News Archives

A New Guide to Exploring the Protein Universe
March 31, 2005: Sung-Hou Kim, a chemist who holds a joint appointment with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Chemistry Department, has constructed a protein-structure space map (SSM) based on the distribution in 3-D space of the 1,898 known unique protein structures. "Because proteins with similar structures and functions are clustered together in the SSM," Kim says, "when the structure of a new protein is first identified it can be placed in the appropriate location on the map to reveal its neighbors and its evolutionary history." Theinformation can then be used to predict the protein's function when it cannot be predicted from amino acid sequence information or structural similarity, the two most commonly used methods. The new method improves on previous protein mapping techniques by looking not only at architectural domains, but also protein structures that may contain more than one domain. Read the full story in Science@Berkeley Lab.

Holbrook Receives DOE Outstanding Mentor Award
March 15, 2005: Physical Bioscientist Stephen Holbrook received a 2004 DOE Outstanding Mentor Award for his continuing mentorship of DOE program students. Dr. Holbrook has been working with undergraduates for the past five years, through such programs as SULI, CCI, and PST. Dr. Holbrook received the award at a special ceremony in March, along with four other Berkeley Lab members. In addition to his regular research and mentoring responsibilities, Dr. Holbrook is an active member of Berkeley Lab’s Diversity Council, which makes recommendations to the Lab leadership for creating a world-class work environment that can recruit and retain a workforce reflecting the diversity of the local community and the nation.

A new home for Synthetic Biology
Berkeley Lab and UC Berkeley have joined forces to establish a multidisciplinary research facility in synthetic biology, cell and molecular biology, cancer research, and quantitative biology. The 72,000 square-foot space, with its excellent laboratory facilities and prime location in the heart of the Bay Area bioscience hub, is perfectly suited to the technical demands of today’s biosciences. The facility also represents a major step in consolidating and strengthening the Division's efforts to continue delivering on the promises of synthetic biology. More about the biosciences center -->

Fleming named Deputy Director of Berkeley Lab
February 18, 2005: Lab director Steve Chu has chosen internationally recognized spectroscopist and Physical Biosciences division director Graham Fleming to be his deputy director. "Graham will be working closely with me on scientific policy and program development,” said Chu, “as well as on more fully integrating operations and administration activities with the scientific programs."

Fleming will succeed Pier Oddone, who announced in December that he will leave this spring to become Fermilab’s fifth director. This and other changes in the Lab's leadership come as the University of California and Berkeley Lab recently submitted their proposal to the Source Evaluation Board to continue their management partnership for the Department of Energy.

A distinguished researcher, teacher and administrator both here and on the UC Berkeley campus since 1997, Fleming is a world leader in the field of time-resolved spectroscopy. His campus service has included positions as co-director of the California Institute for Quantitative Biomedical Research (QB3), and faculty lead and advisor to the chancellor on the Stanley Hall replacement building. Berkeley Lab plans to be involved in both projects.

At a Division Town Hall meeting on March 4, Division Deputy Heinz Frei thanked Fleming on behalf of the entire division for his leadership and successes in the eight years since he established the Physical Biosciences Division, which has grown incredibly both in terms of people and programs. More on the Lab's leadership changes is found in the Berkeley Lab View.

02/05/05. Computational and theoretical biologist Gavin Crooks joined the Physical Biosciences Division this week as Divisional Fellow. Crooks accepted the position from Director Graham Fleming, who noted that "Gavin will provide a superb theoretical complement in a wide range of PBD experimental programs, such as our world-leading single-molecule studies." Crooks comes to PBD from the Computational Genomics Research Group at UC Berkeley, where as postdoctoral fellow he collaborated with PBD scientists Steven Brenner and Stephen Holbrook, among others. Crooks is interested in the stochastic dynamics of biological systems, especially those that cannot be described by equilibrium statistical mechanics or studied using traditional computational simulations. Said Crooks: "I'm excited to be a part of a division with so many esteemed colleges, and I look forward to many fruitful collaborations and discussions." More about Crooks' research can be found at http://threeplusone.com. Welcome, Gavin!

