REBECCA ABERGEL
Decontamination, Separation, and Radiotherapeutic Strategies for Heavy Metals

nuclear engineering

Therapeutic Interventions for Post-MRI Gadolinium Toxicity

Gadolinium-based contrast agents have been widely used in clinical magnetic resonance imaging - MRI - studies. However, despite their initial safety reputation, serious toxicity issues associated with the use of these agents have emerged in the last several years, with studies demonstrating the release of gadolinium (Gd) and subsequent deposition in bone tissue and in the brain in patients with normal renal function and intact blood-brain barriers. The only practical therapy to reduce the health consequences of gadolinium deposition is treatment with chelating agents that form excretable complexes, although gadolinium, like other heavy metals, is among the most intractable elements to decorporate. Initially driven by the civilian need for post-exposure medical countermeasures against nuclear threats, Rebecca Abergel’s group has pursued the development of small molecular chelators as therapeutics for heavy element decontamination. The lead investigational drug identified in this program will be further developed into a gadolinium removal product, which could be provided as a post-MRI therapeutic or just bundled with contrast agent administration shortly after the MRI procedure. A comprehensive and detailed assessment of past and future patients having received contrast agents will also be conducted to identify clinical and demographic factors that may predispose individuals to Gd retention and/or the onset of related symptoms.

Rebecca Abergel is an Associate Professor of Nuclear Engineering. Her research group studies the chemistry of heavy elements and inorganic isotopes with a variety of applications in clean energy, defense, and public health. She received her B.Sc. from the Ecole Normale Supérieure of Paris, France, and her Ph.D. from UC Berkeley. She joined the UC Berkeley faculty in 2018.

JAMES ANALYTIS
Condensed Matter Physics and Materials Science

physics

Topological Mott Magnonics

Computation, the process of generating information, requires fast electrical manipulation and recall that often relies on non-linear electrical processes of the material platforms, dissipating large amounts of heat. In this proposal, we aim to address this challenge with a new technology that is rooted in the flow of spin that leverages the collective behavior of the electrons rather than the flow of individual particles. The solution we propose leverages a novel class of AFM materials known as Mott insulators (MIs). Spin and charge channels of dissipation are separated in such materials, so that information carried by the spin sector will not diffuse into the electronic sector, with potential to greatly reduce dissipation and enhance processor speeds.

James Analytis is an Associate Professor in UC Berkeley’s Department of Physics. He joined the faculty in January 2013 as the Charles Kittel Chair in condensed matter physics.

BOUBACAR KANTE
Physical Electronics and Energy

electrical engineering and computer sciences

Ultra-Compact lasers for mobility, sensing, and communication

Semiconductor lasers are ubiquitous in today’s electronics/photonics market due to a multitude of applications ranging from on-chip communication, communication across-the-globe internet connectivity, to laser imaging, detection, and ranging (LIDAR). Moreover, future technologies such as self-driving cars, drones, automated robots, and advanced monitoring and sensing systems will also greatly benefit from an ultra-compact laser system. This project aims at developing a multifunctional laser system that can simultaneously tune its emission wavelength, steer its beam, be energy efficient, and be ultracompact. Such a system will immediately find a unique position in the multibillion dollars market represented by applications of lasers. The project will investigate a unique laser system that we recently invented and that we called Bound State in Continuum Surface Emitting Lasers (BICSEL).  BICSELs could become ubiquitous in future technologies in need of lasers because they have the potential to decrease the cost of lasers when produced at large scale while being energy efficient.

Boubacar Kante is the inaugural Chenming Hu endowed Chaired Associate Professor at UC Berkeley’s Department of Electrical Engineering and Computer Science.

JAY KEASLING
Skin Disease Treatment

Chemistry and biomolecular engineering

Skin probiotics to treat disease

Aging and disease cause damaged, inflamed skin. Multiple factors can cause and aggravate the skin, including protein imbalances, inflammatory cytokines, reactive oxygen species, and harmful bacteria. Conventional topical creams often fail to address these conditions due to the limited lifetime of their active ingredients. After all, our bodies naturally produce compounds to continuously maintain and revitalize our skin. Resvita Biosciences seeks to restore and maintain the vitality of the skin by properly considering the skin microbiome as part of the human body. A harmless skin probiotic will continuously deliver the therapy that a body would to maintain skin health. Simply put, the treatment comes from the outside-in, instead of the inside-out.

Through synthetic biology and metabolic engineering, our goal is to develop a safe and versatile skin microbial platform that can address the causes of skin aging and disease. We have a unique patented approach, a rich product pipeline, clear regulatory advantages, and an experienced scientific management team. Within the next three years, we are confident that we will deliver multiple anti-aging products to market, an IND to treat an orphan skin disease with fast-track FDA designation, and exciting preclinical data to treat multiple inflammatory skin diseases like eczema and psoriasis.

Jay Keasling is a Professor in the Department of Chemical & Biomolecular Engineering and Bioengineering. He is also Senior Faculty Scientist at the Lawrence Berkeley National Laboratory, and his research interests include metabolic engineering of microorganisms.

CECILIA MARTINEZ-GOMEZ
Microbial Rare Earth Element Recovery

plant and microbial biology

Bacterial Enhanced Gadolinium Recovery from Clinical Waste and Waste Water

Rare earth elements (REEs) are critical components of clean energy, consumer, and medical technologies with increasing global demand. However, extraction and refinement of REEs from raw materials using current methods is energy-intensive and environmentally destructive. One REE, Gadolinium (Gd), is widely used in the medical industry to generate contrast agents for magnetic resonance imaging (MRI) because of its unparalleled paramagnetic properties. Yet, in free form, Gd is severely toxic to humans. Unmetabolized contrast agents, excreted in the urine, are cause for concern as rising anthropogenic Gd in surface water correlates with increasing annual MRI exams. Currently, there is no effective method to recycle Gd from medical waste or contaminated water. My research group has developed a microbial platform for efficient, bio-safe leaching and recovery of light REEs (e.g. neodymium), from low-grade sources, such as electronic waste, using the model bacterium Methylorubrum extorquens. Recently, we isolated a genetic variant (evo-HLn) of M. extorquens capable of efficient acquisition of heavy (e.g. Gd) instead of light REEs. The variant is so efficient that it can sequester Gd from common MRI contrast agents. We aim to optimize evo-HLn growth conditions using medical waste and contaminated wastewater. Then, we will engineer the strain to increase its capacity for Gd leaching and Gd recovery. Finally, we will translate the process to a bioreactor setup to identify operation parameters at scale. Once tuned for Gd acquisition, our microbial REE recovery platform will recycle the highly valuable Gd and reduce groundwater contamination.

Cecilia Martinez-Gomez is an Assistant Professor of Plant and Microbial Biology. She conducts research in microbial metabolism, particularly one-carbon metabolism, and builds bacterial platforms to help solve environmental issues.

BAOXIA MI
Heavy Metal Decontamination

civil and environmental engineering

2D Nanomaterial-Enabled Technology for Lead Removal from Drinking Water

Point-of-use (POU) filters that can be installed in households to effectively remove heavy metals (e.g. lead) from drinking water are urgently needed considering recent nation-wide outbreaks of lead contamination of drinking water (e.g., Flint MI, Newark NJ). We discovered that two-dimensional (2D) MoS2 nanosheets demonstrate the highest lead removal capabilities among all materials that have ever been reported in the literature. For example, MoS2 exhibits the highest adsorption capacity as well as the strongest selectivity/affinity toward lead, which are a few orders of magnitude higher than other lead adsorption materials. The high selectivity of MoS2 ensures the successful removal of lead without being interfered by other common ions in drinking water. Filters assembled by stacking MoS2 nanosheets exhibit much higher water productivity than typical reverse osmosis membranes while effectively reducing heavy metal concentration from ppm level to less than 10 ppb. It outperforms other state-of-the-art membranes or novel filters made of various new materials. These results demonstrate that the layer-stacked MoS2 filter has great potential as an innovative POU device for lead removal from drinking water.

Dr. Baoxia Mi is Associate Professor in the Civil and Environmental Engineering Department. Her research focuses on advanced membrane processes and nanotechnology to address some challenging issues in sustainable water supply, including desalination, drinking water quality, wastewater reuse, renewable energy production, and public health protection.

SIMON SCHLEICHER
3D Printing in Home Architecture

Architecture

Robotic 3D Printing of Lightweight Roofs for Affordable Housing

Large-scale 3D printing is a revolutionary innovation that is currently gaining global traction as a faster, inexpensive and more efficient way to build affordable housing. On closer inspection, however, most 3D-printed building projects today, reveal a fundamental weakness of the technology, namely the unresolved question of how to print long-span structures such as roofs and floor slabs. To further reduce construction costs and fabricate not only walls but also lightweight and material-efficient roofs using the same 3D printing manufacturing process, Simon Schleicher and his research team developed the novel idea of printing layers of ultra-high performance concrete and other recycled material alternatives directly onto a double-curved, minimal formwork. The innovation here lies in the special technological interplay between robotic non-planar 3D printing and formwork design. By extending the capabilities of architectural 3D printing beyond the common application of vertical walls, and further developing new methods to fabricate long-span roof structures, this research provides an important milestone on the path towards constructing entire houses from the same cost- and material-efficient additive manufacturing process.

Simon Schleicher is an Associate Professor of Architecture. His specializations include Bio-inspired Structures and Kinetic Systems, Bending-active Structures and Advanced Digital Fabrication, 3D Printing of Compliant Mechanisms and Fixtures, and Adaptive Shading Systems for Freeform Glass Facades. He conducts his research through his research group, Design Innovation from Nature.

MARIA PAZ GUTIERREZ
Indoor Health and Microengineered Biowalls

Architecture

Lichen Building Blocks

Indoor air toxicity is a pressing environmental and health challenge for urban dwellers, who typically spend around 85-90% of their time indoors. Urban air toxicity makes traditional natural ventilation strategies increasingly unviable. Current indoor air detoxification technologies include cumbersome mechanical systems and biological systems in the form of biowalls. Mechanical systems require energy and often disbalance the health of indoor spaces.  Biowalls made of plants require a high level of maintenance and increase humidity from evapotranspiration, making them costly and de facto unsustainable. Gutierrez proposes a radically new approach to biological systems for indoor detoxification through multiscale engineered lichen modules that demand zero energy or infrastructure, have moisture buffering capacity, and are entirely self-regulated and maintenance-free. Lichen Building Blocks is a lightweight structural module system of 3D extruded lichen/recycled plant composites that enable carbon sequestration and VOC removal. The blocks are deployable and scalable for a wide range of indoor spaces and climates. Lichen Building Blocks can revolutionize our capacity for indoor air detoxification at low cost, addressing an increasing environmental and health imperative. 

Maria Paz Gutierrez is an Associate Professor in the Department of Architecture. Her research and design focus on pressing challenges in the intersection of the energy-water-air of the built environment. She explores natural materials innovation and microbial environments as contextual, technological, and cultural implications intersecting architecture, engineering, and science. Gutierrez received her BArch from U.F.T in Chile, M Arch from the University of Pennsylvania, and Ph.D. (AV) from the University of Cambridge. Her construction technology innovations are recognized to bridge gaps in the nexus of sustainability, culture, and health from the nano to the building scale.

RIKKY MULLER
Brain-Computer Interfaces

Electrical Engineering and Computer Sciences

EarEEG – Hearables That Read Your Mind

Smart earbuds and hearing aids known as hearables have transformed the headphone and audiology landscape. In addition to enhancing enjoyment of music and conversation, technologically advanced electronic in-ear devices controlled by touch, movement or voice are being applied to medical monitoring, fitness tracking and more. Rikky Muller’s research group has developed EarEEG, which uses lightweight in-ear earbuds to detect the brain’s electrical activity. Electroencephalography (EEG) is recorded non-invasively from the ear canal and transmitted wirelessly to the user’s smartphone. Her goal is to enable the seamless connection of mind to device in a variety of user interface, consumer and healthcare applications.

Rikky Muller is an Assistant Professor in the Department of Electrical Engineering and Computer Sciences where she holds the S. Shankar Sastry Professorship in Emerging Technologies. Her research group focuses on wearable and implantable medical devices and in developing low-power, wireless microelectronic and integrated systems for neurological applications. She received her B.S. and M. Eng. degrees from the Massachusetts Institute of Technology, and her Ph.D. from UC Berkeley.

KRISTOFER PISTER
Microbatteries

Electrical Engineering and Computer Sciences

Printed Microbatteries for the Internet of Things

The global sensor market has expanded dramatically in recent years, driven by applications in

the Internet of Things, healthcare, wearables and more. Hundreds of billions of sensors are already embedded in a vast array of networked physical objects, measuring changes in the physical environment and reporting this data electronically. UC Berkeley’s Swarm Lab estimates that nearly ten trillion sensors will be deployed in networked devices by the end of the century.  Sensors for many of these applications will require high capacity power and small size unavailable in current microbatteries.  Kristofer Pister will address this need by integrating high density lithium ion microbatteries directly within the chips that enable sensors to function. His technology uses a combination of microfabrication and stencil printing methods to deliver a small, long lived, high energy density and low cost micro-battery to power our connected world.

Kristofer Pister is Professor of Electrical Engineering and Computer Sciences, and a  Co-Director of the Berkeley Sensor and Actuator Center (BSAC).  His research is at the intersection of microelectromechanical systems and integrated circuits.  He received his B.S. from UC San Diego, and M.S. and Ph.D. from UC Berkeley.

JAIJEET ROYCHOWDHURY
Combinatorial Optimization

Electrical Engineering and Computer Sciences

Oscillator Ising Machines for Combinatorial Optimization

In our information-dominated world, combinatorial optimization problems are ubiquitous. Logistics/transportation, intelligent robots, autonomous cars, smart grids, drug design, and communication networks all involve finding the optimal solution from among  millions or billions of possibilities.   “Quantum annealing” machines have been proposed to solve such problems quickly, but they are large, expensive, and difficult to scale to solve ever-larger problems. Jaijeet Roychowdhury and his graduate student, Tianshi Wang, have invented a new approach, OIMs (Oscillator Ising Machines), that solves combinatorial optimization problems using coupled electronic oscillator circuits.  Because OIMs are based on conventional integrated circuit technology, they are a far smaller, less expensive and more scalable alternative.  OIM chips may become a standard technology, as GPUs are for graphics computations.

Jaijeet Roychowdhury is Professor of Electrical Engineering and Computer Sciences. His research interests include machine learning, novel computational paradigms, and the analysis, simulation, verification and design of cyber-physical, electronic, biological, nanoscale and mixed-domain systems. He received his B. Tech. from the Indian Institute of Technology, Kanpur, India, and his M.S. and Ph.D. in Electrical Engineering and Computer Sciences at UC Berkeley.  He and Tianshi Wang were awarded the 2019 Bell Labs Prize for their work on OIMs.

RUSSELL VANCE
Immunotherapy

molecular and cell biology

Can We Harness Virus-Triggered Immunity for Cancer Immunotherapy?

Immunotherapy has revolutionized the treatment of cancer. However, many patients fail to respond to current cancer immunotherapies. Recent data suggest that immunotherapy resistant tumors lack infiltration of the immune cells necessary for therapeutic responses. One of the characteristics of these so-called “cold” tumors is the absence of a gene expression signature characteristic of type I interferons, a class of secreted signaling proteins that elicit potent anti-tumor immune responses. Russell Vance’s lab will identify the pathways that silence type I interferon production in tumors and develop novel small molecule inhibitors of these pathways, to unleash anti-tumor interferon responses.  This approach is unique as its goal is to reverse the silencing itself, rather than to induce interferon expression within a tumor.

Russell Vance is Professor of Immunology and Pathogenesis in the Department of Molecular and Cell Biology, and an Investigator of the Howard Hughes Medical Institute.  A B.Sc. and M.A. graduate of Queen’s University in Kingston, Ontario Canada, he received his Ph.D. from UC Berkeley and did postdoctoral research at Harvard Medical School. The Vance Lab studies the complex interrelationship between pathogens and their hosts, including the innate immune response characterized by the production of type I interferons.

NORMAN YAO
Physics

Materials ENGINEERING

The NV-DAC: A Quantum Sensor at High Pressures

Characterizing the behavior of matter under pressure and strain is essential for the development of next generation technologies, ranging from solar cells to auxetic and “smart” materials. The workhorse of such studies is the diamond anvil cell (DAC), which has had a transformative impact on materials science, chemistry, physics, and engineering by providing a tabletop apparatus capable of reaching megabar pressures. However, due to the enormous stress gradients generated, it is challenging to position a sensor near the sample in order to measure local material properties. This prevents access to essential pieces of information from within the sample chamber: for example, does material failure and fracture nucleate from a specific point? Are there inhomogeneities in the viscous and elastic properties of a sample? As a Bakar Fellow, Norman Yao will develop the NV-DAC system, which is capable of measuring material properties under pressure with sub-micron spatial resolution and at temperatures ranging from 4K to room temperature.

Norman Yao received his A.B. and Ph.D. from Harvard University.  He joined the faculty of the Department of Physics as an Assistant Professor in 2016, after completing postdoctoral research at UC Berkeley as a Miller Fellow.  His laboratory employs a variety of theoretical, numerical and experimental tools to investigate problems at the interface between atomic, molecular and optical physics, condensed matter, and quantum information science.

MICHAEL YARTSEV
Autonomous Navigation

BIOENGINEERING

Re-Inventing the Wheel: Biologically Inspired Innovations for Autonomous Vehicles

Autonomous transportation is the way of the future. A necessary requirement of any autonomous vehicle is to sense and respond to objects in the external environment; both stationary, such as curbs and barriers, and in motion, such as pedestrians and vehicles.  Present efforts focus on video-scene analysis, which is computationally expensive and highly challenged in cluttered environments.  Michael Yartsev will take an alternative, biologically-inspired approach towards solving these problems by leveraging solutions obtained by biological systems. A major focus will be the bat whose flight activity can be analyzed individually at the level of neural activity and collectively as interactive behavior. These findings will be translated into computational algorithms that enable optimal processing of incoming sonar-based sensory inputs and uncover the most efficient “rules of the road”  for the design and operation of autonomous vehicles.

