Argonne-University of Chicago joint venture bolsters
genomic sequencing capabilities
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ARGONNE, Ill. (June 9, 2008)—The Institute
for Genomics and Systems Biology (IGSB), a joint venture of the U.S. Department of Energy's (DOE) Argonne
National Laboratory and the University
of Chicago, has acquired two new instruments
that provide an enhanced ability to sequence genomes more quickly and broadly.
Argonne's genomics research is primarily funded DOE's Office
of Science, which supports research that provides a fundamental scientific
understanding of plants and microbes necessary to develop strategies
for sequestering carbon gases, producing biofuels and cleaning up waste. |
"Sequencing used to be like locating a golf ball by searching only on
the fairway, but not the rough," said IGSB Director Kevin White. "It
used to be that only species that could be cultivated, or grown in pure culture,
could be sequenced. The capabilities of the new Roche 454 FLEX and Illumina
Solexa Genome Sequencer now allow scientists that use the machines to skip
the cultivation step. Eliminating that step will save time and speed up the
research process, while maintaining accurate sequencing results."
The 454 FLEX is ideally suited for studying microbial communities by de
novo sequencing. It provides 400,000 DNA fragments of about 250 base
pairs each – or 100 million base pairs per run – that represent either a
significant part of the genome of a single organism or a random snapshot
of parts of multiple genomes.
The Solexa Genome Sequencer is targeted at resequencing. Compared to the Roche
454 FLEX, it generates more but shorter reads, creating 40 million reads with
a current read length of 18 to 36 base pairs – or about 1 billion base pairs
per run – depending on the application.
The machines were purchased to facilitate research for three Argonne Laboratory-Directed
Research and Development projects. A project led by Michael Miller, a terrestrial
ecologist, and Folker Meyer, a computational biologist in IGSB, will enhance
our understanding of soil CO2 sequestration capability on the microbial level.
In another project, Argonne's soil ecology group is using metagenome sequencing
to study the microbial population in chronoseries plots at DOE's Fermi National
Accelerator Laboratory. In a third project, Argonne's environmental remediation
program is studying the role played by microbial communities in subsurface
remediation of inorganic contaminates using metagenome sequencing.
IGSB's sequencing group plays an active role in the design and optimization
of experiments using DNA sequencing technology, such as developing and optimizing
protocols for DNA isolation from environment as diverse as subsurface soil
and plant leaves. The group also works with researchers to develop protocols
for DNA extraction and to conduct downstream bioinformatics analyses.
The new machines are also open to other Argonne and University of Chicago
researchers who need genetic samples sequenced. In the near future, the sequencing
instruments will be available to select peer-reviewed proposals from researchers
from other organizations.
Argonne's genomics research is primarily funded DOE's Office
of Science,
which supports research that provides a fundamental scientific understanding
of plants and microbes necessary to develop strategies for sequestering carbon
gases, producing biofuels and cleaning up waste.
Argonne National Laboratory brings the world's brightest scientists and engineers
together to find exciting and creative new solutions to pressing national problems
in science and technology. The nation's first national laboratory, Argonne
conducts leading-edge basic and applied scientific research in virtually every
scientific discipline. Argonne researchers work closely with researchers from
hundreds of companies, universities, and federal, state and municipal agencies
to help them solve their specific problems, advance America 's scientific leadership
and prepare the nation for a better future. With employees from more than 60
nations, Argonne is managed by UChicago
Argonne, LLC for the U.S.
Department of Energy's Office
of Science.
For more information, please contact Angela Hardin (630/252-5501
or ahardin@anl.gov) at Argonne.
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