The UC Davis Bioenergy Research Group (BERG)

UC Davis has substantial expertise in biomass energy conversion, biosystems engineering, biotechnology, plant sciences, genomics, proteomics, fuels and power, and transportation systems (Figure 1) and is ranked 1st in Agricultural Sciences by NSF in total R&D expenditures (2003).

UC Davis Bioenergy Highlights:

• UC Davis is host to the California Biomass Collaborative (CBC), and the California Institute of Food and Agricultural Research (CIFAR). The Collaborative, a mostly state-funded organization, provides statewide coordination among industry, government, academic, and environmental sectors involved in biomass management and utilization in California. CIFAR has maintained research programs in bioconversion for fuels and chemicals since its inception. Both organizations conduct forums, meetings, and conferences to enhance dissemination of information on bioenergy.

• The UC Davis Genome Center provides state-of-the art genomics, genotyping, bioinformatics and proteomics expertise. Genome Center faculty conduct basic research in plant and microbial genomics, proteomics and metabolomics.

• The College of Agricultural and Environmental Sciences supports a biobased products initiative, and the Institute of Transportation Studies (ITS), an Organized Research Unit founded in 1991 and staffed by over 150 faculty, staff, and graduate student researchers, is increasing focus on biofuels for mobile applications through its Sustainable Transportation Pathways (STEPS) Program to be launched in January 2007 with the mission of providing transparent and detailed comparisons of current and proposed vehicle fuel infrastructures.

• UC Davis has more faculty conducting research in plant biology than any other leading university. Fundamental advances in genomics, genetics, breeding, engineering, plant physiology, evolutionary biology, and environmental science are underway to improve bioenergy crop performance and production. Faculty carry out basic research on biosynthesis and biodegradation of plant cell walls, crop production systems, sustainable agriculture, and energy crops. Logistics, harvesting and handling systems for bioenergy crops are being improved.

• The UC Davis Plant Genomics Program, comprised of 38 faculty members from 17 departments, has expertise in virtually all aspects of plant genomics and has established leading NSF-funded programs in genetic engineering, breeding and genomics of grass species, models for key bioenergy crops.

• The Center for Entrepreneurship provides academic training in technology transfer and commercialization to energy scientists and graduate students in management to serve as research assistants, helping faculty and campus labs to develop commercialization plans and business models for bringing advanced research to field trials, and ultimately the market.

• UC Davis has a long history of engineering research on biomass conversion to energy and products. The Biomass and Bioenvironmental Engineering Laboratories in the Department of Biological and Agricultural Engineering conduct research into thermochemical and biochemical biomass conversion for power, heat, fuels, chemicals and other products. Research is also conducted on harvesting systems, feedstock processing, transportation, and storage, as well as process integration, systems engineering, and optimization.

• The Long Term Research on Agricultural Systems (LTRAS) project also provides support for biomass feedstock development. LTRAS conducts long term research into sustainable agricultural systems, critical to energy crop production. Selection of preferred energy crop plant species for diverse conditions in California is a goal of current LTRAS activity.

• The Institute for Data Analysis and Visualization (IDAV) at UC Davis is an Organized Research Unit whose main mission is the development of data analysis, interactive data exploration, and visualization technology with relevance to biotechnology and bioinformatics. Today, IDAV is recognized internationally as one of the world's leading research units in scientific data analysis and visualization. The Institute has over ten affiliated UC Davis faculty members, supports around 75 graduate student and undergraduate student researchers, and employs several full-time researchers and post-doctoral fellows.

• UC Davis has substantial expertise in Molecular and Cellular Biology and Microbiology including biodegradative enzyme research (cellulases, amylases, pectinases, xylanases) and exploration of the biology of unique strains in the UC Davis microbial culture collection.

