DOE Bioenergy Research Center (BRC) - jbei.org · JBEI contacts Jay Keasling, Chief Executive...

DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute

Monthly Progress Report – December 2014

Fiscal Year: 2015

Year / Period: Year 8 / Month 3 / December 1 - 31, 2014

Department of Energy’s Joint BioEnergy Institute is supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, through Contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy.

JBEI contacts Jay Keasling, Chief Executive Officer, [email protected], 510-495-2620 Nick Everson, Chief Operating Officer, [email protected], 510-486-6268

Executive Summary This Monthly Progress Report provides a summary of JBEI’s activities for the month of December 2014, third month of fiscal year 2015:

Item Count Highlights

Publications in Print 9 "A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis"

"Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform"

Publications in Press 3 "Isoprenoid drugs, biofuels and chemicals - artemisinin, farnesene and beyond (review)"

Media Citations 16 One story released: “Sweet Smell of Success: JBEI Researchers Boost Methyl Ketone Production in E. coli”.

Presentations Given 8 Presentations were given at the “BESC Biomass Characterization Workshop” in Athens, GA and at the “Globes International Economic Conference” in Tel Aviv, Israel.

On-Site Seminars 15 Dajiang Liu, Department of Chemistry, Penn State University, PA.

Pulakesh Mukherjee, Principal, BASF Venture Capital America Inc.

Tours & Visits 6 China Lake High Tech Consortium

Industry Interactions 3 Interactions with BASF Ventures, Mass Insight and Abengoa

Honors & Awards 1 Jay Keasling was named fellow of the National Academy of Inventors.

FY15 Milestones On track. Despite their delay, the milestones below are expected to meet their deadlines:

Feedstocks - “Heterologous screening of transferases to promote in planta design of polysaccharides (SB)”

Fuels Synthesis - “Improve overall xylose utilization capability in S. cerevisiae strains and examine performance in industrially relevant yeast strains.”

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Dashboard – December 2014 - DOE

FY 2015 Dashboard For Period: December 1 – 31, 2014

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Publications

In Print

Alonso-Gutierrez, J., Kim, E., Batth, T. S., Cho, N., Hu, Q., Chan, L. J., Petzold, C. J., Hillson, N. J., Adams, P. D., Keasling, J. D., Garcia-Martin, H., & Soon Lee, T. (2014). "Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering". Metab Eng. doi, 10.1016/j.ymben.2014.11.011 http://www.ncbi.nlm.nih.gov/pubmed/25554074

Furtado, A., Lupoi, J. S., Hoang, N. V., Healey, A., Singh, S., Simmons, B. A., & Henry, R. J. (2014). "Modifying plants for biofuel and biomaterial production". Plant Biotechnol J, 12(9), 1246-1258. doi, 10.1111/pbi.12300. http://onlinelibrary.wiley.com/doi/10.1111/pbi.12300/full

George, A., Brandt, A., Zahari, S., Klein-Marcuschamer, D., Parthasarathi, R., Sun, N., Sathitsuksanoh, N., Shi, J., Stavila, V., Tran, K., Singh, S., Holmes, B. M., Welton, T., Simmons, B., & Hallett, J. (2014). "Design of Low-Cost Ionic Liquids for Biomass Pretreatment". [ ]. Green Chem. doi, 10.1039/c4gc01208a http://dx.doi.org/10.1039/C4GC01208A

Gondolf, V. M., Stoppel, R., Ebert, B., Rautengarten, C., Liwanag, A., Loque, D., & Scheller, H. V. (2014). "A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis". BMC Plant Biol, 14(1), 344. doi, 10.1186/s12870-014-0344-x http://www.ncbi.nlm.nih.gov/pubmed/25492673

Mingardon, F., Clement, C., Hirano, K., Nhan, M., Luning, E. G., Chanal, A., & Mukhopadhyay, A. (2014). "Improving olefin tolerance and production in E. coli using native and evolved AcrB". Biotechnol Bioeng, n/a-n/a. doi, 10.1002/bit.25511. http://onlinelibrary.wiley.com/doi/10.1002/bit.25511/abstract

