Reset

Director

Adam Arkin is the Dean A. Richard Newton Memorial Professor in the Department of Bioengineering at the University of California, Berkeley and Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. He and his laboratory develop experimental and computational technologies for discovery, prediction, control and design of microbial and viral functions and behaviors in environmental contexts.

He is the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA(Ecosystems and Networks Integrated with Genes and Molecular Assemblies, http://enigma.lbl.gov), designed to understand, at a molecular level, the impact of microbial communities on their ecosystems with specific focus on terrestrial communities in contaminated watersheds. He also directs the Department of Energy Systems Biology Knowledgebase (KBase) program: (http://kbase.us) an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants and their communities, and for sharing results and methods with other scientists. He is director of the newly announced Center for Utilization of Biological Engineering in Space which seeks microbial and plant-based biological solutions for in situ resource utilization that reduce the launch mass and improves reliability and quality of food, pharmaceuticals, fuels and materials for astronauts on a mission to Mars. Finally, he is the Co-Director of the Berkeley Synthetic Biology Institute, which brings together U.C. Berkeley and Lawrence Berkeley National Laboratory Scientists with Industry Partners to forward technology and applications for sustainable biomanufacturing.

Faculty

Doug Clark is the Gilbert Newton Lewis Professor in the Department of Chemical and Biomolecular Engineering and the Dean of the College of Chemistry of the University of California Berkeley.

Dr. Clark’s research interests are in biochemical engineering and biocatalysts. His research is in the field of biochemical engineering, with particular emphasis on enzyme technology, biomaterials, and bioenergy. Current projects include the structural characterization and activation of enzymes in non-aqueous media, the development of metabolic biochips for high-throughput catalysis and bioactivity screening, protein design and assembly for the development of advanced biomaterials, and enhanced conversion of lignocellulosic feedstocks to biofuels.
 

Dr. Coleman-Derr received his graduate education at the University of California at Berkeley in the lab of Dr. Daniel Zilberman in the Plant and Microbial Biology Department, studying mechanisms of epigenetic regulation of transcription in the model plant Arabidopsis. He then completed a post-doctoral research position at the Joint Genome Institute in the group of Dr. Susannah Tringe studying the microbial ecology of the root systems of desert succulents; in this role he also served as bioinformatic support on multiple JGI collaborative metagenomic research efforts involving analysis of 16S rRNA tag data from a variety of environmental and host-associated samples. Dr. Coleman-Derr now leads a research team for the United States Department of Agriculture’s Agricultural Research Service, where he aims to improve our understanding of the effect of abiotic stress on the plant microbiome, and to help identify plant growth promoting microbes capable of alleviating drought stress in their plant hosts. Current research involves several projects related to drought stress response in Sorghum bicolor (sorghum), including investigations into the changes in rhizosphere community composition under drought stress, a genome wide association study to reveal host loci controlled by drought tolerance-inducing root endophytes, and a screen of a collection of cereal endophytes for the ability to confer drought tolerance in sorghum. Dr. Coleman-Derr was awarded the USDA’s Scientist of the Year Award in 2017 for his contributions in this area.
 

Ali Mesbah is an Assistant Professor in the Department of Chemical and Biomolecular Engineering at the University of California Berkeley. Dr. Mesbah's research interests are in optimization-based systems analysis, fault diagnosis, and predictive control of uncertain and stochastic systems.

Before joining UC Berkeley, Dr. Mesbah was a senior postdoctoral associate at MIT. He holds a Ph.D. degree in systems and control from Delft University of Technology. Dr. Mesbah is a senior member of the IEEE and AIChE. He was awarded the AIChE's 35 Under 35 Award in 2017 for his contributions in the area of systems and process control.

