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.
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."
Karen McDonald is a Professor of Chemical Engineering at the University of California at Davis. She also previously served as the Faculty Director and Co-PI of the UC Davis ADVANCE Institutional Transformation program, a NSF-funded program to recruit, retain, and advance women STEM faculty. She is the Institutional Co-I for CUBES at UC Davis and Division Lead for the Food and Pharmaceutical Synthesis Division.
Prior to leading the UC Davis ADVANCE program, she served as Associate Dean for Research and Graduate Studies in the College of Engineering for 13 years. She is a member of the graduate program/groups in Chemical Engineering, Biomedical Engineering, and Plant Biology and the Designated Emphasis in Biotechnology program. From 2003-2015 she served as the Co-Director of the NIH Training Grant in Biomolecular Technology at UC Davis, an innovative multidisciplinary research and educational training for doctoral students working at the interface of life sciences and engineering/physical sciences in application areas related to human health. From 2006-2013, she was the PI and Director of the NSF Collaborative Research and Education in Agricultural Technologies and Engineering (CREATE) IGERT, an interdisciplinary graduate training program with Tuskegee University focused on applications of plant biotechnology to biopharmaceuticals, biorefineries and sustainable agriculture.
Dr. McDonald and her collaborators apply synthetic biology tools in plants for the development of novel expression systems as well as applying bioprocess engineering technologies to produce recombinant proteins (including human therapeutic proteins, enzymes for cellulose degradation, and biopolymers for materials applications) using whole plants, harvested plant tissues, or plant cells grown in bioreactors. As a biochemical engineer, she is interested in translational research and strives to develop novel biomanufacturing processes that are scalable, cost effective, and meet a variety of design constraints. She has lead large multidisciplinary research teams such as a Defense Threat Reduction Agency-funded project to develop a platform for plant-based production of bioscavengers against biothreat agents.
Amor Menezes is an Assistant Professor in the Department of Mechanical and Aerospace Engineering at the University of Florida. He is the Science Principal Investigator of the five-year, multi-university, Center for the Utilization of Biological Engineering in Space (CUBES), a NASA Space Technology Research Institute in biomanufacturing for deep space exploration. He also leads the Systems Design and Integration Division of CUBES.
Dr. Menezes' research interests are in dynamical systems theory and control, with applications to the fields of systems biology and synthetic biology. He is an IEEE Senior Member. He was a 2015 Emerging Leader in Biosecurity and a 2015 fellow of the Synthetic Biology Leadership Excellence Accelerator Program.
He was an Associate Project Scientist in the California Institute for Quantitative Biosciences (QB3) at the University of California, Berkeley from 2016 to 2017, and a QB3 Postdoctoral Scholar from 2011 to 2016. He was a Research Fellow between 2010 and 2011 in the Department of Aerospace Engineering at the University of Michigan, where he received a Ph.D. as an NSERC Post-Graduate Scholar and Michigan Teaching Fellow in 2010, and a Master of Science in Engineering as a Milo E. Oliphant Fellow in 2006. He graduated from the University of Waterloo in 2005 with a Bachelor of Applied Science in Mechanical Engineering with Distinction, Dean's Honors (top 10%), and the Sandford Fleming Co-op Medal.
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.
Bruce Bugbee is Professor in the Department of Plants, Soils, and Climate at Utah State University. He received his PhD from Penn State University and his MS from the University of California at Davis. He joined the faculty at Utah State University in 1981.
Dr. Bugbee uses controlled environments to examine plant-environment interactions. His research has included phytoremediation, algal biofuels, photobiology, and plant water relations. His career has been guided by the idea that teaching is the highest form of understanding. He has mentored 33 graduate students, eight of whom are now on the faculty at other universities. He was awarded the Utah Governor's Medal for Science in 2012, the D. Wynne Thorne lifetime research achievement award in 2016, and the Distinguished alumni award from Penn State University in 2017. He recently gave a TEDx talk titled, “Turning water into food.”
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.
Somen Nandi is an Adjunct Professor in the Department of Chemical Engineering and the Managing Director of Global HealthShare® initiative at the University of California, Davis.
