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.
Technical Staff
Cassandra is a highly motivated and curious senior undergraduate in the Bioengineering department at UC Berkeley, with a specific focus on cell and tissue engineering. She has previously worked in immunology research, where she formulated antibody-conjugated lipid nanoparticles and assessed their transfection into antigen presenting cells for their possible use as mRNA therapeutic delivery vehicles. She has also worked in polymer research, where she contributed to the standardization of nanoindentation as a modality for retrieval analysis of the polymer component from total knee replacement. Through her coursework and research experiences, she has developed a strong interest in the field of synthetic biology which she hopes to utilize to solve problems caused by the climate crisis, with the increasingly necessary exploration of space being one of these issues. Currently, she is working with Gwyneth Hutchinson and NASA CUBES to engineer Spirulina for pharmaceutical and flavor production with applications for supporting human exploration of space. She hopes that through this work and further research done through a PhD program and beyond, she will be able to assist in finding solutions to climate-related issues. In her free time, you can catch her at the roller rink, or on a hike in the Berkeley hills. She also enjoys crocheting and reading novels.
Postdoctoral Scholar
Sulogna Chatterjee is a Postdoctoral Fellow in Criddle-group at Stanford University where she is working on Metabolic Engineering of autotrophic microorganism for better carbon efficiency and production of high-performance bioplastics.
Dr. Sulogna is a DST Inspire Fellow, holds a PhD degree in "Environmental Biotechnology & Microbiology" from "CSIR- Indian Institute of Chemical Technology", India. Her research interest is carbon conversion, waste valorization, bioprocess designing, bioreactor operations, fermentation technologies, bioenergy production and circular biorefinery systems.
During her PhD she has published several high impact research papers and has been awarded the “Research Excellence Award” by BRSI-India and "Best Research Fellow Award" by CSIR-India. She has also represented 'India' in C3E- Women in Clean Energy Education Empowerment Symposium organized by U.S Department of Energy, MIT Energy Initiative, Stanford Energy and Texas A&M University, 2019.
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.
Graduate Student
Jackson is primarily interested in the discovery and creation of novel biological systems that can be used in faucets of bioremediation, human health, and space exploration. He has researched bacteriophages in depth, has discovered and annotated novel phages, and has investigated bacteriophage mechanisms of lysis. He has also done bioinformatics work regarding intrinsic disorder in Merkel Cell Polyomavirus and has explored HECTD3's involvement in cancer. He is a proponent of undergraduate research and learning and has developed a program to certify undergraduates in basic lab techniques to better prepare them for academic research. Currently, he is pursuing a PhD at UF and is teaching, taking courses, and working with Dr. Averesch researching bioplastic production.
Brendan obtained a B.S. in Horticulture from the University of Georgia in 2017 and graduated in 2019 with a dual M.S. in Crop and Soil Science and Sustainable Agriculture from the University of Georgia and Università degli Studi di Padova, respectively. He is presently working toward completion of a Ph.D. in Plant Science at Utah State University's Crop Physiology Laboratory. His graduate research work encompasses photobiological studies and development of novel resource supply, monitoring and control approaches for the plant root-zone in microgravity that are capable of sustaining multiple, successive plant generations.
Noah received a double B.S. in Biochemistry and Biology from the University of Wisconsin - Stevens Point in 2020. He is currently pursuing a Ph. D. in Plant Science as a graduate research assistant in the Crop Physiology Lab at Utah State University in Logan, Utah. Noah's interests include optimizing hydroponics systems and plant nutrition for efficient production in closed systems. Outside of CUBES, he enjoys backpacking, geocaching, and flying general aviation airplanes.
Vrinda Sharma is a graduate student in the CEE department at Stanford. She is working in the Criddle group on engineering autotrophic microorganisms for P4HB polymer production. She received a B.A. in Biological Sciences from Cornell University in 2022 and worked on impact of biocides like Triclosan on soil microorganisms Stenotrophomonas maltophilia in Hay Lab. Post graduation, she worked as Research Associate I in the Microbial Engineering team in Pivot Bio where she got interested in synthetic biology for environmental applications
Wienke is a graduate student in the Bioscience Engineering program at Ghent University, specializing in biochemistry and biotechnology. Currently, she is a visiting student intern at the University of Florida, collaborating with Dr. Nils Averesh on microbial physiology and metabolic engineering, with a particular focus on carbon metabolism and biopolymer synthesis.
