Next Generation Sediment toxicity Testing via DNA Microarrays

The current SBIR solicitation states that the EPA is seeking better sampling, analysis and monitoring technologies to improve hazardous waste management. Development of new methods for testing contaminated sediments is an area of particular concern because many industrial chemical such as pesticides, polycyclic aromatic hydrocarbons, chlorinated hydrocarbons and heavy metals accumulate in sediments and can pose a significant threat to both human health and the environment. Currently available Toxicity Identification and Evaluation/ Toxicity Reduction Evaluation (TIE/TRE) methodologies for examining sediments are difficult, time consuming, and expensive. DNA microarrays have the potential be a practical technology for identifying, characterizing, and monitoring biologically relevant toxins in complex sediment backgrounds, however there are no microarrays for sediment testing organisms. Here we propose the development of a microarray for one of the most commonly used sediment monitoring organisms, the non-biting midge Chironomul tentants. In Phase I, high-throughput sequencing of a normalized cDNA library will be used to design a 72,000 element oligonucleotide array representing at least 10,000 distinct genes. In Phase II, we will demonstrate the feasibility of using these microarrays to identify toxins in TIE/TRE studies by showing that distinctive signatures for a series of model toxins can be identified when presented within the context of complex sediment backgrounds. By the end of Phase II work, we will have commercially available environmental toxicity testing microarrays for sediments.