Towards environmental toxicogenomics - development of a flow-through, high-density DNA hybridization array and its application to ecotoxicity assessment

Assessment of the environmental hazard posed by soils/sediments containing low to moderate levels of contaminants using standard analytical chemical m ethods is uncertain due (in part) to a lack of information on contaminant b ioavailability, the unknown interactive effects of contaminant mixtures, ou r inability to determine the species of a metal in an environmental matrix, and the relative sensitivity of bioassay species. Regulatory agencies comp ensate for this uncertainty by lowering cleanup goals, but in this process they effectively exclude otherwise attractive cleanup options (i.e. bioreme diation). Direct evaluations of soil and sediment toxicity preclude uncerta inty from most of these sources. However, the time and cost of chronic toxi city tests limits their general application to higher levels of tiered toxi city assessments. Transcriptional level (mRNA) toxicity assessments offer g reat advantages in terms of speed, cost and sample throughput. These advant ages are currently offset by questions about the environmental relevance of molecular level responses. To this end a flow-through, high-density DNA hy bridization array (genosensor) system specifically designed for environment al risk assessment was developed. The genosensor is based on highly regular microchannel glass wafers to which gene probes are covalently bound at dis crete (200-mum diameter spot) and addressable (250-mum spot pitch) location s. The flow-through design enables hybridization and washing times to be re duced from approximately 18 h to 20 min. The genosensor was configured so t hat DNA from 28 environmental samples can be simultaneously hybridized with up to 64 different gene probes. The standard microscopic slide format faci litates data capture with most automated array readers and, thus high sampl e throughput (> 350 sample/h). In conclusion, hardware development for mole cular analysis is enabling very tractable means for analyzing RNA and DNA. These developments have underscored the need for further developmental work in probe design software, and the need to relate transcriptional level dat a to whale-organism toxicity indicators. (C) 2001 Elsevier Science B.V. All rights reserved.