Molecular Genetics Core

The mission of the Molecular Genetics (MG) Facility Core is to provide NIEHS Center investigators a variety of services and technical support in the areas of recombinant DNA technology, gene expression analysis and molecular genetics. To provide such services, the MG Core unites the facilities and expertise of two existing facilities, the Recombinant DNA Laboratory (RDL) and the Molecular Genomics Facility. The RDL is a Core Facility in the Sealy Center for Molecular Science and has been a source of support for the NIEHS Center during both previous funding periods (April 95-March 05). Recombinant DNA technology remains an essential part of the experimental design of many of our current research programs. The MG Core offers standard services such as DNA sequence analysis, plasmid DNA preparation and competent cell production, as well as a variety of more sophisticated support services like site-directed mutagenesis, bacterial and eukaryotic expression constructs and the construction of plasmids to create transgenic mice or null-gene (knock-out) mutants of specific genes. The achievement of sequencing an entire genome (yeast, Drosophila, Arabidopsis, rat, mouse, human) produced a change in the experimental design of much of our research from a “single gene” concept to one with the ability to query the expression of the entire genome. The Molecular Genomics Facility, which was established as an extension of the RDL in May 2000, offers gene expression analysis to Center Investigators using both Affymetrix “Gene Chip” and custom microarray technologies. Validation of the differences in gene expression detected by expression analysis is obtained using MG Core support for real-time quantitative RT-PCR. Single nucleotide polymorphisms (SNP) occur frequently within the human genome (1 in every 1300 bases) and have a low mutation rate, making them an ideal basis for a genetic mapping tool to analyze the frequency of a specific phenotypic trait. The MG Core offers Center Investigators SNP analysis using the Affymetrix “Gene Chip” Mapping Assay. This system will provide the analysis of 100,000 SNPs in a single assay.

The Director of the MG Core, including both the RDL and Molecular Genomics Facility, is Thomas G. Wood, Ph.D. Dr. Wood is a Professor in the Department of Biochemistry and Molecular Biology and a Senior Scientist in the Sealy Center for Molecular Science. and has authored 66 peer-reviewed publications. Before his arrival in 1992 at UTMB, he directed the Recombinant DNA Laboratory, Program Resources/National Cancer Institute, Frederick Cancer Research and Development Center for eight years.

The MG Core provided services to 23 NIEHS Center investigators during the past funding year (Table C). These services provide a significant benefit in cost-effectiveness. For example, competent cells for performing routine transformations with plasmid DNA can be purchased from Invitrogen for $80 a vial. The very same reagent is available from the MG Core for $2 if you are an NIEHS Center investigator. DNA sequence analysis costs $3 per reaction. These are obvious benefits to utilizing a Core-based approach to research support. In addition, the MG Core offers support in areas of technical expertise that may not be common to every laboratory in the Center. Specific techniques that may be outside the primary research areas of an individual investigator’s laboratory are accessible to NIEHS Center Investigators through the MG Core. Technologies like gene expression analysis using either Affymetrix “Gene Chips” or microarrays require equipment and experience that cannot easily be duplicated in individual laboratories within the Center. The Core is an excellent solution to this problem. It reduces the cost in capital equipment and insures that a highly trained and experienced technician performs each of the expression assays

The use of DNA polymorphisms as genetic markers for organisms with complex genomes has made possible the mapping of genes associated with interesting biological traits. Polymorphisms corresponding to differences at a single nucleotide position (substitutions, deletions and insertions) are called single nucleotide polymorphisms (SNPs). During the past funding period the MG Core added SNP assays to our list of services. Two programs have already benefited from this addition. Dr. Abdel-Rahman’s program to examine variation in human response to chemical exposures draws upon this type of analysis in defining variance in susceptibility genes. The MG Core developed a SNP-like assay for the Prakash laboratories that actually determines the frequency of each base’s incorporation at a specific loci. One of the specific aims of their program is to define the role of different bypass processes in the replication of damaged DNA. They developed a plasmid system to analyze the replication repair in response to different site-specific lesions. We developed a SNP assay that will assess the frequency that each base is used in the repair process.

Dr. Allan Brasier’s work on “Signaling in Airway Inflammation” benefited from DNA sequencing support and the results were important to their publication, Choudhary et.al. J. Virol. 79:15302-15313, 2005. The STAT3 mutant that the MG Core created for the Brasier Laboratory played a key role in the work published by Ray et.al. (Gastroenterology 29:1616-1632, 2005). Dr. Randall Goldblum’s program “A Phylogenetic Approach to Plant Allergy Vaccines” uses the Core’s DNA sequence service to assist his team in defining variations in the structure of cedar pollens that the group clones as cDNAs.

The MG Core offers gene expression analysis using Affymetrix “Gene Chip”technology. Affeymetrix “Gene Chips” are a commercial platform for interrogating mRNA expression and this technology offers an exciting discovery-based tool for utilization by Center investigators. Dr. Shakeel Ansari has applied this technology to his program entitled “Mechanisms of TCE-Mediated Autoimmunity” to identify changes in gene expression in the mouse liver with time following TCE exposure. Dr. Cornelius Elferink has used the mouse genome 430 “Gene Chip’ to identify a small group of novel target genes that show a change in their level of expression in primary mouse hepatocytes in response to TCDD. Gene Expression analysis and the use of RT-PCR based real time assays as a means of verifying results from “Gene Chip” experiments is one of the ways that the MG Core fulfills our mission to provide state-of-the art support to NIEHS Center investigators that will enhance the successful attainment of their research goals.

Core Director and Members

Thomas G. Wood, Ph.D., Director, Molecular Genetics Core, NIEHS Center; Professor, The Department of Biochemistry and Molecular Biology; Director/Senior Scientist, Recombinant DNA Laboratory; Director, Molecular Genomics Core; Senior Scientist, Sealy Center for Molecular Medicine

Maribel Acosta, B.S., Member, Molecular Genetics Core, Molecular Biologist, Sealy Center for Molecular Medicine

Richard A. Kanost, M.S., Member, Molecular Genetics Core, Senior Research Assistant, Sealy Center for Molecular Medicine

Deborah J. Prusak, B.S., Member, Molecular Genetics Core, Molecular Biologist, Sealy Center for Molecular Medicine

Yuanfen Wei, M.D., Member, Molecular Genetics Core, Research Associate II, Sealy Center for Molecular Medicine

Important Links

Dr. Wood's Home Page:
http://bmb.utmb.edu/faculty/wood/

Recombinant DNA Laboratory:
http://www.scms.utmb.edu/cores/rdl/rdl.htm

Molecular Genomics Laboratory:
http://www.scms.utmb.edu/genomics/index.htm