi's sarcoma ( KS ) [1] .",
"It is considered as the causing agent of all forms of KS [2] , [3] , [4] ( epidemic , iatrogenic , classic and... | [
"Kaposi's sarcoma associated herpesvirus ( KSHV/HHV-8 ) is the causal agent of all forms of Kaposi sarcoma .",
"Molecular epidemiology of the variable K1 region identified five major subtypes exhibiting a clear geographical clustering .",
"The present study is designed to gain new insights into the KSHV epidemi... | [
"Kaposi's sarcoma associated herpesvirus ( KSHV/HHV-8 ) is the causal agent of one of the most frequent skin tumors found endemically or epidemically associated to HIV in Central and Eastern Africa .",
"This highly variable virus tends to cluster geographically according to specific major subtypes .",
"Its prev... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"chemical compounds",
"vacuoles",
"carbohydrates",
"organic compounds",
"glucose",
"membrane proteins",
"physiological processes",
"fungi",
"homeostasis",
"amino acids",
"cellular structures and organelles",
"proteins",
"chemistry",
"methionine",
"cell m... | The yeast protein kinase Sch9 adjusts V-ATPase assembly/disassembly to control pH homeostasis and longevity in response to glucose availability | journal.pgen.1006835 | null | [
[
"In Saccharomyces cerevisiae , Sch9 is part of the highly conserved TORC1 pathway which plays a central role in the nutrient-induced signaling network , thereby affecting many aspects of yeast physiology such as stress resistance , longevity and cell growth [1–3] .",
"The rapamycin-sensitive TORC1 mediate... | [
"The conserved protein kinase Sch9 is a central player in the nutrient-induced signaling network in yeast , although only few of its direct substrates are known .",
"We now provide evidence that Sch9 controls the vacuolar proton pump ( V-ATPase ) to maintain cellular pH homeostasis and ageing .",
"A synthetic s... | [
"The evolutionary conserved TOR complex 1 controls growth in response to the quality and quantity of nutrients such as carbon and amino acids .",
"The protein kinase Sch9 is the main TORC1 effector in yeast .",
"However , only few of its direct targets are known .",
"In this study , we performed a genome-wide... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"morphogens",
"signal transduction",
"developmental biology",
"embryonic pattern formation",
"cell biology",
"molecular development",
"biology and life sciences",
"morphogenesis",
"cell signaling",
"pattern formation",
"cell fate determination",
"hedgehog signaling"
] | A Mutation in the Mouse Ttc26 Gene Leads to Impaired Hedgehog Signaling | journal.pgen.1004689 | null | [
[
"The Hedgehog ( Hh ) signaling pathway plays critical roles in embryonic development , wound healing , and tumorigenesis [1]–[4] .",
"It is activated when the receptor protein Patched-1 ( Ptch1 ) binds to one of the secreted Hh lipoproteins , Sonic Hh ( Shh ) , Indian Hh , or Desert Hh [5] , [6] .",
"... | [
"The phenotype of the spontaneous mutant mouse hop-sterile ( hop ) is characterized by a hopping gait , polydactyly , hydrocephalus , and male sterility .",
"Previous analyses of the hop mouse revealed a deficiency of inner dynein arms in motile cilia and a lack of sperm flagella , potentially accounting for the ... | [
"The Hedgehog ( Hh ) signaling pathway determines pattern formation in many developing tissues , e . g . , during digit formation in the limbs , by regulating proteins of the Gli family .",
"Activation of these proteins requires their transport to the tip of the primary cilium ( an antenna-like sensory structure ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome sequencing",
"sequence analysis",
"genome complexity",
"metagenomics",
"genome evolution",
"host-pathogen interaction",
"biology",
"genomics",
"evolutionary biology",
"genomic evolution",
"microbiology",
"computational biology",
"bacterial pathogens"
] | Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples | journal.pcbi.1003107 | null | [
[
"Lateral gene transfer ( LGT ) is the transmission of genetic material by means other than direct vertical transmission from progenitors to their offspring , and has been best studied for its ability to transfer novel genotypes between species .",
"LGT occurs most frequently between organisms that are in ... | [
"There are 10× more bacterial cells in our bodies from the microbiome than human cells .",
"Viral DNA is known to integrate in the human genome , but the integration of bacterial DNA has not been described .",
"Using publicly available sequence data from the human genome project , the 1000 Genomes Project , and... | [
"There are 10× more bacterial cells in the human body than there are human cells that are part of the human microbiome .",
"Many of those bacteria are in constant , intimate contact with human cells .",
"We sought to establish if bacterial cells insert their own DNA into the human genome .",
"Such random muta... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data | journal.pcbi.1003246 | null | [
[
"Since its introduction , chromatin immunoprecipitation followed by high throughput sequencing ( ChIP-Seq ) has revolutionized the study of gene regulation .",
"ChIP-Seq is currently the state-of-the-art method for studying protein-DNA interactions genome-wide and is widely used [1]–[5] .",
"ChIP-Seq ... | [
"Chromatin immunoprecipitation followed by high throughput sequencing ( ChIP-Seq ) has been successfully used for genome-wide profiling of transcription factor binding sites , histone modifications , and nucleosome occupancy in many model organisms and humans .",
"Because the compact genomes of prokaryotes harbor... | [
"Chromatin immunoprecipitation followed by high throughput sequencing ( ChIP-Seq ) is widely used for studying in vivo protein-DNA interactions genome-wide .",
"Current state-of-the-art ChIP-Seq protocols utilize single-end tag ( SET ) assay which only sequences ends of DNA fragments in the library .",
"Althoug... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"molecular biology/recombination",
"neuroscience"
] | Gene Activation Using FLP Recombinase in C. elegans | journal.pgen.1000028 | null | [
[
"Every widely-used genetic model organism can be manipulated to express genes introduced by the experimenter .",
"In C . elegans it is simple to create a transgene by injecting DNA containing a complete genomic region .",
"In most cases the transgene will be expressed in its native temporal and spatia... | [
"The FLP enzyme catalyzes recombination between specific target sequences in DNA .",
"Here we use FLP to temporally and spatially control gene expression in the nematode C . elegans .",
"Transcription is blocked by the presence of an “off cassette” between the promoter and the coding region of the desired produ... | [
"Genes turn on and off as a natural part of development .",
"The nematode C . elegans has been an important model system for studying the roles of genes in animal development and physiology .",
"However , worm researchers have had a limited toolkit for controlling gene activation .",
"These drawbacks have bee... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"cdna library screening",
"medicine and health sciences",
"enzyme-linked immunoassays",
"helminths",
"tropical diseases",
"parasitic diseases",
"animals",
"trematodes",
"clonorchis sinensis",
"foodborne trematodiases",
"neglected tropical diseases",
"molecular biology techni... | Cs1, a Clonorchis sinensis-derived serodiagnostic antigen containing tandem repeats and a signal peptide | journal.pntd.0006683 | null | [
[
"Clonorchiasis is a food-borne parasitic disease caused by infection with the liver fluke Clonorchis sinensis , which is mainly endemic in China , South Korea , northern Vietnam , and parts of Russia .",
"It was conservatively estimated that in 2004 around 15 million people were infected , of whom an esti... | [
"Clonorchiasis , caused by the liver fluke Clonorchis sinensis , remains a serious public health issue in Asia , especially in China , and its relationship with cholangiocarcinoma has highlighted the importance of C . sinensis infection .",
"Proteins containing tandem repeats ( TRs ) are found in a variety of par... | [
"Clonorchiasis is a neglected tropical disease .",
"The major factor that prevents the effective management of clonorchiasis is a lack of effective diagnostic tools .",
"Proteins containing tandem repeats ( TRs ) , which have been found in a variety of parasites , are known targets of B-cell responses and can b... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neuroscience/neuronal signaling mechanisms",
"neuroscience/neuronal and glial cell biology"
] | Glia and Muscle Sculpt Neuromuscular Arbors by Engulfing Destabilized Synaptic Boutons and Shed Presynaptic Debris | journal.pbio.1000184 | As synapses grow at the Drosophila neuromuscular junction, they shed membrane material in an activity-dependent manner. Glia and postsynaptic muscle cells are required to engulf this debris to ensure new synaptic growth. | [
[
"The wiring of the nervous system , from initial axon sprouting to the formation of specific synaptic connections , represents one of the most dramatic and precise examples of directed cellular outgrowth .",
"Developing axons navigate sometimes tortuous routes as they seek out the appropriate target cells... | [
"Synapse remodeling is an extremely dynamic process , often regulated by neural activity .",
"Here we show during activity-dependent synaptic growth at the Drosophila NMJ many immature synaptic boutons fail to form stable postsynaptic contacts , are selectively shed from the parent arbor , and degenerate or disap... | [
"The synapse is the fundamental unit of communication between neurons and their target cells .",
"As the nervous system matures , synapses often need to be added , removed , or otherwise remodeled to accommodate the changing needs of the circuit .",
"Such changes are often regulated by the activity of the circu... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"plant science",
"signaling",
"plant growth and development",
"molecular development",
"plant genetics",
"biology"
] | Photoactivated UVR8-COP1 Module Determines Photomorphogenic UV-B Signaling Output in Arabidopsis | journal.pgen.1004218 | null | [
[
"Light is a critical environmental stimulus that regulates a number of developmental and physiological processes of living organisms .",
"In sessile plants , perception of light is the initial and decisive step in light signaling transduction , and is achieved by several groups of photosensory receptor pr... | [
"In Arabidopsis , ultraviolet ( UV ) -B-induced photomorphogenesis is initiated by a unique photoreceptor UV RESISTANCE LOCUS 8 ( UVR8 ) which utilizes its tryptophan residues as internal chromophore to sense UV-B .",
"As a result of UV-B light perception , the UVR8 homodimer shaped by its arginine residues under... | [
"Higher plants are able to sense and interpret diverse light signals to modulate their growth .",
"In response to long-wavelength and low-intensity ultraviolet-B ( UV-B ) light , plants establish photomorphogenic development and stress acclimation .",
"UV RESISTANCE LOCUS 8 ( UVR8 ) is a unique UV-B photorecept... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"genetics and genomics"
] | Caenorhabditis elegans HCF-1 Functions in Longevity Maintenance as a DAF-16 Regulator | journal.pbio.0060233 | Caenorhabditis elegans HCF-1 is a new longevity factor that functions to antagonize the transcriptional activities of DAF-16/FOXO by forming a complex with DAF-16/FOXO and preventing a fraction of DAF-16/FOXO from accessing its target gene promoters. | [
[
"Recent studies in various model system have revealed multiple evolutionarily conserved genes and genetic pathways important for longevity [1–6] .",
"One of the best characterized longevity determinants is the forkhead box O ( FOXO ) family of transcription factors , which function as major effectors of t... | [
"The transcription factor DAF-16/forkhead box O ( FOXO ) is a critical longevity determinant in diverse organisms , however the molecular basis of how its transcriptional activity is regulated remains largely unknown .",
"We report that the Caenorhabditis elegans homolog of host cell factor 1 ( HCF-1 ) represents... | [
"One of the key molecules that modulate longevity in evolutionarily diverse organisms is the transcription factor DAF-16/FOXO .",
"Despite its importance in aging and other biological processes , how DAF-16/FOXO activity is regulated in the nucleus is largely unknown .",
"We report a new player important for ag... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Global Genome and Transcriptome Analyses of Magnaporthe oryzae Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evolution | journal.ppat.1004801 | null | [
[
"Rice ( Oryza sativa ) is one of the most important staple food crops for more than half of the global human population [1] .",
"However , the rice production is severely impacted by the blast disease caused by the fungus Magnaporthe oryzae , despite the cultivation of various disease-resistance cultivars... | [
"Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution , in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates .",
