TAG: "Biotechnology"

What about BOB?


Berkeley Lab proposal for an open biofoundry passes crucial first test.

BOB, the Berkeley Open Biofoundry, would be housed in the EmeryStation East building in Emeryville along with DOE’s Joint BioEnergy Institute.

Picture an industrial-sized manufacturing plant in which workers are turning out a valuable chemical product, say a pharmaceutical drug, or an exotic material such as a truly biodegradable plastic, or a clean-burning carbon-neutral transportation fuel. Now picture that plant as being void of smokestacks venting carbon dioxide into the atmosphere, or receptacles for the collecting of toxic, non-recyclable waste. This is the promise of biomanufacturing, in which biological organisms or systems are used to make desired molecules, and it has the potential to become one of the defining technologies of the 21st century.

A Berkeley Lab proposal submitted to the Defense Advanced Research Projects Agency (DARPA) for the establishment of a scientific center for biomanufacturing has passed a crucial first test. DARPA has awarded Berkeley Lab $1.5 million to proceed with a “Task Area 1” (TA1) design and study phase for what is being called “BOB” – for Berkeley Open Biofoundry. By providing the science and technology that will enable the engineering of biological systems to produce valuable chemical products on a commercial scale, BOB is conceived to do for biology what the Molecular Foundry does for nanomaterials.

“The idea behind BOB is to create a new type of user facility in which industrial, academic and government stakeholders will have access to engineered biological systems, including microbes, plants and tissues, at all stages of the engineering process, including design, building, testing and learning,” says Mary Maxon, the head of strategic planning and development for biosciences at Berkeley Lab who is spearheading this proposal along with Jay Keasling, Berkeley Lab’s associate lab director for biosciences. “BOB represents an important step along a pathway that will ultimately lead to a biomanufacturing center for excellence. This center of excellence is envisioned to be a Silicon Valley-style ecosystem of engineering for biology where designs and start-up systems are created but manufacturing is done elsewhere.”

Manufacturing is defined as the human transformation of materials from one form to another, more valuable form. Whereas many traditional manufacturing processes deplete natural resources and damage the environment, biomanufacturing can be both sustainable and environmentally benign. The primary challenges to biomanufacturing have been complexity and cost. Despite these challenges, biomanufacturing now accounts for more than $190 billion annually in U.S. revenues, with California, the birthplace of genetic engineering, accounting for roughly 22 percent of that figure.

“Biomanufacturing could be a significantly larger fraction of the U.S. economy if biology were easier and cheaper to engineer,” says Keasling, who provided a look into what biomanufacturing can offer with the engineering of a strain of yeast that can be used to produce artemisinin, the world’s most powerful anti-malaria drug. When exclusively produced from the wormwood plant, the supply of artemisinin was unreliable and its price too high for the people in developing nations who need it most. With the arrival of a microbial-based form of the drug, the supply has stabilized and the price has become affordable.

“The construction of the artemisinin-producing yeast required $25 million in funding and 150 person-years of work, typical of similar-sized bioengineering projects,” Keasling says. “New synthetic biology and computational technologies are needed to accelerate the development of productive biological systems and  reduce their costs, and industry needs access to them if traditional manufacturing is to be transformed by biomanufacturing.”

“Within the first five years of BOB, if it is fully funded by DARPA and corporate users, we will aim to speed the design time for developing desired biological systems so that it will be 50 times faster than it is today,” Maxon says. “We’ll also aim to make construction time five times faster than it is now and reduce costs by a factor of 20. The goal is to generate 350 molecules that currently can’t be manufactured with biological methods, including some that currently rely on petroleum sources and traditional manufacturing.”

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New DNA-editing technology spawns bold UC initiative


$10M gift will support the UC Berkeley, UCSF effort.

Jennifer Doudna, UC Berkeley

The University of California, Berkeley, and UC San Francisco are launching the Innovative Genomics Initiative (IGI) to lead a revolution in genetic engineering based on a new technology already generating novel strategies for gene therapy and the genetic study of disease.

The Li Ka Shing Foundation has provided a $10 million gift to support the initiative, establishing the Li Ka Shing Center for Genomic Engineering and an affiliated faculty chair at UC Berkeley. The two universities also will provide $2 million in startup funds.

