Superfund Research Program
Genomics and Analytical Chemistry
Project Leader: Daniel K. Nomura
Co-Investigator: Martyn T. Smith
Grant Number: P42ES004705
Funding Period: 2006-2017
Project Summary (2011-2017)
This Core combines the expertise of Drs. Christine Skibola and Evan Williams, the two co-leaders of the Core, who have broad experience in the application of cutting-edge technologies to support the projects of the Berkeley Superfund Research Program (SRP). The overall goals of the Berkeley SRP are to use 'omic' technologies and modern analytical methods to develop biological markers for application in human studies and site remediation to allow better detection and remediation of Superfund priority chemicals and emerging contaminants in the environment; and to better evaluate the risk they pose to human health. This Core is set up specifically for the purpose of providing the laboratory infrastructure and expertise for project researchers to achieve these goals. To meet many of the aims of several projects and ensure their success, investigators require access, know-how, and technical support to apply cutting edge technologies such as functional genomics, transcriptomics, proteomics, genetics and epigenetics. The "Arsenic Biomarker Epidemiology" is an epidemiological study that requires effective handling and management of biological samples so that these technologies can be applied. To accomplish these goals, detailed collection and storage protocols have been designed and the Core provides facilities for the genetic and proteomic studies that will be conducted in several projects. This project and the "Nanotechnology-Based Environmental Sensing" project also require a sophisticated mass spectrometry analysis that is provided by the QB3/Chemistry Mass Spectrometry Facility. The Core also provides support for high-throughput analysis of toxic metabolites for the project "Oxidative Remediation of Recalcitrant Contaminants with Persulfate" through the Berkeley Screening Center.
The specific aims of the Core are to:
- Process, maintain and store biological samples and cell lines
- Provide facilities and methodologies for gene expression and epigenetic studies
- Provide analytical support for proteomic studies, for the identification of proteins and organic and inorganic compounds through the Berkeley QBS/Chemistry Mass Spectrometry Facility, and toxicity screening support
- Provide facilities and methodologies to analyze genetic polymorphisms
- Provide sequencing capabilities at the Berkeley QB3 DNA sequencing facility. The Core provides expertise and analytical support in all required areas that, along with the computational biology skills of the Quantitative Biology Core, that allows for the successful completion of several projects of the Berkeley SRP.