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Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being directed toward examining systems biology in complex multi-cellular organisms, the bulk of system-level analyses conducted to date have focused on the biology of microbes. In, Microbial Systems Biology: Methods and Protocols expert researchers in the field describe the utility and attributes of different tools (both experimental and computational) that are used for studying microbial systems.
Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Systems Biology: Methods and Protocols introduces and aids scientists in using the various tools that are currently available for analysis, modification and utilization of microbial organisms.
Part I: Sample Pre-partion and Identification
1. Flow Cytometry in Environmental Microbiology: A Rapid Approach for the Isolation of Single-Cells for Advanced Molecular Biology Analysis Ferrari BC., Winsley T., Bergquist PL. and van Dorst, J
2. Pressure Cycling Technology in Systems Biology Bradford S. Powell, Alexander V. Lazarev, Greta Carlson, Alexander R. Ivanov, and David A. Rozak
3. Targeted Isolation of Proteins from Natural Microbial Communities Living in an Extreme Environment Steven W. Singer
4. Bacterial Identification and Subtyping Using DNA Microarray and DNA Sequencing Sufian F. Al-Khaldi, Magdi M. Mossoba, Marc M. Allard, E. Kurt Lienau, and Eric D. Brown
Part II: Experimental Genomic Analyses
5. Genetic Manipulation of the Obligate Chemolithoautotrophic Bacterium Thiobacillus denitrificans Harry R. Beller, Tina C. Legler, and Staci R. Kane
6. Genome-wide Mapping of the Binding Sites of Proteins that Interact with DNA Stephen Spiro
Part III: Protein and Lipid Analyses
7. MICROBIAL PROTEOMICS USING MASS SPECTROMETRY Harry B. Hines
8. Fourier Transform Infrared Spectroscopy for Molecular Analysis of Microbial Cells Jesus J. Ojeda
Part IV: Metabolomic Analyses
9. Mass Spectrometry-based Microbial Metabolomics Edward E. K. Baidoo, Peter I. Benke and Jay D. Keasling
10. Fast Sampling of the Cellular Metabolome Walter M. van Gulik, Andre B. Canelas, Hilal Taymaz-Nikerel, Rutger D. Douma, Lodewijk P. de Jonge and Joseph J. Heijnen
Part V: Analyses of Cellular Metabolism
11. Metabolic Pathway Determination and Flux Analysis in Non-model Microorganisms through 13C-isotope Labeling Xueyang Feng, Wei-Qin Zhuang, Peter Colletti, Yinjie J. Tang
12. Biolog Phenotype Microarrays April Shea, Mark Wolcott, Simon Daefler, and David Rozak
13. NanoSIP: NanoSIMS Applications for Microbial Biology Jennifer Pett-Ridge and Peter K. Weber
Part VI: Kinetic Modeling of Cellular Processes
14. Electrophysiological-metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis Max Fontus and Peter Ortoleva
15. Simulating Microbial Systems: Addressing Model Uncertainty/Incompleteness via Multiscale and Entropy Methods A. Singharoy, H. Joshi, S. Cheluvaraja, Y. Miao, D. Brown and P. Ortoleva
Part VII: Genome-Scale Computational Studies
16. Bacterial Genome Annotation Nicholas Beckloff, Shawn Starkenburg, Tracey Freitas, and Patrick Chain
17. LeishCyc: a Guide to Building a Metabolic Pathway Database and the Visualization of Metabolic Data Eleanor C. Saunders, James I. MacRae, Thomas Naderer, Milica Ng, Malcolm J. McConville and Vladimir A. Likic
18. Development of Constraint-base System-level Models of Microbial Metabolism Ali Navid
19. Complex Network Analysis in Microbial Systems: Theory and Examples Zahra Zavareh, Eivind Almaas
20. Modeling a Minimal Cell Michael L. Shuler, Patricia Foley, Jordan Atlas