At the core of the initiative is a revolutionary technology discovered two years ago at UC Berkeley by Jennifer A. Doudna, executive director of the initiative and the new faculty chair. The technology, precision “DNA scissors” referred to as CRISPR/Cas9, has exploded in popularity since it was first published in June 2012 and is at the heart of at least three start-ups and several heavily-attended international meetings. Scientists have referred to it as the “holy grail” of genetic engineering and a “jaw-dropping” breakthrough in the fight against genetic disease. In honor of her discovery and earlier work on RNA, Doudna received last month the Lurie Prize of the Foundation for the National Institutes of Health.

“Professor Doudna’s breakthrough discovery in genomic editing is leading us into a new era of possibilities that we could have never before imagined,” said Li Ka-shing, chairman of the Li Ka Shing Foundation. “It is a great privilege for my foundation to engage with two world-class public institutions to launch the Innovative Genomics Initiative in this quest for the holy grail to fight genetic diseases.”

In the 18 months since the discovery of this technology was announced, more than 125 papers have been published based on the technique. Worldwide, researchers are using Cas9 to investigate the genetic roots of problems as diverse as sickle cell anemia, diabetes, cystic fibrosis, AIDS and depression in hopes of finding new drug targets. Others are adapting the technology to re-engineer yeast to produce biofuels and wheat to resist pests and drought.

“We now have a very easy, very fast and very efficient technique for rewriting the genome, which allows us to do experiments that have been impossible before,” said Doudna, a professor of molecular and cell biology in the California Institute for Quantitative Biosciences (QB3) and an investigator in the Howard Hughes Medical Institute at UC Berkeley. “We are grateful to Mr. Li Ka-shing for his support of our initiative, which will propel ground-breaking advances in genomic engineering.”

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How an entrepreneurial engineering education nurtured a biotech startup


UC San Diego alum Michael Benchimol is working to make chemotherapy more effective.

Michael Benchimol

Identify a real-world problem. Engineer a solution. And, if the solution works, figure out how it can be commercially viable. That’s what Michael Benchimol said he learned over seven years of working in the laboratory of Sadik Esener, a professor in the departments of nanoengineering and electrical and computer engineering at the University of California, San Diego. In Benchimol’s (Ph.D., electrical engineering, ’12) case, it specifically means building a company to advance a targeted drug delivery platform that could make chemotherapy more effective and less toxic to the healthy tissue in the body.

“I like to build things. That’s the engineering side of me,” said Benchimol, who also earned a master’s in electrical engineering at UC San Diego in 2008. “Creating a company was just a different form of creating something from nothing. I always had that interest and I saw that there was an opportunity here.”

The opportunity is a method of delivering chemotherapy drugs directly to cancerous tumors in the body, a longtime goal of next-generation cancer therapy research due to the toxic effects the drugs can have on the rest of the body. The field is enjoying a research heyday in part thanks to advances specifically in the area of nanotechnology. Benchimol says nanotechnology is enabling cancer researchers to leverage the best properties of cancer drugs and biocompatible materials, in a single therapy that can circulate undetected by the body’s immune system.

His company, Sonrgy, recently entered an exclusive licensing agreement with UC San Diego to further develop the company’s technology, which resulted from his Ph.D. and postdoctoral research at the Jacobs School of Engineering and UCSD Moores Cancer Center, where Esener, also directs the NanoTumor Center. Benchimol’s solution is unique in that it doesn’t rely on “tumor receptors” that the nanoparticle can seek out and “stick to” before releasing the drug. Rather, the Sonrgy platform, called SonRx, uses nanocarriers smaller than human cells that carry chemotherapy drugs through the body where they can be released at the tumor site by a doctor deploying ultrasound. The technology is in the preclinical stage.

“The SonRx technology addresses longstanding challenges related to stability and controlled release in nano-scale drug delivery,” said Michael Benchimol, who is Sonrgy’s chief technology officer, in a company statement about the licensing agreement.

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Puzzling quesiton in bacterial immune system answered


Berkeley researchers uncover the key to self-awareness in genome editor.

Short DNA sequences known as “PAM” (shown in yellow) enable the bacterial enzyme Cas9 to identify and degrade foreign DNA, as well as induce site-specific genetic changes in animal and plant cells. The presence of PAM is also required to activate the Cas9 enzyme. (Illustration by KC Roeyer.)

