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Division Director

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Karen A. McDonald

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.   

Faculty

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.

Senior Scientist

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.

Graduate Student

Katie is a PhD student in the Biomedical Engineering Graduate Group at UC Davis working in the McDonald/Nandi Lab. She received her BS in Biomedical Engineering from the University of Oklahoma, where she worked under the NASA EPSCoR STEM Workforce Development grant to develop targeted nanoparticles for therapeutic delivery. Her current work uses plant viruses to separate antibodies and Fc-fusion proteins from crude feedstocks for the production of biopharmaceuticals in space.

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Gwyneth Hutchinson

Gwyneth graduated from UC Berkeley in 2020 where she did nearly 3 years of research and a fellowship in reproductive neuroendocrinology, chronobiology, and cellular biology. She then transitioned to the UCSF-Gladstone Institute of Neurological Disease where she pursued novel research into the contributions of cellular energy metabolism and bioenergetic failure into neurodegenerative disease pathogenesis. Following this, she worked as a Senior Research Associate at Conception Biosciences where she focused on the development of biotechnologies to turn stem cells into viable eggs for individuals and couples to overcome physiological, age-based, and sexuality-based barriers to reproductive success. With NASA CUBES, Gwyneth is developing innovative approaches to build on the Arkin Lab’s recent successes engineering Spirulina for nutrient, pharmaceutical, and flavor production with applications for supporting human exploration of space. She is devising innovative ways to further improve the efficiency of engineering this previously recalcitrant organism and determining the best routes for metabolic engineering of these critical products. She is also interested in pursuing questions surrounding human physiology and reproduction in space with the goal of improving health outcomes for astronauts and space travelers both during missions and upon return to Earth. When she’s not in the lab, Gwyneth loves to spend time with her puppies—Willow and Pandora—and play guitar. She also fancies herself an amateur shark diver and is on the Board of Directors for a literacy nonprofit.

Lorenzo is a Master's degree student in Agro-food Biotechnology in Verona (IT). He earned his Bachelor's degree in Biotechnology in Pavia (IT) and he works as a research student in Davis. His previous experience mostly concerns plant biotechnology as he worked in molecular biology and protein purification of Zeaxanthin epoxidase.

Tressa is a PhD candidate in the Biochemistry, Molecular, Cellular and Developmental Biology graduate group at UC Davis. She earned her B.S. in Environmental Systems: Ecology, Evolution and Behavior at UC San Diego. Previously she worked on harnessing microalgae for production of lipids for biofuels, as well as production of recombinant therapeutic proteins. Her current work is focused on producing recombinant therapeutic proteins for use in space by engineering whole plant systems.

Justin is a PhD student in the Chemical Engineering Department at the University of California, Davis. He earned his B.S. in Chemical Engineering at Northeastern University and worked as a bioprocess development engineer for Synlogic before returning to school. His current research focuses on using modified plant viral particles for the purification of antibodies and Fc-fusion proteins, and the production of pharmaceuticals in transgenic plants

Undergraduate Student

Hue is an undergraduate student studying Bioengineering and Electrical Engineering and Computer Science at UC Berkeley. She is interested in exploring the intersection between synthetic and computational biology with hopes of harnessing an application towards enhancing biomedicine and sustainability. She is working with Dr. Hilzinger in the FPSD division of CUBES to help develop innovative approaches toward improving the metabolic engineering of A. platensis for small molecule production. By enhancing the production of pharmaceuticals, nutrients, and flavors in Spirulina, the project aims to support human exploration of space. In her free time, Hue enjoys traveling, watching sunsets at the beach, swimming, and crocheting.

Ishan is a 1st year undergraduate student studying Microbial Biology at UC Berkeley. He is passionate about biopharmaceuticals and its application across diverse fields of study, including in space exploration. Ishan is working under Dr. Hilzinger on the CUBES project to develop genetic tools in A. platensis for improved metabolic engineering. Additionally, he is investigating CRISPR/Cas-9 and its use in developing new plasmids for this bacterium.

Kylie Akiyama is a second-year undergraduate student at UC Berkeley majoring in bioengineering. She is especially interested in the field of synthetic biology and how we can utilize it in the context of space exploration. Kylie is currently within the FPSD division of CUBES, working to improve the group's capacity to metabolically engineer A. platensis for small molecule production.

Eliana Matos is a highly motivated student pursuing her studies in Bioengineering, with a specific focus on cell and tissue engineering. She has experience working and volunteering with a myriad of organizations, which range from nonprofit hospitals to YMCA Camp Campbell. Here, she effectively applies her optimistic outlook and critical thinking skills. Throughout her undergraduate career, Eliana has explored a broad range of classes and clubs, delving into fields such as neurotechnology, health care advocacy, as well as advanced mathematics and sciences related to engineering. While she expresses an interest in the path towards medical school, she remains fascinated by the multitude of opportunities that bioengineering could potentially offer her. For instance, during her first year of college, she co-authored a research paper on the potential for bioengineering in space exploration, an experience that utterly astounded her. The prospect of integrating her major with space exploration filled her with an exhilarating sense of anticipation.

Eliana, as an individual, is extremely optimistic and consistently seeks the positive aspects in every situation. When she is passionate about a project, her perfectionism surfaces, propelling her to ensure that she executes every task to the best of her abilities. Eliana is willing to devote extra time to projects that pique her interest and often finds herself thrilled when encountering new challenges from which she can learn and grow. She places a high value on efficiency and aims to accomplish tasks correctly on the first attempt. Additionally, she prioritizes constructive criticism and communication, cherishing the opportunity to receive advice and learn new methods for tasks or adapt to new work environments.

Eliana also has a keen interest in applying what she has learned to make a positive impact on her community and the wider world.

Katie is an undergraduate from New York City studying Bioengineering and Electrical Engineering and Computer Science at UC Berkeley. She is interested in exploring the interdisciplinary connections between computer science and synthetic biology for therapeutic applications. Her past research experience includes altering strain specificity of phage-like molecules and developing small molecule therapeutics for immunosuppression.

Through CUBES, she will be working under the FPSD division towards metabolically engineering A. platensis for small molecule production. Katie hopes to pursue a PhD in Bioengineering after graduation to strength her experimental planning and scientific analysis skills. In her free time, she enjoys trying new foods, traveling, hammocking, crafting, and spending time with friends and family.

Justin Wahyudi is an undergraduate student at UC Berkeley studying Bioengineering and Electrical Engineering and Computer Science. Justin is interested in exploring synthetic biology and understanding the various applications that the field offers in healthcare and pharmaceutical settings. He is currently working under Dr. Jacob Hilzinger in the FPSD division of CUBES to help genetically engineer A. platensis for the purpose of pharmaceutical production and supporting advances made in space exploration.

Xina Wang is an undergraduate student at UC Berkeley studying chemical biology and data science. She is interested in the potential of harnessing biosystems found in nature for applications in biomanufacturing and biomedicine through the intersection of synthetic biology and computational tools. Currently, she is engaged in engineering microbes to produce bioplastics for human space exploration as well as for industrial or environmental applications on Earth.

Alumni

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.

Sophia is a sophomore at UC Berkeley studying Molecular & Cellular Biology and Economics. She was initially drawn to CUBES because of their work with In-situ Resource Utilization and is interested in studying different forms of life in strenuous environments. In her free time she enjoys surfing, playing soccer and reading novels.

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.

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. 

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Imran Khan

Imran Khan received PhD fellowship from German Academic and Exchange Service (DAAD) for his doctoral study at Institute for Molecular Biotechnology, RWTH Aachen University, Germany. He also served Vienna Institute for Biotechnology, Vienna, Austria, as researcher where he investigated expression and targeting of recombinant proteins in plant tissues. He also received research funding as PI and supervised PhD and master students working as Assistant Professor at Center for Interdisciplinary Research, Islamabad, Pakistan. He completed his postdoctoral study from University of Bonn, Germany that was also funded by DAAD, Germany. In 2019, Imran received Penn Biomedical Postdoctoral fellowship for postdoctoral study at School of Dental Medicine at University of Pennsylvania, Philadelphia, USA, where he worked on oral delivery of plant made biopharmaceuticals using Chloroplast production system, in collaboration with Takeda, Japan. He joined Dr. McDonald/Nandi lab in 2021 at University of California, Davis, USA, as Assistant Project Scientist. His current research focus on development of platform technologies for bio-manufacturing on Mars to provide food and pharmaceuticals for colonists, funded by National Aeronautics and Space Administration (NASA), USA.

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.

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.
 

Patrick is a first-year student in the Chemical Engineering department at UC Davis, where he works in the McDonald-Nandi lab. He earned his BS in Chemical Engineering at UC Berkeley. Patrick joined CUBES because he is passionate about biotechnology and hopes to improve the safety and feasibility of space missions.

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.

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. 

Kyle Valgardson bachelors of science Biochemistry from Utah Valley University and is currently pursuing a doctorate degree in biochemistry at Utah State University.

Anya is a graduate student at the University of Florida getting her Ph.D. in Biomedical Engineering with Professor Menezes. Her interests include the application of synthetic biology for medical use in space to better support human space exploration.

Prior to the University of Florida, she received her B.S. in Biomedical Engineering at Columbia University in New York City, where she also competed as the Payload Lead on the university’s rockets team. There, Anya also worked on developing microfluidic devices for cancer diagnostics.

She is originally from Fort Lauderdale, Florida and in her spare time enjoys painting and arts and crafts!

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 earned a BS in Chemical Engineering with minors in Electrical Engineering and Mathematical Sciences from Michigan Technological University. He has a strong interdisciplinary background from his time working in a variety of industries. His PhD research involves the production of pharmaceuticals in transgenic plants within the scope of the NASA CUBES project.