Michael Yartsev is an Assistant Professor of Bioengineering and Neuroscience. His laboratory studies the echolocating bat to understand the neural basis of complex spatial, social and acoustic behaviors in mammals. He received his B.Sc. and M.Sc. from Ben-Gurion University and his Ph.D. from the Weizmann Institute in Israel and was a postdoctoral fellow at Princeton University. He joined the UC Berkeley faculty in 2015.

The Bakar Innovation Fellows are creative and entrepreneurial graduate students and postdoctoral scientists who are working with a Bakar Faculty Fellow to translate their laboratory discoveries and innovations to the commercial sector. 

2017-2019 Bakar Innovation Fellows Alumni: Michael Chen, Ph.D. (Laura Waller); Sean Chen, Ph.D. (Lin He); Eric Copenhaver, Ph.D. (Holger Müller); Raissa Estrela, Ph.D. (Jamie Cate); Aaron Friedman, Ph.D. (Daniela Kaufer); Meghan Hauser, Ph.D. (Ke Xu); Tammy Hsu, Ph.D. (John Dueber); Nadja Mannowetz, Ph.D. (Polina Lishko); Vlad Senatorov, Ph.D. (Daniela Kaufer); Zack Phillips, Ph.D. (Laura Waller)

ARASH KOMEILI
Biomining

Plant and Microbial Biology

Synthetic Bacterial Compartments for Biomining of Metals

The traditional mining industry is facing a major crisis. Dwindling sources of easily accessible ores are increasing the costs of exploration and extraction of economically relevant metals. Meanwhile, the environmental consequences of extraction from ores are dire and present companies with costly cleanup protocols. To combat these problems, the budding "biomining" industry seeks to use naturally occurring microbial activities to liberate metals from minerals and subsequently isolate them with electrolysis. As a Bakar Fellow, Arash Komeili will leverage a poorly studied microbial phenomenon, the precipitation of metals in intracellular organelles, to engineer microorganisms capable of biomining important metals. His platform will create hybrid bacterial vehicles that will simultaneously produce iron-based magnetic particles as well as concentrate metals of interest. In this manner, specific metals can be sequestered from environmental sources and easily purified via magnetic separation. 

Arash Komeili is Professor of Plant and Microbial Biology. His laboratory uses a combination of cell biological, genetic and biochemical approaches to understand the genesis and function of magnetosomes, miniature magnets synthesized by some bacteria to concentrate iron for use in as a compass. He received his B.S. from the Massachusetts Institute of Technology, and his Ph.D. from U.C. San Francisco.

MARKITA LANDRY 
Agricultural Nanotechnology

CHEMICAL AND BIOMOLECULAR ENGINEERING

Genetic Engineering of Agriculturally Relevant Crops

Plants are vastly underrepresented among the many biological systems in which genetic engineering is routine. Technologies to genetically manipulate plants yield random DNA integration into the plant genome, are inefficient, and require transgene segregation through laborious breeding if labeling as a genetically modified organism (GMO) is to be avoided. As such, with current approaches, it can take months to years to obtain and test a plant genetic variant. One main bottleneck facing efficient plant genetic modification is efficient biomolecule delivery into plant cells through the rigid and multi-layered cell wall.  The Landry lab has developed a nanotechnology that enables high-throughput delivery of biomolecules to plants without requiring expensive equipment or refrigeration of reagents. The method results in transient protein expression without incorporation of foreign DNA into the plant genome, potentially avoiding classification of modified plants as GMO. Her Bakar Fellows Spark Award will enable her group to extend this platform to genome editing in plants of agricultural relevance such as corn, pepper, soy, rice, and tomato.  

Markita Landry is an Assistant Professor in the Department of Chemical and Biomolecular Engineering.  Her research group merges the fields of single-molecule biophysics and nanomaterials research to develop tools to image and genetically edit biological systems in vitro and in vivo. She received her B.S. and B.A. degrees from the University of North Carolina, her Ph.D. and a certificate in Business Administration from the University of Illinois at Urbana- Champaign, and was a postdoctoral fellow at the Massachusetts Institute of Technology.

ALESSANDRA LANZARA
Quantum Computing

pHYSICS

A New Quantum Detection Tool for Quantum Information Science

There is a worldwide race to build quantum computers that will allow for complex and currently impossible calculations, such as in cryptography and protein modeling. The science that will underpin this revolution in computing is an understanding of how to build a quantum bit, or “qubit,” the basic unit of information in a quantum computer. The spin, an intrinsic property of all elementary particles, i.e. the quantum-mechanical counterpart of the classical angular momentum, is viewed as one of the leading candidates for realization of qubits. Scientists will need new tools to access and control the spin quantum number, especially in those materials such as superconductors and topological insulators that hold great promise for realizing qubits. Alessandra Lanzara’s research group has developed a one-of-a-kind tool, the spin-Time of Flight (spin-TOF), which allows mapping and manipulation of the spin-property of materials and is 1000-fold more efficient than any other existing tool.  Her Bakar Fellows Spark Award will enable her to commercialize the spin-TOF to researchers in the quantum materials/computing field while, in parallel, undertaking research and development of the next generation tool for industry applications.

Alessandra Lanzara is the Charles Kittel Professor of Physics and a Senior Faculty Scientist at the Lawrence Berkeley National Laboratory.   She is also the Chair of the Far West section of the American Physical Society.  She received her M.S. and Ph.D. from the Universita’ di Roma La Sapienza, and did postdoctoral research at Stanford University. Her research is focused on understanding electron behavior and fundamental interactions in quantum materials and on their manipulation with coherently sculpted field of light.

ROYA MABOUDIAN
Air Quality Monitoring

CHEMICAL AND BIOMOLECULAR ENGINEERING

Carbon Dioxide Sensing for Indoor Air Quality Monitoring

Inexpensive and efficient carbon dioxide detectors are desirable for many applications, including air quality assessment, food storage, microbial investigation and patient care. The infrared sensors most commonly in current use are expensive and remain difficult to miniaturize.  With her Bakar Fellows Spark Award, Roya Maboudian will produce an inexpensive alternative based on colorimetric sensing.  These sensors will be simple and user-friendly, exhibiting a color change visible to the human eye, yet sensitive enough to detect minor variations useful in air quality monitoring.  They will be fabricated from a porous crystalline class of materials, called metal organic frameworks, composed of metal clusters connected by organic linking molecules. This material system can be tailored to strongly interact with carbon dioxide, and by incorporating a dye that changes color based on the amount of bound gas, a highly sensitive CO2 detector can be realized.

Roya Maboudian is Professor of Chemical and Biomolecular Engineering, and Co-Director of the Berkeley Sensor & Actuator Center.  Her laboratory applies its expertise in materials, surfaces and interfaces to diverse applications including sustainable and renewable energy, and chemical sensing. She was a postdoctoral researcher at Penn State University and a research associate at UC Santa Barbara after receiving her B.S. from the Catholic University of America, and her M.S. and Ph.D. from Caltech. 

NIREN MURTHY
Point-of-Care Diagnostics

BIOENGINEERING

A Rapid Diagnostic for Drug-Resistant High-Risk Urinary Tract Infections

Urinary tract infections caused by bacteria that produce extended spectrum β-lactamases (ESBLs) have become particularly difficult to treat because these infections are also frequently multidrug resistant, making them impervious to a range of commonly prescribed antibiotics. Rapid detection of ESBL-producing bacteria has the potential to significantly improve patient treatment because it will inform healthcare providers, at the time of diagnosis, whether first-line antibiotics should not be prescribed and alternative agents should be used. To address this need, Niren Murthy’s group has developed a novel biochemical test that enables the detection of bacterially produced ESBLs directly from a patient’s urine sample, within the clinical setting. They have successfully demonstrated the efficacy of the first-generation test against a subgroup of ESBLs.   His Bakar Fellows Spark Award will enable the Murthy group to extend this work to include additional probes capable of detecting all known ESBL variants, and to bring this simple point-of-care diagnostic to clinical trials.

Niren Murthy is Professor of Bioengineering.  The Murthy laboratory is focused on developing new materials for molecular imaging, drug delivery and other medical applications.  He was a postdoctoral researcher in the Department of Chemistry at UC Berkeley, after receiving his B.S. from the University of Redlands, M.S. from the University of Illinois at Chicago, and Ph.D. from the University of Washington, Seattle.

RALUCA ADA POPA
Computer Security

ELECTRICAL ENGINEERING AND COMPUTER SCIENCE

Secure Collaborative Learning

Organizations that own sensitive data often wish to conduct collaborative studies informed by the aggregate data from all of these organizations, but they cannot do so because their data cannot be shared due to privacy concerns or regulations. With her Bakar Fellows Spark Award, Raluca Ada Popa will design and build a data encryption platform that will enable collaborative machine learning studies by performing these multi-party computations under encryption. Each participating group will have a private key to encrypt its own data before submitting it for analysis.  Training will be performed on the combined encrypted data from all collaborating groups, and the resulting final model, also encrypted, can be decrypted by each organization using its own private key.  In this way, the organizations will not share their sensitive data with any other party, yet they will all learn the results of the study. Examples of such uses could be hospitals seeking to predict influenza hot spots or better cancer treatments, or banks seeking to share information to detect money laundering or fraud, potentially saving thousands of lives and millions of dollars annually.

Raluca Ada Popa is an Assistant Professor of Computer Science. Her research is in the area of computer security, systems and applied cryptography, with an emphasis on computing on encrypted data.  She received her B.S., M.Eng.,and Ph.D. from the Massachusetts Institute of Technology.

KENICHI SOGA
Infrastructure Management

CIVIL AND ENVIRONMENTAL ENGINEERING

Smart Infrastructure using Real-time Distributed Sensing Technology

Infrastructure is a large part of nation’s assets and efficient management is vital to society. Infrastructure is constructed to last for decades, but its usage is linked to community needs that change more frequently. Infrastructure owners are increasingly looking for solutions to make their infrastructure more intelligent. The technology that is addressed in this research is Distributed Fiber Optic Sensing (DFOS). When light travels through an optical fiber, the majority of it travels through, but a small fraction is backscattered at every location. Thousands of DFOS analyzers; strain gauges, thermo-couples or accelerometers, quantify the back scattered signals along the length of the cable for distances up to 50km. The Soga lab is developing a new low cost real-time dynamic DFOS system and deploying it in real construction and infrastructure sites. With support of the Bakar Fellows Program, he and his research team aim to create a larger market for DFOS in the infrastructure industry and to promote the technology as part of innovation in engineering design and decision-making processes.

Kenichi Soga is a Chancellor’s Professor in the Civil and Environmental Engineering Department. He received his BEng and MEng in Civil Engineering from Kyoto University in Japan and PhD in Civil Engineering from the University of California at Berkeley. He was Professor of Civil Engineering at the University of Cambridge before joining UC Berkeley in 2016. His current research activities are infrastructure sensing, city scale modeling of infrastructure systems, performance based design and maintenance of underground structures and energy geotechnics.

STEVEN CONOLLY
Medical Imaging

BIOENGINEERING, ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

MPI Tracers for Quantitative, High-Resolution Tracking of Advanced Cancer Immunotherapies without Radiation

Many of today's most advanced diagnostic and therapeutic methods rely on injected cells, such as stem cells and modified immune cells. For example, the most exciting breakthroughs in oncology are in the field of immunotherapy, where the patient's own white blood cells are engineered to better recognize and kill tumors.  Development of these therapies has been slowed because it is extremely challenging to track injected cells within the body. Currently available nuclear medicine imaging methods; scintigraphy, PET, or SPECT, require radioactive reporters which can alter the viability of the cells under study. The Conolly laboratory is developing a high-resolution three-dimensional imaging method, Magnetic Particle Imaging, which does not use any radiation and has unprecedented sensitivity. Conolly’s Bakar Fellows project is to develop a high-resolution, safe and biocompatible tracer to enable MPI-based single-cell detection for immunotherapy optimization.  This high-resolution tracer will also be useful for tracking stem cell therapies, and could potentially revolutionize diagnosis of pulmonary embolisms, stroke, and gastro-intestinal bleeds.  This research may eventually compete for a significant fraction of the global contrast agent market, which now totals $4.57 billion annually.

Steven Conolly holds the Montford G. Cook Chair in the College of Engineering, where he is Professor of Bioengineering, and Electrical Engineering and Computer Sciences.  He is a medical imaging innovator, with particular emphasis on Magnetic Particle Imaging. He received his B.S in Electrical Engineering from Boston University, and his M.S. and Ph.D. in Electrical Engineering from Stanford University. 

POLINA LISHKO
Non-Hormonal Contraception

MOLECULAR AND CELL BIOLOGY

Plant-Derived Molecular Condoms as Non-Toxic Contraceptives

The urgent need for contraception worldwide concerns more than 200 million women. Almost a quarter of American women discontinue using hormonal methods of birth control within the first year, and ~54% of men discontinue using condoms within the same timeline, representing a large unmet demand for reliable, reversible and non-hormonal contraceptive compounds with minimal side effects.  Polina Lishko has discovered several nontoxic plant-derived compounds that effectively inhibit the sperm “drilling” mode that is essential for successful fertilization.  As a Bakar Fellow, she and colleagues will continue to evaluate these compounds’ safety and efficacy in blocking fertilization, using both in vitro and animal assays. They will also perform chemical screens for structurally related compounds with potentially even greater efficacy and begin to assess delivery routes for use in human contraceptive products.

Polina Lishko is Assistant Professor of Cell and Developmental Biology in the Department of Molecular and Cell Biology.  Her laboratory investigates the molecular mechanisms that regulate sperm motility, with the goal of developing safe unisex contraceptives, and diagnostic tests for male infertility. She graduated Summa Cum Laude from the Taras Shevchenko National University and received her Ph.D. at the National Academy of Sciences, both in Kiev, Ukraine. After completing postdoctoral research at Harvard University, she joined the UC Berkeley faculty in 2012.

DAVID SCHAFFER
Gene Therapy

CHEMICAL AND BIOMOLECULAR ENGINEERING, BIOENGINEERING & MCB

Advancing Gene Therapy Systems Through Investigating Mechanisms of Adeno-Associated Virus Replication

Gene therapy - the delivery of therapeutic genes to treat disease - has been increasingly successful in the past 10 years. In particular, delivery vehicles or vectors based on the adeno-associated virus (AAV) have achieved success in clinical trials for rare diseases including hemophilia B, hemophilia A, spinal muscular atrophy and others. However, natural AAV did not evolve as a pharmaceutical gene delivery vehicle, and the difficulty of producing sufficient quantities of AAV to treat incurable diseases is a major impediment to the goal of bringing gene therapy into routine clinical use.  Therapeutic AAV vectors are obtained by purification of virus particles produced within infected host cell lines grown in tissue culture.  David Schaffer is using high throughput approaches to engineer cells for enhanced AAV vector production.  With the support of the Bakar Fellows Program, he will use this information to engineer improved AAV vector production systems by creating virus producing cell lines that can generate many-fold higher levels of AAV vector than the current industry standard, bringing gene therapy one step closer to feasibility.

David Schaffer is Professor of Chemical and Biomolecular Engineering, Bioengineering and Molecular and Cell Biology, and Director of the Berkeley Stem Cell Center. His laboratory is focused on both basic biology and product development for stem cell and gene therapies, using a combination of chemical, genetic and genomic engineering approaches. He studied chemical engineering at Stanford University (B.S.) and the Massachusetts Institute of Technology (Ph.D), and did postdoctoral research at The Salk Institute in gene delivery and stem cell biology. 

MING WU
Photonic Switching

ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

Silicon Photonic Switches for Data Center Networks

Currently, data center servers are interconnected by optic fibers and electronic switches, in which photons travel through optical fibers, are routed by electronic switches, and are then converted back to optical signals. Such optical-electrical-optical conversion has become a bottleneck as data rate has increased. Ming Wu has invented a novel optical (silicon photonic MEMS) switch that demonstrates superior performance relative to all other integrated switches, including the highest port count, lowest on-chip loss, digital switching with sub-microsecond switching time, broadband operation, and low power consumption.   Several major data center operators and telecom companies are collaborating with his group on the applications of this novel switch, which, if successfully commercialized, would transform data centers by greatly increasing their capacity and reducing their energy consumption. His Bakar Fellows support will accelerate commercialization of this invention by enabling him to improve fiber packaging and reliability, and to identify a partner for fabrication of the switches on a large scale.

Ming Wu is the Nortel Distinguished Professor of Electrical Engineering and Computer Sciences, Co-Director of the Berkeley Sensor and Actuator Center, and Faculty Director of Berkeley Marvell Nanolab.  He received his B.S. from National Taiwan University in Taipei, and M.S. and Ph.D. from U.C. Berkeley. His research program includes projects in silicon photonics, optoelectronics, nanophotonics, optical MEMS, and optofluidics. 

TING XU
Biodegradable Plastics

MATERIALS SCIENCE AND ENGINEERING

Commercialization of Polymer/Enzyme Complexes for Controlled Degradation of Plastics

Although plastics are attractive, they are lethal to our vulnerable ecosystem. Even so-called biodegradable plastics degrade slowly, and the resulting small particles can be more harmful than the intact material. Enzymes effectively digest plastics to re-useable monomers but to date can only erode polymers from the surface, rendering enzymatic degradation too slow to be technologically relevant.   Ting Xu recently designed protein-like polymers, “RHPs,” that can stabilize and protect enzymes in harsh environments such as those encountered during plastic fabrication. RHPs can be incorporated into plastics by controlled dispersion during conventional processing techniques, enabling their planned spatial distribution during fabrication and removing the diffusion barrier to degradation at the end of the product’s lifespan. Her Bakar Fellows funding will enable her to optimize and scale up production of RHP-based products for use in the biomedical, food, and green plastic industries.

Ting Xu is Professor of Materials Science and Engineering, and Associate Co-Director of the Tsinghua-Berkeley-Shenzhen Institute Center for Precision Medicine and Healthcare. She received her B.S. from Dalian University of Technology in China, a M.S. from the Chinese Academy of Sciences, and M.S. and Ph.D. from the University of Massachusetts, Amherst. The Xu lab studies the hierarchical self-assembly of complex systems involving artificial proteins, block copolymers, and nanoparticles, and designs, synthesizes and characterizes novel peptides to serve as building blocks for functional biomaterials.
 

