Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

BACKGROUND: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria. RESULTS: To explore conservation and variations in the Shewanella transcriptional networks we analyzed the repertoire of transcription factors and performed genomics-based reconstruction and comparative analysis of regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors and their DNA binding sites, 8 riboswitches and 6 translational attenuators. Forty five regulons were newly inferred from the genome context analysis, whereas others were propagated from previously characterized regulons in the Enterobacteria and Pseudomonas spp.. Multiple variations in regulatory strategies between the Shewanella spp. and E. coli include regulon contraction and expansion (as in the case of PdhR, HexR, FadR), numerous cases of recruiting non-orthologous regulators to control equivalent pathways (e.g. PsrA for fatty acid degradation) and, conversely, orthologous regulators to control distinct pathways (e.g. TyrR, ArgR, Crp). CONCLUSIONS: We tentatively defined the first reference collection of ~100 transcriptional regulons in 16 Shewanella genomes. The resulting regulatory network contains ~600 regulated genes per genome that are mostly involved in metabolism of carbohydrates, amino acids, fatty acids, vitamins, metals, and stress responses. Several reconstructed regulons including NagR for N-acetylglucosamine catabolism were experimentally validated in S. oneidensis MR-1. Analysis of correlations in gene expression patterns helps to interpret the reconstructed regulatory network. The inferred regulatory interactions will provide an additional regulatory constrains for an integrated model of metabolism and regulation in S. oneidensis MR-1.

Acute Decompensated Heart Failure and the Kidney: Physiological, Histological and Transcriptomic Responses to Development and Recovery.

BACKGROUND Acute decompensated heart failure (ADHF) is associated with deterioration in renal function-an important risk factor for poor outcomes. Whether ADHF results in permanent kidney damage/dysfunction is unknown. METHODS AND RESULTS We investigated for the first time the renal responses to the development of, and recovery from, ADHF using an ovine model. ADHF development induced pronounced hemodynamic changes, neurohormonal activation, and decline in renal function, including decreased urine, sodium and urea excretion, and creatinine clearance. Following ADHF recovery (25 days), creatinine clearance reductions persisted. Kidney biopsies taken during ADHF and following recovery showed widespread mesangial cell prominence, early mild acute tubular injury, and medullary/interstitial fibrosis. Renal transcriptomes identified altered expression of 270 genes following ADHF development and 631 genes following recovery. A total of 47 genes remained altered post-recovery. Pathway analysis suggested gene expression changes, driven by a network of inflammatory cytokines centered on IL-1ß (interleukin 1ß), lead to repression of reno-protective eNOS (endothelial nitric oxide synthase) signaling during ADHF development, and following recovery, activation of glomerulosclerosis and reno-protective pathways and repression of proinflammatory/fibrotic pathways. A total of 31 dysregulated genes encoding proteins detectable in urine, serum, and plasma identified potential candidate markers for kidney repair (including CNGA3 [cyclic nucleotide gated channel subunit alpha 3] and OIT3 [oncoprotein induced transcript 3]) or long-term renal impairment in ADHF (including ACTG2 [actin gamma 2, smooth muscle] and ANGPTL4 [angiopoietin like 4]). CONCLUSIONS In an ovine model, we provide the first direct evidence that an episode of ADHF leads to an immediate decline in kidney function that failed to fully resolve after ≈4 weeks and is associated with persistent functional/structural kidney injury. We identified molecular pathways underlying kidney injury and repair in ADHF and highlighted 31 novel candidate biomarkers for acute kidney injury in this setting.

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus.

Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensylvanica). Our chromosome-level Vespula assemblies each contain 176-179 Mb of total sequence assembled into 25 scaffolds, with 10-200 unanchored scaffolds, and 16,566-18,948 genes. We annotated gene sets relevant to the applied management of invasive wasp populations, including genes associated with spermatogenesis and development, pesticide resistance, olfactory receptors, immunity and venom. These genomes provide evidence for active DNA methylation in Vespidae and tandem duplications of venom genes. Our genomic resources will contribute to the development of next-generation control strategies, and monitoring potential resistance to chemical control.

Effect of cold storage and different ions on the thermal resistance of B. cereus NZAS01 spores- analysis of differential gene expression and ion exchange.

Bacillus cereus spores in food are able to survive pasteurization, and if conditions are favourable, subsequently germinate, grow and produce toxins causing food poisoning. The objectives of this study were to firstly determine the impact of cold storage and ion uptake on the thermal resistance of B. cereus spores and secondly to use differential gene expression to help elucidate possible molecular mechanisms for the changes detected in their thermal resistance. B. cereus spores were held at 4 °C in either 0.05 or 0.5 M solutions of cations (Na+, Ca2+ Mg2+,K+, Zn2+) for 6 days and their D88-values were estimated. In the presence of sodium chloride (0.05 and 0.5 M), sodium phosphate buffer, (pH 7, 0.05 and 0.5 M) or zinc acetate (0.05 M), D88 values decreased by 8.8, 10.9, 11.2, 12.9, and 10.2 min respectively, with no evidence of germination (plating methods). Exposure of spores to Na+ in sodium phosphate buffer (pH 7, 0.05 and 0.5 M) or sodium chloride (0.05 and 0.5 M) resulted in the accumulation of Na+ (66.0 ±â€¯2.9, 193.1 ±â€¯4.6, 136.2 ±â€¯9.9 and 70.5 ±â€¯2.7 µg/g) by spores at the significant expense of K+ (10.8 ±â€¯0.5, 7.5 ±â€¯0.2, 8.1 ±â€¯0.4 and 3.6 ±â€¯0.4 µg/g respectively). The mechanism behind the loss of resistance in sodium phosphate buffer (0.05 M) was further investigated by monitoring the differential gene expression using mRNA sequencing. Genes encoding for uracil permease (BC_3890), Mg2+ P-type ATPase-like protein (BC_1581), ABC transporter ATP-binding protein (BC_0815), and 2-keto-3-deoxygluconate permease (BC_4841) were significantly (FDR value ≤0.05) upregulated. This upregulation indicated a possible increase in permeability, which is suggested to account for the increased uptake of sodium ions and the reduction measured in the spore's thermal resistance. This data suggests that during storage at 4 °C in the presence of sodium ions, spores should not be considered to be completely dormant.