Poust, S., Hagen, A., Katz, L., & Keasling, J. D. (2014). "Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform". Curr Opin Biotechnol, 30C(0), 32-39. doi, 10.1016/j.copbio.2014.04.011 http://www.sciencedirect.com/science/article/pii/S0958166914000834

Simmons, C. W., Reddy, A. P., D’haeseleer, P., Khudyakov, J., Billis, K., Pati, A., Simmons, B. A., Singer, S. W., Thelen, M. P., & VanderGheynst, J. S. (2014). "Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw". Biotechnology for Biofuels, 7(1). doi, 10.1186/s13068-014-0180-0 http://www.biotechnologyforbiofuels.com/content/7/1/495/abstract

Singh, S., Cheng, G., Sathitsuksanoh, N., Wu, D., Varanasi, P., George, A., Balan, V., Gao, X., Kumar, R., Dale, B., Wyman, C., & Simmons, B. (2014). "Comparison of Different Biomass Pretreatment Techniques and their Impact on Chemistry and Structure". [Original Research]. Frontiers in Energy Research, 2. doi, 0.3389/fenrg.2014.00062 http://journal.frontiersin.org/Journal/10.3389/fenrg.2014.00062/abstract

Woo, H., Ballor, N., Hazen, T., Fortney, J., Simmons, B., Davenport, K., Goodwin, L., Ivanova, N., Kyrpides, N., Mavromatis, K., Woyke,



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Publications

In Print

T., Jansson, J., Kimbrel, J., & DeAngelis, K. (2014). "Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2". Standards in Genomic Sciences, 9(1), 19. doi, 10.1186/1944-3277-9-19 http://www.standardsingenomics.com/content/9/1/19

In Press

George, K. W., Alonso-Gutierrez, J., Keasling, J. D. & Lee, T. S. (2015). "Isoprenoid drugs, biofuels and chemicals - artemisinin, farnesene and beyond (review)". Adv Biochem Eng Biotechnol.

Eudes, A.,Noppadon, S., Baidoo, E., George, A., Liang, Y., Yang, F., Singh, S., Keasling, J. D., Simmons, B. A. & Loque, D. (2014). “Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency”. Plant Biotechnology Journal.

Tanger, T., Vega-Sánchez, M. E., Fleming, M., Tran, K., Singh, S., Abrahamson, J. B., Jahn, C. E., Santoro, N., Naredo, E. B., Baraoidan, M., Danku, J. M. C., Salt, D. E., McNally, K. L., Simmons, B. A., Ronald, P. C., Leung, H., Bush, D. R., McKay, J. K., Leach, J. E. (2015). “Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype”. BioEnergy Research.

News Citations

Date Article Source

Dec 1 Sweet smell of success Science Codex

Dec 1 Sweet smell of success: Researchers boost methyl ketone production in E. coli Phys.org

Dec 1 Sweet smell of success: Researchers boost methyl ketone production in E. coli (e)Science News

Dec 1 Sweet Smell of Success: JBEI Researchers Boost Methyl Ketone Production in E. coli my Science.org

Dec 1 Sweet smell of success Press-News.org

Dec 2 Sweet Smell Of Success: JBEI Researchers Boost Methyl Ketone Production In E. Coli Technology.org

Dec 2 Sweet Smell of Success ScienceNewsline - Biology

Dec 2 Sweet Smell of Success ScienceNewsline –



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News Citations

Date Article Source

Physics & Chemistry

Dec 2 Bacteria producing sweet-smelling compound for greener fuels EcoSeed

Dec 2 JBEI boosts E. coli methy ketone production 160-fold in two years Biofuels Digest

Dec 2 Sweet smell of success R&D Magazine

Dec 16 Researchers Bioengineering Bacteria Produce Renewable Gasoline Top Secret Writers

