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Division Director

Karen A. McDonald headshot
Karen A. McDonald

Karen McDonald is a Professor of Chemical Engineering at the University of California at Davis.  She also serves as the Faculty Director and Co-PI of the UC Davis ADVANCE Institutional Transformation program (http://ucd-advance.ucdavis.edu/), 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 is a co-chair of 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 vitro 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

Bruce Bugbee headshot
Bruce Bugbee
Areas of Interest:

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.”  
 

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.
 

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 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.
 

Senior Scientist

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.

Postdoctoral Scholar

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

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

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. 

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.
 

Graduate Student

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.

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. 
 

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.

Undergraduate Student

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.