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Latest Articles

  • Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality
    Research Article | Clinical Science and Epidemiology
    Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality

    Around 20% of human cancers are associated with viruses. Epstein-Barr virus (EBV) contributes to gastric cancer, nasopharyngeal carcinoma, and certain lymphomas, but its role in other cancer types remains controversial. We assessed the prevalence of EBV in RNA-seq from 32 tumor types in the Cancer Genome Atlas Project (TCGA) and found EBV to be present in >5% of samples in 12 tumor types. EBV infects epithelial cells and B cells and...

    Sara R. Selitsky, David Marron, Lisle E. Mose, Joel S. Parker, Dirk P. Dittmer
    25 Sep 2018
  • Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes
    Editor's Pick Research Article | Applied and Environmental Science
    Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

    In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of...

    Karen G. Lloyd, Andrew D. Steen, Joshua Ladau, Junqi Yin, Lonnie Crosby
    25 Sep 2018
  • Transmission of Hepatitis B and D Viruses in an African Rural Community
    Research Article | Clinical Science and Epidemiology
    Transmission of Hepatitis B and D Viruses in an African Rural Community

    This study revealed that the prevalence of HBV and HDV in a rural area of Cameroon is extremely high, underlining the pressing need for the improvement of control strategies. Systematic serological and phylogenetic analyses of HBV sequences turned out to be useful tools to identify networks of virus transmission within and between households. The high HBsAg carriage rate found among children demonstrates that implementation of the HBV...

    Carlos Augusto Pinho-Nascimento, Martin W. Bratschi, Rene Höfer, Caroline Cordeiro Soares, Louisa Warryn, Jūlija Pečerska, Jacques C. Minyem, Izabel C. N. P. Paixão, Marcia Terezinha Baroni de Moraes, Alphonse Um Boock, Christian Niel, Gerd Pluschke, Katharina Röltgen
    18 Sep 2018
  • Characterization of <span class="named-content genus-species" id="named-content-1">Aspergillus niger</span> Isolated from the International Space Station
    Research Article | Molecular Biology and Physiology
    Characterization of Aspergillus niger Isolated from the International Space Station

    A thorough understanding of how fungi respond and adapt to the various stimuli encountered during spaceflight presents many economic benefits and is imperative for the health of crew. As A. niger is a predominant ISS isolate frequently detected in built environments, studies of A. niger strains...

    Jillian Romsdahl, Adriana Blachowicz, Abby J. Chiang, Nitin Singh, Jason E. Stajich, Markus Kalkum, Kasthuri Venkateswaran, Clay C. C. Wang
    18 Sep 2018
  • Comprehensive Functional Analysis of the <span class="named-content genus-species" id="named-content-1">Enterococcus faecalis</span> Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF
    Resource Report | Novel Systems Biology Techniques
    Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF

    The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome...

    Jennifer L. Dale, Kenneth B. Beckman, Julia L. E. Willett, Jennifer L. Nilson, Nagendra P. Palani, Joshua A. Baller, Adam Hauge, Daryl M. Gohl, Raymond Erickson, Dawn A. Manias, Michael J. Sadowsky, Gary M. Dunny
    11 Sep 2018
  • Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> to Stationary Phase
    Research Article | Molecular Biology and Physiology
    Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase

    During the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form...

    Hideji Yoshida, Tomohiro Shimada, Akira Ishihama
    11 Sep 2018
  • Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities
    Research Article | Ecological and Evolutionary Science
    Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities

    Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite...

    Ashley R. Coenen, Joshua S. Weitz
    28 Aug 2018
  • Coproporphyrin III Produced by the Bacterium <em>Glutamicibacter arilaitensis</em> Binds Zinc and Is Upregulated by Fungi in Cheese Rinds
    Research Article | Applied and Environmental Science
    Coproporphyrin III Produced by the Bacterium Glutamicibacter arilaitensis Binds Zinc and Is Upregulated by Fungi in Cheese Rinds

    Bacterium-fungus interactions play key roles in the assembly of cheese rind microbial communities, but the molecular mechanisms underlying these interactions are poorly characterized. Moreover, millions of people around the world enjoy eating cheeses and cheese rinds, but our understanding of the diversity of microbial metabolites ingested during cheese consumption is limited. The discovery of zinc coproporphyrin III as the cause of...

    Jessica L. Cleary, Shilpa Kolachina, Benjamin E. Wolfe, Laura M. Sanchez
    21 Aug 2018
  • Genomic Characterization and Copy Number Variation of <em>Bacillus anthracis</em> Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains
    Research Article | Ecological and Evolutionary Science
    Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains

    Bacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B. anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the...

    Angela Pena-Gonzalez, Luis M. Rodriguez-R, Chung K. Marston, Jay E. Gee, Christopher A. Gulvik, Cari B. Kolton, Elke Saile, Michael Frace, Alex R. Hoffmaster, Konstantinos T. Konstantinidis
    14 Aug 2018
  • Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation
    Research Article | Host-Microbe Biology
    Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

    Ruminant animals, such as cows, live in a tight symbiotic association with microorganisms, allowing them to feed on otherwise indigestible plant biomass as food sources. Methane is produced as an end product of the anaerobic feed degradation in ruminants and is emitted to the atmosphere, making ruminant animals among the major anthropogenic sources of the potent greenhouse gas methane. Using newly developed quantitative...

    Andrea Söllinger, Alexander Tøsdal Tveit, Morten Poulsen, Samantha Joan Noel, Mia Bengtsson, Jörg Bernhardt, Anne Louise Frydendahl Hellwing, Peter Lund, Katharina Riedel, Christa Schleper, Ole Højberg, Tim Urich
    7 Aug 2018

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