QB3-Berkeley News and Media Archive – 2012

Highlights of QB3-Berkeley Research, Awards, and Events News from 2012.

December 19, 2012 – What Do Leeches, Limpets and Worms Have in Common?
As much as one-third of marine life, including clams, octupuses and worms, fall into a group called the lophotrochozoa, ancient creatures that originated more than 500 million years ago. Daniel Rokhsar spearheaded a team that has now sequenced the genomes of 3 of these creatures, a limpet, a polychaete worm and a freshwater leech, to learn more about their evolution. More >

December 17, 2012 – To Revert Breast Cancer Cells, Give Them the Squeeze
Daniel Fletcher and his research colleagues have found that compression can guide malignant breast cells back to a normal growth pattern. The findings, presented at the American Society for Cell Biology meeting, demonstrate the influence of mechanical forces on a cell’s destiny. More >

December 11, 2012 – New Energy Biosciences Building Dedicated
State legislators and city officials joined nearly 100 UC Berkeley researchers and administrators on Monday, Dec. 10, to dedicate the new Energy Biosciences Building and celebrate the fifth anniversary of the Energy Biosciences Institute, a partnership between the campus, Lawrence Berkeley National Laboratory, the University of Illinois at Urbana-Champaign and the energy company BP. More >

November 12, 2012 – A Better Route to Xylan
After cellulose, xylan is the most abundant biomass material on Earth, and therefore represents an enormous potential source of stored solar energy for the production of advance biofuels. Jay Keasling and his colleagues have identified a gene in rice plants whose suppression improves both the extraction of xylan and the overall release of the sugars needed to make biofuels. More >

November 7, 2012 – Sweet Diesel! Discovery Resurrects Process to Convert Sugar Directly to Diesel
A long-abandoned fermentation process is being resurrected by Douglas Clark and his research group to produce compounds to feed a catalytic reaction that produces a fuel that looks and acts just like diesel. The fuel has a higher energy content than ethanol, and could help replace nonrenewable transportation fuels. More >

October 30, 2012 – Folding Funnels Key to Biomimicry
Carolyn Bertozzi and her research team have shown that a concept widely accepted as describing the folding of a single individual protein is also applicable to the self-assembly of multiple proteins. Their findings provide important guidelines for future biomimicry efforts, particularly for device fabrication and nanoscale synthesis. More >

October 18, 2012 – Berkeley iGEM Team Wins Regional Jamboree on Its Way to World Championship
The UC Berkeley team for the International Genetically Engineered Machine competition (iGEM) won first place and the best presentation award at the Americas West Regional Jamboree held at Stanford Oct. 12-14, ensuring their participation at the World Championships at MIT in November. More >

October 8, 2012 – A Welcome Predictability
Adam Arkin and his research team have developed an “adaptor” that makes the genetic engineering of microbial components substantially easier and more predictable. More >

October 4, 2012 – QB3-Berkeley Scientists Win NSF Early Career Awards
2012 has been a rewarding year for three of QB3-Berkeley’s scientists. Chris Anderson, John Dueber, and Andy Martin have all been selected for National Science Foundation Faculty Early Career Development (CAREER) Program awards, given to young researchers in science and engineering who also translate their work into significant education activities. More >

September 14, 2012 – Scientists Create First 3-D Model of a Protein Critical to Embryo Development
Researchers led by Eva Nogales have constructed the first detailed and complete picture of a protein complex that is tied to human birth defects as well as the progression of many forms of cancer. Knowing the architecture of this protein, PRC2, should be a boon to its future use in the development of new and improved therapeutic drugs. More >

August 14, 2012 – New PhD Program in Computational Biology
The University of California has approved the Center for Computational Biology’s plan for an interdisciplinary PhD program in Computational Biology. The doctoral program, which offers an innovative curriculum of study for students interested in conducting research at the interface of the computational and biological sciences, will begin accepting applications this fall for students who will start in Fall 2013. More >

August 13, 2012 – QB3 Helps Laid-Off Workers Retool for New Careers
Laid-off workers are getting hands-on training in microfabrication at Berkeley’s Biomolecular Nanotechnology Center through a collaborative technical-education initiative with Oakland’s Laney College. More >

July 24, 2012 – Healy and Lee Get NIH Award for Tissue Chip
Kevin Healy and Luke Lee and collaborators have been awarded a two-year, $1.7 million grant from the NIH to develop on-chip models of living human heart and liver tissue. The grant is part of the Tissue Chip for Drug Screening program, an initiative to help predict the safety of drugs more quickly and cost-effectively, and thereby speed the development of effective therapeutics. More >

