Horizontal Gene Transfer : Methods and Protocols / edited by Fernando de la Cruz.

Format:

Book

Contributor:

Cruz, Fernando de la (Cruz Calahorra), editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1064-3745 ; 2075.

Methods in Molecular Biology, 1064-3745 ; 2075

Language:

English

Subjects (All):

Microbial genetics.

Microbial genomics.

Bacteriology.

Microbial Genetics and Genomics.

Local Subjects:

Microbial Genetics and Genomics.

Bacteriology.

Physical Description:

1 online resource (XV, 413 pages) : 62 illustrations, 52 illustrations in color.

Edition:

First edition 2020.

Contained In:

Springer eBooks

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2020.

System Details:

text file PDF

Summary:

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.

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).

Other Format:

Printed edition:

ISBN:

978-1-4939-9877-7

9781493998777

Access Restriction:

Restricted for use by site license.