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This book expands on the previous volumes with new chapters exploring emerging themes and methodologies in bacterial virus research. The chapters in this book are divided into 4 parts and cover topics such as: iron chloride flocculation of bacteriophages from seawater; encapsulation of Listeria phage A511 by alginate; examining genome termini of bacteriophage through high-throughput sequencing; genome sequencing of dsDNA-containing bacteriophages directly from a single plaque; characterizing bacteriophages by biology, taxonomy, and genome analysis; phage genome annotation using the RAST pipeline; and the use of RP4::mini-Mu for gene transfer. Written in the highly successful Methods in Molecular Biology series format, 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.
Cutting edge and authoritative, Bacteriophages: Methods and Protocols, Volume III is a valuable resource for both established and novice phage scientists.
List of contents
Basic Phage Mathematics.- Analysis of Host-Takeover during SPOi Infection of Bacillus subtilis.- Practical Advice on the One-Step Growth Curve.- Iron Chloride Flocculation of Bacteriophages from Seawater.- Purification of Bacteriophages using Anion-Exchange Chromatography.- Encapsulation Strategies of Bacteriophages (Felix O1) for Oral Therapeutic Application.- Encapsulation of Listeria Phage A511 by Alginate to Improve its Thermal Stability.- Application of a Virucidal Agent to Avoid Over-Estimation of Phage Kill during Phage Decontamination Assays on Ready-to-Eat Meats.- Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes.- Identification of DNA Base Modifications by Means of Pacific Biosciences RS Sequencing Technology.- Analyzing Genome Termini of Bacteriophage Through High-Throughput Sequencing.- Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques using SISPA.- Genome Sequencing of dsDNA-Containing Bacteriophages Directly from a Single Plaque.- Preparing cDNA Libraries from Lytic Phage Infected Cells for Whole Transcriptome Analysis by RNA-Seq.- Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis.- Annotation of Bacteriophage Genome Sequences using DNA Master: An Overview.- Phage Genome Annotation using the RAST Pipeline.- Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams.- Transposable Bacteriophages as Genetic Tools.- Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes.- Use of RP4::mini-Mu for Gene Transfer.- Muprints and Whole Genome Insertion Scans: Methods for Investigating Chromosome Accessibility and DNA Dynamics using Bacteriophage Mu.
Summary
This book expands on the previous volumes with new chapters exploring emerging themes and methodologies in bacterial virus research. The chapters in this book are divided into 4 parts and cover topics such as: iron chloride flocculation of bacteriophages from seawater; encapsulation of Listeria phage A511 by alginate; examining genome termini of bacteriophage through high-throughput sequencing; genome sequencing of dsDNA-containing bacteriophages directly from a single plaque; characterizing bacteriophages by biology, taxonomy, and genome analysis; phage genome annotation using the RAST pipeline; and the use of RP4::mini-Mu for gene transfer. Written in the highly successful Methods in Molecular Biology series format, 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.
Cutting edge and authoritative, Bacteriophages: Methods and Protocols, Volume III is a valuable resource for both established and novice phage scientists.
