Kinetically-Defined Component Actions in Gene Repression
The mode and position of action of four factors is qualitatively identical in gene repression to that previously found in gene ... We describe the conditions under which a theoretical model for gene repression reveals the kinetically-defined mechanism and ... This insight and simplification should facilitate clinical efforts to maximize desired outcomes in gene induction or repression ... the same cannot be said of cofactors that modulate steroid-regulated gene activity. ...https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004122
PLOS Genetics: Publishing science, accelerating research
Mutation of the Mouse Syce1 Gene Disrupts Synapsis and Suggests a Link between Synaptonemal Complex Structural Components and ... Mutation of the Mouse Syce1 Gene Disrupts Synapsis and Suggests a Link between Synaptonemal Complex Structural Components and ... Gene Dosage Effects of the Imprinted Delta-Like Homologue 1 (Dlk1/Pref1) in Development: Implications for the Evolution of ... A Gene-Based Linkage Map for Bicyclus anynana Butterflies Allows for a Comprehensive Analysis of Synteny with the Lepidopteran ...https://journals.plos.org/plosgenetics/issue?id=10.1371/issue.pgen.v05.i02
The Cardiac Acetyl-Lysine Proteome
Gene Ontology annotation of broad Cellular Components (Table 1) was obtained from the Ensembl Gene annotation. More detailed ... Sheet 3: Gene set enrichment of ontologies related to cellular components. These Tables include only terms deemed statistically ... Gene ontologies Is the Subject Area "Gene ontologies" applicable to this article? Yes. No. ... BINGO Analysis. Sheet 1: Gene set enrichment of ontologies related to biological processes. Sheet 2: Gene set enrichment of ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067513
PLOS Pathogens: Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two...
Here we have shown using whole genome sequencing of 10 S. aureus strains and gene replacement experiments on sequential S. ... Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component ... B) Amino acid sequences of the walR and walK genes. Domains are highlighted in color according to figure 1A. Identified ...http://journals.plos.org/plospathogens/article/figure?id=10.1371/journal.ppat.1002359.g001
A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci
These latest associated regions add to the growing repertoire of gene networks predisposing to T1D. ... uncovering the genes contributing to this disease has proven challenging. However, in the past three years there has been ... Author Summary Despite the fact that there is clearly a large genetic component to type 1 diabetes (T1D), ... Despite the fact that there is clearly a large genetic component to type 1 diabetes (T1D), uncovering the genes contributing to ...https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002293
Patterns of Cis Regulatory Variation in Diverse Human Populations
We identify ∼5,700 genes whose expression levels are associated with genetic variation located physically close to the gene, ... We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover ... We analyzed genome-wide gene expression in human cell lines derived from 726 unrelated individuals representing 8 global ... and studies have identified regions of the genome harboring genetic variation affecting gene expression levels. To assess the ...https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002639
Identification of Novel Components Influencing Colonization Factor Antigen I Expression in Enterotoxigenic Escherichia coli
To identify novel components modulating CF surface expression, 20 components relevant to the intestinal environment were ... Effects of individual components on surface expression of the archetype CF, CFA/I, were screened using a fractional factorial ... Seven components, including porcine gastric mucin, lincomycin, glutamine, and glucose were found to induce CFA/I surface ... The optimum concentration for each component was identified, thereby generating a novel culture media, SP1, for CFA/I ...http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141469
Web-Based Genome-Wide Association Study Identifies Two Novel Loci and a Substantial Genetic Component for Parkinson's Disease
The suggestively associated SNP rs28233572 lies in a gene-poor region with only one candidate gene downstream, USP25, encoding ... in ). In early-onset PD, mutations in six specific genes (SNCA, PRKN, PINK1, DJ1, LRRK2, and GBA) have been reported to ... synuclein) ,  and LRRK2 (leucine-rich repeat kinase 2) ,  genes. Autosomal recessive factors include mutations in ... th principal component of the genotype data matrix. Reported odds ratios for each SNP relative to the minor allele were defined ...http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002141&imageURI=info:doi/10.1371/journal.pgen.1002141.t003
Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes
Author Summary We delineate a logical model encompassing 48 components and 82 regulatory interactions controlling mesoderm ... Reim I, Frasch M. The Dorsocross T-box genes are key components of the regulatory network controlling early cardiogenesis in ... Gene regulation Is the Subject Area "Gene regulation" applicable to this article? Yes. No. ... Gene expression Is the Subject Area "Gene expression" applicable to this article? Yes. No. ...https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005073
