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frog and bacteria genomes
At the Joint Genome Institute
(JGI) operated by the Lawrence Livermore, Lawrence Berkeley, and
Los Alamos national laboratories, researchers have been decoding
the DNA of one organism after another. They recently sequenced the
fugu, a tasty but potentially toxic Japanese pufferfish whose compact
genome is similar in many respects to the human genome. (See S&TR,
Applied Science Is a Hallmark of This Laboratory.) They then
went on to map the DNA of a diminutive, fast-growing African frog,
Frogs are of interest to
biologists because their growth from eggs to tadpoles to mature
organisms provides information about the development of cells and
organs. The X. tropicalis has a genetic structure that is
smaller and easier to decode than that of other frog species. Says
Robert Grainger, a leading Xenopus researcher from the University
of Virginia, Studies on frogs have long been instrumental
in understanding such fundamental processes as cell division and
how cells in the embryo communicate with one another. Because these
are the processes that go awry when birth defects occur or cancer
strikes, we must seek a better understanding of them. This genome
project will provide a major step in that direction.
JGI researchers have also
been analyzing the DNA of various lactic acid bacteriathat
is, bacteria that ferment sugars into lactic acidto help food
scientists enhance the preservation and safety of fermented foods.
Not only are these probiotic, or good, bacteria important in food
production, but they can also contribute to the health and balance
of the intestinal tract and to fighting illness and disease. The
JGI has sequenced the genomes of 11 lactic acid bacteria targeted
by the Lactic Acid Bacteria Genome Consortium, a group of molecular
scientists from a dozen U.S. universities.
In early October, scientists
from around the nation gathered at JGI to examine the genomes of
nine of these economically and scientifically important microbes.
David Mills, a food microbiologist and assistant professor of viticulture
and enology at the University of California at Davis, said that
looking at these bacteria would help food producers use their genetic
traits to make better products as well as to retard or prevent food
spoilage. Furthermore, he said, To our knowledge, no one has
ever sequenced such a large number of genetically related microbes
before. This gives us an unprecedented opportunity to learn about
genome evolution within a defined, related group.
Contact: Charles Osolin (925) 296-5643 (firstname.lastname@example.org).
water holds clues about climate change
Climate scientists from the
Laboratory are making progress toward reconstructing past climate
from the chemistry of water moving through the vadose zone, the
region between the land surface and groundwater aquifers. In their
initial studies, the researchers needed to confirm a long-held assumption
that water migrating to deep water tables may be 10,000 to 100,000
years old. Then they needed to determine how large an effect changes
in surface temperature and rainfall amountsthat is, climatemight
have on water chemistry.
To resolve these issues,
they used supercomputers to simulate the chemical interaction of
water with the rocks through which it migrates. The changing type
and abundance of minerals in rocks affect the chemical composition
of the water as it flows through. Scientists can determine the chemistry
changes along the path of the water flow as a function of flow rate.
In arid environments where water tables are hundreds of meters deep,
scientists have assumed that it would take tens of thousands of
years for surface water to reach the water table. The simulations
confirmed that and also showed that climate changes had a measurable
effect on water chemistry, even after thousands of years and after
migrating hundreds of meters through the vadose zone.
What this implies in
principle is that one could use a combination of water temperature,
water chemistry, abundance of water, and isotopic signatures to
reconstruct past climate conditions on a regional scale on most
continents. This is one of the things needed to test and verify
global climate change models, says William Glassley, leader
of the research team.
To go forward in interpreting
the climate record, the researchers need to conduct highly detailed
computer simulations using a vast amount of rock property data that
are not usually measured. They also need to obtain some as yet unestablished
property data, such as how much surface area of a mineral a migrating
water would travel through. But their progress indicates that they
soon will be able to reconstruct a 100,000-year-old climate record.
Contact: William Glassley (925) 422-6499 (email@example.com).
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January 10, 2003