July 19, 2012 – Bakar Fellows Advance Commercially Promising Research
Research innovations by early-career faculty members Amy Herr and Michael Rape are getting a significant boost toward commercial development from UC Berkeley’s Bakar Fellows Program. With Bakar support, Herr is developing a screening strategy aimed to improve testing for prostate cancer. Rape is working on a systematic method to screen for compounds that could yield potent drugs against a group of human enzymes with links to cancer. More >

July 16, 2012 – Not Your Typical Summer Job for High School Students
A summer job for eight high school students from the East Bay means working in a state-of-the art microbiology research laboratory on the next-step in bioenergy. The iCLEM program is a paid summer internship for high school students from economically disadvantaged backgrounds who fall outside the typical curve of academic enrichment. More >

July 12, 2012 – Discovery Opens Door to Attacking Biofilms That Cause Chronic Infections
Using super-resolution microscopy and continuous fluorescent imaging, Steven Chu, Jan Liphardt, and their research team have for the first time revealed the structure of bacterial biofilms, which are responsible for the tenacious nature of bacterial diseases such as cholera and chronic sinusitus. The picture provides new targets for the development of drugs that can tear down these structures. More >

June 28, 2012 – Programmable DNA Scissors Found for Bacterial Immune System
Jennifer Doudna co-led an international team of researchers that has discovered a programmable RNA complex in the bacterial immune system that guides the cleaving of DNA at targeted sites. This discovery opens a new door to genome editing with implications for the green chemistry microbial-based production of advanced biofuels, therapeutic drugs, and other valuable chemical products.

June 11, 2012 – Kumar Lab Explains Fast Tumor Migration
Tight spaces have the counterintuitive effect of aiding the spread of tumor cells, according to a new study led by Sanjay Kumar. His research team developed a 3D model to study the biophysical environment factors influencing tumor invasion and found that narrow channels gave cells traction to help them move faster. The findings have implications for certain cancers, including malignant brain tumors, which tend to infiltrate most rapidly along tissue interfaces and confined spaces, such as blood vessels and nerve tracts. More >

June 6, 2012 – The Real Culprit Behind Hardened Arteries? Stem cells, Says Landmark Study
Vascular diseases are actually a type of stem cell disease, according to a new study by Song Li and his research team. The discovery challenges a long-standing belief that smooth muscle cells contribute to clogged blood vessels, and could revolutionize research into therapies for heart attacks and strokes, which account for one in three deaths in the United States. More >

May 13, 2012 – Scientists Generate Electricity from Viruses
Seung-Wuk Lee and his research team have developed a way to generate power using harmless viruses that convert mechanical energy into electricity. The milestone could lead to tiny devices that harvest electrical energy from the vibrations of everyday tasks. It also points to a simpler way to make microelectronic devices. That’s because the viruses arrange themselves into an orderly film that enables the generator to work. Self-assembly is a much sought after goal in nanotechnology. More >

May 3, 2012 – From Soil Microbe to Super-Efficient Biofuel Factory?
Chris Chang and his research colleagues are exploring whether a common soil bacterium can be engineered to produce liquid transportation fuels much more efficiently than the ways in which advanced biofuels are made today. The process would be powered only by hydrogen and electricity. The goal is a biofuel – or electrofuel, as this new approach is called – that doesn’t require photosynthesis. More >

April 19, 2012 – First Atomic-Scale Real-Time Movies of Platinum Nanocrystal Growth in Liquids
Paul Alivisatos’ research group has developed a technique for encapsulating liquids of nanocrystals between layers of graphene so that chemical reactions in the liquids can be imaged with an electron microscope. With this technique, movies can be made that provide unprecedented direct observations of physical, chemical and biological phenomena that take place in liquids on the nanometer scale. More >

April 11, 2012 – Marqusee Lauded for Protein-Folding Research and ‘Encouragement of the Next Generation’ of Scientists
The American Society for Biochemistry and Molecular Biology has named Susan Marqusee, professor of molecular and cell biology at the University of California, Berkeley, and Berkeley director of the California Institute for Quantitative Biosciences, the winner of the society’s William C. Rose Award. More >

April 9, 2012 – Exciting New Field of Bioorthogonal Chemistry Owes a Debt to Curiosity-Driven Research from Previous Eras
In her Kavli Lecture at the American Chemical Society’s spring meeting, Carolyn Bertozzi described how her ground-breaking bioorthogonal chemistry research made use of experiments nearly a century ago by two German chemists whose work rose from scientific curiosity. More >

March 26, 2012 – Pilot Program to Bolster Biophysical Sciences’ Innovation Pipeline
UC Berkeley is launching the Bakar Fellows Program, a pilot project that will target faculty research with a high degree of commercial promise across the fields of engineering, computer science, chemistry and biological and physical sciences, with the goal of guiding more discoveries from the research lab to the marketplace. More >

