Abstract

Functional genomics analyses of an organism's transcriptome can be informative of the interaction of genetic, disease and environmental factors. Here we used a combination of microarrays and machine-learning analytical approaches to understand the impact of environmental stressors and infection on marine organisms. In particular, we studied marine mammals because they are a good model for the assessment of immunological responses to pathogens and contaminants.^1,2 In fact, as mammals that live their entire life (or most of it) in the sea, they act as integrators of the stressors present in the marine environment.³ Marine mammals may have the potential to predict contaminant effects on human health, and to be indicators of infectious disease that may impact humans who have contact with the marine ecosystem through residence, work, or recreation near the coast.

We tested the hypotheses that 1) individual wild dolphins could be associated with a specific PCBs contamination load and 2) individual sea lions could be assigned to a specific disease status category, using only their blood transcriptomic signatures as classifiers. The tools used were a newly developed dolphin oligo microarray representing 24,418 unigene sequences and a custom oligo microarray generated from cross-hybridization probing of a canine microarray. Microarray data from 74 wild bottlenose dolphin blood samples and 73 California sea lion blood samples were analyzed using gene expression profile analysis, including machine-learning approaches. We were able to correctly classify dolphins according to the contaminant load accumulated in their blubber and measured at the site of sampling, and sea lions according to their disease status. These results suggest that a combination of microarrays and machine-learning analytical approaches would significantly improve coastal managers' knowledge about the marine environment/organism interactions.

Acknowledgements

Research supported by awards from the National Ocean Services/NOAA (NCNS4000-4-0054). The construction and characterization of the dolphin microarrays was supported by the NOAA Oceans and Human Health Initiative. The California sea lion work was supported by the Oiled Wildlife Foundation and NOAA Oceans and Human Health Initiative.

References

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