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The Laboratory
in the News

Lab garners four R&D 100 Awards
Livermore researchers turned in a strong showing in the annual R&D 100 awards competition for top industrial inventions, winning four awards. Each year, R&D Magazine presents these awards to the top 100 industrial, high-technology inventions submitted to its competition for outstanding achievements in research and development.
The four Livermore inventions honored are as follows:
• Biological Aerosol Mass Spectrometry system, which is an instrument that can analyze individual aerosol particles in real time and at high rates to almost instantly identify the presence and concentration of harmful biological particles in air samples.
• Adaptable Radiation Area Monitor, which could play an important role in protecting the nation from radiological or nuclear attack. The highly sensitive system uses a thallium sodium iodide crystal to detect small amounts of nuclear material in a number of different applications. Livermore researchers and Innovative Survivability Technologies of Goleta, California, share this R&D 100 Award.
• NanoFoil®, which is a nanoengineered heat source that heats only the interface being joined and permits large and small components to be metallically bonded with no thermal damage. NanoFoil is sold by Reactive NanoTechnologies of Hunt Valley, Maryland, for a variety of commercial applications. Reactive NanoTechnologies shares this award with Livermore researchers and Johns Hopkins University.
• VisIt, which is a visualization tool for the parallel processing of large amounts of data, including simulations comprising trillions of bytes of data. To date, 4,000 users from throughout the world have downloaded this free, interactive tool.
S&TR’s October issue will feature detailed reports on these award-winning inventions and the teams that created them.
Contact: Ron Franck (925) 422-9977 (franck1@llnl.gov).

New bioinformatics method for analyzing DNA
Scientists at Lawrence Livermore and the Linnaeus Centre for Bioinformatics at Uppsala University in Sweden have developed a new bioinformatics technique for systematically analyzing key regions in DNA that help control gene activity.
Understanding the complex regulatory mechanisms that tell genes when to switch on and off is one of the toughest challenges facing researchers attempting to discover how life works. Binding sites, or areas of DNA that interact with proteins to help control gene expression, can be a long distance on the DNA strand from the genes they influence. In addition, gene expression can be controlled by several regulatory proteins working together at a combination of different binding sites. These regulatory proteins are known as transcription factors. Transcription is the first step in the process by which the genetic information in DNA is decoded by the cell to manufacture proteins, the building blocks of life.
The project’s goal was to deduce how many transcription factors at a time, or combinations of factors, are coming together physically and how these combinations regulate genes. The researchers mathematically modeled general rules that could associate known binding sites and gene expression in yeast, which is one of the most widely studied organisms. “The next step,” says Krzysztof Fidelis, a computational biologist in Livermore’s Biosciences Directorate, “is to test this approach on different organisms, including microbes and vertebrates.”
Other institutions collaborating on the project were Warsaw University in Poland and the Polish Academy of Sciences. A report on the joint work appears in the June 2005 issue of Genome Research. Primary funding for the research was provided by Livermore’s Laboratory Directed Research and Development Program, the Knut and Alice Wallenberg Foundation, and the Swedish Foundation for Strategic Research.
Contact: Krzysztof Fidelis (925) 423-4752 (fidelis1@llnl.gov).

Trigger for rare bone disease found
A research team from Lawrence Livermore and Lawrence Berkeley national laboratories, the Novartis Institutes for BioMedical Research in Switzerland, and the Department of Energy’s (DOE’s) Joint Genome Institute in Walnut Creek have tracked down the biological trigger that gives rise to Van Buchem disease. This hereditary, disfiguring bone disorder can cause blindness and deafness. In June 2005, the research team, led by Gabriela Loots of Livermore’s Genome Biology Division, reported its findings in the online version of Genome Research.
The team found the culprit is a regulatory element in a missing 52,000-base-pair stretch of DNA. This segment of DNA normally directs the sclerostin, or SOST, gene to produce a protein that maintains control of bone formation rates. Without this regulator, bone production goes up, progressively increasing bone density, or osteosclerosis.
Noncoding DNA segments—long stretches of DNA that do not code for proteins and were once thought to have no biological function—are now being found to contain regions that play a key role in switching distant genes on and off. Loot’s study is one of the first to pinpoint a disease-associated mutation that alters one of these long-range regulatory elements.
To locate the specific enhancer sequence responsible for SOST regulation, the team compared human and mouse DNA and found seven common segments within the 140,000-base-pair SOST region. Scientists assume DNA segments that have been “conserved” from one organism to another during evolution play a biological role, or they would have been discarded as organisms evolved. By introducing the conserved segments into cells similar to osteoblasts (bone-forming cells), the team found that a 250-base-pair conserved region named ECR5 was able to drive SOST expression.
The findings provide insight into long-range gene regulation and could lead to new treatments for osteoporosis and other crippling bone disorders. Funding for the research was provided by DOE’s Office of Science and by the National Institutes of Health.
Contact: Gabriela Loots (925) 423-0923 (loots1@llnl.gov).

BlueGene/L retains Top500 ranking
Livermore’s BlueGene/L reaffirmed its ranking as the world’s most powerful computer on the Top500 list, the leading industry authority for high-performance computing. The Top500’s new list was announced June 22 at the 2005 International Supercomputing Conference in Heidelberg, Germany. IBM’s BlueGene/L system, developed in partnership with the National Nuclear Security Administration (NNSA) and with the collaboration of Livermore scientists, demonstrated a sustained performance of 136.8 trillion operations per second (teraops) on the industry standard LINPACK benchmark. The Laboratory’s Thunder machine is seventh on the list, with a sustained performance of 19.94 teraops.
Researchers are running science applications with BlueGene/L’s 32 racks—half the final 64-rack configuration. “Even as we are bringing the machine to its full configuration, we are doing science critical to NNSA’s mission to ensure the safety, security, and reliability of the nation’s nuclear stockpile,” says Dona Crawford, associate director for Computation. “This represents a great team effort led by NNSA’s Advanced Simulation and Computing (ASC) Program. Working with our partners at IBM and Los Alamos and Sandia national laboratories, we are simultaneously advancing scientific discovery and the high-performance computing that makes it possible. The capabilities we are now beginning to apply to our national security missions will also be applicable to other domains.”
According to Dimitri Kusnezov, director of the NNSA ASC Program, “Once complete, NNSA will have available the kind of national security tool needed to rapidly analyze urgent nuclear weapon stockpile aging issues. It will be used to run a broad range of simulation codes that support certification of our stockpile.
Contact: Dona Crawford (925) 422-1985 (crawford13@llnl.gov).

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UCRL-52000-05-9 | September 6, 2005