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December 7, 2000

New institute integrates powerful tools of physical, mathematics, and engineering sciences with biomedical research

By Elizabeth Irwin, UCSC; Bill Gordon, UCSF; and Catherine Zandonella, UCB

UC Santa Cruz will play a key role in one of three new California Institutes for Science and Innovation established today (December 7) by Governor Gray Davis. The Institute for Bioengineering, Biotechnology and Quantitative Biomedical Research (QB3) will be centered at UC San Francisco with major research components at UC Santa Cruz and UC Berkeley.

The institute promises to lead the next revolution in biomedical research. It will integrate physical, mathematical, and engineering sciences to create powerful new techniques for attacking biological problems of such enormous complexity that they have simply remained unapproachable--until now. This integration of sciences could open the way for discovery of treatments and cures for some of our most intractable diseases, such as brain disorders, cancer, and diabetes.

UC Santa Cruz is also a partner in a fourth institute that Gov. Davis said he would urge the state legislature to fund next year. (See Governor Davis's press release.) The Center for Information Technology Research in the Interest of Society (CITRIS) will be headquartered at UC Berkeley, with partners at UCSC, UC Davis, and UC Merced.

The QB3 institute will foster new technology and collaborations for projects such as development of artificial tissues that mimic those found in the human body, to be used to make replacement blood vessels, bone implants, and synthetic replacement organs. Better imaging techniques and computer-assisted analysis developed at the institute will improve the detection and treatment of diseases such as prostate and breast cancer.

Another focus will be bioinformatics--computing methods to sift through the volumes of data generated by the human genome project and other new developments in biomedical research. Bioinformatics includes techniques that may allow scientists to do experiments on computers rather than in the lab. The institute's bioinformatics program will be based at UC Santa Cruz.

"The sequencing of the human genome and other advances in molecular genetics have ushered in an exciting and promising new era in biomedical research," said UCSC Chancellor M.R.C. Greenwood. "Through creative interdisciplinary collaborations, this institute will deliver new discoveries, new products, and new technologies for the benefit of human health, and we are very pleased that some of the research strengths of UC Santa Cruz will contribute."

Each of the three partner campuses brings unique strengths to the institute. UCSF is a world-wide leader in biomedical research, with strong programs in both fundamental biological research and in research directly related to disease. UCSC is internationally recognized as a leader in the mathematical and computer sciences related to genomics. And UC Berkeley will provide expertise in both the biological sciences and in analytical fields including physics, chemistry, engineering, and computer science.

"This institute will represent an unprecedented collaboration among the three campuses, breaking down the traditional boundaries of scientific disciplines. The result should be a greatly enhanced understanding of the human organism, new approaches to the prevention and treatment of disease, and powerful stimuli to the economy of California," said UCSF Chancellor J. Michael Bishop.

UC Berkeley Chancellor Robert M. Berdahl said, "Tackling today's most challenging health problems requires scientists and scholars from many fields building upon one another's expertise. This institute does just that. Equally important, it will help us to train students to excel in this new way of doing health science research."

Organized around three research and education modules--Bioengineering and Biotechnology, Structural and Chemical Biology, and Bioinformatics and the Analysis of Complex Biological Systems--the institute will focus on developing techniques for storing and analyzing vast quantities of biological information and using imaging and mathematical modeling to view molecules, cells, and single organ systems as parts of functional networks. These technologies will allow scientists to understand interactions and predict outcomes and to reconstruct parts of living systems in the laboratory to improve human health.

The sequencing of the human genome is one of several major advances that are revolutionizing biomedical research. Genome sequencing and other "high-throughput" investigative techniques, such as DNA "chips" or microarrays, are enabling scientists to gather enormous amounts of data on gene regulation, protein interactions, and other aspects of the intricate biomolecular ballet that makes life possible.

These powerful techniques, however, present major computational challenges because they generate such large and complex datasets. The field of bioinformatics has emerged to meet those challenges, applying advanced information technology to complex problems in biology. QB3's Bioinformatics module will provide the mathematical and computational expertise essential for much of the institute's work.

"As experimental methods become more sophisticated and the amount of data skyrockets, the role for bioinformatics is dramatically expanding," said David Haussler, professor of computer science and director of the Center for Biomolecular Science and Engineering at UC Santa Cruz.