The Bakar Innovation Fellows are creative and entrepreneurial graduate students and postdoctoral scientists who are working with a Bakar Faculty Fellow to translate their laboratory discoveries and innovations to the commercial sector. The program introduces Innovation Fellows to campus resources and advisors to help them transition from academic researcher to startup founder.

The 2019-20 Bakar Innovation Fellows:

Jonathan Bachman, Ph.D. is President and CTO of Flux Technology, operating under a SSUFIE agreement the laboratory of his mentor to create composite polymer membranes for purifying natural gas.
Bakar Faculty Fellow: Jeffrey Long 

Christopher Barnes, Ph.D. candidate in Bioengineering, is working to make widespread clinical use of gene therapy feasible by increasing production efficiency of therapeutic-grade viral vectors.
Bakar Faculty Fellow: David Schaffer

Prashant Chandrasekharan, Ph.D., postdoctoral scientist in Bioengineering, is formulating novel iron oxide nanoparticle tracers to optimize resolution of Magnetic Particle Imaging, a new non-invasive, non-radioactive imaging modality.
Bakar Faculty Fellow: Steven Conolly

Chase (Qixi) Chen, M.Eng. candidate in Materials Science and Engineering, is employing a new transition material to increase the sensitivity and resolution of infrared radiation detectors.
Bakar Faculty Fellow: Junqiao Wu

Adrian Davey, Ph.D. candidate in Chemical and Biomolecular Engineering, is developing a sensitive, inexpensive miniaturized carbon dioxide sensor with a readily visible color change readout.
Bakar Faculty Fellow: Roya Maboudian

Eduardo González Grandío, Ph.D., postdoctoral scientist in Chemical and Biomolecular Engineering, is developing a biomolecule delivery technique based on carbon nanotubes that will help accelerate non-GMO plant breeding.
Bakar Faculty Fellow: Markita Landry

Johannes Henriksson, Ph.D. candidate, and postdoctoral scientist Kyungmuk Kwon, Ph.D., both in Electrical Engineering and Computer Sciences, are perfecting a newly invented silicon photonic MEMS switch, with the potential to greatly increase the speed and efficiency of optical communication networks and data centers.
Bakar Faculty Fellow: Ming Wu

Postdoctoral scientist Lingqing Lu, Ph.D., and  Ph.D. candidate Andrew Yeskoo, both in Civil and Environmental Engineering, are incorporating distributed fiber optic cables into new and retrofit construction to assess infrastructure performance and maintenance requirements.
Bakar Faculty Fellow: Kenichi Soga 

Mehran Mirramezani, Ph.D. candidate in Mechanical Engineering, is developing computational frameworks for analyzing fractional flow reserve computerized tomography (FFR_CT) images to non-invasively assess coronary artery obstruction.
Bakar Faculty Fellow: Shawn Shadden

Rishabh Poddar, Ph.D. candidate in Computer Science, is building a data encryption platform that will enable participating organizations to collaboratively process confidential information such as health outcomes, sharing the results without revealing their individual data to each other.
Bakar Faculty Fellow: Raluca Ada Popa

Heather Upton, Ph.D., postdoctoral scientist in Molecular and Cell Biology, is devising highly efficient methods of sequencing small RNA or DNA molecules as a rapid, reliable and affordable biomarker diagnostic.
Bakar Faculty Fellow: Kathleen Collins

Jyoti Taneja, Ph.D., postdoctoral scientist in Plant and Microbial Biology, is engineering powdery mildew resistant variants of important California crops such as tomatoes, grapes and strawberries.
Bakar Faculty Fellow: Mary Wildermuth

Storm Weiner, Ph.D. candidate in Physics, and Xuejian Wu, Ph.D., postdoctoral scientist in Physics, are creating miniaturized atomic sensors for applications in navigation, mineral exploration, surveillance, and civil engineering.
Bakar Faculty Fellow: Holger Müller

JAMIE CATE
Biotechnology

Chemistry and Molecular and Cell Biology

Engineering Kluyveromyces marxianus as a New Industrial Synthetic Biology Platform

Throughout history, S. cerevisiae has served as a central industrial and model microorganism due to its use in food production and the many genetic and genomic tools available to probe its biology. However, it is imperfect for industrial use because it has a narrow preference for carbon sources, has proven difficult to engineer to expand the products it can produce, and suffers from performance limitations in harsh industrial conditions. Other yeasts are far more robust and might serve as better industrial hosts. Among “non-standard” yeasts, Kluyveromyces marxianus has outstanding potential as an industrial host due to its appealing traits: thermotolerance, a broad range of carbon source utilization, and one of the highest growth rates among eukaryotes. We propose to use synthetic biology tools for K. marxianus recently developed in our lab to establish the species as a platform that can replace S. cerevisiae as a host for industrial production of value-added renewable chemicals.

Jamie Cate is a Professor in the Departments of Chemistry and Molecular and Cell Biology. He joined the UC Berkeley faculty in 2001 from the Whitehead Institute and Massachusetts Institute of Technology. He received his BS from the University of Denver and his PhD from Yale University, and was a postdoctoral fellow at UC Santa Cruz.  The Cate laboratory develops novel means of biofuel and renewable chemical production, and studies the basic biology of protein synthesis.

NICHOLAS DE MONCHAUX
Sustainability

Architecture, Urban Design and Berkeley Center for New Media

Local Code: Connecting CAD & GIS for Networked and Sustainable Urban Design

Our work connects two previously separate worlds of information and design in the built environment; Geographic Information Systems (GIS) and Computer-Aided Design (CAD).  Over the last five years, we have shown how a robust integration between CAD and GIS can produce unprecedented and essential design work, such as our 3,659 individual proposals for distributed ecological infrastructure in San Francisco, Los Angeles, and New York. Such proposals accomplish much of what large, single infrastructure proposals would accomplish for the city, but at a reduced cost, and with far greater resilience and investment in at-risk communities.  As well as a way to make better cities and landscapes, however, the methods we have prototyped are potentially instrumental for a range of design markets. From locally optimizing solar energy installations to effectively configuring ecological prefabricated housing on many sites, we believe our work can play a key role in a wide range of new, digital connections between how we map the world and how we make it.

Nicholas de Monchaux is Associate Professor of Architecture and Urban Design and Director of the Berkeley Center for New Media. His design work has been exhibited widely, including at the Biennial of the Americas, the Venice Architecture Biennale, the Lisbon Architecture Triennial, SFMOMA, and the Chicago MCA. He received his B.A. with distinction in Architecture, from Yale, and his Professional Degree (M.Arch.) from Princeton. 

DANIEL FLETCHER
Digital Health

Bioengineering

Mobile Phone-Based Eye Care

Routine eye exams are required for effective diagnosis and management of diabetic retinopathy, glaucoma, and other major causes of blindness. Despite coverage of exam costs by insurance and Medicare, many people forgo necessary screening. A low-cost handheld retinal imaging tool could increase access to routine eye exams by making high-quality retinal imaging available from primary care physicians and other healthcare professionals. Together with collaborators, we have developed a mobile phone-based ophthalmoscope capable of capturing wide-field retinal images for rapid screening of retinal diseases.

Daniel Fletcher is the Chatterjee Professor of Engineering Biological Systems and Chair of the Department of Bioengineering. His laboratory develops medical devices and studies biophysical mechanisms of disease, with a particular interest in infectious diseases and global health. He received his BS from Princeton University, his D.Phil from Oxford University as a Rhodes Scholar, and his PhD from Stanford University.

LIN HE
Genome Editing

Molecular and Cell Biology

Highly Efficient Mammalian Genome Editing by CRISPR RNP Electroporation of Zygotes

Today, standard CRISPR-editing practice in mice involves microinjection of Cas9 DNA/mRNA into zygotes to directly generate modified animals. While a significant improvement over previous genome engineering methods, microinjection is a costly and time-consuming procedure. We have developed a novel electroporation-based strategy, CRISPR-EZ, to deliver preassembled Cas9 ribonucleoproteins (RNPs) for genome editing. This method enables high-efficiency and high-throughput genome editing in vivo with an optimal embryo survival rate at a fraction of the cost of microinjection-based methods.  We propose to further increase the overall editing efficiency of CRISPR-EZ, and to enable more complex genome engineering schemes in mice. In collaboration with experts in animal reproduction biology, we propose to expand the utility of CRISPR-EZ to engineer the genomes of other mammalian species. Given the advantages of CRISPR-EZ technology in editing efficiency and embryo survival, it has considerable potential to be the preferred CRISPR genome editing technology in mammals.

Research in the He laboratory is directed toward understanding the functions of non-coding genomic elements in normal development and disease, including micro-RNAs, long non-coding RNAs, and retroposons, using a variety of mouse genetics, genomics, cell and molecular biology approaches. Dr. He received her BS from Tsinghua University and PhD from Stanford University. After postdoctoral research at the Cold Spring Harbor Laboratory, she joined the UC Berkeley faculty in 2008.  Dr. He was awarded a MacArthur Foundation “genius” award in 2009, and a carcinogenesis young investigator award in 2014. She is currently an HHMI faculty Scholar. 

JUNQIAO WU
ENERGY EFFICIENCY

Materials Science and Engineering

Multi-Smart Thermal Materials

We propose to develop, understand, and exploit a special class of phase transition materials as multi-functional coatings for smart thermal management. Thanks to a thermally-driven metal-insulator phase transition, these materials switch their thermal radiation reflectivity and thermal conductivity at the transition temperature, and the transition temperature can be tuned by the material composition.  These unusual switching properties enable self-regulated, intelligent management of heat exchanges (both heat radiation and heat conduction) of a system with its environment for much improved thermal energy utilization. The technology would save a large amount of energy that is currently wasted due to poor heat management in those systems. For example, currently in buildings, ~ 50% of the energy consumption is used for heating and air conditioning, while in transportation, ~ 60% of the heat produced in combustion engines is directly wasted. If the coatings we develop would improve efficiency of these processes by only 5%, the net effect would save energy costs in the USA on the order of billions of dollars.

Junqiao Wu received his BS from Fudan University, MS from Peking University, and his PhD from UC Berkeley, and was a postdoctoral researcher at Harvard University. He is currently a faculty member in the Department of Materials Science and Engineering and Co-Deputy Director of the Tsinghua-Berkeley Shenzhen Institute.  Dr. Wu was a recipient of the Presidential Early Career Award for Scientists and Engineers (PECASE) from the White House in 2013. The Wu laboratory explores novel materials properties and applications, phase transitions at the nanometer scale, and thermoelectrics and optoelectronics of semiconductor films, nanostructures, interfaces and composites. 

Amy E. Herr is the faculty director of the Bakar Fellows program. She was part of the inaugural 2012-13 Bakar Fellows cohort with support for her start-up, Zephyrus Biosciences to develop research tools enabling protein analysis at the single cell level. The company was acquired in March 2016 by Bio-techne. She is the Lester John and Lynne Dewar Lloyd Distinguished Professor in Bioengineering at UC Berkeley, Alfred P. Sloan Foundation Research Fellow in Chemistry, and co-inventor of the scWestern technology. She is an internationally recognized leader in microanalytical tool innovation. She earned her Ph.D. and M.S. degrees in mechanical engineering from Stanford and holds a B.S. in engineering & applied science from Caltech.

Please contact bakarfellows@berkeley.edu with any questions you may have about the program, or your application to join the program.  

Paul Alivisatos is UC Berkeley's Executive Vice Chancellor and Provost.  In addition he is the Samsung Distinguished Professor of Nanoscience and Nanotechnology, the Founding Director of the Kavli Energy Nanoscience Institute (ENSI), and Director Emeritus of Lawrence Berkeley National Laboratory.  He holds professorships in UC Berkeley's departments of chemistry and materials science. In addition, he is a founder of two prominent nanotechnology companies, Nanosys and Quantum Dot Corp, now a part of Thermo Fisher. Groundbreaking contributions to the fundamental physical chemistry of nanocrystals are the hallmarks of Dr. Alivisatos' distinguished career. He received his B.A. from the University of Chicago and his Ph.D. from UC Berkeley. 

Barbara Bass Bakar former Chief Executive Officer for several major retail firms, serves as the President of the Barbara and Gerson Bakar Foundation and the Gerson Bakar Foundation.  She also leads the ACHIEVE Program, a high school scholarship and enrichment program that she created and oversees. She is a member of the UC Berkeley Board of Visitors and the UCSF Foundation Board. She is a former chair of the UCSF Foundation and a former director of Starbucks Corporation and DFS Group, Ltd.

David Breslauer is co-founder and Chief Technology Officer of Bolt Threads, making sustainable biomaterials for consumer apparel and products. Bolt Threads grew out of his PhD thesis on the material science of spider silk, work performed in the UCSF/UC Berkeley Bioengineering Graduate Group. Bolt Threads currently produces Mylo(TM), a mycelium-based leather replacement, Microsilk(TM), a spider silk-based apparel fiber, and bsilk(TM), a silk-based silicone-replacement for personal care. In addition, David serves an advisor to startups inventing sustainable materials and food. David received his B.S. in Bioengineering from UC San Diego in 2005, and Ph.D. in 2010.

Kelly Gardner is Director of Marketing at ProteinSimple. Previously, she was CEO and co-founder at Zephyrus Biosciences, a venture-backed start-up company she spun out from her Ph.D. work to commercialize a microfluidic based platform for single-cell analysis.  She led Zephyrus from incorporation through to acquisition. In 2016, MIT Technology Review named Gardner to the “35 Innovators Under 35” list of entrepreneurs. She completed her Ph.D. in bioengineering in Professor Amy Herr’s Lab at UC Berkeley and holds an M.B.A.-equivalent from Cambridge University as a Gates Scholar, and a B.S. from Yale University.

Rachel Haurwitz is co-founder of Caribou Biosciences and has been President and CEO since its inception. She has a research background in CRISPR-Cas biology, and is also a co-founder of Intellia Therapeutics. In 2014, she was named by Forbes Magazine to the "30 Under 30" list in Science and Healthcare, and in 2016, Fortune Magazine named her to the "40 Under 40" list of the most influential young people in business. Haurwitz is an inventor on several patents and patent applications covering multiple CRISPR-derived technologies, and she has co-authored scientific papers in high impact journals characterizing CRISPR-Cas systems. Haurwitz earned an A.B. in biological sciences from Harvard, and received her Ph.D. in molecular and cell biology from UC Berkeley.

Amy E. Herr is the faculty director of the Bakar Fellows program. She was part of the inaugural 2012-13 Bakar Fellows cohort with support for her start-up, Zephyrus Biosciences to develop research tools enabling protein analysis at the single cell level. The company was acquired in March 2016 by Bio-techne. She is the Lester John and Lynne Dewar Lloyd Distinguished Professor in Bioengineering at UC Berkeley, Alfred P. Sloan Foundation Research Fellow in Chemistry, and co-inventor of the scWestern technology. She is an internationally recognized leader in microanalytical tool innovation. She earned her Ph.D. and M.S. degrees in mechanical engineering from Stanford and holds a B.S. in engineering & applied science from Caltech.

Randy H. Katz serves as UC Berkeley’s Vice Chancellor for Research and  is the United Microelectronics Corporation Distinguished Professor of Electrical Engineering and Computer Sciences. A Fellow of the Association for Computing Machinery, the Institute of Electrical and Electronics Engineers, and the American Association for the Advancement of Science, and a member of the National Academy of Engineering and the American Academy of Arts and Sciences, he has published over 350 refereed technical papers, book chapters, and books. His textbook, Contemporary Logic Design, has sold over 100,000 copies in two editions.  VCR Katz has received numerous awards for excellence in teaching, from UC Berkeley and professional societies. In the late 1980s, with colleagues at Berkeley, he developed Redundant Arrays of Inexpensive Disks (RAID), a $15 billion per year industry sector. On secondment to DARPA in 1993-1994, he established whitehouse.gov and connected the White House to the Internet. His current research interests are data analytics from distribute sensors and actuators (RISELab) and Smart Cities through Intelligent Energy/Buildings/Transportation Infrastructures (BETS). He received his B.S. from Cornell University, and his M.S. and Ph.D. from UC Berkeley.

Rich Lyons is UC Berkeley's Chief Innovation & Entrepreneurship Officer. From 2008 to 2018 he served as dean of UC Berkeley's Haas School where he currently holds the William and Janet Cronk Chair in Innovative Leadership. He was acting dean of the Haas School from 2004 to 2005 and executive associate dean from 2005 to 2006. For the two years prior to serving as dean he was the Chief Learning Officer at Goldman Sachs. He received his BS with highest honors from UC Berkeley (business) and PhD from MIT (economics). Before (re)joining Berkeley, Rich was for six years on the the business faculty at Columbia University. His research and teaching expertise is in international finance and his top applied interest is the "how and why" of setting strong institutional cultures. 

Michelle Meng-Hsiung Kiang is a technologist turned serial entrepreneur, bringing leading-edge innovation to commercial successes. She is a Venture Partner at ITIC focusing on early stage investment in deep tech. Most recently, she was Founder and CEO of Chirp Microsystems, a venture-backed company providing low-power, ultrasonic 3D sensing solutions initially developed at UC Berkeley/ Davis. After Chirp was acquired in 2018 by TDK, Michelle became VP and General Manager of the ultrasound sensor business under TDK’s MEMS Business Group. Prior to Chirp, she co-founded and led market development and business strategy for PINC Solutions, a leading provider of sensor-fusion enabled supply chain management SaaS solutions, and Onix Microsystems, a pioneer in MEMS-based optical networking products. While not working on her startups, she served in executive roles at Micron Technology and NeoPhotonics in Strategic Planning and Corporate Development. Dr. Kiang received the M.S. and Ph.D. degrees from UC Berkeley, and the B.S. degree from National Taiwan University, all in Electrical Engineering. She is the recipient of the David Sakrason Award for her outstanding thesis work at UC Berkeley.

Tsu-Jae King Liu is Vice Provost for Academic and Space Planning at UC Berkeley. She also holds a distinguished professorship endowed by TSMC in the department of electrical engineering and computer sciences. She has been on Intel’s board of directors since summer 2016. Previously she has held research and engineering positions at the Xerox Palo Alto Research Center and Synopsys Inc. Liu has received numerous awards for her research, including the Intel Outstanding Researcher in Nanotechnology Award (2012) and the SIA University Researcher Award (2014). Currently, her research is focused on nanometer-scale logic and memory devices, and advanced materials, process technology and devices for energy-efficient electronics. She received her B.S., M.S. and Ph.D. degrees in electrical engineering from Stanford University.

