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News & Events 2011

CAD-type tools for engineering RNA componentsDecember 22, 2011 - CAD for RNA
Jay Keasling and his colleagues have developed computer assisted design (CAD)-type tools for engineering RNA components to control genetic expression in microbes. This holds enormous potential for microbial-based production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals. More >


Sensory neuronsDecember 7, 2011 - Research could help people with declining sense of smell
Neuroscientist John Ngai and colleagues have discovered a genetic trigger in olfactory stem cells that makes the nose renew its smell sensors, providing hope for new therapies for people who have lost their sense of smell due to trauma or old age. More >


E. coli bacteriaNovember 29, 2011 - E. Coli bacteria engineered to eat switchgrass and make transportation fuels
Strains of E. coli bacteria have been engineered by Jay Keasling and his research team to digest switchgrass biomass and synthesize its sugars into gasoline, diesel, and jet fuel. The switchgrass, which is among the most highly touted of the potential feedstocks for advanced biofuels, was pre-treated with ionic liquid, a key to the success of a new study. More >


Desulfovibrio vulgarisNovember 9, 2011 - Researchers create first of its kind gene map of sulfate-reducing bacterium
Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a study by Adam Arkin and his colleagues. The researchers have created a first-of-its-kind gene map of Desulfovibrio vulgaris, which can be used to identify the genes that determine how these bacteria interact with their surrounding environment. More >


BiotinOctober 31, 2011 - Scientists develop new tool for the study of spatial patterns in living cells
By embedding fixed arrays of gold nanoparticles into fluid lipid bilayers, scientists, led by Jay Groves, can study with unprecedented detail how the spatial patterns of chemical and physical properties on membranes can determine the fate of a cell – whether it lives or dies, remains normal or turns cancerous. More >


Woo-Jae Chung & Seung-Wuk LeeOctober 19, 2011 - Viruses turned into molecular Legos
Researchers, led by Seung-Wuk Lee, have turned a benign virus into building blocks for assembling structures that mimic collagen, one of the most important structural proteins in nature. The "self-templating assembly" process they developed could eventually be used to manufacture materials with tunable optical, biomedical, and mechanical properties. More >


Carolyn BertozziOctober 17, 2011 - Bertozzi named to Institute of Medicine
Carolyn Bertozzi, professor of chemistry and of molecular and cell biology, has been named to the prestigious Institute of Medicine (IOM), one of the highest national honors in the fields of health and medicine. Her lab focuses on profiling changes in the cell surface associated with cancer, inflammation and bacterial infection for development of diagnostic and therapeutic approaches. More >


Dept. of Transportation photoSeptember 27, 2011 - Scientists identify new microbe-produced advanced biofuel as an alternative to diesel fuel
Jay Keasling and his research colleagues have identified a terpene called bisabolane as a potential biofuel for replacing diesel fuel. They have also engineered two strains of microbe – a bacteria and a yeast – that can be used in the biosynthetic production of this clean, green, renewable and domestic alternative to diesel fuel. More >


MiscanthusSeptember 23, 2011 - Lessons to be learned from nature in photosynthesis
Lessons to be learned from nature could lead to the development of an artificial version of photosynthesis that would provide us with an absolutely clean and virtually inexhaustible energy source, says QB3 photosynthesis authority Graham Fleming and three international colleagues. More >


Reprogrammed muscle cellsSeptember 22, 2011 - Bioengineers reprogram muscles to combat degeneration
Irina Conboy and her research team have turned back the clock on mature muscle tissue, coaxing it back to an earlier stem cell stage to form new muscle. Moreover, they showed in mice that the newly reprogrammed muscle stem cells could be used to help repair damaged tissue. The achievement is described in the Sept. 23 issue of the journal Chemistry & Biology. More >


Doudna Nogales seahorseSeptember 22, 2011 - Close up look at a microbial vaccination program
Researchers, led by Jennifer Doudna and Eva Nogales, used a combination of cryo-electron microscopy and 3-D image reconstruction to determine the structure of Cascade, a protein complex that plays a key role in the microbial immune system by detecting and inactivating the nucleic acid of invading pathogens. Microbial immune systems in the human microbiome are critical to the preservation of the health of their human host. More >


A More Flexible Protein Ensemble (Image courtesy James Fraser)September 13, 2011 - Proteins better analyzed at room temperature
Proteins are jittery things – continually moving, flopping around and waving their molecular arms. But the practice of freezing protein crystals for analysis – a mainstay of biology for 40 years – erases most of the information about these motions, leading scientists to miss vital clues about how these molecules operate, according to a report by Tom Alber and his colleagues. More >


