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    • Latest Articles
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    • mSphere of Influence: Commentaries from Early Career Microbiologists
    • Archive
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transcriptomics

  • Open Access
    The Putative APSES Transcription Factor RgdA Governs Growth, Development, Toxigenesis, and Virulence in <span class="named-content genus-species" id="named-content-1">Aspergillus fumigatus</span>
    Research Article | Molecular Biology and Physiology
    The Putative APSES Transcription Factor RgdA Governs Growth, Development, Toxigenesis, and Virulence in Aspergillus fumigatus

    Immunocompromised patients are susceptible to infections with the opportunistic human-pathogenic fungus Aspergillus fumigatus. This fungus causes systemic infections such as invasive aspergillosis (IA), which is one of the most life-threatening fungal diseases. To control this serious disease, it is critical to identify new antifungal drug targets. In fungi, the...

    Sang-Cheol Jun, Yong-Ho Choi, Min-Woo Lee, Jae-Hyuk Yu, Kwang-Soo Shin
  • Open Access
    Transcriptional Profiling Suggests T Cells Cluster around Neurons Injected with <span class="named-content genus-species" id="named-content-1">Toxoplasma gondii</span> Proteins
    Research Article | Host-Microbe Biology
    Transcriptional Profiling Suggests T Cells Cluster around Neurons Injected with Toxoplasma gondii Proteins

    Like other persistent intracellular pathogens, Toxoplasma gondii, a protozoan parasite, has evolved to evade the immune system and establish a chronic infection in specific cells and organs, including neurons in the CNS. Understanding T. gondii’s persistence in neurons holds the potential to identify novel, curative drug targets. The work presented here...

    Emily F. Merritt, Hannah J. Johnson, Zhee Sheen Wong, Adam S. Buntzman, Austin C. Conklin, Carla M. Cabral, Casey E. Romanoski, Jon P. Boyle, Anita A. Koshy
  • Open Access
    Integrative Analysis of Proteome and Transcriptome Dynamics during <span class="named-content genus-species" id="named-content-1">Bacillus subtilis</span> Spore Revival
    Research Article | Molecular Biology and Physiology
    Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival

    This study demonstrated the progress of macromolecular synthesis during Bacillus subtilis spore germination and outgrowth. The transcriptome analysis has additionally allowed us to trace gene expression during this transformation process. For the first time, the basic survival kit for spore-based life has been identified. In addition, in this analysis based on...

    Bhagyashree Swarge, Wishwas Abhyankar, Martijs Jonker, Huub Hoefsloot, Gertjan Kramer, Peter Setlow, Stanley Brul, Leo J. de Koning
  • Open Access
    The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen <span class="named-content genus-species" id="named-content-1">Candida orthopsilosis</span>
    Research Article | Ecological and Evolutionary Science
    The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis

    How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.

    Hrant Hovhannisyan, Ester Saus, Ewa Ksiezopolska, Toni Gabaldón
  • Open Access
    mSphere of Influence: Predicting Immune Responses and Susceptibility to Influenza Virus—May the Data Be with You
    Commentary | Host-Microbe Biology
    mSphere of Influence: Predicting Immune Responses and Susceptibility to Influenza Virus—May the Data Be with You

    Irene Ramos works in the field of immunology to viral infections. In this mSphere of Influence article, she reflects on how “Global analyses of human immune variation reveal baseline predictors of postvaccination responses” by Tsang et al. (Cell 157:499–513, 2014, https://doi.org/10.1016/j.cell.2014.03.031) and “A crowdsourced analysis to identify ab initio molecular signatures...

    Irene Ramos
  • Open Access
    Transcriptomic and Proteomic Approaches to Finding Novel Diagnostic and Immunogenic Candidates in <em>Pneumocystis</em>
    Editor's Pick Research Article | Host-Microbe Biology
    Transcriptomic and Proteomic Approaches to Finding Novel Diagnostic and Immunogenic Candidates in Pneumocystis

    The current report enhances our understanding of Pneumocystis biology in a number of ways. First, the current study provided a preliminary annotation of the Pneumocystis murina genome, addressing a long-standing issue in the field. Second, this study validated two novel transcripts enriched in the two predominant life forms of Pneumocystis. These...

    Taylor Eddens, Waleed Elsegeiny, David Ricks, Meagan Goodwin, William T. Horne, Mingquan Zheng, Jay K. Kolls
  • Open Access
    Analysis of the <em>In Vivo</em> Transcriptome of <span class="named-content genus-species" id="named-content-1">Bordetella pertussis</span> during Infection of Mice
    Research Article | Host-Microbe Biology
    Analysis of the In Vivo Transcriptome of Bordetella pertussis during Infection of Mice

    In vitro growth conditions for bacteria do not fully recapitulate the host environment. RNA sequencing transcriptome analysis allows for the characterization of the infection gene expression profiles of pathogens in complex environments. Isolation of the pathogen from infected tissues is critical because of the large amounts of host RNA present in crude lysates of infected organs. A filtration method was developed that enabled...

    Ting Y. Wong, Jesse M. Hall, Evan S. Nowak, Dylan T. Boehm, Laura A. Gonyar, Erik L. Hewlett, Joshua C. Eby, Mariette Barbier, F. Heath Damron
  • Open Access
    <em>csrB</em> Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in <em>Vibrio tasmaniensis</em> LGP32
    Research Article | Molecular Biology and Physiology
    csrB Gene Duplication Drives the Evolution of Redundant Regulatory Pathways Controlling Expression of the Major Toxic Secreted Metalloproteases in Vibrio tasmaniensis LGP32

    The conserved CsrB sRNAs are an example of sibling sRNAs, i.e., sRNAs which are present in multiple copies in genomes. This report illustrates how new copies arise through gene duplication events and highlights two evolutionary advantages of having such multiple copies: differential regulation of the multiple copies allows integration of different input signals into the regulatory network of which they are parts, and the high redundancy...

    An Ngoc Nguyen, Elena Disconzi, Guillaume M. Charrière, Delphine Destoumieux-Garzón, Philippe Bouloc, Frédérique Le Roux, Annick Jacq
  • Open Access
    Mechanism of High-Level Daptomycin Resistance in <em>Corynebacterium striatum</em>
    Research Article | Therapeutics and Prevention
    Mechanism of High-Level Daptomycin Resistance in Corynebacterium striatum

    Antimicrobial resistance threatens the efficacy of antimicrobial treatment options, including last-line-of-defense drugs. Understanding how this resistance develops can help direct antimicrobial stewardship efforts and is critical to designing the next generation of antimicrobial therapies. Here we determine how Corynebacterium striatum, a skin commensal and...

    Nicholas K. Goldner, Christopher Bulow, Kevin Cho, Meghan Wallace, Fong-Fu Hsu, Gary J. Patti, Carey-Ann Burnham, Paul Schlesinger, Gautam Dantas
  • Open Access
    Shifts in the Gut Metabolome and <span class="named-content genus-species" id="named-content-1">Clostridium difficile</span> Transcriptome throughout Colonization and Infection in a Mouse Model
    Research Article | Host-Microbe Biology
    Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model

    Clostridium difficile is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring C. difficile growth. Here we used metabolomics and...

    Joshua R. Fletcher, Samantha Erwin, Cristina Lanzas, Casey M. Theriot

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