Genetic Evolution of a Helicobacter pylori Acid-Sensing Histidine Kinase and Gastric Disease

Helicobacter pylori is the strongest risk factor for gastric adenocarcinoma, which develops within a hypochlorhydric environment. We sequentially isolated H. pylori (strain J99) from a patient who developed corpus-predominant gastritis and hypochlorhydia over a 6-year interval. Archival J99 survived significantly better under acidic conditions than recent J99 strains. H. pylori arsRS encodes a 2-component system critical for stress responses; recent J99 isolates harbored 2 nonsynonymous arsS mutations, and arsS inactivation abolished acid survival. In vivo, acid-resistant archival, but not recent J99, successfully colonized high-acid-secreting rodents. Thus, genetic evolution of arsS may influence progression to hypochlorhydia and gastric cancer

Crosstalk between the HpArsRS two-component system and HpNikR is necessary for maximal activation of urease transcription

Helicobacter pylori NikR (HpNikR) is a nickel dependent transcription factor that directly regulates a number of genes in this important gastric pathogen. One key gene that is regulated by HpNikR is ureA, which encodes for the urease enzyme. In vitro DNA binding studies of HpNikR with the ureA promoter (P-ureA) previously identified a recognition site that is required for high affinity protein/DNA binding. As a means to determine the in vivo significance of this recognition site and to identify the key DNA sequence determinants required for ureA transcription, herein, we have translated these in vitro results to analysis directly within H. pylori. Using a series of GFP reporter constructs in which the P-ureA DNA target was altered, in combination with mutant H. pylori strains deficient in key regulatory proteins, we confirmed the importance of the previously identified HpNikR recognition sequence for HpNikR-dependent ureA transcription. Moreover, we identified a second factor, the HpArsRS two-component system that was required for maximum transcription of ureA. While HpArsRS is known to regulate ureA in response to acid shock, it was previously thought to function independently of HpNikR and to have no role at neutral pH. However, our qPCR analysis of ureA expression in wildtype, Delta nikR and Delta arsS single mutants as well as a Delta arsS/nikR double mutant strain background showed reduced basal level expression of ureA when arsS was absent. Additionally, we determined that both HpNikR and HpArsRS were necessary for maximal expression of ureA under nickel, low pH and combined nickel and low pH stresses. In vitro studies of HpArsR-P with the P-ureA DNA target using florescence anisotropy confirmed a direct protein/DNA binding interaction. Together, these data support a model in which HpArsRS and HpNikR cooperatively interact to regulate ureA transcription under various environmental conditions. This is the first time that direct cross-talk between HpArsRS and HpNikR at neutral pH has been demonstrated

Suppression of Integrin Activation: A Novel Function of a Ras/Raf-Initiated MAP Kinase Pathway

AbstractRapid modulation of ligand binding affinity (“activation”) is a central property of the integrin cell adhesion receptors. Using a screen for suppressors of integrin activation, we identified the small GTP-binding protein, H-Ras, and its effector kinase, Raf-1, as negative regulators of integrin activation. H-Ras inhibited the activation of integrins with three distinct α and β subunit cytoplasmic domains. Suppression was not associated with integrin phosphorylation and was independent of both mRNA transcription and protein synthesis. Furthermore, suppression correlated with activation of the ERK MAP kinase pathway. Thus, regulation of integrin affinity state is a novel, transcription-independent function of a Ras-linked MAP kinase pathway that may mediate a negative feedback loop in integrin function

Polymorphisms of the acid sensing histidine kinase gene arsS in Helicobacter pylori populations from anatomically distinct gastric sites

Phase variation is frequently utilized by bacterial species to affect gene expression such that phenotypic variants are maintained within populations, ensuring survival as environmental or host conditions change. Unusual among Helicobacter pylori phase variable or contingency genes is arsS, encoding a sensory histidine kinase involved in the acid acclimation of the organism. The presence of a 3\u27 homopolymeric cytosine tract of variable length in arsS among Helicobacter pylori strains allows for the expression of various functional ArsS isoforms, differing in carboxy-terminal protein domains. In this study, we analyzed this 3\u27 arsS region via amplified fragment length polymorphism (AFLP) and sequencing analyses for H. pylori populations from 3 different gastric sites of 12 patients. Our data indicate the presence of multiple arsS alleles within each population of H. pylori derived from the gastric antrum, cardia, or corpus of these patients. We also show that H. pylori, derived from the same anatomical site and patient, are predicted to express multiple ArsS isoforms in each population investigated. Furthermore, we identify a polymorphic deletion within arsS that generates another alternate ArsS C-terminal end. These findings suggest that four C-terminal variations of ArsS adds to the complexity of the ArsRS acid adaptation mechanism as a whole and may influence the ability of H. pylori to persist in the gastric niche for decades. (c) 2012 Elsevier Ltd. All rights reserved

Genetic Signatures for \u3cem\u3eHelicobacter pylori\u3c/em\u3e Strains of West African Origin

Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of H. pylori strains from seven globally distributed populations or subpopulations and identified encoded proteins that exhibited the highest levels of sequence divergence. These included secreted proteins, an LPS glycosyltransferase, fucosyltransferases, proteins involved in molybdopterin biosynthesis, and Clp protease adaptor (ClpS). Among proteins encoded by the cag pathogenicity island, CagA and CagQ exhibited the highest levels of sequence diversity. We then identified proteins in strains of Western African origin (classified as hspWAfrica by MLST analysis) with sequences that were highly divergent compared to those in other populations of strains. These included ATP-dependent Clp protease, ClpS, and proteins of unknown function. Three of the divergent proteins sequences identified in West African strains were characterized by distinct insertions or deletions up to 8 amino acids in length. These polymorphisms in rapidly evolving proteins represent robust genetic signatures for H. pylori strains of West African origin

