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USE OF SERIAL ANALYSIS OF GENE EXPRESSION (SAGE) TO STUDY GENETIC RESPONSES TO THE PRESENCE OF THE TNT OR RDX BY ARABIDOPSIS THALIANA
Citation:
Ekman, D R., W. W. Lorenz, S C. McCutcheon, AND N L. Wolfe. USE OF SERIAL ANALYSIS OF GENE EXPRESSION (SAGE) TO STUDY GENETIC RESPONSES TO THE PRESENCE OF THE TNT OR RDX BY ARABIDOPSIS THALIANA. Presented at Sixth International Symposium on Environmental Biotechnology and Fourth International Symposium on Cleaner Bioprocesses and Sustainable Development, Vera Cruz, Mexico, June 9-12, 2002.
Impact/Purpose:
Elucidate and model the underlying processes (physical, chemical, enzymatic, biological, and geochemical) that describe the species-specific transformation and transport of organic contaminants and nutrients in environmental and biological systems. Develop and integrate chemical behavior parameterization models (e.g., SPARC), chemical-process models, and ecosystem-characterization models into reactive-transport models.
Description:
Phytoremediation is currently being explored for its potential to clean-up of the large number of military sites that have been contaminated by explosives such as 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Although some of the enzymes responsible for the metabolism of explosives have been identified, little is known about plant responses to these pollutants at a genetic level. In light of this fact, a comprehensive genomics approach known as SAGE (Velculescu et al. 1995) is now being employed to improve the situation. Using SAGE, genes important in the metabolism of both TNT and RDX will be identified, giving the field a more detailed understanding of the plant mechanisms involved. Like many other genomic techniques (e.g. microarrays, oligo-based gene chips, differential display, etc.), SAGE provides for comparisons of genetic expression between organisms experiencing different stimuli. Thus, comparisons will be made in the genetic expression of plants grown in the presence of either TNT or RDX and in the absence (control). For the true power of the technique to be realized a plant species with a known genome must be utilized and thus the flowering plant Arabidopsis thaliana was chosen. Currently, the TNT-SAGE library has been completed and genes are being identified. Prior to the SAGE analysis, the concentration of explosive necessary to produce a response without killing the plants was determined by growing the plants in sterile liquid media (MS media) in a variety of explosive (either TNT or RDX) concentrations. In this way the SAGE analysis will identify genes that the plant is expressing to "deal" with the explosive and not genes that are simply involved in the process of cell death