Andre Marquis is the Executive Director of the Lester Center for Entrepreneurship at the Haas School of Business at UC Berkeley. He has many years of experience starting successful biotechnology and IT ventures. Two companies Marquis helped start became publicly traded and a third was acquired by Amazon for over $190 million. He was also a founder and CEO of Amplyx Pharmaceuticals, an early stage drug development company backed by Life Science Angels and Tech Coast Angels. Marquis was a member of Boston-based CommonAngels and a founder of Incubator, LLC, a Berkeley-based business incubator. He received his B.A in cognitive science from University of Rochester and an M.B.A. from UC Berkeley’s Haas School of Business. 

Edward E. Penhoet is currently associate dean of biology at UC Berkeley and a member of the board of directors of the UCSF Benioff Children's Hospitals. He is also chairman of the board of Immune Design Corporation.  He was dean of the UC Berkeley School of Public Health  from 1998-2002, and  was a director of Alta Partners, a health sciences venture capital firm from 2000 to 2016.  Penhoet also was a co-founder of Chiron Corporation, where he served as the company’s President and Chief Executive Officer from its formation in 1981 until April 1998. He served as Vice-Chair of the governing board of the Independent Citizens Oversight Committee for the California Institute of Regenerative Medicine (CIRM) from 2005 to 2010, and served as the President of the Gordon and Betty Moore Foundation from 2004 to 2008. From 2008 to 2016 Penhoet served on President Obama's Council of Advisors on Science and Technology (PCAST), an advisory group comprised of 20 of the nation’s leading scientists and engineers. Penhoet is an emeritus faculty member of both molecular and cell biology and of public health at UC Berkeley  He received his A.B. from Stanford and his Ph.D. from the University of Washington.

Arnold N. Silverman is a principal of Discovery Ventures, LLC, a venture capital firm focused on early-stage investment in software companies with market leadership potential in emerging technologies. Prior to Discovery Ventures, Silverman was President of Dymo Industries, a NYSE multinational company, he then went on to become CEO of Icot Corporation. He was a found board member of, and was an early-stage investor in, numerous leading software companies including Oracle, Informatica, iOwn, Luna Information Systems, Times Ten, and Business Objects. He received his B.S. and M.S. in electrical engineering and computer science from UC Berkeley and holds an M.B.A. from Columbia.

Darlene Solomon is a Senior Vice President and CTO at Agilent where her responsibilities include Agilent Research labs, and Agilent's programs in university relations, external research and venture investment. In her leadership role she works closely with Agilent's businesses to define the company's technology strategy and R&D priorities. She joined Hewlett-Packard Laboratories as a research scientist and soon moved into leadership as the R&D manager for the Chemical and Biological Systems Department. When Agilent Technologies was spun out from H-P in 1999, she became responsible for R&D/Technology for Agilent's Life Sciences and Chemical Analysis business. She was promoted to VP and Director, Agilent Laboratories in 2003, and has been Agilent's CTO and VP since 2006. Solomon earned her BS in chemistry from Stanford University and a doctorate in bioinorganic chemistry from MIT and completed Stanford's Executive Development Program. Solomon serves on the board of directors at Materion Corporation and participates in multiple academic and government advisory and review boards. She is a member of the National Academy of Engineering, a Fellow of the American Institute for Medical and Biological Engineering, received the USC Viterbi School of Engineering's Daniel J Epstein Engineering Management Award, and was named by Healthcare Technology Report to its Top 25 Women in Biotech. 

Robert Tjian was president of the Howard Hughes Medical Institute from April 2009 through August 2016. Trained as a biochemist, he has made major contributions to the understanding of how genes work during his three decades on the faculty at UC Berkeley. Tjian studies the biochemical steps involved in controlling how genes are turned on and off – information that is key to decoding the human genome. Findings from Tjian's laboratory have illuminated the relationship between disruptions in the transcription process and disorders such as cancer, diabetes, and Huntington's disease. More recently, his team has begun studying how transcription factors control the differentiation of embryonic stem cells into muscle, liver, and neurons. Early in his career Tijan cofounded the start-up company Tularik. Which was acquired by Amgen for $1.3billion in 2004. Tjian received a B.S. in biochemistry from UC Berkeley and a Ph.D. from Harvard University.

KATHY COLLINS
Biotechnology and Health

Molecular and Cell Biology

New Reverse Transcriptase Technologies: Tools for Diagnosis and Health Status

Molecular signatures of an individual’s current heath status remain largely unread, at enormous cost. DNA sequence tests can inform disease risk but rarely report on current health. RNA sequence has the promise to meet the need for a broadly informative, readily interpretable, and affordable read-out of health status. RNA is DNA in action: quantitative and qualitative variations in RNA provide extra layers of information and are filtered for irrelevant genomic DNA sequence. Because cells secrete packets of RNA into the bloodstream, particularly cancer and dying cells, a simple blood draw will allow disease detection independent of the tumor type or type of tissue dysfunction. Our startup, KarnaTeq, has developed new tools for RNA sequencing that can be used by scientists now and health providers in the future.

Kathleen Collins is a Professor of Biochemistry, Biophysics and Structural Biology in the Department of Molecular and Cell Biology and a member of the Berkeley Stem Cell Center. Her investigations of RTs that copy RNA to make DNA, and RNA polymerases that convert single-stranded RNA to double-stranded RNA, establish the biological and biochemical mechanisms of nucleic acid synthesis beyond the central dogma. She joined the Berkeley faculty in 1995 after training at Yale, M.I.T. and Cold Spring Harbor Laboratory.

JAMES HURLEY
Neurodegenerative Disease

Molecular and Cell Biology

Activating Autophagy to Fight Neurodegeneration: Using Molecular Structure to Fight Neurodegeneration

Autophagy (literally “self-eating”) is the cell’s major mechanism for clearing out intracellular debris, and is central to maintaining health at the cellular level. Neurons are the cells that are the most vulnerable to damage when autophagy slows down in aging and disease, and a reduction in autophagic capacity is linked to neurodegenerative diseases such as Parkinson’s Disease. The machinery that carries out autophagy in cells consists of a series of protein complexes, including complexes known as “ULK1” and “PI3KC3-C1”. We are using insights into the structures of these complexes, and their dynamic changes during activation and inactivation, to develop therapies that will promote healthy autophagic function and combat neurodegenerative disease.

 James H. Hurley is a Professor and Judy C. Webb Chair in the Department of Molecular and Cell Biology studying protein-membrane interactions important in neurodegenerative diseases and AIDS. He received his B.A. and M.S. in Physics from San Francisco State University and his Ph. D. in Biophysics from UC San Francisco.

ALI JAVEY
Health Monitoring

Electrical Engineering and Computer Science

Wearable Sweat Sensors: Instantaneous Health Monitoring

Wearable sensor technologies play a significant role in realizing personalized medicine. Sweat contains metabolites that indicate physiological information and is an excellent candidate for non-invasive, continuous monitoring of health status. Our flexible sensors and integrated circuits bridge the technology gap in wearable sensors, enabling a wide range of personalized real-time diagnostics.

Ali Javey is a Professor in Electrical Engineering and Computer Science. He received a Ph.D. degree in chemistry from Stanford University in 2005, and was a Junior Fellow of the Harvard Society of Fellows from 2005 to 2006. He then joined the faculty of the University of California at Berkeley where he is currently a professor of Electrical Engineering and Computer Sciences. He is also a faculty scientist at the Lawrence Berkeley National Laboratory where he serves as the program leader of Electronic Materials (E-Mat). He is an associate editor of ACS Nano. He is the co-director of Berkeley Sensor and Actuator Center (BSAC), and Bay Area PV Consortium (BAPVC).

JEFFREY LONG
Carbon Capture

Chemistry

Development of Solid Adsorbents for Low-Cost Carbon Capture: Chemical Cooperativity in Action

Fossil fuel-fired power plants are the largest stationary point sources of anthropogenic carbon dioxide (CO2), which overwhelming evidence indicates is the leading greenhouse gas contributing to climate change. Although renewable energy technologies are being actively pursued, global dependence on fossil fuels is not likely to abate within the next two or more decades, and therefore carbon capture (and sequestration) is essential for reducing CO2 emissions. The prohibitive energy and cost expenses associated with current amine solvent-based capture technologies present a major impediment to large-scale commercial deployment, however. Our innovative solid adsorbents, consisting of diamine-appended metal-organic frameworks (MOFs), exhibit an unprecedented cooperative mechanism for CO2 binding that enables remarkable gas uptake, low-temperature regeneration, and uniquely positions them to revolutionize carbon capture. We will pursue the development, optimization, and large-scale commercial production of these adsorbents in pelletized form for implementation in coal- and natural gas-fired power plants.

Jeffrey Long is a Professor in the Departments of Chemistry and Chemical and Biomolecular Engineering. His research focuses on the development of new porous materials for applications in gas storage and separations relevant to clean energy technologies, as well as on the development of molecular and porous materials with novel catalytic, magnetic, and conductive properties. He received a BA in Chemistry from Cornell University, a PhD from Harvard University, and went on to postdoctoral studies at UC Berkeley before joining the Chemistry faculty in 1997. 

JIE YAO
Optics

Material Science and Engineering

Reconfigurable Photonics for the Next Generation Consumer Optics: Making Cameras Smarter and More Compact

Today conventional lenses are still used in smart phones, microscopes and many other devices. They are bulky and can only achieve a fixed functionality. With reconfigurable photonic devices, multiple functionalities can be achieved in one "smart lens". One can choose from the functionalities which one to use. Moreover, such lenses are going to be much more compact than their conventional counterparts.

Jie Yao is an Assistant Professor in the Department of Materials Science and Engineering. His research includes the study of novel optical materials and their applications in nanophotonics. He received his BS/MS degrees from Nanjing University, China and PhD in Applied Science and Technology from UC Berkeley.

Tsu-Jae King Liu was born in Ithaca, NY in 1963. She received the B.S., M.S. and Ph.D. degrees in Electrical Engineering from Stanford University in 1984, 1986 and 1994, respectively.  She joined the Xerox Palo Alto Research Center as a Member of Research Staff in 1992, to research and develop polycrystalline-silicon thin-film transistor technologies for high-performance flat-panel display and imaging applications. During her tenure with Xerox PARC, she served as a Consulting Assistant Professor of Electrical Engineering at Stanford University. In August 1996 she joined the faculty of the University of California at Berkeley, where she is now the Conexant Systems Distinguished Professor of Electrical Engineering and Computer Sciences (EECS) and Chair of the Department of Electrical Engineering and Computer Sciences.  From 2000 to 2004 and from 2006 to 2008, she served as the Faculty Director of the UC Berkeley Microfabrication Laboratory.  From 2003 to 2004, she also served as Vice Chair for Graduate Matters in the EECS Department. In 2000 Dr. Liu founded Progressant Technologies, which developed negative differential resistance transistor technology. The company was acquired by Synopsys, Inc. in 2004 for an undisclosed amount. In 2004-2006 she was Senior Director of Engineering in the Advanced Technology Group of Synopsys, Inc. (Mountain View, CA).  From July 2008 through June 2012 she was Associate Dean for Research in the College of Engineering. 

Dr. Liu's awards include the Ross M. Tucker AIME Electronics Materials Award (1992) for seminal work in polycrystalline silicon-germanium thin films, an NSF CAREER Award (1998) for research in thin-film transistor technology, the DARPA Significant Technical Achievement Award (2000) for development of the FinFET, the Electrical Engineering Award for Outstanding Teaching at UC Berkeley (2003), the IEEE Kiyo Tomiyasu Award (2010) for contributions to nanoscale MOS transistors, memory devices, and MEMs devices, the Electrochemical Society Dielectric Science and Technology Division Thomas D. Callinan Award (2011) for excellence in dielectrics and insulation investigations, the Intel Outstanding Researcher in Nanotechnology Award (2012), and the SIA University Researcher Award (2014).  Her research activities are presently in nanometer-scale logic and memory devices, and advanced materials, process technology, and devices for energy-efficient electronics.  She has authored or co-authored over 450 publications and holds over 90 patents. 

Dr. Liu is a Fellow of the Institute of Electrical and Electronics Engineers (IEEE) and a past member of The Electrochemical Society (ECS), the Society for Information Display (SID), and the Materials Research Society (MRS). She has served on committees for many technical conferences including the Device Research Conference, the International Conference on Solid State Devices and Materials, the International Electron Devices Meeting, and the Symposium on VLSI Technology, and was a member of the IEEE EDS VLSI Technology and Circuits Technical Committee.  From 1999 to 2004, she served as an Editor for the IEEE Electron Device Letters. 

Alan Sachs is the Chief Scientific Officer for Thermo Fisher Scientific. He served as the Chief Scientific Officer for Life Technologies/Life Sciences Solutions Group within Thermo Fisher between 2012 and 2015.  Prior to this role, Dr. Sachs was the Vice President of Exploratory and Translational Sciences at Merck Research Laboratories. During his ten years at Merck, he built and directed the global RNA Therapeutics Department, led the Rosetta Inpharmatics group, and led the Department of Molecular Profiling.  Before joining Merck, Dr. Sachs was an Associate Professor of Molecular and Cell Biology at the University of California at Berkeley, and a Whitehead Institute Fellow at the Whitehead Institute in Cambridge, MA.  Dr. Sachs’ academic work focused on understanding of the role of the poly(A) tail in translation and mRNA stability.  Dr. Sachs graduated from Cornell University with a B.A. in Biochemistry, received his Ph.D. with Roger Kornberg in Cell Biology at Stanford Medical School, received his M.D. from Stanford Medical School, and completed a post-doctoral fellowship with Ron Davis in the Department of Biochemistry, Stanford Medical School.

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Innovators portal for the UC Berkeley community | innovators.berkeley.edu

Berkeley’s vibrant entrepreneurial ecosystem extends across virtually every corner of campus and the broad Cal community — from middle and high school students involved with the Young Entrepreneurs at Haas through the energetic undergraduate and graduate student ranks, to world-class postdocs and faculty, and thousands of alumni around the world. Berkeley inventors and entrepreneurs — like Apple’s legendary Steve Wozniak ’86, groundbreaking biologist Jay Keasling, and visionary businessman Dave Gilboa ’03 — have changed the world.

We’re here to help you be part of Berkeley’s community of innovators. Our team of University Development and Alumni Relations and cross-campus staff will guide you through the breadth and depth of the innovation enterprise at UC Berkeley. At innovators.berkeley.edu, our team members have extensive campus and alumni networks, and experience across multiple campus areas.

• We help stakeholders engage with Berkeley in mutually beneficial ways.
• We facilitate connections among faculty, students, alumni, industry, and key university staff.
• We help alumni navigate the many Berkeley research programs, initiatives, groups, and events of interest to the innovation community.
• We help develop philanthropic and corporate partnerships with Berkeley.
• We find creative, efficient ways to support Cal and to strengthen the Berkeley network.

Map of the bottom-up UC Berkeley entrepreneurial community | Cal’s Entrepreneurial Ecosystem

QB3 is a resource for UC Berkeley entrepreneurs | qb3.org

Opportunities for MBA Students to Work with Bakar Fellows

If you would like to work with a Bakar Fellow please contact Program Manager Heather Youngs (hlyoungs@berkeley.edu)

Fellows Seeking Market Assessments

Daniela Kaufer: Creating new diagnostics and therapeutics for trauma induced epilepsy

Mary Wildermuth: Fighting fungal diseases in major California crops including strawberries and grapes

Tanja Cuk: Creating new materials for large-scale batteries with faster charging and longer life to support renewable energy

 Laura Waller: Extremely high resolution imaging for semiconductor manufacturing and non-destructive tissue analysis for medical diagnostics and biological research

Neil Tsutsui: Using ant-style communication to control a common pest without toxic pesticides

PIETER ABBEEL
Robotics

Electrical Engineering and Computer Sciences

A Robot in Every Home: Artificial Intelligence to Power Home Robots

Today, robots exist that, mechanically, are capable of performing many household chores. Equipping these robots with the artificial intelligence to perform such chores autonomously, however, has proven difficult.  This effort will pursue the development of machine learning algorithms that will enable robots to learn to perform chores from watching human demonstrations and through their own trial and error.  The practical benefits to society include enabling elderly and disabled to live independently well beyond what is possible now, as well as enable all of us to live more productive lives.

Pieter Abbeel is an Associate Professor in the Department of Electrical Engineering and Computer Science studying artificial intelligence (AI), control, intelligent systems and robotics (CIR), and machine learning. He received a BS/MS in electrical engineering from KU Leuven in Belgium and PhD in computer science from Stanford University.

MICHAEL LUSTIG
MRI TechnologyECHNOLOGY

Electrical Engineering & Computer Science

Clinical Dissemination of Compressive Sensing Methods for Robust Rapid MRI: Making MRI Safer, Cheaper, and more Available

MRI is an excellent tool for disease diagnosis and monitoring, yet MRI scans are inherently slow, which reduces throughput, increases cost, and limits applications such as cardiovascular and fetal/pediatric imaging. By enabling faster scans with improved image quality, our work in compressed scanning, motion sensing, and reconstruction algorithms can provide clear benefits to patients and their doctors. This technology could translate into fast, robust, broadly applicable pediatric MRI protocols with less anesthesia, making MRI safer, cheaper, and more available. We also envision new MRI applications for in both pediatric and adult disease diagnosis. We are currently working with radiologists at Lucille Packard Children’s hospital and will soon expand to other bay area facilities.

Michael (Miki) Lustig is an Assistant Professor in Electrical Engineering and Computer Science. His research focuses on medical imaging, particularly Magnetic Resonance Imaging (MRI), signal processing, and  scientific computing. He received a BSc from the Technion, Israel Institute of Technology and a MSc and PhD in Electrical Engineering from Stanford University.

HOLGER MÜLLER
Navigation

Physics  

Pyramidal Atom Inferometric Inertial Sensor: Unlocking New Applications in Navigation

Atom interferometry is a powerful tool for the precision measurements of gravity, acceleration, and rotation. It has already been applied for geophysics and geology, mineral exploration and inertial navigation. However, currently used systems are large, heavy and very expensive. Our breakthrough in miniaturization of these devices will unlock new applications in commercial and military aviation, robotic aircraft (drones), and other emerging technologies.

