Mycobacteria Protocols

ISBN-13: 9781071614594 / Angielski / Twarda / 2021 / 736 str.

Tanya Parish; Anuradha Kumar

Spis treści

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

Blurb

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.