Quantum Secrets of Photosynthesis Revealed
Through photosynthesis, green plants and cyanobacteria are able to transfer sunlight energy to molecular reaction centers for conversion into chemical energy with nearly 100-percent efficiency. Speed is the key – the transfer of the solar energy takes place almost instantaneously so little energy is wasted as heat. How photosynthesis achieves this near instantaneous energy transfer is a long-standing mystery that may have finally been solved. Full story

Keasling named Discover Scientist of the Year
For his breakthroughs in the field of synthetic biology, including treatments for malaria, AIDS, and cancer as well as discoveries of new fuel resources, Discover Magazine awarded Division Director Jay Keasling with its prestigious Scientist of the Year award on November 15th in New York City. Bob Guccione, Jr., CEO of Discover media, says, “Dr. Keasling is a visionary whose ingenuity merits special recognition. Discover believes what separates Dr. Keasling from other scientists, who also have done groundbreaking work, is his spirit and his determination to help those who cannot help themselves. He is a true humanitarian.” More at the Discover website.

Lab, Fluidigm get NIH funds for protein crystal chip
Fluidigm Corporation in South San Francisco and Berkeley Lab have received funding from the National Institutes of Health to develop a microfluidic chip for collection of in situ X-ray diffraction data. The diffraction-capable chip will be designed so that protein crystals can be screened at a synchrotron without having to first remove them from the chip. James Holton, with the Lab's Physical Biosciences Division, is a principal investigator. Read the press release

Nanomedicine Center will use light to turn cells on and off
A new research center at Berkeley Lab and UC Berkeley aims to put light-sensitive switches in the body's cells that could potentially be used to trigger chemical reactions, initiate muscle contraction, activate a drug, or stimulate nerve cells - all at the flash of a light. A major goal of the UC Berkeley-LBNL Nanomedicine Development Center is to equip cells of the retina with photoswitches, essentially making blind nerve cells see, restoring light sensitivity in people with degenerative blindness such as macular degeneration. "We're asking the question, 'Can you control biological nanomolecules - in other words, proteins - with light?'" said center director Ehud Isacoff. "If we can control them by light, then we could develop treatments for eye or skin diseases, even blood diseases, that can be activated by light. This challenge lies at the frontier of nanomedicine." Read the press release

KGO-TV's Dr. Dean Edell reports that Berkeley Lab and UC Berkeley researchers, headed by Physical Biosciences Division Director Jay Keasling, are one step closer to finding a drug to prevent and treat malaria, Currently scientists extract a drug from a plant called Artemisia Annua. But it is incredibly costly and time consuming to harvest the drug. In an important breakthrough, Keasling's team has identified the drug-producing gene in Artemisia. And they've done that several years ahead of schedule, which is a major victory. View Dr. Edell's video report and read more.

Learning how nature splits water
PBD scientists Junko Yano and Vittal Yachandra have led an international team or researchers toward a major new understanding about how plants and photosynthetic lifeforms use sunlight to split water molecules into protons, electrons and oxygen, the cornerstone of photosynthesis. Their work, detailed in the November 3, 2006 issue of the journal Science, shows the precise structure of a catalyst composed of four manganese atoms and one calcium atom that drives this water-splitting reaction. The findings could help researchers synthesize molecules that mimic this catalyst, which is a central focus in the push to develop clean energy technologies that rely on sunlight to split water and form hydrogen to feed fuel cells or other non-polluting power sources. “This is the first study to combine x-ray absorption spectroscopy and crystallography in such a detailed manner to determine the structure of an active metal site in a protein, especially something as complicated as the photosynthetic Mn4Ca cluster,” said Junko Yano. More at science@berkeley lab.

Two major grant awards to BCSB will speed structure solution
New grants totaling $13M will increase the high-throughput capabilities at the Berkeley Center for Structural Biology (BCSB). The Howard Hughes Medical Institute has awarded $4.8 million to upgrade the robotic capabilities of their crystallography beamlines at the Advanced Light Source, and the National Institutes of Health has awarded an $8.2 million grant to further develop a software program called PHENIX, which automates crystallography data acquisition and analysis. The funding will allow the Center to provide its users with even faster methods of identifying protein and nucleic acid structures. “More and more scientists have come to realize that automating macromolecular crystallography leads to better results,” said Paul Adams, an authority on crystallography who heads the BCSB. “In the time it takes to screen one or two crystals by hand, automation enables ten or twenty crystals to be screened. The ability to screen many samples prior to data collection enables researchers to focus their studies on the very best samples.” More about the awards and upgrades at Science@Berkeley Lab