"This same principle applies to the rice blast pathogen Magnaporthe or... | [
"Genetic variations in pathogens , such as the causal agent of rice blast Magnaporthe oryzae , often lead to circumvention of disease-resistance cultivars .",
"Previous genome-wide analyses of model organisms suggest that pathogen effectors are also rapidly evolving , especially in regions with high genome plasti... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration | journal.pcbi.1004295 | null | [
[
"Advances in developmental biology and regenerative medicine require a mechanistic understanding of the generation and repair processes that construct and repair complex anatomical structures [1] .",
"For example , a salamander can regenerate complete limbs , eyes , tails , and jaws [2]; a tail grafted to... | [
"Transformative applications in biomedicine require the discovery of complex regulatory networks that explain the development and regeneration of anatomical structures , and reveal what external signals will trigger desired changes of large-scale pattern .",
"Despite recent advances in bioinformatics , extracting... | [
"Developmental and regenerative biology experiments are producing a huge number of morphological phenotypes from functional perturbation experiments .",
"However , existing pathway models do not generally explain the dynamic regulation of anatomical shape due to the difficulty of inferring and testing non-linear ... | 2015 |
[
"Introduction",
"Current status",
"Challenges to the growth of bioinformatics in Jordan",
"Future directions",
"Conclusion"
] | [
"jordan",
"geographical locations",
"database searching",
"scientists",
"genome analysis",
"science and technology workforce",
"research and analysis methods",
"perspective",
"sequence analysis",
"computer and information sciences",
"genomics",
"sequence alignment",
"bioinformatics",
"peop... | Bioinformatics in Jordan: Status, challenges, and future directions | journal.pcbi.1007202 | null | [
[
"Previously published studies on the development of bioinformatics in several countries [1–7] inspired us to investigate the status of bioinformatics in Jordan .",
"Bioinformatics is a vast multidisciplinary field that has developed computational tools to analyze and manage constantly growing amounts of b... | [
"Bioinformatics plays a key role in supporting the life sciences .",
"In this work , we examine bioinformatics in Jordan , beginning with the current status of bioinformatics education and research , then exploring the challenges of advancing bioinformatics , and finally looking to the future for how Jordanian bi... | [
"Bioinformatics is an important multidisciplinary field for many life sciences .",
"Mathematics , statistics , computer science , and the life sciences join together to breathe life into the discipline of bioinformatics .",
"In Jordan , rapid progress in life science , research , and healthcare have created a d... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"cell cycle and cell division",
"cell processes",
"hematologic cancers and related disorders",
"mathematical computing",
"mathematics",
"stem cells",
"cell growth",
"mesenchymal stem cells",
"adult stem cells",
"computer and information sciences",... | Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis | journal.pcbi.1003599 | null | [
[
"Myelodysplastic syndromes are clonal disorders which are characterized by ineffective hematopoiesis , peripheral cytopenia and a high risk of disease progression towards acute myeloid leukemia ( AML ) [1]–[3] .",
"They arise from an aberrant HSC that gains growth advantage over normal hematopoiesis resul... | [
"Myelodysplastic syndromes ( MDS ) are triggered by an aberrant hematopoietic stem cell ( HSC ) .",
"It is , however , unclear how this clone interferes with physiologic blood formation .",
"In this study , we followed the hypothesis that the MDS clone impinges on feedback signals for self-renewal and different... | [
"Myelodysplastic syndromes are diseases which are characterized by ineffective blood formation .",
"There is accumulating evidence that they are caused by an aberrant hematopoietic stem cell .",
"However , it is yet unclear how this malignant clone suppresses normal hematopoiesis .",
"To this end , we generat... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"neural networks",
"neuroscience",
"mathematics",
"network analysis",
"distribution curves",
"neuronal tuning",
"research and analysis methods",
"statistical distributions",
"curve fitting",
"computer and information sciences",
"mathematical functions",
"animal cells",
"mathematical and stat... | Inferring neural circuit structure from datasets of heterogeneous tuning curves | journal.pcbi.1006816 | null | [
[
"Neural responses in many brain areas are tuned to external parameters such as stimulus- or movement-related features .",
"Tuning curves characterize the dependence of neural responses on such parameters , and are a key descriptive tool in neuroscience .",
"Experimentally measured tuning curves often ... | [
"Tuning curves characterizing the response selectivities of biological neurons can exhibit large degrees of irregularity and diversity across neurons .",
"Theoretical network models that feature heterogeneous cell populations or partially random connectivity also give rise to diverse tuning curves .",
"Empirica... | [
"Neurons in the brain respond selectively to some stimuli or for some motor outputs , but not others .",
"Even within a local brain network , neurons exhibit great diversity in their selectivity patterns .",
"Recently , theorists have highlighted the computational importance of diverse neural selectivity .",
... | 2019 |
[
"Introduction",
"Results and discussion",
"Materials & methods"
] | [
"bacteriology",
"horizontal gene transfer",
"chromosomal inversions",
"microbiology",
"gene transfer",
"dna replication",
"materials science",
"bacterial genetics",
"dna",
"microbial genetics",
"oligomers",
"microbial genomics",
"materials by structure",
"bacterial genomics",
"chromosome... | Chromosome architecture constrains horizontal gene transfer in bacteria | journal.pgen.1007421 | null | [
[
"The evolutionary histories of genes within bacterial genomes have long been shown to be highly incongruent [1]; [2–4] .",
"Horizontal Gene Transfer ( HGT ) between species enables bacteria to acquire and potentially utilize any gene that it encounters in the biosphere , thus catalysing exploration of nov... | [
"Despite significant frequencies of lateral gene transfer between species , higher taxonomic groups of bacteria show ecological and phenotypic cohesion .",
"This suggests that barriers prevent panmictic dissemination of genes via lateral gene transfer .",
"We have proposed that most bacterial genomes have a fun... | [
"The potential success of horizontal gene transfer events is historically equated to the benefits conferred by encoded products .",
"Here we show that gene transfer events are observed less frequently if the introduced genes disrupt important patterns of genomic information , suggesting that this disruption would... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Mitochondrial Transcription Terminator Family Members mTTF and mTerf5 Have Opposing Roles in Coordination of mtDNA Synthesis | journal.pgen.1003800 | null | [
[
"The mitochondrial genome and its expression are essential to maintain oxidative phosphorylation ( OXPHOS ) , a central metabolic process in higher eukaryotes .",
"OXPHOS failure during development leads to developmental arrest in a diverse range of metazoans , including both insects [1] , [2] and vertebr... | [
"All genomes require a system for avoidance or handling of collisions between the machineries of DNA replication and transcription .",
"We have investigated the roles in this process of the mTERF ( mitochondrial transcription termination factor ) family members mTTF and mTerf5 in Drosophila melanogaster .",
"Th... | [
"All genomes require a system for preventing collisions between the machineries of DNA replication and transcription .",
"We have investigated the roles in this process of two proteins of the mTERF ( mitochondrial transcription termination factor ) family in Drosophila .",
"These factors , mTTF and mTerf5 , sha... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"genetics and genomics",
"microbiology",
"molecular biology"
] | Irradiation-Induced Deinococcus radiodurans Genome Fragmentation Triggers Transposition of a Single Resident Insertion Sequence | journal.pgen.1000799 | null | [
[
"Stress-induced transposition has been an attractive notion for some time since it is potentially important in creating diversity to facilitate adaptation of the host to severe environmental conditions .",
"One common major stress is DNA damage .",
"This induces a variety of responses including change... | [
"Stress-induced transposition is an attractive notion since it is potentially important in creating diversity to facilitate adaptation of the host to severe environmental conditions .",
"One common major stress is radiation-induced DNA damage .",
"Deinococcus radiodurans has an exceptional ability to withstand ... | [
"Induction of transposition in prokaryotes under cell stress conditions is potentially important in creating diversity facilitating adaptation to severe environments .",
"In Deinococcus radiodurans , the most radiation-resistant organism known , despite abundance of resident insertion sequences ( IS ) , transposi... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [] | Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection | journal.pcbi.1004694 | null | [
[
"The molecular evolution and adaptation of the human immunodeficiency virus ( HIV ) within infected individuals is exceptionally fast .",
"This evolution is generated by a combination of high rates of mutation and recombination , large population sizes and short generation times , and has important conseq... | [
"Analysis of HIV-1 gene sequences sampled longitudinally from infected individuals can reveal the evolutionary dynamics that underlie associations between disease outcome and viral genetic diversity and divergence .",
"Here we extend a statistical framework to estimate rates of viral molecular adaptation by consi... | [
"Since some common approaches to the study of molecular adaptation may not be optimal for answering questions regarding within-host virus evolution , we have developed an alternative approach that estimates an absolute rate of molecular adaptation from serially-sampled viral populations .",
"Here , we extend this... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"virology/diagnosis",
"infectious diseases/viral infections",
"public health and epidemiology/infectious diseases"
] | Use of Saliva for Early Dengue Diagnosis | journal.pntd.0001046 | null | [
[
"Dengue is one of the most prevalent mosquito-borne diseases in humans .",
"This disease is best controlled by regular Aedes source reduction activities .",
"However , total eradication of Aedes in a densely populated urban area where the vector has established itself is a daunting task .",
"Dengu... | [
"The necessity of a venous blood collection in all dengue diagnostic assays and the high cost of tests that are available for testing during the viraemic period hinder early detection of dengue cases and thus could delay cluster management .",
"This study reports the utility of saliva in an assay that detects den... | [
"The importance of laboratory diagnosis of dengue cannot be undermined .",
"In recent years , many dengue diagnostic tools have become available for various stages of the disease , but the one limitation is that they require blood as a specimen for testing .",
"In many incidences , phlebotomy in needle-phobic f... | 2011 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"biophysics/cell signaling and trafficking structures"
] | Positional Information Generated by Spatially Distributed Signaling Cascades | journal.pcbi.1000330 | null | [
[
"Cascades of covalent protein modification cycles convey signals from cell-surface receptors to target genes in the nucleus .",
"Each cycle consists of two or more interconvertible protein forms , for example , a phosphorylated and unphosphorylated protein , and an active , phosphorylated protein signals ... | [
"The temporal and stationary behavior of protein modification cascades has been extensively studied , yet little is known about the spatial aspects of signal propagation .",
"We have previously shown that the spatial separation of opposing enzymes , such as a kinase and a phosphatase , creates signaling activity ... | [
"Living cells detect environmental cues and propagate signals into the cell interior employing signaling cascades of protein modification cycles .",
"A cycle consists of a pair of opposing enzymes controlling the activation and deactivation of a protein , where the active form transmits the signal to the next cas... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Material and Methods"
] | [
"animal models",
"zebrafish",
"cellular structures",
"gram negative",
"model organisms",
"immune cells",
"cytoskeleton",
"immunity",
