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Project Details
Title:Establishment of a National Oceanic and Atmospheric Administration Center of Excellence in Oceans and Human Health within the Hollings Marine Laboartory at Charleston, South Carolina. Functional Genomic Approaches.
Dates: 06/01/2004 - 06/01/2004
Amount Requested: $266,574
Agency Submitted To: NOAA
PI: Greg Warr
Agency: MUSC
Collaborators:
Abstract:
"Rationale: Functional genomics is an established technology in biomedical science (e.g., Afshari et al. 2002) that has proven predictive power not available from traditional environmental toxicology (Waring et al., 2001). The rationale for a functional genomics approach to assessing the health of populations is that many (although not necessarily all) stressors encountered by an organism will perturb the dynamics of gene expression (as measured by messenger RNA levels) in characteristic ways, producing diagnostic and predictive ""transcriptional signatures"". The application of this technology to marine toxicology has great potential (Snape et al., 2004). Functional genomic research involves, as an essential first step, the collection of the expressed gene sequences of a species. When applied to little-studied marine organisms, significant novel gene discovery is a certain outcome (Gueguen et al., 2003; Jenny et al., 2002; Gross et al., 2001). For example, important insight into the antimicrobial peptides of shrimp immune systems has emerged from the initial genomic studies of these species carried out by the HML Marine Genomics team (Cuthbertson et al., 2002). The goal of this project is to develop and test functional genomics as a tool for assessing exposure and organism health for the oyster, Crassostrea virginica. Two related hypotheses will be tested in a laboratory setting: (1) transcriptional signatures can distinguish oysters exposed to specific individual and multiple challenges (metals, infection, organic toxicants) from control, unchallenged oysters; and (2) a suite of transcriptional signatures will be diagnostic of particular stressor exposures. If lab findings are promising, a field test will be conducted with the Monitoring and Assessment Core in years 3, 4 and 5 of this project. At present, nearly 7500 unique genes from Crassostrea species are available (and in-hand at HML) for spotting to microarrays, along with a suite of genes from Perkinsus marinus, a major oyster pathogen (common name, Dermo). This gene collection was compiled with collaborators from Auburn, France (Montpellier), Norway (Bergen, Sars Institute) and Center of Marine Biotechnology (COMB) of the University of Maryland. When spotted on a microarray this collection allows the detection of alterations in expression of a broad suite of oyster genes (representing a range of physiological and biochemical processes), as well as an assessment of the expression of the genes of Perkinsus. In addition, low density linkage maps, Bacterial Artificial Chromosome libraries, polymorphic microsatellite markers and other essential tools are available for the oyster (www.genome.clemson.edu/orders/; www.marinegenomics.org/). This information will provide a broader genomic context for the information derived in the proposed study, and the potential to link genetic variation in the population to the response to stressors. Major Tasks The goal of this project is to apply functional genomic approaches to marine toxicology and to assess the potential value of such approaches in assessing the impact of multiple stressors on marine organisms. The project will initially address the development and testing of functional genomic tools in the oyster, Crassostrea virginica, utilizing the resources and expertise of the Marine Genomics Core, and building upon preliminary studies that demonstrate the potential for success of the approach in oysters. It is recognized that the number of potential stressors that could have been chosen is large, and that all possible concentrations and interactions cannot be assessed, especially when natural variables such as salinity, hypoxia and temperature are planned for eventual inclusion. Thus, in years 1 and 2 the experiments will utilize single toxicant exposures at concentrations that are known from the literature to induce physiological responses. These data will be used to develop models of transcript profiles in response to exposure to individual metals. The project will also take advantage of the Monitoring and Assessment