Holger Müller is an assistant professor in the Department of Physics. He received a BS from the University of Konstanz, Germany, a PhD from Homboldt-University, Berlin, and conducted post-doctoral research at Stanford University. He successfully applied for his first patent at age 14.

RONALD RAEL
Additive Manufacturing

Architecture

Developing Advanced Building Material Applications Using Additive Manufacturing: Transforming the Built Environment

In the US alone, the construction industry produced 143.5 million tons of building-related construction and demolition debris in 2008 and buildings, in their consumption of energy, produce more greenhouse gases than automobiles or industry. Our research combines exploration of waste materials in additive manufacturing (commonly known as 3D printing) – a viable and transformative tool to create sustainable, intelligent building materials that are responsive and reparable to the environment – and novel assemblies to create efficient architectural systems for building construction. Our technology could transform current building manufacturing and delivery systems. Warehousing material would no longer be necessary because material manufacturing could be on-site and on-demand, using locally derived and recycled materials. We can also add new design features such as recycled ceramic bricks that can act as passive air-conditioning and seismically stable structures. See some of the possibilities at http://www.emergingobjects.com/

Ronald Rael is an Associate Professor in the Departments of Architecture and Art Practice. His research and creative work relies upon a deep understanding of place, and its inherent resources, and makes careful links between a broad spectrum of tools that come from manual, industrial and digital approaches to making architecture. Rael received a BED from the University of Colorado and an MA at Columbia University. Based in San Francisco, his creative practice, Rael San Fratello, established in 2002 with Virginia San Fratello, is an internationally recognized award-winning studio whose work lies at the intersection of architecture, art, culture, and the environment.

KE XU
Microscopy

Chemistry

Spectrally-Resolved Super-Resolution Microscopy: Redefining the Way We See the World

Microscopy, in particular light (optical) microscopy, is an indispensable tool for modern research, medical diagnosis, and quality control. The resolution of conventional optical microscopy is limited by the diffraction of light to about 300 nanometers. Emerging super-resolution microscopy methods, including our recent developments, have overcome this limit by reinventing how a light signal is generated and processed. In recent years, achieve optical resolutions of better than 10 nanometers. Beyond pursuing high spatial resolution, we are developing next-generation methods to integrate super-resolution microscopy with spectroscopy to achieve spectrally-resolved super-resolution microscopy. By exploiting the largely unexplored spectral dimension of fluorophores, our research could enable super-resolution microscopy for infinite color channels with minimal crosstalk between different channels. That could give scientists unprecedented information about the interactions between different molecular components in biological and other complex systems, thus opening up exciting new possibilities for future research and diagnostics. We also plan to make our technology work with conventional commercial microscope systems so it can be readily adapted by researchers in different fields.

Ke Xu is Assistant Professor in the Department of Chemistry and holds the Chevron Chair in Chemistry. His lab works on the development of microscopy, spectroscopy, and other physiochemical tools to visualize biological structures and nanomaterials at the nanoscale. He obtained his B.S. from Tsinghua University, Ph.D. from Caltech, and performed postdoctoral research at Harvard University before joining UC Berkeley.

PIETER ABBEEL
Robotics

Electrical Engineering and Computer Sciences

Pieter Abbeel is teaching robots to learn with the vision that someday every home will have a robotic helper. Abbeel’s approach could help robots deal with three big challenges in navigating complex tasks: translatable perception, environmental variability and uncertainty, which will make robots much more adaptable and useful.

REBECCA ABERGEL
Decontamination, Separation, and Radiotherapeutic Strategies for Heavy Metals

nuclear engineering

Rebecca Abergel has worked with her research group to develop small molecular chelators as therapeutics for heavy element decontamination. She and her team are developing a drug that can be used as a post-MRI treatment to help remove these contaminants from the body, allowing patients to receive their MRI tests with peace of mind.

JAMES ANALYTIS
Condensed Matter Physics and Materials Science

PHYSICS

James Analytis is developing new technology which involves the flow of spin that leverages the collective behavior of the electrons as opposed to the flow of individual particles. This technology involves a novel class of AFM materials known as Mott insulators (MIs), with the benefits being a reduction of dissipation (which causes the electronics to heat up) and enhancing processor speeds.

ANA CLAUDIA ARIAS
MRI Technology

Electrical Engineering and Computer Sciences

Ana Claudia Arias is working on a new, customized hardware to allows Magnetic Resonance Imaging (MRI) with screen-printed receiver coils arrays.  She is working with partners at UCSF and Stanford Children’s Hospital to test the devices in a clinical setting.

JOSE CARMENA
Brain-Machine Interface

Electrical Engineering & Computer Sciences/H. Wills Neuroscience Inst.

Jose Carmena is developing new technology — known as brain-machine interface, or BMI — that enables people with spinal cord injuries, stroke or other motor disabilities to control prostheses simply by thought. His team studies how to exploit brain plasticity and machine learning to accelerate learning and boost performance of the prosthesis.

JAMIE CATE
Biotechnology

Chemistry and Molecular and Cell Biology

Jamie Cate is engineering the yeast Kluyveromyces marxianus as a new host for industrial scale green chemistry applications. His goal is to employ K. marxianus as a highly efficient producer of lipids for use in cosmetics, soaps and detergents. 

KATHY COLLINS
Biotechnology and Health

Molecular and Cell Biology

Kathy Collins is working to see that RNA sequence fulfill's its promise as an informative and affordable read-out of health status. Cells secrete packets of RNA into the bloodstream. Her startup, KarnaTeq, has developed new tools for RNA sequencing that can be used by scientists now, and health providers in the future, to detect disease independent of the type of tumor type or tissue dysfunction with a simple blood draw.  

STEVEN CONOLLY
Medical Imaging

BIOENGINEERING, ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

Steven Conolly is developing a non-radioactive tracer for use with the new medical imaging technology, Magnetic Particle Imaging (MPI).    This research could enable noninvasive early-stage cancer diagnosis and personalized assessment of cancer immunotherapies.  These safe magnetic tracers could also be a breakthrough in high resolution quantitative tracking of cells transplanted for regenerative medicine.

TANJA CUK
Energy Storage

Chemistry

Tanja Cuk received a Bakar fellowship to advance her research on “supercapacitors” — devices that can deliver more power than batteries, and more quickly, but as yet don’t store energy as well. Cuk’s goal is a new generation of supercapacitors optimized for energy delivery and storage. 

NICHOLAS DE MONCHAUX 
Sustainability

Architecture, Urban Design and Berkeley Center for New Media

Nicholas de Monchaux’s Local Code integrates Geographic Information Systems (GIS) and Computer Aided Design (CAD) software systems to enable designers to plan optimally distributed small infrastructure projects such as solar arrays, open space and housing.  The resulting projects will accomplish the goals of large infrastructure proposals, but with reduced cost, greater resilience and shared community benefits.

JOHN DUEBER
Green Dyes

Bioengineering

John Dueber is working to employ metabolite protecting groups for a sustainable indigo dyeing process. The new technology has the potential to transform the Jeans (and related textile) dyeing industry – currently a polluting industry with most of its manufacturing located outside of the United States – into a “green business” using dye processes that would comply with modern regulations ensuring environmental safeguards.

FELIX FISCHER
Graphene Nanoribbons

Chemistry

Felix Fischer plans to develop electronic devices and sensors based on a hot new material: graphene nanoribbons. These are narrow strips of graphene – a sheet of carbon atoms – that are small enough to exhibit quantum weirdness.

DANIEL FLETCHER  
Digital Health

Bioengineering

Daniel Fletcher is engineering a mobile phone-based ophthalmoscope, the RetinaScope, capable of capturing diagnostic quality wide-field retinal images in general practice and clinical settings.   Readily available screening with the RetinaScope will promote early detection of treatable causes of vision loss. 

MARIA PAZ GUTIERREZ
Indoor Health and Microengineered Biowalls

ARCHITECTURE

Maria Paz Gutierrez is introducing a new approach to indoor air detoxification, balancing healthy microbiomes, humidity, and heat regulation. Her new technology comprises engineered lichen blocks that are lightweight, scalable, self-regulated, require no energy, and are virtually maintenance-free, applicable to a wide range of spaces for transforming the health and comfort of indoor spaces.

LIN HE 
Genome Editing

Molecular and Cell Biology

Lin He is perfecting a new method to facilitate genome engineering of research and agricultural animals, by rapidly and efficiently introducing CRISPR/Cas9 ribonucleoproteins into fertilized oocytes.

AMY HERR
Cancer Screening

Bioengineering

Amy Herr is introducing screening strategies that isolate, characterize and measure dozens of proteins in thousands cells, with single-cell resolution. The tool harnesses microarray and microfluidic design to link the burgeoning field of proteomics - the analysis of protein abundance and function - with development of new diagnostics and pharmaceutical compounds.

JAMES HURLEY
Neurodegenerative Disease

Molecular and Cell Biology

James Hurley is developing therapies to regulate autophagy, the cell’s major mechanism for clearing out intracellular debris, to combat neurodegenerative conditions such as Parkinson's Disease. Neurons are the cells most vulnerable to damage when autophagy slows down with aging and disease. His insights will be used to develop therapies that will promote healthy autophagic function.

ALI JAVEY
Health Monitoring

Electrical Engineering and Computer Science

Wearable sensor technologies play a significant role in realizing personalized medicine. Sweat contains metabolites that indicate physiological information and is an excellent candidate for non-invasive, continuous monitoring of health status. Our flexible sensors and integrated circuits bridge the technology gap in wearable sensors, enabling a wide range of personalized real-time diagnostics.

BOUBACAR KANTE
Physical Electronics and Energy

ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

Boubacar Kante is building an ultra-compact laser system called the Bound State in Continuum Surface Emitting Lasers (BICSEL) that has the benefit of being both lower in cost and more energy efficient to meet the demands of rapidly developing technologies.

DANIELA KAUFER
Preventing Epilepsy

Integrative Biology

Daniela Kaufer is focused on a way to prevent the development of epilepsy in people who have had brain injuries, such as from trauma, stroke, infection or cancer. Her studies have shown that disruption of the blood-brain barrier that normally protects the brain may follow such injuries, and is followed by activation of a pathological signaling cascade, that leads to the development of epilepsy. Kaufer identified pharmacological means to target this signaling cascade, and protect the brain.

JAY KEASLING
Skin Disease Treatment

CHEMISTRY AND BIOMOLECULAR ENGINEERING

Jay Keasling is harnessing the power of skin probiotics that would enhance the skin microbiome, equipping the skin with the tools it needs to heal itself. By continuing his research in synthetic biology and metabolic engineering, he hopes to develop a skin microbial platform that can not only treat aging, but also skin diseases such as eczema and psoriasis.

ARASH KOMEILI
Biomining

PLANT AND MICROBIAL BIOLOGY

Arash Komeili is engineering bacteria to concentrate metals of interest for biomining. The goal of the project is to efficiently isolate valuable metals from minerals while minimizing the environmental damage caused by traditional mining approaches.

MARKITA LANDRY
Agricultural Nanotechnology

CHEMICAL AND BIOMOLECULAR ENGINEERING

Markita Landry has developed a nanoparticle-based method for delivering DNA and other biomolecules to a wide range of plant species, enabling high-throughput and high-yield genetic engineering.

ALESSANDRA LANZARA
Quantum Computing

PHYSICS

Alessandra Lanzara and her group have invented an instrument that enables scientists to directly map and control in the momentum space the spin quantum number of electrons. This device will facilitate the creation of materials to realize quantum computing, the next revolution in information technology.

POLINA LISHKO
Non-Hormonal Contraception

MOLECULAR AND CELL BIOLOGY

Polina Lishko has discovered non-toxic plant compounds capable of preventing fertilization by inhibiting sperm activation. She plans to adapt these for use in non-hormonal on-demand contraceptive products.

JEFFREY LONG
Carbon Capture

Chemistry

Jeffrey Long is designing innovative solid adsorbents to revolutionize carbon capture. His startup Mosaic Materials will pursue the development, optimization and large-scale commercial production of diamine-appended metal-organic frameworks (MOFs), that exhibit an unprecedented cooperative mechanism for CO2 binding and low-temperature regeneration, which uniquely positions them to revolutionize carbon capture in coal- and natural gas-fired power plants.

MICHAEL LUSTIG
MRI Technology

Electrical Engineering & Computer Science

Michael Lustig wants to make MRI scanning better, stronger, faster. Using compression scanning, he can reduce time in the machine and create smaller, better resolution images. He is working with radiologists at Lucille Packard Children's Hospital to refine his technology.

ROYA MABOUDIAN
Air Quality Monitoring

CHEMICAL AND BIOMOLECULAR ENGINEERING      

Roya Maboudian has produced an environmentally-friendly porous crystalline material with a strong affinity for carbon dioxide. By incorporating a pH sensitive dye into this material, she will produce an inexpensive and highly sensitive colorimetric carbon dioxide detector.

MICHEL MAHARBIZ
Smart Prosthesis

Electrical Engineering and Computer Sciences      

Michel Maharbiz focuses on building interfaces between the biotic and the abiotic. He is currently focused on developing next-generation neural interface technology. He is the co-inventor of Neural Dust, a method for tetherless electrical recording of neural activity, and is a co-founder of Cortera Neurotechnologies. 

ANDREAS MARTIN
Drug Development

Molecular and Cell Biology

Andreas Martin has developed novel systems and strategies to screen for compounds that selectively inhibit protein turnover in the cell and may lead to new drugs against cancer. His research elucidates important mechanisms of protein degradation and makes the involved enzymes amenable for in-vitro biochemistry, high-throughput screening, and structure-based drug design.

CECILIA MARTINEZ-GOMEZ
Microbial Rare Earth Element Recovery

PLANT AND MICROBIAL BIOLOGY

Cecilia Martinez-Gomez and her research team have developed a microbial platform for bio-safe leaching and recovery of light REEs from low-grade sources, such as electronic waste, using Methylorubrum extorquens. They isolate a genetic variant (evo-HLn) of M. extorquens that is able to acquire heavy REEs (e.g. Gd) instead of light REEs. Their team hopes to engineer the strain to increase its capacity for Gd leaching and Gd recovery, ultimately allowing them to recycle the Gd and reduce groundwater contamination.

BAOXIA MI
Heavy Metal Decontamination

CIVIL AND ENVIRONMENTAL ENGINEERING

Baoxia Mi is working to solve the lead-contamination issue that is inhibiting access to safe drinking water. She and her team discovered that two-dimensional (2D) MoS2 nanosheets are highly effective at removing lead from water. In fact, it is more effective than all materials reported in scientific literature thus far. This can be used as a Point-of use (POU) filter than can be installed in households, making clean water available to communities in need.

HOLGER MüLLER
Navigation

Physics   

Holger Müller is making "finding yourself" a lot easier. His miniaturized multi-axial interferometric inertial sensor can determine its own location without any external cues. By simultaneously measuring four independent combinations of acceleration and rotation, the device can even find materials underground, without the help of a satellite.

RIKKY MULLER
Brain-Computer Interfaces

ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

Rikky Muller is developing wireless earbuds that record the neural activity of the wearer’s brain and use this information to directly interface with smartphones in a variety of user interface, consumer and healthcare applications.

NIREN MURTHY
Point-of-Care Diagnostics

BIOENGINEERING

Niren Murthy is developing a chemical amplification system, termed DETECT, which is designed to rapidly identify bacterial drug resistance.  If successful, DETECT will identify patients that need to be treated with special classes of antibiotics, and will improve the treatment of bacterial infections.

KRISTOFER PISTER
Microbatteries

ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

Kristofer Pister is designing and fabricating in-chip lithium ion microbatteries to deliver longer lived, smaller and less expensive electronic sensors to power the Internet of Things.

RALUCA ADA POPA
Computer Security

ELECTRICAL ENGINEERING AND COMPUTER SCIENCE

Raluca Popa is designing a secure computation platform that will enable organizations to perform collaborative machine learning studies on their aggregate data, while maintaining the privacy of their data and without sharing it with each other.

RONALD RAEL
Additive Manufacturing

Architecture

Ronald Rael wants to change building construction forever. Rael has been expanding 3-D printing to use materials from sawdust to tire to salt. His designs and use local, sustainable materials to explore new architectural applications that can be beautiful, functional and made on-site.

MICHAEL RAPE
Cancer Drugs

Molecular and Cell Biology

Michael Rape has developed the first systematic strategy to screen for compounds that could yield potent drugs against a group or class of human enzymes with links to cancer. Rape‘s company, Nurix,  provides not only a complete new approach to drug discovery, but now also a source of jobs in California. 

JAIJEET ROYCHOWDHURY
Combinatorial Optimization

ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

Jaijeet Roychowdhury and his group have invented OIM, a new approach to solving combinatorial optimization problems. OIMs may revolutionize applications including logistics, autonomous vehicles and smart grids.

DAVID SCHAFFER
Gene Therapy

CHEMICAL AND BIOMOLECULAR ENGINEERING, BIOENGINEERING & MCB

David Schaffer is using molecular engineering to improve production of the viral vectors needed to transport therapeutic genes into target cells. The goal of this work is to enable rapid and efficient generation of large quantities of clinical grade AAV virus for use for clinical gene therapy.

SIMON SCHLEICHER
3D Printing in Home Architecture

ARCHITECTURE

Simon Schleicher and his research team are advancing the field of large-scale 3D printing through their innovative idea to print layers of high-performance concrete and other recycled material alternatives directly onto a double-curved, minimal formwork. This paves the way for a future where entire houses, not just vertical walls, can be constructed at a lower cost using 3D printing.

SHAWN SHADDEN
Diagnostic Tools

Mechanical Engineering

Shawn Shadden integrates diagnostic imaging with computational modeling to better diagnose stroke severity in patients. Using standard CT or MR angiography, a vascular flow model is used to quantify blood flow pre- and post-stroke. This enables estimation of how much disruption of flow has occurred, and improves the ability to risk-stratify patients for their eventual clinical outcome. He will work with a UC Berkeley start-up, O.N. Diagnostics (founded by Tony Keaveny) to bring his technology to market.

KENICHI SOGA
Infrastructure Management

CIVIL AND ENVIRONMENTAL ENGINEERING

Kenichi Soga is developing next generation sensor systems for understanding the performance of infrastructure systems and quantifying the extent of their aging and remaining life, based upon the dynamic distributed fiber optic sensing technology developed in his research group.