Peidong Yang headshot
Peidong Yang
Areas of Interest:

Peidong Yang received a B.S. in chemistry from University of Science and Technology of China in 1993 and a Ph.D. in chemistry from Harvard University in 1997. He did postdoctoral research at University of California, Santa Barbara before joining the faculty in the department of Chemistry at the University of California, Berkeley in 1999. He is currently professor in the Department of Chemistry, Materials Science and Engineering; and a senior faculty scientist at the Lawrence Berkeley National Laboratory. He is S. K. and Angela Chan Distinguished Chair Professor in Energy. He was recently elected as MRS Fellow, and as a member of the National Academy of Sciences and American Academy of Arts and Sciences.

He is the director for California Research Alliance by BASF, and co-director for the Kavli Energy Nanoscience Institute. He is one of the founding members for DOE Energy Innovation Hub: Joint Center for Artificial Photosysnthesis (JCAP) and served as its north director for the first two years.  Yang is an associate editor for Journal of the American Chemical Society and also serves on editorial advisory board for number of journals including Acct. Chem. Res. and Nano. Lett. He was the founder of the Nanoscience subdivision within American Chemical Society. He has co-founded two startups Nanosys Inc. and Alphabet Energy Inc. He is the recipient of MacArthur Fellowship, E. O. Lawrence Award, ACS Nanoscience Award, MRS Medal, Baekeland Medal, Alfred P. Sloan research fellowship, the Arnold and Mabel Beckman Young Investigator Award, National Science Foundation Young Investigator Award, MRS Young Investigator Award, Julius Springer Prize for Applied Physics, ACS Pure Chemistry Award, and Alan T. Waterman Award. According to ISI (2002-2012, Thomas Reuters), Yang is ranked as No. 1 in materials science and No. 10 in chemistry based on average citation per paper. His main research interest is in the area of one dimensional semiconductor nanostructures and their applications in nanophotonics and energy conversion
 

Senior Scientist

Jeffrey Skerker's research focuses on engineering complex traits in microbes using a systems metabolic engineering approach. He has worked on a variety of non-model bacteria and fungi and is particularly interested in developing methods for high-throughput genetics and genome engineering. In the CUBES program, he will help develop Arthrospira platensis (commonly known as Spirulina) as a source of nutrition and medicine. In the initial phase of this project, a basic genetic toolbox will be developed for this organism and then as proof of concept, a two-gene pathway for the production of acetaminophen (i.e. Tylenol) will be integrated into the genome. Although Spirulina is widely grown at the industrial scale as a nutritional supplement, very little strain genetic engineering has been reported in the scientific literature. 

Technical Staff

Shunsuke Yamazaki graduated Tokyo University, Japan, where he investigated the mechanism of bacterial lipoprotein transport in the laboratory of Hajime Tokuda. He is then hired Ajinomoto Co., Inc. and joined Research Institute for Bioscience Products and Fine Chemicals, Kawasaki, Japan, where he worked on breeding strains and developing several processes for production of amino-acids and pharmaceuticals. He was currently in charge of investigation of pharmaceutical production using enzymatic conversion process. He became a visiting scholar researcher of Adam Arkin lab at UC Berkeley, CA, USA.

Postdoctoral Scholar

Daniel received his Ph.D. in Plant Biology with a designated emphasis in biotechnology from the University of California, Davis in 2017. Daniel’s research utilized a multidimensional approach to better understand the immune response initiated by XA21, a rice immune receptor that provides resistance to bacterial leaf blight (BLB) disease. As part of his Ph.D. studies, Daniel also performed research at the International Rice Research Institute in the Philippines, where he used marker-assisted selection to develop stacked resistance to BLB in the Swarna-Sub1 rice variety, which is tolerant to flooding and favored by millions of subsistence farmers in India. Daniel also interned with East-West Seed Group in Thailand, where he developed genetic markers to distinguish isolates of Colletotrichum spp. causing pepper anthracnose and Fusarium oxysporum f. sp. momordicae causing Fusarium wilt on bitter gourd. 

