Bacteriophages: Methods and Protocols, Volume 2: Molecular and Applied Aspects

ISBN-13: 9781617379109 / Angielski / Miękka / 2010 / 373 str.

Martha R. J. Clokie; Andrew M. Kropinski

Opis

Ranging from the evolution of pathogenicity to oceanic carbon cycling, the many and varied roles that bacteriophages play in microbial ecology and evolution have inspired increased interest within the scientific community. Bacteriophages: Methods and Protocols pulls together the vast body of knowledge and expertise from top international bacteriophage researchers to provide both classical and state-of-the-art molecular techniques. With its well-organized modular design, Volume 2: Molecular and Applied Aspects examines a multitude of topics, including the bacteriophage genomics, metagenomics, transcriptomics, and proteomics, along with applied bacteriophage biology. Written in the highly successful Methods in Molecular Biology series format, chapters consist of brief introductions to the subject, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and a Notes section which details tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Bacteriophages: Methods and Protocols is a valuable reference for experienced bacteriophage researchers as well as an easily accessible introduction for newcomers to the subject."

Spis treści

Preface Contributors Introduction Section 1: Bacteriophage Genomics 1. Preparation of Bacteriophage Lysates and Pure DNA Derek John Juan Pickard 2. Approaches to the Compositional Analysis of DNA Richard A. Manderville and Andrew M. Kropinski 3. Determination of Bacteriophage Genome Size by Pulsed-Field Gel Electrophoresis Erika Lingohr, Shelley Frost, and Roger P. Johnson 4. Preparation of a Phage DNA Fragment Library for Whole Genome Shotgun Sequencing Elizabeth J. Summer 5. PCR and Partial Sequencing of Bacteriophage Genomes Martha R. J. Clokie 6. In Silico Identification of Genes in Bacteriophage DNA Andrew M. Kropinski, Mark Borodovsky, Tim J. Carver, Ana M. Cerdeño-Tárraga, Aaron Darling, Alexandre Lomsadze, Padmanabhan Mahadevan, Paul Stothard, Donald Seto, Gary Van Domselaar, and David S. Wishart 7. Determining DNA Packaging Strategy by Analysis of the Termini of the Chromosomes in Tailed-Bacteriophage Virions Sherwood R. Casjens and Eddie B. Gilcrease 8. In silico Characterization of DNA Motifs with Particular Reference to Promoters and Terminators Rob Lavigne, André Villegas, and Andrew M. Kropinksi 9. Molecular Phylogenetics: Testing Evolutionary Hypotheses David A. Walsh and Adrian K. Sharma Section 2: Bacteriophage Transcriptomics and Proteomics 10. Preparation of RNA from Bacteria Infected with Bacteriophages: A Case Study from the Marine Unicellular Synechococcus sp. WH7803 Infected by Phage S-PM2 Jinyu Shan and Martha R. J. Clokie 11. Quantification of Host and Phage mRNA Expression during Infection Using Real-Time PCR Martha R. J. Clokie 12. Oligonucleotide Microarrays for Bacteriophage Expression Studies Andrew D.Millard and Bella Tiwari 13. Purification of Bacteriophages and SDS-PAGE Analysis of Phage Structural Proteins from Ghost Particles Pascale Boulanger 14. Phage Proteomics: Applications of Mass Spectrometry Rob Lavigne, Pieter-Jan Ceyssens, and J. Robben Section 3: Community Bacteriophage Approaches 15. Isolation Independent Methods of Characterizing Phage Communities 1: Strain Typing Using Fingerprinting Methods Clemens Pausz, Jessica L. Clasen, and Curtis A. Suttle 16. Isolation Independent Methods of Characterizing Phage Communities 2: Characterizing a Metagenome K. Eric Wommack, Shellie R. Bench, Jaysheel Bhavsar, David Mead, and Tom Hanson Section 4: Applied Aspects of Bacteriophage Biology 17. Phage Typing Irina Chirakadze, Ann Perets, and Rafiq Ahmed 18. A Genetic Screen to Identify Bacteriophage Lysins Raymond Schuch, Vincent A. Fischetti, and Daniel Nelson 19. General M13 Phage Display: M13 Phage Display in Identification and Characterization of Protein-Protein Interactions Kirsten Hertveldt, Tim Beliën, and Guido Volckaert 20. Isolation of Monoclonal Antibody Fragments from Phage Display Libraries Mehdi Arbabi-Ghahroudi, Jamshid Tanha, and Roger MacKenzie 21. Internet Resources of Interest to Bacteriophage Workers Andrew M. Kropinski