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Final Progress Reports: University of Washington: Functional Genomics and Bioinformatics Core Laboratory

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Superfund Research Program

Functional Genomics and Bioinformatics Core Laboratory

Project Leader: Theodor K. Bammler
Co-Investigator: James W. MacDonald
Grant Number: P42ES004696
Funding Period: 2000-2023
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Final Progress Reports

Year:   2016  2014  2008  2005 

The FGBC provides state-of-the-art molecular, statistical and bioinformatics support to each UW SRP project investigating physiological and neurological effects caused by Superfund toxicants. The FGBC developed a custom q-RT-PCR array for Evan Gallagher, Ph.D. to measure expression of genes involved in olfactory function. The research team found that low-level Cadmium (Cd) exposure associated with polluted waterways can induce persistent olfactory dysfunction in salmon (Williams et al., 2016). The FGBC also performed transcriptional profiling of salmon olfactory rosettes exposed to organophosphate pesticide (OP) mixtures. Researchers identified molecular pathways of olfactory impairment that underlie neurobehavioral injury associated with the neurotoxic effects of environmentally relevant exposure to OP mixtures (Wang et al., 2016). The Core furnished RNA-Seq analysis investigating gene expression in salmon sampled from three different field sites with varying levels of pollution with Superfund chemicals. The FGBC assisted in developing a panel of antioxidant genes using the QuantiGene Plex (QGP) platform. QGP is a q-RT-PCR alternative to rapidly assess the potential for chemicals to elicit oxidative stress (Mills et al., 2017).

PON2 is the only paraoxonase expressed in brain tissue and is able to mitigate oxidative stress. For Clement Furlong, Ph.D. and Lucio Costa, Ph.D.’s project, the FGBC measured PON2, PON1 and PON3 gene expression in the brain and liver of mice through development to identify potential age windows of susceptibility to oxidative stress (Garrick et al., 2016).

For the UW SRP project directed by Rebecca Neumann, Ph.D. and Zhengui Xia, Ph.D., the Core provided proactively technical consultation as to meaningfully utilizing RNA-Seq and q-RT-PCR technologies in their research.

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