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).