The award supports the further design and implementation of Expresso — a sophisticated computational system for microarray bioinformatics. Microarrays (sometimes called DNA chips) are an approach to studying simultaneously the expression of hundreds or thousands of genes in a given organism.
The funded project will address all stages involved in microarray experiments — design, processing, analysis, and interpretation of the biological results. Expresso's design automates many of the tedious methodological aspects of conducting microarray experiments and analyzing subsequent data. It will serve as a tool of powerful synergy between traditional laboratory work and the high-level goals of experimental biologists. The grant project is a multidisciplinary collaboration between computer scientists and biologists, who will use the developed management infrastructure of the Expresso software to conduct their investigations.
According to two of the investigators for the grant, Naren Ramakrishnan and Lenwood S. Heath of Virginia Tech’s computer science department, Expresso is a software system that can be used to conduct a variety of experimental biology research projects. For example, with colleagues at North Carolina State University, the group is using microarrays and Expresso to identify genes that allow Loblolly Pine trees to resist periods of drought. The result will be hardier pine trees that will be economically valuable for the forest industry, the researchers said.
Also, with Malcolm Potts of biochemistry and Rich Helm of wood science and forest products, both at Virginia Tech, the researchers are analyzing microarray data from both bacteria and human tissue to identify genes whose expression changes in the face of drying out. "The result will be human tissue that can be dried out and later reconstituted with water. This can help make the military less dependent on supply lines," Ramakrishnan said. There are also other medical applications.
In collaboration with the International Potato Institute in Lima, Peru, the group is developing microarrays for the study of environmental stress and enhanced production of antioxidants in Andian potato varieties. "The result will be more economically productive and nutritious potato crops, which will benefit the farmer and consumer as well," Heath said.
The team includes Ramakrishnan, Heath, and Layne T. Watson of Virginia Tech’s Department of Computer Science in the College of Arts and Sciences, Ruth Grene Alscher of Plant Pathology, Physiology, and Weed Science in the College of Agriculture, and Jennifer Weller of the Virginia Bioinformatics Institute. Ramakrishnan, Heath, and Watson are members of the problem-solving environment (PSE) group at Virginia Tech; this award is the third Next Generation Software award to the PSE group. The Expresso award is among the largest made in this year's competition.
Additional contacts:
Dr. Lenwood Heath 540-231-4352 heath@vt.edu
Dr. Layne Watson 540-231-7540 ltw@vt.edu
Dr. Ruth Grene Alscher 1 540-231-6761 ralscher@vt.edu
PR CONTACT: Sally Harris (540) 231-6759 slharris@vt.edu