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Expression Analysis

With the availability of genome sequences, techniques for measuring and comparing the expression of thousands of genes have been developed. DNA microarrays provide a powerful tool with which to study gene expression on a whole-genome scale and determine how gene transcription is affected by growth phases (e.g., log to stationary phase) and morphological differentiation or environmental cues and mutations. Both oligonucleotide-based and cDNA arrays have been used in gene expression analyses of pathogenic fungi, in particular C. albicans, for which the genome sequence information was first available. Custom Affymetrix GeneChip arrays have been used for transcriptional profiling of C. albicans during iron limitation and during phenotypic switching of C. albicans strain WO-1 [75, 76]. Other examples of the growing numbers of DNA microarray analyses in C. albicans include transcriptional profiling of yeast-to-hyphae transition [77], cAMP signaling [78], pH response [79] and biofilm formation [80] using cDNA microarrays.

In vivo expression technology (IVET) is a system that has been developed initially for bacterial pathogens to identify genes that are specifically induced in host tissue [81, 82]. Recently IVET has been adapted for use in C. albicans (see Fig. 18.1 and Ref. [83]) and H.capsulatum [84]. In C. albicans IVET revealed the temporal and spatial expression patterns of the SAP genes, demonstrating a high degree of differential gene regulation, even to the level of individual SAP2 alleles [85, 86].

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