Horizontal gene transfer : methods and protocols
著者
書誌事項
Horizontal gene transfer : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2075）（Springer protocols）
Humana Press, c2020
大学図書館所蔵 全1件
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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