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",
"Methods"
] | [] | High Accuracy Decoding of Dynamical Motion from a Large Retinal Population | journal.pcbi.1004304 | null | [
[
"Our current understanding of how sensory neurons collectively encode information about the environment is limited .",
"Being able to “read out” this information from neural ensemble activity is a major challenge in neuroscience .",
"Discriminating among a discrete set of stimuli based on their sensor... | [
"Motion tracking is a challenge the visual system has to solve by reading out the retinal population .",
"It is still unclear how the information from different neurons can be combined together to estimate the position of an object .",
"Here we recorded a large population of ganglion cells in a dense patch of s... | [
"It remains unclear how the brain is able to track the location of moving objects by reading the spike trains received from the retina .",
"To address this question , we recorded a large population of ganglion cells , the retinal output , in a dense patch of salamander and guinea pig retinas while displaying a ba... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/immunomodulation",
"immunology/antigen processing and recognition",
"virology/immune evasion"
] | Varicellovirus UL49.5 Proteins Differentially Affect the Function of the Transporter Associated with Antigen Processing, TAP | journal.ppat.1000080 | null | [
[
"Evolving under the selective pressure of the host immune system , herpesviruses have developed countermeasures to prevent recognition of infected cells by cytotoxic CD8+ T lymphocytes ( CTLs ) .",
"CTLs recognize viral antigens presented as peptides bound to major histocompatibility complex ( MHC ) class... | [
"Cytotoxic T-lymphocytes play an important role in the protection against viral infections , which they detect through the recognition of virus-derived peptides , presented in the context of MHC class I molecules at the surface of the infected cell .",
"The transporter associated with antigen processing ( TAP ) p... | [
"Herpesviruses have the conspicuous property that they persist for life in the infected host .",
"This is also the case for varicelloviruses , a large subfamily of herpesviruses with representatives in humans ( varicella zoster virus or VZV ) , cattle ( bovine herpesvirus 1 or BHV-1 ) , pigs ( pseudorabies virus ... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"ecology",
"virology",
"biology",
"microbiology",
"biodiversity",
"host-pathogen interaction"
] | Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System | journal.ppat.1002796 | null | [
[
"Understanding the relationship between the risk of infectious diseases and host ecology is a long-standing goal of biological research , central for the management of current infectious diseases and for preventing the emergence of new ones .",
"Indeed , changes in host ecology are among the most frequent... | [
"The effect of biodiversity on the ability of parasites to infect their host and cause disease ( i . e . disease risk ) is a major question in pathology , which is central to understand the emergence of infectious diseases , and to develop strategies for their management .",
"Two hypotheses , which can be conside... | [
"Biodiversity has been proposed as a major ecological factor determining disease prevalence .",
"However , the relationship between biodiversity and disease risk remains underexplored .",
"Few studies focus on host-virus systems and , particularly on plant viruses .",
"To address this subject the prevalence o... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"biochemistry",
"physiology",
"mus (mouse)",
"neuroscience",
"genetics and genomics"
] | Inducible and Reversible Clock Gene Expression in Brain Using the tTA System for the Study of Circadian Behavior | journal.pgen.0030033 | null | [
[
"Most organisms possess an endogenous circadian system that drives the daily timing of many physiological and behavioral processes .",
"Genetic screens , spontaneous mutants , and gene-targeting approaches have been key in unraveling the essential set of genes underlying the circadian mechanism in mammals... | [
"The mechanism of circadian oscillations in mammals is cell autonomous and is generated by a set of genes that form a transcriptional autoregulatory feedback loop .",
"While these “clock genes” are well conserved among animals , their specific functions remain to be fully understood and their roles in central ver... | [
"Although significant progress has been made in unraveling the molecular mechanism of circadian clocks in mammals , previous work has focused on germline mutations and in vitro methods for analysis .",
"To address the function of clock genes , it is necessary to develop tools to manipulate circadian genes in a co... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis",
"microbiology/immunity to infections"
] | Importance of the Collagen Adhesin Ace in Pathogenesis and Protection against Enterococcus faecalis Experimental Endocarditis | journal.ppat.1000716 | null | [
[
"Enterococci are gram-positive cocci of intestinal origin first reported as a cause of infective endocarditis ( IE ) in 1899 [1] .",
"They were recognized as the 3rd most common cause of IE as early as the 1920's , and have remained the 3rd most common cause of community onset IE since then with Enterococ... | [
"Ace is an adhesin to collagen from Enterococcus faecalis expressed conditionally after growth in serum or in the presence of collagen .",
"Here , we generated an ace deletion mutant and showed that it was significantly attenuated versus wild-type OG1RF in a mixed infection rat endocarditis model ( P<0 . 0001 ) ,... | [
"Enterococcus faecalis was recognized as a common cause of infective endocarditis ( IE ) by the early 1900s .",
"It is still third in community-onset IE , but is the second most common cause of hospital-associated IE .",
"Complications due to E . faecalis IE include congestive heart failure , septic emboli and ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Characterization of a Novel Human-Specific STING Agonist that Elicits Antiviral Activity Against Emerging Alphaviruses | journal.ppat.1005324 | null | [
[
"The innate immune system includes an array of sentinel proteins termed pattern recognition receptors ( PRRs ) that sense and react to microbe- and danger-associated molecular patterns ( reviewed in [1] ) .",
"These patterns are often constituents or replication intermediates of intracellular ( especially... | [
"Pharmacologic stimulation of innate immune processes represents an attractive strategy to achieve multiple therapeutic outcomes including inhibition of virus replication , boosting antitumor immunity , and enhancing vaccine immunogenicity .",
"In light of this we sought to identify small molecules capable of act... | [
"STING is a pattern recognition receptor of cyclic dinucleotides as well as an innate immune adaptor protein that enables signaling from cytoplasmic receptors to the transcription factor interferon regulatory factor 3 .",
"Initiation of these pathways leads to the expression of type I interferons and proteins ass... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine and health sciences",
"honey bees",
"sociology",
"social sciences",
"animals",
"reproductive physiology",
"social systems",
"developmental biology",
"mutation",
"nutrition",
"nonsense mutation",
"sequence motif analysis",
"bees",
"research and analysis methods"... | A genetic switch for worker nutrition-mediated traits in honeybees | journal.pbio.3000171 | In honeybees, nutrition drives dimorphic size development of reproductive organs in fertile queens and sterile workers. A study using the first induced morphological mutants in honeybees demonstrates that this developmental plasticity requires a genetic program that is switched on by the “feminizer” gene. | [
[
"Highly social insects are characterized by caste dimorphism , with morphologically and physiologically distinct reproductive queens and more or less sterile workers [1–3] .",
"In honeybees , the development of two distinct phenotypes is controlled by different nutrition , and it is a prominent example of... | [
"Highly social insects are characterized by caste dimorphism , with distinct size differences of reproductive organs between fertile queens and the more or less sterile workers .",
"An abundance of nutrition or instruction via diet-specific compounds has been proposed as explanations for the nutrition-driven quee... | [
"In honeybees , nutrition drives dimorphic size development of reproductive organs in fertile queens and sterile workers .",
"The first induced morphological mutants in honeybees demonstrate that this developmental plasticity requires a genetic program that is switched “ON” by the feminizer ( fem ) gene ."
] | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"bacterial diseases",
"infectious diseases",
"bacteremia",
"sepsis",
"infectious disease modeling",
"critical care and emergency medicine"
] | NOD2-mediated Suppression of CD55 on Neutrophils Enhances C5a Generation During Polymicrobial Sepsis | journal.ppat.1003351 | null | [
[
"Sepsis is a complex dysregulated inflammatory response in infection , which causes multiple organ dysfunction and coagulopathy , often resulting in death [1] , [2] .",
"Pro-inflammatory cytokines contribute to an overwhelming inflammatory immune response in the early phase of sepsis , whereas anti-inflam... | [
"Nucleotide-binding oligomerization domain ( NOD ) 2 is a cytosolic protein that plays a defensive role in bacterial infection by sensing peptidoglycans .",
"C5a , which has harmful effects in sepsis , interacts with innate proteins .",
"However , whether NOD2 regulates C5a generation during sepsis remains to b... | [
"Nucleotide-binding oligomerization domain ( NOD ) 2 is a cytosolic protein that senses peptidoglycans of bacteria and exerts a defensive effect on bacterial infection .",
"Sepsis is a complex dysregulated inflammatory response in bacterial infection , causing multiple organ dysfunction , coagulopathy , and fatal... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"infectious disease epidemiology",
"influenza",
"pathogens",
"social sciences",
"human mobility",
"population biology",
"human geography",
"infectious diseases",
"geography",
"epidemiology",
"disease vectors",
"population... | Differential mobility and local variation in infection attack rate | journal.pcbi.1006600 | null | [
[
"The spatial heterogeneity of infectious disease incidence at large scales presents numerous intervention opportunities and challenges .",
"Maps of malaria prevalence [1] have been used to target additional surveillance and to prioritize countries and geographical regions for additional intervention inves... | [
"Infectious disease transmission is an inherently spatial process in which a host’s home location and their social mixing patterns are important , with the mixing of infectious individuals often different to that of susceptible individuals .",
"Although incidence data for humans have traditionally been aggregated... | [
"We know that some places have higher rates of infectious disease than others .",
"At the moment , we usually only measure these differences for large towns and cities , though modern data allows us to track movement at much higher resolution .",
"In this paper , we used a computer simulation of an epidemic to ... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"gut bacteria",
"helminths",
"tropical diseases",
"geographical locations",
"india",
"parasitic diseases",
"parasitic protozoans",
"animals",
"protozoans",
"enterobacteriaceae",
"escherichia",
"neglected tropical diseases",
"cellular struc... | Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India | journal.pntd.0007444 | null | [
[
"Visceral leishmaniasis ( VL ) , also known as kala-azar , is a potentially fatal disease caused by obligate intracellular parasites of the Leishmania donovani species complex .",
"VL is a serious public health problem in indigenous and rural populations in India , causing high morbidity and mortality , a... | [
"Visceral leishmaniasis ( VL ) caused by Leishmania donovani remains of public health concern in rural India .",
"Those at risk of VL are also at risk of other neglected tropical diseases ( NTDs ) including soil transmitted helminths .",
"Intestinal helminths are potent regulators of host immune responses somet... | [
"Visceral leishmaniasis ( VL ) , also known as kala-azar , is a potentially fatal disease caused by intracellular parasites of the Leishmania donovani complex .",
"VL is a serious public health problem in rural India , causing high morbidity and mortality , as well as major costs to local and national health budg... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"public health and epidemiology",
"epidemiology",
"infectious disease epidemiology",
"ophthalmology",
"neglected tropical diseases",
"trachoma"
] | Relationship between Immediate Post-Operative Appearance and 6-Week Operative Outcome in Trichiasis Surgery | journal.pntd.0001718 | null | [
[
"Despite a World Health Organization ( WHO ) initiative in 1998 to eliminate trachoma by 2020 , this disease continues to plague poor regions of many developing countries .",
"Even if active trachoma were to be eradicated today , millions of individuals would be at risk of blindness due to the trichiasis ... | [
"Surgical technique , including suture placement and tension , is believed to contribute to the outcome of bilamellar tarsal rotation surgery for trachomatous trichiasis .",
"However , the immediate post-operative appearance that minimizes the chance of recurrence and other adverse outcomes has not been investiga... | [
"Trichiasis is a potentially blinding consequence of trachoma .",
"The World Health Organization has promoted the bilamellar tarsal rotation ( BLTR ) procedure as a treatment for trichiasis from trachoma .",
"Even if trachoma were to be eradicated today , a great number of individuals would still develop trichi... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"antimicrobials",
"infectious diseases",
"medicine and health sciences",
"pathology and laboratory medicine",
"emerging infectious diseases",
"host-pathogen interactions",
"virology",
"emerging viral diseases",
"microbial control",
"biology and life sciences",
"viral structure",
"microbiology"... | Binding of Glutathione to Enterovirus Capsids Is Essential for Virion Morphogenesis | journal.ppat.1004039 | null | [
[
"Enteroviruses , belonging to the family of the Picornaviridae , are non-enveloped , icosahedral viruses with a positive , single-stranded genome .",
"Enteroviruses comprise many important pathogens of humans and animals .",
"Although most enterovirus infections subside asymptomatically or mildly , th... | [
"Enteroviruses ( family of the Picornaviridae ) cover a large group of medically important human pathogens for which no antiviral treatment is approved .",
"Although these viruses have been extensively studied , some aspects of the viral life cycle , in particular morphogenesis , are yet poorly understood .",
"... | [
"Enteroviruses contain many significant human pathogens , including poliovirus , enterovirus 71 , coxsackieviruses and rhinoviruses .",
"Most enterovirus infections subside mild or asymptomatically , but may also result in severe morbidity and mortality .",
"Here , we report on the mechanism of antiviral action... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Low-level Laser Therapy to the Mouse Femur Enhances the Fungicidal Response of Neutrophils against Paracoccidioides brasiliensis | journal.pntd.0003541 | null | [
[
"Paracoccidioides brasiliensis ( Pb ) is a non-sexual thermodimorphic fungus that exists in either a mycelium or a yeast form; the latter being pathogenic to humans and can cause an important and neglected systemic infection called paracoccidioidomycosis ( PCM ) .",
"The likelihood of infection and its se... | [
"Neutrophils ( PMN ) play a central role in host defense against the neglected fungal infection paracoccidioidomycosis ( PCM ) , which is caused by the dimorphic fungus Paracoccidioides brasiliensis ( Pb ) .",
"PCM is of major importance , especially in Latin America , and its treatment relies on the use of antif... | [
"PCM triggers a typical granulomatous inflammatory reaction with PMN playing a major role; these inflammatory cells are crucial in the initial stages of PCM , participating in the innate immune reaction and also directing the acquired immune response in the later stages .",