Daniel is currently a post-doctoral scholar in Devin Coleman-Derr’s group at the University of California, Berkeley where he is exploring ways to minimize the challenges of extraterrestrial farming, including finite resources and limited growing space within controlled-environment agricultural systems. Focusing on rice, Daniel is using a microbiome-based approach to select plant growth promoting bacteria that enhance phosphorus and water-use efficiencies. Additionally, he is using CRISPR/Cas9 based-gene editing to generate rice plants with increased conversion efficiency of light into edible biomass.
 

Jake hails from the far-away lands of the Midwest. He received his Bachelor's degree in Genetics from the University of Wisconsin-Madison where he was introduced to the world of scientific research through the study of the evolution of gene expression regulation in the yeast Saccharomyces cerevisiae. Upon graduation, Jake began his graduate work in Marine Studies at the University of Delaware where he studied the regulation of energy metabolism in green sulfur bacteria (the Chlorobiaceae). Being a microbiologist that had always admired synthetic biology from a distance, and one that was enamored with space exploration, Jake joined the Arkin Lab at the University of California-Berkeley as a postdoc to pursue applications of microbial engineering to space exploration and colonization. Jake's research interests include environmental microbiology, microbial physiology/systems biology, genetics, synthetic biology, and space bioengineering. 
 

kbsander [AT] berkeley [DOT] edu

Kyle Sander grew up in Portland, Oregon and attended Oregon State University earning a B.S. in Chemical Engineering.  He interned at a Georgia-Pacific Containerboard Mill for a year as an Environmental/Process Engineer, and then went on to earn an M.S. degree in Biological and Ecological Engineering studying life cycle effects of algae production for fuels and co-products. He also investigated rapid sand filtration as an algal dewatering process step and enzymatic degradation of, and simultaneous saccharification and ethanol production from, of algal cell biomass.

Kyle earned his PhD from the University of Tennessee, Knoxville conducting his thesis research within the BioEnergy Science Center at Oak Ridge National Laboratory.  Kyle focused on characterizing and engineering regulatory genes and related cellular redox in two candidate lignocellulolytic, ethanol-producing biocatalysts; Clostridium thermocellum and Caldicellulosiruptor bescii.  Basic redox metabolism was characterized in C. thermocellum, yielding an expanded view of redox metabolism in this organism, as well as a set of promising redox-active metabolic loci which were targeted in subsequent engineering for ethanol yield improvement done by others.  Single-gene deletion mutants of promising regulatory gene targets in C. bescii were generated and screened in bioprocessing-relevant conditions to assess the engineering potential of each gene target.  Deletion of a global redox sensing transcription factor (Rex) enabled C. bescii to synthesize 75% more ethanol and allowed us to comprehensively describe the unique Rex regulon in this organism.  A genotype-phenotype relationship was identified between the FapR local fatty acid biosynthesis repressor and this organism’s tolerance to elevated osmolarity conditions, a highly complex, bioprocess-limiting, and difficult-to-engineer trait.

Outside of the lab, Kyle enjoys running, reading, rock-climbing, spending time with family and friends, and becoming more familiar with his new Berkeley and California surroundings.

Yuexiao Shen joined Prof. Peidong Yang’s group at UC Berkeley as a postdoc in October, 2017. He finished his Ph.D. from the department of Chemical Engineering at Penn State in 2016. During his Ph.D., he worked on several projects in the interdisciplinary areas of chemical engineering, biology, chemistry and material science. He was focused on developing bioinspired membranes using membrane proteins that mimic the rapid and selective transport as seen in biological membranes. He extended to explore the potential of mimicking biological channels and lipids using supramolecular chemistry and investigating them using biophysical techniques. Yuexiao finished his bachelor and master degrees at Tsinghua University, where he studied environmental engineering. His academic accomplishments include several high-quality publications in journals such as PNAS, JACS and Journal of Membrane Science (JMS), and have been recognized by nationwide academic organizations with a number of very competitive awards. Yuexiao has already been offered an assistant professor position at Department of Civil, Environmental, and Construction Engineering at Texas Tech.
 

