Bacteriophages: Methods and Protocols, Volume 3 / Edition 2

by Martha R.J. Clokie, Andrew M. Kropinski, Rob Lavigne

Overview

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 prools, and tips on troubleshooting and avoiding known pitfalls.

Cutting edge and authoritative, Bacteriophages: Methods and Prools, Volume IIIis a valuable resource for both established and novice phage scientists.

Product Details

ISBN-13:	9781493973415
Publisher:	Springer New York
Publication date:	11/15/2017
Series:	Methods in Molecular Biology , #1681
Edition description:	1st ed. 2018
Pages:	316
Product dimensions:	6.97(w) x 10.00(h) x (d)

Table of Contents

Preface…
Table of Contents…
Contributing Authors…

Part I Key Basics of Phage Biology


1. Basic Phage Mathematics
Stephen T. Abedon and Tena I. Katsaounis

2. Analysis of Host-Takeover during SPOi Infection of Bacillus subtilis
Charles Stewart

3. Practical Advice on the One-Step Growth Curve
Andrew M. Kropinski

4. Iron Chloride Flocculation of Bacteriophages from Seawater
Bonnie T. Poulos, Seth G. John, and Matthew B. Sullivan

5. Purification of Bacteriophages using Anion-Exchange Chromatography
Dieter Vandenheuvel, Sofie Rombouts, and Evelien M. Adriaenssens

6. Encapsulation Strategies of Bacteriophages (Felix O1) for Oral Therapeutic Application
Golam S. Islam, Qi Wang, and Parviz M. Sabour
7. Encapsulation of Listeria Phage A511 by Alginate to Improve its Thermal Stability
Hanie Ahmadi, Qi Wang, Loong-Tak Lim, and Sampathkumar Balamurugan

8. Application of a Virucidal Agent to Avoid Over-Estimation of Phage Kill during Phage Decontamination Assays on Ready-to-Eat Meats
Andrew Chibeu and S. Balamurugan


Part II Sequencing Analysis of Bacteriophages


9. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes
Daniel A. Russell

10. Identification of DNA Base Modifications by Means of Pacific Biosciences RS Sequencing Technology
Philip Kelleher, James Murphy, Jennifer Mahony, and Douwe van Sinderen

11. Analyzing Genome Termini of Bacteriophage Through High-Throughput Sequencing
Xianglilan Zhang, Yahui Wang, and Yigang Tong

12. Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques using SISPA
Derick E. Fouts

13. Genome Sequencing of dsDNA-Containing Bacteriophages Directly from a Single Plaque
Witold Kot

14. Preparing cDNA Libraries from Lytic Phage Infected Cells for Whole Transcriptome Analysis by RNA-Seq
Bob Blasdel, Pieter-Jan Ceyssens, and Rob Lavigne



Part III Phage-Related Bioinformatics Tools



15. Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis
Ramy K. Aziz, Hans-Wolfgang Ackermann, Nicola K. Petty, and Andrew M. Kropinski

16. Annotation of Bacteriophage Genome Sequences using DNA Master: An Overview
Welkin H. Pope and Deborah Jacobs-Sera

17. Phage Genome Annotation using the RAST Pipeline
Katelyn McNair, Ramy K. Aziz, Gordon D. Pusch, Ross Overbeek, Bas E. Dutilh, and Robert Edwards

18. Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams
Dann Turner and J. Mark Sutton, Darren M. Reynolds, Eby M. Sim, and Nicola K. Petty



Part IV Bacteriophage Genetics



19. Transposable Bacteriophages as Genetic Tools
Ariane Toussaint

20. Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes



Saija Haapa-Paananen and Harri Savilahti




21. Use of RP4::mini-Mu for Gene Transfer
Frédérique Van Gijsegem

22. Muprints and Whole Genome Insertion Scans: Methods for Investigating Chromosome
Accessibility and DNA Dynamics using Bacteriophage Mu
N. Patrick Higgins