01/25/05. The New York Times reports on the battle against malaria. Reporter Donald G. McNeil, Jr. explains how researchers like Jay Keasling are fighting to save millions of lives by creating next-generation malaria drugs via synthetic biology. The January 25, 2005 article discusses the challenges of creating the perfect medicine, which must be "powerful enough to kill a parasite that can twist a capillary-surfing red blood cell into a clotted lump, but still safe enough to give to a malnourished child whose hospital is a mud hut and whose nurse is a fretful mother who cannot read." Keasling and others are racing to bring the high-tech drugs to the developing world at a mere 25 cents per treatment, while malaria becomes increasingly resistant to current treatments. NY Times article about malaria (login required) -->

01/20/05. PBD researchers have solved an important mystery in how plants protect themselves from excess radiation. The research, led by Graham Fleming, identified one of the key molecules that help protect plants from oxidation damage as the result of absorbing too much light. Fleming, along with Kris Niyogi, Nancy Holt, and others in the Fleming Lab, determined that when chlorophyll molecules in green plants take in more solar energy than they are able to immediately use, molecules of zeaxanthin, a member of the carotenoid family of pigment molecules, carry away the excess energy. The results are reported in the January 21, 2005 issue of the journal Science. details about the Fleming discovery -->

01/10/05. Carlos Bustamante, head of the Advanced Microscopies Department, received received the Richtmyer Award for conveying physics to public audiences at the January 10 meeting of the American Association of Physics Teachers (AAPT). Bustamante, who is also a Howard Hughes Medical Institute Investigator and UC Berkeley professor of molecular and cell biology, physics and chemistry, has worked on new methods of manipulating just one molecule at a time, and is the creator of optical tweezers, which use light to move objects as small as a single atom. The Richtmyer Award, which includes a gift of $7,500, is named after Floyd K. Richtmyer, a distinguished physicist, teacher, and administrator who served the physics community in many ways. read UCB press release -->

12/17/05. Research led by Synthetic Biology Department head Jay Keasling resulted in the creation of a simple and much less expensive means of making one of the most promising and potent of all the new anti-malarial drugs. This, in turn, has led to an announcement from the Bill & Melinda Gates Foundation of a $42.6 million grant to take Keasling’s development to the production level. The ultimate payoff will be an affordable, accessible cure for malaria, a disease that kills more than a million children each year. Read about the Gates Foundation award in the Berkeley Lab View

09/30/04. Working through Synthetic Biology Department Head Jay Keasling, UC Berkeley signed a landmark agreement with the Samoan government for exclusive rights to a native tree with enormous therapeutic potential as an anti-AIDS drug. Under this agreement, Keasling and his research group will seek to genetically engineer a strain of E. coli bacteria that can cheaply synthesize and mass-produce prostratin, the chemical compound that comes from the mamala tree. The drug currently is being studied by scientists around the world because of its potential to force the AIDS virus out of hibernation in the body's immune cells and into the line of fire of anti-AIDS drugs now in use. Read the full article in the Berkeley Lab View -->

09/24/04. Using a computational analysis of crystallographic data, Paul Adams has visualized the dynamic changes the chaperonin GroEL undergoes while helping proteins in the cell fold correctly. In doing so he has outlined a method for revealing the motions of molecular machines while they do their work. As a result of stresses such as heat shock, a protein can lose its natural fold, enabling it to aggregate with other unfolded proteins. If this process isn't combated then cells die. Chaperonins are proteins found in everything from microbes to humans, that come to the rescue to help mis-folded proteins regain their correct fold so they can work properly within the cell. Paul Adams and his collaborators examined crystallographic data from the chaperonin GroEL, found in E. coli, and were able to extract information about the large scale motions of the molecule during different stages of its reaction cycle. These results derived from experimental data are similar to those that previously could only be predicted by computational modeling studies. The technique may provide a method for examining other large complexes to further our understanding of molecular machines. The full results of Adams’ study are published in the September 3rd 2004 issue of the Journal of Molecular Biology.

