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The Laboratory
in the News

Gene expression from extreme environments
In a collaboration involving Lawrence Livermore and Oak Ridge national laboratories, the University of California (UC) at Berkeley, and Xavier University in New Orleans, researchers are finding that communities of microorganisms are assembled from several disparate organisms that function together to survive. That is, microorganisms will adapt to extreme conditions, such as high temperature and toxicity, by evolving to specialize and cooperate with each other. The research team, led by UC Berkeley professor Jill Banfield, examined more than 2,000 proteins produced by five species in a community that thrives in the hot, highly acidic conditions of an abandoned mine at Iron Mountain, California.
“We found large numbers of proteins that don’t resemble any other proteins we know about,” says team member Michael Thelen, a protein biochemist in Livermore’s Biosciences Directorate. “Also, many of these proteins are enzymes whose main function is to maintain the correct structure of other proteins exposed to this harsh environment.”
The complex interaction of microbes, water, and exposed ore at the mine has generated dangerously high levels of sulfuric acid and toxic heavy metals. The microorganisms found there—called extremophiles for their affinity to harsh environments—grow as densely packed pink biofilm that floats on the mine water’s surface. The millimeter-thick biofilm is a self-sustaining system, using carbon and nitrogen from the atmosphere within the mine and deriving energy from the iron that has leached from the iron sulfide rock.
The team’s results, published in the June 24, 2005, issue of Science, indicate that many functions, such as nitrogen fixation, are handled by specialized microbes. Thelen adds that studies such as this one will help researchers learn how biofilm functions in different environments, what mechanisms are involved in assembling microbial communities, and how metabolic tasks and resources are partitioned.
Contact: Michael Thelen (925) 422-6547 (mthelen@llnl.gov).

Measuring the composition of Titan’s atmosphere
Livermore is collaborating with the National Aeronautics and Space Administration (NASA), the University of British Columbia (UBC), and NASA’s Jet Propulsion Laboratory (JPL) to measure the temperature, winds, and chemical composition of Titan’s atmosphere. Led by principal investigator F. Michael Flasar of NASA’s Goddard Space Flight Center, the team is using the Cassini Composite Infrared Spectrometer (CIRS) on the Cassini-Huygens spacecraft to record data from Titan’s atmosphere.
CIRS measures the intensity of far-infrared radiation, light with wavelengths between those of radar and near-infrared light. The abundance of methane in Titan’s atmosphere is determined by comparing the intensity of spectral emission lines from the atmosphere with laboratory measurements. Livermore physicist Edward Wishnow measured the spectrum of methane at temperatures and densities similar to Titan’s—about 113 kelvins and about 1 atmosphere of pressure. Because the laboratory absorption spectra correspond well with the Titan spectral lines, the laboratory results can be used to determine the amount of methane in Titan’s upper atmosphere. UBC scientists Herbert Gush, Irving Ozier, and Mark Halpern collaborated on the laboratory work, and JPL scientist Glenn Orton helped interpret the data.
Titan is the only moon in the solar system with a substantial atmosphere, and that atmosphere is primarily composed of nitrogen, making it similar to Earth’s. Scientists want to study Titan’s atmosphere because the organic chemistry occurring there is analogous to the processes that may have occurred in the early terrestrial atmosphere. CIRS observations of Titan’s stratosphere also indicate that its winter (northern) pole has many properties in common with Earth’s. Titan’s cold temperatures, strong circumpolar winds, and concentrations of several compounds are analogs to the polar winds and ozone hole on Earth. Both also have strong winds that isolate the polar air and inhibit mixing with air at lower latitudes.
Cassini-Huygens is an international collaboration between NASA and the European and Italian space agencies. Cassini is the first spacecraft to explore the Saturn system of rings and moons from orbit. Results from the team’s research appeared in the May 13, 2005, issue of Science.
Contact: Edward H. Wishnow (925) 422-7208 (wishnow@llnl.gov).

New approach to the study of microbes
Scientists from the Department of Energy’s Joint Genome Institute have developed an approach that uses information-rich snippets of DNA from Minnesota farm soil and whalebones recovered from a mile underwater to analyze terrestrial and aquatic habitats. Called environmental genomic tags (EGTs), these indicators capture a DNA profile of a particular niche and reflect the presence and levels of light, nutrients, pollutants, and other features. Led by JGI scientist Susannah Green Tringe, the researchers compared the DNA pieces to determine site-specific motifs. Then they used this information to detect environments under stress and evaluate the progress of remediation efforts.
The abundances of genes in the EGT data reflect the demands of a particular setting. For example, genes involved in breaking down plant material are overrepresented in soil and absent in seawater. In seawater, genes involved in the passage of sodium, a major chemical component of salt water, are particularly abundant. By evaluating the EGT data, scientists can determine what is happening in an environment without identifying the microbes that live there.
A report on the team’s research appeared in the April 22, 2005, issue of Science.
Contact: Art Kobayashi (925) 296-5765 (akobayashi@llnl.gov).

Human effects on global climate
A joint study by scientists in the Laboratory’s Program for Climate Model Diagnosis and Intercomparison (PCMDI) and at the Scripps Institution of Oceanography concluded that the warming of the world’s oceans is a clear signal of human effects on global climate. The recent study—which also involved scientists at the University of Reading and the National Center for Atmospheric Research—compared climate model simulations with observed estimates of how ocean temperatures changed over the second half of the 20th century. Previous research had linked recent ocean warming to human activities, and the new work significantly strengthens this conclusion.
The study focuses on the complex vertical structure of ocean warming and shows that computer models capture this structure if they are run with natural external forcings (solar irradiance and volcanic aerosols) combined with changes in human-induced forcings (well-mixed greenhouse gases, ozone, and sulfate aerosols). Models run with natural forcings alone do not explain the observed ocean warming. Results from this project appeared in the July 8, 2005, issue of Science Express.
The researchers used fingerprinting, a technique for determining how different climate forcings affect temperature. A climate model provides the physically based estimates of the shape, size, and evolution of the fingerprint. Researchers then compare the model fingerprint to past records of observed climate. In the PCMDI–Scripps study, the models depicted a warming signal in the upper 700 meters of the major ocean basins, which correlates well with past measurements of observed climate. Because the simulations reproduce the structure in such fine detail, the researchers concluded that the models are capturing the physical mechanisms involved in the penetration of the ocean warming signal.
Contact: Benjamin Santer (925) 422-2486 (santer1@llnl.gov).

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UCRL-52000-05-7/8 | July 8, 2005