Her ongoing research, a collaboration with Lucerne University of Applied Sciences and Arts and the European Space Agency (ESA), investigates the effects of microgravity on gene expression patterns in intervertebral discs (IVD), offering insights into cellular adaptation in space environments.
Previously, Wienke worked on projects involving the engineering of advanced enzybiotics as next-generation antimicrobial agents, employing molecular biology techniques to develop effective treatments. She has also focused on enzyme immobilization, using concanavalin A to create carriers for β-galactosidase, and contributed to the development of designer cellulosomes for biofuel production by optimizing enzyme cascades for efficient biomass degradation.
Undergraduate Student
Milan is an undergraduate student at Rice University studying Electrical and Computer Engineering with a Data Science & Systems specialization. He is interested in utilizing synthetic biology and environmental biotechnology and combining it with artificial intelligence to create sustainable methods of food production, mitigate issues caused by rapid climate change, and assist in deep space exploration.
At CUBES, he is currently working with Dr. Hilzinger to build a cyanobacteria pan genome and utilizing it to understand and analyze the evolution of important phenotypes across different variants (e.g. multicellularity) using machine learning.
Hanen is an undergraduate at UC Berkeley studying Bioengineering. He is interested in utilizing computational and synthetic biology to reduce plastic pollution, develop new drugs and diagnostics, and improve food production and the environment, especially in poorer regions of the world. At CUBE, he is focusing on engineering microbes to produce bioplastics useful for applications in space missions as well as on Earth.
After undergrad, Hanen plans to pursue a PhD in bioengineering or biotechnology to grow as a scientist. He aims to start a company one day focusing on using bioengineering to address environmental and food insecurity issues around the globe.
As a San Franciscan native, Hanen enjoys exploring the Bay Area, sports, and reading in his free time.
Alumni
Skyler Chan is studying Electrical Engineering and Computer Science at UC Berkeley, and he has wanted to become an astronaut since he was 3. In high school, he learned how to fly gliders, and was involved in various student-led space organizations. One of his goals is to make humanity an interplanetary species within our lifetime, and he joined CUBES to advance this mission. Currently, he builds in the Systems Design and Integration Division of CUBES. He is interested in exploring sustainable design on Mars, such as, how to build the first self-sufficient Martian cities. To Skyler, the idea that the choices we make designing the first Martian habitats today will have an impact on the future of humanity never gets old. In his free time, he can be found flying drones, PR-ing at the gym, and filming videos with friends.
Calvin (Tae Hyun) is pursuing his PhD in Civil and Environmental Engineering at the University of Alberta, Canada, under the supervision of Professor Bipro Dhar. His research scholarly pursuits center around advancing microbial electrochemical technologies, focusing on the development of bioelectrochemical sensors for the detection of naphthenic acids in oil sands process water, as well as exploring microbial electrolysis cell-assisted anaerobic digestions and microbial electrosynthesis systems for the conversion of carbon dioxide into biomethane and for biogas upgrading applications. Presently, he is a visiting scholar in Professor Craig Criddle's laboratory at Stanford University. As part of the CUBES project, Calvin works under the mentorship of Professor Craig Criddle and Dr. Nils Averesch, where he is involved in converting methane and methanol into para-hydroxybenzoic acid (pHBA) using methanotrophs through metabolic and genetic engineering. His academic excellence is also recognized through prestigious awards such as the Izaak Killam Memorial Graduate Scholarship and the Canada Graduate Scholarship from the Natural Sciences and Engineering Research Council of Canada.
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.
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.
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.
Daphne is an undergraduate student at Purdue University studying Engineering Technology Education with minors in Computer Information Technology, Global Studies, Biological Sciences, Biotechnology, and Design & Innovation. She has previously been involved with the HHMI SEA-PHAGES project at Purdue University discovering and characterizing novel bacteriophages. Additionally, she has previously written and edited for a variety of science communication publications.
Within CUBES, she is working with Kyle Sanders on the Numerical Modeling team as a SULI intern, where she is using Julia to analyze relationships within a microbial ecosystem for implantation into the rhizosphere of O. sativa.