"immunologic subspecialties",
"innate immunity",
"immunity to infections",
"immunology",
"host-pathogen interaction",
"biology",
"microbiology",
"molecul... | The Zebrafish as a New Model for the In Vivo Study of Shigella flexneri Interaction with Phagocytes and Bacterial Autophagy | journal.ppat.1003588 | null | [
[
"Macroautophagy ( hereafter referred to as autophagy ) is an intracellular degradation process by which cytosolic materials are delivered to the lysosome .",
"The canonical autophagy pathway involves the initiation and elongation of double-membrane autophagosomes to sequester cargo , and this process requ... | [
"Autophagy , an ancient and highly conserved intracellular degradation process , is viewed as a critical component of innate immunity because of its ability to deliver cytosolic bacteria to the lysosome .",
"However , the role of bacterial autophagy in vivo remains poorly understood .",
"The zebrafish ( Danio r... | [
"Autophagy , an ancient and highly conserved intracellular degradation process , is viewed as a critical component of innate immunity because of its ability to deliver cytosolic bacteria to the lysosome .",
"However , a complete understanding of the molecules and mechanisms restricting cytosolic bacteria has not ... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"plant science",
"medicine and health sciences",
"population modeling",
"infectious disease epidemiology",
"epidemiology",
"influenza",
"plant pathology",
"biology and life sciences",
"infectious disease modeling",
"computational biology",
"viral diseases",
"epidemiolo... | Determinants of Influenza Transmission in South East Asia: Insights from a Household Cohort Study in Vietnam | journal.ppat.1004310 | null | [
[
"Three to five millions severe illnesses and 250 , 000 to 500 , 000 deaths worldwide are due to the influenza virus each year [1] .",
"To guide control policies , it is important that the determinants of influenza transmission are fully characterized .",
"Such assessment is complex because the risk of... | [
"To guide control policies , it is important that the determinants of influenza transmission are fully characterized .",
"Such assessment is complex because the risk of influenza infection is multifaceted and depends both on immunity acquired naturally or via vaccination and on the individual level of exposure to... | [
"Influenza causes an estimated three to five million severe illnesses worldwide each year .",
"In order to guide control policies it is important to determine the key risk factors for transmission .",
"This is often done by studying transmission in households but in the past , analysis of such data has suffered... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing techniques",
"genome-wide association studies",
"animal types",
"vertebrates",
"pets and companion animals",
"dogs",
"animals",
"mammals",
"long non-coding rnas",
"genome analysis",
"mammalian genomics",
"molecular biology techniques",
"rna sequencing",
"zoology",
"research a... | A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies | journal.pgen.1006482 | null | [
[
"Inherited peripheral neuropathies are neurodegenerative diseases of the peripheral nervous system ( PNS ) , including the Charcot-Marie-Tooth diseases ( CMT ) and Hereditary Sensory and Autonomic Neuropathies ( HSANs ) [1] .",
"They are categorized based on the degree of involvement of motor , sensory an... | [
"Human Hereditary Sensory Autonomic Neuropathies ( HSANs ) are characterized by insensitivity to pain , sometimes combined with self-mutilation .",
"Strikingly , several sporting dog breeds are particularly affected by such neuropathies .",
"Clinical signs appear in young puppies and consist of acral analgesia ... | [
"In this study , we present a canine neuropathy characterized by insensitivity to pain in the feet , sometimes combined with self-mutilation described in four sporting breeds .",
"This particular phenotype has the clinical hallmarks of human Hereditary Sensory Autonomic Neuropathies ( HSAN ) .",
"As we hypothes... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Heat Shock Transcription Factor σ32 Co-opts the Signal Recognition Particle to Regulate Protein Homeostasis in E. coli | journal.pbio.1001735 | The bacterial heat shock transcription factor, σ32, maintains proper protein homeostasis only after it is targeted to the inner membrane by the signal recognition particle (SRP), thereby enabling integration of protein folding information from both the cytoplasm and cell membrane. | [
[
"The heat shock response ( HSR ) maintains protein homeostasis ( proteostasis ) in all organisms .",
"The HSR responds to protein unfolding , aggregation , and damage by the rapid and transient production of heat shock proteins ( HSPs ) and by triggering other cellular protective pathways that help mitiga... | [
"All cells must adapt to rapidly changing conditions .",
"The heat shock response ( HSR ) is an intracellular signaling pathway that maintains proteostasis ( protein folding homeostasis ) , a process critical for survival in all organisms exposed to heat stress or other conditions that alter the folding of the pr... | [
"All cells have to adjust to frequent changes in their environmental conditions .",
"The heat shock response is a signaling pathway critical for survival of all organisms exposed to elevated temperatures .",
"Under such conditions , the heat shock response maintains enzymes and other proteins in a properly fold... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"physics",
"chemistry",
"chemical biology",
"chemical physics",
"biophysics"
] | Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases? | journal.pcbi.1002501 | null | [
[
"Polyglutamine ( polyQ ) diseases involve a set of nine late-onset progressive neurodegenerative diseases caused by the expansion of CAG triplet sequence repeats [1] .",
"These repeats result in the transcription of proteins with abnormally long polyQ inserts .",
"When these inserts expand beyond a no... | [
"We have characterized the conformational ensembles of polyglutamine peptides of various lengths ( ranging from to ) , both with and without the presence of a C-terminal polyproline hexapeptide .",
"For this , we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to ch... | [
"Nine neurodegenerative diseases are caused by polyglutamine ( polyQ ) expansions greater than a given threshold in proteins with little or no homology except for the polyQ regions .",
"The diseases all share a common feature: the formation of polyQ aggregates and eventual neuronal death .",
"Using molecular dy... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [] | Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches | journal.pntd.0003759 | null | [
[
"Fascioliasis or hepatic distomatosis , caused by the food-borne trematodes Fasciola hepatica and Fasciola gigantica , is considered one of the most important parasitic diseases , which constitutes a serious public health problem and has a significant veterinary relevance .",
"Economically important anima... | [
"Fasciola hepatica is the causative agent of fascioliasis , a disease affecting grazing animals , causing economic losses in global agriculture and currently being an important human zoonosis .",
"Overuse of chemotherapeutics against fascioliasis has increased the populations of drug resistant parasites .",
"F ... | [
"Fascioliosis is considered an emerging disease in humans , causing important losses in global agriculture through the infection of livestock animals .",
"The outcome of resistant parasites has increased the search for new drugs which may contribute to disease control .",
"In recent decades , Fasciola cathepsin... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"medicine and health sciences",
"pathology and laboratory medicine",
"helminths",
"parasitic diseases",
"animals",
"parasitology",
"developmental biology",
"gastropods",
"sporocysts",
"genome analysis",
"snails",
"research and analys... | A multistrain approach to studying the mechanisms underlying compatibility in the interaction between Biomphalaria glabrata and Schistosoma mansoni | journal.pntd.0005398 | null | [
[
"Schistosomes are the causative agents of schistosomiasis , which is one of the most important neglected human tropical diseases in the world .",
"Schistosomes infect over 200 million people worldwide , causing both acute and chronic debilitating diseases [1 , 2] .",
"There is no effective vaccine aga... | [
"In recent decades , numerous studies have sought to better understand the mechanisms underlying the compatibility between Biomphalaria glabrata and Schistosoma mansoni .",
"The developments of comparative transcriptomics , comparative genomics , interactomics and more targeted approaches have enabled researchers... | [
"Schistosomiasis is the second most widespread human tropical parasitic disease after malaria .",
"It is caused by flatworms of the genus Schistosoma , and poses a considerable threat for human health in numerous Asian , African and South American countries .",
"The World Health Organization has set the goal of... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"medicine and health sciences",
"toxins",
"immune physiology",
"pathology and laboratory medicine",
"crystal structure",
"immunology",
"condensed matter physics",
"vertebrates",
"animals",
"toxicology",
"toxic agents",
"reptiles",
"dna",
"crystallography",
"antibodies",
"venoms",
"im... | A Heterologous Multiepitope DNA Prime/Recombinant Protein Boost Immunisation Strategy for the Development of an Antiserum against Micrurus corallinus (Coral Snake) Venom | journal.pntd.0004484 | null | [
[
"Envenomation by snakebite is a common and generally harmful , environmental and occupational neglected tropical disease that constitutes a highly relevant public health problem with worldwide mortality estimated to be around 50 , 000 deaths annually [1] .",
"In the Americas , although most of the registe... | [
"Envenoming by coral snakes ( Elapidae: Micrurus ) , although not abundant , represent a serious health threat in the Americas , especially because antivenoms are scarce .",
"The development of adequate amounts of antielapidic serum for the treatment of accidents caused by snakes like Micrurus corallinus is a cha... | [
"Coral snakes are a group of deadly venomous snakes that exhibit a characteristic red , yellow/white , and black coloured banding pattern .",
"Accidents involving these snakes tend to be very severe or even lethal , causing peripheral nervous system depression with muscle paralysis and vasomotor instability .",
... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology",
"cardiovascular disorders"
] | Neuropilin-1/GIPC1 Signaling Regulates α5β1 Integrin Traffic and Function in Endothelial Cells | journal.pbio.1000025 | The transmembrane protein neuropilin-1 promotes endothelial cell attachment to the extracellular matrix by enhancing active integrin treadmilling at cell-adhesion sites. | [
[
"In vertebrates , the development of a hierarchically organized and functional vascular tree relies on the dynamic interaction of endothelial cells ( ECs ) with the surrounding extracellular matrix ( ECM ) , which is mediated by heterodimeric αβ integrin adhesive receptors [1] .",
"During evolution , vert... | [
"Neuropilin 1 ( Nrp1 ) is a coreceptor for vascular endothelial growth factor A165 ( VEGF-A165 , VEGF-A164 in mice ) and semaphorin 3A ( SEMA3A ) .",
"Nevertheless , Nrp1 null embryos display vascular defects that differ from those of mice lacking either VEGF-A164 or Sema3A proteins .",
"Furthermore , it has be... | [
"The vascular system is a hierarchical network of blood vessels lined by endothelial cells that , by means of the transmembrane integrin proteins , bind to the surrounding proteinaceous extracellular matrix ( ECM ) .",
"Integrins are required for proper cardiovascular development and exist in bent ( inactive ) an... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing techniques",
"sequence analysis",
"biochemistry",
"protein synthesis",
"protein interactions",
"genome evolution",
"proteins",
"protein folding",
"chaperone proteins",
"protein structure",
"evolutionary modeling",
"biology and life sciences",
"molecular biology techniques",
"co... | Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks | journal.pcbi.1003674 | null | [
[
"Protein evolution is central to adaptation and ultimately survival of all species [1] .",
"Proteins evolve through mutation and selection , and given the marginal stability of their native state and the sensitivity of protein structure to mutation [2] , major questions arise concerning how the emergence ... | [
"Evolution is driven by mutations , which lead to new protein functions but come at a cost to protein stability .",
"Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability .",
"Accordingly , organisms must balance the benefit of acceptin... | [
"Evolutionary innovation through mutation is important for adaptation , thus ultimately survival of all species .",
"Proteins , the main actors of cellular life , are generally only marginally stable in the cell and sensitive to mutations .",