Dynein Modifiers in C. elegans: Light Chains Suppress Conditional Heavy Chain Mutants
The identification and initial characterization of this group of genes represents a route to identify genes that are not ... Additionally, we identified four dynein components that appear to negatively regulate the force-generating dynein heavy chain. ... We determined that 20 of the 49 genes we identified specifically influenced the viability of dynein mutant strains but not the ... We have performed a genome-wide screen to isolate genes that are involved in dynein-dependent processes. ...http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0030128
Secondary Evolution of a Self-Incompatibility Locus in the Brassicaceae Genus Leavenworthia
As with LaLal2, however, the genes with highest similarity are found in A. lyrata: genes NCBI Gene ID 9302985 and NCBI Gene ID ... SI is a complex phenotype whose functioning requires co-evolution among several interacting components . It has been ... Genes were annotated with the A. thaliana reference genome, and the NCBI Gene ID numbers for A. lyrata genes are also given. ... An SRK gene sequence was identified in a genome region between gene orthologs of A. thaliana PUB8 and ARK3. Genes were ...https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001560
Colony Foundation in an Oceanic Seabird
Gene flow among Atlantic colonies. Most individuals sampled in source colonies originated in their own colony but recent gene ... b) Relationship between body size estimated as the first principal component (PC1) of a PCA analysis and the loadings in the ... Contemporary gene flow among Atlantic colonies. Since Galician colonies were grouped within an Atlantic genetic deme, and to ... We also assigned sex to sampled individuals by PCR amplification of the CHD genes [82, 83]. Blood was boiled in 100mM NaOH for ...https://journals.plos.org/plosone/article?id=info%3Adoi%2F10.1371%2Fjournal.pone.0147222
Association of the Innate Immunity and Inflammation Pathway with Advanced Prostate Cancer Risk
... and four genes in these sub-pathways (TLR1, TLR6, OAS1, and OAS2) were nominally associated with advanced prostate cancer risk ... located in 46 genes involved in this pathway, with disease risk using 494 cases with advanced disease and 536 controls from ... To adjust for genetic ancestry in all analyses, we included the first principal component of the principal component analysis ... 5 genes), and 6) selenoproteins (2 genes). The genes SELS and SEP15 coding for selenoproteins were included because of their ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051680
Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability
We also show that Cyclin G-induced FA correlates with the activation of genes involved in translation and the repression of ... genes involved in energy production. We suggest that fine-tuned control of these key functions is important for developmental ... A large amount of data converges towards the importance of hubs-i.e. the most connected genes-in gene networks. Deregulating ... We did not observe any significant overlap between Cyclin G-bound genes and binding sites for Calypso, the second component of ...https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007498
Candidate Gene Association Study in Type 2 Diabetes Indicates a Role for Genes Involved in β-Cell Function as Well as Insulin...
The absence of large single gene effects and the detection of multiple small effects confirms the genetic complexity of type 2 ... The genes encoding the two molecular components of the voltage-gated potassium channel of the pancreatic β-cell are located ... 2003) Candidate Gene Association Study in Type 2 Diabetes Indicates a Role for Genes Involved in β-Cell Function as Well as ... Correction: Candidate Gene Association Study in Type 2 Diabetes Indicates a Role for Genes Involved in β-Cell Function as Well ...http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0000020
Longitudinal Analysis Is More Powerful than Cross-Sectional Analysis in Detecting Genetic Association with Neuroimaging...
... analysis detected more regional phenotypes associated with the two SNPs and indicated another significant SNP rs439401 in gene ... In particular, at the genome-wide significance level, both SNP rs429358 in gene APOE and SNP rs2075650 in gene TOMM40 were ... Shete S, Chen J, Zhou X, Amos C (2000) Modeling age x major gene interaction by a variance component approach. Genetic ... 2012) Principal interactions analysis for repeated measures data: application to gene-gene and gene-environment interactions. ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102312
Atypical speech versus non-speech detection and discrimination in 4- to 6- yr old children with autism spectrum disorder: An...
Temporal components (Cognitive component (N330), Late Slow Wave component (LSW-P600).. A repeated measures ANOVA carried out on ... EEG was recorded continuously using a 128-channel Hydrocel Geodesic Sensor Net (Electrical Geodesics, Eugene, Oregon) with a ... the ERP components observed included a negative going component peaking at 150 ms (N150), a positive going component peaking at ... The ERP components recorded over the frontal-central region were as follows: a positive going component peaking at 140 ms (P150 ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181354
The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory...