LYDIA SOHN
Cancer Screening

Mechanical Engineering

Lydia Sohn  looks 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. Sohn’s label-free method of screening cells, Node-Pore Sensing (NPS) was named one of five “Revolutionary Platform Technologies for Advancing Life Sciences Research” at a recent White House event. Sohn established her start-up company Nodexus in February 2014.

NEIL TSUTSUI
Agricultural Pests

Environmental Science, Policy and Management

Neil Tsutsui develops environmentally safe ways to control populations of Argentine ants — the no. 1 pest problem in homes and businesses, and a serious threat to California’s vitally important agriculture industry. Tsutsui leads efforts to reduce population growth by turning the ants’ own communication pheromones against them. 

RUSSELL VANCE
Immunotherapy

MOLECULAR AND CELL BIOLOGY

Russell Vance is taking a new approach to enhancing the efficacy of immunotherapy.  His goal is to identify small molecules that block the anti-interferon defenses of tumors.

LAURA WALLER
Microscopy

Electrical Engineering and Computer Sciences

Laura Waller is working on computational imaging methods for quantitative phase microscopy, which enables one to map the shape and/or density of invisible samples in a non-invasive way. Her group is developing simple experimental architectures and efficient post-processing algorithms for phase recovery, applied in a variety of scientific and industrial settings.

FENG WANG
Optoelectronic Devices

Physics

Feng Wang focuses on graphene, which has remarkable electrical, optical and nanofabrication properties that make it an exciting platform for new optoelectronic devices integrated on a single silicon chip. 

MARY WILDERMUTH
Plant Defense

Plant and Microbial Biology

Mary Wildermuth is looking for ways to help plants resist a common pathogen, powdery mildews, that have a devastating impact on California agriculture. This could obviate the need for extensive chemical treatments used to limit damage from the fungus. The Bakar Fellowship has enabled initial translation of this research to relevant agronomic species and allows for prioritization and formulation of strategies for commercialization. 

JUNQIAO WU 
Energy Efficiency

Materials Science and Engineering

Junqiao Wu is developing a new class of phase transition material-based coatings to improve the efficiency of thermal energy utilization. These materials may revolutionize energy handling in buildings and automobiles by automatically reflecting heat to the environment when cooling is required, but allowing it to enter to contribute to heating. 

MING WU
Photonic Switching

ELECTRICAL ENGINEERING AND COMPUTER SCIENCES

A current bottleneck for optical networks and data centers is the rate at which switches can direct data to the correct pathway.  Ming Wu’s silicon photonic switch has higher capacity, lower latency and better energy efficiency than current technology, and promises to transform data center operations.

KE XU
Microscopy

Chemistry

Ke Xu is extending the resolution of fluorescence microscopy to achieve optical resolution of better than 10 nm, a range previously accessible only through electron microscopy. His super-resolved microscopy with infinite color channels could give scientists unprecedented information about the interactions between different molecules in complex systems.

TING XU
Biodegradable Plastics

MATERIALS SCIENCE AND ENGINEERING

Ting Xu has designed novel protein-like RHP polymers that complex with enzymes to protect their structure and activity in harsh chemical environments.  This can lead to new materials with prescribed fate, enhanced ability to be recycled, and green chemistry. 

JIE YAO
Optics

Material Science and Engineering

Jie Yao wants to improve your cell phone. He is developing a "smart lens" or reconfigurable photonic devices with multiple functionalities that are much more compact than a conventional lens. His tunable optics can be used in other devices as well including microscopes, other cameras, scanners, detectors and scopes.

NORMAN YAO
Physics

MATERIALS ENGINEERING

Norman Yao has designed a highly sensitive and accurate probe for assessing the performance of new materials under pressure and strain. His NV-DAC system integrates quantum spin defects directly into diamond anvil cells and enables the measurement of material properties under pressure with sub-micron spatial resolution at a wide range of temperatures.

MICHAEL YARTSEV
Autonomous Navigation

BIOENGINEERING

Michael Yartsev is using insights gained from the study of bat navigation to design algorithms to control safe and efficient autonomous vehicles.

ANA CLAUDIA ARIAS
MRI Technology

Electrical Engineering and Computer Sciences

Customized Hardware for Magnetic Resonance Imaging (MRI): Screen-Printed Receiver Coils Arrays

Magnetic Resonance Imaging (MRI) is widely used in clinical settings as a diagnostic tool that offers superior contrast when compared to other imaging techniques. However, the RF receive coils represent a limiting factor on signal to noise ratio (SNR) which translates into notoriously slow scans. Current receive coils are often anatomically unmatched for the human body, heavy, inflexible, restrictive, and poorly tolerated by many patients. We propose the use of printed electronics as a powerful new approach for the design and manufacturing of MRI receive arrays. Printing enables highly flexible, lightweight, and inexpensive devices that conform easily to a patient’s body, much like a tailor-made (bespoke) garment. These printed arrays will address the performance gap where lack of body proximity and conformity is the dominating factor in SNR. Prof. Arias and Prof. Lustig have shown that this technology can be adapted to different body types, presenting excellent in vivo results. In this project we will conduct an in-depth study of the characteristics of printed components, together with SNR characterization of coil arrays tuned to operate in 1.5T and 3T clinical scanners. Our goal is to mature the technology to demonstrate large-area printed multi-channel MRI coil arrays, integrated into clothing which will give MRI access to a much broader human population, specially children. 

Ana Claudia Arias is Associate Professor in the Department of Electrical Engineering and Computer Sciences. Prior to UC Berkeley, she was the manager of the Printed Electronic Devices Area at PARC, a Xerox Company. She received her PhD in Physics from the University of Cambridge, UK. Her current research focuses on flexible printed devices and integration that leads to mechanically flexible electronic systems.

JOHN DUEBER
Green Dyes

Bioengineering

Employing Metabolite Protecting Groups for a Sustainable Indigo Dyeing Process

A major challenge for green chemistry is the maintenance of unstable intermediates under the mild conditions that make green chemistry green.  One excellent example is the dyeing of blue jeans using indigo, a process that currently depends on hazardous reducing agents to generate and maintain an unstable, soluble intermediate.  We propose to develop a biomimetic process that produces a natural indigo precursor by applying an easily-removed, easily-recycled protecting group during biosynthesis.  This stable, soluble product eliminates the need for the chemical reducing agents, making the process cleaner and safer.  Indigo dye solubility is the first of many green chemistry challenges that we believe will be addressable with this concept of biological protecting groups.

John Dueber is Assistant Professor in the Department of Bioengineering and a Principal Investigator with the Energy Biosciences Institute at UC Berkeley. His research employs protein engineering and synthetic biology approaches to gain designable control over biological systems. He earned his PhD at the University of California, San Francisco, in 2005 and joined the UC Berkeley faculty in 2010 after postdoctoral studies there as a QB3 Distinguished Fellow.

ANDREAS MARTIN
Drug Development

Molecular and Cell Biology

Jamming up Protein Turnover: Development of Specific Inhibitors for Deubiquitinating Enzymes

Reversible attachment of ubiquitin to proteins plays essential roles in protein trafficking, signaling, and degradation, and thus the control of many vital processes in eukaryotic cells. Important for this regulation is the rapid ubiquitin removal by deubiquitinating enzymes (DUBs), which therefore represent potent pharmacological targets for the treatment of cancers and neurodegenerative diseases. Protein degradation by the 26S proteasome critically depends on deubiquitination by the DUB Rpn11, a metalloprotease of the JAMM family. However, strategies for the selective inhibition of JAMM proteases are still missing. Our recent progress in recombinant expression, biochemical characterization, and structure-determination of Rpn11 offers unprecedented opportunities for the development of inhibitors for Rpn11 and related JAMM proteases by means of high-throughput screening. Specific activity assays will allow us to identify and validate new small-molecule antagonists, which are then tested for their effects on cancer-cell growth in established model systems. Identified inhibitors will be licensed to industry partners or used as the basis for starting a new company.

Andreas Martin is Assistant Professor in the Department of Biochemistry, Biophysics and Structural Biology. His research goals are to decipher the fundamental principles that govern substrate engagement, deubiquitination, unfolding, and translocation by the eukaryotic 26S proteasome.

SHAWN SHADDEN 
Diagnostic Tools

Mechanical Engineering

Image-Based Modeling for Acute Stroke Diagnosis

Diagnostic imaging, including CT and MRI, has transformed medicine by enabling noninvasive view of tissue inside the body. Using this technology to reliably diagnose cardiovascular problems is hindered by the fact that functional information about blood flow can be difficult to glean from medical images. Moreover, while diagnostic imaging may be useful to spot a problem, it does not provide the predictive power needed to test whether a given intervention may have anticipated benefit. The integration of diagnostic imaging with computational modeling can help address these two critical needs. In regards to ischemic stroke, we aim to develop a quantitative metric derived from image-based blood flow modeling at the time of diagnosis to risk-stratify the patient for a given treatment. The physician can then use this information, along with the patient's clinical data, to make a more informed and accurate treatment decision for that particular patient.

Shawn Shadden is Assistant Professor in the Department of Mechanical Engineering. His research focuses on the advancement of theoretical and computational methods to quantify complex fluid flow. Shawn received his PhD in Control and Dynamical Systems from the California Institute of Technology and his BS from the University of Texas, Austin in Aerospace Engineering.

LAURA WALLER
Microscopy

Electrical Engineering and Computer Sciences

Quantitative Phase Microscopy

This project aims to develop new methods of quantitative phase imaging, for applications in biological microscopy and semiconductor lithography. Phase imaging is a useful contrast mechanism that allows transparent samples to be visualized and quantified in a label-free non-invasive manner. From phase images, we can recover accurate height maps of cells or microfabricated surfaces, with nanometer-level sensitivity and diffraction-limited lateral resolution. Our methods use only a few images captured at various focus settings of a microscope. Thus, they are particularly simple and easy to incorporate into existing microscopes without specialized hardware. We aim to develop software that can interface with existing microscope hardware for adding quantitative phase capabilities to any commercial microscope, with real-time computation and easy automation of focus tracking and image segmentation.

Laura Waller is Assistant Professor in the Department of Electrical Engineering and Computer Sciences. She heads the Computational Imaging Lab, which develops new methods for optical imaging, with optics and computational algorithms designed simultaneously. The specific focus is on measuring and controlling wave effects (such as phase, coherence or nonlinearity) in microscopes and cameras. Laura was a Postdoctoral Research Associate in Electrical Engineering and Lecturer of Physics at Princeton University from 2010-2012 and received her BS, MEng, and PhD degrees in Electrical Engineering and Computer Science from the Massachusetts Institute of Technology (MIT) in 2004, 2005, and 2010, respectively.

By: Wallace Ravven
February 12, 2014

“Ballistic transport ” – it sounds like a blast into the future. And it is. 

By fabricating strips of carbon only one-atom thick and less than 15 atoms wide, researchers aim to create molecular-scale “wires” capable of carrying information thousands of times faster than is possible today.

Crammed into integrated circuits, these microscopic strips known as graphene nanoribbons could increase by more than 10,000 times the number of transistors per area in computer chips. The exceptionally fast current transport along graphene nanoribbons would not only increase chip performance, but could refine the sensitivity of sensors to monitor circuit performance or subtle environmental changes.

First conceived only ten years ago, nanoribbon technology is, of course, a very hot field. To successfully exploit graphene’s great promise, though, the absolute dimensions of the nanoribbons and their internal symmetry must be precise and predictable. Variations in structure generate performance uncertainty and inefficiency. Today’s fabrication techniques aren’t yet up to the job.

Felix Fischer, a chemist at Berkeley, is using his support from the Bakar Fellows Program to develop a totally new and extraordinarily precise way to create nanoribbons.

Fischer is also a recipient of a David and Lucille Packard Foundation Fellowship, awarded this year to 16 of the nation’s most innovative young scientists and engineers.

The conductivity and other electrical properties of nanoribbons are essentially defined by their dimensions. This, in turn, derives from their absolute atomic structure. Adding just one or two carbon atoms to a 15-atom-wide ribbon, for example, degrades its ability to work at room temperature.

Current fabrication methods rely on relatively crude physical means to create the microscopic strips – if something at the scale of less than a billionth of an inch can truly be called crude.  

“The conventional approach uses a focused beam to carve nanoribbons from sheets of graphene,” Fischer says.  “You chisel out the structure you want from a larger chunk of carbon. It can be done relatively quickly, but you don’t have precise control over the position of each carbon atom in the ribbon.

“We want nanoribbons in which we know exactly where each atom is.”

Instead of physically sculpting strips of graphene, Fischer chemically concocts them. By creating nanoribbons from their molecular subunits, he can control the position and number of each atom in the ribbon and achieve predictable control over their performance, he says.

His lab synthesizes molecular building blocks made from rings of carbon and hydrogen atoms, similar to the chemical structure of benzene. They then heat the molecules to link the building blocks into linear daisy-chains. In a second heating step the excess hydrogen atoms are stripped from the carbon skeleton yielding a uniform backbone of carbon-carbon bonds. 

The assembly’s atomic arrangement and its supporting substrate look like snakeskin or a tire track – though at a phenomenally small scale. If 10,000 nanoribbons were placed side by side they would form a structure about as wide as a human hair.

Electrons can travel along the uniform graphene ribbon essentially with no atoms to block their way. Their straight trajectory enables them to transport current thousands of times faster over short distances than they would through a traditional metallic conductor like copper wire.

That, in turn, means that transistors can be switched on and off much faster – one of the keys to increasing a circuit’s speed.
 
Fischer has found that nanoribbons can operate as room temperature semiconductors when they are between 10 to 20 atoms wide.

“The wider the ribbon, the narrower the band gap (a determinant of electrical conductance),” he says. “If you go to much wider ones, the properties we need fizzle out.”

The graphene strips could enable much faster transport, storage, and retrieval of data than can today’s semiconductors. Their structure also dissipates heat well, which would allow computers and other large electronic devices circuits to work longer and more efficiently.

Leaning back in his chair, arms folded behind his head and a cheery smile on his face, Fischer likens his interest in nanoribbons to the excitement of a child dreaming of being an astronaut. “It’s being somewhere where no one has been before. In chemistry, you can make new things every day. You’re only limited by your imagination and creativity.”

He mentions the often-cited Moore’s Law that predicts the performance to computer chips to double every two years. “Many manufacturers have worried that we might be hitting a ceiling. You have to think of how you can produce electronic devices that can work faster without generating more heat. These nanoribbons might be a key to keeping up with Moore’s Law.”

Certainly imagining that possibility is the first step.
 
____________________________

The Bakar Fellows Program supports innovative research by early career faculty at UC Berkeley with a special focus on projects that hold commercial promise.  For more information, see http://bakarfellows.berkeley.edu.

FELIX FISCHER
Graphene Nanoribbons

Chemistry

Molecular Electronics and Sensing Based on Graphene Nanoribbons

The potential of single layer graphene based electronic devices has been recognized mostly due to its exceptionally high charge carrier mobility. While the extended two-dimensional hexagonal carbon lattice is a semimetal or a zero-gap semiconductor, structural confinement to an essentially one-dimensional graphene ribbon opens a band-gap large enough to expose room temperature semiconductor properties. The primary goal of Felix’s research is the development of a rational synthetic bottom-up approach towards atomically defined graphene nanoribbons that enables him to harness the exotic electronic and magnetic properties emerging from quantum confinement effects at the nanometer scale. His design of a new generation of high-performance electronic materials paves the way to meet the ever increasing demand for smaller, faster, and more energy efficient electronic devices.

Felix R. Fischer is an Assistant Professor in the Department of Chemistry at UC Berkeley. He is interested in the development of atomically unambiguously defined nanomaterials and their incorporation into functional electronic devices such as organic field-effect transistors, photovoltaic cells and integrated molecular circuits. Prior to joining the faculty at UC Berkeley, Felix was a German National Academy of Sciences Leopoldina Postdoctoral Research Fellow at Columbia University in New York. Learn more.

DANIELA KAUFER
Preventing Epilepsy

Integrative Biology

Blood-Brain Barrier Dysfunction as a Biomarker and a Therapeutic Target for the Prevention of Acquired Epilepsy

The protection of the brain from blood-borne toxins, proteins and cells is critical to the brain’s normal function. Insults to the brain, including traumatic brain injuries, stroke, infections, and brain tumors are associated with Blood-Brain Barrier (BBB) dysfunction, and significant increase in the risk for epilepsy. However, there is no clinically applicable strategy to identify at-risk patients, or prevent the development of epilepsy in them. Daniela Kaufer, in collaboration with Dr. Alon Friedman from Ben Gurion University, will build on previous findings demonstrating that the blood protein albumin activates TGFß signaling cascade in astrocytes and initiates an epileptogenic process following BBB compromise. Kaufer and Friedman have demonstrated that blocking TGFß signaling following injury prevents the development of epilepsy, and identified an FDA-approved drug that effectively blocks the development of epilepsy and eliminates delayed seizures following BBB insult in rats and mice. Now they propose a preventive approach that includes screening BBB integrity as a marker to identify at-risk patients, and administration of losartan or alternative TGFß signaling blockers to prevent epilepsy development in these patients.

Daniela Kaufer is an Associate Professor in the Department of Integrative Biology and the Helen Wills Neuroscience Institute at UC Berkeley. She was born and raised in Israel where she studied Biological Sciences at Technion, and received her Ph.D. in Molecular Biochemistry at Hebrew University. She was a Human Frontiers Post-doctoral Fellow at Stanford University, before joining the UC Berkeley faculty in 2005. Daniela’s lab studies brain plasticity throughout life in face of stress and neurological insults, with a particular focus on plasticity involving adult neural stem cells and across the neurovascular unit – neurons, astrocytes, oligodendrocytes and the components of blood brain barrier. Learn more.