Dec 16 Berkeley innovators named fellows of National Academy of Inventors UC Berkeley Newscenter

Dec 24 You Can Turn E.Coli Bacteria into Microscopic Fuel Factories GOOD Magazine

Dec 24 JBEI Offers Biofuel Technologies For License Downstream Business

Dec 24 Bay Area Company Develops Drug Process to Cure Malaria ABC7 News



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Presentations

Date Division Presenter(s) Title Presentation Location

Dec 1 Feedstocks Chiu, T.-Y. Molecular Mechanisms of Pollen Development and Future Applications

National Chiayi University, Chiayi, Taiwan

Dec 1 Deconstruction Simmons, B. A. Advances in Biomass Pretreatment at JBEI

Beijing University of Chemical Technology, Beijing, China

Dec 6 Fuels Synthesis

Lee, T. S. Joint Efforts for Biomass to Biofuel Researches - the Joint BioEnergy Institute (JBEI)

KOLIS (Korean Life Scientist in the SF Bay Area) Winter Conference, San Francisco, CA


Keasling, J. D. Biomanufacturing in California and Israel

Globes International Economic Conference, Tel Aviv, Israel


Keasling, J. D. Advanced Plants to Advanced Fuels

Eilat-Eilot Renewable and Green Energy Conference, Eilat, Israel

Dec 15 Deconstruction Parthasarathi, R., Simmons, B.A., and Seema Singh, S.

Biomass Pretreatment using Designer Ionic Liquids

Postdoctoral Technical Showcase, Sandia National Laboratories, Livermore, CA

Dec 17 Deconstruction Simmons, B. A. Driving the Future: Advanced Biomass Conversion and Biofuel Production Technologies at JBEI

Kanazawa University, Kanazawa, Japan

Dec 18 - 19 Feedstocks Mortimer, J. C. Characterising unknown polysaccharide structures: primary wall xylan as an example

BESC Biomass Characterization Workshop, Athens, GA



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Onsite Seminars

Date Type Presenter Title Affiliation

Dec 1 General Seminar Deconstruction Guest

Jipeng Yan Hot-water based biorefinery: kinetic interpretation and sugar quantification

Interview Candidate


Glen Li Novel Pretreatment Technology using Alkaline Peroxide and Organometallic Catalysts

Interview Candidate


Dajiang Liu Catalytic Biomass Conversion & Upgrading into Platform Chemicals & Liquid Fuels

Department of Chemistry, Penn State University, University Park, PA,

Dec 3 JBEI Seminar Series Patrick Shih Developing synthetic biology tools for plant genetic engineering

Cell Wall Engineering/Feedstocks


Jijiao Zeng Characterization, Modification and Catalytic Valorization of Lignin

Department of Agriculture & Biological Engineering, IFAS, University of Florida, Gainesville, FL


Rangana Wijayapala Catalytic Conversion of Biomass to Bio-Fuels

Department of Chemistry Mississippi State University

Dec 3 Group Seminar Ee-Been Goh To the limit: strategies to further improve methyl ketones production

Fuels Synthesis Division

Dec 3 Group Seminar Itay Budin Using lipid engineering to elucidate cellular roles for membrane viscosity




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Dec 8 Group Seminar Edward Baidoo 1) Establishing a CE-QTOF MS platform for metabolomics in the Fuels Synthesis division. 2) Understanding the metabolic consequences of expressing the mevalonate pathway and overexpressing DXP synthase in E. coli


Dec 8 Group Seminar James Kirby GC-MS overview; Isoprenoid pathway yields


Dec 16 General Seminar Fuels Synthesis Guest

Jesus Barrajas Structural insights into cyclization and release of polyketide and nonribosomal peptide intermediates.

Interview Candidate

Dec 17 General Seminar Tech Transfer Guest

Pulakesh Mukherjee, Principal

BASF Venture Capital - Investing in chemistry and material related start up

BASF Venture Capital America Inc.