"This raises the question how the emergence of new functions is balan... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"oncology",
"developmental biology",
"mathematics",
"cell biology",
"in vitro",
"computational biology",
"chemical biology",
"animals",
"mus (mouse)"
] | Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control | journal.pcbi.0030130 | null | [
[
"Self-renewal is one of the defining characteristics of embryonic stem cells ( ESCs ) [1] .",
"This fate choice is influenced by ligand–receptor-mediated activation of intracellular signaling pathways .",
"Significant work is being done to understand the signaling proteins and pathways that control se... | [
"Directing stem cell fate requires knowledge of how signaling networks integrate temporally and spatially segregated stimuli .",
"We developed and validated a computational model of signal transducer and activator of transcription-3 ( Stat3 ) pathway kinetics , a signaling network involved in embryonic stem cell ... | [
"Directing stem cell fate requires knowledge of how intracellular signaling pathways integrate environmental stimuli to make decisions to stay as stem cells ( self-renew ) or to differentiate into specific functional cell types .",
"We developed and validated a computational model of signal transducer and activat... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/virion structure, assembly, and egress",
"cell biology/morphogenesis and cell biology",
"cell biology",
"virology",
"infectious diseases/viral infections"
] | Electron Tomography Reveals the Steps in Filovirus Budding | journal.ppat.1000875 | null | [
[
"Marburg virus ( MARV ) and Ebola virus , the two genera in the family Filoviridae , cause fulminant hemorrhagic disease in humans and nonhuman primates , resulting in high mortality rates [1] , [2] , [3] .",
"Outbreaks of MARV disease in sub-Saharan Africa underline the emerging potential of this virus ,... | [
"The filoviruses , Marburg and Ebola , are non-segmented negative-strand RNA viruses causing severe hemorrhagic fever with high mortality rates in humans and nonhuman primates .",
"The sequence of events that leads to release of filovirus particles from cells is poorly understood .",
"Two contrasting mechanisms... | [
"The filoviruses , Marburg and Ebola , cause lethal hemorrhagic fever and are highest-priority bioterrorism agents .",
"Filovirus particles contain a rod-like nucleocapsid and are normally filamentous , though other shapes are seen .",
"It is poorly understood how such large filamentous particles are assembled ... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"host-pathogen interaction",
"biology",
"microbiology"
] | Leishmania mexicana Infection Induces IgG to Parasite Surface Glycoinositol Phospholipids that Can Induce IL-10 in Mice and Humans | journal.pntd.0002224 | null | [
[
"Leishmania is an intracellular protozoan parasite that causes 2 million new infections yearly and is a major cause of death worldwide [1] .",
"Drug toxicity and the development of resistance have made leishmaniasis an ever-challenging set of diseases [2] , [3] , [4] .",
"While a vaccine is likely the... | [
"Infection with the intracellular protozoan parasite Leishmania mexicana causes chronic disease in C57BL/6 mice , in which cutaneous lesions persist for many months with high parasite burdens ( 107–108 parasites ) .",
"This chronic disease process requires host IL-10 and FcγRIII .",
"When Leishmania amastigotes... | [
"Leishmania mexicana is a single-celled parasite that causes chronic skin disease in humans and mice .",
"Antibodies on the surface of parasites lead to the production of a protein called interleukin-10 ( IL-10 ) , which blocks an effective immune response needed to kill parasites and resolve skin lesions .",
"... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"cell physiology",
"gene regulation",
"purification techniques",
"regulatory proteins",
"membrane staining",
"dna-binding proteins",
"fungi",
"transcription factors",
"cellular structures and organelles",
"extraction techniques",
"protein purification",
"research and analy... | The C-terminal region of Net1 is an activator of RNA polymerase I transcription with conserved features from yeast to human | journal.pgen.1008006 | null | [
[
"RNA polymerase I ( Pol I ) transcribes the precursor for three out of the four ribosomal RNAs ( rRNAs ) , which are essential components of ribosomes , required for cell growth and proliferation .",
"In proliferating cells of S . cerevisiae ( hereafter called yeast ) , Pol I activity accounts for over 50... | [
"RNA polymerase I ( Pol I ) synthesizes ribosomal RNA ( rRNA ) in all eukaryotes , accounting for the major part of transcriptional activity in proliferating cells .",
"Although basal Pol I transcription factors have been characterized in diverse organisms , the molecular basis of the robust rRNA production in vi... | [
"The production of ribosomes , cellular factories of protein synthesis , is an essential process driving proliferation and cell growth .",
"Ribosome biogenesis is controlled at the level of synthesis of its components , ribosomal proteins and ribosomal RNA .",
"In eukaryotes , RNA polymerase I is dedicated to t... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neurological disorders/neuromuscular diseases",
"neurological disorders/spinal disorders",
"genetics and genomics/genetics of disease",
"neurological disorders/neurogenetics",
"neuroscience/neurobiology of disease and regeneration"
] | Conserved Genes Act as Modifiers of Invertebrate SMN Loss of Function Defects | journal.pgen.1001172 | null | [
[
"Decreased Survival of Motor Neuron ( SMN ) protein function underlies most Spinal Muscular Atrophy ( SMA ) cases [1] .",
"The SMN protein is ubiquitously expressed [2] , [3] , yet SMA pathology is remarkably specific .",
"Patients lose spinal α-motorneurons and experience muscular dysfunction with at... | [
"Spinal Muscular Atrophy ( SMA ) is caused by diminished function of the Survival of Motor Neuron ( SMN ) protein , but the molecular pathways critical for SMA pathology remain elusive .",
"We have used genetic approaches in invertebrate models to identify conserved SMN loss of function modifier genes .",
"Dros... | [
"Spinal Muscular Atrophy ( SMA ) is a common , untreatable , and often fatal neuromuscular disease predominately caused by reduced Survival Motor Neuron ( SMN ) protein function .",
"Here , we use invertebrate models to identify and validate conserved genes that play a critical role in SMN loss of function neurom... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/membranes and sorting",
"microbiology/cellular microbiology and pathogenesis",
"biophysics/membrane proteins and energy transduction"
] | Helicobacter pylori VacA Toxin/Subunit p34: Targeting of an Anion Channel to the Inner Mitochondrial Membrane | journal.ppat.1000878 | null | [
[
"Helicobacter pylori is a gram-negative bacterium infecting the human gastric mucosa , causing gastritis and peptic ulcer and , in some cases , gastric cancer [1]–[5] .",
"One of the major virulence factors of the bacteria is the vacuolating toxin VacA , a protein of about 90 kDa [1] , [6] , [7] .",
"... | [
"The vacuolating toxin VacA , released by Helicobacter pylori , is an important virulence factor in the pathogenesis of gastritis and gastroduodenal ulcers .",
"VacA contains two subunits: The p58 subunit mediates entry into target cells , and the p34 subunit mediates targeting to mitochondria and is essential fo... | [
"VacA is a toxic protein produced by Helicobacter pylori , the bacteria that cause gastritis and ulcer diseases .",
"p34 , the toxic component of VacA , is known to damage mitochondria , defined cell organelles in the target cells .",
"However , both the mechanism of mitochondrial targeting and the toxic activi... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing techniques",
"organismal evolution",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"invertebrate genomics",
"viruses",
"dna viruses",
"phylogenetic analysis",
"genome analysis",
"microbial evolution",
"sequence motif analysis",
... | The Ancient Evolutionary History of Polyomaviruses | journal.ppat.1005574 | null | [
[
"Murine polyomavirus ( MPyV ) was discovered in the mid-1950s as a filterable infectious agent that could induce salivary tumors in experimentally exposed mice [2 , 3] .",
"It was quickly established that the virus is potently carcinogenic , causing many different types of tumors ( Greek poly + oma ) in v... | [
"Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds .",
"To investigate the deeper evolutionary history of the family , we used a combination of viral metagenomics , bioinformatics , and structural modeling approaches to identify and characterize polyomavirus sequences ass... | [
"Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates , including humans .",
"In this report , we describe our discovery of highly divergent polyomaviruses associated with various marine fish .",
"Searches of public deep sequencing databases unexpectedly reve... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Characterization of Metabolically Quiescent Leishmania Parasites in Murine Lesions Using Heavy Water Labeling | journal.ppat.1004683 | null | [
[
"A number of medically important bacterial , fungal and protozoan pathogens are associated with persistent chronic infections that can reactivate to cause acute disease long after initial infection [1–5] .",
"With few exceptions [6] , very little is known about the growth rate or physiological state of th... | [
"Information on the growth rate and metabolism of microbial pathogens that cause long-term chronic infections is limited , reflecting the absence of suitable tools for measuring these parameters in vivo .",
"Here , we have measured the replication and physiological state of Leishmania mexicana parasites in murine... | [
"Microbial pathogens can adapt to changing conditions in their hosts by switching between different growth and physiological states .",
"However , current methods for measuring microbial physiology in vivo are limited , hampering detailed dissection of host-pathogen interactions .",
"Here we have used heavy wat... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"mutation",
"haplotypes",
"genetic polymorphism",
"natural selection",
"genetics",
"population genetics",
"biology",
"population biology",
"evolutionary biology",
"genetics and genomics"
] | An EAV-HP Insertion in 5′ Flanking Region of SLCO1B3 Causes Blue Eggshell in the Chicken | journal.pgen.1003183 | null | [
[
"Avian eggshell coloration is the result of crypsis or mimetism and plays important roles in filtering solar radiation and strengthening the eggshell [1] .",
"Blue eggshell color has been proposed as post-mating signals of female phenotypic quality to their mates and is related to fitness of the offspring... | [
"The genetic determination of eggshell coloration has not been determined in birds .",
"Here we report that the blue eggshell is caused by an EAV-HP insertion that promotes the expression of SLCO1B3 gene in the uterus ( shell gland ) of the oviduct in chicken .",
"In this study , the genetic map location of the... | [
"The eggshell color of birds is of wide interest , but the molecular basis remained unknown until our discovery , reported here .",
"The blue eggshell is found not only in wild birds but also in domestic fowls .",
"In this study , we identified that blue eggshell in chickens from different geographical regions ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Coherent Motion of Monolayer Sheets under Confinement and Its Pathological Implications | journal.pcbi.1004670 | null | [
[
"An epithelial sheet is comprised of a group of cells that are connected to each other via cadherin bonds to form a monolayer .",
"Many experimental observations have demonstrated that cells in this network are persistently motile , and upon reaching a critical density show collective migration behavior [... | [
"Coherent angular rotation of epithelial cells is thought to contribute to many vital physiological processes including tissue morphogenesis and glandular formation .",
"However , factors regulating this motion , and the implications of this motion if perturbed , remain incompletely understood .",
"In the curre... | [
"Epithelial and endothelial cells that line various cavities and the vasculature in our bodies , are tightly connected to each other and exist as sheets .",
"Upon confinement in two-dimensional geometries , these cells exhibit rotational motion , which has also been observed in vivo and implicated in physiologica... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant pests",
"plant science",
"model organisms",
"plant and algal models",
"plant growth and development",
"genetics",
"plant genetics",
"plant pathology",
"biology",
"arabidopsis thaliana"
] | The bHLH Subgroup IIId Factors Negatively Regulate Jasmonate-Mediated Plant Defense and Development | journal.pgen.1003653 | null | [
[
"Plant hormones are essential for the regulation of plant growth , differentiation , development , reproduction , and survival [1]–[3] .",