Short DNA sequences known as “PAM” (shown in yellow) enable the bacterial enzyme Cas9 to identify and degrade foreign DNA, as well as induce site-specific genetic changes in animal and plant cells. The presence of PAM is also required to activate the Cas9 enzyme.

A central question has been answered regarding a protein that plays an essential role in the bacterial immune system and is fast becoming a valuable tool for genetic engineering. A team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley have determined how the bacterial enzyme known as Cas9, guided by RNA, is able to identify and degrade foreign DNA during viral infections, as well as induce site-specific genetic changes in animal and plant cells. Through a combination of single-molecule imaging and bulk biochemical experiments, the research team has shown that the genome-editing ability of Cas9 is made possible by the presence of short DNA sequences known as “PAM,” for protospacer adjacent motif.

“Our results reveal two major functions of the PAM that explain why it is so critical to the ability of Cas9 to target and cleave DNA sequences matching the guide RNA,” says Jennifer Doudna, the biochemist who led this study. “The presence of the PAM adjacent to target sites in foreign DNA and its absence from those targets in the host genome enables Cas9 to precisely discriminate between non-self DNA that must be degraded and self DNA that may be almost identical. The presence of the PAM is also required to activate the Cas9 enzyme.”

With genetically engineered microorganisms, such as bacteria and fungi, playing an increasing role in the green chemistry production of valuable chemical products including therapeutic drugs, advanced biofuels and biodegradable plastics from renewables, Cas9 is emerging as an important genome-editing tool for practitioners of synthetic biology.

“Understanding how Cas9 is able to locate specific 20-base-pair target sequences within genomes that are millions to billions of base pairs long may enable improvements to gene targeting and genome editing efforts in bacteria and other types of cells,” says Doudna who holds joint appointments with Berkeley Lab’s Physical Biosciences Division and UC Berkeley’s Department of Molecular and Cell Biology and Department of Chemistry, and is also an investigator with the Howard Hughes Medical Institute (HHMI).

Doudna is one of two corresponding authors of a paper describing this research in the journal Nature. The paper is titled “DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.” The other corresponding author is Eric Greene of Columbia University. Co-authoring this paper were Samuel Sternberg, Sy Redding and Martin Jinek.

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UCSF, Quest Diagnostics launch collaboration to advance precision medicine


Areas of focus will include autism, oncology, neurology and women’s health.

June Lee, UC San Francisco

June Lee, UC San Francisco

UC San Francisco and Quest Diagnostics, the world’s leading provider of diagnostic information services, have formed a collaboration to accelerate the translation of biomedical research into advanced diagnostics in the field of precision medicine, for improved patient care, treatment and outcomes.

Initial clinical areas of focus include autism, oncology, neurology and women’s health.

The collaboration, which combines the research discoveries and capabilities of UCSF with the national testing database and technical and clinical development capability of Quest Diagnostics, has an overarching aim of enabling holistic and integrated diagnostic solutions that close gaps in care or enable new clinical value.

Under the terms of the agreement, scientists will jointly research, develop and validate diagnostic innovations to solve specific clinical problems and provide actionable information to improve patient care. The organizations will focus on diagnostics to advance precision medicine, an emerging field of medical science that aims to integrate the most informative data from molecular, clinical, population and other research to create predictive, preventive and precise medical solutions for patients. Quest Diagnostics would independently develop and validate any lab-developed tests for clinical use that emerge from the collaboration’s research.

Researchers will utilize laboratory-based diagnostics, imaging procedures and population analysis based on Quest’s national Health Trends database, the largest private clinical database in the U.S., based on more than 1.5 billion patient encounters, to advance precision medicine.

The alliance is the first master agreement that UCSF’s Office of Innovation, Technology and Alliances has signed with a clinical laboratory testing company and augments the university’s efforts to translate laboratory research into new therapies. The broad agreement lays the groundwork for multiple projects between the two organizations.

“Advances in technology and science have identified many promising opportunities to improve outcomes through insights revealed by novel diagnostic solutions, yet fulfilling the full potential of these opportunities often hinges on translational clinical studies which validate their value,” said Jay Wohlgemuth, M.D., senior vice president, science and innovation, Quest Diagnostics. “This unique collaboration between UCSF and Quest brings together the finest researchers and clinicians in the country to accelerate the development of a ‘product pipeline’ of scientific discoveries as clinically valuable diagnostic solutions that enable precision medicine for improved outcomes.”