Dr. Nandi has been working on molecular breeding technology to produce the heterologous proteins in different platforms for past 18 years. He has extensive experience on the application of bioprocess engineering technologies to produce recombinant proteins (including human therapeutic proteins and enzymes) using seeds, whole plants, harvested tissues or cells grown in vitro in bioreactors as hosts, improve efficacy of target molecule by enzymatic glycan modification and performing techno-economic analyses. This multidisciplinary effort led to the development of five products, now in the market and two molecules in human clinical trials. He is interested in translational research and continually strives to develop processes that are scalable, cost effective, and meet quality specifications and regulatory requirements. Somen leads large multifaceted programs and is experienced teaching and mentoring both in developing and developed countries, including managing teams with diverse expertise, cultural, and ethnic backgrounds. Somen’s research efforts in CUBES are to produce therapeutic proteins and food via optimization of plant metabolic engineering and in limited resource environment like Mars.
Dr. Trenton (Trent) Smith is an Associate Professor of Biology at Simpson University in Redding, California. He received his Ph.D. in the lab of Dr. Vicki Vance at the University of South Carolina in 2001, studying viral suppression of RNA interference in plants. Specifically, he generated and studied suppression of RNAi in transgenic Arabidopsis thaliana expressing the helper component proteinase from Turnip Mosaic Virus. In early 2018, Dr. Smith joined with the lab of Dr. Karen McDonald and Dr. Somen Nandi at UC Davis, as a visiting scientist. He is designing systems to express cell wall-degrading enzymes in potato, as part of the biofuels work of CUBES.
Robert Waymouth is the Robert Eckles Swain Professor in the Department of Chemistry at Stanford University. Dr. Waymouth investigates new catalytic strategies to create useful new molecules, including sustainable polymers, synthetic fuels, and bioactive molecules. In one such breakthrough, Professor Waymouth and IBM researcher Jim Hedrick opened a new path for production of environmentally sustainable plastics and improved plastics recycling, earning recognition in the 2012 Presidential Green Chemistry Award.
The Waymouth Group applies mechanistic principles to develop new concepts in catalysis, with particular focus on the development of organometallic and organic catalysts for the synthesis of complex macromolecular architectures. In organometallic catalysis, the group devised a highly selective alcohol oxidation catalyst that selectively oxidizes unprotected polyols and carbohydrates to alpha-hyroxyketones. The Waymouth group pioneered the development of catalysts that can access multiple kinetic states during a polymerization reaction in order to control sequence distribution. They devised a novel strategy for the synthesis of elastomeric polypropylene utilizing a metallocene catalyst whose structure was designed to interconvert between chiral and achiral coordination geometries on the timescale of the synthesis of a single polymer chain.
In collaboration with Jim Hedrick of IBM laboratories, the Waymouth Group has developed an extensive platform of organic catalysts for the controlled ring-opening polymerization of lactones, carbonates and other heterocyclic monomers. Mechanistic studies of nucleophilic N-heterocyclic carbene catalysts revealed an unusual zwitterionic ring-opening polymerization method which enabled the synthesis of high molecular weight cyclic polymers, a novel topology for these biodegradable and biocompatible macromolecules. In collaboration with the Wender group, the Waymouth group has devised selective organocatalytic strategies for the synthesis of functional degradable polymers and oligomers that function as "molecular transporters" to deliver drugs and probes into cells. These efforts combine elements of mechanistic organic and organometallic chemistry, polymer synthesis, and homogeneous catalysis to rationally design new macromolecular structures.
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
Dr. Takashi Nakamura received his Ph.D. in Aeronautics and Astronautics from MIT and his B.S. in Aeronautical Engineering from the University of Tokyo. Currently, he is the manager of Space Exploration Technologies at Physical Sciences Inc. (PSI), and has been involved in numerous R&D programs sponsored by NSF, NASA, DoE and DoD.
Dr. Nakamura has been developing, with funding from the Air Force and NASA, a unique space solar power system for power generation, propulsion, materials processing, and plant lighting in space. This concept is based on the use of optical fibers for transmission of solar radiation, the concept Dr. Nakamura pioneered in 1976 while he was at Japan's Electrotechnical Laboratory. Dr. Nakamura is an Associate Fellow of AIAA, a member of AAS and Sigma Xi.
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.
