Main description:

This fully updated edition explores the latest techniques to study the challenging, and at times dangerous, genus of bacteria known as mycobacteria with basic methods that are still required for mycobacteriology along with the newer or improved methods that have been developed. The volume features chapters on the basics of DNA isolation, protein isolation, and lipid isolation, as well as more sophisticated techniques for isolation of ribosomes, and continues with sections involving analyzing subcellular fractions, culture methods, sequencing technology, in vitro models, molecular methods, as well as drug discovery applications. Written for the highly successful Methods in Molecular Biology series, 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 up-to-date, Mycobacteria Protocols, Fourth Edition serves as an ideal guide for those starting out with their mycobacteria research and also for those who have worked with it for decades.

Contents:

1. Culturing Mycobacteria

Elizabeth Wallace, Debra Hendrickson, Nicholas Tolli, Carolina Mehaffy, Maria Pena, Jerry A. Nick, Phillip Knabenbaur, Jackson Watkins, Anne Simpson, Anita G. Amin, Delphi Chatterjee, Karen M. Dobos, Ramanuj Lahiri, Linda Adams, Michael Strong; Max Salfinger, Rebecca Bradford, Timothy T. Stedman, Marco A. Riojas, and Manzour Hernando Hazbon

2. DNA Isolation from Mycobacteria

Heena Jagatia and Daire Cantillon

3. Extraction and Separation of Mycobacterial Proteins

Megan Lucas, Joan M. Ryan, Jackson Watkins, Kala Early, Nicole A. Kruh-Garcia, Carolina Mehaffy, and Karen M. Dobos

4. Lipid and Lipoarabinomannan Isolation and Characterization

Marie-Antoinette Laneelle, Lucie Spina, Jerome Nigou, Anne Lemassu, and Mamadou Daffe

5. Purification of Hibernating and Active C- Ribosomes from Zinc-Starved Mycobacteria

Yunlong Li, Pooja Keshavan, Jamie H. Corro, Ravi K. Koripella, Rajendra K. Agrawal, and Anil K. Ojha

6. Macrophage Infection Models for Mycobacterium tuberculosis

Benjamin K. Johnson, Sean M. Thomas, Andrew J. Olive, and Robert B. Abramovitch

7. Novel Single-Cell and High Throughput Microscopy Techniques to Monitor Dictyostelium discoideum-Mycobacterium marinum Infection Dynamics

Manon Mottet, Cristina Bosmani, Nabil Hanna, Jahn Nitschke, Louise Lefrancois, and Thierry Soldati

8. Single-Cell Analysis of Mycobacteria Using Microfluidics and Time-Lapse Microscopy

Giulia Manina and Neeraj Dhar

9. Measuring Efflux and Permeability in Mycobacteria

Liliana Rodrigues, Jose A. Ainsa, and Miguel Viveiros

10. Drug Susceptibility Screening Using In Vitro Models of Hypoxic Non-Replicating Persistent Mycobacteria

Savannah E.R. Gibson, James Harrison, and Jonathan A.G. Cox

11. Flow Cytometry Analysis of Mycobacteria and Mycobacteria-Infected Immune Cells

Sydney L. Solomon and Bryan D. Bryson

12. Electroporation of Mycobacteria

Tanya Parish

13. Gene Switching and Essentiality Testing

Amanda Claire Brown

14. Oligo-Mediated Recombineering and Its Use for Making SNPs, Knockouts, Insertions, and Fusions in Mycobacterium tuberculosis

Kenan C. Murphy

15. Using Proteolytic Hypomorphs to Detect Small Molecule Mechanism of Action

Eachan O. Johnson and Deborah T. Hung

16. CRISPR Interference (CRISPRi) for Targeted Gene Silencing in Mycobacteria

Andrew I. Wong and Jeremy M. Rock

17. Exploiting Fluorescent Proteins to Understand Mycobacterium tuberculosis Biology

David Giacalone, Lu Huang, and Shumin Tan

18. Metabolic Labeling of Live Mycobacteria with Trehalose-Based Probes

Nicholas Banahene and Benjamin M. Swarts

19. Identification and Characterization of Mycobacterial Species Using Whole Genome Sequences

Marco A. Riojas, Andrew M. Frank, Samuel R. Greenfield, Stephen P. King, Conor J. Meehan, Michael Strong, Alice R. Wattam, and Manzour Hernando Hazbon

20. Whole Genome Sequencing of Mycobacterium tuberculosis Directly from Sputum Samples

Amanda Claire Brown

21. Experimental and Computational Workflow for RNA Sequencing in Mycobacterium tuberculosis: From Total RNA to Differentially Expressed Genes

Shuyi Ma, Richard M. Jones Jr., Natalie S. Gleason, Jessica Farrow-Johnson, and David R. Sherman

22. RNA Sequencing for Transcript 5'-End Mapping in Mycobacteria

M. Carla Martini, Huaming Sun, and Scarlet S. Shell

23. Methods for Proteomic Analyses of Mycobacteria

Carolina Mehaffy, Megan Lucas, Nicole A. Kruh-Garcia, and Karen M. Dobos

24. Targeted Lipidomics of Mycobacterial Lipids and Glycolipids

Emilie Layre

25. Metabolomics of Mycobacterium tuberculosis

Kyle A. Planck, Madhumitha Nandakumar, Luiz Pedro S. de Carvalho, and Kyu Rhee

26. Determining Minimum Inhibitory Concentrations in Liquid Cultures or on Solid Medium

Qinglan Wang and Helena I.M. Boshoff

27. A Multi-Stress Model for High Throughput Screening Against Non-Replicating Mycobacterium tuberculosis

Ben Gold, Thulasi Warrier, and Carl Nathan

28. Antimicrobial Susceptibility Testing for Mycobacterium sps in High Throughput Format

Esther Perez-Herran and Alfonso Mendoza

29. High-Content Analysis Monitoring Intracellular Trafficking and Replication of Mycobacterium tuberculosis Inside Host Cells

Nathalie Deboosere, Imene Belhaouane, Arnaud Machelart, Eik Hoffmann, Alexandre Vandeputte, and Priscille Brodin

30. Efficient Measurement of Drug Interactions with DiaMOND (Diagonal Measurement of N-Way Drug Interactions)

Nhi Van, Yonatan Degefu, and Bree B. Aldridge

31. Drug Sensitivity Testing of Mycobacterium tuberculosis Growing in a Hollow Fiber Bioreactor

Brett Mason and Veronique Dartois