The collaboration is launching with two specific projects already under way. One project involves Quest’s national database of molecular testing data to facilitate participation in research and development efforts related to genetic variations of autism, based on Quest’s CGH microarray ClariSure technology, which can help identify genetic mutations associated with autism and other developmental disorders. While there currently is no treatment for autism, a test that aids its diagnosis could help identify individuals who might be appropriate candidates for research studies that could lead to future therapies.

The second project aims to identify biomarkers to determine which children with glioma brain tumors may benefit from a drug that is currently available to treat the disease. That project will integrate molecular biomarker testing with advanced MRI imaging technologies. This project is the first phase of larger collaborative studies to develop and validate integrated care pathways, which would include laboratory diagnostics, imaging data and other clinical information to be used in the management of patients with brain cancer and neurological diseases.

UCSF has been at the forefront of the movement toward precision medicine, for which UCSF Chancellor Susan Desmond-Hellmann, M.D., M.P.H., co-authored the initial National Academy of Sciences paper that defined the new field. That paper set the vision of harnessing the vast amounts of genetic, environmental and health data worldwide to make health care more predictive, precise and targeted.

“There are many diagnostics projects underway at UCSF for which Quest could partner and contribute a great deal of value in turning an isolated research project into a diagnostic service or other technology that directly benefits patients,” said June Lee, M.D., F.A.C.C.P., director of early translational research at the UCSF Clinical and Translational Science Institute, which initiated the collaboration with Quest after several scientists from both organizations had formed isolated, but successful, research collaborations. “This agreement will give UCSF researchers access to Quest expertise in developing diagnostics, as well as in understanding the market conditions for projects on campus.”

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Schekman receives Nobel Medal in Stockholm ceremony


UC’s 13th Nobel laureate in medicine calls for more support of basic research.

Newly minted Nobel laureate Randy Schekman used his Nobel acceptance speech Dec. 10 in Stockholm to encourage more support for basic research, the “freedom of inquiry (that) nourished the careers of today’s laureates,” he said.

Schekman, a UC Berkeley professor of molecular and cell biology, delivered his brief remarks at the lavish Nobel banquet as he accepted the 2013 Nobel Prize in Medicine or Physiology on behalf of his two co-winners: Thomas Südhof of Stanford University and James Rothman of Yale University.

Since the prize was announced Oct. 7, Schekman has used the spotlight to push for increased funding of basic research – the wellspring of his own seminal discoveries in yeast – and of public universities, which were underrepresented in this year’s American Nobel lineup. Of the nine American Nobelists, Schekman was the only one from a public institution.

“I wish particularly to acknowledge the Nobel Foundation for its recognition of basic science,” he said. “This year’s laureates in the natural sciences reflect the value of curiosity-driven inquiry, unfettered by top-down management of goals and methods.”

Schekman was referring to the increasing desire of U.S. funding agencies “to want to manage discovery with expansive so-called strategic science initiatives at the expense of the individual creative exercise we celebrate today.”

The banquet was the crowning event of a weeklong series of celebrations honoring the new Nobelists, during which Schekman delivered a lengthier speech on Dec. 7 about his research on yeast secretion. This work, which Schekman pursued purely out of curiousity, turned out to be critical to the success of the biotechnology industry.

Schekman traveled to Stockholm with his wife, Nancy Walls, their son and daughter and his father. During his banquet acceptance speech, he expressed appreciation for a broad range of friends and colleagues.

“I view this occasion as one of the great moments of my life, one that I am thrilled to share with my wife and children, my father, and family, friends, colleagues and the students of mine who made this day possible,” he said.

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Single-cell genome sequencing gets better


New approach exhibits comparatively little “amplification bias.”

Jeff Gole

Jeff Gole worked on this project as a Ph.D. student at UC San Diego.

Researchers led by bioengineers at UC San Diego have generated the most complete genome sequences from single E. coli cells and individual neurons from the human brain. The breakthrough comes from a new single-cell genome sequencing technique that confines genome amplification to fluid-filled wells with a volume of just 12 nanoliters.

The study was published in the journal Nature Biotechnology on Nov. 10. An animated video describing the new approach, which is called the Microwell Displacement Amplification System or MIDAS, is available here.

