Bacteriophages: Methods and Protocols, Volume 3

✍ Scribed by Martha R.J. Clokie, Andrew M. Kropinski, Rob Lavigne (eds.)

• Publisher: Humana Press
• Year: 2018
• Tongue: English
• Leaves: 311
• Series: Methods in Molecular Biology 1681
• Edition: 1
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xi
Front Matter ....Pages 1-1
Basic Phage Mathematics (Stephen T. Abedon, Tena I. Katsaounis)....Pages 3-30
Analysis of Host-Takeover During SPO1 Infection of Bacillus subtilis (Charles R. Stewart)....Pages 31-39
Practical Advice on the One-Step Growth Curve (Andrew M. Kropinski)....Pages 41-47
Iron Chloride Flocculation of Bacteriophages from Seawater (Bonnie T. Poulos, Seth G. John, Matthew B. Sullivan)....Pages 49-57
Purification of Bacteriophages Using Anion-Exchange Chromatography (Dieter Vandenheuvel, Sofie Rombouts, Evelien M. Adriaenssens)....Pages 59-69
Encapsulation Strategies of Bacteriophage (Felix O1) for Oral Therapeutic Application (Golam S. Islam, Qi Wang, Parviz M. Sabour)....Pages 71-87
Encapsulation of Listeria Phage A511 by Alginate to Improve Its Thermal Stability (Hanie Ahmadi, Qi Wang, Loong-Tak Lim, S. Balamurugan)....Pages 89-95
Application of a Virucidal Agent to Avoid Overestimation of Phage Kill During Phage Decontamination Assays on Ready-to-Eat Meats (Andrew Chibeu, S. Balamurugan)....Pages 97-105
Front Matter ....Pages 107-107
Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes (Daniel A. Russell)....Pages 109-125
Identification of DNA Base Modifications by Means of Pacific Biosciences RS Sequencing Technology (Philip Kelleher, James Murphy, Jennifer Mahony, Douwe van Sinderen)....Pages 127-137
Analyzing Genome Termini of Bacteriophage Through High-Throughput Sequencing (Xianglilan Zhang, Yahui Wang, Yigang Tong)....Pages 139-163
Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques Using SISPA (Derick E. Fouts)....Pages 165-178
Genome Sequencing of dsDNA-Containing Bacteriophages Directly from a Single Plaque (Witold Kot)....Pages 179-184
Preparing cDNA Libraries from Lytic Phage-Infected Cells for Whole Transcriptome Analysis by RNA-Seq (Bob Blasdel, Pieter-Jan Ceyssens, Rob Lavigne)....Pages 185-194
Front Matter ....Pages 195-195
Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis (Ramy Karam Aziz, Hans-Wolfgang Ackermann, Nicola K. Petty, Andrew M. Kropinski)....Pages 197-215
Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview (Welkin H. Pope, Deborah Jacobs-Sera)....Pages 217-229
Phage Genome Annotation Using the RAST Pipeline (Katelyn McNair, Ramy Karam Aziz, Gordon D. Pusch, Ross Overbeek, Bas E. Dutilh, Robert Edwards)....Pages 231-238
Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams (Dann Turner, J. Mark Sutton, Darren M. Reynolds, Eby M. Sim, Nicola K. Petty)....Pages 239-260
Front Matter ....Pages 261-261
Transposable Bacteriophages as Genetic Tools (Ariane Toussaint)....Pages 263-278
Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes (Saija Haapa-Paananen, Harri Savilahti)....Pages 279-286
Use of RP4::Mini-Mu for Gene Transfer (Frédérique Van Gijsegem)....Pages 287-302
Muprints and Whole Genome Insertion Scans: Methods for Investigating Chromosome Accessibility and DNA Dynamics using Bacteriophage Mu (N. Patrick Higgins)....Pages 303-314
Back Matter ....Pages 315-316

✦ Subjects

Microbiology