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

Project-Specific Links

Final Progress Reports

Year:   2016  2014  2008  2005 

In 2008, the Superfund Functional Genomics and Bioinformatics Core Laboratory (SFGBCL) increased the number of genotyping and gene expression assays available, continued the development and testing of new instrumentation and methodologies (e.g. oligonucleotidebased DNA microarray analyses) and added appropriate software. Thus, capabilities for ongoing Superfund-based projects were expanded. Over 90 hours of consultation were furnished to Superfund researchers.

SFGBCL made significant progress, as follows;

• For Dr. Woods, SFGBCL processed samples from a Portugal Children’s study, elderly population cohort, and a dental workers’ study, all involving mercury exposure, atypical porphyrinogenic response, and neuro/motor function. These 3 study populations were genotyped for genetic variants including 7 SNPs tagSNPs in the TDO2 gene; the HFEC282Y, HFE H63D, and CPOX4 N272H, COMT Val158Met, BDNF Val66Met, and 5-HTTLPR polymorphisms. 100 autism cohort subjects were also genotyped for these alleles. SFGBCL contributed to the publication: Heyer N, Echeverria D, Farin FM and Woods JS. The association between serotonin transporter gene promoter polymorphism (5-HTTLPR), self-reported symptoms and dental mercury exposure. J. Tox. Environ. Health 2008;71(19):1318-26.
• RNA extraction, QC and microarray processing of over 180 mouse/human samples for Affymetrix arrays and subsequent bioinformatics analyses were carried out.  The study examined the transcriptional profiles of human U87-MG cells and SHSY5Y cells treated with the jet fuel lubricants Durad 125 and Durad 150.
• In support of Dr. Costa’s project Ongoing work was incorporated into a manuscript titled ‘Serum cholinesterase inhibition in relation to paraoxonase (PON1) status among organophosphate-exposed agricultural pesticide handlers’. The lab also contributed to two manuscripts with Dr. Checkoway’s group:
  • Brighina L, Checkoway H, Maraganore DM, et al. Alphasynuclein,pesticides, and Parkinson disease: a case-control study.Neurology. 2008 Apr15;70(16 Pt 2):1461-9
  • Costa-Mallen P, Checkoway H, et al. The functional polymorphismof the hemoglobin-binding protein haptoglobin influences susceptibility to idiopathic Parkinson's disease. Am J Med Genet B Neuropsychiatr Genet. 2008 Mar 5;147B(2):216-22.
• Working with Dr. Gallagher’s group, the SFGBC contributed to three manuscripts:
  • Lefebvre KA, Tilton SC, Bammler TK, Beyer RP, Srinouanprachan S, Stapleton PL, Farin FM, Gallagher EP. Gene expression profiles in zebrafish brain after acute exposure to domoic acid at symptomatic and asymptomatic doses. Toxicol Sci. 2008 Oct 20
  • Matsuo AY, Gallagher EP, Trute M, Stapleton PL, Levado R, SchlenkD. Characterization of Phase I biotransformation enzymes in coho salmon (Oncorhynchuskisutch).Comp Biochem Physiol C Toxicol Pharmacol. 2008 Jan;147(1):78-84
  • Lefebvre KA, Tilton SC, Bammler TK, Beyer RP, Srinouanprachan S, Stapleton PL, Farin FM, and Gallagher EP. Gene expression profiles in zebrafish brain after acute exposure to domoic acid at symptomatic and asymptomatic doses. Toxicological Sciences 2009.
• In support of Dr. Strand’s project (Phytoremediation of Organic Pollutants Using Transgenic Plants), SFGBCL processed 16 poplar samples processed on Affymetrix arrays and bioinformatic analysis is ongoing. Numerous other poplar-related samples were processed and RT/PCR analysis was carried out for rabbit CYP2E1, poplar 325.1 and four genes of another poplar species for microarray result verification. RT-PCR analysis for XplA in 12 samples grass was measured. 12 hours of consultation were provided.