HR: 1330h
AN: B33E-21    [Abstracts]
TI: Application of Whole Genome Expression Analysis to Assess Bacterial Responses to Environmental Conditions
AU: * Vukanti, R V
EM: rvukanti@kent.edu
AF: Department of Biological Sciences, Kent State University, Kent, OH 44242 United States
AU: Mintz, E M
EM: emintz@kent.edu
AF: Department of Biological Sciences, Kent State University, Kent, OH 44242 United States
AU: Leff, L G
EM: lleff@kent.edu
AF: Department of Biological Sciences, Kent State University, Kent, OH 44242 United States
AB: Bacterial responses to environmental signals are multifactorial and are coupled to changes in gene expression. An understanding of bacterial responses to environmental conditions is possible using microarray expression analysis. In this study, the utility of microarrays for examining changes in gene expression in Escherichia coli under different environmental conditions was assessed. RNA was isolated, hybridized to Affymetrix E. coli Genome 2.0 chips and analyzed using Affymetrix GCOS and Genespring software. Major limiting factors were obtaining enough quality RNA (10⁷-10⁸ cells to get 10μg RNA)and accounting for differences in growth rates under different conditions. Stabilization of RNA prior to isolation and taking extreme precautions while handling RNA were crucial. In addition, use of this method in ecological studies is limited by availability and cost of commercial arrays; choice of primers for cDNA synthesis, reproducibility, complexity of results generated and need to validate findings. This method may be more widely applicable with the development of better approaches for RNA recovery from environmental samples and increased number of available strain-specific arrays. Diligent experimental design and verification of results with real-time PCR or northern blots is needed. Overall, there is a great potential for use of this technology to discover mechanisms underlying organisms' responses to environmental conditions.
DE: 9810 New fields (not classifiable under other headings)
DE: 9903 NABS Student Award Methodology
SC: Biogeosciences [B]
MN: 2005 Joint Assembly