Talk from Salish Sea Conference 2014

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

5. e
Physiology

6. Very easy to get billions of A,C,T, and Gs

7. e
Physiology

8. DNA Variation
Gene Expression
Proteins
Epigenetic Alterations - DNA Methylation
Biological Indicators of Ecosystem Health

9. DNA Variation
Gene Expression
Proteins
Epigenetic Alterations - DNA Methylation
Biological Indicators of Ecosystem Health

11. Physiological
Response of
Oysters in
Puget
Sound
Gene Expression

12. urban, agriculture, water
fowl, marinas, seals
low population, low fecal
coliform

13. urban, agriculture, water
fowl, marinas, seals
low population, low fecal
coliform

14. urban, agriculture, water
fowl, marinas, seals
low population, low fecal
coliform
with replication / validation -> signature

15. 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

16. Olympia oyster
PROPS v2

17. Application of qPCR

18. Very easy to get billions of A,C,T, and Gs

19. Very easy to get thousands of genes online

20. DNA Variation
Gene Expression
Proteins
Epigenetic Alterations - DNA Methylation
Biological Indicators of Ecosytem Health

21. Epigenetic Alterations - DNA Methylation
DNA Methylation
Histone
Modification
Small Interfering
RNA

22. • controls normal developmental processes
• implicated in human diseases including cancer
• possible means for adaptation of changing
environmental condition
- heritable for several generations
Epigenetics

23. Contaminants and DNA Methylation

24. DNA methylation and oysters
sites
Gavery, unpublished

25. Gavery - Friday 9:00 - #383DMRs

26. 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.

27. Acknowledgements
Mackenzie Gavery
Claire Olson
Sam White
Brent Vadopalas
Jake Heare
EPA
STAR
Aquaculture Program
DNA methylation
oystergen.es
@sr320