Physical Biosciences Division One Stop
PBD Scientists Create Collagen-Like Building Blocks Out of Viruses
Using a simple, single-step process, PBD scientists recently developed a technique to direct benign, filamentous viruses called M13 phages to serve as structural building blocks for materials with a wide range of properties.
The materials created could eventually be used to create complex biological tissues, such as cornea, skin and bones, or to manufacture materials with tunable optical, biomedical and mechanical properties.
The scientific team, led by PBD Faculty Scientist and UC Berkeley bioengineer Seung-Wuk Lee and his student and lead author Woo-Jae Chung, published their findings in the Oct. 20, 2011, issue of Nature. More>
Paul Adams Recognized As Significant Contributor to Field of Crystallography
We are all familiar with the cliché “publish or perish”. What is absent in such terminology is the assessment of the value of a particular publication. A common measure of the value of a particular publication is the degree to which it is referred to or “cited” in the works of one’s peers. In recognition of this measure of value, the journal Acta Crystallographica Section D has collected the twenty publications in Biological Crystallography that are most cited by other authors. Quite remarkably, our very own Deputy Division Director, Paul Adams is author on five of those twenty most cited papers. This is clear testament to the truly valuable contributions he is making to the field. Please join us in congratulating Paul for this remarkable achievement.
Acta Crystallographica Section D now has an Impact Factor of 6.326, and to celebrate, has put together a collection of their highly cited articles, which can be viewed at: http://journals.iucr.org/d/services/highly_cited_articles.html
Krishna Niyogi Wins Howard Hughes Award
Krishna K. Niyogi is one of only 15 scientists nationwide to be chosen for an extensive new program that is part of an initiative to boost much-needed funding for fundamental plant research. Niyogi, a scientist in the Physical Biosciences Division as well as a professor in Plant & Microbial Biology in the College of Natural Resources at UC Berkeley, has spent two decades studying photosynthesis. He has made fundamental discoveries that help scientists understand the strategies plants use to adapt to their environment. The new grant is a joint effort of the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation. More>
Dr. Henrik Scheller named Vice President for Feedstocks at JBEI
PBD is pleased to announce that Dr. Henrik Scheller has been named the Vice President for Feedstocks at the Joint BioEnergy Institute (JBEI). His new position will be in addition to his role as Director of Cell Wall Biosynthesis.
Additionally, Henrik has accepted an invitation by Division Director, Adam Arkin to serve on the Division Staff Committee for PBD. The Division Staff Committee is an advisory committee to the Division Director on matters related to the Division's professional research staff including hiring and reviewing cases for promotion (career-track and career appointments).
Biological Circuits for Synthetic Biology: Keeping it Simple
Adam Arkin, director of the Physical Biosciences Division, along with Julius Lucks and Lei “Stanley” Qi, led the development of the first RNA-based regulatory system that can independently control the transcription activities of multiple targets in a single cell. This is a significant advance for the design and construction of programmable genetic networks. Also contributing to this work were Vivek Mutalik and Denise Wang. More
JBEI Researchers Counteract Biofuel Toxity in Microbes
Researchers at the Joint BioEnergy Institute (JBEI) have created a library of microbial efflux pumps that reduce toxicity and boost production of biofuels in engineered strains of microbes. This should serve as a valuable new tool for the development of advanced biofuels and other areas of biotechnology as well. Aindrila Mukhopadhyay, a chemist with JBEI’s Fuels Synthesis Division, is leading this research. More
Paul Adams to Serve as Member of NIH Scientific Review Panel
Paul Adams, Deputy Director for the Lab's Physical Biosciences Division and Vice President for Technology for the Joint BioEnergy Institute has accepted the invitation to serve as a member of the Macromolecular Structure and Function D Study Section, Center for Scientific Review, for the National Institute of Health (NIH), for the term beginning July 1, 2011 and ending June 30, 2015. Members are selected on the basis of their demonstrated competence and achievements in their scientific discipline as evidenced by the quality of research accomplishments, publications in scientific journals, and other significant scientific activities, achievements and honors.
Study sections review grant applications submitted to the NIH, make recommendations of these applications to the appropriate NIH national advisory council or board, and survey the status of research in their fields of science. These functions are of great value to medical and allied research in this country. We congratulate Paul Adams for his scientific stature and his contributions.
PBD Scientists Recipients of NSF CAREER Awards
PBD Faculty Scientists and UCB Bioengineering Assistant Professors Amy Herr and Sanjay Kumar have received 2011 National Science Foundation Faculty Early Career Development (CAREER) Program awards.
Herr is a leading researcher in microscale biomarker detection technology. Her award was given from the Chemical, Environmental, Bioengineering, and Transport Systems (CBET) Division for her proposal in "microMOSAIC Frameworks for Next-Generation Proteomic Technology".