PBD scientist Kimmen Sjölander is being honored along with two other LBNL scientsts with the nation's highest award for scientists at the early stages of their careers — 2003 Presidential Early Career Award for Scientists and Engineers. Sjölander's work in computational biology seeks to understand the evolution of proteins, the workhorses of all life. She is developing algorithms to unlock the mysteries of how protein superfamilies evolve novel functions and structures, and how evolutionary relationships between proteins help predict structure and function. Her projects, which involve regular collaborations with experimental biologists, include the study of how proteins confer disease resistance in both plants and animals. full story in Berkeley Lab View -->

08/23/04. UC Berkeley researcher Leor Weinberger (a Lab guest) and his colleague were contemplating the failure of conventional therapies to get to grips with HIV. "The vast majority of scientists don't believe it's possible to eliminate the virus or to develop a protective vaccine," he says. So he got to thinking of an entirely different approach: rather than destroying the virus, try instead to live with it. The result of his research is the design for a genetically modified virus that he hopes will be every bit as pervasive as HIV. "I'm apprehensive," admits Adam Arkin, a Berkeley Lab physical bioscientist and leader of the research team. "We are 99.99 percent certain nothing bad will happen, but you don't want to use a treatment like this until your understanding is good enough." Full story

7/14/04. What began as a simple study of how a human enzyme binds nitric oxide blossomed into a collaborative effort resulting in a richer understanding of how organisms sense and use oxygen. Guanlyate cyclase is a human enzyme that detects nitric oxide, which is important in relaxing and dilating blood vessels, and has roles in central nervous system and immune function. Michael Marletta was studying the human enzyme when he came across GCY-35, an almost genetically identical enzyme in the nematode Caenorhabditis elegans. Now, Marletta and a group of researchers from across the nation have pieced together how the nematode actually uses GCY-35 to sense oxygen in its environment. The group believes this helps the nematode find areas of low oxygen concentration, where its oxygen-devouring bacterial food is most likely to be found. Because of the similarities between human and nematode enzymes, the findings may have significance in human health, such as healthy blood pressure. The research team’s findings are reported in the July 15 edition issue of Nature, as well as Berkeley Lab’s Research News.

7/11/04. At the crossroads of chemical engineering, chemistry, physics, and biophysics, Arup Chakraborty probes the subtle workings of the immune system. Using sophisticated theoretical and computational methods developed in his lab to study this and other complex systems, Chakraborty reports in Nature Immunology how he developed a molecular model describing how CD4 enhances T cell sensitivity to antigenby coordinating Lck accumulation at the immunological synapse. Read the Nature article here

7/9/04. By delicately stretching a protein to its limits, Carlos Bustamante and a team of researchers have begun to show how the ubiquitous condensin molecule helps coil an entire meter of DNA into each human cell. Discovered just ten years ago, condensins are found in all organisms, from bacteria to humans. Bustamante and the team were able to stretch condensin-compacted DNA molecules between two beads, observing the results as the bonds between the condensin molecules snapped. From the details, published in the June edition of Science, the team could infer how condensin molecules are assembled within the DNA fiber. This mechanistic approach to characterizing proteins complements methods such as crystallography, genetics and biochemistry, and these particular results promise insight into a family of proteins with such crucial functions as DNA repair and meiosis. Read the Science article here

06/25/04. Gerry McDermott, Operations Head of the Berkeley Center for Structural Biology (BCSB), has been recognized as a 2003 Outstanding Mentor for the Department of Energy. McDermott was one of four LBNL mentors selected for the award based on how long they have been mentoring, their contribution to DOE and Lab educational goals, and their contribution to encouraging student professional and academic success. McDermott was presented with the award, signed by the Secretary of Energy, at a special event on June 25.

6/17/04. John Kuriyan and his team have solved the protein structure of an important complex involved in DNA replication. Their findings, which appear in this month’s Nature, help illustrate the mechanism by which DNA polymerase – the protein responsible for DNA duplication – attaches to DNA to begin its work. DNA polymerase must begin replication right where double-stranded DNA becomes a single strand. This involves the DNA sliding clamp, a ring-shaped protein that helps DNA polymerase hold on to and slide down a single strand of DNA. The Kuriyan Lab determined the exact structure of this ring-shaped clamp protein and a larger five-protein complex known as the clamp loader, which helps direct DNA polymerase to exactly the right spot, thus enabling rapid replication. Read the Nature article here

5/14/04. Adam Arkin tells Wired News how it took him and UC Berkeley professor David Schaffer just $200,000 and a grad student to develop a potential treatment for AIDS. And that scares them. That's because the therapy itself is a virus. They created a virus altered to latch onto HIV and mute its ability to become AIDS. They've tested the theory in a computer model and in cells in a dish. The results have been promising, and if they continue in that vein, the researchers could begin animal testing by the end of this year.

