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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

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

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. 

Postdoctoral Scholar

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. 
 

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. 

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

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.

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.
 

Undergraduate Student

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.

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.