A candidate using BNC UV beamSeptember 7, 2011 - UC Berkeley and Laney College team up to train workers in medical device technology
A group of Laney College students, all of them displaced workers looking for a new job field, got specialized training this summer in medical device technology at UC Berkeley through a new collaboration between UC Berkeley and Peralta Community College District staff. At least two students have already received Bay Area job offers as a result. More >


Nano Precision MedicalAugust 31, 2011 - Movin' on up
Nano Precision Medical, a biomedical startup incubated at the QB3 Garage@Berkeley, recently expanded to occupy two benches and two private offices at the QB3 East Bay Innovation Center in Berkeley. More >


BioBuilderAugust 25, 2011 - High school teachers explore the engineering of biology at BioBuilder Workshop
When 27 high school science teachers return to their classrooms this fall, they will bring with them new approaches to teaching science and engineering, thanks to a week-long workshop sponsored by the Synthetic Biology Engineering Research Center (SynBERC) and held at MIT in August. More >


ABPDUAugust 18, 2011 - Berkeley Lab opens advanced biofuels facility
Berkeley Lab has opened the Advanced Biofuels Process Demonstration Unit (ABPDU), a state-of-the art facility, designed to help expedite the commercialization of advanced next-generation biofuels by providing industry-scale test beds for discoveries made in the laboratory. More >


iCLEMJuly 21, 2011 - Bay Area students get hands-on science experience and a salary
Now in its fourth year, the iCLEM (Introductory College Level Experience in Microbiology) program, which is aimed at high school students who trend outside the typical curve of academic enrichment programs, is bigger and stronger than ever. Eight high school students from the East Bay Area will earn $2,000 upon completion of an eight-week program in which they work in a state-of-the art microbiology laboratory on a research project related to bioenergy. More >


Pines-NMRJuly 6, 2011 - Researchers apply NMR/MRI to microfluidic chromatography
By pairing remote-detection NMR/MRI with a unique chromatography separation medium, researchers led by Alex Pines have opened the door to a portable system for highly sensitive chemical analysis that would be impractical if not impossible with conventional technologies. More >


Pines-microflow-imageWebJuly 1, 2011 - Breaking Kasha’s Rule
Paul Alivasatos and members of his research group have created tetrapod molecules of semiconductor nanocrystals and watched them break a fundamental principle of photoluminescence known as “Kasha’s rule.” The discovery holds promise for multi-color light emission as well as medical technologies. More >


Serous adenocarcinoma in bilateral ovariesJune 29, 2011 - Ovarian cancer genome mapped, opens door to personalized medicine
John Ngai joined hundreds of scientists from more than 80 institutions to develop the first comprehensive catalog of the genetic aberrations responsible for an aggressive type of ovarian cancer. This effort could lead to targeted treatment based on a person’s cancer fingerprint. More >


Pines-microflow-imageWebJune 22, 2011 - QB3 team wins R&D 100 Award
QB3 researchers won an 2011 R&D 100 award, also known as the "Oscar of Innovation." The winning invention was a new version of MRI technology – called Magnetic Resonance Microarray Imaging – that delivers results a million times faster than conventional MRI. More >


3D plasmon rulerJune 16, 2011 - Taking the 3D measure of macromolecules
A team led by Paul Alivisatos has developed the world’s first three-dimensional plasmon rulers, capable of measuring nanometer-scale spatial changes in macromolecular systems. These 3D plasmon rulers could provide unprecedented details on such critical dynamic events in biology as the interaction of DNA with enzymes, the folding of proteins, the motion of peptides or the vibrations of cell membranes. More >


Ecoli circuitsMay 26, 2011 - Biological circuits for synthetic biology
Using the tools of synthetic biology, a research team led by Adam Arkin has engineered 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.
More >


Motion of the small ribosomal subunit,May 19, 2011 - Atomic-scale structures of ribosome could help improve antibiotics
In a development that could lead to better antibiotics, Jamie Cate and other researchers have derived atomic-scale resolution structures of the cell’s protein-making machine, the ribosome, at key stages of its job. The structures reveal that the ribosome’s ability to rotate an incredible amount without falling apart is due to the never-before-seen springiness of molecular widgets that hold it together.
More >


