Horizontal gene transfer : methods and protocols

著者

    • Cruz, Fernando de la

書誌事項

Horizontal gene transfer : methods and protocols

edited by Fernando de la Cruz

（Methods in molecular biology / John M. Walker, series editor, 2075）（Springer protocols）

Humana Press, c2020

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注記

Includes index

内容説明・目次

内容説明

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.

目次

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, Luisa 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 Leon Sampedro, Luisa 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 Cabezon and Ignacio Arechaga 11. Identification of Relaxase-DNA Covalent Complexes and DNA Strand Transfer Reaction Products by Polyacrylamide Gel Electrophoresis Maria Lucas and Gabriel Moncalian 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, Celine Loot, Jose Antonio Escudero, Aleksandra Nivina, and Didier Mazel 15. Methods to Identify and Analyze Vesicle-Protected DNA Transfer Alba Blesa and Jose Berenguer 16. Measuring Plasmid Stability in Gram-Negative Bacteria Damian Lobato Marquez 17. Methods for the Analysis and Characterization of Defence Mechanisms against Horizontal Gene Transfer: CRISPR Systems Alicia Calvo-Villamanan, 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 Jorgensen, and Lars Hestbjerg Hansen 19. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan Jean Cury, Sophie Abby, Olivia Doppelt-Azeroual, Bertrand Neron, 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 Garcillan-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 Maria de Toro, Val F. Lanza, Luis Vielva, Santiago Redondo-Salvo, and Fernando de la Cruz 24. Statistical Analysis of Accessory Genome Miguel D. Fernandez-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 Andres 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 Tomas Aparicio, Victor de Lorenzo, and Esteban Martinez-Garcia 28. Conjugative Assembly Genome Engineering (CAGE) Marc Guell

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