Microbial Systems Biology

Methods and Protocols

Editors:

ISBN: 978-1-61779-826-9 (Print) 978-1-61779-827-6 (Online)

Table of contents (20 protocols)

  1. Front Matter

    Pages i-xii

  2. Sample Prepartion and Identification

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-26

      Flow Cytometry in Environmental Microbiology: A Rapid Approach for the Isolation of Single Cells for Advanced Molecular Biology Analysis

    3. No Access

      Book Protocol

      Pages 27-62

      Pressure Cycling Technology in Systems Biology

    4. No Access

      Book Protocol

      Pages 63-72

      Targeted Isolation of Proteins from Natural Microbial Communities Living in an Extreme Environment

    5. No Access

      Book Protocol

      Pages 73-95

      Bacterial Identification and Subtyping Using DNA Microarray and DNA Sequencing

  3. Experimental Genomic Analyses

    1. Front Matter

      Pages 97-97

    2. No Access

      Book Protocol

      Pages 99-136

      Genetic Manipulation of the Obligate Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    3. No Access

      Book Protocol

      Pages 137-156

      Genome-Wide Mapping of the Binding Sites of Proteins That Interact with DNA

  4. Protein and Lipid Analyses

    1. Front Matter

      Pages 157-157

    2. No Access

      Book Protocol

      Pages 159-186

      Microbial Proteomics Using Mass Spectrometry

    3. No Access

      Book Protocol

      Pages 187-211

      Fourier Transform Infrared Spectroscopy for Molecular Analysis of Microbial Cells

  5. Metabolomic Analyses

    1. Front Matter

      Pages 213-213

    2. No Access

      Book Protocol

      Pages 215-278

      Mass Spectrometry-Based Microbial Metabolomics

    3. No Access

      Book Protocol

      Pages 279-306

      Fast Sampling of the Cellular Metabolome

  6. Analyses of Cellular Metabolism

    1. Front Matter

      Pages 307-307

    2. No Access

      Book Protocol

      Pages 309-330

      Metabolic Pathway Determination and Flux Analysis in Nonmodel Microorganisms Through 13C-Isotope Labeling

    3. No Access

      Book Protocol

      Pages 331-373

      Biolog Phenotype Microarrays

    4. No Access

      Book Protocol

      Pages 375-408

      NanoSIP: NanoSIMS Applications for Microbial Biology

  7. Kinetic Modeling of Cellular Processes

    1. Front Matter

      Pages 409-409

    2. No Access

      Book Protocol

      Pages 411-431

      Electrophysiological-Metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis

    3. No Access

      Book Protocol

      Pages 433-467

      Simulating Microbial Systems: Addressing Model Uncertainty/Incompleteness via Multiscale and Entropy Methods

  8. Genome-Scale Computational Studies

    1. Front Matter

      Pages 469-469

    2. No Access

      Book Protocol

      Pages 471-503

      Bacterial Genome Annotation

    3. No Access

      Book Protocol

      Pages 505-529

      LeishCyc: A Guide to Building a Metabolic Pathway Database and Visualization of Metabolomic Data

    4. No Access

      Book Protocol

      Pages 531-549

      Development of Constraint-Based System-Level Models of Microbial Metabolism

    5. No Access

      Book Protocol

      Pages 551-571

      Complex Network Analysis in Microbial Systems: Theory and Examples

    6. No Access

      Book Protocol

      Pages 573-610

      Modeling a Minimal Cell

  9. Back Matter

    Pages 611-615