Dec 17 Group Seminar Ryan Phelan Design of polyketide synthases for the engineered production of highly-reduced compounds


Dec 17 Group Seminar Chris Shymansky Automating conversion of raw 13C MFA data into fluxes



Tyrone Wells Trees into Fat: Bioconversion of Lignocellulosic Pretreatment Effluent via Oleaginous Rhodococcus opacus DSM 1069

Interview Candidate



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Tours and VIP Visits at JBEI

Date Company Attendees

Dec 1 Tianjin Economic-Technological Development Area Hongwei Liu, Wei Ning, Liqun Zhang, Ying Lan, Bin Wang, Wei Liu, Wanjun Mu, Yanmei Liu, Peng Hou, Jiaguo Shang, Zhengjian Lyu, Huiwen Xiao, Jianghao Li, Meng Xiao, Donghui Lin, Yajing Li, Chunhua Sun, Zhigang Cui

Dec 2 China Lake High Tech Consortium/Navy Lawrence Merwin, Stephen Fallis, Gregory Ostrom, Zachary Sechrist, Dylan Riley, Marc Stockbauer, Bill Hogan

Dec 3 Hydropower and New Energy Division of Yunnan Provincial Energy Administration

Wu Zhi Qiang, Jin Mei,Jing Ming, Xie Da Peng, Yang Guo Quan, Xia Cong Shi, Li Ming Hong, Wang Yin Long, Dao Jun Hua, Shi Li, Shi Yun Huai, Yang Zi Li, Tian Chun Hing, Song Zheng Xian, Tian Li Ming

Dec 4 Indian Institute of Technology - Bombay Pramod Wangikar

Dec 4 Total New Energy Division Anne-Sophie Wunenburger, Alina Dora Crisan

Dec 9 Ajinomoto Co., Inc Hiroaki Ozawa, Research Scientist, R&D Planning Dept



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Honors and Awards

Name Honors and Awards

Jay Keasling Fellows of National Academy of Inventors

Industry Interactions

Date Company / Contact

Dec 17 BASF Ventures / Pulakesh Mukherjee

Dec 19 Mass Insight / Tom Gilman

Area of interest: Licensing

Dec 19 Abengoa / Juan Ramos and Rosario Gomez

Area of interest: Status of collaborative projects



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Milestones

Feedstocks Division

Area Initiatives Milestone/Deliverables Due % Complete

Plant Cell Wall Biosynthesis and Its Regulation

Novel acetyl and feruloyltransferase activities characterized (CWB) Sept. 2015 26

Genetic characterization of mutant candidates from rice stem saccharification screen (GG)

Sept. 2015 24

Correlation between cell wall modification and environmental interactions investigated (GG)

Sept. 2015 24

Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 25

Characterization of novel GT activities (SB) Sept. 2015 26

Lignin and Hemicellulose Modification for Fuels Production

Evaluation of engineered plants with new lignin traits (including analysis with the Deconstruction and Technology Divisions) (CWE)

Sept. 2015 25

Transgenic plants with dominant repressors of hemicellulose biosynthesis characterized (CWB)

Sept. 2015 24

Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 26

Optimization of translation control technologies to improve tissue-specific expression (CWE)

Sept. 2015 28

Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 20

Heterologous screening of transferases to promote in planta design of polysaccharides (SB).

Sept. 2015 3



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Milestones

Feedstocks Division (continued)


Engineering of Modifications in Different Plant Species

Cell wall related genes in switchgrass functionally annotated, integrated into phylogenomics databases, and integrated with Kbase (GG)

Sept. 2015 24

Resequencing of Kitaake mutants (with JGI) and a database set up for hi throughput in silico screening (GG).

