
USDA: New Gene Data Center and
Gene-Analyzing Machines Will Speed DiscoveriesBy Marcia
Wood January 17, 1999SAN DIEGO, Jan. 17--The
U.S. Department of Agriculture announced
here today that it will establish a new gene data research center at
Cornell University in Ithaca, N.Y. USDA
also will acquire eight new automated machines allowing the department's
researchers to speed their analyses of plant, animal and microbial genes, said
Judy St. John. Based in Beltsville Md., she is Associate Deputy Administrator
for Crop Production,
Product Value and Safety with USDA's Agricultural Research Service. "Together, these two initiatives will accelerate genetic discoveries to
benefit our agriculture, food supply, environment and consumers," St. John
said at the Plant and Animal Genome VII
Conference held today through Jan. 21 at San Diego's Town and Country
Convention Center. "The new DNA analyzers are very fast, highly automated machines,"
St. John said at a conference workshop on federal funding of plant gene
research. "These state- of-the-art tools will make USDA's
Agricultural Research Service the single
most powerful force in genome sequencing within the public agricultural
research sector." The analyzers should begin arriving this spring at ARS
labs in California, Florida, Georgia, Iowa, Maryland, Nebraska, New York and
Pennsylvania. ARS will operate the new Center for Bioinformatics and Comparative Genomics
at sites in Ithaca and Geneva, N.Y., where ARS already has research labs, St.
John said. Genomics is the study of the genome, which refers to
essentially all the genetic material of an organism.
Bioinformatics is the use of computers to help researchers answer
life-science questions, mainly through studying genetic information in
electronic databases. "The USDA-funded center at Cornell," she said, "will aid
researchers around the country and the world in the quest to discover all the
genes in grains--like corn, wheat and rice--and plants in the family that
includes tomatoes, potatoes and peppers." "ARS and Cornell," she said, "already maintain the foremost
computerized, publicly accessible data bases for information about the
structure of genes in grain crops and the Solanaceae family that includes
tomatoes, potatoes and peppers. The center will establish a new partnership to
strengthen this effort." "This partnership will bring in the expertise of Cornell's computer
theory center to apply advanced computer tools to analyze gene information.
This research is urgent, because databases are required that can handle the
deluge of information these gene data banks will receive as a result of
increased federal funding of gene-sequencing projects," St. John said. Once a gene's structure is discovered, scientists can use computers to look
for similar structures in genome databases of plants, humans, mice and other
life forms. Similar structure often connotes similar function, thus shortening the time
to find out what job a gene performs. And once a gene's function, such as
disease-resistance, is identified, biotechnologists can begin experiments to
see if that gene can be re-built to make it more effective. Plants with improved resistance to disease, for example, should require less
chemical pesticides. Or, the genes could be moved into plants that currently
lack resistance. St. John said plans for the Center for Bioinformatics and Comparative
Genomics at Cornell will be implemented through increased ARS funding, with the
addition of several ARS bioinformatics specialists. Cornell faculty in the
Department of Plant
Breeding and Biometry and the Cornell
Theory Center will join the ARS staff in the new genomics center. ARS bioinformatics specialists and Cornell faculty in the Plant Breeding and
Biometry Department currently maintain the gene data banks known as GrainGenes,
SolGenes (for solanaceous crops) and RiceGenes. The ARS labs receiving the new DNA analyzers are in Albany, Calif.; Ft.
Pierce, Fla.; Athens, Ga.; Ames, Iowa; Beltsville, Md.; Clay Center, Neb.;
Orient Point, N.Y.; and Wyndmoor, Pa. "The machines will greatly accelerate the speed at which the
researchers discover the structure of genes of plants, farm animals and other
living things, such as microorganisms important in food safety," St. John
said. At ARS' Plum Island
Animal Disease Center in Orient Point, N.Y., scientists will use the new
instrument to detail the genetic makeup of microbes deadly to livestock.
"Discovering the genetic structure of those microbes," said St. John,
"could enable researchers to develop new, more effective techniques to
protect farm animals." At ARS' Beltsville (Md.) Agricultural
Research Center, researchers in the Livestock and Poultry Sciences
Institute will put their DNA analyzer to work on genes important in cow mammary
glands. The scientists want to find genes responsible for resistance to
diseases of the mammary gland. In Albany, Calif., biotechnologists will use one of the instruments at the
ARS Western Regional Research Center and
at the Plant Gene Expression
Center operated by ARS and the University of California, Berkeley. The
scientists will examine genetic material from microbes as well as from rice,
wheat and a flowering plant called Arabidopsis thaliana, a member of the
mustard family. "Arabidopsis has become a premier model for
hastening discovery of important genes in crop plants," said St. John.
"The new DNA analyzers should enhance USDA's contribution to international
projects to sequence all the genes in Arabidopsis and rice." The Perkin-Elmer ABI model 3700 DNA sequencers purchased by ARS can boost a
lab's productivity an estimated 50 times and decrease costs, according to
Perkin-Elmer Corp., Norwalk, Conn. The sequencers can run unattended for 24
hours, enabling labs to process tens of thousands of samples a week. ARS research on plant genomes is a critical federal component in support of
the National
Plant Genome Initiative. Through research in the public and private
sectors, the initiative aims to improve plants to address regional, national
and global problems. These include problems of food supply, human nutrition and
health, environmental quality, agricultural and forestry resource supply and
quality, energy supply, and rural economies. The NPGI is coordinated by an interagency working group of the
cabinet-level
National
Science and Technology Council. Federal competitive grant funds in support
of the initiative come largely from USDA,
the National Science Foundation, the
Department of Energy and the
National Institutes of Health. More than 1,000 scientists and others from around the country and the world
have registered to attend the Plant and Animal Genome VII Conference. USDA is a
co-sponsor along with universities and nonprofit and industry groups. Scientific contacts: Judy St. John, ARS Associate Deputy
Administrator for Crop
Production, Product Value and Safety, Beltsville Md., phone (301) 504-6252,
fax (301) 504-6191, [email protected];
Caird E. Rexroad, Jr., ARS Associate Deputy Administrator for
Animal Production,
Product Value and Safety, Beltsville Md., phone (301) 504-7050, fax (301)
504-6720, [email protected]. During the Plant and Animal Genome VII Conference, St. John may be reached
from Jan. 17-21 at the Town and Country Hotel, phone (619) 291-7131. The number
for the conference registration desk in the hotel's Atlas Foyer is (619)
291-7131, ext. 3939. U.S. Department of Agriculture | |