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National Institute of Environmental Health Sciences

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Your Environment. Your Health.

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

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
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

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Final Progress Reports

Year:   2016  2014  2008  2005 

For Dr. Gallagher's project (Biotransformation Gene-Environment Interactions in Coho Salmon Neurotoxicity), the Functional Genomics and Bioinformatics Core (FGBCL) provided pathway analysis of a microarray experiment that investigated the effect of Cd on the liver and the olfactory system in zebra fish. The core also provided rigorous statistical analysis of a complex behavioral data set that assessed the effect of Cd on olfactory function in coho salmon. In addition, the core visualized this complex data via a combination of boxplots and violin plots to capture all the essential information contained in the data.

The FGPCL assisted Dr. Zhang (Plasma Biomarkers for Parkinsonism in Welders) in the analysis of a proteomics data set that was generated to identify potential biomarkers of Parkinson's disease. The Core also provided significant support in the preparation of a manuscript reporting this data. This manuscript has been published (Shi et al., Mol Cell Proteomics. 2015 Jan 2. pii: mcp.M114.040576).

The FGBCL assisted Drs. Furlong and Costa (Biomarkers of Susceptibility to Environmentally-Induced Diseases) in the analysis of a microarray data set that assessed the effect of gestational Chlorpyrifos exposure in PON1(+/+), PON1-knockout (PON1(-/-)), and tgHuPON1R192 and tgHuPON1Q192 transgenic mice. The core also provided support in the preparation of a manuscript that reported these data and has been published (Cole et al., Toxicol Sci. 2014 Oct;141(2):409-22). In addition, the core performed statistical analysis of a mouse behavioral data set that investigated the effect of Mn exposure on the behavior of WT and PON2 knockout mice.

Dr. Checkoway's research (Parkinsonism and Metal Exposures Among Welders) focused on the potential role of Mn exposure in Parkinson's disease. The FGPCL provided data analysis support and assisted with the preparation of three manuscripts, all of which have been published [1) Searles Nielsen et al., Parkinsonism & Related Disorders, in press 2015; 2) Ahmed et al., PLoS Genet. 2014;10:e1004788. doi: 10.1371/journal.pgen.1004788; 3) Searles Nielsen et al., Environ Res. 2015 Jan;136:75-81].

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