Can we realize tangible benefits from using complex ‘omics tools when assessing soil quality?

Spurgeon, D.; Kille, P.. 2012 Can we realize tangible benefits from using complex ‘omics tools when assessing soil quality? [Lecture] In: 6th SETAC World Congress / SETAC Europe 22nd Annual Meeting, Berlin, 20-24 May 2012. (Unpublished)

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‘Omics approaches are no longer novel but rather serve as powerful tools which can substantially enrich and enhance ecotoxicological investigations. Some proteomic and metabolomic methods have exploited for approaching 20 years whilst after a decade of the exploitation of microarrays based gene measurements we may soon see this technology retired in deference to the more robust New Generation Sequencing based digitial transcriptomics. The maturation of some of these technologies provides an opportunity to appraise what has been learnt so far during their application for chemical hazard assessment. An appraisal of this type considering aquatic ecosystems, and especially fish (Fent and Sumpter 2011, Aquat. Tox. 1055, 25-29), concluded that despite some notable technical achievements and scientific advances, the application of profiling techniques to aquatic ecotoxicology was not yet sufficiently proven for application in either prospective risk assessment or routine environmental monitoring. In this paper, we will discuss the current status and application of systems biology methods for assessing the biological consequences of soil contamination. The analysis will start from an assessment of the lessons learnt from traditional single biomarker analysis conducted at the Avonmouth smelter contaminated site (e.g. expression analysis for an individual gene or protein) both in terms of absolute sensitivity of gene expression measurements and also variation in biomarker responses. An understanding of biomarker sensitivity and variability can lead to hypotheses related to micro-evolutionary processes that can be tested either through exquisitely targeted analysis or genome wide screening. Such analyses can use standard methods or the emerging potential of Next Generation Sequencing. Although often forgotten in the push to move to expression analysis, the genome resources generated as precursors to expression profiling can in themselves offer a resource from which to identify potential mode and mechanisms of action coupled to the biological effects associated with chemical exposure. Linking wider gene expression analysis to physiological observations can provide support for physiological models that categorise chemicals according to their effects on relevant endpoints. Finally, the holy grail of diagnostic based monitoring can become a reality provided that the test case is clearly defined and the molecular assessment is supported by sound environmental chemistry and anchored to physiological analysis of the monitored population(s).

Item Type: Publication - Conference Item (Lecture)
Programmes: CEH Topics & Objectives 2009 - 2012 > Biogeochemistry > BGC Topic 1 - Monitoring and Interpretation of Biogeochemical and Climate Changes
CEH Sections/Science Areas: Hails
NORA Subject Terms: Biology and Microbiology
Date made live: 22 Jan 2013 14:31 +0 (UTC)

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