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Bacteriophages

Methods and Protocols, Volume 3

  • Book
  • © 2018

Overview

Editors:
  1. Martha R.J. Clokie

    1. Department Infection, Immunity & Inflammation, University of Leicester School of Medicine, Leicester, United Kingdom

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    You can also search for this editor in PubMed   Google Scholar

  2. Andrew M. Kropinski

    1. University of Guelph, Guelph, Canada

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    You can also search for this editor in PubMed   Google Scholar

  3. Rob Lavigne

    1. KU Leuven, Laboratory of Gene Technology, Leuven, Belgium

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1681)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xi
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  2. Key Basics of Phage Biology

    1. Front Matter

      Pages 1-1
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    2. Basic Phage Mathematics

      • Stephen T. Abedon, Tena I. Katsaounis
      Pages 3-30

    3. Analysis of Host-Takeover During SPO1 Infection of Bacillus subtilis

      • Charles R. Stewart
      Pages 31-39

    4. Practical Advice on the One-Step Growth Curve

      • Andrew M. Kropinski
      Pages 41-47

    5. Iron Chloride Flocculation of Bacteriophages from Seawater

      • Bonnie T. Poulos, Seth G. John, Matthew B. Sullivan
      Pages 49-57

    6. Purification of Bacteriophages Using Anion-Exchange Chromatography

      • Dieter Vandenheuvel, Sofie Rombouts, Evelien M. Adriaenssens
      Pages 59-69

    7. Encapsulation Strategies of Bacteriophage (Felix O1) for Oral Therapeutic Application

      • Golam S. Islam, Qi Wang, Parviz M. Sabour
      Pages 71-87

    8. Encapsulation of Listeria Phage A511 by Alginate to Improve Its Thermal Stability

      • Hanie Ahmadi, Qi Wang, Loong-Tak Lim, S. Balamurugan
      Pages 89-95

    9. 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

  3. Sequencing Analysis of Bacteriophages

    1. Front Matter

      Pages 107-107
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    2. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes

      • Daniel A. Russell
      Pages 109-125

    3. 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

    4. Analyzing Genome Termini of Bacteriophage Through High-Throughput Sequencing

      • Xianglilan Zhang, Yahui Wang, Yigang Tong
      Pages 139-163

    5. Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques Using SISPA

      • Derick E. Fouts
      Pages 165-178

    6. Genome Sequencing of dsDNA-Containing Bacteriophages Directly from a Single Plaque

      • Witold Kot
      Pages 179-184

    7. 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

  4. Phage-Related Bioinformatics Tools

    1. Front Matter

      Pages 195-195
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    2. 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

    3. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview

      • Welkin H. Pope, Deborah Jacobs-Sera
      Pages 217-229
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Keywords

About this book

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.

Editors and Affiliations

  • Department Infection, Immunity & Inflammation, University of Leicester School of Medicine, Leicester, United Kingdom

    Martha R.J. Clokie

  • University of Guelph, Guelph, Canada

    Andrew M. Kropinski

  • KU Leuven, Laboratory of Gene Technology, Leuven, Belgium

    Rob Lavigne

Bibliographic Information

  • Book Title: Bacteriophages

  • Book Subtitle: Methods and Protocols, Volume 3

  • Editors: Martha R.J. Clokie, Andrew M. Kropinski, Rob Lavigne

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7343-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7341-5Published: 15 November 2017

  • Softcover ISBN: 978-1-4939-8458-9Published: 23 August 2018

  • eBook ISBN: 978-1-4939-7343-9Published: 10 November 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 316

  • Number of Illustrations: 25 b/w illustrations, 36 illustrations in colour

  • Topics: Microbiology

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