5/13/04. RNA, like protein, can sometimes function as an enzyme (ribozyme) to speed biochemical reaction rates. But how does RNA, a simple polymer with just four different chemical building blocks, enhance reaction rates by at least a million fold? Recently, a group including PBD scientists Jennifer Doudna and Jamie Cate obtained high-resolution x-ray crystallographic structures of a ribozyme trapped in different states of its catalytic cycle, showing how a change in the RNA conformation governs the reaction mechanism. Most ribozymes catalyze the cutting and pasting of RNA molecules at specific sites, snipping out (cleaving) extraneous sequences not needed in the final functional form of an RNA. In the hepatitis delta virus (HDV), a human pathogen with a small circular RNA genome, a ribozyme contained within the viral sequence cuts the RNA at a single site during replication to enable packaging of new virions, the extracellular virus particles that allow the virus to infect a host and replicate. Understanding how the ribozyme works is of interest both for defining the fundamental principles of RNA-catalyzed reactions and for discovering a possible Achilles' heel in this deadly pathogen. The findings were reported in the May 13 edition of Nature.

5/13/04. Graham Fleming, director of the Physical Biosciences Division, was selected by the photochemical societies of Europe, Asia, and the Americas to receive the Porter Medal. The medal honors Fleming's life-long work in the field of photochemistry. It is presented every two years on the occasion of the International Union of Pure and Applied Chemistry (IUPAC) symposium. The 2004 medal will be awarded to Fleming this July during a ceremony in Spain.

4/30/04. Biolog, Inc., of Hayward, CA and Berkeley Lab's Physical Biosciences Division announced a partnership to introduce a new phenotype microarray technology that will enable high-throughput, simultaneous analysis of cellular traits. This capability will further the goals of the Department of Energy's Genomes-to-Life program, which involves the structural, functional and comparative analysis of genomes and gene products from organisms that affect the environment. Lab scientist Terry Hazen said the new technology "will further our understanding of microbes' functions." Read the press release

4/26/04. Jay Keasling appears this month's Scientific American magazine in an article entitled "Synthetic LIfe." Keasling and other leaders in synthetic biology discuss the challenges and potential benefits of building libraries of interchangeable DNA parts that can be assembled inside microbes to create programmable, living machines. The complete story can be viewed online here.

4/06/04. Haw Yang has received the NSF's Faculty Early Career Development (CAREER) Award for his innovative studies involving single-molecule microscopy of individual biomolecules. The CAREER Program is the National Science Foundation’s most prestigious award for new faculty members, recognizing and supporting early career-development activities of those most likely to become the academic leaders of the 21st century. In his award-winning project entitled "Optical Single-Molecule Studies of Reaction Pathways of Biological Macromolecules," Yang will conduct experiments to probe the conformational flexibility of biomolecules using single-molecule spectroscopic techniques combined with systematic mutation of a ubiquitous prototype system - - the adenylate kinase family of enzymes. Besides building a research program that will provide insight to the understanding of the motions of biomolecules, Yang's research will provide research opportunities for undergraduate, graduate and post-doctoral researchers. The H. Yang Group's research theme is to develop single-molecule biotechnologies and to study the behavior of individual molecules, aiming at achieving a better understanding of the manner by which a living cell sustains its life.

4/06/04. Thomas Earnest and colleagues collaborating with the bioinstrumentation group of the Engineering Division have developed protein crystal automounter robots at the ALS that are doing for protein crystallography what facilities like the Joint Genome Institute have done for high-throughput genome sequencing. The protein crystallography team, which includes PBD scientists Gyorgy Snell and Carl Cork, describes its accomplishments and techniques in the journal Structure this month. Automating protein crystallography is not simply a matter of making life easier for scientists: By eliminating the human errors that inevitably set in during a repetitious procedure, and by coupling the robots to a unique software program that enables researchers to cull their best data, Earnest and his colleagues have also been able to improve the quality of work being done at their beamlines. Earnest said, “Thanks to our automounter robots, in less than three years of operation we’ve been able to screen more than 10,000 protein crystals and collect complete structural datasets on several hundred of them.” Read the Berkeley Lab press release