May 17, 2011 - Nuclear magnetic resonance with no magnets
Nuclear magnetic resonance (NMR) is a powerful tool for chemical analysis and, in the form of magnetic resonance imaging (MRI), an indispensable technique for medical diagnosis. But its uses have been limited by the need for strong magnetic fields and big, expensive, superconducting magnets. Now Alex Pines and his colleagues have demonstrated that they can do NMR in a zero magnetic field without using any magnets at all. More >


May 11, 2011 - Striking the right balance: researchers counteract biofuel toxicity in microbes
Jay Keasling and his fellow researchers have created a library of microbial efflux pumps that reduce toxicity and boost production of biofuels in engineered strains of microbes. This library and the bioprospecting strategy behind it should serve as valuable new tools for the development of advanced biofuels and other areas of biotechnology as well. More >


April 2011 - Tuning into our genetic inheritance
One of the most common nutritional deficiencies in the United States, folic acid deficiency has been linked to conditions as serious as spina bifida. Geneticist Jasper Rine, whose research focuses on exploring human gene variation, has sequenced the genes involved in folic acid metabolism in an effort to unravel the genetic basis of this disease. His hope: that someday we may be able to prevent or treat a variety of medical conditions with something as simple as a nutritional supplement. More >


April 20, 2011 - Starting a new metabolic path
Berkeley researchers have demonstrated a new technique for the metabolic engineering of microbes that speeds up and improves the identification and quantification of proteins within a cell or organism. The new technique is called "targeted proteomics." More >


April 19, 2011 - Synthetic biology institute launched
An alliance of top researchers has formed the Synthetic Biology Institute (SBI), advancing UC Berkeley's efforts to engineer cells and biological systems in ways that promise to transform technology in health and medicine, energy, the environment, new materials, and a host of other critical arenas. The new institute is launching a collaborative effort with its first industry member, Agilent Technologies Inc. More >


DeloitteApril 11, 2011 - QB3, Deloitte collaborate to drive California bioscience innovation
QB3 has entered into a collaboration with Deloitte to help the institute in its efforts to convert bioscience innovation into a driver for jobs, companies, and improved health in California. More >


TataMarch 31, 2011 - CCB and Tata Consultancy Services partner to advance understanding of personal genomic variation
The Center for Computational Biology, a UC Berkeley strategic initiative and QB3-Berkeley affiliated center, is partnering with Tata Consultancy Services in a new initiative to develop a pioneering software platform to analyze genomic differences and bring closer the era when one’s personal genome will be a starting point for health and medical advice. More >


Molecular machinery that helps transport messenger RNA from a cell’s nucleusMarch 28, 2011 - RNA-exporting machine deciphered
The molecular machinery that helps export messenger RNA from a cell’s nucleus to the cytoplasm where it guides the synthesis of proteins has been structurally mapped by QB3 scientists. In addition to new insights on cell mechanics, the research could advance understanding of certain congenital diseases. More >


Systems biologyMarch 17, 2011 - Arkin and Schaffer highlight the key insights of systems biology
Systems biology holds promise for advances in such important areas as pharmaceuticals, environmental remediation, and sustainable energy; but, as an essay by Adam Arkin and David Schaffer explains, its most profound impact is that it might one day provide an answer to the central question: What is life? More >


Tether-free SIMBAS chip March 16, 2011 - New blood analysis chip could lead to disease diagnosis in minutes
A major milestone in microfluidics could soon lead to stand-alone, self-powered chips that can diagnose diseases within minutes. The device, developed by researchers at UC Berkeley, Dublin City University in Ireland, and Universidad de Valparaíso Chile, is able to process whole blood samples without the use of external tubing or external components. More >


DNAMarch 14, 2011 - Genome-scale sequencing expands at Berkeley
Resources to support DNA research have expanded dramatically with the recent acquisition of state of the art equipment for QB3 core research facilities, removing a bottleneck and making it possible to produce massive amounts of DNA sequence. In addition, a new bioinformatics training and resource facility has been formed to assist researchers with the flood of DNA sequence information now available to them. More >


Butanol biosynthetic pathwayMarch 1, 2011 - Turning bacteria into butanol biofuel factories
While ethanol is today’s major biofuel, researchers aim to produce fuels more like gasoline. Butanol is the primary candidate, now produced primarily by Clostridium bacteria. Michelle Chang has transplanted the enzyme pathway from Clostridium into E. coli and gotten the bacteria to churn out 10 times more n-butanol than competing microbes, close to the level needed for industrial scale production.
More >


