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December 2002

The Laboratory
in the News

Commentary by
Jay Davis

Emerging from the Cold War: Stockpile Stewardship and Beyond

Machines from Interlocking Molecules

Laser Zaps Communication Bottleneck




The Laboratory
in the News

Sequencing 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, October 2002, Applied Science Is a Hallmark of This Laboratory.) They then went on to map the DNA of a diminutive, fast-growing African frog, Xenopus tropicalis.
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 bacteria—that is, bacteria that ferment sugars into lactic acid—to 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 (

Migrating 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 amounts—that is, climate—might 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 (



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UCRL-52000-02-12 | January 10, 2003