2019 - 2020 Fellows
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.
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.
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.
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.
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
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.
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.