"In some PCM patients , these immune me... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology",
"geography",
"gis",
"zoology",
"entomology",
"epidemiology",
"earth sciences",
"biology",
"population biology",
"spatial epidemiology",
"cartography"
] | Spatial Heterogeneity and Risk Maps of Community Infestation by Triatoma infestans in Rural Northwestern Argentina | journal.pntd.0001788 | null | [
[
"Over the past 15 years , the burden of Chagas disease has been significantly reduced ( from an estimated ∼30 million human cases in 1990 to ∼9–11 million in 2006 ) as a consequence of direct actions promoted by several multinational regional initiatives [1] , [2] .",
"The key for such success has been th... | [
"Fifty years of residual insecticide spraying to control Triatoma infestans in the Gran Chaco region of northern Argentina , Paraguay and Bolivia shows that vertically coordinated interventions aiming at full coverage have limited effects and are unsustainable .",
"We quantified the spatial distribution of T . in... | [
"In the Southern Cone countries of South America , vectorborne transmission of Chagas disease persists in the Gran Chaco region of northern Argentina , Paraguay and Bolivia , where Triatoma infestans is the main vector .",
"More than 50 years of vector control in this region demonstrate that vertically coordinate... | 2012 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"computational chemistry",
"chemistry",
"microbiology",
"biology",
"biophysics",
"computational biology"
] | Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach | journal.pcbi.1003113 | null | [
[
"Microbial resistance presents a major challenge in the development of novel antibiotics because bacteria are continually developing new resistance mechanisms [1] .",
"The bacterial ribosome is a target for over 60% of antibiotics [2] , [3] , which bind at vital sites within both the 30S and 50S ribosomal... | [
"Resistance to macrolide antibiotics is conferred by mutation of A2058 to G or methylation by Erm methyltransferases of the exocyclic N6 of A2058 ( E . coli numbering ) that forms the macrolide binding site in the 50S subunit of the ribosome .",
"Ketolides such as telithromycin mitigate A2058G resistance yet rema... | [
"Bacterial resistance to antibiotics is a serious public health problem that requires the continuous development of new antibiotics .",
"Bacteria acquire resistance to macrolide antibiotics by ( 1 ) effluxing the drug from the cell , ( 2 ) modifying the drug , or ( 3 ) modifying the drug target ( i . e . , the 50... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Evaluation of Cardiac Involvement in Children with Dengue by Serial Echocardiographic Studies | journal.pntd.0003943 | null | [
[
"Infection by dengue viruses ( DENV ) results in clinical presentation ranging from asymptomatic infection to a fatal viral hemorrhagic fever characterized by plasma leakage and bleeding [1–3] .",
"Plasma leakage in dengue occurs around the time of defervescence , is localized primarily in the serosal cav... | [
"Infection with dengue virus results in a wide range of clinical manifestations from dengue fever ( DF ) , a self-limited febrile illness , to dengue hemorrhagic fever ( DHF ) which is characterized by plasma leakage and bleeding tendency .",
"Although cardiac involvement has been reported in dengue , the inciden... | [
"Dengue is a viral infection with a wide range of symptoms from a self-limiting fever called dengue fever ( DF ) to dengue hemorrhagic fever ( DHF ) which is characterized by leaky blood vessels and bleeding that can lead to shock in severe cases .",
"Abnormal heart function has been reported but the frequencies ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"open science",
"medicine and health sciences",
"diagnostic radiology",
"functional magnetic resonance imaging",
"social sciences",
"light",
"electrophysiology",
"neuroscience",
"electromagnetic radiation",
"magnetic resonance imaging",
"cognitive psychology",
"luminance",
"brain mapping",
... | The role of inferior frontal junction in controlling the spatially global effect of feature-based attention in human visual areas | journal.pbio.2005399 | null | [
[
"Attentional selection is the mechanism by which a subset of incoming information is processed preferentially .",
"Numerous studies have demonstrated that attentional selection can be based on a spatial location [1–7] .",
"Alternatively , attention can also select specific features independent of thei... | [
"Feature-based attention has a spatially global effect , i . e . , responses to stimuli that share features with an attended stimulus are enhanced not only at the attended location but throughout the visual field .",
"However , how feature-based attention modulates cortical neural responses at unattended location... | [
"Attentional selection is the mechanism by which relevant sensory information is processed preferentially .",
"Feature-based attention plays a key role in identifying an attentional target in a complex scene , because we often know the features of the target but not its exact location .",
"The ability to quickl... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal models",
"neurobiology of disease and regeneration",
"medicine and health sciences",
"model organisms",
"neurology",
"biology and life sciences",
"neuroscience",
"research and analysis methods"
] | The Wnt Receptor Ryk Reduces Neuronal and Cell Survival Capacity by Repressing FOXO Activity During the Early Phases of Mutant Huntingtin Pathogenicity | journal.pbio.1001895 | A study of Huntington's disease reveals that neurons might fail to cope with maintaining their function during the pre-symptomatic, pathogenic phases of HD, possibly due to the early repression of key longevity-promoting transcription factors by abnormal developmental signaling. | [
[
"Cell stress response factors are important for cells to maintain function in a large variety of normal and pathological contexts , including diseases linked to proteotoxicity [1] .",
"Among these factors , the FOXO family of Forkhead transcription factors is central to longevity and cellular homeostasis ... | [
"The Wnt receptor Ryk is an evolutionary-conserved protein important during neuronal differentiation through several mechanisms , including γ-secretase cleavage and nuclear translocation of its intracellular domain ( Ryk-ICD ) .",
"Although the Wnt pathway may be neuroprotective , the role of Ryk in neurodegenera... | [
"Neuronal cell decline in neurodegenerative disease can be caused by inherited mutations and involves neuronal dysfunction followed by neuronal death .",
"The ability of neurons to cope with the chronic stress induced by mutant protein expression may determine the course of their decline and eventual demise .",
... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"medicine and health sciences",
"body fluids",
"abdomen",
"geographical locations",
"vector-borne diseases",
"parasitic diseases",
"parasitic protozoans",
"invertebrate genomics",
"north america",
"protozoans",
"central america",
"guatemala",
"infectious diseases",
"animal genomics",
"pe... | Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata | journal.pntd.0006730 | null | [
[
"Chagas disease ( American trypanosomiasis ) is caused by the protozoan parasite Trypanosoma cruzi .",
"Considered a neglected disease by the World Health Organization , it is widespread in the Americas , where an estimated 70 million people are at risk of contracting the infection [1] .",
"The diseas... | [
"Chagas disease , considered a neglected disease by the World Health Organization , is caused by the protozoan parasite Trypanosoma cruzi , and transmitted by >140 triatomine species across the Americas .",
"In Central America , the main vector is Triatoma dimidiata , an opportunistic blood meal feeder inhabiting... | [
"Chagas disease is caused by the parasite Trypanosoma cruzi , which is spread by triatomine kissing bugs .",
"There are many biotic factors that influence the risk of disease transmission , including the strain of the parasite , the vector movement patterns , the community of microbes interacting with the parasit... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/fungal infections",
"infectious diseases/antimicrobials and drug resistance"
] | PKC Signaling Regulates Drug Resistance of the Fungal Pathogen Candida albicans via Circuitry Comprised of Mkc1, Calcineurin, and Hsp90 | journal.ppat.1001069 | null | [
[
"Microbial survival depends critically upon coordination of sensing environmental stimuli with control of the appropriate cellular responses .",
"As a consequence , microbes have evolved elaborate mechanisms to sense and respond to diverse environmental stresses , including oxidative stress , osmotic stre... | [
"Fungal pathogens exploit diverse mechanisms to survive exposure to antifungal drugs .",
"This poses concern given the limited number of clinically useful antifungals and the growing population of immunocompromised individuals vulnerable to life-threatening fungal infection .",
"To identify molecules that abrog... | [
"Treating fungal infections is challenging due to the emergence of drug resistance and the limited number of clinically useful antifungal drugs .",
"We screened a library of 1 , 280 pharmacologically active compounds to identify those that reverse resistance of the leading human fungal pathogen , Candida albicans... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"leptospira",
"pathology and laboratory medicine",
"pathogens",
"tropical diseases",
"microbiology",
"vertebrates",
"animals",
"mammals",
"dogs",
"bacterial diseases",
"neglected tropical diseases",
"molecular biology techniques",
"bacteria",
"bacterial pa... | Human Leptospirosis on Reunion Island, Indian Ocean: Are Rodents the (Only) Ones to Blame? | journal.pntd.0004733 | null | [
[
"Leptospirosis is a bacterial systemic infection , occasionally fatal , caused by the pathogenic spirochetes of the genus Leptospira .",
"Though claimed as the most widespread zoonosis in the world [1 , 2] , the disease is considered as emerging in many parts of the world .",
"Leptospirosis is most pr... | [
"Although leptospirosis is a zoonosis of major concern on tropical islands , the molecular epidemiology of the disease aiming at linking human cases to specific animal reservoirs has been rarely explored within these peculiar ecosystems .",
"Five species of wild small mammals ( n = 995 ) as well as domestic anima... | [
"Leptospirosis is a zoonosis caused by infection with pathogenic Leptospira species .",
"A broad range of animals , including rodents , pets and livestock , are maintenance hosts for leptospires .",
"However , assessing the relative importance of each host in the contamination of the environment and , in fine ,... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"organoids",
"medicine and health sciences",
"luciferase",
"vesicular stomatitis virus",
"pathology and laboratory medicine",
"enzymes",
"pathogens",
"biological cultures",
"enzymology",
"microbiology",
"viruses",
"rna viruses",
"organ cultures",
"digestive system",
"research and analysi... | Differential induction of interferon stimulated genes between type I and type III interferons is independent of interferon receptor abundance | journal.ppat.1007420 | null | [
[
"During viral infection interferons ( IFNs ) are the predominant cytokines made to combat viral replication and spread .",
"Following binding to specific receptors , IFNs induce a JAK/STAT signaling cascade which results in the production of interferon stimulated genes ( ISGs ) .",
"These ISGs will th... | [
"It is currently believed that type I and III interferons ( IFNs ) have redundant functions .",
"However , the preferential distribution of type III IFN receptor on epithelial cells suggests functional differences at epithelial surfaces .",
"Here , using human intestinal epithelial cells we could show that alth... | [
"The human intestinal tract plays two important roles in the body: first it is responsible for nutrient absorption and second it is the primary barrier which protects the human body from the outside environment .",
"This complex tissue is constantly exposed to commensal bacteria and is often exposed to both bacte... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"humoral immunity",
"medicine",
"infectious diseases",
"immunity",
"dengue fever",
"neglected tropical diseases",
"immunology",
"biology",
"viral diseases",
"dengue",
"immune response"
] | Therapeutic Efficacy of Antibodies Lacking FcγR against Lethal Dengue Virus Infection Is Due to Neutralizing Potency and Blocking of Enhancing Antibodies | journal.ppat.1003157 | null | [
[
"The four serotypes of dengue virus ( DENV ) are transmitted by Aedes aegypti and Ae .",
"albopictus mosquitoes and are endemic predominantly in tropical and sub-tropical regions of the world [1] , [2] .",
"Syndromes associated with DENV infection range from inapparent infection to classic dengue feve... | [
"Dengue hemorrhagic fever and dengue shock syndrome ( DHF/DSS ) are life-threatening complications following infection with one of the four serotypes of dengue virus ( DENV ) .",
"At present , no vaccine or antiviral therapies are available against dengue .",
"Here , we characterized a panel of eight human or m... | [
"The four dengue virus serotypes ( DENV1-4 ) cause the most prevalent mosquito-transmitted viral disease globally , infecting 50–100 million people annually in tropical and sub-tropical regions worldwide , yet no vaccine or therapy has been licensed to prevent or treat dengue .",
"The greatest risk factor for sev... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology",
"microbiology/cellular microbiology and pathogenesis",
"microbiology"
] | Biofilm Development on Caenorhabditis elegans by Yersinia Is Facilitated by Quorum Sensing-Dependent Repression of Type III Secretion | journal.ppat.1001250 | null | [
[
"The human pathogenic Yersiniae ( Yersinia pseudotuberculosis , Yersinia enterocolitica and Yersinia pestis ) share a high degree of DNA identity , but cause distinct diseases ranging from enterocolitis ( Y . enterocolitica and Y . pseudotuberculosis ) to pneumonic , bubonic or septicaemic plague ( Y . pestis... | [
"Yersinia pseudotuberculosis forms biofilms on Caenorhabditis elegans which block nematode feeding .",
"This genetically amenable host-pathogen model has important implications for biofilm development on living , motile surfaces .",
"Here we show that Y . pseudotuberculosis biofilm development on C . elegans is... | [
"Many Gram-negative bacteria communicate by producing and sensing the presence of chemical signal molecules such as the N-acylhomoserine lactones ( AHLs ) .",
"Bacterial cells use AHLs to convey information about their environment , metabolism and population size .",
"This type of chemical signalling is called ... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"population genetics",
"cereal crops",
"plant science",
"mathematics",
"forecasting",
"statistics (mathematics)",
"crops",
"plant genomics",
"mammalian genomics",
"population biology",
"plants",
"research and analysis methods",
"curve fitting",
"grasses",
"crop science... | Using Genetic Distance to Infer the Accuracy of Genomic Prediction | journal.pgen.1006288 | null | [
[
"Predicting unobserved phenotypes using high-density SNP or sequence data is the foundation of many applications in medical diagnostics [1–3] , plant [4 , 5] and animal [6] breeding .",
"The accuracy of genomic predictions will depend on a number of factors: relatedness among genotyped individuals [7 , 8]... | [
"The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics .",
"Statistical models used for this task are usually tested using cross-validation ,... | [
"The availability of increasing amounts of genomic data is making the use of statistical models to predict traits of interest a mainstay of many applications in life sciences .",
"Applications range from medical diagnostics for common and rare diseases to breeding characteristics such as disease resistance in pla... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"enzyme-linked immunoassays",
"onchocerca volvulus",
"pathology and laboratory medicine",
"tropical diseases",
"geographical locations",
"parasitic diseases",
"animals",
"onchocerca",
"parasitology",
"neglected tropical diseases",
"onchocercia... | Evidence for Suppression of Onchocerciasis Transmission in Bioko Island, Equatorial Guinea | journal.pntd.0004829 | null | [
