Horizontal gene transfer : methods and protocols

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. Front Matter ....Pages i-xv Front Matter ....Pages 1-1 Plasmid DNA Isolation and Visualization: Isolation and Characterization of Plasmids from Clinical Samples (Kaitlin A. Tagg, Carola Venturini, Muhammad Kamruzzaman, Andrew N. Ginn, Sally R. Partridge)....Pages 3-20 Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health (Ana R. Freitas, Carla Novais, Luísa Peixe, Teresa M. Coque)....Pages 21-38 Detection, Isolation, and Characterization of Plasmids in the Environment (Khald Blau, Sven Jechalke, Kornelia Smalla)....Pages 39-60 Bacteriophage Isolation and Characterization: Phages of Escherichia coli (Juan Jofre, Maite Muniesa)....Pages 61-79 Detection and Characterization of Transposons in Bacteria (Catherine Guynet, Phan Thai Nguyen Le, Michael Chandler, Bao Ton-Hoang)....Pages 81-90 Front Matter ....Pages 91-91 Measuring Plasmid Conjugation Using Antibiotic Selection (Jorge Rodriguez-Grande, Raul Fernandez-Lopez)....Pages 93-98 Measuring Plasmid Conjugation Using Fluorescent Reporters (Carolina Palencia-Gandara, Raul Ruiz, Raul Fernandez-Lopez)....Pages 99-110 Methods to Quantify DNA Transfer in Enterococcus (Carla Novais, Ana R. Freitas, Ricardo León-Sampedro, Luísa Peixe, Teresa M. Coque)....Pages 111-122 Quantifying and Characterizing Distributive Conjugal Transfer in Mycobacterium smegmatis (Ryan R. Clark, Todd A. Gray, Keith M. Derbyshire)....Pages 123-134 Spectrophotometric Assays to Quantify the Activity of T4SS ATPases (Elena Cabezón, Ignacio Arechaga)....Pages 135-143 Identification of Relaxase-DNA Covalent Complexes and DNA Strand Transfer Reaction Products by Polyacrylamide Gel Electrophoresis (María Lucas, Gabriel Moncalián)....Pages 145-156 First Biochemical Steps on Bacterial Transposition Pathways (Catherine Guynet, Emilien Nicolas, Bao Ton-Hoang, Jean-Yves Bouet, Bernard Hallet)....Pages 157-177 Natural Transformation in Escherichia coli (Yoko Komiyama, Sumio Maeda)....Pages 179-187 Integron Identification in Bacterial Genomes and Cassette Recombination Assays (Claire Vit, Céline Loot, José Antonio Escudero, Aleksandra Nivina, Didier Mazel)....Pages 189-208 Methods to Identify and Analyze Vesicle-Protected DNA Transfer (Alba Blesa, José Berenguer)....Pages 209-221 Measuring Plasmid Stability in Gram-Negative Bacteria (Damián Lobato-Márquez)....Pages 223-233 Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems (Alicia Calvo-Villamañán, Aude Bernheim, David Bikard)....Pages 235-249 Front Matter ....Pages 251-251 The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements (Patrick Denis Browne, Witold Kot, Tue Sparholt Jørgensen, Lars Hestbjerg Hansen)....Pages 253-264 Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan (Jean Cury, Sophie S. Abby, Olivia Doppelt-Azeroual, Bertrand Néron, Eduardo P. C. Rocha)....Pages 265-283 PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS) (Alessandra Carattoli, Henrik Hasman)....Pages 285-294 MOBscan: Automated Annotation of MOB Relaxases (M. Pilar Garcillán-Barcia, Santiago Redondo-Salvo, Luis Vielva, Fernando de la Cruz)....Pages 295-308 Plasmid Typing and Classification (Laura Villa, Alessandra Carattoli)....Pages 309-321 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, Fernando de la Cruz)....Pages 323-339 Statistical Analysis of Accessory Genome (Miguel D. Fernández-de-Bobadilla, Teresa M. Coque, Val F. Lanza)....Pages 341-353 Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits (Luis Delaye, Carlos Vargas, Amparo Latorre, Andrés Moya)....Pages 355-369 Methods to Study Fitness and Compensatory Adaptation in Plasmid-Carrying Bacteria (Javier DelaFuente, Jeronimo Rodriguez-Beltran, Alvaro San Millan)....Pages 371-382 A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria (Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García)....Pages 383-398 Conjugative Assembly Genome Engineering (CAGE) (Marc Güell)....Pages 399-409 Back Matter ....Pages 411-413 "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." -- prové de l'editor 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. -- Back cover