Genomic Science Program

Genomic Science Program Research Awards

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Shewanella Federation

Pacific Northwest National Laboratory
Principal Investigator: Jim Fredrickson
Oak Ridge National Laboratory
Principal Investigator: Jizhong Zhou
BIATECH
Principal Investigator: Eugene Kolker

Research Partners:

• Michigan State University
• Argonne National Laboratory
• Marine Biological Laboratory
• University of Southern California
• Desert Research Institute

The Shewanella Federation is a multi-investigator and cross-institutional consortium formed to characterize and model the biology of the metabolically versatile bacterium Shewanella oneidensis MR-1. Information gathered from systems-level investigations will be used to model cellular-networks to construct a computation model predicting the biology of S. oneidensis MR-1.

Abstracts and Presentations

• 2005 Contractor-Grantee Workshop
  • Shewanella Federation (PDF, 242 kb)
  • The Shewanella Federation: Functional Genomic Investigations of Dissimilatory Metal- Reducing Shewanella
  • Global Profiling of Shewanella oneidensis MR-1: Expression of ‘Hypothetical’Genes and Improved Functional Annotations
  • Respiratory Pathways and Regulatory Networks of Shewanella oneidensis Involved in Energy Metabolism and Environmental Sensing
  • Functional Analysis of Shewanella, A Cross Genome Comparison
  • Optical Methods for Characterization of Expression Levels and Protein-Protein Interactions in Shewanella oneidensis MR-1
  • Reverse-Engineering Microbial Networks in Escherichia coli and Shewanella oneidensis MR-1 via Large-Scale Perturbation Studies
  • Comparative Analysis of Gene Expression Profiles of Shewanella oneidensis MR-1 Following Exposure to Ionizing Radiation and Ultraviolet Radiation
  • The Microbial Proteome Project: A Database of Microbial Protein Expression in the Context of Genome Analysis
• 2004 Contractor-Grantee Workshop
  • Abstracts
    • Global and Physiological Responses to Substrate Shifts in Continuous and Controlled Batch Cultures of Shewanella oneidensis MR-1
    • Integrated Analysis of Gene Functions and Regulatory Networks Involved in Anaerobic Energy Metabolism of Shewanella oneidensis MR-1
    • Profiling Shewanella oneidensis Strain MR-1: Converting Hypothetical Genes into Real, Functional Proteins
    • Systems Biology of Shewanella oneidensis MR-1: Physiology and Genomics of Nitrate Reduction, the Radiation Stress Response, and Bioinformatics Applications
    • Development and Application of Optical Methods for Characterization of Protein-Protein Interactions in Shewanella oneidensis MR-1
    • Annotation of Genes and Metabolism of Shewanella oneidensis MR-1
• 2003 Contractor-Grantee Workshop
  • Presentations
    • "Microarray-Based Functional Analysis," Jizhong (Joe) Zhou. (web-browsable files or PDF)
    • "2DE Proteomics for Shewanella Federation," Carol Giometti. (web-browsable files or PDF)
    • “Interdisciplinary Study of Shewanella oneidensis MR-1’s Metabolism & Metal Reduction,” Eugene Kolker. (web-browsable files or PDF)
    • "The Shewanella Federation," Jim Fredrickson. (web-browsable files or PDF)
    • "Shewanella and Genomes to Life," Ken Nealson. (web-browsable files or PDF)
    • "Approach for High Throughput Microbial Proteomics," Richard D. Smith. (web-browsable files or PDF)
    • "Tenets for Successful Integrated Research," Yuri A. Gorby. (web-browsable files or PDF)
  • Abstracts
    • Environmental Sensing, Metabolic Response, and Regulatory Networks in the Respiratory Versatile Bacterium Shewanella oneidensis MR-1
    • Progress in Development of Genetic Tools for Shewanella oneidensis MR-1
    • Integrated Analysis of Protein Complexes and Regulatory Networks Involved in Anaerobic Energy Metabolism of Shewanella oneidensis MR-1
    • Analysis of the Shewanella oneidensis Proteome in Cells Grown in Continuous Culture
    • The Microbial Proteome Project: A Database of Microbial Protein Expression in the Context of Genome Analysis
    • Genomes to Proteomes to Life: Application of New Technologies for Comprehensive, Quantitative and High Throughput Microbial Proteomics
• Related Abstracts
  • Integrating “Top-Down” and “Bottom-Up” Mass Spectrometric Approaches for Proteomic Analysis of Shewanella oneidensis, Nathan C. VerBerkmoes, et al. Journal of Proteome Research 2002, 1, 239-252. (Requires subscription to view article.)
  • Abstracts from DOE Genome Program Contractor-Grantee Workshop, January 27-31, 2002, Oakland, CA
• Genome-Wide Functional Analysis of the Metal-Reducing Bacterium Shewanella oneidensis MR-1: Progress Summary, Alexander Beliaev, Dorothea K. Thompson, Carol S. Giometti, Kenneth H. Nealson, Alison E. Murray, James M. Tiedje, and Jizhong Zhou
• Global Characterization of Proteins Associated With S. oneidensis MR-1 Outer Membrane Vesicles, Margaret F. Romine, Jim Fredrickson, Yuri Gorby, Jeff McLean, Mary S. Lipton, Ljiljana  Pasa-Tolic, Alexander Tsapin, Kenneth Nealson, Carol Giometti, Sandra Tollaksen, and Richard D. Smith
• Shewanella Federation: Data Analysis and Integration, Eugene Kolker
• Integrated Analysis of Protein Complexes and Regulatory Networks Involved in Anaerobic Energy Metabolism of Shewanella oneidensis MR-1, Jizhong Zhou, Frank Larimer, James M. Tiedje, Kenneth H. Nealson, Richard Smith, Timothy Palzkill, Bernhardt O. Palsson, Carol Giometti, Dong Xu, Mary Lipton, Alex S. Beliaev, Dorothea K. Thompson, Matthew W. Fields, James R. Cole, and Joel Klappenbach