Horizontal Gene Transfer, 1st ed. 2020
Methods and Protocols
Methods in Molecular Biology Series, Vol. 2075

Coordinator: de la Cruz Fernando

Language: English

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Horizontal Gene Transfer
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Support: Print on demand

Approximative price 189.89 €

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Horizontal Gene Transfer
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413 p. · 17.8x25.4 cm · Hardback
This book focuses on technologies used to study horizontal gene transfer (HGT) in prokaryotes. Beginning with a section on the detection and isolation of mobile genetic elements (MGEs), the volume continues with sections concentrating on the analysis of conjugation, transformation, and transduction in HGT as well as a series of methods to analyze the adaptation and evolution of MGEs, with special attention paid to bioinformatics tools. 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 practical, Horizontal Gene Transfer: Methods and Protocols serves as an ideal guide to the further study of this pervasive, all-important mechanism of genetic originality.

Part I: Methods for the Detection and Isolation of Mobile Genetic Elements

 

1. Plasmid DNA Isolation and Visualization: Isolation and Characterization of Plasmids from Clinical Samples

            Kaitlin A. Tagg, Carola Venturini, Muhammad Kamruzzaman, Andrew N. Ginn, and Sally R. Partridge

 

2. Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health

            Ana R. Freitas, Carla Novais, Luísa Peixe, and Teresa M. Coque

 

3. Detection, Isolation, and Characterization of Plasmids in the Environment

            Khald Blau, Sven Jechalke, and Kornelia Smalla

 

4. Bacteriophage Isolation and Characterization: Phages of Escherichia coli

            Juan Jofre and Maite Muniesa

 

5. Detection and Characterization of Transposons in Bacteria

            Catherine Guynet, Le Phan Thai Nguyen, Michael Chandler, and Bao Ton-Hoang

 

Part II: Methods to Quantify and Characterize Horizontal Gene Transfer

 

6. Measuring Plasmid Conjugation Using Antibiotic Selection

            Jorge Rodriguez-Grande and Raul Fernandez-Lopez

 

7. Measuring Plasmid Conjugation Using Fluorescent Reporters

            Carolina Palencia-Gandara, Raul Ruiz, and Raul Fernandez-Lopez

 

8. Methods to Quantify DNA Transfer in Enterococcus

            Carla Novais, Ana R. Freitas, Ricardo León Sampedro, Luísa Peixe, and Teresa M. Coque

 

9. Quantifying and Characterizing Distributive Conjugal Transfer in Mycobacterium smegmatis

            Ryan Clark, Todd A. Gray, and Keith M. Derbyshire

 

10. Spectrophotometric Assays to Quantify the Activity of T4SS ATPases

            Elena Cabezón and Ignacio Arechaga

 

11. Identification of Relaxase-DNA Covalent Complexes and DNA Strand Transfer Reaction Products by Polyacrylamide Gel Electrophoresis

            María Lucas and Gabriel Moncalián

 

12. First Biochemical Steps on Bacterial Transposition Pathways

            Catherine Guynet, Emilien Nicolas, Bao Ton-Hoang, Jean-Yves Bouet, and Bernard Hallet

 

13. Natural Transformation in Escherichia coli

            Yoko Komiyama and Sumio Maeda

 

14. Integron Identification in Bacterial Genomes and Cassette Recombination Assays

            Claire Vit, Céline Loot, José Antonio Escudero, Aleksandra Nivina, and Didier Mazel

 

15. Methods to Identify and Analyze Vesicle-Protected DNA Transfer

            Alba Blesa and José Berenguer

 

16. Measuring Plasmid Stability in Gram-Negative Bacteria

            Damián Lobato Márquez

 

17. Methods for the Analysis and Characterization of Defence Mechanisms against Horizontal Gene Transfer: CRISPR Systems

            Alicia Calvo-Villamañán, Aude Bernheim, and David Bikard

 

Part III: OMICs, Bioinformatics, Mathematical Modeling, and Technological Applications of HGT

 

18. The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements

            Patrick Denis Browne, Witold Kot, Tue Sparholt Jørgensen, and Lars Hestbjerg Hansen

 

19. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

            Jean Cury, Sophie Abby, Olivia Doppelt-Azeroual, Bertrand Néron, and Eduardo P.C. Rocha

 

20. PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole Genome Sequencing (WGS)

            Alessandra Carattoli and Henrik Hasman

 

21. MOBscan: Automated Annotation of MOB Relaxases

            M. Pilar Garcillán-Barcia, Santiago Redondo-Salvo, Luis Vielva, and Fernando de la Cruz

 

22. Plasmid Typing and Classification

            Laura Villa and Alessandra Carattoli

 

23. Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets

            María de Toro, Val F. Lanza, Luis Vielva, Santiago Redondo-Salvo, and Fernando de la Cruz

 

24. Statistical Analysis of Accessory Genome

            Miguel D. Fernández-de-Bobadilla, Teresa M. Coque, and Val F. Lanza

 

25. Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits

            Luis Delaye, Carlos Vargas, Amparo Latorre, and Andrés Moya

 

26. Methods to Study Fitness and Compensatory Adaptation in Plasmid-Carrying Bacteria

            Javier DelaFuente, Jeronimo Rodriguez-Beltran, and Alvaro San Millan

 

27. A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria

            Tomás Aparicio, Víctor de Lorenzo, and Esteban Martínez-García

 

28. Conjugative Assembly Genome Engineering (CAGE)

            Marc Güell

Includes cutting-edge techniques

Provides step-by-step detail essential for reproducible results

Contains key implementation advice from the experts