Kumar is a pioneer in molecular cell dynamics and the mechanobiology of the cytoskeleton. He was recognized by the Directorate for Engineering (ENG), CMMI Division, Biomechanics and Mechanobiology (BMMB) Program for his project: "Microscale Mechanobiology of Actomyosin Stress Fiber Bundles: An Integrated Program for Research and Education in Cellular Bioengineering"
The CAREER Program is a Foundation-wide activity that offers the National Science Foundation's most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations. Such activities should build a firm foundation for a lifetime of leadership in integrating education and research.
Essay by PBD Scientists featured in the journal Cell takes a look at systems biology and cellular networking
Adam Arkin, Director of the Physical Biosciences Division and a leading computational biologist, is the corresponding author of an essay in the journal Cell which describes in detail key technologies and insights that are advancing systems biology research. The paper is titled “Network News:Innovations in 21st Century Systems Biology.” Co-authoring the article is David Schaffer, also a PBD Scientist and a chemical engineer with Berkeley Lab’s Physical Biosciences Division. More>
A Second Pathway for Antidepressants: Berkeley Lab Reports New Fluorescent Assay Reveals TREK1 Mechanism
Using a unique and relatively simple cell-based fluorescent assay they developed, scientists with PBD and UC Berkeley have identified a means by which fluoxetine, the active ingredient in Prozac, suppresses the activity of the TREK1 potassium channel. TREK1 activity has been implicated in mood regulation and could be an important target for fluoxetine and other antidepressant drugs.
Ehud Isacoff of PBD is the corresponding author on a paper reporting the results of this study that appears in the Proceedings of the National Academy of Science (PNAS). More>
Physical Bioscientist Wins NAS Molecular Biology Award
James Berger of the Lab’s Physical Biosciences Division has won the 2011 National Academy of Sciences (NAS) Molecular Biology Award for “elucidating the structures of topoisomerases and helicases and providing insights into the biochemical mechanisms that mediate the replication and transcription of DNA.” Using Beamline 8.3.1 at the Advanced Light Source, Berger researches the crystal structures of protein motors that play pivotal roles in gene expression and replication, and are vital to the survival of all biological cells. The NAS Molecular Biology Award, which is sponsored by Pfizer Inc., consists of a $25,000 prize to recognize a recent notable discovery in molecular biology by a young scientist. More>
PBD Scientist Wins 2010 ACS Division of Analytical Chemistry Spectrochemical Analysis Award
Stephen Cramer, a Berkeley Lab Physical Biosciences Faculty Scientist and a UC Davis Professor of Applied Sciences, received the American Chemical Society’s 2010 ACS Division and Analytical Chemistry Spectrochemcial Analysis Award. The award recognizes individuals who through scholarly activity have definitively and uniquely advanced the field of spectrochemical analysis and optical spectrometry. Cramer researches the structure of metal-containing molecules, high-resolution x-ray fluorescence and x-ray Raman spectroscopy, soft x-ray spectroscopy and x-ray magnetic circular dichroism; EXAFS, Mo and V nitrogenase, and hydrogenase and other Ni metalloproteins.
PBD Scientist Wins Remsen Award for 2011
Graham Fleming, Senior Faculty Scientist and former Division Director at the Physical Biosciences Division, former LBNL Deputy Laboratory Director, and Vice Chancellor for Research at UC Berkeley, has been chosen by the Maryland Section of the American Chemical Society as the recipient of the prestigious Remsen Award for 2011.
The Remsen Award was established in 1946 to commemorate the career of Ira Remsen, first Professor of Chemistry and second President of the Johns Hopkins University, as a chemist, educator, and administrator. The Remsen Award Lecturers are chemists of outstanding achievement, in keeping with Ira Remsen's long and devoted career as an exponent of the highest standards in teaching and research in chemistry.
PBD Scientist Wins PECASE Award
Two scientists with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) were among the 85 researchers named by President Barack Obama to receive the prestigious Presidential Early Career for Scientists and Engineers (PECASE) Award, the highest honor bestowed by the United States government on early-career researchers.
The Berkeley Lab recipients were Gavin Crooks, a theoretical chemist with Berkeley Lab’s Physical Biosciences Division, and Trent Northen, a staff scientist with Berkeley Lab’s Life Sciences Division and with the Joint BioEnergy Institute (JBEI). They join 11 other DOE recipients of the 2010 PECASE Award, which will be received later this year at a White House ceremony. In addition to a citation and a plaque, each PECASE winner will receive DOE funding for up to five years to advance his or her research.. More
Berkeley Lab Scientists Reveal Path to Protein Crystallization
Scientists at Berkeley Lab’s Molecular Foundry, including Sungwook Chung, Seong-Ho Shin, James DeYoreo and Carolyn Bertozzi, have imaged in real-time how bacterial surface-layer proteins form crystals in a cell-like environment. This direct observation of protein assembly could provide researchers with insight into how micoorganisms stave off antibiotics or lock carbon dioxide into minerals. More
Article Featured as Cover and "Paper of the Week" in Journal of Biological Chemistry (JBC), September 3, 2010
LBNL Scientists Jose H. Pereira, Corie Ralston, and Paul D. Adams team with other scientists to publish article, "Crystal Structures of a Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle". On The Cover: Chaperonins are large protein complexes consisting of two stacked multisubunit rings, which open and close in an ATP-dependent manner to create a protected environment for protein folding. The cover figure shows the first crystal structure of a group II chaperonin in an open conformation. We have obtained structures of the archaeal chaperonin from Methanococcus maripaludis in both a peptide acceptor (open) state and a protein folding (closed) state. For details see the article by Pereira et al., pages 27958–27966.