Weakly- and Semi-Supervised Panoptic Segmentation

We present a weakly supervised model that jointly performs both semantic- and instance-segmentation -- a particularly relevant problem given the substantial cost of obtaining pixel-perfect annotation for these tasks. In contrast to many popular instance segmentation approaches based on object detectors, our method does not predict any overlapping instances. Moreover, we are able to segment both "thing" and "stuff" classes, and thus explain all the pixels in the image. "Thing" classes are weakly-supervised with bounding boxes, and "stuff" with image-level tags. We obtain state-of-the-art results on Pascal VOC, for both full and weak supervision (which achieves about 95% of fully-supervised performance). Furthermore, we present the first weakly-supervised results on Cityscapes for both semantic- and instance-segmentation. Finally, we use our weakly supervised framework to analyse the relationship between annotation quality and predictive performance, which is of interest to dataset creators.Comment: ECCV 2018. The first two authors contributed equall

Repetitive Sequence Variations in the Promoter Region of the Adhesin-Encoding Gene sabA of Helicobacter pylori Affect Transcription

The pathogenesis of diseases elicited by the gastric pathogen Helicobacter pylori is partially determined by the effectiveness of adaptation to the variably acidic environment of the host stomach. Adaptation includes appropriate adherence to the gastric epithelium via outer membrane protein adhesins such as SabA. The expression of sabA is subject to regulation via phase variation in the promoter and coding regions as well as repression by the two-component system ArsRS. In this study, we investigated the role of a homopolymeric thymine [poly(T)] tract -50 to -33 relative to the sabA transcriptional start site in H. pylori strain J99. We quantified sabA expression in H. pylori J99 by quantitative reverse transcription-PCR (RT-PCR), demonstrating significant changes in sabA expression associated with experimental manipulations of poly(T) tract length. Mimicking the length increase of this tract by adding adenines instead of thymines had similar effects, while the addition of other nucleotides failed to affect sabA expression in the same manner. We hypothesize that modification of the poly(T) tract changes DNA topology, affecting regulatory protein interaction(s) or RNA polymerase binding efficiency. Additionally, we characterized the interaction between the sabA promoter region and ArsR, a response regulator affecting sabA expression. Using recombinant ArsR in electrophoretic mobility shift assays (EMSA), we localized binding to a sequence with partial dyad symmetry -20 and +38 relative to the sabA + 1 site. The control of sabA expression by both ArsRS and phase variation at two distinct repeat regions suggests the control of sabA expression is both complex and vital to H. pylori infection

Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

3-Methylpiperidinium ionic liquids

[EN] A wide range of room temperature ionic liquids based on the 3-methylpiperdinium cation core were produced from 3-methylpiperidine, which is a derivative of DYTEKs (R) A amine. First, reaction with 1-bromoalkanes or 1-bromoalkoxyalkanes generated the corresponding tertiary amines (Rm beta pip, R = alkyl or alkoxyalkyl); further quaternisation reactions with the appropriate methylating agents yielded the quaternary [Rmm(beta)pip]X salts (X-= I-, [CF3CO2]-or [OTf](-); Tf = -SO2CF3), and [Rmm(beta)pip][NTf2] were prepared by anion metathesis from the corresponding iodides. All [NTf2]-salts are liquids at room temperature. [Rmm(beta)pip]X (X-= I-, [CF3CO2]-or [OTf](-)) are low-melting solids when R = alkyl, but room temperature liquids upon introduction of ether functionalities on R. Neither of the 3-methylpiperdinium ionic liquids showed any signs of crystallisation, even well below 0 degrees C. Some related non-C-substituted piperidinium and pyrrolidinium analogues were prepared and studied for comparison. Crystal structures of 1-hexyl-1,3-dimethylpiperidinium tetraphenylborate, 1-butyl-3-methylpiperidinium bromide, 1-(2-methoxyethyl)1- methylpiperidinium chloride and 1-(2-methoxyethyl)-1-methylpyrrolidinium bromide are reported. Extensive structural and physical data are collected and compared to literature data, with special emphasis on the systematic study of the cation ring size and/or asymmetry effects on density, viscosity and ionic conductivity, allowing general trends to be outlined. Cyclic voltammetry shows that 3-methylpiperidinium ionic liquids, similarly to azepanium, piperidinium or pyrrolidinium counterparts, are extremely electrochemically stable; the portfolio of useful alternatives for safe and high-performing electrolytes is thus greatly extended.We would like to acknowledge the EPSRC NCS in Southampton for the single crystal X-ray diffraction data collection and INVISTA Intermediates for funding.Belhocine, T.; Forsyth, SA.; Gunaratne, HQN.; Nieuwenhuyzen, M.; Nockemann, P.; Vaca Puga, A.; Seddon, KR.... (2015). 3-Methylpiperidinium ionic liquids. Physical Chemistry Chemical Physics. 17(16):10398-10416. doi:10.1039/C4CP05936KS10398104161716C. Mikolajczak , M.Kahn, K.White and R. T.Long, Lithium-ion Batteries Hazard and Use Assessment, Springer, New York, 2012Choi, N.-S., Chen, Z., Freunberger, S. A., Ji, X., Sun, Y.-K., Amine, K., … Bruce, P. G. (2012). Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors. 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