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.
Wenyu Gu is currently a postdoc at Stanford University.
Mackenzie Jones received her B.S. in Botany from Utah Valley University. She is currently a graduate student at Utah State University working in the Crop Physiology Laboratory in pursuit of a Ph.D. in Plant Science. Her interests of study include plant nutrition, soil fertility, and nutrient cycling. For the CUBES effort, Mackenzie's research will focus on optimizing plant nutrition in controlled environments for long-term space travel.
Paul Kusuma received a bachelor’s degree in horticulture from the University of Florida, and is now pursuing a PhD in plant physiology at Utah State University.
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)!
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.
Lauren Payne is a second year undergraduate student at Utah State University studying Plant Science. She interns at the USU Crop Physiology Lab, assisting graduate students with experiments involving plant growth conditions. In CUBES, she aids Noah Langenfeld with projects in nitrogen recycling and nutrient optimization in hydroponic systems.
Kim is a second-year undergraduate student studying Bioengineering. She is interested in the applications of engineering and science in space exploration. In CUBES, she will be working on exploring species of cyanobacteria and developing a pan-genome.
Tiago is a visiting doctoral student from the Humans on Mars project of the University of Bremen, Germany. As a part of his doctorate project, he is looking to convert cyanobacterial biomass produced on Mars from in-situ resources into a plant fertilizer and other products of interest. To carry out this conversion both anaerobic digestion and bioelectrochemical systems are employed and explored within a wet lab and modelling context. The overarching goal is to explore Mars sustainably by harnessing local resources and reducing shipped payload mass. During his research stay, he will be working on the bioplastic production by C. necator and the modelling of the cyanobacterial biomass processing.
Fengzhe is an undergraduate at Beijing Jiaotong University and now an exchange student at UC Berkeley studying computer science. He is interested in data mining, deep learning and interdisciplinary tasks. In CUBES, Fengzhe mainly works on modeling deep learning methods in dynamic systems. Previously, he worked in a computer science lab at Peking University on an information retrieval and recommender system.
Divya is a third year undergraduate student at UC Berkeley majoring in Bioengineering. She screens Spirulina mutants as they are generated and help in the development of better transformation methods for this organism in FPSD.
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.
Gretchen Vengerova is a third year undergraduate student at UC Berkeley, studying bioengineering. She is interested in applying bioengineering concepts to conservation efforts. Previously she worked at CSU San Marcos, studying the transcriptomics of algae. In CUBES, she is working to study potential loop closure processes in a Martian biomanufactory. In the future, she hopes to use loop closures concepts to decrease terrestrial waste and pollution, but she would also enjoy more opportunities to merge bioengineering with space.
Tyler Wallentine is an undergraduate student at Utah State University pursuing Bachelor of Science degrees in biochemistry and biological engineering. Tyler is originally from Meridian, Idaho and comes from a family of nine. He has a passion for space exploration and wants to see the establishment of a Martian colony within his lifetime. He intends to apply his education in engineering and chemistry to help in this endeavor. His interests include chemical engineering, space system development, and environmental biotechnology. He enjoys 3D design and printing, both as a hobby and as a means of accomplishing his engineering goals. He intends to pursue a Ph.D. in bioengineering following his undergraduate studies to further progress towards a research career.
Tyler is currently working with the Microbial Media and Feedstocks Division (MMFD) of NASA CUBES. He has been continuing development of an anaerobic photobioreactor for Rhodopseudomonas palustris NifA*. He is also evaluating the effectiveness of R. palustris to utilize planetary base wastewater to grow and perform nitrogen fixation, to maximize in-situ resource utilization.
Tyler is an avid runner, having participated in both track and cross country in high school. During that time, he ran a marathon and has a personal mile record of 4:44. He also boxes in his free time. He enjoys drawing, painting, and graphic design. He also enjoys movies, camping, and writing.
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.
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.
Liangzi is a graduate student in Criddle-group at Stanford University. She is working on improving the metabolic function in autotrophic microorganisms to enhance carbon efficiency and produce high-performance bioplastics as part of CUBES.
She is interested in sustainable biomanufacturing, bioremediation, as well as carbon capture and utilization.