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PCR and Partial Sequencing of Bacteriophage Genomes

PCR is a quick and effective way of identifying the presence and ‘affiliation’ of bacteriophages, or phage-encoded genes from environmental samples, bacterial cells or purified viruses. The limitations are that you have to know what you are looking for in order to find it. Although the bacterio ...

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In silico Characterization of DNA Motifs with Particular Reference to Promoters and Terminators

Knowledge of the regulatory elements contained within bacteriophage genomes forms the basis for understanding genomic expression and organization. The in silico prediction of promoter and terminator sequences in phage genomes is a first step towards this understanding. In this c ...

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Determining DNA Packaging Strategy by Analysis of the Termini of the Chromosomes in Tailed-Bacteriophage Virions

Tailed-bacteriophage virions contain a single linear dsDNA chromosome which can range in size from about 18 to 500 kbp across the known tailed-phage types. These linear chromosomes can have one of several known types of termini as follows: cohesive ends (- or -single-strand extensions), circ ...

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Molecular Phylogenetics: Testing Evolutionary Hypotheses

A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage ev ...

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Preparation of RNA from Bacteria Infected with Bacteriophages: A Case Study from the Marine Unicellular Synechococcus sp. WH7803 Infected by Phage S-P

Bacteriophages manipulate bacterial gene expression in order to express their own genes or influence bacterial metabolism. Gene expression can be studied using real-time PCR or microarrays. Either technique requires the prior isolation of high quality RNA uncontaminated by the p ...

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Quantification of Host and Phage mRNA Expression During Infection Using Real-Time PCR

Real-time, or quantitative PCR, is a valuable technique useful in bacteriophage research to quantify the abundance of phage or host gene transcripts. It can be used during the infection cycle both to monitor the expression of individual viral transcripts and to compare relative gene expres ...

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Purification of Bacteriophages and SDS-PAGE Analysis of Phage Structural Proteins from Ghost Particles

Concentration and purification of infectious particles are prerequisites for structural and functional characterization of bacteriophages. The methods detailed in the first part of this chapter outline the protocols commonly used to obtain purified phages: the concentrat ...

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Oligonucleotide Microarrays for Bacteriophage Expression Studies

Gene expression microarrays offer the ability to monitor the expression of all phage genes over an infection cycle. However, there are relatively few reports to date of microarrays being used to investigate phage biology. This chapter aims to provide an overview of how to design and implement a m ...

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Isolation Independent Methods of Characterizing Phage Communities 1: Strain Typing Using Fingerprinting Methods

Since most of the phage genomes isolated from natural samples are previously unknown sequences, an isolation-independent approach is necessary to quantify the diversity of natural viral communities. Currently, two different methodological approaches are widely used to obtain ...

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Phage Proteomics: Applications of Mass Spectrometry

Current techniques in mass spectrometry (MS) allow sensitive and accurate identification of proteins thanks to the in silico availability of these protein sequences within databases. This chapter provides a short overview of MS techniques used in the identification of phage struct ...

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Isolation Independent Methods of Characterizing Phage Communities 2: Characterizing a Metagenome

Current appreciation of the vast expanse of prokaryotic diversity has largely come through molecular phylogenetic exploration of sequence diversity within the universally conserved gene for small subunit ribosomal RNA (16S rDNA). A plethora of methodologies for characteriz ...

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Phage Typing

Phage typing is a rapid, economical, reliable, and reproducible technique, requiring no specialized equipment, for fingerprinting disease-causing agents for epidemiological investigation and surveillance.

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General M13 Phage Display: M13 Phage Display in Identification and Characterization of ProteinProtein Interactions

In M13 phage display, proteins and peptides are exposed on one of the surface proteins of filamentous phage particles and become accessible to affinity enrichment against a bait of interest. We describe the construction of fragmented whole genome and gene fragment phage display libraries ...

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A Genetic Screen to Identify Bacteriophage Lysins

Lysins are phage-encoded, peptidoglycan (cell wall) hydrolases that accumulate in the bacterial cytoplasm during a lytic infection cycle. Late during infection, the lysins undergo holin-mediated translocation across the inner membrane into the peptidoglycan matrix where th ...

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Isolation of Monoclonal Antibody Fragments from Phage Display Libraries

Techniques developed over the past 20 years for the display of foreign peptides and proteins on the surfaces of filamentous bacteriophages have been a major driving force in the rapid development of recombinant antibody technology in recent years. With phage display of antibodies as one of i ...

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Internet Resources of Interest to Bacteriophage Workers

The Internet provides a myriad of useful tools for the phage worker including access to culture collections, specific databases, tools for gene identification, and whole genome comparisons, lecture notes, information on upcoming scientific meetings, books, etc.

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Sampling Sediment and Soil: Use of Coring Devices

Individually, molecular and classical microbial ecology techniques are powerful tools in microbial ecology, but both are limited with respect to relating the presence and/or diversity of microorganisms to their function/activity in that environment (1,2). By combining the two ap ...

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Establishment of Experimental Biofilms Using the Modified Robbins Device and Flow Cells

Recent studies have shown that biofilms (a complex organization of bacterial cells present at a surface or interface, which produces a slime-like matrix) represent the principal form of bacterial growth in all environments studied to date (1). There are numerous advantages to bacteria gr ...

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Some Problems Posed by Natural Environments for Monitoring Microorganisms

The history and emergence of microbiology as a scientific discipline are intimately linked with developments of methods for isolation, enrichment, growth, and maintenance of microorganisms in the laboratory as pure cultures to enable subsequent biochemical and genetic analys ...

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Experimental Biofilms and Their Applications in the Study of Environmental Processes

The trend in research in recent years has been to extrapolate results from studies of planktonic bacteria into environmental systems. This method of studying planktonic bacteria under in vitro conditions has undoubtedly yielded important data in a wide range of areas; however, the exami ...

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