[
"Onchocerciasis or \"river blindness\" is a chronic parasitic neglected tropical disease caused by the filarial nematode Onchocerca volvulus ( O . volvulus ) .",
"It is transmitted to humans through exposure to repeated bites of infected blackflies of the genus Similium [1] .",
"Adult worms live in su... | [
"Onchocerciasis or \"river blindness\" is a chronic parasitic neglected tropical disease which is endemic both in mainland and insular Equatorial Guinea .",
"We aim to estimate the current epidemiological situation of onchocerciasis in Bioko Island after vector elimination in 2005 and more than sixteen years of C... | [
"Onchocerciasis or “river blindness” is a chronic parasitic disease which is mainly found in Sub-Saharan Africa .",
"Onchocerciasis is endemic in both mainland and insular Equatorial Guinea .",
"Huge achievements have been made on onchocerciasis control in Bioko Island in the last years , and the country is mov... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"protein transport",
"cell processes",
"vertebrates",
"animals",
"animal models",
"osteichthyes",
"developmental biology",
"model organisms",
"organism development",
"glycosylation",
"embryos",
"extraction techniques",
"research and analysis methods",
"erk signaling cascade",
"embryology... | Liver-Enriched Gene 1, a Glycosylated Secretory Protein, Binds to FGFR and Mediates an Anti-stress Pathway to Protect Liver Development in Zebrafish | journal.pgen.1005881 | null | [
[
"The process of liver development includes",
"1 ) the specification of hepatoblasts from the endoderm ,",
"2 ) proliferation of hepatoblasts to form the liver primordium ( liver bud ) , and",
"3 ) differentiation and proliferation of hepatocytes to form the embryonic liver [1–5] .",
"Liver org... | [
"Unlike mammals and birds , teleost fish undergo external embryogenesis , and therefore their embryos are constantly challenged by stresses from their living environment .",
"These stresses , when becoming too harsh , will cause arrest of cell proliferation , abnormal cell death or senescence .",
"Such organism... | [
"Although being challenged by stresses from their living environment during embryogenesis , teleost fish harbor a robust genetic program dictating liver development as long as any environmental change , including temperature or natural UV irradiation , is not detrimental .",
"It is therefore of interest to explor... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide association studies",
"genome sequencing",
"genome analysis tools",
"biology",
"genomics",
"computational biology"
] | Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data | journal.pgen.1003959 | null | [
[
"In the field of human genetics research , there has been increasing interest in the role of low frequency variation in complex human disease ( defined in this text as variants with a minor allele frequency between 0 . 5%–3% ) .",
"This is in many ways a response to changing technology , but more importan... | [
"Analyses investigating low frequency variants have the potential for explaining additional genetic heritability of many complex human traits .",
"However , the natural frequencies of rare variation between human populations strongly confound genetic analyses .",
"We have applied a novel collapsing method to id... | [
"Low frequency variants are likely to play an important role in uncovering complex trait heritability; however , they are often continent or population specific .",
"This specificity complicates genetic analyses investigating low frequency variants for two reasons: low frequency variant signals in an association ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"carbohydrate metabolism",
"medicine and health sciences",
"chemical compounds",
"monomers",
"phosphates",
"carbohydrates",
"glucose metabolism",
"organic compounds",
"parasitic protozoans",
"glucose",
"parasitic diseases",
"protozoans",
"amino acids",
"digestive system",
"polymer chemis... | Gluconeogenesis is essential for trypanosome development in the tsetse fly vector | journal.ppat.1007502 | null | [
[
"Trypanosomes of the Trypanosoma brucei species complex are the etiological agents of Human African Trypanosomiasis , a parasitic disease that affects about 20 countries in sub-Saharan Africa [1] .",
"T . brucei adapts to the different environments encountered in its insect ( tsetse fly ) and mammalian ho... | [
"In the glucose-free environment that is the midgut of the tsetse fly vector , the procyclic form of Trypanosoma brucei primarily uses proline to feed its central carbon and energy metabolism .",
"In these conditions , the parasite needs to produce glucose 6-phosphate ( G6P ) through gluconeogenesis from metaboli... | [
"Trypanosoma brucei , the parasite responsible for sleeping sickness in humans , is transmitted by the tsetse fly that primarily uses amino acids for its energy production .",
"In the glucose-free environment encountered between the insect blood meals , T . brucei needs to produce through gluconeogenesis glucose ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology"
] | A Competition between Stimulators and Antagonists of Upf Complex Recruitment Governs Human Nonsense-Mediated mRNA Decay | journal.pbio.0060111 | Human mRNAs with premature termination codons are detected and degraded by nonsense-mediated decay when 3' untranslated region-associated proteins, such as poly(A)-binding protein, are absent from the proximity of the terminating ribosome. | [
[
"The process of nonsense-mediated decay ( NMD ) subjects mRNAs with premature termination codons ( PTCs ) to rapid decay .",
"This helps rid the cell of aberrant mRNAs that have acquired PTCs through mutation or faulty processing [1–3] .",
"Moreover , several lines of evidence suggest that NMD is also... | [
"The nonsense-mediated decay ( NMD ) pathway subjects mRNAs with premature termination codons ( PTCs ) to rapid decay .",
"The conserved Upf1–3 complex interacts with the eukaryotic translation release factors , eRF3 and eRF1 , and triggers NMD when translation termination takes place at a PTC .",
"Contrasting ... | [
"The nonsense-mediated mRNA decay pathway is responsible for rapidly degrading mRNAs with premature termination codons .",
"This is important because it prevents the production of potentially deleterious truncated proteins from aberrant mRNAs , such as those that have undergone erroneous processing .",
"How doe... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Strategy for O-Glycoproteomics of Enveloped Viruses—the O-Glycoproteome of Herpes Simplex Virus Type 1 | journal.ppat.1004784 | null | [
[
"Enveloped viruses contain one or more membrane proteins important for adhesion and entry to host cells [1] .",
"The majority of envelope membrane proteins are predicted or confirmed to be covered with glycans with important functions in protein folding , transport , formation of infectious particles , en... | [
"Glycosylation of viral envelope proteins is important for infectivity and interaction with host immunity , however , our current knowledge of the functions of glycosylation is largely limited to N-glycosylation because it is difficult to predict and identify site-specific O-glycosylation .",
"Here , we present a... | [
"Information on site-specific O-glycosylation of viral envelope glycoproteins is generally very limited despite important functions .",
"We present a powerful mass-spectrometry based strategy to globally identify O-glycosylation sites on viral envelope proteins of a given virus in the context of a productive infe... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"cell death",
"medicine and health sciences",
"immune cells",
"cardiovascular anatomy",
"nervous system",
"immunology",
"tropical diseases",
"brain",
"cell processes",
"parasitic diseases",
"neuronal death",
"cytotoxic t cells",
"white blood cells",
"animal cells",
"bloo... | CD8+ T Cells Induce Fatal Brainstem Pathology during Cerebral Malaria via Luminal Antigen-Specific Engagement of Brain Vasculature | journal.ppat.1006022 | null | [
[
"Malaria , a disease caused by protozoan parasites of the genus Plasmodium , is a leading cause of morbidity and mortality in the developing world .",
"Of the 627 , 000 annual deaths due to malaria , the vast majority are caused by Plasmodium falciparum infections [1] .",
"Human cerebral malaria ( HCM... | [
"Cerebral malaria ( CM ) is a severe complication of Plasmodium falciparum infection that results in thousands of deaths each year , mostly in African children .",
"The in vivo mechanisms underlying this fatal condition are not entirely understood .",
"Using the animal model of experimental cerebral malaria ( E... | [
"Cerebral malaria ( CM ) is a severe and potentially fatal complication of malaria in humans that results in swelling and bleeding within the brain .",
"The mechanisms that cause this fatal disease in humans are not completely understood .",
"We studied an animal model known as experimental cerebral malaria to ... | 2016 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genetics of disease",
"genetics and genomics/gene discovery",
"genetics and genomics/population genetics"
] | Association of Variants at UMOD with Chronic Kidney Disease and Kidney Stones—Role of Age and Comorbid Diseases | journal.pgen.1001039 | null | [
[
"Chronic kidney disease ( CKD ) is a common disorder that can progress to kidney failure and is associated with an increased risk of cardiovascular disease and mortality [1] , [2] .",
"The cause of CKD is not always known and frequently appears multifactorial with hypertension ( HTN ) and diabetes mellitu... | [
"Chronic kidney disease ( CKD ) is a worldwide public health problem that is associated with substantial morbidity and mortality .",
"To search for sequence variants that associate with CKD , we conducted a genome-wide association study ( GWAS ) that included a total of 3 , 203 Icelandic cases and 38 , 782 contro... | [
"Chronic kidney disease ( CKD ) is a common condition that is associated with substantial morbidity and mortality and has been recognized as a major public health problem worldwide .",
"Common causes of CKD include hypertension , diabetes , and inflammatory disorders .",
"Previous studies have shown a significa... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"developmental biology",
"innate immune system",
"white blood cells",
"immune cells",
"cytokines",
"cell biology",
"animal cells",
"nk cells",
"immunity",
"molecular development",
"antigen-presenting cells",
"immunity to infections",
"biology and life sciences",
"cellular ... | Syk Signaling in Dendritic Cells Orchestrates Innate Resistance to Systemic Fungal Infection | journal.ppat.1004276 | null | [
[
"Candida albicans is the most prevalent fungal pathogen in humans causing local infections of skin , nails , oral cavity and genital tract [1] .",
"In some instances , Candida can spread systemically via the bloodstream and lodge in the kidneys , which then act as the major site of fungal replication [2] ... | [
"Host protection from fungal infection is thought to ensue in part from the activity of Syk-coupled C-type lectin receptors and MyD88-coupled toll-like receptors in myeloid cells , including neutrophils , macrophages and dendritic cells ( DCs ) .",
"Given the multitude of cell types and receptors involved , elimi... | [
"Multiple cell types bearing a vast array of immune receptors with different modes of signaling ensure that the host response to infection is both robust and reliable .",
"For this reason , loss of a single signaling pathway in a given cell type is often not enough to impact host resistance .",
"Here , we find ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"pattern recognition receptors",
"medicine and health sciences",
"molecular dynamics",
"immunology",
"lipoprotein receptors",
"lipid structure",
"immune system proteins",
"lipids",
"proteins",
"lipoproteins",
"chemistry",
"physics",
"biochemistry",
"biochemical simulations",
"signal tran... | Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach | journal.pcbi.1006165 | null | [
[
"Apolipoprotein E ( apoE ) is a member of the superfamily of exchangeable apolipoproteins .",
"It mediates cellular uptake of cholesterol-rich lipoproteins by acting as a high affinity ligand for cell surface receptors belonging to the low-density lipoprotein ( LDL ) receptor family [1] .",
"An imbala... | [
"Apolipoprotein E ( apoE ) is a forefront actor in the transport of lipids and the maintenance of cholesterol homeostasis , and is also strongly implicated in Alzheimer’s disease .",
"Upon lipid-binding apoE adopts a conformational state that mediates the receptor-induced internalization of lipoproteins .",
"Du... | [
"Among the proteins involved in the transport of lipids and their distribution to the cells , apolipoprotein E ( apoE ) mediates the internalization of cholesterol rich lipoproteins by acting as a ligand for cell-surface receptors .",
"In the central nervous system , while apoE is the major cholesterol transport ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota | journal.pgen.1005413 | null | [
[
"Primary and nosocomial bacterial infections are a major source of morbidity and mortality worldwide [1] .",
"In the United States alone , community-acquired bacterial infections represent a leading cause of death , particularly among the elderly [2 , 3] , while healthcare-associated bacterial disease aff... | [
"Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology , but it has not yet been applied systematically or comprehensively within a clinical context .",
"Here , over the course of one year , we performed prospective collection and whole genome sequencing of nearly all... | [
"Bacterial whole genome sequencing is becoming increasingly common to microbiological research , but despite its great potential , has not yet been meaningfully integrated into clinical care .",
"Here , we generated whole genome sequencing data from nearly all of the bacterial isolates prospectively collected fro... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"immunology/cellular microbiology and pathogenesis",
"physiology/immunity to infections",
"virology/animal models of infection",
"infectious diseases/viral infections",
"virology/viruses and cancer",
"pathology/immunology",
"oncology/myelomas and lymphoproliferative diseases",
"immunology/immunity to ... | Clonal Structure of Rapid-Onset MDV-Driven CD4+ Lymphomas and Responding CD8+ T Cells | journal.ppat.1001337 | null | [
[
"Virus driven lymphoid oncogenesis is a serious consequence of infection with a wide range of herpes and retroviral pathogens in a variety of hosts .",
"Major lymphoma-associated infections of humans include Epstein Barr virus ( EBV ) and Human T cell lymphotropic virus ( HTLV ) [1] , [2] .",
"With bo... | [
"Lymphoid oncogenesis is a life threatening complication associated with a number of persistent viral infections ( e . g . EBV and HTLV-1 in humans ) .",
"With many of these infections it is difficult to study their natural history and the dynamics of tumor formation .",
"Marek's Disease Virus ( MDV ) is a prev... | [
"Many viral infections target the immune system , making use of the long lived , highly proliferative lymphocytes to propagate and survive within the host .",
"This characteristic has led to an association between some viruses such as Epstein Barr Virus ( EBV ) , Human T cell Lymphotrophic Virus-1 ( HTLV-1 ) and ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"t helper cells",
"medicine and health sciences",
"immune cells",
"immune physiology",
"spleen",
"immunology",
"tropical diseases",
"parasitic diseases",
"parasitic protozoans",
"cell differentiation",
"parasitology",
"parasitemia",
"developmental biology",
"protozoans",
... | P2X7 receptor drives Th1 cell differentiation and controls the follicular helper T cell population to protect against Plasmodium chabaudi malaria | journal.ppat.1006595 | null | [
[
"Despite efforts to develop vaccines and antimalarial drugs , Plasmodium infection still causes the death of about half a million people yearly [1] .",
"The most prevalent Plasmodium species , Plasmodium falciparum and Plasmodium vivax , persist for very long time periods in the bloodstream of infected in... | [
"A complete understanding of the mechanisms underlying the acquisition of protective immunity is crucial to improve vaccine strategies to eradicate malaria .",