Faculty and Research Scientists

More than one hundred UC Davis faculty, research scientists, and administrators in seven major campus units have been identified as possible participants in the group (Table 1). Examples of some individual faculty research areas:

Julian Alston, Professor of Agricultural and Resource Economics and head of the Science and Technology Program of the Agricultural Issues Center at UC Davis, studies agricultural markets, agricultural research and productivity, and the economics of government policy.

Charlie Bamforth, Anheuser-Busch Endowed Professor of Brewing Science, is a leading authority on wheat and barley biochemistry, with special focus on brewery and malting science.

Alison Berry, Professor of Plant Sciences, works on Acidothermus cellulolyticus, the bacterial species whose cellulolytic enzyme has improved efficiency of biomass degradation 10% and is now in use by Genencor. She heads the international genome project for Acidothermus, working to identify genes of interest for lignocellulose degradation.

David Block, Associate Professor of Viticulture & Enology and Chemical Engineering & Materials Science, studies fermentation process optimization to predict the kinetics of alcohol production in yeasts, as well as the role of yeast cell membrane lipid composition on ethanol and higher alcohol tolerance of production organisms. He also has extensive experience in optimizing the production of secondary metabolites in bacterial and fungal systems.

Eduardo Blumwald, Professor and Will W. Lester Endowed Chair of Plant Sciences, studies the production of drought and salt tolerant crops. His lab is particularly interested in transgenic crop plants with increased yields under limited environmental conditions and focuses its efforts on rice, wheat, and cotton, as well as grasses.

Kyria Boundy-Mills, curator of the Phaff Yeast Culture Collection, manages one of the world's largest collections of wild yeasts, including thousands of yeasts isolated from decaying plant material. Yeasts from this collection are used in research on campus and by academic, agency, and industrial researchers worldwide, including research on cellulases and conversion of waste biomass to biofuels.

Abhaya Dandekar, Professor of Plant Sciences and Faculty Director of the Ralph M. Parsons Foundation Plant Transformation Center at UC Davis, focuses his research on genetic engineering of woody tree crops to optimize them for use as bioenergy and biomaterials substrates through modification of carbon allocation, and fat, tannins, and starch composition, as well as disease and pest resistance.

Cristina E. Davis, Assistant Professor of Mechanical and Aeronautical Engineering, develops cutting edge technologies for use in extremely precise analytical sensors and actuators, important in the optimization of process steps in biofuel production. Her work with graduate students on senior design projects could also be used to develop novel biofuel processing equipment.

Roger Davis, Professor of Mechanical & Aeronautical Engineering, studies fluid dynamics and propulsion, and runs combustion simulations in his research characterizing biofuels. He also leads a team at UC Davis working towards a DARPA proposal, developing a biofuel for jet engines that will replace the JP8 standard.

Michael Delwiche, Professor of Biological and Agricultural Engineering, focuses his research in sensors, instrumentation, and control systems to improve biological and agricultural production.

Roy Doi, Distinguished Professor of Molecular and Cellular Biology and National Academy Fellow, is an expert in cellulosome machinery and cellulose degrading enzymes.

Jorge Dubcovsky, Professor of Plant Sciences and leader of a national applied genomics consortium for marker assisted selection in wheat, studies wheat straw utilization as a substrate for biofuels. His lab is developing a TILLING knockout population in collaboration with the UC Davis Genome Center and has recently cloned and patented a gene that regulates transport to wheat grain, potentially allowing for late lignin and hemicellulose modifications.

Nael El-Farra, Assistant Professor of Chemical Engineering & Materials Science, focuses his research on the development and application of advanced process control and monitoring systems for chemical and biochemical processes.

Roland Faller, and Marjorie Longo, Associate Professors of Chemical Engineering and Materials Science, work towards a biophysical understanding of alcohol tolerance in micro-organisms. They explore mechanisms for alcohol's deleterious effect on cell membranes and study the impact of membrane composition on ethanol tolerance, employing microscopy and computer modeling techniques to gain further knowledge of the structure, transport, thermodynamics, and mechanics of simple synthetic monolayer and bilayer membrane systems.