Currently Su is a postdoctoral researcher working with Professor Peidong Yang at University of California, Berkeley. His current research focuses on the bioelectrochemical CO2 fixation and N2 reduction. He received his Ph.D. degree in Chemistry on September 2017, with Professor Peidong Yang at University of California, Berkeley. During the Ph.D., he was awarded the MRS Graduate Student Award and the Chinese Government Award for Outstanding Self-financed Student Abroad. Su obtained his B.S. degree in Chemistry from University of Science and Technology of China on 2012, before joining the Peidong Yang Group as a graduate student.

Graduate Student

Anthony Abel is a Ph.D. student in Chemical Engineering in the Clark Laboratory at UC Berkeley. Previously, he earned his B.S. in Chemical Engineering and M.S. in Materials Science at Drexel University in Philadelphia, PA, where he developed solution deposition techniques for inexpensive semiconductor materials. He has previously worked for the National Renewable Energy Laboratory, where he designed reactors for the sustainable production of hydrogen via photoelectrochemical water splitting. 

Anthony’s research interests lie at the intersection of chemical engineering, materials science, and microbial synthesis. Within CUBES, he will focus on the simulation and design of hybrid bioinorganic reactors and engineering microbes to function optimally within this artificial environment.

In his spare time, Anthony is a mentor for Bay Area Graduate Pathways to STEM, and enjoys reading science fiction and playing squash.
 

Aaron Berliner is a Bioengineering graduate student in the Arkin Laboratory at UC Berkeley/UCSF. He studied bioengineering, control theory, synthetic and systems biology, and nanotechnology at Boston University. In 2012, he began working as a research associate at the NASA Ames Research Center on projects involving 3D printing, bioelectrochemistry, and astrobiology. In 2013, he started as a research scientist in the Life Sciences group of Autodesk Research in San Francisco. At Autodesk, Aaron’s work ran the gamut from bioprinting, software engineering, synthetic virology, and DNA origami until 2016 when he moved back to space biology. Forming a partnership between UC Berkeley, Autodesk, and NASA Ames, Aaron began construction for Crucible, an open-source reactor for space synthetic biology experiments until 2017 when he started as a graduate student with Adam Arkin. He enjoys playing with his Mars-in-a-jar reactors. Aaron helped author the STRI grant that launched CUBES and is an NSF graduate fellow. His alternative scientific interests are terraforming and radiation biology. Aaron likes whiteboards and dry erase markers and dirty models with clean math.
 

Stefano Cestellos-Blanco is a Ph.D. student in Materials Science & Engineering in the Yang Group under the direction of Professor Peidong Yang at the University of California, Berkeley. He received his B.S. degree in Chemical Engineering from Stanford University in 2016. His research interests lie at the intersection of inorganic materials and molecular biology. He envisions a future in which nanoengineered materials work in cooperation with the natural world. Stefano is investigating biohybrid catalytic systems for the fixation and utilization of CO2 and N2 in the MMFD division of CUBES. 
 

George earned a B.S. in Chemical Engineering and a M.S. in "Process, Simulation, Optimization, and Control" from the University of Patras (Greece) in 2016 and 2018, respectively. While there, he was a member of the “Laboratory of Fluid Mechanics and Rheology” where his research focused on the rheology and numerical simulation of flows involving complex yield-stress fluids. He is now pursuing a PhD in Chemical Engineering at University of California, Berkeley, working in the “Process Systems and Control Laboratory”. His current research interests lie in learning-based optimal control of complex systems that intrinsically contain uncertainties. As a member of CUBES, he will be part of the SDID, focusing on systems engineering, process modelling, dynamic optimization and control. His motivation for studying Chemical Engineering was his particular interest in mathematics as a high-school student, as well as his enthusiasm in applying scientific principles towards solving real-world problems.

Alex graduated from Georgetown University in 2014 with a B.S. in Environmental Biology with a focus in community ecology. Following graduation, he moved to the University of Kentucky to study how bacterial symbionts mediate insect ecology in agricultural systems.

