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New USDA Gene Data Center and DNA Analyzers

USDA: New Gene Data Center and Gene-Analyzing Machines Speed Discoveries

ARS News Service
Agricultural Research Service, USDA
Marcia Wood, (510) 559-6070,
January 17, 1999

SAN 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

"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

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 NSF, 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,; and 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,

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.
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