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 2005, the Bioanalytical Core Laboratory increased the number and types of genotyping and quantitative gene expression assays available, continued the development and testing of new molecular biology-related instrumentation and methodologies such as oligonucleotide-based DNA microarray analyses and, incorporated additional molecular biology-associated software.  As a result, the Superfund Bioanalytical Core Laboratory has expanded the number and scope of ongoing Super Fund based projects.  In addition, over 275 hours of consultation were furnished to researchers associated with the Bioanalytical Core Laboratory.  Therefore, the services provided by the Bioanalytical Core Laboratory represent significant progress toward each of the specific aims and are listed below according to Project number and investigator.

Project 1 (Kavanagh) - Genotyping of the three known polymorphisms in the GCL gene for studies involving end stage renal disease and cystic fibrosis.  Development of novel TaqMan-based gene dosage assays for validation of microarray-generated gene expression analyses.  Over 200 gene expression analyses for endogenous mouse and transgene GCLc and GCLm genes.  Project 2 (Woods) – 4 Manuscripts: Heyer NJ, Echeverria D, Farin FM, Woods JS, et al. Chronic low-level mercury exposure, BDNF polymorphism, and associations with self-reported symptoms and mood.  Toxicol Sci. 2004; 81:354-363, 2004.  Woods JS, Echeverria D, Farin FM, et al. The association between genetic polymorphisms of CPOX and an atypical porphyrinogenic response to mercury exposure in humans. Toxicol. Appl. Pharmacol. 2005; (in press). Echeverria D, Woods JS, Farin FM, et al. Chronic low-level mercury exposure, BDNF polymorphism, and associations with memory, attention and motor function. Neurotox Teratol 2005a (in press).  Echeverria, D, Woods, Farin, FM, et al. The association between CPOX polymorphism and neurobehavioral domains in response to mercury exposure in humans. Toxicol Sci 2005b (in press).  Project 3 (Costa) – Development of new genotyping for polymorphisms in the DAT1 gene for studies involving Parkinson’s Disease.  Over 20 hours of consultation was given to participants of project #3.  Project 5 (Checkoway) - Mononuclear cell isolation, serum separation, DNA extraction, and archival storage of ~ 50 new PD study samples followed by subsequent genotyping of over 50 PD study samples for the COMT Val158Met CYP2D6A, CYP2D6B, CYP2E1 5' flanking RsaI, CYP1A1m2, GSTP1A, GSTP1B, GSTM1*0/GSTM1*0, and GSTT1*0/GSTT1*0 polymorphisms. 1 Manuscript: Nielsen SS, Mueller BA,  Farin FM, Checkoway H, et al. Risk of brain tumors in children and susceptibility to organophosphorus insecticides:  The potential role of paraoxonase (PON1). Environmental Health Perspectives 2005 (in press).  Project 6 (Morgan) - Development of new RT-PCR assays for verification of one-color human oligonucleotide-based microarray analyses. Further development and verification of other multiple RNA amplification procedures for human peripheral blood mononuclear cells.  Project 7 (Hooper) – Over 40 hours of consultation were specifically rendered to this project.  Project 10 (Ferguson) – Development of new TaqMan-based assays to quantitate D. ethenogenes  and S. multivorans  in environmental samples and analyses of 50 samples. A manuscript was submitted to Environmental Microbiology: Pietari, J.M.H., Herwig, R.P. and J.F. Ferguson, Characterization of PCE or cDEC dechlorinating microcosms with T-RFLP and PCR of dechlorinating bacteria.