De La Cruz Fernando (ed.) Horizontal Gene Transfer: Methods and Protocols

Humana Press, 2019. — 411 p. — (Methods in Molecular Biology 2075) — ISBN: 978-1-4939-9876-0This 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.Plasmid DNA Isolation and Visualization: Isolation and Characterization of Plasmids from Clinical Samples
Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health
Detection, Isolation, and Characterization of Plasmids in the Environment
Bacteriophage Isolation and Characterization: Phages of Escherichia coli
Detection and Characterization of Transposons in Bacteria
Measuring Plasmid Conjugation Using Antibiotic Selection
Measuring Plasmid Conjugation Using Fluorescent Reporters
Methods to Quantify DNA Transfer in Enterococcus
Quantifying and Characterizing Distributive Conjugal Transfer in Mycobacterium smegmatis
Spectrophotometric Assays to Quantify the Activity of T4SS ATPases
Identification of Relaxase-DNA Covalent Complexes and DNA Strand Transfer Reaction Products by Polyacrylamide Gel Electrophoresis
First Biochemical Steps on Bacterial Transposition Pathways
Natural Transformation in Escherichia coli
Integron Identification in Bacterial Genomes and Cassette Recombination Assays
Methods to Identify and Analyze Vesicle-Protected DNA Transfer
Measuring Plasmid Stability in Gram-Negative Bacteria
Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems
The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements
Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan
PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS)
MOBscan: Automated Annotation of MOB Relaxases
Plasmid Typing and Classification
Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets
Statistical Analysis of Accessory Genome
Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits
Methods to Study Fitness and Compensatory Adaptation in Plasmid-Carrying Bacteria
A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria
Conjugative Assembly Genome Engineering (CAGE)