Oliver Fiehn, Associate Professor of Molecular and Cellular Biology at the UC Davis Genome Center, performs metabolic phenotyping. By exploiting various mass spectrometric approaches, including capturing and querying experimental designs by generalized GxE frameworks, metabolite identifications and databases, and multivariate statistics, his lab seeks to create and optimize new molecular breeding tools.

Bruce Gates, Professor of Chemical Engineering and Materials Science, has extensive experience in fundamental catalysis and catalysis of fuel upgrading. Currently he is studying solid superacids with room temperature butane isomerization activities, potentially providing the first practical route to low-temperature paraffin isomerization for clean-burning gasoline.

Sham Goyal, Plant Physiologist in the Department of Plant Sciences, has extensive agronomy and field agriculture expertise, and studies the regulation of nitrogen uptake, metabolism, and usage efficiency in plants, as well as the physiology of abiotic stress and stress tolerance.

Andrew Hargadon, Associate Professor of Technology Management, is Director of Technology Management Programs and Chancellor's Fellow at the Graduate School of Management. Hargadon is also Director of the newly formed UC Davis Energy Efficiency Center.

Bruce Hartsough, Professor and Chair of Biological and Agricultural Engineering, investigates methods for harvesting, collecting, processing and transporting dedicated woody biomass crops, forest thinnings, and forest residues.

William Horwath, Associate Professor of Land Air and Water Resources, studies the use of wastes in the fertilization of biomass energy crops and nutrient use efficiency in biomass crop production. He also focuses his research on carbon sequestration in managed and natural ecosystems and looks at the effect of sustainable agricultural practices on long-term soil fertility and water quality.

You-Lo Hsieh, Professor of Fiber and Polymer Science, studies cellulose structure, synthesis and reactions, as well as functional nanofibers and polymers from synthetic and biologically derived molecules.

Kentaro Inoue, Assistant Professor of Plant Sciences, researches the mechanisms by which nuclear-encoded proteins are targeted to specific compartments within the chloroplasts, as well as the regulatory mechanism for the biosynthesis of carotenoids, processes important to the optimization of biofuel generation.

Bryan Jenkins, Professor of Biological and Agricultural Engineering, conducts research into thermochemical conversion of biomass and optimization of biomass systems and directs the California Biomass Collaborative, a statewide coordinating program for biomass technology and policy.

Steve Kaffka, extension agronomist, directs the Long Term Research on Agricultural Systems project at the CAES, focusing on agricultural sustainability. He also works on oil seed and sugar crops like safflower, canola, and sugar beets suitable for biofuels use. He leads a multi-disciplinary research group focusing on the use of saline and other waste waters for biomass production as a means of salinity management in California, and is active in the UC water quality work group.

Masoud Kayhanian, Associate Director of the Center for Environmental and Water Resources Engineering and Senior Development Engineer of Civil and Environmental Engineering, researches the conversion of biomass and organic wastes into energy, the kinetics of bioconversion processes, and water quality and contaminant particle dynamics.

Dan Kliebenstein, Assistant Professor of Plant Sciences, has expertise conducting and interpreting high-throughput plant metabolic analyses for the purpose of interpreting and modifying metabolic networks involved in plant growth and resistance.

John Labavitch, Professor of Plant Sciences, and Alan Bennett, Associate Vice Chancellor for Research, are studying plant development related cell wall metabolism, elucidating how expansin interacts with other plant cell wall modifying enzymes, and the value of developmentally timed expression in plants of these fungal enzymes in the bioconversion of wall polysaccharides.

F. Thomas Ledig, Adjunct Professor for the Department of Plant Sciences, began a program to genetically test and select eucalypt species for renewable biomass energy on marginal lands in 1979 that is still in progress today at 22 sites in California, Chile, and India. He has consulted around the globe for governments and industry in the field of biomass fuel breeding.