Skyler Friedline received his BS in Biochemistry and Molecular Biology from UC Santa Barbara in 2016. He is new to the fields of synthetic biology and microbial engineering but is motivated to learn quickly and make an impact. He began working as a research associate and lab manager in Adam Arkin's UC Berkeley Lab in 2019. He is interested in the development of microbes enabling closed loop living in space and on earth.
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.
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.
Rong Cai is a postdoc in the Yang Group at the University of California, Berkeley. She received her Ph.D. degree in Chemistry Department from the University of Utah in 2019. Her research focuses on understanding the electron metabolism of microbes and designing inorganic material to deliver electron to bacteria efficiently.
Anna received her B.S in Biotechnology from National Technical University of Ukraine and M.S. in Microbiology from the University of Oklahoma, where she was a Fulbright Scholar. She got her Ph.D. in Biological Engineering from Utah State University. Her M.S. thesis research focused on characterization of ultra-small microorganisms from anoxic sulfur-rich pond using bioinformatics. For her Ph.D. research, Anna worked with local municipal and industrial wastewater treatment facilities to improve microbial transformation of organic waste compounds and algal biomass into valuable bioproducts, such as biogas and bioplastic. She also developed a computational model describing anaerobic microbial granulation in the upflow anaerobic sludge blanket reactors.
Anna is currently a postdoc in the group of Prof. Lance Seefeldt at Utah State University and is working on engineering nitrogen-fixing purple non-sulfur bacteria and bioprocess design.
Soumyajit Sen Gupta has been a member of the SDID division of the CUBES since March 2018. Prior to joining the CUBES as a post doctoral research associate with Dr. Amor Menezes, he was a doctoral research scholar at Indian Institute of Technology, Bombay since 2012. His doctoral thesis was on integrated plant-wide optimization of microalgae biorefinery, co-producing fuel, food and chemicals. He is a Bachelors' (2010 batch) from Jadavpur University and Masters' (2012 batch) from Indian Institute of Technology, Kharagpur; both these degrees have been in the discipline of Chemical Engineering. His research interests are in the area of systems design, modeling and optimization, renewable energy and process systems engineering.
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.
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.
Sunggeun Woo earned his B.S. and M.S. from Yonsei University in South Korea. During his B.S. and M.S. programs, he studied in the civil and environmental engineering department and he narrowed down his research focus to environmental biotechnology in his M.S. program, where he wrote fifteen papers for about two and a half years including five of them as the lead-author. At that time, the research topics were various in the field of environmental biotechnology including wastewater treatment systems, isolation and cultivation of microorganisms and harnessing renewable bio-diesel from microalgae. Based on the wide range of understandings, Sunggeun Woo joined the Criddle group for his Ph.D. program in September, 2012 focusing on the Coupled Aerobic-anoxic Nitrous Decomposition Operation (CANDO) project. Sunggeun Woo participated in developing the CANDO process which produces a renewable energy, nitrous oxide (N2O), from nitrogen pollutants through microorganisms. During his Ph.D. program, Sunggeun Woo's main focus was to elucidate the microbial members that produce N2O and the metabolic pathways in them related to N2O and polyhydroxybutyrate (PHB) production. He graduated from Ph.D. program in January, 2018 and he is now continuing his research as a post-doctoral scholar in the Criddle group. His research is currently focusing on the recovery of renewable energy and materials from waste or wastewater using microorganisms.
He is currently working as a Researcher with Professor Dr. Lance C. Seefeldt at Utah State University. He received his PhD in Organic Chemistry from Nankai University, Tianjin, China in 2007 and PhD in Biochemistry from Utah State University in 2013. After that, he continuously worked with Dr. Lance Seefeldt as postdoctoral fellow focusing on understanding nitrogenase mechanism with a broad range of interdisciplinary strategies, including biochemical, biophysical, and electrochemical methods. His research interests include metalloenzymes, small molecule activation, and relevant catalyst design and mechanistic studies.
Shuyang is a post-doctoral research associate working with Dr. Bruce Bugbee in the Crop Physiology Laboratory at the Utah State University. Her current research is focused on improving the understanding of whole-plant photosynthetic and morphological responses of food crops to light quality and quantity, primarily under artificial light in controlled environments. She received her PhD from the horticulture department at the University of Georgia in August 2017.
