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Functional Genomics Research Project
Project Goal
The goal of this project is to develop and test functional genomic tools to assess exposure and organism health for the oyster, Crassostrea virginica. Learn more about the background information for this project »
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Abstract
The basic tools and methods have been developed for investigating oyster transcriptomic and proteomic responses to challenges and stressors present in the marine environment, such as changes in salinity, temperature, oxygenation, pollution and infectious diseases. Data derived from the use of microarrays in oyster, shrimp and dolphin suggests that transcriptomic approaches will be a highly sensitive and informative method for assessing the interaction of marine organisms with multiple stressors. The completion of these studies will provide methods for the accurate and effective assessment of the health status of the marine environment and of some potential hazards that it might pose to the health of humans consuming fish and shellfish, living beside the ocean, and using it for recreation or commerce.
Short-Term Objectives
Objectives of this project are to develop microarray tools that will permit, through “transcriptional signatures”, the diagnosis of the multiple stressors to which the organism has been exposed and to assess the microarray as a tool for the diagnosis and prognosis of oyster exposure and health in the marine environment. In addition to defined laboratory challenge studies, oysters will be sampled from field sites in the marine estuarine environment, and the results from the microarrays will be combined with those from traditional measures of oyster health (e.g., assays of hemocyte function; levels of glutathione and of lipid peroxidation) and environmental health (e.g., sediment contaminant levels; benthic community composition) to test the hypothesis that functional genomics techniques and information can provide a sensitive assessment of environmental health.
Expected Results
The Functional Genomics project will generate physical products that include collections of cloned oyster genes. Importantly, other products will include new knowledge of the genetic response of the oysters to environmental challenges and their value as diagnostic and prognostic tools and new methods making use of linkages between oyster genetic signatures and ecosystem health information. Looking at the larger picture, the major contribution of the Functional Genomics Research Project is development of the technology needed to integrate information, from the molecular to organism levels, into assessments of the health status of marine ecosystems. In collaboration with the Marine Organisms as Disease Vectors project, the Functional Genomics Research Project will study linkages between the health status of oysters and human health risks resulting from bioaccumulation of human pathogens.
Accomplishments:
- A validated cDNA microarray containing both oyster genes (both C. virginica and C. gigas) has been developed, in collaboration with the international Oyster Genome Consortium. This tool is being made available to, and will be widely used by, the oyster research community and marine ecosystem managers to assess the health status of oysters and their responses to environmental stressors.
- Two laboratory-based experiments utilizing the microarray to understand the response of the oyster to stressors have been conducted. In the first, 216 oysters were exposed to single and multiple exposures of copper, zinc and cadmium, at concentrations ranging from low to high. RNA was isolated from gills and hepatopancreas and hybridized to the microarrays, and actual metal burden, glutathione levels and lipid peroxidation were measured for each oyster. In addition, the Oysters as Disease Vectors Group (as referenced in the Report of this Group) measured a suite of physiological parameters, including hemocyte count, pO 2, pCO 2 and pH. In the second experiment, oysters challenged by sterile wounding and by wounding accompanied by exposure to heat-killed bacteria and fungi were conducted (in collaboration with Drs Cunningham and Jenny). RNA samples from these oysters have also been hybridized to the microarray. The results from the second study have been analyzed and are presented in detail in the Report of the Bioinformatics Core (Dr Robert Chapman), but in summary it is clear that the transcriptomes of control oysters, sterile wounded oysters, and septic wounded oysters can be reliably distinguished.
- Publications describing the generation of BAC libraries in C. virginica and C. gigas and the regulation of metallothionein genes of C. viriginica in response to metals exposure and immune challenge have been published. These articles will be of value to researchers in oyster physiology and to researchers in ecology by advancing our understanding of marine environmental science at a molecular and genomic level. Research presentations on oyster genomics and their transcriptomic responses to stressors were made at the Tenth Congress of the International Society for Developmental and Comparative Immunology held in Charleston, SC in July 2006. Drs Chapman and Warr attended the Workshop on Biodiversity and Human Health, organized by NOAA, EPA and Yale University and held at the Smithsonian Institution on September 14 and 15. At this Workshop they presented the approach developed by the OHHI team at Hollings Marine Laboratory to understanding the biological response of the environment to multiple stressors.
Transfer of Results
The following products will be transferred as appropriate to user groups as stages in their development are complete.
| Deliverables | User Group |
|---|---|
| Annotated physical clone collections of oyster ESTs | Oyster research community, shellfish biologists, aquaculture producers |
| Validated oyster⁄Perkinsus microarrays | Oyster research community, marine ecosystem managers |
| Oyster genes responsive to single and multiple stressors | Oyster research community, public health agencies |
| Scientific articles relating to “Ecogenomics” | Bioinformatics and ecology researchers |
| Transcriptomic tools for monitoring the health of the marine environment | Marine ecosystem managers, public health officials |
Publications:
Cunningham C, Hikima J, Jenny MJ, Chapman RW, Fang G-C, Saski C, Lundqvist ML, Wing RA, Cupit PM, Gross PS, Warr GW, Tomkins JP. (2006) New Resources for Marine Genomics: BAC libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas) Marine Biotechnology. In Press
Jenny MJ, Warr GW, Ringwood AH, Baltzegar DA, Chapman RW. (2006) Regulation of Metallothionein Genes in the American Oyster (Crassostrea virginica): Ontogeny and Differential Expression in Response to Different Stressors. Gene, 379, 156-165.
Public Information and Outreach:
Oyster and shrimp cDNA microarrays have been delivered to the national and international community of oyster and shrimp health researchers. The marine genomics website provides a publicly accessible database and set of analytical tools for understanding the genomics of selected marine organisms (including the American oyster, Atlantic white shrimp, grass shrimp and the Atlantic bottlenose dolphin) and assessing their health using transcriptomic methods.
For More Information
Contact: Paul Gross, (843) 762.8859
Email: GrossP@musc.edu
Contact: Greg Warr, (843) 762.8869
Email: WarrG@musc.edu