Gray Davis & Gavin NewsomFebruary 24, 2011 - QB3 celebrates 10 years of bioscience innovation
QB3 celebrates a decade of driving the bioeconomy and spells out its goal of helping the state foster science and innovation to benefit society. More >


Michael MarlettaFebruary 22, 2011 - Scripps Research Institute names Marletta as president
Chemistry professor Michael Marletta has been named the next president of The Scripps Research Institute. Marletta will join the Scripps faculty and will become the President-elect on July 1, 2011, and he will become President and CEO on January 1, 2012. More >


Herr and KumarFebruary 14, 2011 - Herr and Kumar receive NSF CAREER awards
Bioengineering Assistant Professors Amy Herr and Sanjay Kumar have received 2011 National Science Foundation Faculty Early Career Development (CAREER) Program awards. CAREER awards are given to young researchers in science and engineering who have also translated their work into significant educational activities. More >


McKone Grand ChallengesFebruary 8, 2011 - Challenges for biofuels – new life cycle assessment report
Energy Biosciences Institute researchers have produced a report that presents seven grand challenges for addressing the social, economic, and environmental issues that must be confronted before advanced biofuels can replace gasoline on a widescale basis. More >


Neurospora colonyFebruary 7, 2011 - A new pathway for antidepressants
Using a unique and relatively simple cell-based fluorescent assay they developed, Ehud Isacoff and other researchers have identified a means by which fluoxetine, the active ingredient in the antidepressant Prozac, suppresses the activity of the TREK1 potassium channel. TREK1 activity could be an important target for fluoxetine and other antidepressant drugs.
More >


Jan LiphardtJanuary/February 2011 - Fighting cancer across the disciplines
Biophysicist Jan Liphardt believes that a new, multidisciplinary approach to understanding fundamental aspects of cancer is key to making progress in the ongoing war against this disease. As director of the new $15 million Bay Area Physical Sciences-Oncology Center, one of 12 such centers funded by the National Cancer Institute, Liphardt is in position to have a significant impact on this national effort. More >


Neurospora colonyJanuary 31, 2011 - Prize winners in DNA contest announced
In a demonstration of "reverse-ecology," Rachel Brem and other UC Berkeley biologists have shown that one can determine an organism's adaptive traits by looking first at its genome and checking for variations across a population. The study offers a powerful new tool in evolutionary genetics research, one that could be used to help monitor the effects of climate change and habitat destruction.
More >


DNA winnersJanuary 26, 2011 - Prize winners in DNA contest announced
A precocious research proposal for testing dietary health, a parody of Lady Gaga’s “Telephone” music video and a philosophical essay on genetic testing have won prizes from UC Berkeley’s “Bring Your Genes to Cal” program. More >


James BergerJanuary 20, 2011 - National Academy of Sciences honors Berger
James Berger is among 13 individuals to be honored by the National Academy of Sciences (NAS) for their extraordinary scientific achievements in the areas of biology, chemistry, physics, economics, and psychology. Berger, recipient of the NAS Award in Molecular Biology, is being honored for elucidating the structures of topoisomerases and helicases and providing insights into the biochemical mechanisms that mediate the replication and transcription of DNA. Sponsored by Pfizer Inc., the award consists of a $25,000 prize to recognize a recent notable discovery in molecular biology by a young scientist. More >


Polymer membranesJanuary 11, 2011 - Polymer membranes with molecular-sized channels that assemble themselves
Ting Xu and a team at QB3-Berkeley and LBNL have developed a solution-based method for inducing polymer membranes with molecular-sized channels to assemble themselves. Fully compatible with commercial membrane-fabrication, this new technique is believed to be the first example of organic nanotubes fabricated into a functional membrane over macroscopic distances. The material might be applied in a number of fields, including desalination. More >


Rogers Family FoundationJanuary 3, 2011 - A booster rocket for proof-of-concept research: the 2010 Rogers Awards
John Kuriyan and Art Weiss have won a Rogers Bridging-the-Gap Award. The awards, which are granted by the Rogers Family Foundation of Oakland in an annual competition coordinated by QB3, are renewable for a second year and provide up to $250,000 for projects that could benefit society and have a strong chance of commercialization. Kuriyan and Weiss plan is use the award to conduct screening for drug compounds that turn T cells off by inhibiting a key enzyme called ZAP70. More >



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