3/31/04. Carolyn Larabell and Mark Le Gros have been awarded $2.5 million from NIH and DOE to establish a first-of-its-kind x-ray microscope to perform “cat scans” of biological cells, and other unprecedented capabilities for cell and molecular biology studies. The new microscopy resource also promises a better understanding of human diseases at the molecular level and possibly new discoveries for treating those diseases. The microscope, dubbed XM-2, is poised to bridge the gap between light microscopy and electron microscopy. “X-ray microscopy can bridge this gap by combining some of the best features associated with light and electron microscopy, plus bringing in some entirely new capabilities,” Larabell recently said during a Berkeley Lab View interview. At a resolution of 10 nm (about the size of a protein), a complete data set for an x-ray tomography image should require less than three minutes, compared to the days and even weeks required for electron microscopy. The microscope will be an NIH Biomedical Technology Resource Center at the ALS, which means the instrument will be available to biomedical researchers throughout the nation. In addition to construction funding, NIH and DOE will contribute about $1.3 million to run the microscope for each of its first five years of operation. Click here to view QuickTime tomographic images from the center.

3/8/04. Robert Glaeser was awarded the Microscopy Society of America's 2004 Distinguished Scientist Award for the Biological Sciences. The award was present for Gleaser's internationally recognized research accomplishments and distinguished contributions to microscopy.

2/13/04. Arup Chakraborty was elected to the National Academy of Engineering (NAE) for his accomplishments in applying theoretical chemistry to practical problems in immune system recognition, polymer interfaces, sensor technology, and catalysis. Election to the National Academy of Engineering is among the highest professional distinctions accorded to an engineer. Academy membership honors those who have made "important contributions to engineering theory and practice, including significant contributions to the literature of engineering theory and practice," and those who have demonstrated accomplishment in "the pioneering of new fields of engineering, making major advancements in traditional fields of engineering, or developing/implementing innovative approaches to engineering education." Chakraborty is the Warren and Katherine Schlinger Distinguished Professor and Chair, Department of Chemical Engineering, University of California, Berkeley, and Department Head of Computational and Theoretical Biology for our Division. "I am very pleased to be recognized by the National Academy," said Chakraborty. "It reflects the wonderful environment for doing research at Berkeley Lab and the campus."

1/26/04. Scientists are finding a computer program called Elves to be a nearly magical solution to the tedious and time-consuming task of determining the 3-D shape of proteins from X-ray diffraction data. According to Elves developer James Holton of the Physical Biosciences Division — who now operates an X-ray beamline devoted to protein crystallography at the Advanced Light Source — researchers can unleash Elves on a set of X-ray diffraction data and go on to other things while the computer spits out a protein structure. Read Robert Sanders’ UC Berkeley press release here, or read Holton's paper here.

1/16/04. Carlos Bustamante was one of 16 individuals selected by the National Academy of Sciences (NAS) to receive awards honoring their outstanding scientific achievements. The awards will be presented on April 19 at a ceremony in Washington, D.C., during the Academy's 141st annual meeting. Bustamante was awarded the Alexander Hollaender Award in Biophysics – a prize of $20,000 awarded every three years for excellence in biophysics. The NAS cited Bustamante "for his ingenious use of atomic force microscopy and laser tweezers to study the biophysical properties of proteins, DNA, and RNA, one molecule at a time." The award was established by a bequest from Henrietta W. Hollaender in honor of her husband and was first presented in 1998.

1/8/04. Jay Groves appears in this month's Nature journal, where he and co-authors describe how microscopic glass beads coated with lipid membranes provide a sensitive detector of interactions between proteins and ligands. The findings pave the way for a deeper understanding of the molecular architecture of and biochemical processes within the cell membranes of all living organisms. The entire article appears here in Nature. Groves' work is also nicely summarized here in Nature Online's News and Views section.