"Jasmonates ( JAs ) , a class of cyclic fatty acid-derived plant hormones originating from plastid membrane α-linolenic acid [4] , [5] , regulate diverse aspects of pl... | [
"Plants have evolved sophisticated systems for adaptation to their natural habitat .",
"In response to developmental and environmental cues , plants produce and perceive jasmonate ( JA ) signals , which induce degradation of JASMONATE-ZIM-Domain ( JAZ ) proteins and derepress the JAZ-repressed transcription facto... | [
"Plants live in fixed places and have to evolve sophisticated systems for adaptation to their frequently changing environment .",
"Plant hormones are essential for the regulation of these sophisticated systems which coordinately control plant growth , development , reproduction and defense .",
"Jasmonates ( JAs... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/germ cells",
"developmental biology/embryology",
"molecular biology/histone modification",
"molecular biology/centromeres",
"developmental biology/aging",
"cell biology/developmental molecular mechanisms",
"genetics and genomics/chromosome biology",
"molecular biology/chromosome... | Loss of Maternal ATRX Results in Centromere Instability and Aneuploidy in the Mammalian Oocyte and Pre-Implantation Embryo | journal.pgen.1001137 | null | [
[
"Heterochromatin formation in eukaryotic cells is essential for the maintenance of nuclear architecture , the control of gene expression and chromosome segregation [1]–[6] .",
"In the mouse genome , constitutive heterochromatin consists of two closely related chromosomal sub-domains with distinct structur... | [
"The α-thalassemia/mental retardation X-linked protein ( ATRX ) is a chromatin-remodeling factor known to regulate DNA methylation at repetitive sequences of the human genome .",
"We have previously demonstrated that ATRX binds to pericentric heterochromatin domains in mouse oocytes at the metaphase II stage wher... | [
"The transmission of an abnormal chromosome complement from the gametes to the early embryo , a condition called aneuploidy , is a major cause of congenital birth defects and pregnancy loss .",
"Human embryos are particularly susceptible to aneuploidy , which in the majority of cases is the result of abnormal mei... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"gene function",
"developmental biology",
"growth control",
"cell fate determination",
"organism development",
"stem cells",
"animal cells",
"cell biology",
"regeneration",
"genetics",
"biology and life sciences",
"cellular types",
"morphogenesis",
"cell differentiation",
"adult stem cel... | JNK Controls the Onset of Mitosis in Planarian Stem Cells and Triggers Apoptotic Cell Death Required for Regeneration and Remodeling | journal.pgen.1004400 | null | [
[
"The regeneration of missing tissues requires tight coordination between stem cell proliferation , differentiation , and cell death .",
"However , it remains unclear how these processes are integrated to generate a well-proportioned organism .",
"We addressed this question using the freshwater planari... | [
"Regeneration of lost tissues depends on the precise interpretation of molecular signals that control and coordinate the onset of proliferation , cellular differentiation and cell death .",
"However , the nature of those molecular signals and the mechanisms that integrate the cellular responses remain largely unk... | [
"Planarians , thanks to their extraordinary regenerative capacity , represent a unique model of animal regeneration .",
"After amputation , new animals regenerate from each individual piece of tissue , leading Dalyell to describe them as “immortal under the edge of the knife” in 1814 .",
"Planarians also contin... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Regulation of Insulin Receptor Trafficking by Bardet Biedl Syndrome Proteins | journal.pgen.1005311 | null | [
[
"Insulin is critically involved in the regulation of glucose and lipid metabolism in various tissues ensuring the coordinated uptake and storage of the products of digestion .",
"Insulin binding to its receptor initiates a myriad of intracellular events resulting in downstream activation of glucose uptake... | [
"Insulin and its receptor are critical for the regulation of metabolic functions , but the mechanisms underlying insulin receptor ( IR ) trafficking to the plasma membrane are not well understood .",
"Here , we show that Bardet Biedl Syndrome ( BBS ) proteins are necessary for IR localization to the cell surface ... | [
"A main function of the hormone insulin in the body is to regulate metabolism of glucose .",
"The hormone causes body cells in different organs and tissues to utilize glucose from the bloodstream , storing the excess amount .",
"Insulin resistance which reflects the inability of insulin to properly regulate glu... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/disease models",
"genetics and genomics/animal genetics",
"genetics and genomics",
"genetics and genomics/comparative genomics"
] | Balancing Selection of a Frame-Shift Mutation in the MRC2 Gene Accounts for the Outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle | journal.pgen.1000666 | null | [
[
"The Belgian Blue Cattle breed ( BBCB ) is notorious for its exceptional muscular development known as “double-muscling” .",
"This extreme phenotype is due in part to an 11-bp loss-of-function deletion in the myostatin gene that has been fixed in the breed ( e . g . [1] ) , as well as to ongoing selection... | [
"We herein describe the positional identification of a 2-bp deletion in the open reading frame of the MRC2 receptor causing the recessive Crooked Tail Syndrome in cattle .",
"The resulting frame-shift reveals a premature stop codon that causes nonsense-mediated decay of the mutant messenger RNA , and the virtual ... | [
"Livestock are being subject to intense artificial selection aimed at ever-increasing , sometimes extreme , production phenotypes .",
"This is well-illustrated by the exceptional muscular hypertrophy characterizing the “double-muscled” Belgian Blue Cattle Breed ( BBCB ) .",
"We herein identify a loss-of-functio... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacterial diseases",
"infectious diseases",
"medicine and health sciences",
"protozoan infections",
"biology and life sciences",
"immunology",
"microbiology",
"listeriosis",
"infectious disease control",
"parasitic diseases",
"toxoplasmosis"
] | Toxoplasma gondii Profilin Promotes Recruitment of Ly6Chi CCR2+ Inflammatory Monocytes That Can Confer Resistance to Bacterial Infection | journal.ppat.1004203 | null | [
[
"Toxoplasma gondii is an obligate intracellular Apicomplexan parasite that can infect nearly any nucleated cell of all warm blooded animals .",
"Within warm blooded hosts , T . gondii replicates as a fast growing tachyzoite form , which disseminates throughout the body during acute infection .",
"Over... | [
"Ly6C+ inflammatory monocytes are essential to host defense against Toxoplasma gondii , Listeria monocytogenes and other infections .",
"During T . gondii infection impaired inflammatory monocyte emigration results in severe inflammation and failure to control parasite replication .",
"However , the T . gondii ... | [
"Toxoplasma gondii is an apicomplexan parasite that can infect all warm blooded animals , but rodent species are considered the primary reservoirs .",
"Mice that are infected with T . gondii become more resistant to lethal infection with other pathogens .",
"Ly6C+ inflammatory monocytes are innate immune cells ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"phosphorylation",
"learning",
"medicine and health sciences",
"action potentials",
"nervous system",
"membrane potential",
"social sciences",
"electrophysiology",
"neuroscience",
"learning and memory",
"cognitive psychology",
"mathematics",
"cognition",
"memory",
"distribution curves",
... | Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons | journal.pcbi.1005306 | null | [
[
"Traditionally , increased synaptic response is believed to reflect activity dependent synaptic plasticity , in which the association between different inputs is strengthened through synaptic-specific potentiation .",
"We have previously shown that acquiring the skill to perform in a particularly difficul... | [
"Intense spiking response of a memory-pattern is believed to play a crucial role both in normal learning and pathology , where it can create biased behavior .",
"We recently proposed a novel model for memory amplification where the simultaneous two-fold increase of all excitatory ( AMPAR-mediated ) and inhibitory... | [
"Amplifying the strength of a neuronal assembly that underlies a behavioral choice can lead to a particularly long lasting dominant memory .",
"We report experimental and theoretical evidence for a long-term mechanism that amplifies the response of a neuronal assembly which we termed “memory amplification mechani... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetic mutation",
"gene function",
"mutation",
"phylogenetics",
"protein folding",
"protein structure",
"molecular genetics",
"divergent evolution",
"forms of evolution",
"proteins",
"biology",
"evolutionary systematics",
"biophysics",
"physics",
"mutagenesis",
"biochemistry",
"gen... | Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor | journal.pgen.1002117 | null | [
[
"A central goal in studies of molecular evolution is to reveal the genetic , structural , and biophysical mechanisms by which protein functions have evolved [1]–[6] .",
"Ancient proteins and DNA are seldom directly available , but the traces of their evolutionary history are found in their extant descenda... | [
"Understanding the genetic , structural , and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies .",
"Ancestral sequence reconstruction ( ASR ) offers an experimental approach to these questions .",
"Here we use ASR to shed light on the earliest fu... | [
"A central question in molecular evolution is how changes in the genetic , structural , and biophysical properties of proteins generate new functions .",
"Ancestral sequence reconstruction ( ASR ) allows long-extinct proteins to be resurrected and characterized in the laboratory and allows the mechanisms for evol... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"bacteriology",
"biochemistry",
"gram negative",
"medicine and health sciences",
"pathology and laboratory medicine",
"host-pathogen interactions",
"medical microbiology",
"small molecules",
"microbial pathogens",
"biology and life sciences",
"microbiology",
"chemical biolog... | The Transcriptional Activator LdtR from ‘Candidatus Liberibacter asiaticus’ Mediates Osmotic Stress Tolerance | journal.ppat.1004101 | null | [
[
"The rapid expansion of Huanglongbing ( HLB; also known as “citrus greening” ) disease caused a crisis in the citrus industry worldwide , with no solution visible in the near future .",
"Experts estimate that without pro-active measures , the citrus industry in affected areas ( like Florida ) will be sign... | [
"The causal agent of Huanglongbing disease , ‘Candidatus Liberibacter asiaticus’ , is a non-culturable , gram negative , phloem-limited α-proteobacterium .",
"Current methods to control the spread of this disease are still limited to the removal and destruction of infected trees .",
"In this study , we identifi... | [
"The rapid expansion of Huanglongbing disease ( HLB ) has caused a severe crisis in the citrus industry , with no solution visible in the near future .",
"The causative agent , ‘Candidatus Liberibacter asiaticus’ , is an unculturable bacterium under common laboratory conditions , which has made it difficult to ga... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational chemistry",
"molecular complexes",
"cell biology",
"molecular dynamics",
"biophysics theory",
"biology and life sciences",
"chemistry",
"physical sciences",
"computational biology",
"molecular cell biology",
"biophysics",
"molecular biology",
"biophysical simulations"
] | Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin | journal.pcbi.1003552 | null | [
[
"Myosin II , the conventional myosin responsible for muscle contraction , generates mechanical force by interacting with actin filament .",
"Our understanding of this actomyosin motor has greatly increased by X-ray analyses of myosin structures [1]–[3] and by electron microscopy ( EM ) of actomyosin compl... | [
"An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation .",
"On the basis of structural observations of myosins and actins , the widely held lever-arm hypothesis has been proposed , in which proteins are assumed to show sequential struct... | [
"Myosin II is a molecular motor that is fueled by ATP hydrolysis and generates mechanical force by interacting with actin filament .",
"Comparison among various myosin structures obtained by X-ray and electron microscope analyses has led to the hypothesis that structural change of myosin in ATP hydrolysis cycle i... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"pesticides",
"genome sequencing",
"genome expression analysis",
"immunity",
"pest control",
"innate immunity",
"immunology",
"biology",
"genomics",
"microbiology",
"host-pathogen interaction",
"genetics and genomics",
"agriculture"
