Microbial Genetics and Genomics
Description / Table of Contents:
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 Defence 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)
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
XV, 413 p. 62 illus., 52 illus. in color. : online resource.
1st ed. 2020.