Genomic approaches to
assessing ecosystem health
Steven Roberts
School of Aquatic and Fishery Sciences
University of Washi...
Open Science
• You are free to Share!
• Our lab practices open notebook
science
• Slides and more available
robertslab.inf...
e
Physiology
Very easy to get billions of A,C,T, and Gs
e
Physiology
DNA Variation
Gene Expression
Proteins
Epigenetic Alterations - DNA Methylation
Biological Indicators of Ecosystem Health
DNA Variation
Gene Expression
Proteins
Epigenetic Alterations - DNA Methylation
Biological Indicators of Ecosystem Health
Physiological
Response of
Oysters in
Puget
Sound
Gene Expression
urban, agriculture, water
fowl, marinas, seals
low population, low fecal
coliform
urban, agriculture, water
fowl, marinas, seals
low population, low fecal
coliform
urban, agriculture, water
fowl, marinas, seals
low population, low fecal
coliform
with replication / validation -> signatu...
qPCRlowpopulation,
lowfecalcoliform
urban,agriculture,
waterfowl,
marinas,seals
metalloproteinase inhibitor 3
Gavery, Mack...
Olympia oyster
PROPS v2
Application of qPCR
Very easy to get billions of A,C,T, and Gs
Very easy to get thousands of genes online
DNA Variation
Gene Expression
Proteins
Epigenetic Alterations - DNA Methylation
Biological Indicators of Ecosytem Health
Epigenetic Alterations - DNA Methylation
DNA Methylation
Histone
Modification
Small Interfering
RNA
• controls normal developmental processes
• implicated in human diseases including cancer
• possible means for adaptation ...
Contaminants and DNA Methylation
DNA methylation and oysters
sites
Gavery, unpublished
Gavery - Friday 9:00 - #383DMRs
Summary
• Sequencing technology allows for easy integration
of genomic approaches into environmental
studies.
• Practical ...
Acknowledgements
Mackenzie Gavery
Claire Olson
Sam White
Brent Vadopalas
Jake Heare
EPA
STAR
Aquaculture Program
DNA methy...
Genomic approaches to assessing ecosystem health
Genomic approaches to assessing ecosystem health
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

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Genomic approaches to assessing ecosystem health

  1. 1. Genomic approaches to assessing ecosystem health Steven Roberts School of Aquatic and Fishery Sciences University of Washington
  2. 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. 3. e Physiology
  4. 4. Very easy to get billions of A,C,T, and Gs
  5. 5. e Physiology
  6. 6. DNA Variation Gene Expression Proteins Epigenetic Alterations - DNA Methylation Biological Indicators of Ecosystem Health
  7. 7. DNA Variation Gene Expression Proteins Epigenetic Alterations - DNA Methylation Biological Indicators of Ecosystem Health
  8. 8. Physiological Response of Oysters in Puget Sound Gene Expression
  9. 9. urban, agriculture, water fowl, marinas, seals low population, low fecal coliform
  10. 10. urban, agriculture, water fowl, marinas, seals low population, low fecal coliform
  11. 11. urban, agriculture, water fowl, marinas, seals low population, low fecal coliform with replication / validation -> signature
  12. 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. 13. Olympia oyster PROPS v2
  14. 14. Application of qPCR
  15. 15. Very easy to get billions of A,C,T, and Gs
  16. 16. Very easy to get thousands of genes online
  17. 17. DNA Variation Gene Expression Proteins Epigenetic Alterations - DNA Methylation Biological Indicators of Ecosytem Health
  18. 18. Epigenetic Alterations - DNA Methylation DNA Methylation Histone Modification Small Interfering RNA
  19. 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. 20. Contaminants and DNA Methylation
  21. 21. DNA methylation and oysters sites Gavery, unpublished
  22. 22. Gavery - Friday 9:00 - #383DMRs
  23. 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. 24. Acknowledgements Mackenzie Gavery Claire Olson Sam White Brent Vadopalas Jake Heare EPA STAR Aquaculture Program DNA methylation oystergen.es @sr320

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