] | Altered Immunity in Crowded Locust Reduced Fungal (Metarhizium anisopliae) Pathogenesis | journal.ppat.1003102 | null | [
[
"Similar to pathogenic infection , the stress of living conditions alters animal immunity .",
"Changes in population density usually induce polyphenic transition and variations in the immune response of animals [1] .",
"The locust , globally notorious agricultural pests that have been controlled with ... | [
"The stress of living conditions , similar to infections , alters animal immunity .",
"High population density is empirically considered to induce prophylactic immunity to reduce the infection risk , which was challenged by a model of low connectivity between infectious and susceptible individuals in crowded anim... | [
"The wide application of fungal biopesticides for insect management has led to concerns over the development of biopesticide resistance .",
"The migratory locust , a globally notorious agricultural pest , has density-dependent phase changes between solitary and gregarious states .",
"The gregarious locusts disp... | 2013 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"microbiology",
"cloning",
"parasitic diseases",
"parasitic protozoans",
"protozoan life cycles",
"animals",
"developmental biology",
"protozoans",
"molecular biology techniques",
"epimastigotes",
"insect vectors",
"digestive system",
"res... | Trypanosoma cruzi surface mucins are involved in the attachment to the Triatoma infestans rectal ampoule | journal.pntd.0007418 | null | [
[
"Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , is a life-long , debilitating illness of major significance in Latin America , and an emergent threat to global public health [1] .",
"T . cruzi is a very adaptable organism , able to infect a wide range of mammals and more than 140 sp... | [
"Trypanosoma cruzi , the agent of Chagas disease , is a protozoan parasite transmitted to humans by blood-sucking triatomine vectors .",
"However , and despite its utmost biological and epidemiological relevance , T . cruzi development inside the digestive tract of the insect remains a poorly understood process .... | [
"Chagas disease , caused by the protozoan Trypanosoma cruzi , is a life-long and debilitating neglected illness of major significance to Latin America public health , for which no vaccine or adequate drugs are yet available .",
"In this scenario , identification of novel drug targets and/or strategies aimed at co... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"viral immune evasion",
"viral persistence and latency",
"virology",
"biology",
"microbiology"
] | Dendritic Cell-induced Activation of Latent HIV-1 Provirus in Actively Proliferating Primary T Lymphocytes | journal.ppat.1003259 | null | [
[
"Combined antiretroviral therapy ( cART ) is able to suppress the HIV-1 plasma RNA load in patients to undetectable levels .",
"The treatment , however , does not lead to complete virus eradication .",
"Even after many years of successful cART the virus can rebound from latently infected cellular rese... | [
"HIV-1 latency remains a formidable barrier towards virus eradication as therapeutic attempts to purge these reservoirs are so far unsuccessful .",
"The pool of transcriptionally silent proviruses is established early in infection and persists for a lifetime , even when viral loads are suppressed below detection ... | [
"Combination therapy can suppress the viral load in HIV-1 infected individuals to undetectable levels , but does not lead to complete virus eradication .",
"Even after many years of successful therapy the virus is still present in long-lived cells as a latently integrated provirus .",
"HIV-1 can re-establish sy... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"innate immune system",
"medicine and health sciences",
"immune physiology",
"cytokines",
"body fluids",
"dose prediction methods",
"animal models of disease",
"blood counts",
"immunology",
"tropical diseases",
"microbiology",
"developmental biology",
"pharmaceutics",
"mol... | Extended Evaluation of Virological, Immunological and Pharmacokinetic Endpoints of CELADEN: A Randomized, Placebo-Controlled Trial of Celgosivir in Dengue Fever Patients | journal.pntd.0004851 | null | [
[
"Dengue fever is a mosquito-borne viral illness that is endemic in tropical regions around the world , with an estimated 96 million cases of dengue illness annually [1] .",
"Dengue is one of 17 neglected tropical diseases that the World Health Organization ( WHO ) has identified for priority attention due... | [
"CELADEN was a randomized placebo-controlled trial of 50 patients with confirmed dengue fever to evaluate the efficacy and safety of celgosivir ( A study registered at ClinicalTrials . gov , number NCT01619969 ) .",
"Celgosivir was given as a 400 mg loading dose and 200 mg bid ( twice a day ) over 5 days .",
"R... | [
"Dengue virus is currently threatening 40% of the world’s population .",
"An approximately 60% efficacious vaccine has been registered for use in Mexico , Brazil , the Philippines , Paraguay and El Salvador , but there are no approved antiviral treatments available .",
"We have shown that celgosivir , an endopl... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/cellular microbiology and pathogenesis",
"microbiology/immunity to infections",
"microbiology/innate immunity",
"immunology/immunity to infections",
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis",
"microbiology/medical microbiology",
"infe... | Modulation of Neutrophil Function by a Secreted Mucinase of Escherichia coli O157∶H7 | journal.ppat.1000320 | null | [
[
"Enterohemorrhagic Escherichia coli ( EHEC ) of serogroup O157∶H7 is an emerging human diarrheal pathogen associated with numerous food-borne outbreaks in the U . S . Infection of the colon by EHEC causes mild diarrhea that proceeds to bloody colitis and can be acquired following ingestion of fewer than 100 o... | [
"Escherichia coli O157∶H7 is a human enteric pathogen that causes hemorrhagic colitis which can progress to hemolytic uremic syndrome , a severe kidney disease with immune involvement .",
"During infection , E . coli O157∶H7 secretes StcE , a metalloprotease that promotes the formation of attaching and effacing l... | [
"Enterohemorrhagic Escherichia coli ( EHEC ) poses a significant threat to the U . S . food supply , causing foodborne gastrointestinal disease in humans that can progress to hemolytic uremic syndrome ( HUS ) , a potentially fatal kidney disease .",
"Research suggests that EHEC strains are growing more virulent ,... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Chitin Recognition via Chitotriosidase Promotes Pathologic Type-2 Helper T Cell Responses to Cryptococcal Infection | journal.ppat.1004701 | null | [
[
"Pulmonary mycoses , ranging from invasive fungal infection to severe asthma with fungal sensitization , affect millions of people worldwide [1 , 2] .",
"Fungi inhabit a multitude of ecological niches , and consequently , humans continuously encounter potentially pathogenic fungi in the environment .",
... | [
"Pulmonary mycoses are often associated with type-2 helper T ( Th2 ) cell responses .",
"However , mechanisms of Th2 cell accumulation are multifactorial and incompletely known .",
"To investigate Th2 cell responses to pulmonary fungal infection , we developed a peptide-MHCII tetramer to track antigen-specific ... | [
"Humans often inhale potentially pathogenic fungi in the environment .",
"While CD4+ helper T ( Th ) cells are required for protection against invasive disease , a subset of Th cells , called Th2 cells , are associated with increased mortality and allergy/asthma morbidity .",
"Our study aimed to unravel the cel... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | MAN1B1 Deficiency: An Unexpected CDG-II | journal.pgen.1003989 | null | [
[
"Congenital Disorders of Glycosylation ( CDG ) are a group of genetic diseases , due to deficient protein and lipid glycosylation [1] .",
"To date , over 60 distinct disorders have been described , comprising a very broad range of phenotypes [2] .",
"However , the search for the culprit gene in an uns... | [
"Congenital disorders of glycosylation ( CDG ) are a group of rare metabolic diseases , due to impaired protein and lipid glycosylation .",
"In the present study , exome sequencing was used to identify MAN1B1 as the culprit gene in an unsolved CDG-II patient .",
"Subsequently , 6 additional cases with MAN1B1-CD... | [
"Glycosylation concerns the synthesis of sugar chains , their addition onto proteins and/or lipids , and their subsequent modifications .",
"The resulting glycoproteins serve many critical roles in metabolism .",
"The importance of this pathway is illustrated by a group of diseases called Congenital Disorders o... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"gene regulation",
"pathogens",
"regulatory proteins",
"immunology",
"microbiology",
"dna-binding proteins",
"cell differentiation",
"dna transcription",
"viruses",
"developmental biology",
... | EBV epigenetically suppresses the B cell-to-plasma cell differentiation pathway while establishing long-term latency | journal.pbio.2001992 | null | [
[
"Epstein-Barr virus ( EBV ) is a human gamma-herpesvirus that infects about 95% of the world’s adult population .",
"Although infection is nearly always benign , on rare occasions it is etiologically associated with various human cancers , including Burkitt lymphoma ( BL ) , diffuse large B cell lymphoma ... | [
"Mature human B cells infected by Epstein-Barr virus ( EBV ) become activated , grow , and proliferate .",
"If the cells are infected ex vivo , they are transformed into continuously proliferating lymphoblastoid cell lines ( LCLs ) that carry EBV DNA as extra-chromosomal episomes , express 9 latency-associated EB... | [
"Epstein-Barr virus ( EBV ) infection can cause several types of cancer associated with its major target in humans , the mature B cell .",
"Furthermore , EBV is one of the most potent transforming agents ever identified , producing—in vitro—‘immortal’ B lymphoblastoid cell lines ( LCLs ) with outstanding reliabil... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"immunology/genetics of the immune system",
"immunology/immunity to infections"
] | Genetic and Functional Role of TNF-alpha in the Development Trypanosoma cruzi Infection | journal.pntd.0000976 | null | [
[
"Chagas disease is an important chronic infection caused by the protozoan Trypanosoma cruzi .",
"The disease continues to be a major public health problem in most Latin America countries , affecting around 9 million people [1] .",
"In addition , Chagas disease is an emerging health problem in non-ende... | [
"TNF-alpha plays an important role in trypanocidal mechanisms and is related to tissue injury .",
"This cytokine has been detected in the heart of human chagasic patients where it is associated with tissue damage .",
"This study investigated whether TNF-alpha levels and the presence of genetic polymorphisms are... | [
"Chagas disease is an important parasitic disease that has no cure .",
"The pathogenesis of the disease is still not completely understood .",
"Studies using candidate genes are important to better understand the differences between individuals that lead to such heterogenous disease .",
"TNF-alpha is a cytoki... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Cooperative Action of Cdk1/cyclin B and SIRT1 Is Required for Mitotic Repression of rRNA Synthesis | journal.pgen.1005246 | null | [
[
"Posttranslational modification of transcription factors is critical for cell cycle progression in a unidirectional and reversible manner .",
"Cell cycle-dependent oscillation of transcriptional activity is governed by a complex network of regulatory proteins and signaling pathways that respond to various... | [
"Mitotic repression of rRNA synthesis requires inactivation of the RNA polymerase I ( Pol I ) -specific transcription factor SL1 by Cdk1/cyclin B-dependent phosphorylation of TAFI110 ( TBP-associated factor 110 ) at a single threonine residue ( T852 ) .",
"Upon exit from mitosis , T852 is dephosphorylated by Cdc1... | [
"In metazoans , transcription is arrested during mitosis .",
"Previous studies have established that mitotic repression of cellular transcription is mediated by Cdk1/cyclin B-dependent phosphorylation of basal transcription factors that nucleate transcription complex formation .",
"Repression of rDNA transcript... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"bacteriology",
"organismal evolution",
"microbial mutation",
"bacteriophages",
"microbiology",
"viruses",
"mutation",
"genetic predisposition",
"lysogeny",
"microbial evolution",
"population biology",
"viral replication",
"population metrics",
"point mutation",
"bacterial evolution",
... | Leaky resistance and the conditions for the existence of lytic bacteriophage | journal.pbio.2005971 | null | [
[
"The viruses of bacteria and archaea , phage , for brevity and generality , are touted to be the most abundant organisms on Earth [1] .",
"Research with phage , and particularly but not exclusively those that infect E . coli , have played a major role in the development of the contemporary concept of the ... | [
