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University of California-Davis

Superfund Research Program

Integrated Response to Toxic Perturbation

Project Leader: Robert H. Rice
Co-Investigators: Alan R. Buckpitt, J. Bruce German, Dietmar Kültz
Grant Number: P42ES004699
Funding Period: 2000-2010

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Project Summary (2005-2010)

Driven by technological advances and investigator demand, this Core has expanded from the original goal of providing DNA microarray service to include proteomics and metabolomics, thus providing an integrated approach to assessing cell and tissue responses to toxic exposure. First, the microarray service provides transcriptomic profiling for investigation of toxic endpoints. To this end, it prepares glass slides with high density arrays (e.g., 20,000 elements) of long oligonucleotides representing transcribed genes from human, mouse or rat. It also prepares slides on demand containing smaller arrays or (subject to availability) DNA representing transcripts or genes from other species. The Core processes the slides or train lab personnel in this function as requested and, in concert with Core B, assists in data processing. Second, the Core provides proteomics services including profiling (with protein separation and mass spectrometric identification) and analysis of posttranslational modifications (phosphorylation, sulfhydryl oxidation). The Core also provides services for metabolomic investigations such as profiling of metabolic subdomains and metabolic fingerprinting (including phase II metabolism). Validated analyses of metabolic subdomains include the quantitative assessment of both regulatory oxylipids (for the study of tissue responses to inflammatory injury and general repair mechanisms) and structural/energetic lipids (for the study of toxicant effects on cell/organism energy utilization). Metabolic fingerprinting provides tools for an expansive exploration of toxicant effects on the small molecule milieu of tissues, cells, and biofluids. Integrating themes are to find characteristic responses to given agents, identifying biomarkers of early response, and finding no effect levels for the most sensitive biomarkers of effect. The emphasis is on increasing Project productivity and efficiency of resource utilization. Thus highly trained Core personnel help in planning experiments, concentrating their efforts on technically demanding functions, and training Project personnel in conducting their own experiments where feasible. The Core providea data storage and assistance in data analysis.

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