Genome-Wide Mycobacterium tuberculosis Variation (GMTV) Database: A New Tool for Integrating Sequence Variations and Epidemiology

Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains

Ecto-5′-nucleotidase and intestinal ion secretion by enteropathogenic Escherichia coli

Enteropathogenic Escherichia coli (EPEC) triggers a large release of adenosine triphosphate (ATP) from host intestinal cells and the extracellular ATP is broken down to adenosine diphosphate (ADP), AMP, and adenosine. Adenosine is a potent secretagogue in the small and large intestine. We suspected that ecto-5′-nucleotidase (CD73, an intestinal enzyme) was a critical enzyme involved in the conversion of AMP to adenosine and in the pathogenesis of EPEC diarrhea. We developed a nonradioactive method for measuring ecto-5′-nucleotidase in cultured T84 cell monolayers based on the detection of phosphate release from 5′-AMP. EPEC infection triggered a release of ecto-5′-nucleotidase from the cell surface into the supernatant medium. EPEC-induced 5′-nucleotidase release was not correlated with host cell death but instead with activation of phosphatidylinositol-specific phospholipase C (PI-PLC). Ecto-5′-nucleotidase was susceptible to inhibition by zinc acetate and by α,β-methylene-adenosine diphosphate (α,β-methylene-ADP). In the Ussing chamber, these inhibitors could reverse the chloride secretory responses triggered by 5′-AMP. In addition, α,β-methylene-ADP and zinc blocked the ability of 5′-AMP to stimulate EPEC growth under nutrient-limited conditions in vitro. Ecto-5′-nucleotidase appears to be the major enzyme responsible for generation of adenosine from adenine nucleotides in the T84 cell line, and inhibitors of ecto-5′-nucleotidase, such as α,β-methylene-ADP and zinc, might be useful for treatment of the watery diarrhea produced by EPEC infection

The Atmospheric River Tracking Method Intercomparison Project (ARTMIP): Quantifying Uncertainties in Atmospheric River Climatology

Atmospheric rivers (ARs) are now widely known for their association with high‐impact weather events and long‐term water supply in many regions. Researchers within the scientific community have developed numerous methods to identify and track of ARs—a necessary step for analyses on gridded data sets, and objective attribution of impacts to ARs. These different methods have been developed to answer specific research questions and hence use different criteria (e.g., geometry, threshold values of key variables, and time dependence). Furthermore, these methods are often employed using different reanalysis data sets, time periods, and regions of interest. The goal of the Atmospheric River Tracking Method Intercomparison Project (ARTMIP) is to understand and quantify uncertainties in AR science that arise due to differences in these methods. This paper presents results for key AR‐related metrics based on 20+ different AR identification and tracking methods applied to Modern‐Era Retrospective Analysis for Research and Applications Version 2 reanalysis data from January 1980 through June 2017. We show that AR frequency, duration, and seasonality exhibit a wide range of results, while the meridional distribution of these metrics along selected coastal (but not interior) transects are quite similar across methods. Furthermore, methods are grouped into criteria‐based clusters, within which the range of results is reduced. AR case studies and an evaluation of individual method deviation from an all‐method mean highlight advantages/disadvantages of certain approaches. For example, methods with less (more) restrictive criteria identify more (less) ARs and AR‐related impacts. Finally, this paper concludes with a discussion and recommendations for those conducting AR‐related research to consider.Fil: Rutz, Jonathan J.. National Ocean And Atmospheric Administration; Estados UnidosFil: Shields, Christine A.. National Center for Atmospheric Research; Estados UnidosFil: Lora, Juan M.. University of Yale; Estados UnidosFil: Payne, Ashley E.. University of Michigan; Estados UnidosFil: Guan, Bin. California Institute of Technology; Estados UnidosFil: Ullrich, Paul. University of California at Davis; Estados UnidosFil: O'Brien, Travis. Lawrence Berkeley National Laboratory; Estados UnidosFil: Leung, Ruby. Pacific Northwest National Laboratory; Estados UnidosFil: Ralph, F. Martin. Center For Western Weather And Water Extremes; Estados UnidosFil: Wehner, Michael. Lawrence Berkeley National Laboratory; Estados UnidosFil: Brands, Swen. Meteogalicia; EspañaFil: Collow, Allison. Universities Space Research Association; Estados UnidosFil: Goldenson, Naomi. University of California at Los Angeles; Estados UnidosFil: Gorodetskaya, Irina. Universidade de Aveiro; PortugalFil: Griffith, Helen. University of Reading; Reino UnidoFil: Kashinath, Karthik. Lawrence Bekeley National Laboratory; Estados UnidosFil: Kawzenuk, Brian. Center For Western Weather And Water Extremes; Reino UnidoFil: Krishnan, Harinarayan. Lawrence Berkeley National Laboratory; Estados UnidosFil: Kurlin, Vitaliy. University of Liverpool; Reino UnidoFil: Lavers, David. European Centre For Medium-range Weather Forecasts; Estados UnidosFil: Magnusdottir, Gudrun. University of California at Irvine; Estados UnidosFil: Mahoney, Kelly. Universidad de Lisboa; PortugalFil: Mc Clenny, Elizabeth. University of California at Davis; Estados UnidosFil: Muszynski, Grzegorz. University of Liverpool; Reino Unido. Lawrence Bekeley National Laboratory; Estados UnidosFil: Nguyen, Phu Dinh. University of California at Irvine; Estados UnidosFil: Prabhat, Mr.. Lawrence Bekeley National Laboratory; Estados UnidosFil: Qian, Yun. Pacific Northwest National Laboratory; Estados UnidosFil: Ramos, Alexandre M.. Universidade Nova de Lisboa; PortugalFil: Sarangi, Chandan. Pacific Northwest National Laboratory; Estados UnidosFil: Viale, Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentin

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal: A rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes. We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure (SGS) will be higher in more peripheral populations because of lower population density. The study was performed on the predominantly selfing Avena sterilis and included: (1) direct measurement of dispersal in a controlled environment; and (2) analyses of SGS in three natural populations, sampled in linear transects at fixed increasing inter-plant distances. We found that in A. sterilis major seed dispersal is by gravity in close (less than 2 m) vicinity of the mother plant, with a minor additional effect of wind. Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1 m only in the most peripheral desert population, while in the two core populations with Mediterranean conditions, no genetic structure was found. Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within-population gene flow related to low plant density. Our findings also show that predominant self-pollination and highly localized seed dispersal lead to SGS at a very fine scale, but only if plant density is not too high

Data for depositing - field introduction

Field experiment dat

Data from: Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions

Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multi-year reciprocal transplant experiment the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential