QB3-Berkeley news archive – 2013

Highlights of QB3-Berkeley research, awards, and events news from 2013.

December 23, 2013 – Yildiz Receives Early Career Award
Ahmet Yildiz, assistant professor of biochemistry, biophysics and structural biology, is among 102 researchers named by President Obama as recipients of the Presidential Early Career Awards for Scientists and Engineers, the highest honor bestowed by the U.S. government on science and engineering professionals in the early stages of their independent research careers. More >

December 10, 2013 – Carolyn Bertozzi Elected to National Academy of Inventors
Carolyn Bertozzi has been named a Fellow of the National Academy of Inventors (NAI). The honor is based on her outstanding inventions and discoveries, which include the creation of a suite of techniques comprising “bioorthogonal chemistry,” chemical reactions that can take place inside living systems without interfering with native biochemical processes. Her work has inspired several additional bioorthogonal chemical processes used in research on cancer and other diseases. More >

October 29, 2013 – Less Toxic Metabolites, More Chemical Product
By preventing the build-up of toxic metabolites in engineered microbes, a dynamic regulatory system developed by Jay Keasling and his colleagues can help boost production of an advanced biofuel, a therapeutic drug, or other valuable chemical products. The system has already been used to double the production in E. coli of amorphadiene, a precursor to the premier antimalarial drug artemisinin. More >

October 20, 2013 – Physical Cues Help Mature Cells Revert into Embryonic-Like Stem Cells
Song Li and his research group have shown that culturing mature cells on a microgrooved surface boosts the efficiency of reprogramming them back into an embryonic-like, stem cell state. Such pluripotent stem cells have become a research mainstay in regenerative medicine, disease modeling and drug screening. More >

October 10, 2013 – BioBuilder Workshop Benefits High School Science Teachers, and Their Students
For one week in August, the teachers became the students when nine high school educators attended the 2013 BioBuilder program in Berkeley’s Stanley Hall. This year’s workshop was designed to help teachers find innovative ways to introduce synthetic biology into their classrooms and featured wet labs, lunch seminars with professors, and a field trip to the Joint BioEnergy Institute (JBEI). More >

October 2, 2013 – 3D Dynamic Imaging of Soft Materials
Through a combination of transmission electron microscopy (TEM) and a unique graphene liquid cell, Paul Alivisatos and other researchers have recorded the three-dimensional motion of DNA connected to gold nanocrystals, the first reported use of TEM for 3D dynamic imaging of soft materials. More >

September 18, 2013 – Toxoplasma Infection Permanently Shifts Balance in Cat-and-Mouse Game
Infection with the toxoplasma parasite makes mice fearless in the presence of cats. But how? Michael Eisen and other Berkeley researchers looked at the effects of three common strains of toxoplasma and found that they remove the fear of cat urine for as long as four months, apparently making permanent changes in the mouse brain’s neurons. More >

September 17, 2013 – BNC to House NSF-Funded Nanoscale Microscope
Researchers using a new tool in QB3-Berkeley’s Biomolecular Nanotechnology Center (BNC) will investigate matter on an unprecedented scale, thanks to a $2 million NSF grant for the purchase and installation of a new ORION Nanofab microscope. More >

September 4, 2013 – Grant for Newborn Genetic Screening
A research team including computational biologist Steven Brenner has received a $6 million federal grant to study whether it makes sense to perform genetic sequencing as part of the routine screening of all newborns. The researchers will also look at questions of ethics and public interest. More >

August 26, 2013 – Genome Editing Pioneers Gather at Berkeley
More than 300 people gathered August 26 to hear from scientists leading the emerging field of genome editing, at a symposium hosted by QB3-Berkeley and sponsored by Life Technologies. New advances offer precise genetic manipulation and novel approaches to tackling human disease. More >

July 31, 2013 – Acclaimed Molecular Biologist Named New QB3-UCSF Director
QB3 has tapped Nevan Krogan to lead QB3-UCSF. Krogan, a professor of cellular and molecular pharmacology and an investigator at the J. David Gladstone Institutes, is known for his prolific research into developing and using systems biology approaches to help understand complex biological phenomena. More >

July 29, 2013 – Tetrapod Quantum Dots Light the Way to Stronger Polymers
Researchers led by Paul Alivisatos have developed advanced opto-mechanical stress probes based on tetrapod quantum dots (tQDs) that allow precise measurement of the strength of polymer fibers with minimal impact on mechanical properties. These fluorescent tQDs could lead to stronger, self-repairing polymer nanocomposites as well as aid in monitoring effects of drugs on the metastasis of cancer cells. More >

July 15, 2013 – Tiny Bubbles Hold Big Promise for NMR/MRI
Alex Pines and his research team have shown that tiny bubbles carrying hyperpolarized xenon gas hold big promise for imaging technologies, as these xenon carriers can detect the spatial distribution of molecules with far greater sensitivity than conventional NMR/MRI. Applications include imaging of complex chemical and environmental samples, as well as early stage detection and characterization of lung cancer tumors. More >

July 8, 2013 – Berkeley Researchers Win 2013 R&D 100 Awards
QB3-Berkeley researchers are among those who have won 2013 R&D 100 Awards this year. Presented by R&D Magazine, the awards recognize the year’s top 100 technology products from industry, academia, and government-sponsored research, ranging from chemistry to materials to biomedical breakthroughs.
More >

July 1, 2013 – Cancerous Traffic Jams: Biomechanical Factor in Malignancies Identified
A research team led by chemist Jay Groves has demonstrated that the malignant activity of a cellular protein system strongly linked to breast cancer can arise from what essentially are protein traffic jams. More >

June 19, 2013 – Expressly Unfit for the Laboratory
A new study by Adam Arkin and his colleagues challenges the orthodoxy of microbiology, which holds that in response to environmental changes, bacterial genes will boost production of needed proteins and decrease production of those that aren’t. The study found that for bacteria in the laboratory there was little evidence of adaptive genetic response. More >

June 12, 2013 – Researchers Develop Easy and Effective Therapy to Restore Sight
Gene therapy using adeno-associated virus (AAV) has successfully restored sight to people with a rare inherited retinal degeneration, but current therapy requires injecting the virus directly into the retina. David Schaffer and his research colleagues have evolved AAV so that it is able to penetrate the retina, allowing doctors to inject the virus and its gene load into the vitreous to reach all cells of the retina. More >

June 11, 2013 – Bakar Fellows Pursue Path to Marketplace
Lydia Sohn is among five UC Berkeley scientists who have been awarded Bakar Fellowships to help them advance their lab-bench discoveries into the marketplace. Sohn will look for ways to screen for metastatic cancer cells that have been shed from breast tumors and are circulating in the blood threatening to establish satellite tumors. More >

June 5, 2013 – Researchers Increase NMR/MRI Sensitivity Through Hyperpolarization of Nuclei in Diamond
Vikram Bajaj, Alex Pines, Dmitry Budker, and their colleagues have demonstrated the first magnetically-controlled nearly complete hyperpolarization of the spins of carbon-13 nuclei located near synthetic defects in diamond crystals. This spin hyperpolarization, which can be carried out with refrigerator-style magnets at room temperature, enhances NMR/MRI sensitivity by many orders of magnitude. More >

May 24, 2013 – Copper on the Brain
Christopher Chang and his research group have developed unique fluorescent probes for molecular imaging of copper in the brain, and are using these probes to uncover new information critical to a healthy mind. More >

May 15, 2013 – Turning Up the Heat on Biofuels
Douglas Clark and his colleagues have employed a promising technique for improving the ability of cellulase enzymes to operate at advantageously high temperatures. More >

May 9, 2013 – Rape Appointed HHMI Investigator
Michael Rape’s experiments at age 12 on how air pollution killed trees in his native Bavaria, eventually led him to a career studying the impacts of chemicals on biology. His current work on a protein, ubiquitin, found in every cell in the body has resulted in his appointment as a Howard Hughes Medical Institute (HHMI) investigator. More >

May 6, 2013 – Light-Controled Hydrogel for Soft Robotics
Inspired by the way plants plants grow, researchers led by Seung-Wuk Lee have created a hydrogel that can be manipulated by light. This shape-changing gel, a biopolymer made of thin sheets of graphene combined with elastic proteins, could have future applications in the emerging field of soft robotics. More >

April 30, 2013 – Berger Named to National Academy of Sciences
Biochemist and structural biologist James Berger has been elected member of the National Academy of Sciences (NAS), one of the highest honors given to a scientist or engineer in the United States. More >

April 12, 2013 – Launch of Antimalarial Drug a Triumph for Synthetic Biology
The best therapy today for malaria is a drug combination that includes a derivative of artemisinin, now solely available from plants. On April 11, Sanofi began production of the first semi-synthetic version of artemisinin, derived from yeast developed by biotech company Amyris based on discoveries in the laboratory of Jay Keasling. More >

April 11, 2013 – Scientists Map Elusive 3-D Structure of Telomerase Enzyme, Key Actor in Cancer, Aging
Like finally seeing all the gears of a watch and how they work together, Kathleen Collins and her colleagues have, for the first time ever, solved the puzzle of how the various components of an entire telomerase enzyme complex fit together and function in a three-dimensional structure. The research represents a breakthrough that could open up a host of new approaches to fighting disease. More >

April 7, 2013 – Sweet Success: Researchers Find Way to Catalyze More Sugars From Biomass
Using an ultrahigh-precision microscopy technique, Jan Liphardt, Doug Clark, and their colleagues have uncovered a way to improve the collective catalytic activity of enzyme cocktails on cellulosic biomass, boosting the yields of sugars for the production of advanced biofuels. More >