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.
Jeremy Adams is a Ph.D. student in Chemical and Biomolecular Engineering at UC Berkeley, currently working in the Clark Lab. He received a BSE in Chemical Engineering from Arizona State University in 2017. Jeremy’s research interests lie in the intersection of synthetic biology and biochemical engineering, particularly towards the development of sustainable biomanufacturing processes. His work in CUBES involves engineering lithoautotrophic microbes to convert Mars-available resources into useful products, as well as engineering export pathways of those products to simplify downstream separation processes. In his free time, Jeremy enjoys traveling and scuba diving.
Aaron Berliner is a Bioengineering graduate student in the Arkin Laboratory at UC Berkeley/UCSF. He studied bioengineering, control theory, and synthetic and systems biology 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 on 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.
Ji Min Kim is a 1st year Ph.D. student in Materials Science and Engineering at the University of California Berkeley in the Yang Group. She received her B.S. degree in Materials Science and Engineering from Hanyang University in 2016 and M.S. degree in Materials Science and Engineering from Seoul National University in 2018. Her research interest is focused on the CO2 fixation via a semiconductor nanowire-bacteria hybrid system in the MMFD division of CUBES. The system utilizing light capturing high surface area nanowire array and acetogenic anaerobes enables the photoelectrochemical acetic acid production with long-term stability.
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.
Matt received his B.S. in Chemical Engineering from the University of Massachusetts, Amherst. He previously worked as a process engineer for Sanofi Genzyme. His current research focuses on developing a novel biologically-derived bioseparations platform for limited resource environments.
Jorge is originally from Chicago where he attended Loyola University Chicago and received his B.S. in Environmental Science with a Chemistry Minor. After his undergraduate studies, he attended Stanford where he obtained his M.S. in Environmental Engineering and where he has continued as a PhD student working with Professor Craig Criddle. His research focuses on biotechnology with an emphasis on efficiently utilizing waste streams to produce biological materials (e.g., bioplastics, biofuels). As part of the CUBES effort, Jorge's research involves identifying organisms that can thrive on the limited amount of resources available for long-range space travel.
Vince is a first-year Ph.D. student in chemistry at Stanford University; he is interested in creating biodegradable organic materials as well as designing materials processing techniques such as additive manufacturing in order to make functional parts from biodegradable materials feasible for replacing petroleum based plastics. His role in CUBES will be to create and optimism polymeric systems based on methanotrophic polyhydroxyalkanoate production for the closed-loop manufacturing of tools. Before starting his graduate work at Stanford, he studied mechanical engineering and chemistry at Colorado School of Mines where he created block copolymer materials for hydrogen fuel cell membranes and computed degradation mechanisms for small molecule bis-azide species. He also worked as a design engineer at RICOH where he designed, 3D printed, and tested small parts for improving large-scale ink-jet printer functions. Vince likes to hike and carve wood in his free time.
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.
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.
Yongao (Mary) Xiong is a Ph.D. candidate in the Department of Chemical Engineering at UC Davis in the McDonald-Nandi Lab (http://mcdonald-nandi.ech.ucdavis.edu). She received her B.S. in Chemical Engineering from University of Washington, Seattle. She has mastered in recombinant protein production, purification, and functional characterizations using plant systems. Her work includes the process optimization of transient protein expression in leaves/cells utilizing agrobacteria-mediated gene transfer, chromatography method development (resin and membrane-based), and bioassay design. In addition, she is investigating approaches to modify and control protein N-glycosylation profile through subcellular targeting, the incorporation of glycan processing enzyme inhibitors and in vitro enzymatic treatment. Mary examines the effects of N-glycosylation on protein properties and molecular structures. She has started working on fine tuning of downstream process engineering of the recombinant PTH-Fc and functional characterizations using a combination of label-free protein-based assay and cell-based assays.
Kevin is a first year PhD student in Chemical Engineering at the University of California, Davis. He works in the McDonald-Nandi lab, where he develops recombinant plant cell wall degrading enzymes within the scope of NASA's CUBES project. Kevin earned a BS in Chemical Engineering with minors in Electrical Engineering and Mathematical Sciences from Michigan Technological University.