12/23/03. Graham Fleming, along with principal investigator Bill Lester and co-principal investigator Michael Frenklach, are leading a computational science project that has been awarded 1 million hours of supercomputing time at the Lab's NERSC Center. The INCITE grant was awarded by the DOE's Office of Science and is one of just three such awards granted. The project focuses on the electronic structure of carotenoids, a natural compound found in plants and eyes that is important in mitigating free radical cell damage to cells exposed to strong light. Despite the importance of carotenoids, their photoprotective mechanism is not well understood, in large measure because the relevant excited states cannot be studied directly by optical spectroscopy. The planned calculations (around 80,000 hours each) will be the largest rigorous ab initio calculations performed to date on molecular systems. "We expect our results to provide a benchmark for accurate calculations of the electronic structure of biomolecules," said Fleming. Full story

12/8/03. Arup Chakraborty was appointed the Department Head of Theoretical and Computational Biology in the Physical Biosciences Division. Chakraborty will lead the division's efforts to develop new computational strategies to analyze and predict solutions to biological problems. Division Director Graham Fleming said that "Chakraborty's distinguished research in areas as disparate as inter-cellular communication in the immune system and polymer science brings a bold and broad perspective to the rapidly growing demands of theoretical biology." Chakraborty serves as the Warren and Katherine Schlinger Distinguished Professor of Chemical Engineering and Professor of Chemistry, and the Chair of Chemical Engineering at UC Berkeley.

10/9/03. Graham Fleming visited Florida State University as part of the Phi Beta Kappa Visiting Scholar Program, which gives students and faculty the chance to learn from some of science’s leading authorities. Dr. Fleming shared his work on electron transfer in photosynthesis, and specifically discussed how plants optimize their photosynthetic processes during the course of a day in response to brighter and dimmer sunlight. Dr. Fleming also met with chemistry students and faculty in what he described as an essential part of the scientific dialogue. While at FSU, Dr. Fleming visited the National High Magnetic Lab at Florida State University. In an interview with FSU Headlines, Dr. Fleming said that the facility provided students with opportunities that “couldn’t be done or even thought about” at other universities. Other visitors of FSU’s Mag Lab that day: Florida governor Jeb Bush. Listen to an online broadcast of the interview

10/8/03. Rod MacKinnon, a BCSB user and familiar face at the ALS, was awarded the Nobel Prize in Chemistry for studies involving cell membrane channels. Using HHMI beamline 8.2.2, MacKinnon revealed the 3-D structure of ion channels, which regulate the passage of inorganic ions through membranes. Ion channels control heart rate, regulate hormones, and generate electrical signals in the nervous system. MacKinnon differs from many researchers in that he actually collects beamline data himself, rather than delegating the task to students or other scientists. MacKinnon shares the Nobel award with Peter Agre, whose discovery of a water channel eventually revealed an entire family of water channels known as aquaporins. Together, their work is opening new lines of research in biochemistry and biology.

10/7/03. Mark Le Gros received the 2003 Halbach Award for Innovative Instrumentation at the Advanced Light Source. Dr. Le Gros received the award for his design and development of a fully automated cryo-rotation stage for the soft x-ray microscope. This apparatus enables collection of tomographic data sets from whole rapidly frozen cells in three minutes at better than 50 nm resolution. The award is named in honor of Klaus Halbach (1925-2000), a Berkeley Lab physicist best known for his work on permanent magnet insertion devices (such as undulators and wigglers), which made third-generation rings such as the ALS feasible. To commemorate the tenth anniversary of the ALS, Ruth Halbach -- widow of the reknowned physicist -- presented the award to Le Gros at the 2003 ALS User Meeting.

Ruth Halbach presents Mark Le Gros with the Halbach Award

9/23/03. Jay Groves, Faculty Scientist and UC Berkeley Assistant Professor of Chemistry, was named along with two other UCB scientists to the 2003 list of the world's 100 Top Young Innovators by Technology Review magazine, published by the Massachusetts Institute of Technology (MIT). Groves was among 100 individuals "under age 35 whose innovative work in technology has a profound impact on today's world," according to the publication. More info at the UCB press release and Technology Review Online (free registration required).

7/31/03. Jay Keasling was named head of a newly formed Synthetic Biology Department within the Division. The department will integrate a wealth of new data and experimental advances in biology, engineering and nanoscience to develop organisms and biologically-inspired systems that will one day convert plentiful, renewable resources into energy, replace environmentally unfriendly chemical syntheses, seek out and destroy pathogens, and remediate recalcitrant environmental contaminants. The Synthetic Biology Department will expand the division's capabilities and further its mission to forge truly interdependent science at the cutting edge of the biological and physical sciences.