"However , it is still unclear whether recognition of damage signals influences the immune response to Plasmodium infection .",
"Adenosine triphosphate ... | [
"Malaria still causes the death of approximately half a million people yearly despite efforts to develop vaccines .",
"The ability of Plasmodium parasites to survive the immune effector mechanisms indicates how suitable the immune response must be to eliminate the infection .",
"CD4 T cells have a dual role in ... | 2017 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"bacteriology",
"gene networks",
"gene regulation",
"microbiology",
"microbial evolution",
"molecular genetics",
"microbial growth and development",
"bacterial pathogens",
"biology",
"microbial ecology",
"bacterial physiology",
"gram negative",
"genetics",
"bacterial evolution",
"genetic... | The Regulatory Network of Natural Competence and Transformation of Vibrio cholerae | journal.pgen.1002778 | null | [
[
"The bacterium Vibrio cholerae is a facultative pathogen and the causative agent of the disease cholera .",
"Cholera is far from being extinct and is , in fact , considered a re-emerging disease [1] .",
"The destructive capacity of cholera is demonstrated by its current outbreak in Haiti .",
"Acco... | [
"The human pathogen Vibrio cholerae is an aquatic bacterium frequently encountered in rivers , lakes , estuaries , and coastal regions .",
"Within these environmental reservoirs , the bacterium is often found associated with zooplankton and more specifically with their chitinous exoskeleton .",
"Upon growth on ... | [
"The human pathogen Vibrio cholerae is an aquatic bacterium often encountered in rivers , estuaries , and coastal regions .",
"Within this environmental niche , the bacterium often associates with the chitinous exoskeleton of zooplankton .",
"Upon colonization of these chitinous surfaces , V . cholerae switches... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"insulin-dependent signal transduction",
"mitogenic signaling",
"tor signaling",
"cell differentiation",
"animal models",
"developmental biology",
"drosophila melanogaster",
"model organisms",
"stem cells",
"cell growth",
"signaling pathways",
"adult stem cells",
"signaling in cellular proce... | Notch-Mediated Suppression of TSC2 Expression Regulates Cell Differentiation in the Drosophila Intestinal Stem Cell Lineage | journal.pgen.1003045 | null | [
[
"Regenerative processes in somatic tissues require coordinated regulation of stem cell proliferation and daughter cell differentiation to ensure long-term tissue homeostasis [1]–[3] .",
"The Drosophila posterior midgut epithelium has emerged as an excellent model system to study this regulation [4]–[7] ."... | [
"Epithelial homeostasis in the posterior midgut of Drosophila is maintained by multipotent intestinal stem cells ( ISCs ) .",
"ISCs self-renew and produce enteroblasts ( EBs ) that differentiate into either enterocytes ( ECs ) or enteroendocrine cells ( EEs ) in response to differential Notch ( N ) activation .",... | [
"Stem cells maintain tissue homeostasis in metazoans .",
"A productive model to study the regulation of stem cell function is the Drosophila posterior midgut .",
"Notch ( N ) signaling controls intestinal stem cell ( ISC ) differentiation in this tissue , while ISC proliferation is regulated by growth factor si... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality | journal.pcbi.1004506 | null | [
[
"Synthetic lethality ( SL ) occurs when two nonessential genes cause cellular inviability after being knocked out simultaneously . [1]",
"Although SL was originally studied and described in yeast , it can be a powerful tool for studying drug action in humans; for example , SL may guide the development of ... | [
"Synthetic lethality is a genetic interaction wherein two otherwise nonessential genes cause cellular inviability when knocked out simultaneously .",
"Drugs can mimic genetic knock-out effects; therefore , our understanding of promiscuous drugs , polypharmacology-related adverse drug reactions , and multi-drug th... | [
"Synthetic lethality is a genetic interaction that has promising implications for informing novel cancer therapies .",
"Over 200 million pairwise tests would be required to identify all pairwise synthetic lethal interactions in humans–currently , an impossibly large experimental burden .",
"To simplify the proc... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"chemical compounds",
"molecular probe techniques",
"enzymes",
"enzymology",
"immunoblotting",
"carbohydrates",
"organic compounds",
"glucose",
"fungi",
"model organisms",
"experimental organism systems",
"molecular biology techniques",
"research and analysis methods",
... | Whi2 is a conserved negative regulator of TORC1 in response to low amino acids | journal.pgen.1007592 | null | [
[
"The understudied Whi2 protein of Saccharomyces cerevisiae and its fungal homologs share predicted domain structure and sequence similarity with the family of human KCTD proteins [1] ( S1 Fig ) .",
"Despite primary sequence divergences , a homologous SKP1/BTB/POZ domain is identifiable ( IPR011333 ) in th... | [
"Yeast WHI2 was originally identified in a genetic screen for regulators of cell cycle arrest and later suggested to function in general stress responses .",
"However , the function of Whi2 is unknown .",
"Whi2 has predicted structure and sequence similarity to human KCTD family proteins , which have been impli... | [
"Yeast and human cells respond to declining levels of available nutrients to prepare ahead for leaner times .",
"The detailed mechanisms of nutrient sensing are not well understood , but defects in these processes have key roles in diseases such as cancer .",
"The evolutionarily conserved protein complex TORC1 ... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"environmental epidemiology",
"epidemiology",
"neglected tropical diseases"
] | Animal Reservoir, Natural and Socioeconomic Variations and the Transmission of Hemorrhagic Fever with Renal Syndrome in Chenzhou, China, 2006–2010 | journal.pntd.0002615 | null | [
[
"Hemorrhagic fever with renal syndrome ( HFRS ) is a natural focal disease characterized by fever , hemorrhagic manifestations , and acute renal dysfunction .",
"HFRS is mainly transmitted by rodents [1] .",
"In China , HFRS is primarily caused by one of two types of hantaviruses , Hantaan virus ( HTN... | [
"China has the highest incidence of hemorrhagic fever with renal syndrome ( HFRS ) worldwide .",
"Reported cases account for 90% of the total number of global cases .",
"By 2010 , approximately 1 . 4 million HFRS cases had been reported in China .",
"This study aimed to explore the effect of the rodent reserv... | [
"Hemorrhagic fever with renal syndrome ( HFRS ) , a rodent-borne disease caused by hantaviruses , is characterized by fever , haemorrhage , headache , back pain , abdominal pain , and acute kidney injury .",
"China has the highest incidence of HFRS worldwide .",
"Reported cases account for 90% of the total glob... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/gene discovery",
"genetics and genomics/gene function",
"molecular biology/translational regulation",
"microbiology",
"microbiology/microbial physiology and metabolism",
"molecular biology",
"genetics and genomics"
] | Escherichia coli MazF Leads to the Simultaneous Selective Synthesis of Both “Death Proteins” and “Survival Proteins” | journal.pgen.1000390 | null | [
[
"Toxin-antitoxin modules consist of pairs of genes on the bacterial chromosome [1]–[5]: the downstream gene encodes a stable toxin which causes cell death and the upstream gene encodes a labile antitoxin which counteracts the activity of the toxin .",
"In the E . coli chromosome , seven toxin-antitoxin mo... | [
"The Escherichia coli mazEF module is one of the most thoroughly studied toxin–antitoxin systems .",
"mazF encodes a stable toxin , MazF , and mazE encodes a labile antitoxin , MazE , which prevents the lethal effect of MazF .",
"MazF is an endoribonuclease that leads to the inhibition of protein synthesis by c... | [
"The enteric bacterium E . coli , as most other bacteria , carries a pair of genes on its chromosome; one of them specifies a toxin and the other one an antitoxin .",
"Previously , we have shown that that the mazEF toxin–antitoxin system in E . coli is responsible for bacterial cell death under stressful conditio... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"mosquito",
"infectious diseases",
"malaria",
"dynamics"
] | Progression of Plasmodium berghei through Anopheles stephensi Is Density-Dependent | journal.ppat.0030195 | null | [
[
"The availability of the genomes of man , the mosquito and the malarial parasite has enabled penetrating new studies on the molecular organization of Plasmodium in its two hosts .",
"Yet , we do not fully comprehend how parasite population densities may affect transmissibility .",
"Without this knowle... | [
"It is well documented that the density of Plasmodium in its vertebrate host modulates the physiological response induced; this in turn regulates parasite survival and transmission .",
"It is less clear that parasite density in the mosquito regulates survival and transmission of this important pathogen .",
"Num... | [
"Malaria , one of the world's most devastating parasitic diseases , is caused by protozoan parasites of the genus Plasmodium and is transmitted between mammalian hosts by Anopheles mosquitoes .",
"Within the mosquito , the parasite undergoes four sequential developmental transformations as it passes from the bloo... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Neutrophil-Derived MMP-8 Drives AMPK-Dependent Matrix Destruction in Human Pulmonary Tuberculosis | journal.ppat.1004917 | null | [
[
"The lung cavity is a hallmark of pulmonary tuberculosis , a globally important disease of man .",
"The cavity has high bacillary burden and is associated with spread of infection .",
"Polymorphonuclear leukocytes or neutrophils are abundant in areas of TB lung cavities [1] .",
"Excessive neutroph... | [
"Pulmonary cavities , the hallmark of tuberculosis ( TB ) , are characterized by high mycobacterial load and perpetuate the spread of M . tuberculosis .",
"The mechanism of matrix destruction resulting in cavitation is not well defined .",
"Neutrophils are emerging as key mediators of TB immunopathology and the... | [
"Neutrophil infiltration is characteristic of immune-induced pathology in tuberculosis but mechanisms whereby neutrophils cause tissue destruction are not fully understood .",
"In this study , we show that neutrophils secrete the collagenase MMP-8 in response to direct infection with Mycobacterium tuberculosis an... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"gene regulation",
"cell differentiation",
"muscle regeneration",
"developmental biology",
"organism development",
"stem cells",
"morphogenesis",
"small interfering rnas",
"muscle differentiation",
"animal cells",
"gene expression",
"myoblasts",
"genetic loci",
"biochemistry",
"rna",
"... | TEAD transcription factors are required for normal primary myoblast differentiation in vitro and muscle regeneration in vivo | journal.pgen.1006600 | null | [
[
"The TEAD ( 1–4 ) transcription factors [1 , 2] bind to a consensus MCAT ( 5’-CATTCCA/T-3’ ) element , originally identified as the SV40 enhancer GT-II motif [3] [4–6] , through the evolutionarily conserved TEA/ATTS DNA binding domain [7 , 8] .",
"Mammalian TEADs are widely expressed with prominent Tead1 ... | [
"The TEAD family of transcription factors ( TEAD1-4 ) bind the MCAT element in the regulatory elements of both growth promoting and myogenic differentiation genes .",
"Defining TEAD transcription factor function in myogenesis has proved elusive due to overlapping expression of family members and their functional ... | [
"Aspects of muscle differentiation can be reproduced using the C2C12 cell line or primary myoblasts both of which can be differentiated to form myotubes in vitro .",
"While the functions of recognised myogenic proteins such as Myogenin , Myod1 and MEF-family transcription factors in this process have been extensi... | 2017 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"genetics and genomics"
] | Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans | journal.pgen.1001302 | null | [
[
"A central challenge of evolutionary biology is to elucidate the nature of adaptive changes to the genome: do they comprise a negligible or substantial fraction of differences among species ?",
"When they occur , are they driven by strong positive selection or are they fine-tunings of minor consequence to... | [
"In Drosophila , multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common .",
"All suffer from confounding factors , however , such that the interpretation of the evidence—in particular , conclusions about the rate and strength of beneficial substitutions—remains... | [
"Characterizing the nature of beneficial changes to the genome is essential to our understanding of adaptation .",
"To do so , researchers identify and analyze footprints that beneficial changes leave in patterns of genetic variation within and between species .",
"In order to teach us about adaptive evolution ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"nervous system",
"computer hardware",
"light",
"neuroscience",
"electromagnetic radiation",
"luminance",
"brain mapping",
"computational neuroscience",
"visible light",
"neuronal tuning",
"computer and information sciences",
"animal cells",
"connectomics",
... | Could a Neuroscientist Understand a Microprocessor? | journal.pcbi.1005268 | null | [
[
"The MOS 6502 ( and the virtually identical MOS 6507 ) were the processors in the Apple I , the Commodore 64 , and the Atari Video Game System ( VCS ) ( see [10] for a comprehensive review ) .",
"The Visual6502 team reverse-engineered the 6507 from physical integrated circuits [11] by chemically removing ... | [
"There is a popular belief in neuroscience that we are primarily data limited , and that producing large , multimodal , and complex datasets will , with the help of advanced data analysis algorithms , lead to fundamental insights into the way the brain processes information .",
"These datasets do not yet exist , ... | [
"Neuroscience is held back by the fact that it is hard to evaluate if a conclusion is correct; the complexity of the systems under study and their experimental inaccessability make the assessment of algorithmic and data analytic technqiues challenging at best .",
"We thus argue for testing approaches using known ... | 2017 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"immune physiology",
"pathology and laboratory medicine",
"ruminants",
"pathogens",
"immunology",
"geographical locations",
"microbiology",
"vertebrates",
"animals",
"mammals",
"viruses",
"rna viruses",
"antibodies",
"insect vectors",
... | Neutralizing antibodies for orthobunyaviruses in Pantanal, Brazil | journal.pntd.0006014 | null | [
[
"The Bunyaviridae family contains over 300 enveloped viruses divided into five genera , including Orthobunyavirus , Phlebovirus and Nairovirus , which include arboviruses , viruses capable of alternately replicating in vertebrates and arthropods [1] .",
"Orthobunyaviruses are classified into immunological... | [
"The Pantanal is a hotspot for arbovirus studies in South America .",
"Various medically important flaviviruses and alphaviruses have been reported in domestic and wild animals in the region .",
"To expand the knowledge of local arbovirus circulation , a serosurvey for 14 Brazilian orthobunyaviruses was conduct... | [
"In the present study , we report the evidence of various orthobunyaviruses of medical importance in domestic and wild animals of the Pantanal , a large floodplain located in West-Central Brazil .",
"Although various other arboviruses as flaviviruses and alphaviruses have been reported in the region , orthobunyav... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods",
"Acknowledgments"
] | [] | The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients | journal.pcbi.1003203 | null | [
[
"Despite an increasing arsenal and improved potency of antiretroviral drugs , the optimal use of combination antiretroviral therapy against HIV-1 infection remains challenging [1] .",
"Complicating factors include drug interactions and toxicities , adherence to therapy , and development of drug resistance... | [
"The success of combination antiretroviral therapy is limited by the evolutionary escape dynamics of HIV-1 .",
"We used Isotonic Conjunctive Bayesian Networks ( I-CBNs ) , a class of probabilistic graphical models , to describe this process .",