Now, pursuing a PhD in Plant Biology at UC Berkeley, Alex studies plant-associated microbial communities from shoots to roots. In cassava, a tropical root crop, Alex  investigates the phyllosphere ecology and carryover of the microbiome between planting seasons. For CUBES, he aims to construct synthetic bacterial communities via host-mediated selection to better grow rice in space. As both a Trekkie and wannabe farmer, Alex is very excited to be a member of FPSD.

tacken-headshot
Tom Tacken
Areas of Interest:

Tom is a Visiting Scholar from the Netherlands completing the research for his master thesis in the Peidong Yang Group. His work is focused on the microbial synthesis of ammonia from dinitrogen gas. Ammonia is essential for a successful manned mission to Mars. However, it is not feasible to achieve the current production method, the Haber-Bosch process, on Mars due to limited resources. Therefore, the search for an alternative way to produce ammonia is paramount to the success of this mission. The reduction of dinitrogen gas with a solar-driven potential and bacteria as catalysts is a very promising way of achieving this.

Kelly Wetmore is a graduate student in Adam Arkin’s lab at UC Berkeley with over 15 years of experience in microbial physiology and genetics before and during graduate school. She has been instrumental in developing a number of next-generation tools and protocols for microbial functional genomics. Kelly is supporting the CUBES team in applying these tools to optimize the core biomanufacturing microbes in physiologically more-or-less relevant conditions. She is also part of a large DOE environmental systems biology project in which she is developing a new technology to query high-throughput genetic interactions.

HaoZhang headshot
Hao Zhang
Areas of Interest:

Hao Zhang is a 4th year graduate student in Chemistry at University of California Berkeley with Prof. Peidong Yang. She received her B.S in Material Science and Engineering from University of Science and Technology of China (USTC) in 2014.
Her research is focused on the CO2 fixation via photosynthetic biohybrid systems(PBSs) in the MMFD division. The non-photosynthetic bacteria could be photosensitized by using the semiconductors to reduce the CO2 into multicarbon products, such as acetate, ethanol, and other valuable products. Such PBSs inherits both the high light-harvesting efficiency and the superior catalytic performance from solid-state semiconductors and whole-cell microorganisms, respectively.

Undergraduate Student

Brendan, originally from Austin, TX, is a second-year chemical engineering major with a concentration in biotechnology. His research interest lies in the intersection of chemical engineering and synthetic biology. As a part of CUBES, Brendan is currently working with postdoctoral scholar Jacob Hilzinger to genetically engineer cyanobacteria to produce useful biomass in both Earth-based and Mars-based economies.

Mia Mirkovic is a second-year undergraduate student in the Electrical Engineering and Computer Sciences department at the University of California, Berkeley pursuing mixed-signal processing and circuit design. Her interests include systems modeling and control, imaging, representation theory, modern music technology and history, and radio.

She works with Aaron Berliner on the development of Crucible, an open-source, 3D-printable chamber for space synthetic biology experiments, and mathematical models for Martian in-situ resource utilization for life support, power, and an integrated, multi-function, multi-organism bio-manufacturing system to produce fuel, food, and materials. These models will likely underlie a software package for accelerating mission design and simulation. 
 

Sharpless Headshot
Will Sharpless
Areas of Interest:

Will is an undergrad at UC Berkeley studying molecular biology and math. He is captivated by the potential of synthetic biology in communities and in enhanced individuals in regards to productions of biofuels and commodity chemicals, as medicinal substitutes and as agricultural supplements.

Alex Starr is a second year undergraduate at University of California Berkeley with interests in synthetic and molecular biology, applied math, artificial intelligence, and the utilization of biology in space exploration.  As part of CUBES, he is working to develop a system for the detoxification and enrichment of Martian regolith using the perchlorate reducing bacterium Azospira suillum PS.  Prior to joining CUBES, Alex studied expression of genes related to root growth in sunflowers and worked on understanding the genetic basis of drought-tolerant root phenotypes in maize.