Bacteriophages: Methods and Protocols, Volume 3

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