“Our preliminary data suggest that individual neurons from the same brain have different genetic compositions. This is a relatively new idea, and our approach will enable researchers to look at genomic differences between single cells with much finer detail,” said Kun Zhang, a professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering and the corresponding author on the paper.

The researchers report that the genome sequences of single cells generated using the new approach exhibited comparatively little “amplification bias,” which has been the most significant technological obstacle facing single-cell genome sequencing in the past decade. This bias refers to the fact that the amplification step is uneven, with different regions of a genome being copied different numbers of times. This imbalance complicates many downstream genomic analyses, including assembly of genomes from scratch and identifying DNA content variations among cells from the same individual.

Sequencing the genomes of single cells is of great interest to researchers working in many different fields. For example, probing the genetic make-up of individual cells would help researchers identify and understand a wide range of organisms that cannot be easily grown in the lab from the bacteria that live within our digestive tracts and on our skin, to the microscopic organisms that live in ocean water. Single-cell genetic studies are also being used to study cancer cells, stem cells and the human brain, which is made up of cells that increasingly appear to have significant genomic diversity.

“We now have the wonderful opportunity to take a higher-resolution look at genomes within single cells, extending our understanding of genomic mosaicism within the brain to the level of DNA sequence, which here revealed new somatic changes to the neuronal genome. This could provide new insights into the normal as well as abnormal brain, such as occurs in Alzheimer’s and Parkinson’s disease or schizophrenia,” said Jerold Chun, a co-author and professor in the Dorris Neuroscience Center at The Scripps Research Institute.

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Anti-aging research advances featured in QB3 symposium


Chronic diseases of aging are targeted in new ways.

Symposium attendees browse poster presentations on QB3 aging research in Genentech Hall at UCSF's Mission Bay campus.

Symposium attendees browse poster presentations on QB3 aging research in Genentech Hall at UCSF's Mission Bay campus.

Death is a 100 percent certainty, but that doesn’t stop University of California researchers from searching for an end run around aging with the intensity of a football team battling back as the clock runs down.

Eleven leading scientists from the California Institute for Quantitative Biosciences (QB3) – a state-funded consortium founded by UC San Francisco, UC Berkeley and UC Santa Cruz – presented their latest research findings and anti-aging strategies at a daylong symposium earlier this month called “The Science of Staying Younger Longer.”

The goal of this research area is rejuvenation: longer, healthier life, free from the costly and debilitating chronic diseases associated with aging and a too-early demise. Better living in old age is a growing priority as a bulging population of baby boomers enters their golden years.

Thanks primarily to better control over infectious diseases through improved sanitation, vaccines and antibiotics, Americans live on average more than three decades longer than they did a century ago. But today tantalizing research findings from different scientific disciplines – including genetics, immunology, cell biology, diabetes research and microbiology – are raising hopes for another revolutionary increase in life expectancy.

“Perhaps rejuvenation therapies will appear in less than a decade, if we pool our resources and skills,” said Regis Kelly, Ph.D., director of QB3 and organizer of the Oct. 16 event on the UCSF Mission Bay campus.

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Randy Schekman wins Nobel Prize in Medicine


UC Berkeley professor is UC’s 13th Nobelist in medicine.

As photographers capture the moment -- and UC Berkeley Chancellor Nicholas Dirks savors it -- Nobel Prize winner Randy Schekman takes a congratulatory call from UC President Janet Napolitano. (Photo by Peg Skorpinski, UC Berkeley)

As photographers capture the moment -- and UC Berkeley Chancellor Nicholas Dirks savors it -- Nobel Prize winner Randy Schekman takes a congratulatory call from UC President Janet Napolitano.

Randy W. Schekman, professor of molecular and cell biology at the University of California, Berkeley, has won the 2013 Nobel Prize in Physiology or Medicine for his role in revealing the machinery that regulates the transport and secretion of proteins in our cells. He shares the prize with James E. Rothman of Yale University and Thomas C. Südhof of Stanford University.

Discoveries by Schekman about how yeast secrete proteins led directly to the success of the biotechnology industry, which was able to coax yeast to release useful protein drugs, such as insulin and human growth hormone. The three scientists’ research on protein transport in cells, and how cells control this trafficking to secrete hormones and enzymes, illuminated the workings of a fundamental process in cell physiology.

