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transcriptome

  • Open Access
    Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
    Research Article | Host-Microbe Biology
    Decoding the Architecture of the Varicella-Zoster Virus Transcriptome

    Transcription from herpesviral genomes, executed by the host RNA polymerase II and regulated by viral proteins, results in coordinated viral gene expression to efficiently produce infectious progeny. However, the complete coding potential and regulation of viral gene expression remain ill-defined for the human alphaherpesvirus varicella-zoster virus (VZV), causative agent of both varicella and herpes zoster. Here, we present a...

    Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
  • Open Access
    Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <em>Salmonella fis</em> and <em>dps</em> Genes
    Research Article | Molecular Biology and Physiology
    Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the Salmonella fis and dps Genes

    We assessed the impact on Salmonella physiology of reciprocally translocating the genes encoding the Fis and Dps nucleoid-associated proteins (NAPs) and of inverting their growth-phase production patterns such that Fis was produced in stationary phase (like Dps) and Dps was produced in exponential phase (like Fis). Changes to peak binding of Fis were detected by ChIP-seq on the chromosome, as were widespread impacts on the...

    Marina M. Bogue, Aalap Mogre, Michael C. Beckett, Nicholas R. Thomson, Charles J. Dorman
  • Open Access
    The Gene Expression Profile of Uropathogenic <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
    Research Article | Host-Microbe Biology
    The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model

    Different experimental models have been used to study UPEC pathogenesis, including in vitro cultures in different media, tissue culture, and mouse models of infection. The last is especially important since it allows evaluation of mechanisms of pathogenesis and potential therapeutic strategies against UPEC. Bacterial physiology is greatly shaped by environment, and it is therefore critical to understand how closely bacterial...

    Arwen E. Frick-Cheng, Anna Sintsova, Sara N. Smith, Michael Krauthammer, Kathryn A. Eaton, Harry L. T. Mobley
  • Open Access
    Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities
    Research Article | Host-Microbe Biology
    Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities

    HIV enters tissues early after infection, leading to establishment and persistence of HIV reservoirs despite antiretroviral therapy (ART). Viral reservoirs are a major obstacle to the eradication and cure of HIV. CD14+CD16+ (mature) monocytes may contribute to establishment and reseeding of reservoirs. A subset of monocytes, consisting mainly of CD14+CD16+ cells, harbors HIV (HIV+...

    Rosiris León-Rivera, Brenda Morsey, Meng Niu, Howard S. Fox, Joan W. Berman
  • Open Access
    Virulence as a Side Effect of Interspecies Interaction in <em>Vibrio</em> Coral Pathogens
    Research Article | Host-Microbe Biology
    Virulence as a Side Effect of Interspecies Interaction in Vibrio Coral Pathogens

    Vibrio coralliilyticus and Vibrio mediterranei are important coral pathogens capable of inducing serious coral damage, which increases severely when they infect the host simultaneously. This has consequences related to the dispersion of these pathogens among different locations that could enhance...

    Esther Rubio-Portillo, Ana B. Martin-Cuadrado, Andrés M. Caraballo-Rodríguez, Forest Rohwer, Pieter C. Dorrestein, Josefa Antón
  • Open Access
    RhlR-Regulated Acyl-Homoserine Lactone Quorum Sensing in a Cystic Fibrosis Isolate of <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span>
    Research Article | Molecular Biology and Physiology
    RhlR-Regulated Acyl-Homoserine Lactone Quorum Sensing in a Cystic Fibrosis Isolate of Pseudomonas aeruginosa

    Pseudomonas aeruginosa is a prominent cystic fibrosis (CF) pathogen that uses quorum sensing (QS) to regulate virulence. In laboratory strains, the key QS regulator is LasR. Many isolates from patients with chronic CF infections appear to use an alternate QS circuitry in which another transcriptional regulator, RhlR, mediates QS. We show that a LasR-null CF clinical...

    Renae L. Cruz, Kyle L. Asfahl, Sara Van den Bossche, Tom Coenye, Aurélie Crabbé, Ajai A. Dandekar
  • Open Access
    Global Transcriptome Analysis Identifies a Diagnostic Signature for Early Disseminated Lyme Disease and Its Resolution
    Research Article | Host-Microbe Biology
    Global Transcriptome Analysis Identifies a Diagnostic Signature for Early Disseminated Lyme Disease and Its Resolution

    Lyme disease (LD), caused by Borrelia burgdorferi, is the most common tick-borne infectious disease in the United States. We examined gene expression patterns in the blood of individuals with early disseminated LD at the time of diagnosis (acute) and also at approximately 1 month and 6 months following antibiotic treatment. A distinct acute LD profile was observed...

    Mary M. Petzke, Konstantin Volyanskyy, Yong Mao, Byron Arevalo, Raphael Zohn, Johanna Quituisaca, Gary P. Wormser, Nevenka Dimitrova, Ira Schwartz
  • Open Access
    Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span> Infection
    Research Article | Host-Microbe Biology
    Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection

    Tuberculosis is the infectious disease with the worldwide largest disease burden and there remains a great need for better diagnostic biomarkers to detect latent and active M. tuberculosis infection. RNA molecules hold great promise in this regard, as their levels of expression may differ considerably between infected and uninfected subjects. We have measured...

    Leonardo Silva de Araujo, Marcelo Ribeiro-Alves, Thyago Leal-Calvo, Janaína Leung, Verónica Durán, Mohamed Samir, Steven Talbot, Aravind Tallam, Fernanda Carvalho de Queiroz Mello, Robert Geffers, Maria Helena Féres Saad, Frank Pessler
  • Open Access
    Rapid Phenotypic and Metabolomic Domestication of Wild <em>Penicillium</em> Molds on Cheese
    Editor's Pick Research Article | Applied and Environmental Science
    Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese

    Industrial cultures of filamentous fungi are used to add unique aesthetics and flavors to cheeses and other microbial foods. How these microbes adapted to live in food environments is generally unknown as most microbial domestication is unintentional. Our work demonstrates that wild molds closely related to the starter culture Penicillium camemberti can readily lose...

    Ina Bodinaku, Jason Shaffer, Allison B. Connors, Jacob L. Steenwyk, Megan N. Biango-Daniels, Erik K. Kastman, Antonis Rokas, Albert Robbat, Benjamin E. Wolfe
  • Open Access
    A <em>rhlI</em> 5′ UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span>
    Research Article | Molecular Biology and Physiology
    A rhlI 5′ UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in Pseudomonas aeruginosa

    The opportunistic human pathogen Pseudomonas aeruginosa possesses multiple quorum sensing systems that regulate and coordinate production of virulence factors and adaptation to different environments. Despite extensive research, the regulatory elements that play a role in this complex network are still not fully understood. By using several RNA sequencing techniques,...

    Maureen K. Thomason, Maya Voichek, Daniel Dar, Victoria Addis, David Fitzgerald, Susan Gottesman, Rotem Sorek, E. Peter Greenberg

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