"We employed partial order constraints among viral resistance mutat... | [
"Drug resistance remains a challenge in the management of HIV-infected patients .",
"The accumulation of mutations during ongoing viral replication is the origin of drug resistance development .",
"Understanding this evolutionary process in a quantitative manner is an important prerequisite for minimizing the r... | 2013 |
[
"Introduction",
"Results & discussion",
"Materials & methods"
] | [
"biotechnology",
"brassica",
"nucleosome mapping",
"plant science",
"model organisms",
"experimental organism systems",
"plant genomics",
"epigenetics",
"molecular biology techniques",
"plants",
"chromatin",
"structural genomics",
"research and analysis methods",
"arabidopsis thaliana",
... | Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis | journal.pgen.1006988 | null | [
[
"Within the nucleus , higher eukaryotic genomes are packaged in the form of chromatin in which the structural unit is a nucleosome , a ~150 bp of double-stranded DNA wound around an octameric histone protein core .",
"Nucleosomes are arranged in a repetitive manner spaced by a linker region of DNA with a ... | [
"All eukaryotic genomes are packaged as chromatin , with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors ( TF ) and initiation complexes , together forming a dynamic chromatin landscape .",
"Whilst details of nuc... | [
"DNA is packaged by proteins into chromatin , of which the fundamental unit is a complex of histone proteins that wraps ~150bp of DNA into a nucleosome .",
"Digestion of chromatin with enzymes such as micrococcal nuclease cuts the DNA between the protein particles , and by sequencing the cut sites , they can be m... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"medicine and health sciences",
"nervous system",
"enzymes",
"caenorhabditis",
"enzymology",
"electrophysiology",
"neurites",
"neuroscience",
"animals",
"phosphatases",
"animal models",
"caenorhabditis elegans",
"model organisms",
"animal behavior",
"experimental organ... | The receptor protein tyrosine phosphatase CLR-1 is required for synaptic partner recognition | journal.pgen.1007312 | null | [
[
"Perception , thought , and behavior all rely on the faithful transfer of information between neurons .",
"During development , neurons form circuits through a series of well-characterized steps , including neuronal migration , guidance of axons and dendrites into target regions , and finally the formatio... | [
"During neural circuit formation , most axons are guided to complex environments , coming into contact with multiple potential synaptic partners .",
"However , it is critical that they recognize specific neurons with which to form synapses .",
"Here , we utilize the split GFP-based marker Neuroligin-1 GFP Recon... | [
"The nervous system is required for many body functions including perception , behavior and thought .",
"Cells in the nervous system called neurons function in interconnected groups called circuits to carry out these basic functions .",
"While we have learned a great deal about how circuits function , we know m... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Activation of Smurf E3 Ligase Promoted by Smoothened Regulates Hedgehog Signaling through Targeting Patched Turnover | journal.pbio.1001721 | Protein turnover of Patched, the Hedgehog receptor and key negative regulator of Hedgehog signaling, is controlled by the ubiquitin E3 ligase, Smurf, in a manner that depends on activation of signal transducer, Smoothened. | [
[
"Hedgehog ( Hh ) signaling is evolutionarily conserved and is essential for patterning of organs of both invertebrates and vertebrates [1] , [2] .",
"Dysregulation of Hh signaling activity leads to developmental abnormalities and cancers [3] .",
"In Drosophila , genetic and biochemical evidence reveal... | [
"Hedgehog signaling plays conserved roles in controlling embryonic development; its dysregulation has been implicated in many human diseases including cancers .",
"Hedgehog signaling has an unusual reception system consisting of two transmembrane proteins , Patched receptor and Smoothened signal transducer .",
... | [
"Hedgehog ( Hh ) signaling is a pathway renowned for its roles in controlling embryonic development and tumorigenesis .",
"Signaling via this pathway proceeds when Hh ligands bind to the receptor Patched ( Ptc ) , thereby preventing Ptc from inhibiting the signal transducer , Smoothened ( Smo ) , and thus allowin... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Selamectin Is the Avermectin with the Best Potential for Buruli Ulcer Treatment | journal.pntd.0003996 | null | [
[
"Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans , is a chronic debilitating disease of the skin and soft tissue .",
"Although mortality is low , permanent disfigurement and disability is high [1] .",
"BU is mainly found in Africa , South America and the Western Pacific regions and is often lin... | [
"A comprehensive analysis was done to evaluate the potential use of anti-parasitic macrocyclic lactones ( including avermectins and milbemycins ) for Buruli ulcer ( BU ) therapy .",
"A panel containing nearly all macrocyclic lactones used in human or in veterinary medicine was analyzed for activity in vitro again... | [
"Buruli ulcer ( BU ) is a chronic debilitating mycobacterial disease of the skin and soft tissue caused by Mycobacterium ulcerans .",
"It is mainly found in tropical regions and often linked to poverty .",
"BU can be cured in most cases with the standard treatment , a combination of rifampicin and the injectabl... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"tropical diseases",
"geographical locations",
"ebola hemorrhagic fever",
"parasitic diseases",
"diarrhea",
"signs and symptoms",
"gastroenterology and hepatology",
"neglected tropical diseases",
"africa",
"viral hemorrhagic ... | Predicting Ebola infection: A malaria-sensitive triage score for Ebola virus disease | journal.pntd.0005356 | null | [
[
"Prior to the 2013–2015 epidemic of Ebola virus disease ( EVD ) , fifteen outbreaks caused by the virulent Zaire ebolavirus strain had been recorded since the identification of the virus in 1976 [1] .",
"The West African EVD epidemic started in December 2013 , rapidly spreading from Guinea to Liberia and ... | [
"The non-specific symptoms of Ebola Virus Disease ( EVD ) pose a major problem to triage and isolation efforts at Ebola Treatment Centres ( ETCs ) .",
"Under the current triage protocol , half the patients allocated to high-risk “probable” wards were EVD ( - ) : a misclassification speculated to predispose nosoco... | [
"Four decades after the discovery of Ebola virus disease ( EVD ) , the sources , reservoirs and dynamics of infection are still largely unknown and thus the threat of re-emergence remains ever present .",
"As EVD thrives on fragile healthcare systems in the developing world , it is essential that triage tools are... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"chemical compounds",
"enzymes",
"metabolic processes",
"ketones",
"enzymology",
"carbohydrates",
"organic compounds",
"glucose",
"glycolysis",
"pyruvate",
"systems science",
"mathematics",
"metabolites",
"enzyme metabolism",
"enzyme chemistry",
"computer and information sciences",
"... | Stability of Ensemble Models Predicts Productivity of Enzymatic Systems | journal.pcbi.1004800 | null | [
[
"We use the following enzymatic systems as examples for our investigation .",
"Three of these systems have been described previously and some experimental data are available to validate our predictions .",
"The other system ( glucose to isoprene pathway ) has not been experimentally investigated .",
... | [
"Stability in a metabolic system may not be obtained if incorrect amounts of enzymes are used .",
"Without stability , some metabolites may accumulate or deplete leading to the irreversible loss of the desired operating point .",
"Even if initial enzyme amounts achieve a stable steady state , changes in enzyme ... | [
"A method of metabolic simulation called ensemble modelling for robustness analysis is used to predict the behavior intrinsic to the network structure ( stoichiometry and kinetic form ) of four enzymatic systems .",
"Some network structures are shown to be prone to instability .",
"Starting from a stable system... | 2016 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"plants",
"genetics and genomics",
"arabidopsis (thale cress)"
] | Genome-Wide Expression Profiling of the Arabidopsis Female Gametophyte Identifies Families of Small, Secreted Proteins | journal.pgen.0030171 | null | [
[
"The life cycle of plants alternates between haploid gametophyte and diploid sporophyte generations .",
"A central step in plant sexual reproduction is the transfer of sperm cells from the male gametophyte , the pollen grain , to the female gametophyte , the embryo sac , resulting in fertilization and the... | [
"The female gametophyte of flowering plants , the embryo sac , develops within the diploid ( sporophytic ) tissue of the ovule .",
"While embryo sac–expressed genes are known to be required at multiple stages of the fertilization process , the set of embryo sac–expressed genes has remained poorly defined .",
"I... | [
"During the sexual reproduction of flowering plants , a pollen tube delivers sperm cells to a specialized group of cells known as the embryo sac , which contains the egg cell .",
"It is known that embryo sacs are active participants in guiding the growth of pollen tubes , in facilitating fertilization , and in in... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome expression analysis",
"molecular cell biology",
"rna processing",
"gene regulation",
"genetics",
"gene expression",
"molecular genetics",
"biology",
"genomics",
"molecular biology",
"genetics and genomics",
"dna transcription"
] | Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1 | journal.pgen.1002329 | null | [
[
"Early in each transcription cycle RNA polymerase II ( Pol II ) can follow one of two paths; terminate early through the Nrd1-Nab3-Sen1 pathway or continue on to form longer , potentially coding transcripts [1] , [2] .",
"Yeast Nrd1 , Nab3 and Sen1 are part of a complex [3] that interacts both with the ph... | [
"RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs .",
"One major difference between these two classes of transcripts is the mechanism of termination .",
"Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled t... | [
"Transcription in eukaryotes is widespread including both protein-coding transcripts and an increasing number of non-coding RNAs .",
"Here we present the results of transcriptome-wide mapping of a set of yeast RNA–binding proteins that control expression of some protein-coding genes and a number of novel non-codi... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular biology/dna replication",
"molecular biology/recombination",
"genetics and genomics/chromosome biology",
"genetics and genomics/disease models",
"genetics and genomics/gene function",
"molecular biology/dna repair"
] | New Functions of Ctf18-RFC in Preserving Genome Stability outside Its Role in Sister Chromatid Cohesion | journal.pgen.1001298 | null | [
[
"DNA trinucleotide repeats are subject to frequent expansions and contractions in families affected by Huntington's disease ( HD ) and other inherited neurological disorders [1] , [2] .",
"Some expanded triplet repeats also cause chromosome fragility , as in fragile X syndrome [1]–[3] .",
"The complex... | [
"Expansion of DNA trinucleotide repeats causes at least 15 hereditary neurological diseases , and these repeats also undergo contraction and fragility .",
"Current models to explain this genetic instability invoke erroneous DNA repair or aberrant replication .",
"Here we show that CAG/CTG tracts are stabilized ... | [
"DNA trinucleotide repeats are naturally occurring runs of three base-pairs .",
"Genetic mutations that expand ( lengthen ) triplet repeats cause multiple neurological diseases , including Huntington's disease .",
"Triplet repeats also contract ( shorten ) and break .",
"This complex behavior suggests triplet... | 2011 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"cell biology/microbial physiology and metabolism",
"computational biology/literature analysis",
"cell biology/microbial growth and development",
"molecular biology/bioinformatics",
"computational biology/metabolic networks",
"computational biology/signaling networks",
"computational biology/systems bio... | Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization | journal.pcbi.1000312 | null | [
[
"High-throughput experimental technologies enable the production of heterogeneous data , such as expression profiles and proteomic data , for almost any organism of interest .",
"A detailed mathematical representation of the in vivo cellular network is required to obtain a holistic understanding of cellul... | [
"Metabolic network reconstructions represent valuable scaffolds for ‘-omics’ data integration and are used to computationally interrogate network properties .",
"However , they do not explicitly account for the synthesis of macromolecules ( i . e . , proteins and RNA ) .",
"Here , we present the first genome-sc... | [
"Systems biology aims to understand the interactions of cellular components in a systemic manner .",
"Mathematical modeling is critical to the integration and analysis of these components on a conceptual as well as mechanistic level .",
"To date , detailed genome-scale reconstructions of metabolism have become ... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"body fluids",
"diagnostic radiology",
"pathology and laboratory medicine",
"vomiting",
"tropical diseases",
"headaches",
"magnetic resonance imaging",
"urine",
"physiological processes",
"signs and symptoms",
"neglected tropical diseases",
"research and analy... | Post-dengue acute disseminated encephalomyelitis: A case report and meta-analysis | journal.pntd.0005715 | null | [
[
"Dengue , a worldwide prevalent mosquito-borne infectious disease , is a flavivirus spread by several species of Aedes type mosquitos , mainly Aedes aegypti [1] .",
"Dengue has become a dangerous burden and is widely spread in more than 110 countries [2 , 3] .",
"The incidence of dengue has increased ... | [
"Dengue is one of the most common infectious diseases .",
"The aim of this study was to systematically review acute disseminated encephalomyelitis ( ADEM ) and to represent a new case .",
"We searched for articles in nine databases for case reports , series or previous reviews reporting ADEM cases in human .",
... | [
"We presented a 13-year-old girl of ADEM following dengue infection .",
"She was totally alert and had a low grade of fever with no focal neurologic deficits , on admission .",
"We revealed that the prevalence of either ADEM or all neurological disorders among dengue patients was not too rare .",
"Moreover , ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands | journal.pgen.1004941 | null | [
[
"Comparative genomics is a fundamental key to the inner workings of genomes .",
"The identification of genes and other functional elements such as regulatory regions , as well as the understanding of their influence on the fitness of organisms rely essentially on the detection of signatures of natural sel... | [
"The characterization of functional elements in genomes relies on the identification of the footprints of natural selection .",
"In this quest , taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic sig... | [
"Classical population genetics models indicate that the efficiency of selection , and hence adaptation , depends on a number of non-selective factors , such as the size of a population or the intensity of recombination .",
"In the last 10 years , evidence has accumulated that another mechanism called GC-Biased Ge... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"medicine and health sciences",
"outpatient clinics",
"disabilities",
"biopsy",
"tropical diseases",
"geographical locations",
"surgical and invasive medical procedures",
"health care",
"bacterial diseases",
"neglected tropical diseases",
"skin diseases",
"public and occupatio... | Impact of a Reference Center on Leprosy Control under a Decentralized Public Health Care Policy in Brazil | journal.pntd.0005059 | null | [
[
"In 1991 , the World Health Organization ( WHO ) adopted the goal of eliminating leprosy as a public health issue worldwide by the year 2000 .",