Randy Schekman will share the 2013 Nobel Prize in Physiology or Medicine (Photo by Peg Skorpinski, UC Berkeley)

Randy Schekman will share the 2013 Nobel Prize in Physiology or Medicine

Schekman is UC Berkeley’s 22nd Nobel laureate, and the first to receive the prize in the area of physiology or medicine. A total of 60 faculty and researchers affiliated with the University of California have won 61 Nobel Prizes, including 13 in medicine.

In a statement, the 50-member Nobel Assembly lauded Rothman, Schekman and Südhof for making known “the exquisitely precise control system for the transport and delivery of cellular cargo. Disturbances in this system have deleterious effects and contribute to conditions such as neurological diseases, diabetes, and immunological disorders.”

“My first reaction was, ‘Oh, my god!’ said Schekman, 64, who was awakened at his El Cerrito home with the good news at 1:30 a.m. “That was also my second reaction.”

Schekman and Rothman separately mapped out one of the body’s critical networks, the system in all cells that shuttles hormones and enzymes out and adds to the cell surface so it can grow and divide. This system, which utilizes little membrane bubbles to ferry molecules around the cell interior, is so critical that errors in the machinery inevitably lead to death.

“Ten percent of the proteins that cells make are secreted, including growth factors and hormones, neurotransmitters by nerve cells and insulin from pancreas cells,” said Schekman, a Howard Hughes Medical Institute investigator.

In what some thought was a foolish decision, Schekman decided in 1976, when he first joined the College of Letters and Science at UC Berkeley, to explore this system in yeast. In the ensuing years, he mapped out the machinery by which yeast cells sort, package and deliver proteins via membrane bubbles to the cell surface, secreting proteins important in yeast communication and mating. Yeast also use the process to deliver receptors to the surface, the cells’ main way of controlling activities such as the intake of nutrients like glucose.

In the 1980s and ’90s, these findings enabled the biotechnology industry to exploit the secretion system in yeast to create and release pharmaceutical products and industrial enzymes. Today, diabetics worldwide use insulin produced and discharged by yeast, and most of the hepatitis B vaccine used around the world is secreted by yeast. Both systems were developed by Chiron Corp. of Emeryville, now part of Novartis International AG, during the 20 years Schekman consulted for the company.

Various diseases, including some forms of diabetes and a form of hemophilia, involve a hitch in the secretion system of cells, and Schekman is now investigating a possible link to Alzheimer’s disease.

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New electron beam writer enables next-gen biomedical technology


Technology allows researchers to precisely write very small patterns on large substrates.

Ryan Anderson, a process engineer for the Nano3 facility in the Qualcomm Institute, prepares to remove a sample from the Vistec EBPG5200 electron beam writer.

Ryan Anderson, a process engineer for the Nano3 facility in the Qualcomm Institute, prepares to remove a sample from the Vistec EBPG5200 electron beam writer.

The new electron beam writer housed in the Nano3 cleanroom facility at the Qualcomm Institute is important for electrical engineering professor Shadi Dayeh’s two major areas of research. He is developing next-generation, nanoscale transistors for integrated electronics; and he is developing neural probes that have the capacity to extract electrical signals from individual brain cells and transmit the information to a prosthetic device or computer. Achieving this level of signal extraction or manipulation requires tiny sensors spaced very closely together for the highest resolution and signal acquisition. Enter the new electron beam writer.

Electron beam (e-beam) lithography enables researchers to write very small patterns on large substrates with a high level of precision. It is a widely used tool in information technology and life science. Applications range from writing patterns on silicon and compound semiconductor chips for electronic device and materials research to genome sequencing platforms. But the ability to write patterns on the scale afforded by the Nano3 facility — with its minimum feature size of less than 8 nanometers on wafers with diameters that can be as large as 8 inches — is unique in Southern California. Before the facility opened earlier this year, the closest comparable e-beam writer was in Los Angeles. In an e-beam writer, unique patterns are “written” on a silicon wafer coated with a polymer resist layer that is sensitive to electron irradiation. The machine directs a narrowly focused electron beam onto the surface marking the pattern, making parts of the resist coating insoluble and others soluble. The soluble area is later washed away, revealing the pattern which can have sub-10 nanometer feature dimensions.

Bioengineering professor Todd Coleman will use the new e-beam writer as one essential step in the building of his epidermal, or tattoo, electronic devices. The devices are designed to acquire brain signals for a variety of medical applications, from monitoring infants for seizures in neonatal intensive care to studying the cognitive impairment associated with Alzheimer’s disease or dementia, and soldiers struggling with post-traumatic stress syndrome.

