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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.

Division Director

Craig Criddle is a Professor in the Department of Civil and Environmental Engineering at Stanford University, and a Senior Fellow at the Woods Institute for the Environment. He is the Institutional Co-I for CUBES at Stanford and the lead of the Biofuel and Biomaterials Manufacturing Division of CUBES.

Dr. Criddle is interested in the environmental engineering, science, and science literacy needed for clean water, clean energy, and healthy ecosystems. His research focus is environmental biotechnology. He is best known for large interdisciplinary field projects, studies of microbial
ecology in bioreactors, and work on microbial transformations of persistent contaminants. Some current projects include a field-scale evaluation of uranium remediation; DNA-monitoring of microbial community structure at full-scale biological wastewater treatment plants; development of membrane bioreactors for energy recovery and nutrient removal; and studies to elucidate the mechanisms and kinetics of microbial transformation of halogenated solvents. To promote science literacy, he worked with award-winning San Francisco cartoonist, Larry Gonick to write "The Cartoon Guide to Chemistry." "Cartoons can give us an intuitive feeling for the why, and deeper understanding can grow from that intuition."

Lance C. Seefeldt is Professor of Chemistry and Biochemistry at Utah State University.  He received his PhD in Biochemistry from the University of California at Riverside and was a Postdoctoral Fellow in the Center for Metalloenzyme Studies at the University of Georgia.  He joined the faculty at Utah State University in 1993.  He is the recipient of the D. Wynne Thorne Research Award and is a Fellow of the American Association for the Advancement of Science.  He is the Utah State University Institutional PI and lead of the Microbial Media and Feedstock Division of CUBES.

Dr. Seefeldt’s research focus is on biological nitrogen fixation.  He has been investigating the mechanism of activation of N2 by the bacterial enzyme nitrogenase.  This work has recently lead to the insight that metal-hydrides are central to the reduction of N2 to NH3.  He is also investigating how to grow nitrogen fixing bacteria with electrodes as a way to accomplish light-driven reduction of N2 and CO2 as a way to capture and make available these resources from the Martian atmosphere.  

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.
 

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

Dr. Nils Averesch is a Postdoc in the Criddle group at Stanford University, California, USA. Before joining CUBES, Nils was the Synthetic Biology Task Lead with Universities Space Research Association as an Associate Scientist at NASA Ames Research Center in Mountain View, California, USA. He received his PhD in 2016 from the University of Queensland in Brisbane, Australia, where he focused on Metabolic Engineering at the Centre for Microbial Electrochemical Systems. He holds an engineer’s degree (Dipl. Ing.) in Biochemical Engineering, from the Technical University of Dortmund in Dortmund, Germany, having graduated in 2011.

Artavazd Badalyan received a Diploma in chemistry from the Lomonosov Moscow State University in Russia and a Ph.D. in analytical biochemistry in the group of Prof. Ulla Wollenberger from the University of Potsdam in Germany where he focused on the bioelectrochemistry of molybdenum hydroxylases and on the development of electrochemical biosensors. He was a postdoctoral research associate with Prof. Shannon Stahl at the Department of Chemistry at the University of Wisconsin-Madison in the field of organic electrochemistry where he developed a novel bioinspired electrocatalyst system for the low-potential alcohol oxidation. Following a position at the Draegerwerk AG as a project leader in the field of electrochemical sensors, he joined the group of Prof. Lance Seefeldt at the Department of Chemistry and Biochemistry at the Utah State University and works on the (bio)electrocatalysis for nitrogen fixation.

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.
 

Wenyu Gu is currently a postdoc at Stanford University. 
 

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.
 

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. 
 

Wakuna is a PhD candidate in the environmental engineering program working with Prof. Craig Criddle. Her research focuses on the microbial degradation of methane in mixtures (biogas and natural gas) for the production of biodegradable polymers called polyhydroxyalkanoates (PHAs). Wakuna is interested in understanding the impact these methane mixtures have on microbial communities, the dynamics between the microbial interactions under certain complex conditions, while optimizing the polymer production process and bacterial growth rates. In addition to research, Wakuna is quite passionate about tutoring and mentoring.

Rhesa discovered her scientific interest many years ago in a high school chemistry class. Her inspirational teacher, Mr. Best—the stereotypical science geek with large bug-eye glasses—taught Rhesa many scientific lessons, but perhaps the greatest was that science is not just for nerdy boys (as her flawed logic thought), it is for anyone.

Currently, a Ph.D. student in the Department of Chemistry and Biochemistry at Utah State University, Rhesa can be found at the laboratory bench doing research focused on understanding and harnessing the amazing abilities of microorganisms. Specifically, she studies the microbial transformation of nitrogen (N2) to ammonia (NH3). This process is a critical part of nature as the majority organisms cannot utilize N2 directly, but need it in a form like NH3 for growth and reproduction. The few microbes that facilitate this conversion provide valuable insight into one of the most biologically challenging reactions and may serve as a catalyst for developing systems for sustainable ammonia production on Mars. 

In additional to research, Rhesa also serves as a science reporter for Utah Public Radio and plans to pursue a career in science education and/or communication. Her excitement for not only doing science, but communicating it just might stem from growing up doing musical theater, which she loves. She also enjoys experiencing other cultures, and hot-potting is always on her list of things to do (and yes, it’s partly to see the beautiful microbial mats)!

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.

Undergraduate Student

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.