"Elimination was defined as achieving a prevalence rate of lower than 1/10 , 000 inhabitants [1] .",
"The widespread implementation of the multidrug therapy ... | [
"We evaluated the profile of patients referred to the Fiocruz Outpatient Clinic , a reference center for the diagnosis and treatment of leprosy in Rio de Janeiro , RJ , and analyzed the origins and outcomes of these referrals .",
"This is an observational retrospective study based on information collected from th... | [
"Leprosy , a neglected disease , remains endemic in some developing countries despite the existence of a successful program to treat and cure patients .",
"While has been a drastic decrease in the number of patients , but we still have a stable number of new cases that is still very high in countries like India a... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"fungal spores",
"chromosome structure and function",
"centromeres",
"sequence assembly tools",
"fungi",
"model organisms",
"experimental organism systems",
"genome analysis",
"fungal reproduction",
"saccharomyces",
"research and analysis methods",
"genome complexity",
"mycology",
"genomic... | Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch | journal.pbio.2002128 | null | [
[
"A whole-genome duplication ( WGD ) occurred more than 100 million years ago in the common ancestor of 6 yeast genera in the ascomycete family Saccharomycetaceae , including Saccharomyces [1 , 2] .",
"Recent phylogenomic analysis has shown that the WGD was an allopolyploidization—that is , a hybridization... | [
"Many interspecies hybrids have been discovered in yeasts , but most of these hybrids are asexual and can replicate only mitotically .",
"Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility , restoring their ability to perform meiosis and sporulate .",
"H... | [
"It has recently been proposed that the whole-genome duplication ( WGD ) event that occurred during evolution of an ancestor of the yeast S . cerevisiae was the result of a hybridization between 2 parental yeast species that were significantly divergent in DNA sequence , followed by a doubling of the genome content... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant anatomy",
"keratinocytes",
"medicine and health sciences",
"cell cycle and cell division",
"cell processes",
"ovules",
"epithelial cells",
"germ cells",
"zygotes",
"endosperm",
"developmental biology",
"luminescent proteins",
"plant science",
"yellow fluorescent protein",
"embryos... | The Arabidopsis Receptor Kinase ZAR1 Is Required for Zygote Asymmetric Division and Its Daughter Cell Fate | journal.pgen.1005933 | null | [
[
"Asymmetric cell division is a fundamental process which produces daughter cells with different size and cell fate during embryonic and postembryonic development .",
"Irrespective of cell types or organisms , it requires a common set of coordinated events including the establishment and transduction of po... | [
"Asymmetric division of zygote is critical for pattern formation during early embryogenesis in plants and animals .",
"It requires integration of the intrinsic and extrinsic cues prior to and/or after fertilization .",
"How these cues are translated into developmental signals is poorly understood .",
"Here th... | [
"Flowering plants are featured as double fertilization , a process that the egg cell and the central cell of embryo sac fuse with a sperm and give rise to a diploid zygote and a triploid primary endosperm cell , respectively .",
"The zygote develops into embryo after cell division and differentiation , and starts... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"neurochemistry",
"sleep",
"depolarization",
"membrane potential",
"brain electrophysiology",
"brain",
"electrophysiology",
"neuroscience",
"learning and memory",
"surgical and invasive medical procedures",
"physiological processes",
"functional electrical sti... | A Thalamocortical Neural Mass Model of the EEG during NREM Sleep and Its Response to Auditory Stimulation | journal.pcbi.1005022 | null | [
[
"In the human electroencephalogram ( EEG ) the most prominent features of non-rapid eye movement ( NREM ) sleep are neocortical slow oscillations ( SO ) at ∼ 0 . 8 Hz [1] and fast thalamocortical spindles characterized by a waxing and waning waveform , with a frequency of 12 to 15 Hz [2] .",
"The cellular... | [
"Few models exist that accurately reproduce the complex rhythms of the thalamocortical system that are apparent in measured scalp EEG and at the same time , are suitable for large-scale simulations of brain activity .",
"Here , we present a neural mass model of the thalamocortical system during natural non-REM sl... | [
"Sleep plays a pivotal role for the consolidation of memory .",
"While REM sleep had originally been the focus of research due to its similarity with wakefulness , more recent studies suggest that different sleep stages are responsible for the consolidation of different types of memory .",
"To better understand... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | PLZF Regulates Fibroblast Growth Factor Responsiveness and Maintenance of Neural Progenitors | journal.pbio.1001676 | A transcription factor called Promyelocytic Leukemia Zinc Finger (PLZF) calibrates the balance between spinal cord progenitor maintenance and differentiation by enhancing their sensitivity to mitogens that are present in developing embryos. | [
[
"The formation of neural circuits within the developing central nervous system ( CNS ) depends upon the spatially and temporally ordered generation of distinct classes of neurons and glia from multipotent neural stem and progenitor cells ( NPCs ) .",
"An essential feature of this progression is the abilit... | [
"Distinct classes of neurons and glial cells in the developing spinal cord arise at specific times and in specific quantities from spatially discrete neural progenitor domains .",
"Thus , adjacent domains can exhibit marked differences in their proliferative potential and timing of differentiation .",
"However ... | [
"The embryonic spinal cord is organized into an array of discrete neural progenitor domains along the dorsoventral axis .",
"Most of these domains undergo two periods of differentiation , first producing specific classes of neurons and then generating distinct populations of glial cells at later times .",
"In a... | 2013 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"immune physiology",
"chemical compounds",
"enzymes",
"immunology",
"enzymology",
"organic compounds",
"vaccines",
"preventive medicine",
"amino acids",
"infectious disease control",
"antibodies",
"plants",
"flowering plants",
"vaccination and immunization... | Immune response of rats vaccinated orally with various plant-expressed recombinant cysteine proteinase constructs when challenged with Fasciola hepatica metacercariae | journal.pntd.0005451 | null | [
[
"Infection with Fasciola hepatica , a liver fluke , is one of the most significant veterinary problems due to the worldwide distribution of this parasite and a wide spectrum of host organisms [1] .",
"Fasciolosis causes economic losses of US$3 billion annually due to its impact on livestock production , t... | [
"Cysteine proteinases of Fasciola hepatica are important candidates for vaccine antigens because of their role in fluke biology and host-parasite relationships .",
"In our previous experiments , we found that a recombinant cysteine proteinase cloned from adult F . hepatica ( CPFhW ) can protect rats against liver... | [
"Infection with Fasciola hepatica , a liver fluke , is one of the most significant veterinary problems due to the worldwide distribution of this parasite , a wide spectrum of host organisms and the resulting economic loss .",
"Human fasciolosis caused by F . hepatica is recognised by the World Health Organization... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell death",
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"cardiovascular anatomy",
"oxygen",
"cancer treatment",
"cell processes",
"toxicology",
"oncology",
"toxicity",
"pharmaceutics",
"drug administration",
"blood vessels",
"chemistry",
"blood... | Leveraging Hypoxia-Activated Prodrugs to Prevent Drug Resistance in Solid Tumors | journal.pcbi.1005077 | null | [
[
"Solid tumor vasculature is characterized by a disorganized , aberrant network structure of tortuous , hyperpermeable blood vessels [1] .",
"These characteristics lead to nonuniform spatial distributions of drug and oxygen ( as well as other nutrients and growth factors ) throughout tumors , which in turn... | [
"Experimental studies have shown that one key factor in driving the emergence of drug resistance in solid tumors is tumor hypoxia , which leads to the formation of localized environmental niches where drug-resistant cell populations can evolve and survive .",
"Hypoxia-activated prodrugs ( HAPs ) are compounds des... | [
"It has been suggested that one key factor driving the emergence of drug resistance is the spatial heterogeneity in the distribution of drug and oxygen throughout a tumor due to disorganized tumor vasculatures .",
"Researchers have developed a class of novel drugs that penetrate to hypoxic regions where they are ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"urinary system procedures",
"medicine and health sciences",
"innate immune system",
"organ transplantation",
"immune cells",
"body fluids",
"immune physiology",
"cytokines",
"viral transmission and infection",
"immunology",
"microbiology",
"cell differentiation",
"surgical ... | Clinically Relevant Reactivation of Polyomavirus BK (BKPyV) in HLA-A02-Positive Renal Transplant Recipients Is Associated with Impaired Effector-Memory Differentiation of BKPyV-Specific CD8+ T Cells | journal.ppat.1005903 | null | [
[
"Polyomavirus BK ( BKPyV ) establishes a mode of latent infection in the vast majority of the general , immunocompetent population [1 , 2] .",
"However , in immunosuppressed renal transplant recipients ( RTRs ) , BKPyV can escape the weakened immunological response leading to reactivation in up to 60% of ... | [
"Polyomavirus BK ( BKPyV ) frequently reactivates in immunosuppressed renal transplant recipients ( RTRs ) and may lead to graft loss due to BKPyV-induced interstitial nephritis ( BKVN ) .",
"Little is known on the differentiation of CD8+ T cells targeting BKPyV in RTRs .",
"Here we investigated whether BKPyV-s... | [
"In immunosuppressed renal transplant recipients ( RTRs ) , BKPyV frequently reactivates from latency and may cause severe interstitial nephritis in the allograft ( BKVN ) .",
"Not only is there no effective treatment , it also not understood why BKVN arises in some RTRs but not in all .",
"In the current study... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Toxoplasma gondii Relies on Both Host and Parasite Isoprenoids and Can Be Rendered Sensitive to Atorvastatin | journal.ppat.1003665 | null | [
[
"Toxoplasma gondii is an important intracellular pathogen causing disease in humans and animals .",
"Most human infections are uncomplicated but the parasite persists and the chronic infection can be reactivated upon immunosuppression in patients undergoing organ transplants , cancer chemotherapy [1] , or... | [
"Intracellular pathogens have complex metabolic interactions with their host cells to ensure a steady supply of energy and anabolic building blocks for rapid growth .",
"Here we use the obligate intracellular parasite Toxoplasma gondii to probe this interaction for isoprenoids , abundant lipidic compounds essenti... | [
"Toxoplasma gondii is an obligate intracellular parasite and is not able to replicate outside the host cell .",
"The parasite lives in a specialized parasitophorous vacuole in contact with the host cytoplasm through the parasitophorous vacuole membrane .",
"It is highly likely that a very active exchange of met... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Artificial Warthog Burrows Used to Sample Adult and Immature Tsetse (Glossina spp) in the Zambezi Valley of Zimbabwe | journal.pntd.0003565 | null | [
[
"Adult tsetse flies ( Glossina spp , Diptera: Glossinidae ) are the vectors of human and animal trypanosomiasis in Africa and , as such , have been the object of intense study since the early 20th century and the source of an extensive literature on their field biology .",
"Our knowledge of the ( briefly ... | [
"The biology of adult tsetse ( Glossina spp ) , vectors of trypanosomiasis in Africa , has been extensively studied – but little is known about larviposition in the field .",
"In September-November 1998 , in the hot-dry season in Zimbabwe’s Zambezi Valley , we used artificial warthog burrows to capture adult fema... | [
"Adult tsetse , vectors of trypanosomiasis , have been extensively studied for more than 100 years , but little is known about larviposition behaviour in the field .",
"Pupae are generally collected in the field via arduous searches of putative larviposition sites .",
"Females have never been sampled in the fie... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"immune cells",
"cytokines",
"immunity to infections",
"immune suppression",
"immunology",
"adaptive immunity",
"neglected tropical diseases",
"immunoregulation",
"immunomodulation",
"lymphatic filariasis",
"infectious diseases",
"inflammation",
"t cells",
"immune response",
... | Regulatory T Cells in Human Lymphatic Filariasis: Stronger Functional Activity in Microfilaremics | journal.pntd.0001655 | null | [
[
"Lymphatic filariasis ( LF ) , caused by nematodes Wuchereria bancrofti , Brugia malayi and B . timori , affects around 120 million people worldwide and additionally 2 billion people are at risk in endemic areas [1] .",
"Although not life-threatening , chronic manifestation of disease causes major disabil... | [
"Infection with filarial parasites is associated with T cell hyporesponsiveness , which is thought to be partly mediated by their ability to induce regulatory T cells ( Tregs ) during human infections .",
"This study investigates the functional capacity of Tregs from different groups of filarial patients to suppr... | [
"Lymphatic filariasis is a neglected disease still prominent in low-resource settings and is very disabling when it progresses to chronic pathology caused by lymphedema .",
"Until now , studies on the contribution of Tregs to lymphocyte hyporesponsiveness in human filariasis have focused on frequency and phenotyp... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"sequencing techniques",
"engineering and technology",
"gene regulation",
"synthetic biology",
"regulatory proteins",
"microbiology",
"dna-binding proteins",
"invertebrate genomics",
"transcription factors",
"bacterial genetics",
"sequence motif analysis",
"molecular biology ... | The Role of Genome Accessibility in Transcription Factor Binding in Bacteria | journal.pcbi.1004891 | null | [
[
"In order to adapt to different environmental challenges , microorganisms need to precisely control the expression of specific sets of genes at defined magnitudes at any given moment [1 , 2] .",
"This control is mediated by regulatory proteins such as transcription factors ( TF ) that are able to recogniz... | [
"ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression .",
"However , the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions .",
"Furthermore , ChIP-seq data often poorly correlate with in v... | [
"A quantitative description of transcription factor ( TF ) binding in vivo is critical for our understanding of gene regulation .",
"Chromatin Immunoprecipitation followed by sequencing ( ChIP-seq ) provides a genome-scale map of TF-binding .",
"However , a quantitative characterization of the impact of genome ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biomacromolecule-ligand interactions",
"protein interactions",
"microbiology",
"host-pathogen interaction",
"parasitology",
"glycoproteins",
"proteins",
"cell adhesion",
"extracellular matrix",
"biology",
"recombinant proteins",
"proteomics",
"biochemistry",
"transmembrane proteins",
"c... | Semaphorin-7A Is an Erythrocyte Receptor for P. falciparum Merozoite-Specific TRAP Homolog, MTRAP | journal.ppat.1003031 | null | [
[
"Plasmodium falciparum is the etiological agent of the most severe form of malaria causing over one million deaths annually , primarily in African children [1] .",
"The parasite lifecycle is complex and involves distinct stages that can recognise and invade differentiated cell types of both the human host... | [
"The motility and invasion of Plasmodium parasites is believed to require a cytoplasmic actin-myosin motor associated with a cell surface ligand belonging to the TRAP ( thrombospondin-related anonymous protein ) family .",