Electrical engineering Ph.D. candidate Andrew Grieco is using the machine to develop a new type of optical waveguide that promises to improve efficiency and reduce power consumption. Grieco works in the laboratory of Shaya Fainman, professor and chair, Department of Electrical and Computer Engineering. Developing on-chip optical networking devices such as waveguides, switches and amplifiers is a critical step in the development of optical chips. Although information systems rely primarily on fiber-optic networks to connect and share data around the world, the underlying computer technology is still based on electronic chips, causing data traffic jams.

“Any local company that has an investment in nanoscale science and technology should greatly benefit from this machine. It’s a powerful tool that is hard to find in a typical university setting or within local industry,” said Dayeh (Ph.D., 2008 UC San Diego), who joined the faculty in 2012. “It’s a unique tool that is being brought to San Diego.“

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The story behind the anthrax killer


Under the sea, UC San Diego researchers find promising sources to treat human diseases.

Chris Kauffman, a staff research associate at UC San Diego's Scripps Institution of Oceanography, collects samples for biomedical research off Madiera Island.

Chris Kauffman, a staff research associate at UC San Diego's Scripps Institution of Oceanography, collects samples for biomedical research off Madiera Island.

William Fenical made headlines in July when he announced a promising new candidate in the search for novel sources to treat human diseases, the latest in his long and storied biomedical research career at Scripps Institution of Oceanography at UC San Diego.

This time, Fenical identified a new compound from the ocean that effectively kills anthrax, the feared biological weapon, as well as methicillin-resistant Staphylococcus aureus, or MRSA, the bacteria that has proliferated in recent years and proven problematic to treat. Fenical and his colleagues called the new compound “anthracimycin,” and hold hope that one day it will lead to the development of a powerful new drug.

“The real importance of this work is the fact that anthracimycin has a new and unique chemical structure,” said Fenical, a distinguished professor of oceanography and pharmaceutical science at Scripps “The discovery of truly new antibiotic compounds is quite rare. This discovery adds to many previous discoveries that show that marine bacteria are genetically and chemically unique.”

Fenical is quick to share credit for the discovery with a team of researchers in his laboratory. In this case special attention goes to Chris Kauffman, a staff research associate who has been part of Fenical’s team since 1991.

In the depths of Fenical’s research labs, Kauffman operates the group’s fermentation facility, a crucial area for teasing out promising compound candidates from the mind-boggling diversity of chemical structures found in the world’s vast oceans.

Kauffman also has emerged as the group’s field expedition leader in their search near and far for novel materials from the sea. He has logged more than 450 research dives to locations as close as La Jolla and as far as Fiji, Papua New Guinea, Palau, the Philippines, and the Red Sea.

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Scientists devise innovative method to profile, predict behavior of proteins


New technique lets researchers pinpoint, map thousands of enzyme interactions.

Nevan Krogan

Nevan Krogan

An enzyme is a tiny, well-oiled machine.

A class of proteins that are made up of multiple, interlocking molecular components, enzymes perform a variety of tasks inside each cell. However, precisely how these components work together to complete these tasks has long eluded scientists.

But now, a team of researchers has found a way to map an enzyme’s underlying molecular machinery, revealing patterns that could allow them to predict how an enzyme behaves – and what happens when this process disrupted.

In the latest issue of the journal Cell, a team of scientists led by Gladstone Institutes and UC San Francisco investigator Nevan Krogan, Ph.D., Texas A&M University’s Craig Kaplan, Ph.D., and UCSF professor Christine Guthrie, Ph.D., describe a new technique – called the point mutant E-MAP (pE-MAP) approach – that gives researchers the ability to pinpoint and map thousands of interactions between each of an enzyme’s many moving parts.

The researchers focused on a well-known enzyme – called RNA polymerase II (RNAPII) – and used the single-cellular yeast species S. cerevisiae as a model. Researchers had previously mapped the physical structure of RNAPII, but not how various parts of the enzyme work with other proteins within the cell to perform vital functions.

“Scientists know RNAPII’s physical structure, but this large enzyme has many distinct regions that each perform distinct functions,” said Kaplan, who is also a scientist at Texas A&M AgriLife. “We wanted to connect the dots between these regions and their function.”

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