Alex is a second year Aerospace Engineering student at the University of Florida. He is working under Dr. Amor Menezes in the Systems Design and Integration division. He has been a member of CUBES since November 2018. He is interested optimizing mission parameters to minimize mission costs and increase viability. His work at the University of Florida also includes the applications of model-free control to space missions.
Brooklyn Brace is a third year undergraduate student at UC Berkeley studying Molecular and Cell Biology. She has an interest in microbiology and genomics and how they apply to bioengineering. In the Arkin Lab, Brooklyn is currently working in the MMFD division investigating genes important for nitrogen fixation. Previously, Brooklyn worked in a synthetic biology lab at Columbia University working on the development of a multiplexed drug screening platform.
Saige is a fourth year at the University of Florida studying Aerospace Engineering. She is working with Dr. Amor Menezes under the Systems Design and Integration division. She is interested in the effects of space travel on biological systems and using alternative solutions to mitigate problems cause by long term missions.
Avery is a third year undergraduate student at UC Berkeley, currently working towards a double major in Economics and Molecular and Cell Biology with an emphasis in developmental genetics. She is interested in how the intersection of her two academic disciplines come together to further the research behind space exploration. In CUBES, Avery is working towards optimizing an elemental balance in a martian biomanufacturing system. Previously, Avery worked at the University of Michigan on research relating to metabolic control in the immune system and the development of new drugs for the treatment of autoimmunity and cancer.
In the future, Avery would like to pursue a career in the biotechnology industry.
Anderson Lee is a third-year undergraduate student at UC Berkeley studying Bioengineering with a focus on Synthetic and Computational Biology. He is currently optimizing the production of biopharmaceuticals to be utilized during space travel. In previous companies, he has developed an ELISA procedure to determine the concentration of a tumor-detecting drug in biological samples and enhanced a mobile, quick diagnostic machine that scans for viruses. Previous to the Arkin Lab, he worked in Mohammed Mofrad's Cell and Biomechanics Laboratory at UC Berkeley where he used neural networks with backpropagation to predict a virus' host based on the genome of the virus.
In the future, he sees himself using synthetic biology to conquer problems inherent to the nature of space travel. He believes that technology already present in nature and perfected with evolution can be the key to send humans to other planets.
Isaac Lipsky is a second year undergraduate student at UC Berkeley studying environmental science. In concert with Aaron Berliner, he is working on developing cost-benefit metrics for Mars surface operations. His interests include planetary science and the tantalizing prospect of Martian terraforming.
Max Perko is a third year chemistry undergraduate at Stanford, studying biosynthetic polyester vitrimers for additive manufacturing in the Waymouth lab. His research is being performed in conjunction with that of Vince Pane (of the Waymouth lab) and the Criddle lab (Stanford Biology), for the Center for the Utilization of Biological Engineering in Space (CUBES) on their Mars exploration project.
Will is an undergrad at UC Berkeley studying molecular biology and math. He is captivated by the potential of synthetic biology and the application of modern methods of engineering to biology whether in microbes, mammalian cells, or multi-organism communities. In CUBES, Will models and designs microbial communities for agricultural enhancement. Previously, he has worked on metabolic engineering for the production of biofuels and commodity chemicals, directed evolution for the bioremediative degradation of plastic, and microRNA circuits and protein engineering for immunotherapy.
Cindy is a second-year undergrad at UC Berkeley studying computer science. She is interested in applying CS skills to space research. At CUBES, she is working on building object oriented models to simulate and optimize a biologically-driven Mars exploration mission. Outside of academics, she practices Wushu (Chinese martial arts) and goes on spontaneous adventures to the beach.
Dexter is a first year Ph.D. student in Chemical Engineering at UC Davis in the McDonald-Nandi Lab. He received his B.S. in Chemical Engineering from Columbia University, New York and his B.A. in Chemistry from University of Puget Sound, Washington through a Dual Degree Program. He is currently developing stable lines of transgenic lettuce, which express a parathyroid hormone fusion protein.
Jesse Delzio is a third year biochemical engineering undergraduate at the University of California, Davis. He began research with Dr. Somen Nandi and Dr. Karen McDonald in July 2017 and is currently researching drug purification through the functionalization of viral coat proteins to be used for simpler isolation in low resource environments such as Mars. He is currently working under the mentorship of Matthew McNulty. His interests include chemical engineering, biotechnology, and plant engineering. Jesse has investigated the expression and capture of recombinant parathyroid hormone from different lettuce varieties. He has also provided calculations of land area and expression levels required to sustain a team of astronauts on Mars.
