Details
Contaminant Stressor Response In Mytilus Using Genomics: Mussel Monitoring For The New Millennium Website
Principal Investigator(s):
Andrew Y. Gracey - University of Southern California
James Moffett - University of Southern California
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Associate Investigator(s):
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Period: 2/1/2008 - 1/1/2010
| Current Status: Completed | Last Updated: 8/18/2010 | |
| Federal Funds: | State Funds: | |
Objectives:
We propose to couple classic monitoring of contaminants with contemporary molecular analysis of gene expression to provide unprecedented insights into contamination events and their impact on the health of ecosystem inhabitants. Here we will use changes in gene expression as a quantitative assessment of perturbation, with contaminants serving as perturbing agents. We hypothesize that exposure of mussels to contaminants will be evident as a change in gene expression and that this output can discriminate between the severity of the contamination and the identity of the contaminant. Since different contaminants will have different effects of mussel physiology the resulting gene expression change, or signature, will vary correspondingly. Similarly, gene expression responses will change according to the severity of the exposure to match the degree of perturbation or toxicity. We will examine the following EPA Priority Pollutants: copper, cadmium, mercury, zinc and representative polycyclic aromatic hydrocarbons.
Methodology:
First, we will establish a reference database of gene expression signatures that define the changes in mRNA level that occur when mussels are exposed to specific contaminants in a controlled laboratory environment. Both the concentration and duration of treatment will be manipulated to ensure that our expression signatures can discriminate between mild and toxic events. RNA will be isolated from gill tissue of control and exposed animals and their gene expression signatures defined by hybridization to our existing 12,000 gene Mytilus microarray. Then we will use this reference database as a roadmap to interpret the gene expression signatures of mussels collected in the field during a variety of episodic events. In situ passive sampling devices will be deployed adjacent to mussel colonies in the field to assess perturbations in dissolved metal concentrations during episodic events relative to normal conditions to relate to gene expression.
Rationale:
The discharge of heavy metals and other contaminants into coastal receiving waters is regulated by the Clean Water Act using criteria developed through toxicity testing of marine invertebrate larvae, particularly the mussel Mytilus edulis, and related species within the genus. Because these species are highly sensitive to contaminants in their larval stages, the criteria have led to considerable improvement in water quality in many harbors. Criteria that protect receiving waters are based on laboratory toxicity testing, coupled with simple waste load allocation models that cannot provide an accurate picture of complex systems. Newer approaches, based on rapid advances in molecular biology, have yet to be incorporated into a regulatory framework, but have the potential to provide insightful, site-specific information on contaminant fate and transport and community response.
Accomplishments:
Outcomes:
Publications & other print media:
Gracey, A. Y., Chaney, M. L., Boomhower, J. P., Tyburczy, W. R., Connor, K., Somero, G. N. (2008). Rhythms of Gene Expression in a Fluctuating Intertidal Environment. Current Biology. Vol. 18 (19), pp. 1501-1507.
Evans, H., De Tomaso, A., Quail, M., Rogers, J., Gracey, A. Y., Cossins, A. R., Berenbrink, M. (2008). Ancient and modern duplication events and the evolution of stearoyl-CoA desaturases in teleost fishes. Physiological Genomics. Vol. 35, pp. 18-29.
Gracey, A. Y. (2008). The Gillichthys mirabilis Cooper array: a platform to investigate the molecular basis of phenotypic plasticity. Journal of Fish Biology. Vol. 72, pp. 2118-2132.
Williams, D. R., Li, W., Hughes, M. A., Gonzalez, S. F., Vernon, C., Vidal, M. C., Jeney, Z., Jeney, G., Dixon, P., McAndrew, B., Bartfai, R., Oban, L., Trudeau, V., Rogers, J., Matthews, L., Fraser, E. J., Gracey, A. Y., Cossins, A. R. (2008). Genomic resources and microarrays for the common carp Cyprinus carpio L. Journal of Fish Biology. Vol. 72, pp. 2095-2117.