Karen McDonald, Associate Dean, Research & Graduate Studies of the College of Engineering, oversees a teaching and research program in plant biotechnology, production, purification and characterization of natural and recombinant proteins from plants, plant tissues and plant cell suspension cultures.

David Mills, Professor of Microbial Ecology and Bacterial Genetics, and Co-Leader of the Lactic Acid Bacteria Genome Consortium, is leading a nation-wide sequencing project of industrially relevant microbial genomes.

Jeff Mitchell, Cooperative Extension Cropping Systems Specialist in the Department of Plant Sciences, has served as Statewide Chair of the University's Conservation Tillage (CT) Workgroup for the past eight years. This Workgroup consists of over 700 university, NRCS, farmer, private sector, NGO, and public agency members who are working together on developing reduced tillage production alternatives for California.

Deb Niemeier, Professor of Civil and Environmental Engineering, is Director of the John Muir Institute of the Environment, and Director of the federally and state funded UC Davis-Caltrans Air Quality Project. Her current research focus is emissions trading policy development.

Joan Ogden, of the Institute of Transportation Studies and Professor of Environmental Science and Policy, is an expert on hydrogen energy systems and is leading the development of a new program in sustainable transportation energy pathways (STEPS) with an emphasis in biofuels.
Ning Pan, Professor of Textiles and Biological and Agricultural Engineering, studies carbon nanotube formed high efficiency electrodes for supercapacitors and power cells, the conversion of biomass into activated carbon and carbon fibers, and computer modeling and simulation of the phenomena involved.
Dan Parfitt, plant geneticist and breeder, works towards the development of improved and alternative crop plants for the production of biomass to be used as a substrate for the production of biofuels.

David S. Reid, Professor of Food Science and Technology, studies the role of water in foods, particularly water activity issues, and is interested in methods to optimize the balance between storage conditions to maintain high quality and minimize energy costs in the storage environment.

Pamela Ronald, Faculty Assistant to the Provost, Chair of the UCD Plant Genomics program, and Guggenheim Fellow, leads an NSF multi-institutional project to develop whole genome microarrays for rice, and is using proteomics and genetic engineering approaches to elucidate the molecular basis for stress tolerance and disease resistance in rice. She is also developing rice as a model system for energy crops such as switchgrass.

Dewey Ryu, Professor of the Department of Chemical Engineering’s Biochemical Engineering Program, has extensive expertise in enzyme engineering and biocatalysis, bioseparation process design, recombinant bioprocess engineering, and gene expression optimization critical to the optimization of biomass to bioenergy conversion and metabolic pathway engineering.

Kate Scow and Krassi Hristova, Professors of Land Air and Water Resources, are working on the biodegradation, molecular biology and bioremediation of petroleum compounds and additives, research which includes the whole genome sequencing of an MTBE-degrading bacterium and study on its enzymatic pathway involved in breakdown, as well as research on using oxygen to stimulate MTBE in situ and ex situ bioremediation, natural attenuation of petroleum compounds in groundwater under anaerobic conditions, and impacts of ethanol on petroleum spills.

Sharon Shoemaker, Executive Director, California Institute of Food and Agricultural Research leads a DOE-OIT research project to develop new microorganisms for simultaneous conversion of hexoses and pentoses in rice straw to lactic acid, and, in partnership with Argonne National Lab, to produce ethyl lactate as a platform chemical for solvents. In addition, she focuses her research on elucidating the mode of action of cellulases, to develop cellulase and other carbohydrase systems for biomass applications. Through CIFAR, bioproducts and bioenergy activities extend to regional, national and international partners.

Johan Six, soil scientist in the Department of Plant Sciences, focuses his research on the relationship between the carbon and nitrogen cycles and their effect on ecosystem functioning. He is particularly interested in how ecosystem properties are impacted by management practices and global stresses, such as elevated carbon dioxide.