March 26, 2012 – New Synthetic Biology Technique Boosts Microbial Production of Diesel Fuel
Researchers co-led by Jay Keasling have developed a “dynamic sensor-regulator system” that can detect metabolic changes in microbes during the production of fatty acid-based fuels or chemicals and control the expression of genes affecting that production. The result in one demonstration was a threefold increase in the microbial production of biodiesel from glucose. More >

March 23, 2012 – A Shiny New Tool for Imaging Biomolecules
A scientific team led by Jay Groves has embedded artificial membranes with billions of nano-antennas that can boost optical signals from a protein tens of thousands of times. The technique could provide a critical tool in the fight against a wide range of health problems, including cancer. More >

March 13, 2012 – A Fragrant New Biofuel
Jay Keasling and his colleagues have identified methyl ketones, chemical compounds known for their fragrance and flavor, as strong biofuel candidates. Methyl ketones produced from glucose by engineered E. coli yielded high cetane numbers – a diesel fuel rating comparable to the octane number for gasoline.

February 28, 2012 – JBEI Startup Takes Aim at Petrochemicals
Lygos, a tenant of the QB3 East Bay Innovation Center, is engineering enzymes to produce plastic precursors from sugar. The company co-founders include Jay Keasling, a world authority on synthetic biology and metabolic engineering. More >

February 1, 2012 – Professors’ Innovations Benefit Society, Economy
Cutting-edge research is a hallmark of UC Berkeley, and it should come as no surprise that faculty members are eager to see their discoveries put to use. Many, such as chemistry dean Richard Mathies, have formed start-ups to develop their inventions to a point where they become viable in the marketplace, benefiting not only society but the university as well. More >

January 11, 2012 – New Information on the Waste-Disposal Units of Living Cells
Berkeley researchers led by Andreas Martin and Eva Nogales have provided the most detailed look ever at the “regulatory particle” used by the proteasome – one of the most critical protein machines in living cells – to identify and degrade proteins marked for destruction. This new information holds implications for a broad range of vital biochemical processes, including transcription, DNA repair and the immune defense system. More >

Faculty Media Mentions, 2012

December 10, 2012, PNAS
Microfluidic Western Blotting

December 1, 2012, Economist
The Dream of the Medical Tricorder

October 25, 2012, GenomeWeb
Startup DiAssess Creating Device to Detect Protein, Nucleic Acids

September 20, 2012, Chemical & Engineering News
Fluorescent Probe Highlights CO in Cells

September 15, 2012, Contra Costa Times
Ex-Solyndra Workers Find Cure for Joblessness in Laney College Medical Tech Manufacturing Program

September 14, 2012, San Francisco Business Times
QB3 Powers New Wave of Bio Startups

September 10, 2012, WBUR
Questioning Last Week’s Big DNA News

September 1, 2012, Genetic Engineering & Biotechnology News
Lighting Up Live Cells With Fluorescence

August 16, 2012, Daily Californian
UC Berkeley Partner Program Provides Training for Laid-Off Workers

August 6, 2012, KQED – Quest
Newly Discovered Stem Cells Cause Clogged Arteries

June 14, 2012, Technology Review
Parents Could Skip the Doctor’s Office with this Device

June 13, 2012, Bloomberg TV
Microbes Can Convert Waste to Fuel

June 11, 2012, New York Times
A Panoramic View of Energy Innovation

June 8, 2012, Science Friday
Identifying the Real Culprit Behind Killer Vascular Diseases

June 2, 2012, CNTV
Viral Electricity: New Usage of Virus

May 11, 2012, New Scientist
Bug Evolved a Self-propelling Corkscrew

May 9, 2012, JournalStar
Market Should Dictate Crops Used to Produce Biofuels

May 1, 2012, San Francisco Chronicle
UC Berkeley Wins $60 Million for Computer Center

April 25, 2012, Nature
RNA Studies Under Fire

April 9, 2012, ScienceDaily
High-resolution Atomic Imaging of Specimens in Liquid by TEM Using Graphene Liquid Cell

April 9, 2012, Science 2.0
What Blindsight Can Tell Us About the Architecture of the Brain

April 9, 2012, ScienceBlog.com
Diet May Treat Some Gene Mutations

April 2, 2012, Technology Review
Genetic Sensor Boosts Biofuel Production

March 27, 2012, PhysOrg.com
New Field of Chemistry Has Potential for Making Drugs Inside Patients – and More

March 14, 2012, Live Science
How Scientists Are ‘Greening’ Chemistry

February 20, 2012, separationsNOW.com
Microfluidics Go Way Out West: Conducting Western Blotting on a Microfluidic Chip

February 8, 2012, PopTech
Energy Shop Talk: Jay Keasling on Plant-based Fuels

January 6, 2012, Energy shop talk: Jay Keasling on plant-based fuels
Synthetic Biology: Key Field of the Future

January 6, 2012, Fibre2Fashion
University Debuts Cotton Gold-Standard Genome Sequence