实验基础

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 ...

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 ...

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 ...

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 ...

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

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 ...

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 ...

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 ...

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.

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 ...

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 ...

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 ...

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 ...

Monitoring microbial activities in the environment is difficult owing to the lack of suitable methods. For a technique to be useful for monitoring in situ activities, it must possess the following properties: sensitivity, selectivity, stability, the ability to make continuous real-t ...

The increasing trend toward quality assurance programs and hazard analysis, consumer demand for a wide variety of wholesome foods, and legislative pressures (e.g., the U.K. Food Safety Act) have increased the need for more rapid microbiological analyses. Although hazard analysis and cr ...

Reporter gene is a generic term that is used to describe genes whose expression is indicative of the presence of a particular cell, a specific event occurring within that cell, or a reflection of the expression of other, usually targeted genes of interest. For example, the presence of such a gene may make an ...

Dictyostelium discoideum has proven to be a useful lead genetic system for identifying novel genes and pathways responsible for the regulation of sensitivity to the widely used anticancer drug cisplatin. Resistance to cisplatin is a major factor limiting the efficacy of the drug in treat ...

N-glycans modify the great majority of all secreted and plasma membrane proteins, which themselves constitute one-third to one-half of the proteome. The ultimate definition of the glycoproteome would be the identification of all the N-glycans attached to all the modified asparaginyl s ...

Dictyostelium has become a model organism for the study of social evolution because of the stage in its life cycle where thousands of independent amoebae together form a fruiting body. Some individuals die to form a stalk that holds aloft the remaining cells for dispersal to new environments as sp ...

Dictyostelium discoideum is an exceptionally powerful eukaryotic model to study many aspects of growth, development, and fundamental cellular processes. Its small-sized, haploid genome allows highly efficient targeted homologous recombination for gene disruption and k ...