Microbial Systems Biology: Methods and Protocols

ISBN-13: 9781493961924 / Angielski / Miękka / 2016 / 615 str.

Ali Navid

Opis

This Methods in Molecular Biology (TM) volume describes experimental and computational tools used for studying microbial systems, and offers step-by-step, readily reproducible laboratory protocols, with key tips on troubleshooting and avoiding known pitfalls.

Recenzje

From the reviews:

"This book ... deals with one of the most dynamic trends in Biology, namely Systems Biology of Microorganisms. ... Most of the chapters are of direct and immediate usefulness for scientists to start their own experiments with respect to different aspects of systems biology of a given microorganism or community/environment. ... In my opinion, the purpose of this book ... to introduce the reader to some of the established and state-of-the-art technologies that are being used to study microbial systems biology - is fully accomplished." (Ioan I. Ardelean, Romanian Journal of Biochemistry, Vol. 50 (1), 2013)

Spis treści

Part I: Sample Prepartion 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

Jesús 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. Likić

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

Blurb

 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.