"In experimental cultures , when bacteria are mixed with lytic ( virulent ) bacteriophage , bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria .",
"Following the ascent of resistant mutants , the densities of bacteria in these simple communities become limited by... | [
"While it is clear that bacteriophage abound in bacterial communities , their role in the ecology and evolution of these communities remains poorly understood .",
"Fundamental questions remain unanswered , such as , are phage regulating the population densities of their host bacteria ?",
"And how are virulent p... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"parastic protozoans",
"immunity",
"innate immunity",
"toxoplasma gondii",
"immunology",
"protozoology",
"biology",
"microbiology"
] | Inflammasome Sensor NLRP1 Controls Rat Macrophage Susceptibility to Toxoplasma gondii | journal.ppat.1003927 | null | [
[
"Toxoplasma gondii is an obligate intracellular parasite , for which different host species or strains within a species display variable susceptibilities .",
"Different Toxoplasma strains also differ in virulence within the same host , suggesting variation in effectors among parasite strains and/or their ... | [
"Toxoplasma gondii is an intracellular parasite that infects a wide range of warm-blooded species .",
"Rats vary in their susceptibility to this parasite .",
"The Toxo1 locus conferring Toxoplasma resistance in rats was previously mapped to a region of chromosome 10 containing Nlrp1 .",
"This gene encodes an ... | [
"Inflammasomes are multiprotein complexes that are a major component of the innate immune system .",
"They contain “sensor” proteins that are responsible for detecting various microbial and environmental danger signals and function by activating caspase-1 , an enzyme that mediates cleavage and release of the pro-... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"medicine and health sciences",
"reproductive system",
"maternal health",
"obstetrics and gynecology",
"reproductive physiology",
"endocrine physiology",
"epithelial cells",
"women's health",
"pregnancy",
"animal cells",
"proteins",
"endocrinology",
"gene expression",
... | CUZD1 is a critical mediator of the JAK/STAT5 signaling pathway that controls mammary gland development during pregnancy | journal.pgen.1006654 | null | [
[
"In the mammary gland , development of an extensive ductal network during puberty and formation of lobuloalveolar units during pregnancy are critical events required for lactation .",
"These complex developmental processes are regulated by a variety of signaling cues , including the steroid hormones 17β-e... | [
"In the mammary gland , genetic circuits controlled by estrogen , progesterone , and prolactin , act in concert with pathways regulated by members of the epidermal growth factor family to orchestrate growth and morphogenesis during puberty , pregnancy and lactation .",
"However , the precise mechanisms underlying... | [
"In the mammary gland , genetic circuits controlled by the hormones , estrogen , progesterone and prolactin , act in concert with pathways regulated by members of the epidermal growth factor family to orchestrate growth and morphogenesis during puberty , pregnancy and lactation .",
"We have identified CUZD1 as a ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"circuit models",
"motor systems",
"computational neuroscience",
"biology",
"neuroscience",
"neurophysiology"
] | Human Motor Cortical Activity Is Selectively Phase-Entrained on Underlying Rhythms | journal.pcbi.1002655 | null | [
[
"Human motor behaviors such as reaching , grasping and speaking , are executed and controlled by the somatomotor regions of the cerebral cortex , which are located immediately anterior and posterior of the central sulcus .",
"This peri-central system is known to manifest a 12–20 Hz electrical oscillation ... | [
"The functional significance of electrical rhythms in the mammalian brain remains uncertain .",
"In the motor cortex , the 12–20 Hz beta rhythm is known to transiently decrease in amplitude during movement , and to be altered in many motor diseases .",
"Here we show that the activity of neuronal populations is ... | [
"We have long known that there are rhythmic oscillations in the mammalian brain .",
"Although the power in these rhythms changes during behavior , their relevance for brain function has been something of a mystery .",
"In this study , the particular role of rhythms in human motor cortex was studied both during ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology",
"viruses and cancer",
"biology",
"microbiology"
] | HPV16 E7 Protein and hTERT Proteins Defective for Telomere Maintenance Cooperate to Immortalize Human Keratinocytes | journal.ppat.1003284 | null | [
[
"Cell immortality is a hallmark of cancer cells [1] and the high-risk oncogenic HPVs encode two major transforming genes , E6 and E7 , which are required for the immortalization of human primary genital keratinocytes [2] , [3] .",
"These two oncogenes are uniformly retained and expressed in cervical cance... | [
"Previous studies have shown that wild-type human telomerase reverse transcriptase ( hTERT ) protein can functionally replace the human papillomavirus type 16 ( HPV-16 ) E6 protein , which cooperates with the viral E7 protein in the immortalization of primary keratinocytes .",
"In the current study , we made the ... | [
"The human papillomaviruses ( HPVs ) are critical elements in the etiology of cervical cancer , as well as several other human cancers .",
"The E6 protein , in combination with the E7 protein of these viruses , immortalizes epithelial cells and increases the expression of the hTERT protein .",
"In the current s... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Temporal Coordination of Carbohydrate Metabolism during Mosquito Reproduction | journal.pgen.1005309 | null | [
[
"The ability of multicellular organisms to maintain metabolic homeostasis and respond to changing energy requirements during development , reproduction and stress represents an essential adaptation critical for survival and evolutionary success .",
"Thus , it is important to decipher regulatory mechanisms... | [
"Hematophagous mosquitoes serve as vectors of multiple devastating human diseases , and many unique physiological features contribute to the incredible evolutionary success of these insects .",
"These functions place high-energy demands on a reproducing female mosquito , and carbohydrate metabolism ( CM ) must be... | [
"Mosquitoes transmit numerous devastating human diseases due to their obligatory hematophagy that is required for the efficient reproduction .",
"Metabolism must be synchronized with high energetic needs of a female mosquito for host seeking , blood feeding and rapid egg development .",
"Each reproductive cycle... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genomics",
"genetics and genomics/comparative genomics",
"genetics and genomics/functional genomics",
"genetics and genomics/gene expression",
"evolutionary biology/genomics",
"neuroscience/neurodevelopment"
] | Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain | journal.pgen.1000617 | null | [
[
"The mammalian genome displays a complex and extensive pattern of interlaced transcription of protein-coding genes and thousands of non-coding RNA ( ncRNA; see Materials and Methods for definitions ) loci [1] .",
"Exons from ncRNA loci may overlap on the same ( sense ) , or opposite ( antisense ) , strand... | [
"Besides protein-coding mRNAs , eukaryotic transcriptomes include many long non-protein-coding RNAs ( ncRNAs ) of unknown function that are transcribed away from protein-coding loci .",
"Here , we have identified 659 intergenic long ncRNAs whose genomic sequences individually exhibit evolutionary constraint , a h... | [
"Virtually all of the eukaryotic genome is transcribed , yet far from all transcripts encode protein .",
"Very little is known about the functions of most non-coding transcripts or , indeed , whether they convey functions at all .",
"Among all such transcripts , we have chosen to consider long non-coding RNAs (... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant science",
"plant microbiology",
"plant biology",
"plant pathogens",
"microbial pathogens",
"plant pathology",
"biology",
"microbiology"
] | Phytophthora sojae Avirulence Effector Avr3b is a Secreted NADH and ADP-ribose Pyrophosphorylase that Modulates Plant Immunity | journal.ppat.1002353 | null | [
[
"Plant innate immunity , which has been continuously refined by challenges from a diversity of pathogens during evolution , employs at least two defense systems in response to pathogen attacks [1] .",
"One is basal defense through host receptor recognition of conserved pathogen-associated molecular patter... | [
"Plants have evolved pathogen-associated molecular pattern ( PAMP ) -triggered immunity ( PTI ) and effector-triggered immunity ( ETI ) to protect themselves from infection by diverse pathogens .",
"Avirulence ( Avr ) effectors that trigger plant ETI as a result of recognition by plant resistance ( R ) gene produ... | [
"Phytophthora , a group of notorious oomycete pathogens , damages a very wide range of crop , vegetable , pasture and horticultural plants , generating great losses to agricultural production annually .",
"Disease outcomes between plants and Phytophthora pathogens often depend on whether plants carry resistance (... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Failure of PCR to Detect Treponema pallidum ssp. pertenue DNA in Blood in Latent Yaws | journal.pntd.0003905 | null | [
[
"Yaws , caused by infection with Treponema pallidum ssp .",
"pertenue[1] , is targeted for eradication by 2020[2] .",
"The organism is closely related to Treponema pallidum ssp .",
"pallidum , the causative agent of venereal syphilis .",
"The mainstay of the World Health Organization ( WHO ) e... | [
"Yaws , caused by Treponema pallidum ssp .",
"pertenue , is a neglected tropical disease closely related to venereal syphilis and is targeted for eradication by 2020 .",
"Latent yaws represents a diagnostic challenge , and current tools cannot adequately distinguish between individuals with true latent infectio... | [
"Yaws is a bacterial infection closely related to syphilis .",
"The WHO has launched a worldwide campaign to eradicate yaws by 2020 .",
"For each clinically apparent case , many close contacts are infected but do not show clinical signs , which is called latent yaws .",
"Currently , diagnosis for these patien... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"nucleic acid synthesis",
"microbial mutation",
"pathology and laboratory medicine",
"hepacivirus",
"pathogens",
"biological cultures",
"microbiology",
"mathematical models",
"viruses",
"rna viruses",
"cell cultures",
"rna synthesis",
"chemical synthesis",
... | NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains | journal.ppat.1006343 | null | [
[
"Direct-acting antivirals ( DAAs ) targeting the hepatitis C virus ( HCV ) include specific inhibitors of the NS3/4A protease/helicase , the NS5B RNA-dependent RNA polymerase and the NS5A protein .",
"Combination therapies with two or more DAAs can result in a sustained virological response ( SVR ) in mos... | [
"Hepatitis C virus ( HCV ) RNA is synthesized by the replicase complex ( RC ) , a macromolecular assembly composed of viral non-structural proteins and cellular co-factors .",
"Inhibitors of the HCV NS5A protein block formation of new RCs but do not affect RNA synthesis by pre-formed RCs .",
"Without new RC for... | [
"Inhibitors targeting the HCV NS5A protein are a key component of highly effective interferon-free combination therapies for chronic hepatitis C . Despite their high potency against HCV , the precise details of their mode of action are poorly understood .",
"They are known to block assembly and release of virus p... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Y Fuse? Sex Chromosome Fusions in Fishes and Reptiles | journal.pgen.1005237 | null | [
[
"The number of chromosomes is one of the most fundamental features of a eukaryotic genome .",
"Chromosome number varies , both between closely related species and within species , and such variation can contribute to divergent adaptation and speciation [1–5] .",
"Shifts in chromosome number typically ... | [
"Chromosomal fusion plays a recurring role in the evolution of adaptations and reproductive isolation among species , yet little is known of the evolutionary drivers of chromosomal fusions .",
"Because sex chromosomes ( X and Y in male heterogametic systems , Z and W in female heterogametic systems ) differ in th... | [
"Chromosome number is a basic feature of the eukaryotic genome that has important consequences for recombination , segregation , and other processes .",
"Despite a century of research on the evolution of karyotype , however , we still have little understanding of the evolutionary forces that enable chromosomal fu... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"clinical research design",
"tropical diseases",
"plasmodium falciparum",
"parasitic diseases",
"parasitic protozoans",
"parasitology",
"observational studies",
"research design",
"protozoans",