"Current models of invasion usually invoke the existence of specific receptors for the TRAP... | [
"Apicomplexan parasites are one of the most significant groups of pathogens infecting humans and include Plasmodium falciparum , the parasite responsible for malaria .",
"These parasites critically depend on their human host and must invade our cells to multiply; therefore , understanding this invasion process - ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cognitive neuroscience",
"behavioral neuroscience",
"social and behavioral sciences",
"psychology",
"emotions",
"cognition",
"decision making",
"behavior",
"biology",
"neuroscience"
] | Limbic Justice—Amygdala Involvement in Immediate Rejection in the Ultimatum Game | journal.pbio.1001054 | null | [
[
"Research within behavioral economics and psychology has demonstrated that human decisions are based on more dimensions than simply maximization of monetary reward [1]–[3] .",
"One important factor with prominent impact on decision making is the influence of emotional processes [4] .",
"Emotional proc... | [
"Imaging studies have revealed a putative neural account of emotional bias in decision making .",
"However , it has been difficult in previous studies to identify the causal role of the different sub-regions involved in decision making .",
"The Ultimatum Game ( UG ) is a game to study the punishment of norm-vio... | [
"It is well-established that emotions influence decision making .",
"One way of studying this relationship is the Ultimatum Game , which has revealed that subjects punish unfair behavior in others in spite of receiving a concomitant economic loss .",
"Previous brain imaging studies have suggested that this deci... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Disclaimer"
] | [
"taxonomy",
"medicine and health sciences",
"burkholderia pseudomallei",
"pathology and laboratory medicine",
"pathogens",
"melioidosis",
"geographical locations",
"microbiology",
"north america",
"bacterial diseases",
"burkholderia cepacia complex",
"phylogenetics",
"data management",
"ca... | Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico | journal.pntd.0007727 | null | [
[
"The Burkholderia genus is a group of diverse , primarily soil-dwelling , Gram-negative bacteria that have many strategies to survive and persist in soil , including acid tolerance [1] and intrinsic antibiotic resistance [2] .",
"These species employ a wide variety of ecological strategies , including deg... | [
"Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis .",
"The global burden and distribution of melioidosis is poorly understood , including in the Caribbean .",
"B . pseudomallei was previously isolated from humans and soil in eastern Puerto Rico but the abundance and ... | [
"The objective of this study was to examine the distribution and abundance of Burkholderia pseudomallei in the environment in Puerto Rico .",
"B . pseudomallei is a microbe that lives in soil and causes the disease melioidosis .",
"We conducted sampling around Puerto Rico to survey for the presence of B . pseud... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"chicken",
"in vitro",
"vertebrates",
"computational biology"
] | Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model | journal.pcbi.0030076 | null | [
[
"Skeletal pattern formation in the developing vertebrate limb depends on interactions of precartilage mesenchymal cells with factors that control the spatiotemporal differentiation of cartilage .",
"The most fundamental skeletogenic processes involve the spatial separation of precartilage mesenchyme into ... | [
"Cells of the embryonic vertebrate limb in high-density culture undergo chondrogenic pattern formation , which results in the production of regularly spaced “islands” of cartilage similar to the cartilage primordia of the developing limb skeleton .",
"The first step in this process , in vitro and in vivo , is the... | [
"The development of an organism from embryo to adult includes processes of pattern formation that involve the interactions over space and time of independent cells to form multicellular structures .",
"Computational models permit exploration of possible alternative mechanisms that reproduce biological patterns an... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"biochemistry",
"lipids",
"epidemiology",
"genetics",
"biology",
"human genetics",
"genetic epidemiology"
] | Gene-Based Sequencing Identifies Lipid-Influencing Variants with Ethnicity-Specific Effects in African Americans | journal.pgen.1004190 | null | [
[
"The role of the distribution of serum lipids in influencing disease risk is well-established .",
"Serum lipids are under the influence of genetic and non-genetic ( e . g . , dietary ) factors .",
"Lipids are routinely evaluated in the screening for and monitoring of metabolic disorders .",
"Effec... | [
"Although a considerable proportion of serum lipids loci identified in European ancestry individuals ( EA ) replicate in African Americans ( AA ) , interethnic differences in the distribution of serum lipids suggest that some genetic determinants differ by ethnicity .",
"We conducted a comprehensive evaluation of... | [
"Most of the work on the genetic epidemiology of serum lipids in African Americans ( AA ) has focused on replicating findings that were identified in European ancestry individuals .",
"While this can be very informative about the generalizability of lipids loci across populations , African ancestry-specific varia... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology/plant growth and development",
"plant biology/plant genetics and gene expression",
"genetics and genomics/plant genetics and gene expression",
"genetics and genomics/gene expression"
] | Arabidopsis COMPASS-Like Complexes Mediate Histone H3 Lysine-4 Trimethylation to Control Floral Transition and Plant Development | journal.pgen.1001330 | null | [
[
"Histone lysine methylation regulates chromatin structure and gene transcription in eukaryotes .",
"Various lysine residues on histones can be methylated and the ε-amino group of lysines can be mono- , di- and tri-methylated .",
"Lysine methylation is linked with transcriptional activation or repressi... | [
"Histone H3 lysine-4 ( H3K4 ) methylation is associated with transcribed genes in eukaryotes .",
"In Drosophila and mammals , both di- and tri-methylation of H3K4 are associated with gene activation .",
"In contrast to animals , in Arabidopsis H3K4 trimethylation , but not mono- or di-methylation of H3K4 , has ... | [
"Histones can be covalently modified and histone modifications regulate chromatin structure and gene transcription .",
"One such modification is histone H3 lysine-4 ( H3K4 ) methylation , which can be mono- , di- , or tri-methylated .",
"In animals such as fruitfly and mammals , both di- and tri-methylation of ... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biofilms",
"exopolysaccharides",
"gene regulation",
"microbiology",
"genetic elements",
"research and analysis methods",
"sequence analysis",
"sequence alignment",
"bioinformatics",
"gene expression",
"genetic loci",
"biochemistry",
"polysaccharides",
"database and informatics methods",
... | Genome-scale analysis of the genes that contribute to Burkholderia pseudomallei biofilm formation identifies a crucial exopolysaccharide biosynthesis gene cluster | journal.pntd.0005689 | null | [
[
"B . pseudomallei , an environmental saprophyte , is the etiological agent of melioidosis and has been traditionally described as being endemic to Northern Australia and Southeast Asia [1] .",
"However , an increasing body of evidence indicates B . pseudomallei is more widely distributed than previously t... | [
"Burkholderia pseudomallei , the causative agent of melioidosis , is an important public health threat due to limited therapeutic options for treatment .",
"Efforts to improve therapeutics for B . pseudomallei infections are dependent on the need to understand the role of B . pseudomallei biofilm formation and it... | [
"B . pseudomallei , the etiological agent of melioidosis , is an emerging pathogen with limited therapeutic options and no available vaccines .",
"A better understanding of the role of biofilm formation during pathogenesis will aid in melioidosis diagnosis and the development of new therapeutics and vaccines .",
... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"fish",
"otolith",
"vesicles",
"ears",
"vertebrates",
"animals",
"animal models",
"osteichthyes",
"developmental biology",
"inner ear",
"model organisms",
"experimental organism systems",
"embryos",
"cellular structures and organelles",
"research and ana... | Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression | journal.pgen.1008051 | null | [
[
"The otic placode—precursor of the vertebrate inner ear—has the remarkable ability to generate a mirror-image organ with duplicate structures under some experimental conditions in fish and amphibians , as originally described by R . G . Harrison over eighty years ago ( reviewed in [1] ) .",
"Understanding... | [
"In the zebrafish , Fgf and Hh signalling assign anterior and posterior identity , respectively , to the poles of the developing ear .",
"Mis-expression of fgf3 or inhibition of Hh signalling results in double-anterior ears , including ectopic expression of hmx3a .",
"To understand how this double-anterior patt... | [
"Understanding how signalling molecules impart information to developing organ systems , and how this is interpreted through networks of gene activity , is a key goal of developmental genetic analysis .",
"In the developing zebrafish inner ear , differences in gene expression arise between the anterior and poster... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"virology",
"biology",
"microbiology"
] | Silent Circulation of St. Louis Encephalitis Virus Prior to an Encephalitis Outbreak in Cordoba, Argentina (2005) | journal.pntd.0001489 | null | [
[
"The St . Louis encephalitis ( SLE ) , caused by the homonymous virus ( SLEV , genus Flavivirus , family Flaviviridae ) , is a complex zoonoses in the New World [1] .",
"In South America , SLE is an emerging arbovirosis , with febrile illness and encephalitis cases reported in Argentina and Brazil [2] , [... | [
"St . Louis encephalitis virus is a complex zoonoses .",
"In 2005 , 47 laboratory-confirmed and probable clinical cases of SLEV infection were reported in Córdoba , Argentina .",
"Although the causes of 2005 outbreak remain unknown , they might be related not only to virological factors , but also to ecological... | [
"The St . Louis encephalitis is a complex zoonoses in the New World .",
"In South America ( Argentina and Brazil ) , SLE is an emerging arbovirosis .",
"SLEV reemerged in Argentina during 2002 and , since then , outbreaks have been reported in 2005 , 2006 , 2010 and 2011 .",
"During the 2005 outbreak two SLEV... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"medicine and health sciences",
"rna interference",
"nervous system",
"cell processes",
"electrophysiology",
"neuroscience",
"animals",
"animal models",
"drosophila melanogaster",
"model organisms",
"molecular biology techniques",
"epigenetics",
"drosophila",
"research a... | Dbo/Henji Modulates Synaptic dPAK to Gate Glutamate Receptor Abundance and Postsynaptic Response | journal.pgen.1006362 | null | [
[
"Coordinated action and communication between pre- and postsynapses are essential in maintaining synaptic strength and plasticity .",
"Presynaptic strength or release probability of synaptic vesicles involves layers of regulation including vesicle docking , fusion , and recycling , as well as endocytosis ... | [
"In response to environmental and physiological changes , the synapse manifests plasticity while simultaneously maintains homeostasis .",
"Here , we analyzed mutant synapses of henji , also known as dbo , at the Drosophila neuromuscular junction ( NMJ ) .",
"In henji mutants , NMJ growth is defective with appea... | [
"To meet various developmental or environmental needs , the communication between pre- and postsynapse can be modulated in different aspects .",
"The release of presynaptic vesicles can be regulated at the steps of docking , membrane fusion and endocytosis .",
"Upon receiving neurotransmitter stimuli from presy... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"plant anatomy",
"medicine and health sciences",
"immunology",
"brassica",
"plant biotechnology",
"plant science",
"model organisms",
"genetically modified plants",
"plants",
"extraction techniques",
"genetic engineering",
"research and analysis methods",
"arabidopsis thal... | Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity | journal.pgen.1005990 | null | [
[
"In plants , receptors that sense pathogen attack are central players in the biotic stress signaling network .",
"Receptor activation triggers innate immunity pathways to protect cells and tissues from disease .",
"In a first line of defense , surface pattern recognition receptors ( PRRs ) bind microb... | [
"Plants have a large panel of nucleotide-binding/leucine rich repeat ( NLR ) immune receptors which monitor host interference by diverse pathogen molecules ( effectors ) and trigger disease resistance pathways .",
"NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced ... | [
"Plants tune their cellular and developmental programs to different environmental stimuli .",
"Central players in the plant biotic stress response network are intracellular NLR receptors which intercept specific disease-inducing molecules ( effectors ) produced by pathogenic microbes .",
"Variation in NLR gene ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"epistasis",
"mutation",
"genetic mutation",
"mutation types",
"phenotypes",
"genetic screens",
"heredity",
"genetics",
"genetic suppression",
"population genetics",
"biology",
"complex traits",
"gene function"
] | The Conditional Nature of Genetic Interactions: The Consequences of Wild-Type Backgrounds on Mutational Interactions in a Genome-Wide Modifier Screen | journal.pgen.1003661 | null | [
[
"Fundamental to the logic of genetic analysis is that the observed variation in a phenotype for a genetically mediated trait is causally linked to one or more DNA lesions/variants .",
"However , it is well known that the phenotypic effects of many individual mutant alleles are context dependent , with res... | [
"The phenotypic outcome of a mutation cannot be simply mapped onto the underlying DNA variant .",
"Instead , the phenotype is a function of the allele , the genetic background in which it occurs and the environment where the mutational effects are expressed .",
"While the influence of genetic background on the ... | [
"Examining the consequences of how one mutation behaves when in the presence of a second mutation forms the basis of our understanding of genetic interactions , and is part of the fundamental toolbox of genetic analysis .",
"Yet the logical interpretation of such mutational interactions depends on the generality ... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational biology/evolutionary modeling",
"mathematics",
"oncology"
] | Evolution of Resistance to Targeted Anti-Cancer Therapies during Continuous and Pulsed Administration Strategies | journal.pcbi.1000557 | null | [
[
"Alteration of the normal regulation of cell-cycle progression , division and death lies at the heart of the processes driving tumorigenesis .",
"A detailed molecular understanding of these processes provides an opportunity to design targeted anti-cancer agents .",
"The term ‘targeted therapy’ refers ... | [
"The discovery of small molecules targeted to specific oncogenic pathways has revolutionized anti-cancer therapy .",
"However , such therapy often fails due to the evolution of acquired resistance .",
"One long-standing question in clinical cancer research is the identification of optimum therapeutic administra... | [
"Recently , the field of anti-cancer therapy has witnessed a revolution by the discovery of targeted therapy , which refers to compounds targeting specific pathways causing abnormal growth of cancer cells .",
"The clinical success of such drugs has been limited by the evolution of acquired resistance to these com... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide association studies",
"quantitative trait association studies",
"statistical analysis of genetic association",
"inflammation",
"medicine and health sciences",
"genetic association studies",