Dan Sperling, Director, Institute of Transportation Studies and Professor of Civil and Environmental Engineering and Environmental Science and Policy, leads a world-renowned institute with research into advanced vehicles and fuels, including biofuels and hydrogen. Sperling is also Associate Director of the newly formed UC Davis Energy Efficiency Center.

Pieter Stroeve, Professor of Chemical Engineering, conducts research in nanotechnology, bioseparations, colloid science, self-assembled monolayers, surface modification, batteries and electrochemistry.

Peter Thy, project scientist, Department of Geology, studies phase relations and the chemistry of residual silicate, oxide, and carbonate systems from high temperature conversion of biomass fuels.

Jean VanderGheynst, Associate Professor of Biological and Agricultural Engineering, focuses on recombinant protein expression in harvested plant tissues, recombinant protein stability in, and recovery from, plant tissues, and fermentation processes for plant biomass stabilization and conversion to value-added products.

Dave Wilson, Professor of Molecular and Cellular Biology, leads a lab that focuses on the structural biology of xylose assimilation. Using crystal structures to engineer substrate and cosubstrate specificities and catalytic efficiencies of these enzymes, he works to create a yeast strain that can effectively ferment xylose.

Ruihong Zhang, Professor of Biological and Agricultural Engineering, conducts research into anaerobic digestion of biomass and wastes for energy production and nutrient management. A novel two-stage digestion system is currently being developed at the pilot scale for use with multiple feedstocks.

UC Davis Research Facilities

• CAES Genomics Facility
• UCD Biomass Laboratory
• UCD Bioenvironmental Laboratory
• UCD Bioprocessing Laboratory
• Microbial Fermentation Laboratories
• Plant Tissue Culture Teaching and Research Laboratory
• Experimental fields, state of the art greenhouses
• Harvesting equipment
• State of the art brewery pilot plant

Institutes, Centers and Programs

• California Institute of Food and Agricultural Research (CIFAR)
• California Biomass Collaborative
• Institute of Transportation Studies (ITS)
• Sustainable Transportation Pathways Program (STEPS)
• Sustainable Agriculture Research and Education Program (SAREP)
• Sustainable Agriculture Farming Systems Project (SAFS)
• Agricultural Issues Center
• John Muir institute of the Environment (JMIE)
• The UC Davis Genome Center
• The Institute of Global Climate Change
• The UC Davis Plant Genomics Program
• Long Term Research on Agricultural Systems (LTRAS)
  
  
  

Figure 1.

UC Davis Bioenergy Research Group

Molecular and Cellular Biology	Plant Biology and Photosynthetic Organisms	Enzymology	Process and Systems Engineering	Plant Production Systems	Resource Management	Environmental Quality
Non-photosynthetic organisms Cellular Processes Isolation	Photosynthesis Characterization PS Bacteria Algae Woody crops Herbaceous crops Lignins Low-lignin plants	Cellulase Hemi-cellulase Hydrogenase Autolysis enzymes Methane synthase Fatty acid synthase	Biochemical conversion Thermo-chemical conversion Biorefineries Optimization Transportation Power Generation Combined Heat and Power Systems Reaction processes Catalysis Combustion	Energy crop systems Sustain-able Agriculture Carbon sequestra-tion Genetic engineering Genome analyses Systems biology	Forestry Waste manage-ment Watersheds	Air Quality Water Quality Soil and Land Quality Avian and other wildlife impacts Environmental Justice Greenhouse Gases Global Climate Change
Molecular and Cellular Biologists, Biochemists	Molecular and Cellular Biologists, Geneticists, Plant Scientists	Biochemists, Molecular Biologists	Engineers, Biologists, Chemists, Physicists	Agronomists Soil Scientists Plant Scientists Geneticists Engineers	Economists Engineers Ecologists Biologists Resource Scientists	Engineers Atmospheric Scientists

Table 1. Preliminary list of the UCD Bioenergy Research Group.