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The Laboratory
in the News

An improved measure of DNA damage
A team of Livermore researchers led by Paul Henderson of the Chemistry, Materials, and Life Sciences Directorate reported a new understanding of how damaged nucleic acid is incorporated in DNA and subsequently repaired. The findings—which resulted from a study using accelerator mass spectrometry (AMS)—were featured on the cover of the July 3, 2007, issue of the Proceedings of the National Academy of Sciences.
AMS allows patients or cells to be dosed with tiny amounts of radioactive compounds that can be traced in vivo or in vitro without disturbing normal metabolic processes. In this study, which was funded by the National Institutes of Health and the California Breast Cancer Research Program, researchers tagged human breast cancer cells with carbon-14 to track how living cells process oxidized guanosine (8-oxodG), a precursor to one of the most prevalent forms of DNA damage. If not repaired, the damaged DNA can cause cell mutations.
The sensitivity of AMS allowed the researchers to measure the 8-oxodG incorporated into DNA even though the amount in some cells was less than one atom of carbon-14. This minute quantity is too small to be characterized using standard non-AMS methods. Nevertheless, it was orders of magnitude higher than the researchers expected.
In this study, the Livermore team established the mechanism by which 8-oxodG is metabolized. The team hopes that scientists can use this new understanding of mutagenesis to develop treatments aimed at reducing cancer mutation rates.
Contact: Paul Henderson (925) 423-2822 (henderson48@llnl.gov).

Climate models reflect observed ocean temperatures
A study by Laboratory scientists in the Program for Climate Model Diagnosis and Intercomparison in collaboration with colleagues at Scripps Institution of Oceanography shows that climate models are reliable tools for helping researchers better understand the observed record of ocean warming and variability. Results from this collaboration appeared in the June 26, 2007, issue of the Proceedings of the National Academy of Sciences.
The observational record shows substantial variability in ocean heat content over time scales ranging from several years to decades. The Livermore–Scripps team demonstrated that climate models represent this variability much more realistically than previously believed. Using 13 numerical climate models, the researchers found that the apparent discrepancies between modeled and observed variability can be explained by accounting for changes in observational coverage and instrumentation and by including the effects of volcanic eruptions.
The research also casts doubt on recent findings that the 0- to 700-meter layer of the global ocean cooled markedly from 2003 to 2005. Results indicate that the perceived cooling is largely an artifact of a systematic change in the observing system. Previous studies combined ocean temperature observations from several types of instruments, and the averaged measurements indicated an apparent cooling trend. When the Livermore–Scripps researchers looked at readings from individual instruments, they found no cooling. When the climate models included the cooling effects of intermittent volcanic eruptions, modeling results agreed even more closely with observations.
Contact: Benjamin Santer (925) 422-2486 (santer1@llnl.gov).

Laboratory signs technical agreement with BP
Lawrence Livermore has partnered with BP (formerly British Petroleum) to provide technical expertise in developing underground coal gasification (UCG) technology to convert in situ coal deposits into fuels and other products. In a technical cooperation agreement signed in July, Livermore agreed to work with BP to address three areas of UCG technology: determining the feasibility of storing carbon dioxide underground; assessing the environmental risks associated with UCG and developing methods to mitigate those factors; and modeling UCG processes to evaluate test results over time.
Underground coal gasification offers the potential to produce fuels and hydrocarbon feedstock from coal deposits that otherwise cannot be recovered. Introducing a controlled supply of air or oxygen into a coal seam produces syngas, which can be pumped to the surface. The recovered syngas can be used as fuel to generate power or as feedstock to produce chemicals and other hydrocarbon products. Additionally, the carbon dioxide produced in the UCG process can be captured and pumped into the excavated coal seam or into a nearby formation. This capability could dramatically reduce carbon dioxide emissions, which have been linked to global climate change.
Livermore has worked on developing UCG technology for more than 30 years. In the partnership with BP, Laboratory researchers will provide their expertise in advanced computation and modeling, engineering, environmental management, and carbon management, including carbon sequestration.
Contact: Julio Friedmann (925) 423-0585 (friedmann2@llnl.gov).

Detailing algae’s role in nutrient cycle
Scientists from Lawrence Livermore, Portland State University, and the University of Southern California used nanometer-scale secondary-ion mass spectrometry (NanoSIMS) to image and track nutrient uptake in blue-green algae. Blue-green algae are key players in global nutrient cycling. They take in, or fix, nitrogen gas from the atmosphere and convert it into a usable nutrient, enabling photosynthesis in nutrient-poor waters. The bacteria fix both nitrogen and carbon, an intriguing capability. Fixing carbon dioxide during photosynthesis produces oxygen, which inhibits nitrogen fixation. Each blue-green algae species solves this problem in its own way, and many of the methods are poorly understood. The collaboration, which includes Livermore researchers Peter Weber, Jennifer Pett-Ridge, Stewart Fallon, and Ian Hutcheon, focused on the freshwater algae Anabaena oscillariodes, a species that separates the two processes into adjacent cells.
NanoSIMS allows researchers to map distributions of elements and isotopes to a resolution of 50 to 100 nanometers. The research results, published in the August 2007 issue of the International Society for Microbial Ecology Journal, demonstrate that the technique could effectively track the uptake and movement of carbon and nitrogen in two cell types in the algae: carbon-fixing vegetative cells and nitrogen-fixing heterocysts. “We can see cell by cell how newly fixed nitrogen is rapidly exported from the heterocysts to vegetative cells, keeping pace with the nitrogen demands of the growing and dividing vegetative cells,” says Weber. “Now, we can take these results and apply them to poorly understood species.”
Contact: Peter Weber (925) 422-3018 (weber21@llnl.gov).

Dusty mirror experiment inspires new research
A group of researchers at Lawrence Livermore and several American and European institutions have developed a technique for observing the x-ray-induced explosion of microscopic objects. In an experiment using FLASH, the soft x-ray free-electron laser in Hamburg, Germany, the researchers placed an x-ray mirror a short distance behind a spherical plastic target. An x-ray laser pulse directed at the target blows up the plastic sphere and then bounces off the mirror, allowing the researchers to look at the sphere after it explodes. The resolution for this experiment is greater than 3 femtoseconds. Light passing through the sphere combines with light bouncing from the mirror back through the object and causes interference, which forms a hologram, or three-dimensional image, of the object. With this setup, the team can study material dynamics under the extreme conditions created by an intense laser pulse, both during the pulse and as it turns into plasma.
“From previous work at FLASH, we know the target does not explode during the initial 25-femtosecond pulse, which forms the known reference wave of the hologram,” says Livermore physicist Henry Chapman. “We can thus use the reference wave to determine the unknown object wave, which is actually the same object but a few femtoseconds later.”
The experiment design was inspired by Chapman’s visit to the Chabot Space and Science Center in Oakland, California. An optics exhibit at the science museum demonstrated Sir Isaac Newton’s dusty mirror experiment, in which Newton made one of the earliest observations of interference. Chapman realized that his group could create the same effect using laser pulses and x-ray mirrors. The research, which appeared in the August 9, 2007, edition of Nature, is part of a Laboratory Directed Research and Development project to develop the technique and determine the feasibility of single-molecule imaging experiments to be performed at Stanford’s Linac Coherent Light Source.
Contact: Henry Chapman (925) 423-1580 (chapman9@llnl.gov).

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UCRL-52000-07-10 | October 11, 2007