Prior to his research in the McDonald-Nandi lab, Jesse worked as a lab intern for a chemical company in San Diego called Designer Molecules Inc. His main interests were chemistry and physics. He applied to the University of California, Davis and studied chemical engineering for his first two years. After discovering a project involving biomanufacturing for deep space exploration led by Dr. McDonald, Jesse's interest in biotechnology and biology grew, urging him to switch majors to biochemical engineering. He has been researching for the Center for the Utilization of Biological Engineering in Space on their Mars exploration project ever since.
Kristian is an NSERC post-doctoral fellow in Environmental Engineering and Science at Stanford University. His current research focuses on: Hard-wiring bacteria in a microbial battery, salinity gradient energy production from a mixing entropy battery, and PHB bioplastic production from C. Necator. His PhD was in Chemical and Biological Engineering from the University of British Columbia in Vancouver.
Pauline received a bachelor's degree and a master's degree in pharmaceutical sciences from the University of Lyon, France. She is currently a visiting scholar in the Department of Chemical Engineering in the McDonald Laboratory at UC Davis.
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.
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.
Kalimuthu Karuppanan is a Postdoctoral scholar in the Department of Chemical Engineering, at the University of California, Davis. He received his Ph.D. in Biotechnology and M.S. degree in Plant Science from Madurai Kamaraj University, India. Since he has been at UC Davis Dr. Karuppanan has contributed to a number of research projects funded by DARPA, DTRA, and NSF and he has mentored many Ph.D. students and undergraduate researchers. He was the instructor for ECH161L, Bioprocess Engineering Laboratory course, in 2014 at UC Davis. He received the campus-wide Award for Excellence in Postdoctoral Research in 2016 and Phil Thai Memorial Award in Medicine for Lung Research in 2015 for his outstanding research performance. He is a co-inventor in a recently filed patent on Novel Fusion Proteins for Treating Inflammatory Diseases. Dr. Karuppanan is a CUBES Co-PI and member of the Food and Pharmaceutical Synthesis Division.
His research is in protein biotherapeutics for treating infectious and non-infectious diseases. He has extensive experience in recombinant protein bioprocessing in planta. His work includes gene design, designing vector systems for agrobacterial-mediated gene transfer in plants, protein expression using plants and plant cell suspension cultures, protein purification using affinity and traditional chromatography systems, biophysical and functional characterization of recombinant proteins, and drug efficacy improvement by enzymatic glycan modification.
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)!
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.
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.
Mathangi Soundararajan is a PhD candidate from India currently at Utah State University advised by Lance Seefeldt. She has also been awarded the Presidential Doctoral Research Fellow by Utah State University. She majored in biotechnology in her high school, and went on to get her Bachelors in Biomedical Sciences from Sri Ramachandra University. In her junior year, she was awarded the Undergraduate Summer Research Fellowship by Sri Ramachandra University to study the effects of dairy intake on inflammatory biomarkers in people with Type 2 Diabetes. She also worked as a Research Assistant at the Institute of Mathematical Sciences during her final year, where she studied the genetic susceptibility of Type 2 Diabetes patients to colorectal cancer using bioinformatics methods. Graduating at the top of her batch, she was awarded the 'Best Outgoing Student' medal as well. Her current research interest includes understanding and applying biological nitrogen fixation in bioelectrochemical systems. Her undergraduate research experience has also contributed to her interest in understanding metabolism and the effects of derangements in metabolism. When she is not losing track of time in the research lab, you can find her catching up on TV series and Netflixing.
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.
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.
Chris Szikszai worked with the Waymouth group, summer of 2017, testing feasibility of extruding and printing PHBV (poly-3-hydroxybutyrate-co-3-hydroxyvalerate). Aided by Professor Dan Strauss from SJSU and Naomi Clayman, Chris used analytical techniques such as DSC, GPC, and an Instron tensile tester to characterize the biopolymer: before extrusion, prior to printing, and after printing.
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.
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.