This chapter deals with oligonucleotide microarrays for the detection and quantification of microorganisms. Such microarrays contain hundreds of oligonucleotide probes, each one specific for different strains/species/genera of microorganisms. They offer a fast, high-throughput alternative for the parallel detection of microbes from virtually any sample. The application potential of diagnostic microarrays covers most sectors of life sciences, including human, veterinary, food and plant diagnostics, environmental microbiology, water quality control, etc. Identification of human pathogens from clinical samples can be accomplished with a properly designed array within a matter of hours without cultivation and prior information on its approximate nature. Detection of food contaminating microbes, veterinary and plant pathogens can also be accomplished with diagnostic microarrays on a large scale. They can be used to study the effect of soil microbial diversity on soil fertility and sustainable soil quality as well as the response of microbial diversity to agricultural practices. It has only recently been acknowledged that the activity of microorganisms is essential to stabilise the biosphere. Understanding the complex interactions between the highly complex microbial communities and their environments is crucial for a sustainable development. Microbial ecology has only started to scratch the surface of this topic. High-throughput methods for the analysis of microbial diversity are badly needed for further development in this field. The scientific and technical background, the lab protocols, the experimental design and the data mining technique for the creation and application of such microarrays will be described in detail. Actual protocols will be those successfully applied in the author´s lab while references will be given to alternative approaches. Some of the numerous other applications of oligonucleotide microarrays will also be mentioned. Their detailed discussion is beyond the scope of this chapter thus the reader will be referred to more detailed literature on these topics.
|In A Beginner's Guide to Microarrays. Ed. by: Erick Blalock
|Kluwer Academic Publishers
|Veröffentlicht - 2003
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