WALNUT CREEK, CA -- The Department of Energy's Joint
Genome Institute (JGI), whose Production Genomics Facility in Walnut Creek
is one of the fastest and most powerful in the U.S., has been enlisted
to help safeguard public safety by determining the whole genome sequences
of a variety of infectious bacteria -- a first step toward developing
tests that can be used to rapidly identify their presence in the environment.

While the anthrax strains used in recent bioterrorist attacks could be
identified, there are no field tests for dozens of other potentially dangerous
microbes. To develop new tests and improve existing ones, knowing the
whole genomic sequence of each organism and its close relatives can be
vitally important.

JGI is ideally suited to this effort because of its capacity and depth
of experience in sequencing microorganisms. In a little over three years
JGI has sequenced scores of microbes; last year it sequenced 15 bacteria
in a single month and today is capable of sequencing an average microbe's
genome twice over in a single day.

Starting May 7, 2002, JGI's Production Genomics Facility (PGF) will determine
draft genome sequences of several bacteria already under study at Lawrence
Livermore and Los Alamos National Laboratories. JGI was founded in 1997
by these two laboratories and Lawrence Berkeley National Laboratory; all
three laboratories are managed for the Department of Energy by the University
of California.

The first pathogens to be sequenced under the current program are members
of the Bacillus, Brucella, Clostridium, Francisella, Shigella, and Yersinia
groups. In many of these groups, several strains or related species will
be sequenced, for example, two strains of Bacillus anthracis (anthrax)
and one of the similar species Bacillus thuringiensis.

Depending on how quickly the organisms become available, JGI plans to
sequence the whole genomes of many more potentially hazardous bacteria
and a number of their less harmful relatives.

Sequencing at JGI will not involve actual pathogens. Whole organisms
will be received and handled at laboratories equipped with appropriate
containment facilities, like those in place at Livermore and Los Alamos,
where the DNA of each pathogen will be reduced to fragments to be sent
in a disassembled state to JGI's Production Genomics Facility.

The genome of a typical bacterium is a circular piece of DNA containing
approximately two to five million "base pairs" -- pairs of the
chemical bases, integral to the DNA molecule, that form the letters of
the genetic code. Genomes from millions of individual bacteria are fragmented
to create a library of random pieces each about two to three thousand
base pairs long. Each fragment represents only about 0.0005 percent of
the complete genome.

Because intact genomes are not involved, the Centers for Disease Control
and Prevention have registered the PGF to receive this fragmentary DNA
with no change in standard procedures. The PGF will work with multiple
copies of each fragment. Automated equipment determines the exact sequence
of bases on each strand. The data is then assembled by a computer program
to reconstruct the order of the bases in the whole genome.

The completed sequence exists only as a string of letters in a computer's
output. No physical genomes will be handled at JGI, and the standard laboratory
strain of E. coli in which individual DNA fragments are reproduced
will be disposed of after sterilization, according to the standard operating
procedures of the PGF. Draft sequences will be shared with Los Alamos
and Lawrence Livermore laboratories for finishing and annotation.

JGI has been a leader in sequencing organisms of crucial interest to
researchers around the world. For the Human Genome Project, JGI sequenced
human chromosomes 5, 16, and 19, which together constitute some 11 percent
of the human genome. JGI sequenced mouse DNA related to human chromosome
19 to illuminate the molecular evolutionary history of the two species.
Working with an international consortium of universities and industry,
JGI participated in the sequencing of the gene-rich puffer fish (Fugu
rubripes). The 165 million base-pair genome of the sea squirt (Ciona
intestinalis) was sequenced jointly by JGI, Japan's National Institute
of Genetics, and Kyoto University. JGI has also sequenced the environmentally
important white rot fungus (Phanerochaete chrysosporium) and over
50 important microorganisms.

The Joint Genome Institute is one of the largest publicly funded human
genome sequencing institutions in the world. With its main headquarters
and Production Genomics Facility in Walnut Creek, JGI employs about 240
people and has programs in genomic sequencing, computation, functional
genomics, genomic diversity, and new technology development. Funding is
provided predominantly by the Department of Energy's Office of Science;
other agencies that have contributed to funding JGI include DOE's National
Nuclear Security Administration, the National Institutes of Health, the
National Science Foundation, and the U.S. Department of Agriculture.