New Visiting Faculty Somerville Awarded Balzan Prize
Christopher Somerville, who in August became a PBD Visiting Faculty Member, has been awarded the prestigious International Balzan Prize for his work in plant molecular genomics. Not bad, considering that former prize winners include Jean Piaget, Pope John Paul, and Mother Teresa. Along with Eliot Meyerowitz at Caltech, Dr. Somerville helped establish Arabidopsis as a model organism, which the Prize Committee stated has “far reaching implications for plant science, both on a fundamental level and in potential applications." Dr. Somerville is the Director of the Carnegie Institution Department of Plant Biology, and Professor of Biological Sciences at Stanford University. His research interests focus on understanding how plant cell wall polysaccharides are synthesized, how the structures relate to the functions of the cell wall, and how the system is regulated. "I believe that knowledge of cell wall structure and function will facilitate the development of plants with improved utility as sources of renewable materials and as biofuel feedstocks," remarked Somerville, who will play a key role in Division and Lab efforts to develop cellulosic ethanol and other solar-to-fuel science and technology.More about Prof. Somerville's research -->

PBD robotics team awarded Halbach Prize
Carl Cork, John Taylor, Gyorgy Snell, and members of the Engineering Division have received the Klaus Halbach Prize for 2006. The Halbach Prize, given yearly for innovative instrumentation at the Advanced Light Source (ALS), was awarded to the PBD-led team for developing a system that automatically mounts and aligns protein crystals for high-throughput structural biology. The pioneering technology in applying robotics to improve the quality and throughput of x-ray crystallographic data was so successful at the ALS that it expanded to the National Synchrotron Light Source, the Cornell High Energy Synchrotron, and three sectors of the Advanced Photon Source, and continues as part of an instrument development program spanning the four sites. The Halbach Prize is given in honor of LBNL scientist and engineer, Klaus Halbach, whose development of insertion devices such as wigglers and undulators was critical to the now common use of third-generation synchrotrons as research resources. The robotic automation program is funded by the National Institute of General Medical Sciences of the National Institutes of Health. Congratulations to the team for their excellent work!

Ribbon cutting celebrates launch of the National Center for X-Ray Tomography
The National Center for X-ray Tomography (NCXT) was officially dedicated on October 11, 2006, at the Advanced Light Source. This first-of-its-kind x-ray microscope will enable scientists to perform three-dimensional “CAT scans” on biological cells, just one of many unprecedented capabilities for cell and molecular biology studies. X-ray microscopy is expected to bridge the capabilities gap between light and electron microscopy, combining some of the best features of each and adding entirely new ones. For example, hydrated biological samples can be rapidly frozen and scanned without any chemical alteration or staining. The quick turnaround time between sample preparation and data collection will allow scientists to accumulate a large volume of data very quickly, and the images obtained (at 25-nanometer resolution) are ideally suited for quantitative analysis. “X-ray microscopy is an emerging new technology that expands the imaging toolbox for cell and molecular biologists, and we are going to make this technology available to the greater biological community,” said principal investigator and PBD microscopy expert Carolyn Larabell, who built the microscope with co-principal investigator and Berkeley Lab physicist Mark Le Gros.

Christopher Voigt named to TR35
Since 1999, the editors of MIT’s Technology Review have honored the young innovators whose inventions and research they find most exciting. Today that collection is the TR35, a list of technologists and scientists, all under the age of 35. Their work--spanning medicine, computing, communications, electronics, nanotechnology, and more--is changing our world. Synthetic biologist Christopher Voigt was chosen for 2006’s TR35 list for creating an unusual image: the Virgin Mary on a lawn of E. coli. In turning microbes into a "photographic" medium, Voigt and his team have illustrated his approach to synthetic biology: Creating genetic parts that can be used interchangeably to achieve different results. They hooked a light receptor from blue-green algae to a protein that normally controls E. coli genes' response to the cell's surroundings.

PBD leads Lab-effort on cellulosic ethanol
Lab Director Steve Chu considers the search for sustainable, carbon-neutral energy "the most important scientific challenge we face today." That’s why Berkeley Lab is partnering with Lawrence Livermore and Sandia Labs to respond to the DOE's $250M call to develop a major, multidisciplinary Bioenergy Center. The Joint BioEnergy Institute (JBEI) has a goal of using rapidly advancing scientific areas such as nanotechnology and synthetic biology to transform the biofuel industry in California and the entire nation. more at jbei.org -->

Molecular DNA switch found to be the same for all life
The molecular machinery that starts the process by which a biological cell divides into two identical daughter cells apparently worked so well early on that evolution has conserved it across the eons in all forms of life on Earth. Research led by Michael Botchan, Eva Nogales and PBD researcher James Berger revealed that the molecular machinery behind the initiation of DNA replication in Archaea, Bacteria and Eukarya cells is remarkably similar. In two papers concurrently published in the August edition of the journal Nature Structural and Molecular Biology, the team report the identification of a helical substructure within a superfamily of proteins, called AAA+, as the molecular “initiator” of DNA replication in a bacteria, E. coli, and in a eukaryote, Drosophila melanogaster, the fruit fly. Taken with earlier research that identified AAA+ proteins at the heart of the DNA replication initiator in archaea organisms, these new findings indicate that DNA replication is an ancient event that evolved millions of years ago, prior to when Archae, Bacteria and Eukarya split into separate domains of life. Berger, a biochemist and structural biologist who participated in both studies, noted that “[o]ur findings of evolutionary kinship between the DNA initiators in all three domains make sense because, to paraphrase Francois Jacob, the one thing a cell wants to do is to become two cells,” said Berger, “A cell can't do this if it doesn't replicate its DNA in the right place, at the right time, and in the right manner, while simultaneously avoiding over-replication.” More from LBNL science writer Lynn Yarris at Science@Berkeley Lab

