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