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RNA-seq

  • Open Access
    Human Keratinocyte Response to Superantigens
    Research Article | Host-Microbe Biology
    Human Keratinocyte Response to Superantigens

    Staphylococcus aureus and Streptococcus pyogenes are common human pathogens, causing infections that include the skin. Both pathogens produce a family of secreted toxins called superantigens, which have been shown to be important in human diseases. The first cell types encountered by superantigens...

    Patrick M. Schlievert, Francoise A. Gourronc, Donald Y. M. Leung, Aloysius J. Klingelhutz
  • 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
    Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span>
    Research Article | Molecular Biology and Physiology
    Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in Staphylococcus aureus

    Regulatory small RNAs (sRNAs) are a class of RNA molecules that are produced in bacterial cells but that typically do not encode proteins. Instead, they perform a variety of critical functions within the cell as RNA. Most bacterial genomes do not include annotations for sRNA genes, and any type of analysis that is performed using a bacterial genome as a reference will therefore overlook data for sRNAs. In this study, we reexamined...

    Hailee M. Sorensen, Rebecca A. Keogh, Marcus A. Wittekind, Andrew R. Caillet, Richard E. Wiemels, Elizabeth A. Laner, Ronan K. Carroll
  • Open Access
    ClbR Is the Key Transcriptional Activator of Colibactin Gene Expression in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Research Article | Host-Microbe Biology
    ClbR Is the Key Transcriptional Activator of Colibactin Gene Expression in Escherichia coli

    The nonribosomal peptide/polyketide hybrid colibactin can be considered a bacterial virulence factor involved in extraintestinal infection and also a procarcinogen. Nevertheless, and despite its genotoxic effect, colibactin expression can also inhibit bacterial or tumor growth and correlates with probiotic anti-inflammatory and analgesic properties. Although the biological function of this natural compound has been studied extensively,...

    Alexander Wallenstein, Nadine Rehm, Marina Brinkmann, Martina Selle, Nadège Bossuet-Greif, Daniel Sauer, Boyke Bunk, Cathrin Spröer, Haleluya Tesfaye Wami, Stefan Homburg, Rudolf von Bünau, Simone König, Jean-Philippe Nougayrède, Jörg Overmann, Eric Oswald, Rolf Müller, Ulrich Dobrindt
  • Open Access
    Convergence between Regulation of Carbon Utilization and Catabolic Repression in <em>Xanthophyllomyces dendrorhous</em>
    Research Article | Molecular Biology and Physiology
    Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous

    The conditions affecting catabolic regulation in X. dendrorhous are complex and suggest the presence of an alternative mechanism of regulation. The repressors Mig1, Cyc8, and Tup1 are essential elements for the regulation of the use of glucose and other carbon sources. All play different roles but, depending on the growth conditions, can work in convergent,...

    Pilar Martinez-Moya, Sebastián Campusano, Pamela Córdova, Alberto Paradela, Dionisia Sepulveda, Jennifer Alcaíno, Marcelo Baeza, Víctor Cifuentes
  • Open Access
    Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids
    Research Article | Applied and Environmental Science
    Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids

    The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of...

    Justine Cheval, Erika Muth, Gaëlle Gonzalez, Muriel Coulpier, Pascale Beurdeley, Stéphane Cruveiller, Marc Eloit
  • Open Access
    Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis
    Research Article | Host-Microbe Biology
    Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis

    Human papillomavirus (HPV)-associated cancers still remain a big health problem, especially in developing countries, despite the availability of prophylactic vaccines. Although HPV oncogenes have been intensively investigated for decades, a study applying recent advances in RNA-Seq and quantitative proteomic approaches to a precancerous model system with well-defined HPV oncogene expression alongside HPV-negative parental cells has been...

    Ruwen Yang, Jana Klimentová, Elke Göckel-Krzikalla, Regina Ly, Nadine Gmelin, Agnes Hotz-Wagenblatt, Helena Řehulková, Jiří Stulík, Frank Rösl, Martina Niebler
  • Open Access
    Newly Identified Nucleoid-Associated-Like Protein YlxR Regulates Metabolic Gene Expression in <span class="named-content genus-species" id="named-content-1">Bacillus subtilis</span>
    Research Article | Molecular Biology and Physiology
    Newly Identified Nucleoid-Associated-Like Protein YlxR Regulates Metabolic Gene Expression in Bacillus subtilis

    Expression of genes encoding NAPs is often temporally regulated. According to results from single-cell analysis, the ylxR gene is induced by glucose and expressed in a bistable mode. These characteristics have not previously been reported for NAP gene expression. Transcriptional profiling of the ylxR disruptant revealed a change in the expression levels of approximately 400 genes, including genes for synthesis of 12...

    Mitsuo Ogura, Yu Kanesaki
  • Open Access
    Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen <em>Rhizopus delemar</em>
    Editor's Pick Research Article | Molecular Biology and Physiology
    Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar

    Germination is key to the growth of many organisms, including fungal spores. Mucormycete spores exist abundantly within the environment and germinate to form hyphae. These spores are capable of infecting immunocompromised individuals, causing the disease mucormycosis. Germination from spore to hyphae within patients leads to angioinvasion, tissue necrosis, and often fatal infections. This study advances our understanding of how spore...

    Poppy C. S. Sephton-Clark, Jose F. Muñoz, Elizabeth R. Ballou, Christina A. Cuomo, Kerstin Voelz
  • Open Access
    Transcriptome Analysis of <span class="named-content genus-species" id="named-content-1">Neisseria gonorrhoeae</span> during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women
    Research Article | Host-Microbe Biology
    Transcriptome Analysis of Neisseria gonorrhoeae during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women

    Recent emergence of antimicrobial resistance of Neisseria gonorrhoeae worldwide has resulted in limited therapeutic choices for treatment of infections caused by this organism. We performed global transcriptomic analysis of N. gonorrhoeae in subjects with gonorrhea who attended a Nanjing, China,...

    Kathleen Nudel, Ryan McClure, Matthew Moreau, Emma Briars, A. Jeanine Abrams, Brian Tjaden, Xiao-Hong Su, David Trees, Peter A. Rice, Paola Massari, Caroline A. Genco

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