1. Shellfish as indicators of environmental change
Steven Roberts
School of Aquatic and Fishery Sciences
University of Washington
2.
3. Oceans and Human Health
practical
omic approaches ?
medium to large scale characterization of
transcripts, proteins, community members
(metagenome), metabolites, epigenetic
differences....
one health
inter-relationships among human, animal, and
environmental health and seeks to enhance
communication, cooperation, and collaboration
in integrating these areas for the health and
well-being of all species
16. Oceans and Human Health
immune
response
pathogen
physiology
bioindicator
17. Oceans and Human Health
immune
response
How does environmental change impact physiology (populations)?
18. Oceans and Human Health
immune
response
How does environmental change impact physiology (populations)?
How will changes in immune response impact pathogen dynamics?
19. Oceans and Human Health
immune
response
Pacific Oysters
- Vibrio
- Oyster Herpes Virus
20. Oceans and Human Health
immune
response
Pacific Oysters
- Vibrio - Sanger
- Oyster Herpes Virus - HTS
How advances in technology are changing science
24. interleukin 17
•cytokine
•large number of cytokines found in vertebrates are not
found in invertebrates
•interleukin 17 is not similar to other interleukins
•vertebrates- interleukin expressed in
activated memory T cells
27. Oceans and Human Health
immune
response
Pacific Oysters
- Vibrio - Sanger
- Oyster Herpes Virus - HTS
How advances in technology are changing science
51. Ocean Acidification and Emerging Diseases
Acidification will compromise
shell structure in many shellfish
There is little known about
how other physiological
processes will be impacted
Using genomic approaches
to determine how multiple
stressors impact
host-pathogen system
61. low oxygen conditions Chart 6
biosynthesis
response to endogenous stimulus
transport
ion transport
signal transduction
Control
cell communication
transcription
protein metabolism
cell cycle
carbohydrate metabolism
protein biosynthesis
cell organization and biogenesis
response to external stimulus
amino acid and derivative metabolism
morphogenesis
protein modification
generation of precursor metabolites and energy
death
response to abiotic stimulus
Low Oxygen
cell death
cell differentiation
cell homeostasis
nucleic acid metabolism
secondary metabolism
catabolism
lipid metabolism
DNA metabolism
response to stress
0 0.025 0.050 0.075 0.100
62. summary
• proteomic approaches offer global tool to directly examine
functional responses to changes in environmental conditions
(including those that contribute to virulence)
• absence of a known genome makes protein identification
challenging
63. Oceans and Human Health
immune
response
pathogen
physiology
bioindicator
71. Transcriptomics
16 million
~40 bp
HQ reads
16 million
~40 bp
HQ reads
72. 32 million reads
v
17 million matched
Sigenae consensuses
29 thousand features
Upregulated features | min 10 unique hits & 2 fold increase
1329 1316
22 specific 25 specific
78. qPCR
complement C1q
steroid 17-alpha-hydroxylase serine protease inhibitor
TNF-related protein 4
gonadotropin-releasing
calmodulin-like metalloproteinase inhibitor 3
hormone II receptor
79. summary
•HTS offers non-biased, one-stop characterization
•provides ability to identify organismal stressors
without prior knowledge of
contaminant
•natural variation in physiology needs
and genetics needs to be taken into
consideration
practical?
80. Oceans and Human Health
immune
response
pathogen
physiology
bioindicator
transcriptome
epigenome
81. epigenetics
DNA Methylation
Histone Small Interfering
Modification RNA
82. epigenetics
•controls normal developmental processes
•implicated in human diseases including cancer
•possible means for adaptation of changing
environmental condition
- heritable for several generations
83. environmental epigenomics
- agouti viable yellow (Avy)
- no methylation = yellow
- methylation = normal
- maternal BPA exposure
influences offspring
- DNA hypomethylation
84. environmental epigenomics
• Rats treated with the estrogenic pesticide methoxychlor
or the antiandrogenic fungicide vinclozolin during
pregnancy
• Male offspring that have decreased sperm capacity and
fertility
• Compromised fertility is passed through the adult male
germ line for four generations
Anway MD, Cupp AS, Uzumcu M, Skinner MK 2005 Epigenetic
transgenerational actions of endocrine disruptors and male fertility.
Science 308:1466–1469
97. bisulfite sequencing
- Less Practical? Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, et al. (2010)
- Comprehensive Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base
Encoding. PLoS ONE 5(2): e9320. doi:10.1371/journal.pone.0009320
98. summary
• epigenetic processes are important mechanisms by
which changing environmental conditions alter gene
expression pattern
• more research is needed to better understand
mechanism and heritability in marine organisms
99. conclusions & directions
• comparative and evolutionary aspects can provide valuable
insight into predicting ecosystem changes
• characterizing natural populations to better understand
biology and the environment will continue to be complex,
however deep sequencing will prove to be a valuable tool
100. acknowledgements
Yannick Gueguen (Ifremer)
Julien de Lorgeril (Ifremer)
Frederick Goetz (WATER Institute)
Giles Goetz (WATER Institute)
Samuel White (UW)
Colleen Burge (UW)
Carolyn Friedman (UW)
Tatyana Marushchak (UW)
funding
Mackenzie Gavery (UW) USDA-NRAC
Joth Davis (Taylor Shellfish) NOAA SK Program
Dustin Lennon (UW) Washington SeaGrant
Paul Sampson (UW) UW-SAFS