Microarray Genomic Systems Development

In order to identify and characterize microbes using the currently available methods, information on the organisms genetic material is required. Recombinant microbes which contain novel genetic material would not have such information and therefore avoid detection. Previous work has been done to develop a system with array-based genomic fingerprinting technology, which should help to identify the new strains, detect the presence of novel genetic material, and measure gene expressions. The next phase is the development of a test system for rapid species identification in addition to the oligonucleotide fingerprint. The test organisms for this work were Bacillus bacteria 11 species, Escherichia coli TOP10 7 strains, and Geobacillus stearothermophilus. Using standard molecular biology methods, we isolated genomic DNA, digested the DNA to reduce complexity, labelled it with fluorescent dyes, and hybridized the labelled DNA to two types of microarrays, Human Operon 21K chips containing 23,232 features and Bacterial genomic chips containing 5,280 features. The hybridization data was then analyzed with ChromaBlast, an useful analytic tool in Excel, which normalized columnar data, sorted the data into user-selectable range-driven bins, developed colour heat maps from the data, and then output the heat map and bin assortment for review. When the data patterns on the colour heat maps were filtered and sorted, bacteria in different genera could be discriminated with high confidence in certain subsets of the features. However, species or strain differentiations of the test organisms were not as evident in this work. A multipathogen chip was designed to further investigate species and strain differentiation. Due to time limitation on the contract, only one or two sample chips from each test organism has been included thus far. In the next phase, data from more replicate microarray chips should be included in the set of hybridization data.