7/22/03. Carlos Bustamante, leader of our division's Advanced Microscopy Deparment and a professor of molecular and cell biology, physics, and chemistry at UC Berkeley, will receive the Biophysical Society's Founder's Award for his pioneering role in single-molecule biophysics. One criterium for the award is the acceptance and use of the candidate's advance by others in the field, either promptly or over a period of years. The Society will honor Bustamante and eight other scholars next February 16 at its annual meeting, in Baltimore, Maryland. Read more about the Biophysical Society and the Founder's Award.

6/1/03. Jay Keasling, along with Vince Martin and others, have engineered a way to produce a next-generation malaria drug within E. coli. Keasling combined yeast and wormwood genes within E. coli, then optimized the chemical pathway by 10,000 times to produce amorphadiene, the chemical precursor to arteminisin. Keasling's process is simpler, cheaper, and more environmentally friendly than the current method of producing arteminisin, which involves grinding the wormwood plant and purifying the extract. The drug, artemisinin, is a promising antimalarial because of its effectiveness against strains of the malaria parasite now resistant to front-line drugs. It is now too expensive for broad use in countries in Africa and South America where it is most needed. Keasling's research was published online today in Nature Biotechnology and is scheduled to run in the journal's printed edition in July. Read the details here. 5/30/03. Gerry McDermott and colleagues have determined the structure and function of AcrB, a protein that pumps antibiotics and many other molecules out of pathogens. Understanding AcrB pump may have important implications in drug resistance. For example, the results may yield a better understanding of how to design antibiotics that avoid the pump, thereby staying active in the cell. The results of McDermott's research appears in the May 2003 edition of Science. 4/24/03. Gerry McDermott and colleagues have determined the structure of the Nogo receptor (NgR), a protein that is implicated in inhibition of axon regeneration in the adult mammalian central nervous system. A target for drug design for repair of spinal injuries, the NgR structure was determined to 1.5Å on Beamline 8.2.1 by mercury MAD. McDermott's findings appear in the April 24 edition of Neuron. 3/6/03. Steven Brenner was one of 117 scientists and scholars selected as recipients of The Alfred P. Sloan Foundation's Research Fellowship grants for 2003. Brenner was honored with a $40,000 grant in computational molecular biology. The fellowships are awarded annually to recognize and support young scientists and scholars in seven fields: chemistry, computational and evolutionary molecular biology, computer science, economics, mathematics, neuroscience, and physics.
2/17/03. Sung-Hou Kim's research group has created a 3-D map the protein universe. The map shows that protein folds are broadly grouped into four different classes that correspond to scientists' observations of protein structure. This map provides important insight into the evolution and demographics of protein structures and may help scientists identify the functions of newly discovered proteins. The findings were reported in the Proceedings of the National Academy of Sciences. More information about the protein map is available at LBL's Research News site.
	Click to enlarge the 3-D protein map

12/3/02. Keith Henderson and researchers from UT Southwestern Medical Center and HHMI have determined the crystal structure of the protein responsible for controlling the level of cholesterol in the bloodstream. Critical early work was performed on ALS beamline 5.0.2, and the structure was determined from data collected during the commissioning of beamline 8.2.1. The results are featured in the November 29, 2002 edition of Science Magazine and online at Science Express.

11/20/02. Paul Adams will be giving a seminar talk at the Lawrence Berkeley Lab's DC Projects Office on Friday, December 13. Adams' talk, entitled "Getting the Most from Biological Data," discusses how researchers can bridge the gaps among experiment, analysis, and simulation.

11/14/02. Carlos Bustamante is featured in a nicely done article in the November 2002 issue of California Monthly, the magazine of the California Alumni Association. In the article, entitled "Force of Nature," Bustamante shares the origins of his interest in science, the path that ultimately brought him to Berkeley, and his ambitions for the future.

11/8/02. Paul Adams, leader of the Computational Crystallography Initiative (CCI), received an award from Technology Transfer and Lab director Charles Shank for the CCI's progress in commercializing its technology via the PHENIX Industrial Consortium. Adams' group was one of ten recognized for moving LBNL's research into the commercial sector. Congratulations!

Lab Director Charles Shank is pictured here with Paul Adams and other recipients of the Technology Transfer awards.