Scientist Receives $100K Gates Global Health Grant
Jennifer Doudna, a Lab scientist and UC Berkeley professor of molecular and cell biology, has won a Gates foundation grant to "explore bold and largely unproven ways to improve health in developing countries." Doudna's project would use RNA restriction enzymes to detect the RNA specific to viruses or bacteria. These enzymes could be imprinted on paper and made to change color when exposed to viral or bacterial RNA in urine, much the way over-the-counter pregnancy tests change color when exposed to hormones in urine.. Full Story
Lab, JBEI Get Eco Honor From Diablo Magazine
Diablo Magazine, which covers the San Francisco East Bay, recently announced their 2010 Eco Awards, and Berkeley Lab and the Joint BioEnergy Institute were among the winners. The Lab was recognized for its Carbon Cycle 2.0 initiative, which brings the Lab’s energy research under one umbrella to help reduce carbon emissions. JBEI was lauded for its successful engineering of a microbe that could convert biomass into clean-burning biofuel. Full Story
PBD Scientists Get Physical in the Fight Against Cancer
Jay Groves, of the Physical Biosciences Division, and his student, Pradeep Nair, were co-authors of a Science paper in which it was shown that the biochemical activity of a key player in cancer metastasis can be altered by the application of a direct physical force. This research presents a potential new road for future cancer therapies and also suggests how the activity of cancer cells can be affected by surrounding tissue. Other co-authors of the paper included Joe Gray, director of the Life Sciences Division. Full Story
Microbes Produce Fuels Directly from Biomass
A collaboration led by researchers with the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI) has developed a microbe that can produce an advanced biofuel directly from biomass. Deploying the tools of synthetic biology, the JBEI researchers engineered a strain of Escherichia coli (E. coli) bacteria to produce biodiesel fuel and other important chemicals derived from fatty acids. Full Story
Lab Scientist Interviewed in ScienceWatch
Josh Heazlewood, a plant biologist with the Lab’s Physical Biosciences Division and director of the systems biology program in the Feedstocks Division of the Joint BioEnergy Institute, is the subject of an online interview in the November 2009 edition of ScienceWatch.com. In the interview, Heazlewood talks about SUBA, the subcelluar database for Arabidopsis thaliana, one of the model plants for biofuel research. Full Story
National Cancer Institute Names Jan Liphardt As Director of New Cancer Research Unit
Scientists at UC Berkeley and UCSF have formed a research center to explore the physical principles that govern the origin and behavior of cancer cells, and how they multiply in humans. Full Story
Protein structures revealed at record pace
Scientists at LBNL have developed a fast and efficient way to
determine the structure of proteins, shortening a process that often takes
years into a matter of days. PBD scientist, Greg Hura developed the technique
with John Tainer of Berkeley Lab’s Life Sciences Division and the
Scripps Research Institute in La Jolla, CA. Michael Adams and other scientists
from the University of Georgia contributed to the research. Full story
PBD Researchers Identify Photosynthetic Dimmer Switch
In a study of the molecular mechanisms by which plants protect themselves from oxidation damage should they absorb too much sunlight during photosynthesis, a team of researchers has discovered a molecular “dimmer switch” that helps control the flow of solar energy moving through the system of light harvesting proteins. This discovery holds important implications for the future design of artificial photosynthesis systems that could provide the world with a sustainable and secure source of energy. Full story
Higher Temps Yield More Sensitive MRI
Standard magnetic resonance imaging, MRI, is a superb diagnostic tool but one that suffers from low sensitivity, requiring patients to remain motionless for long periods of time inside noisy, claustrophobic machines. A new MRI method, much faster, able to distinguish even among specific target molecules, and many thousands of times more sensitive, has now been developed by researchers in the labs of Berkeley Lab materials scientist Alex Pines and physical bioscientist David Wemmer. Full story.
HIV Enzyme like Swiss Army Knife
Using ingenious molecular espionage, scientists have found how a single key enzyme, seemingly the Swiss army knife in HIV's toolbox, differentiates and dynamically binds both DNA and RNA as part of the virus's fierce attack on host cells. Using single-molecule fluorescent imaging to trace RT's activity in real time, not only reveals novel insights into how this critical viral enzyme functions, but also clarifies how some of the anti-HIV pharmaceuticals work. The research team includes Berkeley Lab physical bioscientist Gregory Bokinsky. Full story.
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 ->
