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systems biology

  • Open Access
    Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection
    Research Article | Host-Microbe Biology
    Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection

    Current molecular tests that identify infection with high-consequence viruses such as Ebola virus and Marburg virus are based on the detection of virus material in the blood. These viruses do not undergo significant early replication in the blood and, instead, replicate in organs such as the liver and spleen. Thus, virus begins to accumulate in the blood only after significant replication has already occurred in those organs, making...

    Emily Speranza, Ignacio Caballero, Anna N. Honko, Joshua C. Johnson, J. Kyle Bohannon, Lisa Evans DeWald, Dawn M. Gerhardt, Jennifer Sword, Lisa E. Hensley, Richard S. Bennett, John H. Connor
  • Open Access
    Asparagine Deprivation Causes a Reversible Inhibition of Human Cytomegalovirus Acute Virus Replication
    Research Article | Host-Microbe Biology
    Asparagine Deprivation Causes a Reversible Inhibition of Human Cytomegalovirus Acute Virus Replication

    HCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, late onset disease remains a significant problem, and prolonged treatment, especially in patients with suppressed immune systems, greatly increases the risk of antiviral resistance. Very few antivirals...

    Chen-Hsuin Lee, Samantha Griffiths, Paul Digard, Nhan Pham, Manfred Auer, Juergen Haas, Finn Grey
  • Open Access
    Editor's Pick Research Article
    Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors

    The majority of our knowledge of the physiology of extracellular electron transfer derives from studies of electrons moving to the exterior of the cell. The physiological mechanisms and/or consequences of the reverse processes are largely uncharacterized. This report demonstrates that when coupled to oxygen reduction, electrode oxidation can result in cellular energy acquisition. This respiratory process has potentially important...

    Annette R. Rowe, Pournami Rajeev, Abhiney Jain, Sahand Pirbadian, Akihiro Okamoto, Jeffrey A. Gralnick, Mohamed Y. El-Naggar, Kenneth H. Nealson
  • Open Access
    Research Article
    Dynamic Proteomics of Herpes Simplex Virus Infection
    Nir Drayman, Omer Karin, Avi Mayo, Tamar Danon, Lev Shapira, Dor Rafael, Anat Zimmer, Anat Bren, Oren Kobiler, Uri Alon
  • Open Access
    Research Article
    Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

    The ubiquitous metabolism of lipids involves refined regulation, and an enriched understanding of this regulation would have wide implications. Various factors can influence lipid metabolism, including the environment and genetics. We demonstrated, using a multi-omics and multifactorial experimental setup, that multiple factors affect lipid accumulation in the yeast Yarrowia lipolytica. Using integrative analysis, we identified...

    Eduard J. Kerkhoven, Young-Mo Kim, Siwei Wei, Carrie D. Nicora, Thomas L. Fillmore, Samuel O. Purvine, Bobbie-Jo Webb-Robertson, Richard D. Smith, Scott E. Baker, Thomas O. Metz, Jens Nielsen
  • Open Access
    Research Article
    Quantitative Kinetic Analyses of Shutting Off a Two-Component System

    Activation of TCSs has been extensively studied; however, the kinetics of shutting off TCS pathways is not well characterized. We present comprehensive analyses of the shutoff response for the PhoR-PhoB system that reveal the impact of phosphatase activity on shutoff kinetics. This allows development of a quantitative framework not only to characterize the phosphatase activity in the natural cellular environment but also to understand...

    Rong Gao, Ann M. Stock
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