Horizontal Gene Transfer

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).