LYDIA SOHN
Cancer Screening

Mechanical Engineering

Label-Free Isolation and Analysis of Circulating Tumor Cells for Metastatic Breast Cancer Biomarker Discovery

Shed from primary solid tumors and entered into the blood stream, circulating tumor cells (CTCs) are believed to play a key role in the metastatic progression of breast cancer. Clinical studies have shown that breast-cancer patients with >5 CTCs/7.5 mL of whole blood prior to therapy have poor overall survival. Very little is known about CTCs, as their isolation and classification are extremely difficult due to their rarity: 1-10 cells/7.5 mL of peripheral blood. Lydia will develop a label-free method of isolating, screening, and sorting CTCs from metastatic breast-cancer patient blood. Metastatic breast-cancer cell lines spiked into healthy donor blood and metastatic breast-cancer patient blood will be used in her studies. She will subsequently molecularly characterize isolated CTCs to discover new biomarkers. Her success would enable a new pathway for determining the course of treatment for metastatic breast cancer patients, monitor cancer therapy, and perform early detection of disease.

Lydia Sohn is an Associate Professor in the Department of Mechanical Engineering at UC Berkeley. Previously she was part of the faculty at Princeton University and was a postdoctoral fellow at AT&T Bell Laboratories in the Semiconductor Physics Research Department, where she developed new methods of lithography with an atomic force microscope. Her research focuses on developing and employing quantitative techniques to analyze single cells. Learn more.

FENG WANG
Optoelectronic Devices

Physics

Graphene-Based Optoelectronics: from Ultrafast Nanophotonic Modulator to High-Sensitivity Optical Sensing

Graphene, a one-atom thick sheet of carbon, is an emerging new material with extraordinary physical properties. Electrically graphene exhibits the highest room-temperature mobility, and electrons move in graphene as if they have zero mass. Optically graphene interacts strongly with light of all wavelengths, and its optical absorption can be easily controlled through electrical gating and structure engineering. In addition, graphene is highly compatible with nanofabrication and can be readily integrated with silicon. This combination of remarkable electrical, optical, and nanofabrication properties makes graphene an exciting platform for new optoelectronic devices--ranging from nanophotonic modulators to optical sensing -- all integrated on a silicon chip. Feng will develop novel integrated graphene-based optoelectronics, in particular ultrafast, energy-efficient nanophotonic modulators for next-generation computing and high-sensitivity optical sensing that significantly surpass currently available alternatives.

Feng Wang received a B.A. from Fudan University, Shanghai, in 1999 and a Ph.D. from Columbia University in 2004. From 2005-2007, he was a Miller Fellow with the Miller Institute for Basic Science at UC Berkeley. He joined the Physics Department at UC Berkeley as an Assistant Professor in 2007. He is interested in light-matter interaction in condensed matter physics, with an emphasis on novel physical phenomena emerging in nanoscale structures and at surfaces and interfaces. Learn more.

MARY WILDERMUTH
Plant Defense

Plant and Microbial Biology

Alteration of Parasite-Induced Plant Processes to Promote Durable Disease Resistance and Enhance Agronomic Product Traits

Powdery mildews are widespread plant parasites with a devastating impact on California agriculture. Currently, extensive chemical treatments are used to limit powdery mildews. Using Arabidopsis thaliana, a small flowering plant that facilitates molecular studies of plant-pathogen interactions, and lasers to isolate specific cells at the infection site, the Wildermuth group identified plant processes that the powdery mildew fungus manipulates to promote its proliferation. Specifically, endoreduplication, an altered cell cycle that is associated with enhanced metabolic capacity, was induced in plant cells underneath the fungal feeding site. Targeted reduction of this process and its downstream impact on metabolism limits powdery mildew proliferation in Arabidopsis and may promote durable powdery mildew resistance in agronomic species. By contrast, increasing endoreduplication or its impacted metabolic pathways could enhance size and nutrient content of specific commodities such as tomato fruit, as well as enhanced bioproduction of specialized plant metabolites. Mary will take the initial translation of this research and apply it to relevant agronomic species and bioproduction platforms, which will allow for the prioritization and formulation of strategies for commercialization.

Mary Wildermuth studied Chemical Engineering at Cornell University and received her Ph.D. in Biochemistry at the University of Colorado, Boulder. From 1998-2002 she was a Postdoctoral Fellow at Harvard Medical School concentrating on molecular genetics. At UC Berkeley since 2003, she is an Associate Professor in the Department of Plant and Microbial Biology. Her research focuses on investigating mechanisms that mediate plant-microbe interactions. Learn more.  

Mr. Silverman is a principal of Discovery Ventures, LLC, a venture capital firm focused on early-stage investment in software companies with market leadership potential in emerging technologies. Prior to Discovery Ventures, Mr. Silverman was president of ICOT Corporation. He has served on the boards of, and was an early-stage investor in, numerous leading software companies including Oracle, Informatica, iOwn, Luna Information Systems, Times Ten, and Business Objects.

He received his B.S. and M.S. in Electrical Engineering and Computer Science from UC Berkeley and holds an MBA from Columbia.

By: Wallace Ravven 
April 22, 2013

Fast, powerful and always ready to go. Qualities that apply to good fullbacks and heavy-duty trucks are also hallmarks of the ideal electric car battery. Conventional car batteries store energy reasonably well, but other technologies can deliver energy more quickly. UC Berkeley’s Tanja Cuk (pronounced “chook”) leads an effort aimed at achieving higher energy densities in these quick technologies.

An assistant professor of chemistry, she is testing how to optimize new devices for both power delivery and energy storage. Her focus is an alternative to conventional batteries, called a “supercapacitor.”

While batteries store energy chemically, supercapacitors store it as an electrical charge which builds up at the interface between electrically charged water molecules, or ions, and an electrode. The charged water molecules move from the supercapacitor chamber to the charged metal electrode. Cuk is testing how combinations of charged metal ions, instead of only water ions, can boost capacitors’ ability to store energy on different types of electrodes.

She aims to increase supercapacitors ability to store energy ten-fold. Her lab has received new momentum in the form of a 2012 Bakar Fellowship award given to UC Berkeley scientists and engineers to help advance innovative research by early career faculty. The program focuses on projects that hold commercial promise.

Supercapacitors generate power by using surface chemical reactions interacting with an internal structure that has a high surface area. The process delivers more power than current batteries. It does so more reliably and with longer lifetimes. But as yet supercapcitors are not as good as batteries in storing energy.

“Current supercapacitors can store small amounts of energy for a long time. I’m working on technologies to store more energy, where the tradeoff might be a shorter storage time. You could use the supercapacitor when you need it for fast power delivery, like speeding up a hill, and then the battery could recharge it. It would be good for quick on-off cycles.”

Essentially, the approach can be thought of as the basis for another kind of hybrid vehicle, with the supercapacitor replacing the battery for bursts of power, and the battery recharging it when it isn’t needed. The strategy will provide a longer battery life for the car overall. Ultimately, Cuk thinks, linking supercapacitors and batteries in an electric car will offer the best of both worlds.

Her Bakar Fellowship supports research to devise supercapacitors that use the chemistry of mixtures of metal ions depositing on an electrode to boost the capacitance and hence, energy stored. Metal ions in a supercapcitor tend to pile up on the electrode. Cuk expects that a mixture of different types will lead the ions to deposit in a more dispersed fashion, speeding up electrical discharge at any voltage.

Cuk’s lab has already felt the impact of the Bakar support. “The focus on commercial application energizes the lab,” she says. “We have an application-oriented project.

“It’s an area I wouldn’t have gone into without this fellowship. It really complements our fundamental research and applies a focus on performance. I am now more aware of studying the tradeoffs between fast and slow energy delivery, and this helps me understand chemical reaction kinetics in a very practical way.”

She hopes to develop a proof-of concept of the capabilities of the new types of supercapacitors in the next year. Bakar support will help shepherd this prototype concept to commercialization.

By: Wallace Ravven
April 15, 2013

Familiarity breeds acceptance among creatures large and small. In fact, it’s the foundation for cooperation in nests of ants, troops of baboons or suburban neighborhoods.

The reverse is also true. Unfamiliarity can breed aggression. Among the world’s most social creature – ants – encounters between workers of the same species, but from different colonies, can lead to torn-off limbs or fights to the death.

The exception are Argentine ants in California, the common household pests that often stream inside when the weather changes, or when they get a whiff of a food source. Argentine ants from different regions in California recognize each other as kin, and don’t attack each other.

Aggressive tendencies have probably become muted among the California ants because they are all descendants of the same group that was originally introduced from South America. They are family, says Neil Tsutsui, an expert in ant genetics and behavior and an associate professor of environmental science, policy and management.

“When we look at the DNA fingerprints of ants from different parts of the state, they are genetically nearly identical,” he says. “You can take an Argentine ant from San Diego and mix it with those in the Bay Area, and they cooperate as if they are the same colony. They will clean each other, and take care of each other’s babies.”

Because Argentine ants have done away with fighting, they can devote all their time and energy to feeding and reproduction. Throughout California, they make up one effective “super-colony,” numbering in the trillions – by far the state’s most common insect, Tsutsui says. And a potential troublemaker.

In some areas, the ants disrupt ecological interactions, repel pollinators and compromise business operations. They also cause significant crop loss, particularly to citrus and grapes, and are considered a significant agricultural pest.

In 2012, Tsutsui received a prestigious Bakar Fellowship which supports innovative research by early career UC Berkeley faculty, with a special focus on projects that hold commercial promise. The program provides support for his lab to develop and test new ways to reduce damage caused by the ants.

Funded by his Bakar Fellowship Tsutsui is now on the trail – literally – of new strategies to repel the invaders. He is experimenting with ways to exploit the ants’ reliance on chemical signaling.

Ants normally distinguish friend from foe by detecting colony-specific molecules called pheromones that coat their bodies. Tsutsui has identified the recognition pheromones and other chemical signals, and has shown in experiments that the ants’ behavior can be tweaked by exposing them to identical, environmentally harmless synthetic pheromones.

He has considered ways of introducing pheromones that spell “invader” to colonies of Argentine ants, in order to boost their aggression. Slight alterations in one of the pheromones can create a false signal to the ants that colony mates are intruders. This can decrease the population either directly through warfare, or indirectly because increased aggression reduces the time and energy the ants use for feeding and reproduction.

His Bakar Fellowship currently supports research to test the pest-control effectiveness of a synthetic version of a natural trail pheromone that Tsutsui discovered. Ants lay down the pheromone as they travel between their nest and potential food for the colony, and it serves as a trail guide.

His lab has drawn trails with a pure version of the pheromone, and shown that the ants will follow these artificial trails too. He aims to introduce synthetic trail pheromones identical to the real ones to draw ants in a chosen direction, perhaps away from a food source – and presumably from crops, businesses, or even into poison traps.

“The Bakar Fellowship is helping us move from discoveries to applications,” he says. We are at the beginning stage, but we hope to start small-scale field experiments this year.”

He has contacted managers at the Charles Krug Winery in the Napa Valley, where Argentine ants live in symbioses with agricultural pests, such as aphids, mealybugs, and scale insects. Winery managers are interested in hosting a field experiment to see if the synthetic trail pheromone strategy can successfully divert the agricultural pests or reduce their impact.

Tsutsui made the connection with Krug Winery through the help of Jeff Burton, the director of UC Berkeley’s Skydeck, a start-up accelerator that serves as a center for training and experience in technology entrepreneurship. Skydeck staff are working with Tsutsui to explore the promise of starting a company to commercialize his pheromone pest-control approach.

First though, the Bakar Fellowship will support proof-of-concept experiments to test the effectiveness of lab – proven techniques in the field. “This is the real problem that the Bakar program addresses,” Tsutsui says. “You see the potential of all these Berkeley discoveries, but there is this gap on moving them that crucial step to having real-world value. This is a great opportunity for us to do just that.”

Over the past two years, Tsutsui’s lab has been working on a strategy to detect bedbugs from the pheromones they emit.  In principle, a hand-held detector could identify the presence of even a single bedbug.  Tsutsui is working with Skydeck  to explore the commercial potential of the technique.

By: Wallace Ravven
April 8, 2013

Ubiquitin –  it sounds like the name of a mythical hero who’s everywhere at once. But it’s an apt term for a molecule that plays a vital role in every cell in our body.  Ubiquitin protects cells from being overrun with junk. It latches on to proteins that have outlived their usefulness and helps ferry them to the cell’s recycling center where they can be broken down for future reassembly.

When a process this critical to survival goes awry, the results can be catastrophic. If ubiquitin fails to connect to its target properly, or does so at the wrong time, the aberration can trigger chronic inflammation, neurodegeneration, even cancer.  

Berkeley’s Michael Rape studies ubiqutins that form chains, “like pearls on a string,” he says. In 2008, his lab discovered a new member of this chain configuration and determined how an enzyme called Ube2S is able to assemble it inside cells. Without the Ube2S enzyme and the ubiquitin chain, he found, cells cannot divide. But with too much Ube2S – and too many ubiquitin chains – cell division runs out of control.   

Rape is now on the trail of a potential drug to block Ube2S and interrupt excessive ubiquitin production to prevent uncontrolled cell division, the hallmark of cancer.  

In 2012, Rape received a prestigious Bakar Fellowship which supports innovative research by early career faculty at UC Berkeley with a special focus on projects that hold commercial promise. The program provides support for his lab to develop strategies needed to screen more than 100,000 compounds to find one that can best block Ube2S, and stop excess ubitqutin from ramping up cell division.

The new funding serves two functions: It helps Rape develop a new tool to understand the “logic” by which ubiquitin controls the cell’s housekeeping needs. And at the same time, the research can zero in on a potential drug to treat cancer.  

“By digging deeper – by understanding the mechanism of action – we can refine our ability to screen for compounds that block UbeS2.,” Rape says. “That would open up a completely new drug strategy for human health.”

The Bakar Fellows Program, he says, allows his lab to go where federal research grants such as those from NIH, would not allow.  

NIH supports basic research on the mechanisms of molecular processes, but usually the support stops there.  “They tend to think it is the job of companies to take it further and search for drugs,” Rape says.

The problem is that companies are reluctant to take on that search until someone has shown the validity of the strategy. It’s an often-unbridgeable gap between research that points to a new drug and the screening needed to find the drug. The pharmaceutical industry, Rape says, is keenly interested in targeting ubiquitins, but most have been waiting for proof of principal – the kind of progress that he now has in his sights. 

“The Bakar support is allowing us to take that next step in our lab. Once we have found a molecule that can target the specific enzyme, we can move to commercial development, or demonstrate to a company that the molecule is a strong enough drug candidate for them to develop further.”

He has already founded a company, called Nurix, which focuses on the development of chemotherapeutics by targeting the ubiquitin system. 

Rape, associate professor of cell and developmental biology, is a native of Bavaria. This year, he gained high honors for his ubiquitin research. He received the prestigious Vilcek Prize for Creative Promise, awarded to only three foreign-born scientists who have made outstanding contributions to society in the U.S. 

Rape believes that if his ubiquitin and Ube2S discoveries can be advanced to the real world of an anti-cancer drug, it would be a “game changer” – certainly the kind of contribution to society the Bakar Fellows Program envisions.

By: Wallace Ravven
April 1, 2013

After age 60, a man faces one chance in six of getting prostate cancer. Unfortunately, the lab test that detects the disease can’t reveal if the cancer poses a real risk. It looks for elevated levels of a protein called PSA. But about 80 percent of cancers that generate high PSA levels grow so slowly that they may never need treatment.

Not knowing if their prostate cancer is likely to metastasize, millions of men undergo often-painful biopsies, and surgeries that can cause serious complications – only to learn that their cancer was not a likely threat.

New research now points the way to a much more refined assessment of proteins and the promise of better diagnosis and treatment of a range of diseases. After proteins have been faithfully produced from our cells’ genetic blueprints, they can naturally undergo chemical changes that dramatically alter their behavior. The alterations, known as post-translational changes, are not coded in our genes, but some of them may be linked to aggressive types of cancer, and to other serious disorders.

In theory, a simple assay – an assessment of an individual’s protein make-up – could improve
diagnosis and treatment of conditions caused by protein variations. In the case of prostate cancer, most men would then be able to breathe easy, and only those at risk could get the treatment they need.

The hitch is that researchers lack a key tool to move these new insights into practical use. They need a fast, efficient way to sort through and identify the modifications, or isoforms, of a single suspect protein. By isolating the different versions of a single protein, scientists have a shot at determining which modifications are linked to disease.

“We need to learn, not only what is encoded in the genome – the blueprint of life – but how that actually translates into protein function in health and disease,” says Amy Herr, associate professor of bioengineering at Berkeley.

Herr is on the front lines of proteomics research – the ambitious effort to determine the variety and function of all human proteins. Her research, supported by the Bakar Fellows Program, which funds innovative research by early career faculty at UC Berkeley with a special focus on projects that hold commercial promise, focuses on developing a more quantitative strategy to assay changes in proteins. This strategy could launch a new generation of diagnostics based on a precise understanding of proteins’ roles in both normal and diseased tissue.

Herr’s lab is developing a way to assay many dozens of human proteins at a time. The technology is designed to assay proteins in extraordinarily small volumes of liquid. This “microfluidic” approach introduces minute samples onto chips similar to those used in the semiconductor industry, except that these chips are designed with microchannels that can each route individual specimens for protein analysis.

The new microfluidic approach allows fast, efficient and automated analysis for the first time – with dozens of individual proteins simultaneously teased apart into their different forms.

The bounty of new biological information can be digitized and archived, Herr explains, allowing findings to be integrated with insights at the genomics level. The strategy provides a new window on potential protein targets for diagnostics and treatments.

And because it employs materials common to industry, the assay strategy can be integrated with existing technology. In a word, it will be “manufacturable.”

Misbehaving proteins may underlie many diseases, so high-volume, automated assays could be a boon to diagnosis and potential treatment well beyond prostate cancer. Variation of individual proteins may play a role in the malformation of proteins in diseases such as Alzheimer’s and Parkinson’s.

Herr’s lab has already begun partnering with major pharmaceutical
companies interested in applying rapid and refined, industrial-scale microfluidic assays. Efficient assay techniques can greatly speed – and reduce the costs of – testing new compounds for their ability to boost or block protein variations that promote devastating diseases.

“Our current understanding of how changes in a given protein affect health and disease has been mostly a black box,” Herr says.

Her lab is showing the way to pry open the box.

By: Wallace Ravven
March 25, 2013

It still sounds futuristic, but the time is approaching when people paralyzed by stroke or spinal cord injury will be able to regain the experience of movement.

They will again be able to hold and manipulate a fork, or maybe a forklift, with a mechanical hand that is controlled by their mind. The connection that had been broken between thinking and doing will be replaced by a new kind of connection that can translate signals from their brain directly to the robotic hand.It still sounds futuristic, but the time is approaching when people paralyzed by stroke or spinal cord injury will be able to regain the experience of movement.

