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genomics

  • Open Access
    Signatures of Selection at Drug Resistance Loci in <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span>
    Research Article | Ecological and Evolutionary Science
    Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis

    Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in...

    Tatum D. Mortimer, Alexandra M. Weber, Caitlin S. Pepperell
  • Open Access
    Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria
    Research Article | Novel Systems Biology Techniques
    Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

    Molecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The...

    Hualan Liu, Morgan N. Price, Robert Jordan Waters, Jayashree Ray, Hans K. Carlson, Jacob S. Lamson, Romy Chakraborty, Adam P. Arkin, Adam M. Deutschbauer
  • Open Access
    Parallel Evolution of Group B <em>Streptococcus</em> Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations
    Research Article | Ecological and Evolutionary Science
    Parallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations

    The incidence of group B Streptococcus (GBS) neonatal disease continues to be a significant cause of concern worldwide. Strains belonging to clonal complex 17 (CC17) are the most frequently responsible for GBS infections in neonates, especially among late-onset disease cases. Therefore, we undertook the largest genomic study of GBS CC17 strains to date to decipher the genetic bases of their remarkable colonization and infection...

    Alexandre Almeida, Isabelle Rosinski-Chupin, Céline Plainvert, Pierre-Emmanuel Douarre, Maria J. Borrego, Claire Poyart, Philippe Glaser
  • Open Access
    Non-Toxin-Producing <em>Bacillus cereus</em> Strains Belonging to the <em>B. anthracis</em> Clade Isolated from the International Space Station
    Research Article | Applied and Environmental Science
    Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station

    The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed...

    Kasthuri Venkateswaran, Nitin K. Singh, Aleksandra Checinska Sielaff, Robert K. Pope, Nicholas H. Bergman, Sandra P. van Tongeren, Nisha B. Patel, Paul A. Lawson, Masataka Satomi, Charles H. D. Williamson, Jason W. Sahl, Paul Keim, Duane Pierson, Jay Perry
  • Open Access
    Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <span class="named-content genus-species" id="named-content-1">Rhodobacter sphaeroides</span>
    Research Article | Molecular Biology and Physiology
    Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

    Knowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in...

    Brian T. Burger, Saheed Imam, Matthew J. Scarborough, Daniel R. Noguera, Timothy J. Donohue
  • Open Access
    Listeriomics: an Interactive Web Platform for Systems Biology of <em>Listeria</em>
    Resource Report | Host-Microbe Biology
    Listeriomics: an Interactive Web Platform for Systems Biology of Listeria

    In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow...

    Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
  • Open Access
    Comparative Genome Analyses of <em>Vibrio anguillarum</em> Strains Reveal a Link with Pathogenicity Traits
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits

    Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were...

    Daniel Castillo, Paul D. Alvise, Ruiqi Xu, Faxing Zhang, Mathias Middelboe, Lone Gram
  • Open Access
    A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses
    Research Article | Novel Systems Biology Techniques
    A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

    This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities...

    Lindsey A. Moser, Lisbeth Ramirez-Carvajal, Vinita Puri, Steven J. Pauszek, Krystal Matthews, Kari A. Dilley, Clancy Mullan, Jennifer McGraw, Michael Khayat, Karen Beeri, Anthony Yee, Vivien Dugan, Mark T. Heise, Matthew B. Frieman, Luis L. Rodriguez, Kristen A. Bernard, David E. Wentworth, Timothy B. Stockwell, Reed S. Shabman
  • Open Access
    ADAGE-Based Integration of Publicly Available <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
    Editor's Pick Research Article | Novel Systems Biology Techniques
    ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

    The quantity and breadth of genome-scale data sets that examine RNA expression in diverse bacterial and eukaryotic species are increasing more rapidly than for curated knowledge. Our ADAGE method integrates such data without requiring gene function, gene pathway, or experiment labeling, making practical its application to any large gene expression compendium. We built a ...

    Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene

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