Equipment for Automated Acquisition of DNA Sequence and DNA Fragment Size Data

Vanderbilt University, Nashville TN

Investigators

Abstract

Abstract for NSF Proposal 0140522 - "Equipment for Automated Acquisition of DNA Sequence and DNA Fragment Size Data" A grant has been awarded to Dr. David E. McCauley at Vanderbilt University to support the purchase of an automated DNA sequencer, a DNA extraction system, and supporting computer hardware. The BaseStation gathers DNA sequence data from slab gels and stores it in a form that can be interpreted by sequence analysis software. The machine can also gather and process other types of DNA fragment size data such as microsatellite DNA genetic markers. In the case of both DNA sequence and microsatellite analysis, products of polymerase chain reaction (PCR) are labeled with a florescent dye and separated by size during electrophoresis. The advantage of the BaseStation is that its 96 well capacity and automated loading allows for high throughput, and its configuration makes it equally suited for gathering sequence and microsatellite data. The associated DNA extraction system will allow for rapid extraction of genomic DNA from a large number of samples. The data gathered by these machines will be used by five P.I.'s (D. McCauley, J. Burke, D. Funk, C. Johnson and N.O. Pellmyr) in a variety of studies in evolutionary and population biology which rely on large quantities of DNA sequence and/or microsatellite data. Some of the specific research projects that will make use of data generated by the equipment include the following. 1) A study designed to use both DNA sequence information and polymorphic microsatellite markers to investigate the population genetics of Silene vulgaris, a plant invasive in North America. Comparison of the genetic characteristics of the plant in North America and in its native Europe should indicate the mechanism or route of invasion. 2) A comparative molecular systematics study of several species of yucca plants and of the moths that pollinate them. This phylogenetic study will help document how highly coevolved plant-pollinator systems develop. 3) A study using polymorphic microsatellite loci that will help to map genes associated with the domestication of sunflowers from their wild relatives. 4) A DNA sequence based study of adaptive radiation and host plant shifts in the Neochlamisus bebbianae beetle complex. 5) A study of the adaptive significance of biological clock genes that follows changes in the frequency of molecular markers in model laboratory populations of cyanobacteria. All of these studies will contribute to understanding basic biological processes such as range expansions, coevolution, host plant shifts and the evolution of the biological clock. However, knowledge coming from these studies will also contribute to the solution of more applied problems such as how invasive species might be controlled, how insects shift feeding from native plant species to plants of economic value, how the genetic manipulation of domesticated species might be made more efficient, or how we might overcome health problems associated with biological rhythm disorders. Finally, the results of all of the studies will contribute to the emerging field of bioinformatics, in that each study will require the P.I. to refine methods of gathering, storing, and analyzing a large volume of genetic information.