Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits.

The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes

Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites

Some strains of the foliar pathogen Pseudomonas syringae are adapted for growth and survival on leaf surfaces and in the leaf interior. Global transcriptome profiling was used to evaluate if these two habitats offer distinct environments for bacteria and thus present distinct driving forces for adaptation. The transcript profiles of Pseudomonas syringae pv. syringae B728a support a model in which leaf surface, or epiphytic, sites specifically favor flagellar motility, swarming motility based on 3-(3-hydroxyalkanoyloxy)alkanoic acid surfactant production, chemosensing, and chemotaxis, indicating active relocation primarily on the leaf surface. Epiphytic sites also promote high transcript levels for phenylalanine degradation, which may help counteract phenylpropanoid-based defenses before leaf entry. In contrast, intercellular, or apoplastic, sites favor the high-level expression of genes for GABA metabolism (degradation of these genes would attenuate GABA repression of virulence) and the synthesis of phytotoxins, two additional secondary metabolites, and syringolin A. These findings support roles for these compounds in virulence, including a role for syringolin A in suppressing defense responses beyond stomatal closure. A comparison of the transcriptomes from in planta cells and from cells exposed to osmotic stress, oxidative stress, and iron and nitrogen limitation indicated that water availability, in particular, was limited in both leaf habitats but was more severely limited in the apoplast than on the leaf surface under the conditions tested. These findings contribute to a coherent model of the adaptations of this widespread bacterial phytopathogen to distinct habitats within its host

RNA-seq Analysis Reveals That an ECF σ Factor, AcsS, Regulates Achromobactin Biosynthesis in Pseudomonas syringae pv. syringae B728a

Iron is an essential micronutrient for Pseudomonas syringae pv. syringae strain B728a and many other microorganisms; therefore, B728a has evolved methods of iron acquirement including the use of iron-chelating siderophores. In this study an extracytoplasmic function (ECF) sigma factor, AcsS, encoded within the achromobactin gene cluster is shown to be a major regulator of genes involved in the biosynthesis and secretion of this siderophore. However, production of achromobactin was not completely abrogated in the deletion mutant, implying that other regulators may be involved such as PvdS, the sigma factor that regulates pyoverdine biosynthesis. RNA-seq analysis identified 287 genes that are differentially expressed between the AcsS deletion mutant and the wild type strain. These genes are involved in iron response, secretion, extracellular polysaccharide production, and cell motility. Thus, the transcriptome analysis supports a role for AcsS in the regulation of achromobactin production and the potential activity of both AcsS and achromobactin in the plant-associated lifestyle of strain B728a

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

RNA-seq analysis of the RND efflux system encoded by the <i>pseABC</i> gene cluster.

a<p>Operon predictions were made using the database of prokaryotic operons (<a href="http://csbl1.bmb.uga.edu" target="_blank">http://csbl1.bmb.uga.edu</a>).</p>b<p>Fold change is reflected as <i>P. syringae</i> pv. syringae B728a in comparison to the <i>ΔacsS</i> deletion mutant; therefore, a positive fold change reflects a decreased level of gene expression in <i>P. syringae</i> pv. syringae B728a <i>ΔacsS</i>.</p

RNA-seq analysis of the mangotoxin gene cluster.

a<p>Operon predictions were made using the database of prokaryotic operons (<a href="http://csbl1.bmb.uga.edu" target="_blank">http://csbl1.bmb.uga.edu</a>).</p>b<p>Fold change is reflected as <i>P. syringae</i> pv. syringae B728a in comparison to the <i>ΔacsS</i> deletion mutant; therefore, a positive fold change reflects a decreased level of gene expression in <i>P. syringae</i> pv. syringae B728a <i>ΔacS</i>.</p

Sequence homology of the achromobactin gene clusters in <i>P. syringae</i> pv. syringae B728a, <i>P. syringae</i> pv. phaseolicola 1448a, and <i>Dickeya dadantii</i> strain 3937.

<p>Sequence homology is shown as a percentage and is in reference to the B728a genome with homologous genes being shown in the same shade and line pattern. Parallel lines reflect a gap in the genome, wherein the genome shown has nucleotides and/or genes that are not found in that location in strain B728a.</p

Primers used for PCR and qRT-PCR amplification.

<p>Primers used for PCR and qRT-PCR amplification.</p

RNA-seq analysis of the achromobactin gene cluster.

a<p>Operon predictions were made using the database of prokaryotic operons (<a href="http://csbl1.bmb.uga.edu" target="_blank">http://csbl1.bmb.uga.edu</a>).</p>b<p>Fold change is reflected as <i>P. syringae</i> pv. syringae B728a in comparison to the <i>ΔacsS</i> deletion mutant; therefore, a positive fold change reflects a decreased level of gene expression in <i>P. syringae</i> pv. syringae B728a <i>ΔacsS</i>.</p

Characterization of Five ECF Sigma Factors in the Genome of <em>Pseudomonas syringae</em> pv. syringae B728a

<div><p><i>Pseudomonas syringae</i> pv. syringae B728a, a bacterial pathogen of bean, utilizes large surface populations and extracellular signaling to initiate a fundamental change from an epiphytic to a pathogenic lifestyle. Extracytoplasmic function (ECF) sigma (σ) factors serve as important regulatory factors in responding to various environmental signals. Bioinformatic analysis of the B728a genome revealed 10 ECF sigma factors. This study analyzed deletion mutants of five previously uncharacterized ECF sigma factor genes in B728a, including three FecI-type ECF sigma factors (ECF5, ECF6, and ECF7) and two ECF sigma factors placed in groups ECF11 and ECF18. Transcriptional profiling by qRT-PCR analysis of ECF sigma factor mutants was used to measure expression of their associated anti-sigma and outer membrane receptor proteins, and expression of genes associated with production of extracellular polysaccharides, fimbriae, glycine betaine and syringomycin. Notably, the B728aΔ<i>ecf7</i> mutant displayed reduced swarming and had decreased expression of CupC fimbrial genes. Growth and pathogenicity assays, using a susceptible bean host, revealed that none of the tested sigma factor genes are required for <i>in planta</i> growth and lesion formation.</p> </div