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,
models, molecular methods, as well as drug discovery applications. Written for the highly successful
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,
M
Table of Contents
1. Culturing Mycobacteria
Elizabeth Wallace, Debra Hendrickson, Nicholas Tolli, Carolina Mehaffy, María Peña, 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 Hazbón
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 Lanéelle, Lucie Spina, Jérôme Nigou, Anne Lemassu, and Mamadou Daffé
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, José A. Aínsa, 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 Hazbón
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 Pérez-Herrán and Alfonso Mendoza
29. High-Content Analysis Monitoring Intracellular Trafficking and Replication of Mycobacterium tuberculosis Inside Host Cells
Nathalie Deboosere, Imène 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 Véronique Dartois
