This grant will provide for the acquisition of an Applied Biosystems 3500xL 24-capillary DNA Analyzer to foster research and research training capabilities at the University of Houston-Clear Lake (UHCL). The ABI 3500xL DNA Analyzer is a fully automated capillary electrophoresis system with a capacity of sequencing up to 400,000 base pairs per day. The requested equipment will be used by at least eight faculty members in biology, biotechnology and environmental science for their research activities as well as for research training of undergraduate and graduate students. The DNA Analyzer will be utilized to detect pesticide resistance-associated gene mutations in Rhipicephalus microplus, to study essential amino acid biosynthesis in Medicago truncatula, to study molecular mechanisms of environmental stress in soft corals, to study molecular mechanisms involved in the maintenance of zinc homeostasis in plants, to study microbial populations in Galveston Bay, and to study regulation of human inducible nitric oxide synthase.

Acquisition of the high-throughput DNA Analyzer will enhance faculty research and advance student learning by enriching courses in genomics and through integration of hands-on exposure for independent research projects using modern instrumentation. Faculty and student researchers will use the equipment to address important problems in the areas of biology, biotechnology and environmental science. For example, the DNA Analyzer will be used to determine the genes responsible for pesticide resistance in the Texas cattle tick, which has led to major loss to the cattle industry. The Analyzer will be used to address problems related to human welfare, such as the role of nitric oxide in the human body, and how to improve the nutritional quality of plant foods, such as legumes, to address the worldwide problem of malnutrition from plant-based diets. The Analyzer will also be used to determine the effects of environmental stress on soft corals, to characterize the microbial community of Galveston Bay, and in other projects important to the environment.

This equipment will greatly enhance the generation of research publications and grant proposals from UHCL and enhance ongoing collaborations with regional and national organizations such as the USDA Children?s Nutrition Research Center, USDA-ARS-Livestock Insect Research Laboratory, Nalco Chemical company, and Baylor College of Medicine. Acquisition of this equipment will address both local and national needs for well-trained B.S. and M.S graduates with research skills in biology, biotechnology and environmental science. At least 50 B.S. and M.S. students per year will use the instrument in independent studies and thesis research and another 30 students in formal training courses. A high percentage of these students will be from groups underrepresented in science. Local 7th to 12th grade science students will also be given opportunities to access data from this equipment to learn how to perform genetic and genomic analysis.

Project Report

have been able to train students in teaching and research labs to perform DNA Sequencing and Fragment Analysis, including sample preparation, running samples, and data analysis. PI Rohde has recently gotten back in the lab and has an MS thesis student and several undergraduate students using the instrument to sequence a cDNA library constructed from RNA derived from the cattle tick Rhipicephalus microplus. His research group is currently analyzing sequences for their involvement in pesticide resistance. A first set of samples has been sequenced and is currently being analyzed. The group is preparing to sequence a second set of samples. Co-PI LZ Santiago-Vázquez initially proposed to use the instrument to analyze the bacterial communities associated to stressed soft corals and to identify expression changes in molecules associated to stress. She was able to analyze the bacterial population of the soft coral Eunicea fusca, showing a switch from mostly gamma-Proteobacteria in controls to the appearance of alpha-Proteobacteria and Actinobacteria with a marked reduction of gamma-Proteobacteria in stressed corals. She is continuing this project with Plexaura homomalla and other corals. The gene expression project has been placed on hold at the moment since the bacterial one has produced many exciting findings. Co-PI Stephens has continued the identifying alleles of the ZIP family transporters in Medicago truncatula. Through the use of the ABI 3500xl Genetic Analyzer, his group has identified 14 alleles in MtZIP1 and 18 alleles in MtZIP5. Stephens is currently characterizing these alleles for changes in activity. In addition, his lab is continuing to identify additional alleles in other ZIP transporters. In collaboration with Dr. George Guillen (UHCL, Biology) and Sybil Glenos (Master thesis) they utilized the Genetic Analyzer to identify genetic variation of Malaclemys terrapin (Diamondback Terrapin) utilizing microsatellites in Galveston Bay populations. Co-PI Mills has recently re-started his research program and in collaboration with Stephens, will begin to look at gene expression changes in Medicago truncatula. Stephens and Santiago-Vázquez along with other new UHCL faculty have incorporated the use and training on the DNA analyzer into several teaching labs. At the moment the use of the Analyzer is standard for the following teaching labs: Lab for Biotechnology (BS), Advance Methods in Biotech I and II Labs (MS), Plant Genomics Analysis (MS), and Bacterial Taxonomy and Biotechnology Lab (MS). In addition to its teaching potential, The DNA Analyzer provides us a tool to annually train over 40 graduate and undergraduate students in research labs. These students have been involved in research projects either conducting thesis work or independent studies. A large number of these students are females. This funded project has resulted in several research presentations in conferences, several manuscripts in preparation to be submitted for publication, several grant proposals, and over 5 MS thesis projects. In addition, many alumni have secured employment in part because of their experience with this instrument.

National Science Foundation (NSF)
Division of Biological Infrastructure (DBI)
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Robert Fleischmann
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University of Houston - Clear Lake
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