"cohort studies",
"neglected tropical diseases",
"zoology",
"res... | Co-infection of Long-Term Carriers of Plasmodium falciparum with Schistosoma haematobium Enhances Protection from Febrile Malaria: A Prospective Cohort Study in Mali | journal.pntd.0003154 | null | [
[
"Malaria and schistosomiasis , caused by the protozoan Plasmodium and the trematode helminth Schistosoma , respectively , impose tremendous public health burdens in tropical and subtropical countries .",
"Whereas malaria afflicts ∼210 million people annually , with ∼0 . 6 million malaria deaths in 2012 ca... | [
"Malaria and schistosomiasis often overlap in tropical and subtropical countries and impose tremendous disease burdens; however , the extent to which schistosomiasis modifies the risk of febrile malaria remains unclear .",
"We evaluated the effect of baseline S . haematobium mono-infection , baseline P . falcipar... | [
"The parasitic diseases malaria and schistosomiasis are tremendous public health burdens , each affecting over 200 million people worldwide with substantial geographic overlap in sub-Saharan Africa .",
"Understanding how schistosomiasis influences the human immune response to Plasmodium , the agent of malaria , c... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"flow cytometry",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"enterococcus infections",
"pathogens",
"immunology",
"cell processes",
"microbiology",
"vertebrates",
"animals",
"animal models",
"osteichthyes",
"bacterial diseases",
... | Bacterial size matters: Multiple mechanisms controlling septum cleavage and diplococcus formation are critical for the virulence of the opportunistic pathogen Enterococcus faecalis | journal.ppat.1006526 | null | [
[
"Enterococci are Gram-positive commensal bacteria colonizing the gastrointestinal tract of humans .",
"They are opportunistic nosocomial pathogens that can cause a wide range of life-threatening infections in immunocompromised patients or following antibiotic-induced dysbiosis [1] .",
"The emergence o... | [
"Enterococcus faecalis is an opportunistic pathogen frequently isolated in clinical settings .",
"This organism is intrinsically resistant to several clinically relevant antibiotics and can transfer resistance to other pathogens .",
"Although E . faecalis has emerged as a major nosocomial pathogen , the mechani... | [
"Enterococcus faecalis is a commensal bacterium that colonizes the gastrointestinal tract of humans .",
"This organism is an opportunistic pathogen that can cause a wide range of life-threatening infections in hospital settings .",
"Despite the identification of several virulence factors , the mechanisms by whi... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"respiratory infections",
"pathology and laboratory medicine",
"viral transmission and infection",
"gene regulation",
"pathogens",
"microbiology",
"orthomyxoviruses",
"pulmonology",
"epithelial cells",
"viruses",
"chronic obstructive pulmonary disease",
"rna v... | Glucocorticoid Insensitivity in Virally Infected Airway Epithelial Cells Is Dependent on Transforming Growth Factor-β Activity | journal.ppat.1006138 | null | [
[
"Exacerbations of asthma and chronic obstructive pulmonary disease ( COPD ) are commonly associated with airway viral infection , including respiratory syncytial virus ( RSV ) , human rhinovirus ( RV ) and influenza A virus ( IAV ) [1 , 2] .",
"RSV infection is a major cause of acute respiratory disease (... | [
"Asthma and chronic obstructive pulmonary disease ( COPD ) exacerbations are commonly associated with respiratory syncytial virus ( RSV ) , rhinovirus ( RV ) and influenza A virus ( IAV ) infection .",
"The ensuing airway inflammation is resistant to the anti-inflammatory actions of glucocorticoids ( GCs ) .",
... | [
"In this study , we investigate how respiratory viral infection interferes with the anti-inflammatory actions of glucocorticoid ( GC ) drugs , which are a highly effective group of anti-inflammatory agents widely used in the treatment of chronic inflammatory airway diseases , including asthma and chronic obstructiv... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"decision making",
"engineering and technology",
"numerical integration",
"signal processing",
"experimental design",
"social sciences",
"neuroscience",
"simulation and modeling",
"research design",
"mathematics",
"cognition",
"vision",
"inhibitions",
"research and analysis methods",
"be... | Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism | journal.pcbi.1004667 | null | [
[
"A number of computational models have been proposed to account for binary decisions based on fluctuating evidence ( see Computational Method for a quantitative description of the models ) .",
"One of these models , the drift–diffusion model ( DDM; [7 , 19 , 30 , 31] employs two accumulators racing each o... | [
"Perceptual decisions are thought to be mediated by a mechanism of sequential sampling and integration of noisy evidence whose temporal weighting profile affects the decision quality .",
"To examine temporal weighting , participants were presented with two brightness-fluctuating disks for 1 , 2 or 3 seconds and w... | [
"An important process that supports decision-making is the integration of evidence over time , which optimizes decision quality by enhancing the signal to noise ratio .",
"The nature of this process depends critically on the weight given to evidence across time: which information has more impact—early , intermedi... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Model"
] | [] | Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network | journal.pcbi.1004535 | null | [
[
"Cell migration in the three dimensional extracellular matrix ( ECM ) plays a crucial role in a wide variety of biophysical processes , such as wound healing , morphogenesis , angiogenesis , tumor growth , and cancer invasion [1 , 2] .",
"Migration dynamics in 3D are significantly different from those obs... | [
"The dynamics of filopodia interacting with the surrounding extracellular matrix ( ECM ) play a key role in various cell-ECM interactions , but their mechanisms of interaction with the ECM in 3D environment remain poorly understood .",
"Based on first principles , here we construct an individual-based , force-bas... | [
"Cell invasion into a 3D ECM requires substantial cellular traction forces as well as the degradation of ECM .",
"We are interested in how filopodia gain traction forces from the surrounding collagen fibers in the degradable ECM .",
"Thereby , to create the overall computational model , we integrated four modul... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/germ cells",
"evolutionary biology/animal genetics",
"genetics and genomics/animal genetics",
"marine and aquatic sciences/genetics, genomics, and barcoding",
"genetics and genomics/gene expression",
"marine and aquatic sciences/evolutionary biology",
"cell biology/developmental m... | Sex Reversal in Zebrafish fancl Mutants Is Caused by Tp53-Mediated Germ Cell Apoptosis | journal.pgen.1001034 | null | [
[
"The existence of two differentiated sexes is common among animals and yet the mechanisms that determine sex are amazingly diverse .",
"Among vertebrates , for instance , some species use primarily genetic factors and others rely on environmental factors to cause embryonic gonads to become testes or ovari... | [
"The molecular genetic mechanisms of sex determination are not known for most vertebrates , including zebrafish .",
"We identified a mutation in the zebrafish fancl gene that causes homozygous mutants to develop as fertile males due to female-to-male sex reversal .",
"Fancl is a member of the Fanconi Anemia/BRC... | [
"Zebrafish has become an important model for understanding vertebrate development and human disease , yet the genetic mechanisms that regulate gonad fate to determine zebrafish sex remain elusive .",
"In this work , we describe a mutation in the fancl gene that causes zebrafish to develop exclusively as male due ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cardiovascular disorders/hypertension",
"genetics and genomics/genetics of disease",
"genetics and genomics/complex traits"
] | Genome-Wide Association Study of Blood Pressure Extremes Identifies Variant near UMOD Associated with Hypertension | journal.pgen.1001177 | null | [
[
"Hypertension is a major cardiovascular risk factor with a global prevalence of 26 . 4% in 2000 , projected to increase to 29 . 2% by 2025 , and is the leading contributor to global mortality[1] , [2] .",
"While epidemiologically BP is a trait continuously associated with an increased risk of cardiovascul... | [
"Hypertension is a heritable and major contributor to the global burden of disease .",
"The sum of rare and common genetic variants robustly identified so far explain only 1%–2% of the population variation in BP and hypertension .",
"This suggests the existence of more undiscovered common variants .",
"We con... | [
"Hypertension is the leading contributor to global mortality with a global prevalence of 26 . 4% in 2000 , projected to increase to 29 . 2% by 2025 .",
"While 50%–60% of population variation in blood pressure can be attributable to additive genetic factors , all the genetic variants robustly identified so far exp... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"inflammatory diseases",
"children",
"medicine and health sciences",
"pathology and laboratory medicine",
"chlamydia trachomatis",
"pathogens",
"immunology",
"tropical diseases",
"microbiology",
"bacterial diseases",
"research design",
"age groups",
"signs and symptoms",
"eye diseases",
... | Progression of scarring trachoma in Tanzanian children: A four-year cohort study | journal.pntd.0007638 | null | [
[
"Sight loss from trachoma , the leading infectious cause of blindness , is the end result of an inflammatory-scarring process .",
"Starting from early childhood , people growing-up in a trachoma endemic community may be repeatedly exposed to ocular challenge with Chlamydia trachomatis , the causative orga... | [
"Trachoma is a progressive blinding disease initiated by infection of the conjunctiva with Chlamydia trachomatis .",
"Repeated infections are thought to cause chronic inflammation , which drives scarring , leading to in-turning of the eyelids .",
"The relationship between C . trachomatis , clinical inflammation... | [
"Trachoma is the leading cause of preventable blindness worldwide and is targeted for elimination as a public health problem by 2020 .",
"The natural history of trachoma is not completely understood however .",
"We conducted a four-year longitudinal study in a trachoma-endemic area of northern Tanzania with det... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immunity",
"immunology",
"microbiology",
"biology",
"parasitology",
"immunotherapy"
] | Use of a Recombinant Cysteine Proteinase from Leishmania (Leishmania) infantum chagasi for the Immunotherapy of Canine Visceral Leishmaniasis | journal.pntd.0002729 | null | [
[
"Zoonotic visceral leishmaniasis ( VL ) is caused by Leishmania ( Leishmania ) infantum chagasi in Mediterranean , Middle-East , Asian countries , and Latin America and dogs are the main domestic reservoirs of this zoonosis which has resulted in an annual incidence of 40 , 100–75 , 000 new human cases [1] , [... | [
"A recombinant cysteine proteinase from Leishmania ( Leishmania ) infantum chagasi ( rLdccys1 ) was previously shown to induce protective immune responses against murine and canine visceral leishmaniasis .",
"These findings encouraged us to use rLdccys1 in the immunotherapy of naturally infected dogs from Teresin... | [
"Visceral leishmaniasis ( VL ) is an important public health problem and dogs are the main domestic reservoirs of zoonotic VL which has resulted in an annual incidence of 40 , 100–75 , 500 new human cases .",
"Because canine VL chemotherapy is limited by the low efficacy of drugs currently used for human VL treat... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Serological proteomic screening and evaluation of a recombinant egg antigen for the diagnosis of low-intensity Schistosoma mansoni infections in endemic area in Brazil | journal.pntd.0006974 | null | [
[
"Schistosomiasis remains as a major worldwide public health problem .",
"Since it is a disease of poverty and limited sanitary facilities , the disease has proved difficult to control for centuries [1] .",
"Schistosomiasis afflicts low-income populations in tropical and subtropical regions with varyin... | [
"Despite decades of use of control programs , schistosomiasis remains a global public health problem .",
"To further reduce prevalence and intensity of infection , or to achieve the goal of elimination in low-endemic areas , there needs to be better diagnostic tools to detect low-intensity infections in low-endem... | [
"Schistosomiasis remains a serious global public health problem .",
"Detecting parasite eggs in patient stool samples using the KK method is the standard diagnostic recommended by the World Health Organization ( WHO ) for infection by S . mansoni .",
"As a result of intensive control strategies , many previousl... | 2019 |
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