April 4, 2013 – Department of Energy Renews Joint BioEnergy Institute for Another Five Years
Reaffirming the Obama administration’s commitment to the development of sustainable alternatives to fossil fuel energy, the U.S. Department of Energy (DOE) has announced a five-year renewal of funding for the Joint BioEnergy Institute (JBEI), a Bay Area multi-institutional scientific partnership. Under the renewal, JBEI, which is led by Jay Keasling, will be funded at the rate of $25 million annually through 2018. More >

April 2, 2013 – President Announces BRAIN Initiative
President Barack Obama has announced a major national initiative to understand how the brain works and how it goes awry. Neuroscientist John Ngai, chemist Paul Alivisatos, and chemical engineer Jay Keasling were on hand at the White House to lend support to the so-called BRAIN initiative, which Ngai termed “our moon project.” More >

March 26, 2013 – Making Living Matter Programmable
A dozen of the pioneers of synthetic biology gathered in Berkeley March 25 to discuss the revolutionary potential of “programming life,” which some compared to the digital revolution. The event was co-hosted by SynBERC and Discover magazine. More >

March 21, 2013 – Computer Simulations Yield Clues to How Cells Interact with Surroundings
Scientists led by Mohammad Mofrad have developed a computer model of a protein that helps cells interact with their surroundings. Like its biological counterpart, the virtual integrin snippet is about twenty nanometers long. It also responds to changes in energy and other stimuli just as integrins do in real life. The result is a new way to explore how the protein connects a cell’s inner and outer environments. More >

March 5, 2013 – Evidence that Comets Could Have Seeded Life on Earth
Richard Mathies and other scientists have shown that complex molecules can form on icy rocks in space, suggesting that comets may have seeded early Earth with the building blocks of life. The team zapped icy snowballs of carbon dioxide and hydrocarbons, producing complex molecules, such as dipeptides, that are capable of catalyzing the formation of more complex structures. More >

February 27, 2013 – Reading the Human Genome
Eva Nogales and members of her research group have achieved a major advance in understanding how genetic information is transcribed from DNA to RNA by providing the first step-by-step look at the biomolecular machinery that reads the human genome. More >

February 11, 2013 – New Details on the Molecular Machinery of Cancer
New details into the activation of a cell surface protein that has been strongly linked to a large number of cancers and is a major target of cancer therapies have been reported by researchers led by Jay Groves, John Kuriyan, and David Wemmer. More >

January 30, 2013 – Endowing Cells with a Magnetic Personality
Taking a hint from magnetotactic bacteria, which make their own tiny bar magnets, Dave Schaffer, Mikhail Shapiro, Arash Komeili, Steve Conolly, and their research team are trying to endow other cells with internal magnets so that they can be tracked with MRI. More >

January 17, 2013 – New Key to Organism Complexity Identified
Researchers led by Eva Nogales have discovered that the transcription factor protein TFIID co-exists in two distinct structural states, a key to genetic expression and TFIID’s ability to initiate the process by which DNA is copied into RNA. More >

January 7, 2013 – Cheap and Easy Technique to Snip DNA Could Revolutionize Gene Therapy
Jennifer Doudna discovered that an enzyme used by bacteria to defend against viruses makes a simple, precise and cheap method of cutting DNA in order to insert new genes. The technique, now proved to work in human cells, could revolutionize genome engineering and transform gene therapy. More >

 Faculty Media Mentions and Awards, 2013

December 19, 2013, Science
Science’s Top 10 Breakthroughs of 2013

November 11, 2013, The Guardian
Biotech Boom Brings New Medicines and Biofuels but Fears About GM Remain

November 7, 2013, The Independent
Jennifer Doudna’s Discovery of ‘Holy Grail’ of Genetic Engineering

September 20, 2013, Wall Street Journal
Daniel Fletcher: Why Your iPhone Upgrade Is Good for the Poor

September 19, 2013, LBL News
A New Player Emerges in Mapping Protein Structures

September 18, 2013, BBC News
Mice ‘Can Lose Innate Fear of Cats’

June 28, 2013, NPR News
Put Down Oil Drill, Pick Up the Test Tube: Making Fuel from Yeast

June 12, 2013, Nature
Be Prepared for the Big Genome Leak

June 4, 2013, USA Today
Bioengineers Invent Light-Controlled Gel

April 10, 2013, Chemistry World
Yeast to Make Malaria Drug on Demand

March 19, 2013, Forbes
This Protein Could Change Biotech Forever

March 12, 2013, The Atlantic
The Sequester Is Going to Devastate U.S. Science Research for Decades

March 12, 2013, Nature
DNA Tool Kit Goes Live Online

March 6, 2013, Daily Mail
Did Life on Earth Arrive on a Comet?

February 28, 2013, PBS: Nova
Why Synthetic Biology Is the Field of the Future

February 27, 2013, HHMI News
A New View of Transcription Initiation

February 13, 2013, Nature
Malaria Drug Made in Yeast Causes Market Ferment

February 8, 2013, CNN
The Next List: Synthetic Biologist Jay Keasling on How Biotechnology Can Solve the Energy Crisis