Olohan, L. A., Li, W., Wulff, T., Jarmer, H., Gracey, A. Y., Cossins, A. R. (2008). Detection of anoxia-responsive genes in cultured cells of the rainbow trout Oncorhynchus mykiss (Walbaum), using an optimized, genome-wide oligoarray. Journal of Fish Biology. Vol. 72, pp. 2170-2186.
McLean, L., Young, I. S., Doherty, M. K., Robertson, D. H., Cossins, A. R., Gracey, A. Y., Beynon, R. B., Whitfield, P. D. (2007). Global Cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics. Vol. 15, pp. 2667-81.
Ahdesmaki, M., Lahdesmaki, H., Gracey, A., Schmulevich, L., Yli-Harja, O. (2007). Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics. Vol. 8, pp. 233.
Gracey, A. Y. (2007). Interpreting physiological responses to environmental change through gene expression profiling. J. Exp. Biol.. Vol. 210, pp. 1593-1601.
Haywood, S. A., Murray, P. A., Cossins, A. R., Gracey, A. Y. (2007). Beyond the lipid hypothesis: mechanisms underlying phenotypic plasticity in inducible cold tolerance. Advances in experimental medicine and biology. Vol. 594, pp. 132-42.
Haywood, S. A., Murray, P. A., Govan, G. G., Gracey, A. Y., Cossins, A. R. (2007). An explicit test of the phospholipid saturation hypothesis of acquired cold tolerance in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. Vol. 104, pp. 5489-5494.
Buckley, B. A., Gracey, A. Y., Somero, G. N. (2006). The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis. J. Exp. Biol.. Vol. 209, pp. 2660-2667.
Cossins, A. R., Fraser, E. J., Hughes, M., Gracey, A. Y. (2006). Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity. J. Exp. Biol.. Vol. 209, pp. 2328-2336.
Fraser, E. J., Vieira de Mello, L., Ward, D., Rees, H. R., Williams, D., Gracey, A. Y., Cossins, A. R. (2006). Hypoxia-inducible myoglobin expression in nonmuscle tissues. Proc. Natl. Acad. Sci. USA. Vol. 103, pp. 2977-2981.
Presentations:
Publicicty:
Video, electronic, and computer products:
| Figure 1. Map of surface layer water toxicity to sea urchins in San Diego Bay associated with Chollas Creek discharges following two separate storm events. The colors show the estimated percent of sea urchin fertilization based upon the toxicity results for water samples (indicated by pie diagrams) and measured salinity in the surface layer. From Schiff et al., 2003 (Schiff 2003). | Table 1 Some representative data for trace metals in California bays, marinas and runoff-derived plumes. Concentrations in ppb. From Schiff et al 2003, 2007 (Schiff 2003; Schiff 2007). |
| Figure 2. Metallothionein gene expression patterns in response to Cd. Panels A and B show the dose-response of metallothionein-10 and metallothionein-20 gene expression in M. californianus excised gill fragments subjected to increasing levels of Cd. Panels C and D show the effects of acclimation to elevated Cd for 2 weeks on the induction of metallothionein genes 24hrs after an exposure to even greater levels of Cd. | Figure 3. Strategy to integrate contaminant-induced expression signatures in field and laboratory mussels. A reference database is constructed that describes the expression signatures of laboratory mussels challenged with a range of contaminants with each gene on the array being ranked by differential expression. Query expression signatures from field mussels are compared to the signatures in the database using either a rank-based or Pearson-correlation based pattern-matching strategy. All signatures in the database are then ranked according to their similarity with the field signature. High-scoring reference signatures indicate that there is a strong likelihood that the field mussels had been exposed to that contaminant. The pattern-matching analysis is repeated many times with permutation of the ranks of genes in the query signature to provide an estimate of statistical significance of the similarity. |