Our observations double the number of known genes present in human islets and indicate that ,60% of the candidate genes for ... Candidate genes for diabetes contribute to this process by acting both at the immune system and, as we suggest here, at the ... We suggest that candidate genes for diabetes function at least in part as ... and other innate immune response/pro-inflammatory components. There was also up-regulation of many genes involved in apoptosis ...https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002552
Genome Mining for Radical SAM Protein Determinants Reveals Multiple Sactibiotic-Like Gene Clusters
Analysis of the thuricin CD-associated gene cluster revealed the presence of genes encoding two highly unusual SAM proteins ( ... Fifteen novel thuricin CD-like gene clusters were identified, based on the presence of TrnC and TrnD homologues in the context ... we performed an in silico screen for novel thuricin CD-like gene clusters using the TrnC and TrnD radical SAM proteins as ... of neighbouring genes encoding potential bacteriocin structural peptides. Moreover, metagenomic analysis revealed that TrnC or ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020852
Glutathione S-Transferase Regulation in Calanus finmarchicus Feeding on the Toxic Dinoflagellate Alexandrium fundyense
Global gene expression analyses agreed with the RT-qPCR results. Furthermore, the RNA-Seq measurements indicated that only four ... Relative expression of three GST genes was measured using RT-qPCR on days 0.5, 1, 2 and 5 in two independent experiments. ... These authors also concluded that detoxification was not a major component of the physiological response of D. pulex feeding on ... To assess relative expression for the tested genes (GSTs), we firstly determined the best reference gene from the three genes: ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159563
Genome-Wide Methylation and Gene Expression Changes in Newborn Rats following Maternal Protein Restriction and Reversal by...
Although the epigenetic and gene expression signatures appeared to underpin largely different biological processes, the gene ... The aim of this study was to evaluate genome-wide DNA methylation and gene expression in the livers of newborn rats exposed to ... The mechanistic basis of such programming is unclear but may involve resetting of epigenetic marks and fetal gene expression. ... On day one postnatally, there were 618 differentially expressed genes and 1183 differentially methylated regions (FDR 5%). The ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082989
miR-K12-7-5p Encoded by Kaposi's Sarcoma-Associated Herpesvirus Stabilizes the Latent State by Targeting Viral ORF50/RTA
Our study revealed that another miRNA, miR-K12-7-5p, targets the viral immediate early gene RTA and that this miRNA contributes ... transfection of miR-K12-7 into 293/Bac36 cells reduced RTA expression and the expression of the downstream early genes ... Because these miRNAs were identified as components of the viral latency program, we speculate that they may contribute to the ... RNA levels of the early genes PAN, ORF57, and ORF59 and the late genes ORF65 and TK were assayed by RT-PCR and quantified ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016224
Multi-Serotype Pneumococcal Nasopharyngeal Carriage Prevalence in Vaccine Naïve Nepalese Children, Assessed Using Molecular...
Additional components of the microarray enabled detection of antibiotic resistance genes and assessed genetic relatedness of ... Presence of Antibiotic Resistance Genes. Antibiotic resistance genes within plate sweep samples were detected by microarray ... Genes conferring resistance to tetracyclines and macrolides were the most frequently identified antibiotic resistance loci ... Table 2. Presence of Antibiotic Resistance Genes in Pneumococcal Positive Array Samples. ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114286
Differences in the Endocannabinoid System of Sperm from Fertile and Infertile Men
The results of qRT-PCR experiments on gene expression of the main components of ECS in sperm from fertile and infertile men are ... In conclusion, we report for the first time the presence of ECS components of 2-AG-related metabolism in human sperm and we ... In this study we characterised, for the first time, all major components of the ECS in sperm of fertile and infertile men. ... In terms of AEA metabolism, NAPE-PLD and FAAH genes were expressed to similar extents in both groups. Instead, a significant ...https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047704
Network Analyses Reveal Novel Aspects of ALS Pathogenesis
By using the power of Drosophila genetics, we performed a large scale genomic screen and identified a number of genes that can ... In this study we sought to identify genes and cellular processes that are involved in the toxicity conferred by the defective ... the human homologues of the fly modifiers can be organized into a network that closely resembles that of the Drosophila genes. ... Several mutations in a gene called hVAPB have shown that this gene is causative of a type of ALS known as ALS8. ...http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005107