"genome analysis",
"genetics",
"biology and life sciences",
"immunology",
"computational biol... | Genome-Wide Association Study of CSF Levels of 59 Alzheimer's Disease Candidate Proteins: Significant Associations with Proteins Involved in Amyloid Processing and Inflammation | journal.pgen.1004758 | null | [
[
"Cerebrospinal fluid ( CSF ) contains promising biomarkers for neurological and psychiatric diseases such as Alzheimer's disease ( AD ) , schizophrenia , and Parkinson's disease [1]–[4] .",
"The brain directly and rapidly influences the composition of CSF , and as such , CSF analytes may provide insights ... | [
"Cerebrospinal fluid ( CSF ) 42 amino acid species of amyloid beta ( Aβ42 ) and tau levels are strongly correlated with the presence of Alzheimer's disease ( AD ) neuropathology including amyloid plaques and neurodegeneration and have been successfully used as endophenotypes for genetic studies of AD .",
"Additio... | [
"The use of quantitative endophenotypes from cerebrospinal fluid has led to the identification of several genetic variants that alter risk or rate of progression of Alzheimer's disease .",
"Here we have analyzed the levels of 58 disease-related proteins in the cerebrospinal fluid for association with millions of ... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology",
"forestry",
"infectious disease epidemiology",
"plant biology",
"statistics",
"population dynamics",
"spatial epidemiology",
"integrated control",
"plant science",
"mathematics",
"pest control",
"plant pathology",
"population biology",
"epidemiology",
"b... | Landscape Epidemiology and Control of Pathogens with Cryptic and Long-Distance Dispersal: Sudden Oak Death in Northern Californian Forests | journal.pcbi.1002328 | null | [
[
"The invasion of ecosystems by non-native plant pathogens and insects [1] , [2] , [3] , [4] poses a growing threat to ecosystem function and conservation as global trade , travel and environmental change create opportunities for introduction and establishment of exotic organisms [5] , [6] , [7] , [8] .",
... | [
"Exotic pathogens and pests threaten ecosystem service , biodiversity , and crop security globally .",
"If an invasive agent can disperse asymptomatically over long distances , multiple spatial and temporal scales interplay , making identification of effective strategies to regulate , monitor , and control diseas... | [
"We discuss principles governing the spread and management of diseases in natural forest ecosystems .",
"Invasive organisms are damaging world forests and agricultural crops at an increasing rate and severity due to global trade and environmental disturbances .",
"While prevention is the best option , practitio... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"peroxidases",
"chemical compounds",
"plant growth and development",
"ethylene signaling cascade",
"ethylene",
"enzymes",
"brassica",
"enzymology",
"organic compounds",
"hormones",
"developmental biology",
"plant science",
"model organisms",
"plant hormones",
"experimental organism syste... | Brassinosteroids regulate root growth by controlling reactive oxygen species homeostasis and dual effect on ethylene synthesis in Arabidopsis | journal.pgen.1007144 | null | [
[
"Roots are important plant ground organs , which absorb water and nutrients to control plant growth and development .",
"In higher plants , root growth is maintained by coordinating cell proliferation and differentiation [1–3] .",
"Plant hormones have been known to play a crucial role in the regulatio... | [
"The brassinosteroids ( BRs ) represent a class of phytohormones , which regulate numerous aspects of growth and development .",
"Here , a det2-9 mutant defective in BR synthesis was identified from an EMS mutant screening for defects in root length , and was used to investigate the role of BR in root development... | [
"Both brassinosteroids ( BRs ) and ethylene have been known to control root growth and development .",
"ROS have been also reported to play an important role in root development .",
"However , the relationship between BRs and ethylene or ROS in root growth and development was not addressed before .",
"In this... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"blood cells",
"taxonomy",
"medicine and health sciences",
"ecology and environmental sciences",
"immune cells",
"microbiome",
"immunology",
"microbiology",
"data management",
"b cell receptors",
"memory b cells",
"thermodynamics",
"microbial genomics",
"ecological metrics",
"immune syst... | Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes | journal.pcbi.1005362 | null | [
[
"The community , i . e . the assemblage of organisms co-existing in a given space and time , is central to much of ecology [1] , and since Darwin’s “entangled bank” [2] one of the great challenges of biology is to explain the observed species diversity in communities mechanistically as a consequence of intera... | [
"The community , the assemblage of organisms co-existing in a given space and time , has the potential to become one of the unifying concepts of biology , especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively .",
"In this spirit we show that a tool from co... | [
"Living things are parts of complex communities , similar to humans living in cities .",
"A quantitative way of describing such communities is to measure the abundance of each species in the community so that a sorted list of abundance numbers is produced , a so-called Rank Abundance Distribution ( RAD ) .",
"W... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"hepatitis",
"hepatitis b",
"dna modification",
"nucleic acids",
"dna viruses",
"viral classification",
"virology",
"dna",
"dna repair",
"biology",
"microbiology",
"molecular cell biology",
"viral diseases"
] | Uracil DNA Glycosylase Counteracts APOBEC3G-Induced Hypermutation of Hepatitis B Viral Genomes: Excision Repair of Covalently Closed Circular DNA | journal.ppat.1003361 | null | [
[
"The hepatitis B virus ( HBV ) is one of the major causative factors of liver cirrhosis and hepatocellular carcinoma .",
"Chronic inflammation due to persistent HBV infection plays a major causative role in these severe liver diseases .",
"However , it is still unknown how HBV establishes persistent i... | [
"The covalently closed circular DNA ( cccDNA ) of the hepatitis B virus ( HBV ) plays an essential role in chronic hepatitis .",
"The cellular repair system is proposed to convert cytoplasmic nucleocapsid ( NC ) DNA ( partially double-stranded DNA ) into cccDNA in the nucleus .",
"Recently , antiviral cytidine ... | [
"Human cytidine deaminases , AID/APOBECs , are restriction factors against various types of viruses .",
"These proteins have the ability to introduce a cytidine-to-uridine ( C-to-U ) hypermutation in the viral DNAs of the hepadnaviruses hepatitis B virus ( HBV ) and duck HBV ( DHBV ) models .",
"It is well know... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"classical mechanics",
"atmospheric science",
"astronomical sciences",
"social sciences",
"light",
"neuroscience",
"electromagnetic radiation",
"probability distribution",
"luminance",
"mathematics",
"reflection",
"visible light",
"skewness",
"research and... | Material and shape perception based on two types of intensity gradient information | journal.pcbi.1006061 | null | [
[
"The physical parameters that affect a retinal image are extremely complex .",
"In addition , the same retinal image can be produced from an infinite number of combinations of materials , shapes , and illuminations in the distal world .",
"Therefore , it is a hard ill-posed problem to estimate what ex... | [
"Visual estimation of the material and shape of an object from a single image includes a hard ill-posed computational problem .",
"However , in our daily life we feel we can estimate both reasonably well .",
"The neural computation underlying this ability remains poorly understood .",
"Here we propose that th... | [
"Objects in our visual world contain a variety of material information .",
"Although such information enables us to experience rich material impressions , it can be a distraction for the estimation of other physical properties such as shapes , albedos , and illuminations .",
"The coupled estimation of these pro... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/hiv infection and aids"
] | Damaged Intestinal Epithelial Integrity Linked to Microbial Translocation in Pathogenic Simian Immunodeficiency Virus Infections | journal.ppat.1001052 | null | [
[
"Persistently elevated immune activation characterized by polyclonal B cell activation [1] , increased T-cell turnover [2] , increased frequencies of T cells with an activated phenotype [3] , and increased levels of pro-inflammatory molecules [4] is a hallmark of disease progression in pathogenic HIV/SIV prim... | [
"The chronic phase of HIV infection is marked by pathological activation of the immune system , the extent of which better predicts disease progression than either plasma viral load or CD4+ T cell count .",
"Recently , translocation of microbial products from the gastrointestinal tract has been proposed as an und... | [
"Persistent activation of the immune system is a hallmark of chronic HIV/SIV infections and predicts disease progression better than either plasma viral load or CD4+ T cell count .",
"While the causes of immune activation during chronic infection are likely multifactorial , recent work has shown that microbial tr... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"urology",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"population genetics",
"tropical diseases",
"microbiology",
"treponematoses",
"bacterial diseases",
"next-generation sequencing",
"sexually transmitted diseases",
"genome ana... | Profile of the tprK gene in primary syphilis patients based on next-generation sequencing | journal.pntd.0006855 | null | [
[
"Syphilis , caused by Treponema pallidum subsp .",
"pallidum , is an ancient sexually transmitted disease that was initially recognized in the 15th century and is a public health threat that cannot be neglected [1 , 2] .",
"The completion of the first whole-genome sequencing of the Nichols strain of T... | [
"The highly variable tprK gene of Treponema pallidum has been acknowledged to be one of the mechanisms that causes persistent infection .",
"Previous studies have mainly focused on the heterogeneity in tprK in propagated strains using a clone-based Sanger approach .",
"Few studies have investigated tprK directl... | [
"Variations in tprK have been acknowledged to be the major contributors to persistent Treponema pallidum infections .",
"Previous studies were based on the clone-based Sanger approach , and most of them were performed in propagated strains using rabbits , which could not reflect the actual heterogeneous character... | 2019 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"bacteriology",
"organismal evolution",
"gut bacteria",
"population genetics",
"microbiology",
"twins",
"developmental biology",
"metagenomics",
"microbial evolution",
"evolutionary adaptation",
"population biology",
"bacteria",
"evolutionary genetics",
"genetics",
"biology and life scie... | Evolutionary dynamics of bacteria in the gut microbiome within and across hosts | journal.pbio.3000102 | A population genetic analysis of human gut metagenomes reveals short-term evolution within individual species of gut bacteria, both within individual hosts, and across the larger population. | [
[
"The gut microbiome is a complex ecosystem comprised of a diverse array of microbial organisms .",
"The abundances of different species and strains can vary dramatically based on diet [1] , host species [2] , and the identities of other co-colonizing taxa [3] .",
"These rapid shifts in community compo... | [
"Gut microbiota are shaped by a combination of ecological and evolutionary forces .",
"While the ecological dynamics have been extensively studied , much less is known about how species of gut bacteria evolve over time .",
"Here , we introduce a model-based framework for quantifying evolutionary dynamics within... | [
"The human gut harbors a diverse microbial community whose composition is shaped by a variety of ecological forces .",
"Given the high rates of turnover , the residents of this community might also have the opportunity to evolve over time by acquiring heritable changes to their genomes .",
"Yet , despite the po... | 2019 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"neural networks",
"caenorhabditis",
"nervous system",
"electrophysiology",
"neuroscience",
"animals",
"motor neurons",
"animal models",
"caenorhabditis elegans",
"model organisms",
"brain mapping",
"experimental organism systems",
"intern... | Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome | journal.pcbi.1005989 | null | [
[
"Neuronal connectivity provides the substrate for integrated brain function .",
"Recent years have seen several systematic and large-scale attempts to generate comprehensive wiring diagrams , or connectomes , of nervous systems [1] in species as diverse as the Caenorhabditis elegans [2 , 3] , Drosophila m... | [
"Studies of nervous system connectivity , in a wide variety of species and at different scales of resolution , have identified several highly conserved motifs of network organization .",
"One such motif is a heterogeneous distribution of connectivity across neural elements , such that some elements act as highly ... | [
"Some elements of neural systems possess many more connections than others , marking them as network hubs .",
"These hubs are often densely interconnected with each other , forming a so-called rich-club that is thought to support integrated function .",
"Recent work in the mouse suggests that connected pairs of... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/microbial growth and development",
"genetics and genomics/gene function",
"microbiology/plant-biotic interactions",
"cell biology/cell signaling"
] | PdeH, a High-Affinity cAMP Phosphodiesterase, Is a Key Regulator of Asexual and Pathogenic Differentiation in Magnaporthe oryzae | journal.ppat.1000897 | null | [
[
"Heterotrimeric G protein signaling utilizes cyclic AMP ( cAMP ) as a second messenger , to mediate the transduction of extracellular stimuli to the intracellular downstream signaling components in several eukaryotes , including the pathogenic fungi .",
"The cAMP pathway is a highly conserved signaling mo... | [
"Cyclic AMP-dependent pathways mediate the communication between external stimuli and the intracellular signaling machinery , thereby influencing important aspects of cellular growth , morphogenesis and differentiation .",
"Crucial to proper function and robustness of these signaling cascades is the strict regula... | [
"Magnaporthe oryzae , an economically important fungal pathogen that causes the blast disease in rice and several cereal crops , is a model organism for studying fungus-host interactions .",
"M . oryzae reproduces asexually by producing spores , which can switch to an infectious disease-causing mode of developmen... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"fish",
"medicine and health sciences",
"vertebrates",
"pigments",
"animals",
"neuroscience",
"alleles",
"epithelial cells",
"animal models",
"osteichthyes",
"developmental biology",
"model organisms",
"stem cells",
"materials science",
"experimental organism systems",
"chromatophores"... | Distinct interactions of Sox5 and Sox10 in fate specification of pigment cells in medaka and zebrafish | journal.pgen.1007260 | null | [
[
"Cell fate specification from multipotent stem cells is a fundamental process during embryonic development .",
"The mechanisms determining how multipotent progenitors choose a diversity of different cell fates is key to understanding the generation of multiple cell types in the animal body .",
"The ne... | [
"Mechanisms generating diverse cell types from multipotent progenitors are fundamental for normal development .",
"Pigment cells are derived from multipotent neural crest cells and their diversity in teleosts provides an excellent model for studying mechanisms controlling fate specification of distinct cell types... | [
"How individual cell fates become specified from multipotent progenitors is a fundamental question in developmental and stem cell biology .",
"Body pigment cells derive from a multipotent progenitor , but while in zebrafish there are three types of pigment cells ( melanocytes , iridophores and xanthophores ) , in... | 2018 |
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