Differential gene expression for investigation of the effect of germinants and heat activation to induce germination in Bacillus cereus spores.

Differential gene expression was used to explore the mechanisms underpinning the differences in the impact of heat activation (70 °C for 30 min) on the germination of Bacillus cereus spores in the presence and absence of a germinant (L-alanine). The number of germinated cells, after heat activation plus L-alanine (3.5 ±â€¯0.02 log CFU/ml) in the spore only initial population was found to be higher than that in only heat activated spores (2.01 ±â€¯0.02 log CFU/ml). The concentration of DPA released by heat activated spores in the presence of L-alanine was 68.3 ±â€¯0.1 and 112.1 ±â€¯0.02 µg/ml after 30 and 60 min, compared to 96.5 and 166.2 ±â€¯0.01 µg/ml after 30 and 90 min, respectively released by spores subjected only to heat activation. Gene (BC0784) encoding for the spore germination protein, gerA operon was up-regulated with a log2-transformed fold change value of 1.2 due to heat activation in the presence of L-alanine. The GerA operon located in the inner membrane is known to be involved in the uptake of L-alanine by B. cereus and has been reported to be involved in L-alanine mediated germination. In addition the up-regulation of genes involved in the uptake of L-alanine is proposed to provide the answer to the synergistic effect of heat and L-alanine in inducing germination in B. cereus spores. In short, heat activation increases the ability of L-alanine to penetrate into the spore's inner membrane, where it can be recognized by the receptors for initiation of the germination pathway. In the current study, the majority of the ribosomal proteins were down-regulated (when spores were heat treated in presence of germinants) this process also appeared to slow down protein synthesis by restricting the protein translation machinery. Differential gene expression revealed the genes responsible for the pathways related to transport and recognition of L-alanine into the spore that could have led to the accelerated germination process along with partial shutting down of protein synthesis pathway and ABC transporters. Knowledge of gene regulation in spores during heat activation will help in the development of approaches to prevent spore germination, which could provide an additional safeguard against bacterial growth and toxin production in improperly cooled heat treated foods.

Allosteric AKT Inhibitors Target Synthetic Lethal Vulnerabilities in E-Cadherin-Deficient Cells.

The CDH1 gene, encoding the cell adhesion protein E-cadherin, is one of the most frequently mutated genes in gastric cancer and inactivating germline CDH1 mutations are responsible for hereditary diffuse gastric cancer syndrome (HDGC). Using cell viability assays, we identified that breast (MCF10A) and gastric (NCI-N87) cells lacking CDH1 expression are more sensitive to allosteric AKT inhibitors than their CDH1-expressing isogenic counterparts. Apoptosis priming and total apoptosis assays in the isogenic MCF10A cells confirmed the enhanced sensitivity of E-cadherin-null cells to the AKT inhibitors. In addition, two of these inhibitors, ARQ-092 and MK2206, preferentially targeted mouse-derived gastric Cdh1-/- organoids for growth arrest. AKT protein expression and activation (as measured by phosphorylation of serine 473) were differentially regulated in E-cadherin-null MCF10A and NCI-N87 cells, with downregulation in the normal breast cells, but upregulation in the gastric cancer cells. Bioinformatic analysis of the TCGA STAD dataset revealed that AKT3, but not AKT1 or AKT2, is upregulated in the majority of E-cadherin-deficient gastric cancers. In conclusion, allosteric AKT inhibitors represent a promising class of drugs for chemoprevention and chemotherapy of cancers with E-cadherin loss.

Rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

Despite New Zealand being a low-tuberculosis (TB) burden country, there are disproportionately high rates of TB in particular populations. Here, we report a rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

Draft Genome Sequences of Two Drug-Resistant Mycobacterium tuberculosis Isolates from Myanmar.

Multidrug-resistant tuberculosis (MDR-TB) and lately, extensively drug-resistant TB (XDR-TB) are increasing global health concerns. Here, we present the genome sequences of two MDR-TB isolates from Myanmar, one of 27 countries with a high MDR-TB burden, and describe a number of mutations consistent with these being XDR-TB isolates.

Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.

Upon exposure of Nitrosomonas europaea to chloroform (7 microM, 1 h), transcripts for 175 of 2,460 genes were found at higher levels in treated cells than in untreated cells and transcripts for 501 genes were found at lower levels. With chloromethane (3.2 mM, 1 h), transcripts for 67 genes were at higher levels and transcripts for 148 genes were at lower levels. Transcripts for 37 genes were at higher levels following both treatments and included genes for heat shock proteins, sigma-factors of the extracytoplasmic function subfamily, and toxin-antitoxin loci. N. europaea has higher levels of transcripts for a variety of defense genes when exposed to chloroform or chloromethane.