Haussler, who holds a UC Presidential Chair and is a Howard Hughes Medical Institute Investigator, is a codirector of the institute. He and his colleagues at UCSC have played a key role in the Human Genome Project, assembling the first publicly available working draft of the human genome sequence. They have also designed a web-based human genome browser that investigators can use to view genes and regions of interest on the assembled genome together with related information in other databases. The web site has drawn the attention of biomedical researchers worldwide. On a typical day, the site receives more than 10,000 requests for information. Researchers are using it to find genes that may someday lead to new treatments for disease.

The use of human genomics in the development of new drugs and new diagnostic tools will undoubtedly require new computational methodologies. The institute will provide unique opportunities for collaborative efforts in these areas, Haussler said.

"Bioinformatics has applications ranging from basic molecular biology to clinical diagnostics and medical imaging. Through the institute, top researchers in all these areas from the three UC campuses will join forces to develop novel technologies for the diagnosis and treatment of diseases," Haussler said.

QB3 will occupy 90,000 square feet of the first building at the new UCSF Mission Bay campus, now under construction about a mile south of San Francisco's Financial District. The 43-acre teaching and research campus is expected to attract one of the nation's most important concentrations of biotechnology and life sciences companies to a private research and development zone surrounding the site. The UCSF buildings will house the Instituteís Bioengineering and Biotechnology module and will include a High-field Magnetic Resonance Imaging system that will be the most powerful in the state and promises to serve as a unique regional resource.

The institute's multidisciplinary approach to health science also complements UC Berkeley's ambitious $500 million Health Sciences Initiative, which seeks to advance health science research through collaboration. The Berkeley campus plans to use QB3 funding to build a new research facility, the first building on campus dedicated to multidisciplinary health sciences research.

At UC Santa Cruz, the Institute's Bioinformatics and Analysis of Complex Biological Systems module will be housed in 11,250 square feet of a new Physical Sciences Building, scheduled for completion in 2002, and in the Baskin Engineering Building.

"Promising advances that will benefit human health in ways we can only imagine today, the QB3 Institute will generate new breakthroughs in science, and will also contribute dramatically to the 21st-century economy. The bioinformatics research strengths of UC Santa Cruz provide a unique and integral element for the new institute," said Gordon Ringold, CEO of Surromed and a UCSC alumnus.

David Agard, a Howard Hughes Medical Institute Investigator and UCSF professor of biochemistry and biophysics, will direct the institute, and the codirectors will be Haussler and Graham R. Fleming, UC Berkeley professor of chemistry and director of the Physical Bioscience Division at Lawrence Berkeley National Laboratory.

As one of three UC institutes selected by the Governor, QB3 will receive state funds totaling $100 million across the three campuses. For every dollar from the state, the institute will provide $2 of outside funding, mainly from private donors.

CITRIS, the fourth institute which Gov. Davis hopes will be funded next year, aims to bring the benefits of information technology to challenging problems in areas such as transportation, education, emergency preparedness, and health care.

"This project is about solving society's most challenging problems, about improving the quality of people's lives," said UC Berkeley Chancellor Berdahl.

"There will be a lot of very interesting technology springing out of CITRIS that will benefit all areas of society," added Richard A. Newton, dean of the UC Berkeley College of Engineering and a professor of electrical engineering and computer sciences.

A small-scale prototype of one type of system envisioned by CITRIS was developed at UCSC. The Real-time Environmental Information Network and Analysis System (REINAS) gathers data on the Monterey Bay coastal environment from an extensive network of remote sensors, stores it in a distributed database, and displays data on command via powerful graphics techniques. With REINAS, weather forecasters and environmental scientists can observe, monitor, and analyze regional oceanographic and meteorological phenomena in real time from their desktops.

Systems based on the REINAS model have a wide range of potential applications, said Patrick Mantey, dean of UCSC's Baskin School of Engineering, who directs the REINAS project.

"In this case it's environmental conditions in Monterey Bay, but it could just as well be traffic patterns or earthquake information," Mantey said.

In addition to UCSC researchers, REINAS also involves scientists at the Naval Postgraduate School and the Monterey Bay Aquarium Research Institute.

Business and private donors have pledged CITRIS more than $173 million over four years, including nearly $50 million from industry and $124.5 million in individual donations. Along with the $100 million from the state and an expected $83 million in private and federal research grants and contracts, CITRIS would receive total funding of more than $356 million over four years. Among the 13 corporate sponsors are Intel Corp., Microsoft Corp., Nortel Networks Corp., and Sun Microsystems, Inc.


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