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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.

Faculty

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.
 

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. 

Technical Staff

Shunsuke Yamazaki graduated Tokyo University, Japan, where he investigated the mechanism of bacterial lipoprotein transport in the laboratory of Hajime Tokuda. He is then hired Ajinomoto Co., Inc. and joined Research Institute for Bioscience Products and Fine Chemicals, Kawasaki, Japan, where he worked on breeding strains and developing several processes for production of amino-acids and pharmaceuticals. He was currently in charge of investigation of pharmaceutical production using enzymatic conversion process. He became a visiting scholar researcher of Adam Arkin lab at UC Berkeley, CA, USA.

Postdoctoral Scholar

Dr. Nils Averesch is a Postdoc in the Criddle group at Stanford University, California, USA. Before joining CUBES, Nils was the Synthetic Biology Task Lead with Universities Space Research Association as an Associate Scientist at NASA Ames Research Center in Mountain View, California, USA. He received his PhD in 2016 from the University of Queensland in Brisbane, Australia, where he focused on Metabolic Engineering at the Centre for Microbial Electrochemical Systems. He holds an engineer’s degree (Dipl. Ing.) in Biochemical Engineering, from the Technical University of Dortmund in Dortmund, Germany, having graduated in 2011.

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.

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.

Graduate Student

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.

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.

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.

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.

Sharpless Headshot
Will Sharpless
Areas of Interest:

Will is an undergrad at UC Berkeley studying molecular biology and math. He is captivated by the potential of synthetic biology in communities and in enhanced individuals in regards to productions of biofuels and commodity chemicals, as medicinal substitutes and as agricultural supplements.

Alex Starr is a second year undergraduate at University of California Berkeley with interests in synthetic and molecular biology, applied math, artificial intelligence, and the utilization of biology in space exploration.  As part of CUBES, he is working to develop a system for the detoxification and enrichment of Martian regolith using the perchlorate reducing bacterium Azospira suillum PS.  Prior to joining CUBES, Alex studied expression of genes related to root growth in sunflowers and worked on understanding the genetic basis of drought-tolerant root phenotypes in maize.