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    • Latest Articles
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    • Special Series: Sponsored Minireviews and Video Abstracts
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  • Topics
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systems biology

  • Open Access
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification
    Research Article | Molecular Biology and Physiology
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

    Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts.

    Anne E. Otwell, Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, Serdar Turkarslan, Sean M. Gibbons, Dwayne A. Elias, David A. Stahl, Gary Siuzdak, Nitin S. Baliga
  • Open Access
    Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation
    Research Article | Novel Systems Biology Techniques
    Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation

    Bacterial persistence is a fascinating phenomenon in which a small subpopulation of bacteria becomes phenotypically tolerant to lethal antibiotic exposure. There is growing evidence that populations of bacteria in chronic clinical infections develop a hyperpersistent phenotype, enabling a substantially larger subpopulation to survive repeated antibiotic treatment. The mechanisms of persistence and modes of increasing persistence rates...

    Anupama Khare, Saeed Tavazoie
  • Open Access
    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
    Research Article | Novel Systems Biology Techniques
    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

    The bacterial communities that live within the human gut have been linked to health and disease. However, we are still just beginning to understand how those bacteria interact and what potential interventions to our gut microbiome can make us healthier. Here, we present a mathematical modeling framework (named MICOM) that can recapitulate the growth rates of diverse bacterial species in the gut and can simulate metabolic interactions...

    Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
  • Open Access
    Conserved Central Intraviral Protein Interactome of the <em>Herpesviridae</em> Family
    Research Article | Molecular Biology and Physiology
    Conserved Central Intraviral Protein Interactome of the Herpesviridae Family

    Herpesviruses are an important socioeconomic burden for both humans and livestock. Throughout their long evolutionary history, individual herpesvirus species have developed remarkable host specificity, while collectively the Herpesviridae family has evolved to infect a large variety of eukaryotic hosts. The development of approaches to fight herpesvirus infections has been hampered by the complexity of herpesviruses’ genomes,...

    Anna Hernández Durán, Kay Grünewald, Maya Topf
  • Open Access
    A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in <em>Trichoderma reesei</em>
    Research Article | Molecular Biology and Physiology
    A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei

    In this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in...

    Amanda Cristina Campos Antonieto, Karoline Maria Vieira Nogueira, Renato Graciano de Paula, Luísa Czamanski Nora, Murilo Henrique Anzolini Cassiano, Maria-Eugenia Guazzaroni, Fausto Almeida, Thiago Aparecido da Silva, Laure Nicolas Annick Ries, Leandro Jose de Assis, Gustavo Henrique Goldman, Roberto Nascimento Silva, Rafael Silva-Rocha
  • Open Access
    The Power of Metabolism for Predicting Microbial Community Dynamics
    Special Issue Perspective | Ecological and Evolutionary Science
    The Power of Metabolism for Predicting Microbial Community Dynamics

    Quantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.

    Jeremy M. Chacón, William R. Harcombe
  • Open Access
    Role of Multiple Infections on Immunological Variation in Wild Populations
    Special Issue Perspective | Ecological and Evolutionary Science
    Role of Multiple Infections on Immunological Variation in Wild Populations

    A central challenge in the fields of evolutionary immunology and disease ecology is to understand the causes and consequences of natural variation in host susceptibility to infectious diseases. As hosts progress from birth to death in the wild, they are exposed to a wide variety of microorganisms that influence their physical condition, immune system maturation, and susceptibility to concurrent and future infection.

    Ann T. Tate
  • Open Access
    Minor Isozymes Tailor Yeast Metabolism to Carbon Availability
    Research Article | Molecular Biology and Physiology
    Minor Isozymes Tailor Yeast Metabolism to Carbon Availability

    Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one...

    Patrick H. Bradley, Patrick A. Gibney, David Botstein, Olga G. Troyanskaya, Joshua D. Rabinowitz
  • Open Access
    Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks
    Research Article | Ecological and Evolutionary Science
    Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks

    Different organisms in a microbial community may drastically affect each other’s growth phenotypes, significantly affecting the community dynamics, with important implications for human and environmental health. Novel culturing methods and the decreasing costs of sequencing will gradually enable high-throughput measurements of pairwise interactions in systematic coculturing studies. However, a thorough characterization of all...

    Demetrius DiMucci, Mark Kon, Daniel Segrè
  • Open Access
    Announcement of the 2019 BLAST Conference: “BLAST XV: 15th International Conference on Bacterial Locomotion and Signal Transduction”
    Editorial
    Announcement of the 2019 BLAST Conference: “BLAST XV: 15th International Conference on Bacterial Locomotion and Signal Transduction”

    An exciting conference showcasing cutting edge research in bacterial signal transduction, chemotaxis, and motility will be held in January 2019. This conference, called Bacterial Locomotion and Signal Transduction (BLAST), will be held in New Orleans, LA, USA, under the auspices of chair Birgit Scharf.

    Christine Josenhans, Robert B. Bourret, Karen Ottemann, Rasika Harshey, Ariane Briegel, Alan Wolfe, Birgit E. Scharf
    and on behalf of the BLAST Board of Directors and the Executive Committee of BLAST XV

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