10/9/02. Adam Arkin is featured in the September 2002 edition of HHMI's quarterly publication, HHMI Bulletin. In the article "Engineering the Cell," Arkin discusses his notion of the cell as a machine, his multidisciplinary approach to biology, and how he hopes to bring molecular biology into the realm of cellular engineering.

9/13/02. Thomas Earnest is in print this month in the September 2002 edition of Genome Technology. In the article "Better Beamlines in Berkeley," Dr. Earnest describes how robotic automation of ALS's beamlines is shortening the time it takes to develop three-dimensional protein structures by three or four fold. You can also read the article online at Genome Technology's website, www.genomeweb.com.

9/12/02. Adam Arkin has been selected to speak for the EECS Joint Colloquium Distinguished Lecture Series. Dr. Arkin's lecture will take place on Wednesday September 18 at the Hewlett Packard Auditorium, 306 Soda Hall, UC Berkeley campus. The title of his presentation will be "Motifs and Modules in Cellular Signal Processing" (read the abstract).

08/06/02. John Kuriyan and fellow researchers have identified specific mutations in a rogue gene that render the drug Gleevec ineffective in some patients who have chronic myeloid leukemia (CML). The findings, published in this month's Cancer Cell, provide new information that may improve the effectiveness of second-generation drugs, thereby minimizing drug resistance. The development may also allow for sophisticated genetic screening to identify best therapies for individual CML patients.

8/5/02. Steven Brenner, PBD Faculty Scientist and Assistant Professor of Plant and Microbial Biology at UC Berkeley, was named a Board Member of the International Society for Computational Biology. Dr. Brenner is also a founding member of the Open Bioinformatics Foundation.

7/23/02. Adam Arkin and Terry Hazen, Co-directors of the Virtual Institute for Microbial Stress and Survival (VIMSS) were awarded $36.6 million over five years as part of the Genomes to Life initiative. This program will provide fundamental research on applied environmental conditions in metal and radionuclide contaminated waste sites. For more information, please see (Currents), (DOE press release) and (Oakland Tribune).

7/29/02. Kenneth Sauer and Vittal K. Yachandra have been selected as Editor's Choice in Science for their paper on the Photosynthetic Water Oxidation Complex (See Editor's Choice, Biochemistry: Cluster Analysis). Knowledge of this biological complex will be of great value in combating global warming. For the full text of the paper please go to PNAS Online.

7/29/92. Jan Liphardt, Carlos Bustamante et. al., have published a report in Science shedding light on Jarzynski's Equality, a remarkable new result in theoretical statistical mechanics. The experimental verification of Jarzynski's Equality provides the first example of its use as a bridge between the statistical mechanics of equilibrium and nonequilibrium systems. For a commentary on this result, see the Perspectives article by D. Egolf.

6/27/02. Berkeley Center for Structural Biology, the High-throughput Nanovolume Crystallization Robot has won a 2002 R & D 100 Award in recognition of being one of the 100 most technologically significant new products/processes of the year. The Crystallization Robot was developed by LBNL engineers in conjunction with industry and academia. The LBNL/Syrrx robot enables protein structure determination at a historically unprecedented rate for the purpose of drug discovery. (R & D Magazine)

06/07/02. Jan Liphardt has proven the ability to make thermodynamic generalizations about nonequilibrium systems at the molecular level. Equilibrium equations historically failed as they approached molecular scales because the increasing proportionality of molecular thermodynamics introduces significant measurement error. In 1997, Jarzynski proved an equality relating the irreversible work to the equilibrium free energy difference (G), showing that it was theoretically possible to obtain equilibrium thermodynamic parameters from processes carried out arbitrarily far from equilibrium. By successfully demonstrating the Jarzynski equality, Jan’s lab provided a bridge between the statistical mechanics of equilibrium and nonequilibrium systems. This work also extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments to areas such as parallel processing. Details of Liphardt's discovery appear here in Nature.

4/30/02. Carlos Bustamante was newly elected as a member of the National Academy of Sciences in Washington DC. Election to this membership is considered one of the highest honors that can be accorded a US scientist or engineer. (National Academy of Sciences)

4/30/02. Jennifer Doudna was newly elected as a member of the National Academy of Sciences in Washington DC. Election to this membership is considered one of the highest honors that can be accorded a US scientist or engineer. (National Academy of Sciences)