Translating Environmental Genomics outputs into Practical Use: Development of Biomonitoring tools using Quantitative, Real-time PCR Arrays.

Important sectors of the UK's economy depend on the quality of its environment and in Scotland this is especially important to industries such as agriculture, fish farming, brewing, whisky distilling and tourism. The Scottish Environment Protection Agency (SEPA) is charged with the task of maintaining and improving the quality of Scotland's environment. Monitoring has traditionally relied on chemistry in combination with ecology and hydrology to assess impacts on the freshwater and marine environments. This multi-disciplinary approach to the regulation of point-source discharges such as sewage works and industrial plants has resulted in steady improvements in water quality. However, new questions are being asked in relation to exposure to a number of new chemicals (e.g. brominated flame retardants) and formulations (e.g. nanoparticles), on the effects of mixtures and on impacts of chemicals at sub-lethal levels and on community or ecosystem health. As a result, biomarkers are increasingly used to indicate biological responses caused by contaminant stress and this project seeks to extend this work taking advantage of 'omics techniques. This proposal consists of two interrelated components: (a) a Knowledge and Information Transfer (KIT) programme, to inform and train SEPA staff in the new 'omics-based techniques and possibilities; and (b) a 'Demonstration Project' that exploits information from genomics studies to develop Quantitative Real time PCR (qPCR) arrays as biomonitoring tools for environmental risk assessment and improvement. The KIT component of the project will consist of a variety of Seminars, Workshops and a Conference. These will provide for SEPA staff, at various levels of seniority and work activities, background information on the nature and applications of 'omics techniques. It will also introduce staff to the Demonstration Project explaining its Aims and Objectives, experimental strategy and plan of development. This information will be continuously updated for 'Core Staff' (those likely to be involved in application of 'omics techniques) at regular intervals by Workshops to be held at SEPA. Additionally, selected staff will receive practical training in PCR by participation in a Theory and Practice Workshop at GCU. A one-day Conference will be held at SEPA at the end of the project to consider the broader possibilities of 'omics and to present the outputs of the Demonstration Project. The intention is to invite speakers and provide information that influences a wider group of staff in relation to the merits of the new technology. The Demonstration Project will develop and test qPCR arrays for two species, the stickleback (Gasterosteus aculeatus), for the freshwater environment, and the blue mussel (Mytilus edulis) for the marine and thus include a vertebrate and invertebrate. The tools will have the capacity to measure multiple gene transcripts simultaneously in single biological samples. Previous work from this group has studied responses in these organisms to copper, dibenzanthracene and ethinyl oestradiol so we shall focus on these compounds which are also highly relevant to the Scottish environment and thus to SEPA's work. SEPA will second, part-time, a member of their staff to work alongside the PDRA in the Demonstration Project. Existing data will be used to identify suitable genes that are diagnostic of exposure and effect in multiple stress-response pathways informative for a variety of stressors. The project plan is to identify suitable gene targets by data-mining and to design and validate qPCR arrays with RNA from experimentally exposed animals. The arrays will then be tested in an environmental context using animals collected at various time-points through the year from contaminated and reference ('clean') sites. Gene expression data will be integrated with chemical data, historic and contemporary, from water column and sediment samples and from body burdens.