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Genomic approaches to assessing ecosystem health
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Genomic approaches to assessing ecosystem health

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Talk from Salish Sea Conference 2014

Talk from Salish Sea Conference 2014

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  • 1. Genomic approaches to assessing ecosystem health Steven Roberts School of Aquatic and Fishery Sciences University of Washington
  • 2. Open Science • You are free to Share! • Our lab practices open notebook science • Slides and more available robertslab.info sr320@uw.edu @sr320 #ssec14
  • 3. e Physiology
  • 4. Very easy to get billions of A,C,T, and Gs
  • 5. e Physiology
  • 6. DNA Variation Gene Expression Proteins Epigenetic Alterations - DNA Methylation Biological Indicators of Ecosystem Health
  • 7. DNA Variation Gene Expression Proteins Epigenetic Alterations - DNA Methylation Biological Indicators of Ecosystem Health
  • 8. Physiological Response of Oysters in Puget Sound Gene Expression
  • 9. urban, agriculture, water fowl, marinas, seals low population, low fecal coliform
  • 10. urban, agriculture, water fowl, marinas, seals low population, low fecal coliform
  • 11. urban, agriculture, water fowl, marinas, seals low population, low fecal coliform with replication / validation -> signature
  • 12. qPCRlowpopulation, lowfecalcoliform urban,agriculture, waterfowl, marinas,seals metalloproteinase inhibitor 3 Gavery, Mackenzie; Roberts, Steven; White, Samuel (2013): qPCR corroboration of an RNA-Seq experiment. figshare. http://dx.doi.org/10.6084/m9.figshare.683879
  • 13. Olympia oyster PROPS v2
  • 14. Application of qPCR
  • 15. Very easy to get billions of A,C,T, and Gs
  • 16. Very easy to get thousands of genes online
  • 17. DNA Variation Gene Expression Proteins Epigenetic Alterations - DNA Methylation Biological Indicators of Ecosytem Health
  • 18. Epigenetic Alterations - DNA Methylation DNA Methylation Histone Modification Small Interfering RNA
  • 19. • controls normal developmental processes • implicated in human diseases including cancer • possible means for adaptation of changing environmental condition - heritable for several generations Epigenetics
  • 20. Contaminants and DNA Methylation
  • 21. DNA methylation and oysters sites Gavery, unpublished
  • 22. Gavery - Friday 9:00 - #383DMRs
  • 23. Summary • Sequencing technology allows for easy integration of genomic approaches into environmental studies. • Practical implementation would involve using targeted assays*. • Significant lack of knowledge concerning toxins and epigenetics in marine invertebrates. This could have significant ecosystem impacts.
  • 24. Acknowledgements Mackenzie Gavery Claire Olson Sam White Brent Vadopalas Jake Heare EPA STAR Aquaculture Program DNA methylation oystergen.es @sr320