The startling capability stems from insights in neuroscience, coupled with refined bioengineering. Known as a brain-machine interface, or BMI, the emerging technology can retrain the brain to think of an artificial hand as its own.

Over the past two decades, scientists have discovered the brain’s impressive plasticity – its capacity to learn new skills throughout life, and its ability to reallocate sets of neurons to new tasks. BMI exploits these capabilities. Electrodes implanted in the brain allow neurons to communicate with external software that can control a prosthetic device.

The technology is being refined in advanced laboratories in several countries, including the United States, Japan, China and several European countries. Berkeley neuroengineer Jose Carmena and bioengineer Michel Maharbiz have joined forces in a project supported by the Bakar Fellows Program aimed to move the technology from the laboratory to the real world. The Bakar Fellows Program supports innovative research by early career faculty at UC Berkeley with a special focus on projects that hold commercial promise.

“The Bakar funding encourages us to look at processes – to think about experiments that we wouldn’t likely be able to pursue with federal research grants,” says Maharbiz, a professor of electrical engineering and the self-professed “gadget man” of the team. “It is helping us look at how to leverage the activity going on in our labs to push commercialization and help people regain movement.”

Carmena, a professor of electrical engineering and of neuroscience, describes the effort as trying to tighten the “closed loop” between the firing of the brain’s neurons and the software that translates the neural signals into instructions for the prosthetics.

The exchange between neurons and the prosthetic device is a two-way street, he explains. Once subjects learn to mentally control the device, their skill at it improves, and this strengthens the neural pathways for control.

Likewise, as researchers learn more about which bundles of neurons are firing, they can update the algorithms, or mathematical instructions, that underlie the communication between the brain and the prosthetic device.

The software is the translator, or decoder. “Think of the decoder as the spinal cord that normally connects thoughts to action”, Carmena says. “In a BMI setting, the decoder is the new spinal cord. And we have shown that no matter what the spinal cord is made of, the brain will learn to use it. That is the power of brain plasticity.”

Many challenges remain – more in the neural implant technology than the robotics, Maharbiz says.

“Having wires implanted into your brain creates physiological complications. Currently, technology allows only temporary implants. That’s not practical.You wouldn’t want to replace a heart pacemaker every few months.”

In addition, the wires themselves appear to irritate, maybe even physically interfere with, neuron firing. Researchers are pursuing different strategies to overcome these problems. Maharbiz is a nano-engineer, and his lab works on fabricating extraordinarily thin, compliant wires – “like super-thin and flexible spaghetti,” he says.

Both Carmena and Maharbiz are also on the trail of greatly boosting the number of neurons, and the locations of neurons that electrodes can reach. The entire enterprise requires a tight collaboration between neuroscientists and their engineering counterparts.

“I think in California, we are poised to make big advances in BMI,” Maharbiz says. “The semiconductor industry has pushed very sophisticated microfabrication and electronics capabilities, and we also have great computer science and neuroscience expertise. There are very few places where you can see all these parts come together.”

UC Berkeley’s Marvell Nanofabrication Lab, with support from the semiconductor, computing and nanotechnology industries, for example, is equipped with sophisticated fabrication facilities to help advance the BMI effort, he says.

The Bakar Fellows Program is also closely connected to Skydeck, a Berkeley-run startup accelerator and a center for training and experience in technology entrepreneurship. Carmena’s and Maharbiz’s graduate students in meet there regularly to brainstorm about potential routes to commercialization of their research.

“The Bakar support has a very interesting effect on us,” Carmena says. “I’ve always thought about bringing this technology all the way from the lab to commercialization to help disabled people. But you’re busy and have many obligations, and the goal gets pushed back.

“The Bakar program changed my mindset. We have access to experts who can help us along this route; resources to understand patent issues. You are almost pushed towards a commercial effort. And that can only help in the long run.”

JOSE CARMENA 
Brain-Machine Interface

Electrical Engineering & Computer Sciences/H. Wills Neuroscience Inst.

A Brain-Machine Interface for Stroke Motor Rehabilitation

Brain-Machine Interface (BMI) technology has tremendous potential to greatly improve the quality of life of millions of people suffering from spinal cord injury, stroke, amyotrophic lateral sclerosis, and other severely disabling conditions. In the long-term, brain-controlled prostheses will be capable of reproducing the wide range of motor functions carried out by the human upper limb, so that patients can enact their voluntary motor intentions simply by thought. The field is currently unbalanced with a variety of robotic solutions to replace missing or paralyzed limbs that clearly exceed the ability of existing neural-interface technology to control them. Here we propose to transform recent advances from our laboratory in the neuroengineering science of BMI into clinically viable solutions. We will exploit neuroplasticity with closed-loop decoding techniques for achieving skillful brain-control of prosthetic devices comparable to natural movements. The Bakar fellowship will facilitate bringing these advances into the clinical and commercial realms.

Jose M. Carmena is an Associate Professor of Electrical Engineering and Neuroscience at UC Berkeley, and Co-Director of the Center for Neural Engineering and Prostheses at UC Berkeley and UC San Francisco. His research program in neural engineering and systems neuroscience is aimed at building the science and engineering base that will allow the creation of reliable neuroprosthetic systems for the severely disabled. Jose is co-inventor of Neural Dust, a new implantable technology that will enable robust and reliable brain-machine interfaces. Learn more...

TANJA CUK 
Energy Storage

Chemistry

Next Generation Supercapacitors: Managing Pseudocapacitance with Metal Ions

Supercapacitors store energy capacitively, as a surface charge; whereas batteries store energy chemically, via oxidation and reduction reactions.  Compared to batteries, they can deliver energy much more rapidly (higher power), show enhanced reliability, and longer charge/discharge cycle lifetimes.  The primary disadvantage of supercapacitors is their low energy density.  It is well known that the capacitance, and hence the energy stored, can be enhanced 10-100 times by exploiting pseudocapacitance—the capacitance that arises from equilibrium charge transfer between molecules in the electrolyte and the electrode.  The purpose of this Bakar fellowship proposal is to increase the number of materials that can be utilized for pseudo-capacitive behavior and explore the limits to energy density stored as a surface charge.  This fundamentally new approach involves placing multiple types of metal ions in solution with transition metal oxide electrodes. The consequences will be monitored with electrochemical measurements, x-ray absorption/photoemission, scanning transmission x-ray microscopy, and optical second harmonic generation.  The result will be a flexible materials system that can be optimized for performance.

Tanja Cuk graduated from Princeton University with a BSE in Electrical Engineering (2000) and Stanford University with a PhD in Applied Physics (2007).  She then went on to complete a Miller Postdoctoral Fellowship at UC Berkeley (2007-2010).  She joined the faculty of the Chemistry Department at UC Berkeley as an Assistant Professor in 2010.  Her research involves understanding catalytic processes at solid-liquid interfaces using ultrafast optical/infrared spectroscopy and in-situ x-ray spectroscopy. Learn more..

AMY HERR
Cancer Screening

Bioengineering

Getting Personal:  Massively Multiplexed Microanalytical Tools for Linking Proteomics to the Drug Development Pipeline

Personalized medicine is imaginable, but not truly realized.  Historically, drug discovery efforts have sought the “blockbuster” drug.  Nevertheless, mounting evidence suggests that individual response to treatment is anything but ‘one-size-fits-all’. A personalized approach to medicine has benefitted from understanding the individual’s genetic make-up (e.g., breast cancer).  Genomics technology has played a key role in yielding a treasure trove of information unimaginable just five years ago.  That said, important individual information is carried at the protein level (i.e., Alzheimer’s disease, prostate cancer) and our protein measurement capabilities are severely lacking.  Slow, labor-intensive, qualitative readouts are the norm.  To bridge this gap, we propose to radically advance the content and fidelity of protein-level measurements by introducing uniquely-suited multiplexed proteomic technology built on a microsystems/nanomaterials framework. Our approach would yield proteomic data suitable for fusion with genetic information, underpinning truly individual medicine. Patient costs, insurer costs, and pharmaceutical costs would all potentially benefit.

Amy E. Herr received her B. S. degree from Caltech and her M.S. and Ph.D. degrees from Stanford in Mechanical Engineering. From 2002-2007, Dr. Herr was a Biosystems Research staff member at Sandia National Laboratories (Livermore). At UC Berkeley since 2007, Professor Herr’s research focuses on instrumentation innovation to advance quantitation in life sciences and clinical problems – impact spans from tools for fundamental research (cell signaling) to near-patient disease diagnostics. Two entrepreneurial ventures have spun out of her research group and have successfully secured seed round funding and are now pursuing product development in University of California incubator facilities.   Learn more...

MICHEL MAHARBIZ
Smart Prostesis

Electrical Engineering and Computer Sciences   

Neural Dust: a Chronic, High Density Interface to the Mammalian Brain

Chronic, high-density neural interfaces will enable new therapies in the restoration of limb motor control, speech prostheses, communication devices for “lock-in” patients, and much more.  Maharbiz proposes a radical technology shift enabling  massive scaling in the number of neural recordings from the brain while providing a path towards truly chronic BMI. These goals are achieved via two fundamental technology innovations: 1)  10 - 100 micron scale, free-floating, ultrasonically-addressable sensor nodes, or neural dust, that detect and report local extracellular electrophysiological data, and 2) a sub-cranial interrogator that establishes power and communication links with the neural dust.  While the vision spans several years, specific technologies will be ready for commercialization and the road to clinical impact immediately. In the shorter term, Maharbiz has co-founded Cortera Neurotechnology to commercialize the related wireless microelectrocorticography (uECoG) technology developed in the Rabaey, Alon and Maharbiz groups.

Michel M. Maharbiz is an Associate Professor of Electrical Engineering and Computer Sciences at UC Berkeley.  He is the co-founder of Cortera Neurotech, Tweedle Technologies, Microreactor Inc. and has served as vice-president for product development at Quswami. Prof. Maharbiz was the recipient of a 2009 NSF Career Award for research into developing microfabricated interfaces for synthetic biology and MIT Tech Review's 2009 TR10 for the development of the world's first radio-controlled flying cyborg insects. Professor Maharbiz’s current research interests include building micro/nano interfaces to cells and organismsand exploring bio-derived fabrication methods. Learn more...

MICHAEL RAPE
Cancer Drugs

Molecular and Cell Biology

Developing First-in-Class Antagonists of Ubiquitin Conjugating Enzymes

Ubiquitylation is a posttranslational modification that is essential for cell division and survival, and its misregulation has been associated with many diseases, including cancer, chronic inflammation, or neurodegeneration. Small molecule inhibitors of ubiquitylation are attractive candidates for therapeutic approaches against these diseases, yet few strategies to target ubiquitylation enzymes have been established. We propose to develop a small molecule platform to target ubiquitin-conjugating E2 enzymes, which play key roles in cancer cell division and survival. Small molecule antagonists of E2 function will be extensively validated in biophysical approaches and tested for effects on cancer cell survival in various established model systems. Our technology will open up a new family of enzymes for drug discovery, allowing us to license it to existing Californian biotechnology companies or to use it as the foundation for starting a company aimed at interfering with disease-related ubiquitylation events.

Michael Rape is a Howard Hughes Investigator and Professor of Molecular and Cell Biology. He founded the biotech company Nurix, a leader in discovering and developing therapies that modulate the ubiquitin proteasome system. Nurix is funded by leading life sciences investors, Third Rock Ventures and the Column Group. Michael’s research focuses on how proteins are modified with ubiquitin and how processes in the cell are regulated by ubiquitination as well as ways to alter ubiquitination to treat diseases. He studied Biochemistry in Bayreuth, Germany and received his Ph.D. at the Max Planck Institute of Biochemistry in Martinsried, Germany. Learn more...

NEIL TSUTSUI
Agricultural Pests

Environmental Science, Policy and Management

Manipulating Insect Pheromones to Control a Widespread and Damaging Insect

Insects cause tremendous damage to agricultural products and are costly to control in businesses and residential settings. Moreover, the use of conventional insecticides degrades water and soil, presents health concerns, and is ecologically damaging. In California, the invasive Argentine ant is the leading pest of households and businesses and causes substantial agricultural losses in vineyards and citrus orchards. Tsutsui is silencing genes for pheromone production as a targeted, environmentally friendly approach to controlling Argentine ants. This project builds on his lab’s extensive prior research on Argentine ant genetics, genomics, behavior, and chemical ecology. The Bakar Fellows Program is supporting field tests of these control techniques to accelerate their transition from the lab to the marketplace.

Neil Tsutsui is a Professor in the Department of Environmental Science, Policy and Management. His research focuses on on ants and bees - how they communicate, why they behave in the ways they do, their ecology, and their evolution. He works in both the field and the lab, using a variety of different approaches. Professor Tsutsui received his B.S. in Biology, specializing in Marine Science from Boston University and his Ph.D. in Ecology and Evolutionary Biology from UC San Diego. Learn more...

What is the Bakar Fellows Program?

What are the benefits for faculty participating in the Bakar Fellows Program?

What are the expectations of the Bakar Fellows?

Who is eligible to apply?

When is the application deadline?

How do faculty apply for the Bakar Fellows Program?

How are the Bakar Fellows selected?

When does support start? And how can it be used?

Which campus unit administers the Bakar Fellows Program? 

Who are the members of the Bakar Fellows Advisory Board?
 

What is the Bakar Fellows Program?

The Bakar Fellows Program enhances UC Berkeley’s impact on the California economy by catalyzing the translation of basic scientific discoveries and engineering innovation to practical benefit. More specifically, the Bakar Fellows Program supports early-stage and commercially promising research by UC Berkeley faculty and their research groups. The Bakar Fellows Program comprises a strong network that assists researchers in introducing their discoveries and innovations to the market. Cal ranks as the top university for serial founders, second for VC-backed start-ups and second for women-led, VC-backed start-ups (Pitchbook), and is one of America’s most entrepreneurial universities (Forbes).

What are the benefits for faculty participating in the Bakar Fellows Program?

Through a competitive application process, faculty members are selected as Bakar Fellows and awarded discretionary research support. Faculty Fellows join a UC Berkeley ecosystem that includes faculty, post-docs, students, staff and alumni. The strong network and numerous entrepreneurial resources at UC Berkeley assist researchers in introducing discoveries to the market. Bakar Fellows benefit from work space in UC Berkeley’s Skydeck, a university incubator-accelerator in downtown Berkeley, interaction with the Haas School of Business and its Lester Center for Entrepreneurship, engagement with the School of Engineering’s Fung Institute for Engineering Leadership, and customized interactions with the Office of Intellectual Property and Industry Research Alliances (IPIRA). The Bakar Fellows harness UC Berkeley’s PI-entrepreneur and alumni networks to facilitate connections to relevant financial and founder communities in their specific domains.

What are the expectations of the Bakar Fellows?

The Bakar Spark Fund is designed to accelerate PI-led UC Berkeley research to tangible, positive societal impact through commercialization. Bakar Faculty Fellows are not expected to commercialize research outcomes during the 2-year Spark Fund period, but are expected to move closer to commercialization through milestones established by each PI.  Tangible evidence of commercialization of Spark Fund supported research makes alumni eligible for the Bakar Prize.  The one-time, up to $300K prize is designed to be a discretionary fund to assist the Fellow further with commercialization of research. During the Spark Fund period, Faculty Fellows will attend Bakar Fellows community events, engage with the Advisory Board, submit annual updates on progress towards goals.  

Who is eligible to apply?

UC Berkeley academic senate faculty who conduct research in the fields of, but not limited to engineering, computer science, chemistry, life sciences, physical sciences or multidisciplinary work in these disciplines are eligible to apply. The topic of the proposed research determines eligibility, not the home department of the applicant.

When is the application deadline?

The application cycle is annual, with initial applications due in early spring. For spring 2021 the application deadline is Monday, March 1, 2021.

How do faculty apply for the Bakar Fellows Program?

The application requires a brief summary of the proposed research project, a statement of how the research will make a key difference once introduced to the commercial marketplace, anticipated milestones for introducing the research to the market and an outline of how support from the Bakar Fellows Program will enhance their research. To apply, please fill out the Bakar Fellows Program Application. 

How are the Bakar Fellows selected?

The Bakar Faculty Fellows are leaders in their fields and exhibit interest in, or a track record of, realizing the commercial potential of their research. More specific selection criteria include:

• The research must be novel and capable of yielding practical benefit to society within a reasonable time-frame.
• The project and team must align with the Bakar Fellows Program goal of catalyzing commercialization of important research results. Examples of desirable outcomes include filing of patent applications, licensing of intellectual property, developing new industry partnerships, and/or the creation of a new company.
• The proposed research must demonstrably gain from Bakar Fellows Program support.

The review process takes place in two phases.  Application materials are initially evaluated, and finalists identified, by an ad hoc Selection Committee. Bakar Faculty Fellows are selected by the standing Bakar Fellows Program Advisory Board, based on finalist short talks presented at the Advisory Board’s annual meeting.  The Bakar Fellows Program Advisory Board is comprised of both academic and industry members.

When does support start? And how can it be used?

Funds are available at the beginning of the fiscal year in July.  Funds are for discretionary use by the faculty fellow. They cannot be used for faculty salaries or to pay for capital improvements. No overhead is assessed on the awards. 

Which campus unit administers the Bakar Fellows Program?

The Bakar Fellows Program is managed by the Office of the Vice Chancellor for Research.

The Bakar Fellows Program at UC Berkeley fosters faculty entrepreneurship in the STEM+ fields including Engineering, Computer Science, Chemistry, Biological Sciences, Physical Sciences, and Architecture. On a competitive basis, Bakar Fellows are awarded discretionary research support to mature & translate their ground-breaking discoveries and innovations into commercial solutions. Started in 2012, the Bakar Fellows Program enriches Berkeley by supporting entrepreneurial faculty & their research groups.

UC Berkeley ranks in the Top 2 universities for serial founders and for VC-backed start-ups (Pitchbook). We rank #3 for women-led, VC-backed start-ups (Pitchbook) and as the #3 most entrepreneurial university (Forbes). Over the last decade, UC Berkeley spin-out companies are estimated to have raised more than $14B (Pitchbook), positively impacting the California, US, and global economies.