Microbial Systems Biology: Methods and Protocols

ISBN-13: 9781071615843 / Angielski / Twarda / 2021 / 340 str.

Ali Navid

Spis treści

1. Parallel Accelerator and Molecular Mass Spectrometry Measurement of Carbon-14 Labeled Analytes

Benjamin J. Stewart and Ted J. Ognibene

 

2. 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

 

3. Investigation of Protein-Lipid Interactions Using Native Mass Spectrometry

Xiao Cong, John W. Patrick, Yang Liu, Xiaowen Liang, Wen Liu, and Arthur Laganowsky

 

4. Western Blot Processing Optimization: The Perfect Blot.

Russ Yukhananov, David P. Chimento, and Laura A. Marlow

 

5. FISHing on a Budget

Gable M. Wadsworth and Harold D. Kim

 

6. NanoSIP: NanoSIMS Applications for Microbial Biology

Jennifer Pett-Ridge and Peter K. Weber

 

7. Construction of Metatranscriptomic Libraries for 5' end Sequencing of rRNAs for Microbiome Research

Marja Tiirola and Anita Mäki

 

8. Computational Approaches for Designing Highly Specific and Efficient sgRNAs

Jaspreet Kaur Dhanjal, Dhvani Vora, Navaneethan Radhakrishnan, and Durai Sundar

 

9. Complex Network Analysis in Microbial Systems: Theory and Examples

André Voigt and Eivind Almaas

 

10. Prokaryotic Genome Annotation

Jeffrey A. Kimbrel, Brendan M. Jeffrey, and Christopher S. Ward

 

11. Functional Annotation from Structural Homology

Brent W. Segelke

 

12. Metabolic Modeling with MetaFlux

Mario Latendresse, Wai Kit Ong, and Peter D. Karp

 

13. Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, And Predict Pathways in an Isolate Genome

Benjamin H. Allen, Nidhi Gupta, Janaka N. Edirisinghe, José P. Faria, and Christopher S. Henry

 

14. Curating COBRA Models of Microbial Metabolism

Ali Navid

 

15. A Beginner’s Guide to the COBRA Toolbox

Ali Navid

 

16. Rules of Engagement: A Guide to Developing Agent-Based Models

Marc Griesemer and Suzanne S. Sindi

Blurb

This second edition provides new and updated chapters describing the utility and attributes of different tools that are used for studying microbial systems. Chapters detail a number of methods, including in silico system level analyses by MetaFlux, Kbase genome-scale model builder, COBRA toolbox, NanoSIP, and PAMMS. 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 tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Microbial Systems Biology: Methods and Protocols, Second Edition aims to introduce and aid scientists in using the various tools that are currently available for analysis, modification, and utilization of microbial organisms.