Keasling participates in CNN Future Summit
Division Head Jay Keasling participated in the first of four roundtable discussions about how technology is shaping our future. In a global initiative, CNN has gathered some of the world's leading futurologists in genetics, stem cells, robotics and cybernetics to examine the ways science is working to fix, augment and duplicate the human body. Originating from Singapore, the show originally aired on CNN International on June 15. Read more about CNN Future Summit -->

First detailed look at “Dicer” enzyme
A team of Berkeley Lab and UC Berkeley scientists has gotten its first detailed look at the molecular structure of an enzyme that Nature has been using for eons to help silence unwanted genetic messages. The researchers — led by Lab biochemist Jennifer Doudna — used x-ray crystallography at the Advanced Light Source to determine the crystal structure of Dicer, an enzyme that plays a critical role in the process known as RNA interference. The Dicer enzyme is able to snip a double-stranded form of RNA into segments that can attach themselves to genes and block their activity. Read the full story -->

Discovering new energy sources: The Helios Project
With so many concerns about energy availability and sustainability these days, it seems natural for Berkeley Lab to consider how new research at the boundary between basic energy sciences and applied fields of energy technology can increase the nation’s energy options for the future. Now, a new Lab-wide program represents a new type of research facility focusing on one of the greatest scientific and technical challenges of our time: To create effective approaches for the exploitation of solar energy. The Helios Project, led by Lab Associate Director Paul Alivisatos and PBD Division Director Jay Keasling, is a multidisciplinary program conceived to provide the people of the United States with energy security as well as unprecedented economic growth, without restrictions imposed by environmental factors, for decades to come. Centering largely on new energy/nano building concept, Helios will cut across traditional research boundaries and programs in profound ways to produce transforming technologies in synthetic biology and nanotechnology, and will fuse the Lab’s core strengths in biological, chemical and physical sciences in the search for a sustainable, C02-neutral source of energy.

The long view on structural genomics
In a January 20 review paper in the journal Science, PBD researchers Steven Brenner and John-Marc Chandonia compare how structural genomics centers perform relative to traditional structural biology labs. They found that the cost of solving a structure at the most efficient SG center in the United States has dropped to one-quarter of the estimated cost of solving a structure by traditional methods. However, the efficiency of the top structural biology laboratories—even though they work on very challenging structures—is comparable to that of SG centers. Such non-center papers are also cited more often, suggesting greater current impact.

Custom microbes, at your service: Synthetic biology featured in NYT
There are bacteria that blink on and off like Christmas tree lights and bacteria that form multicolored patterns of concentric circles resembling an archery target. Yet others can reproduce photographic images. These are not strange-but-true specimens from nature, but rather the early tinkering of synthetic biologists, who seek to create living machines and biological devices that can perform novel tasks. Berkeley Lab's Jay Keasling is trying to take up to 12 genes from the wormwood tree and yeast and get them to work together in E. coli bacteria to produce artemisinin, a malaria drug now extracted from the wormwood tree. More in the Jan 17 issue of the New York Times.

Revealing the secrets of protein synthesis
December 5, 2005: PBD researchers Jennifer Doudna and Eva Nogales have uncovered key information towards understanding the crucial first step in protein synthesis, the process by which the genetic code, harbored within DNA and copied into RNA, is translated into the production of proteins. Their findings help to explain how viruses, such as Hepatitis C, are able to highjack protein synthesis machinery in humans for their own purposes. Nogales (a biophysicist) and Doudna (a biochemist) led a study in which cryo electron microscopy (cryo-EM) was used to create a 3-D model of the protein complex called eukaryotic translation initiation factor 3 (eIF3). The model showed that the eIF3 protein complex employs the same structural mechanics in the loading of either human or viral RNA to ribosomes, the complex machinery in living cells responsible for protein synthesis. “This is the first insight into how the initiation mechanisms of protein synthesis work specifically for humans, and a step towards understanding at the molecular level what happens when a viral infection occurs,” said Doudna.  “A better understanding of these mechanisms could open the door to new and improved therapies for viral infections.” Full story ->

Nanothermometers could help cancer therapies
December 5, 2005: Thermometers only nanometers or billionths of a meter in diameter could boost the effectiveness of heat- or cold-based anti-cancer therapies and optimize genetic analysis devices and electronics design, say experts. While other nanothermometers made with biomolecules and fluorescent compounds exist, those effectively get destroyed after "a few tens of seconds." The latest models ought to prove durable "for very long periods of time," said Berkeley Lab physical bioscientist Jan Liphardt. Full story ->

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