2 Dissecting host-pathogen molecular interactions with microarrays

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This chapter focuses on dissecting host-pathogen molecular interactions with microarrays. Microarrays are a powerful tool for measuring Deoxyribo-nucleic acid (DNA) or Ribo-nucleic acid (RNA) content and become increasingly available and cost-effective. The chapter describes methods for using bacterial cDNA microarrays to explore new territory in pathogen-host interactions. The chapter includes basic protocols for isolating bacterial RNA and for labeling and hybridizing DNA and RNA to microarrays. In addition, the references provide examples of experimental rationale and design. Microarrays can be used to detect genomic differences between strains or closely related pathogens. For example, pathogen arrays can be used to profile DNA isolated from a variety of environmental or clinical sources with the aim of identifying genomic regions that correlate or anti-correlate with virulence. Microarrays also are used to examine changes in mRNA levels in bacterial grown in broth under conditions that are relevant to infection. To obtain high quality data, it is important to conduct a time course experiment or to titrate the condition of interest.

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