Sept. 2015 24

Translation of best technologies developed in Arabidopsis to other plant species (CWE)

Sept. 2015 25



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Milestones

Deconstruction Division


Biomass Pretreatment

Predict and develop task specific ILs for selective lignin or cellulose dissolution and low temperature pretreatment

May 2015 38

Complete characterization of lignin streams from various IL pretreatment process configurations

July 2015 30

Design, synthesis and assessment of lignin and hemicellulose derived IL mixtures for mixed and engineered feedstock pretreatment

Aug. 2015 30

Use multi-scale simulations strategies (from first principle quantum mechanics to force field based) to understand interactions between biomass derived ILs and lignocellulosic biomass

Sept. 2015 22

Enzyme Optimization

Develop an assay for screening lignin degrading enzymes on insoluble lignin and begin populating a lignin degrading enzyme database (LigDB).

Feb. 2015 70

Expand our database of ionic liquid tolerant enzymes, particularly to include enzymes from the GH3, GH5, GH6, GH9, GH10, AA9 and AA10 families.

May 2015 45

Improve the overall sugar yields of our existing thermo and ionic liquid tolerant multi-component enzyme mixture by including enzymes for hydrolysis of both cellulose and hemicellulose and by including LPMOs.

July 2015 30

Demonstrate using directed evolution to engineer enhanced stability -glucosidase in up to 20% [C2mim][OAc].

Sept. 2015 30



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Milestones

Deconstruction Division (continued)


Microbial Communities

Complete characterization of active component of JTherm March 2015 62

Establish complementary thermophilic cellulase cocktail focusing on crystalline substrates

July 2015 35

Identify five bacterial strains capable of metabolizing mixtures of aromatics from pretreatment-derived lignin streams

Sept. 2015 30

Fungal Biotechnology

Design new expression systems based on recent “omics” discoveries in regard to promoters and assess heterologous GH expression

Feb. 2015 70

Initiate ChIP-Seq analysis of histone modifications in A. niger aimed at identifying epigenetic determinants of high productivity

April 2015 45

Optimize cultivation conditions for heterologous enzyme production, including temperature and pH, and initiate ‘omic analysis of optimal vs. baseline conditions

July 2015 40

Validate candidate genes for hyperproduction phenotypes through gene deletion and/or overexpression

Sept. 2015 35



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Milestones



Discovery of Novel Hydrocarbon Biochemistries

In vitro, anaerobic testing of toluene biosynthesis candidates Sept. 2015 25

In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 25

Optimization of Hydrocarbon Biosynthetic Pathways

Improve methyl ketone production in E. coli with NIMS-aided HT screening and metabolic modeling

Sept. 2015 25

E. coli pathway engineering for isopentenol production both in aerobic and anaerobic conditions

Sept. 2015 25

Genes encoding isoprenoid pathway integrated into E. coli chromosome

Sept. 2015 25

Three enzymes in S. cerevisiae glycolytic pathway replaced and impact on fatty acid-derived fuel tested

Sept. 2015 24

Type 1 fatty acid synthases from several organisms expressed in E. coli and production of fatty acid-based fuels tested

March 2015 100

Develop analytical method for LC-MS of MEV and DXP intermediates April 2015 50

Host Engineering Improve overall xylose utilization capability in S. cerevisiae strains and examine performance in industrially relevant yeast strains.

Sept. 2015 10

E. coli membrane editing: With JGI, generate 10-20 single and double mutants and test improvement in expression of beneficial tolerance pump and corresponding tolerance to toxic fuels.

Sept. 2015 37



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Milestones

Fuels Synthesis Division (continued)


Synthetic Bio Informatics

Codon optimization tool (GeneDesign) integrated into the DIVA platform.

Sept. 2015 25

Clonal sequence validation (Sanger and/or MiSeq) pipeline implemented and integrated with DIVA/ICE

Sept. 2015 25

Quantitative Metabolic Modeling for Host and Pathway Engineering

Usage of EDD, MvT and 2S-13C MFA to improve production of fatty acids in S. cerevisiae.

Sept. 2015 40

Perform flux analysis of S. cerevisiae sip1 strain June 2015 85

Implement interactive metabolic engineering on MvT Sept. 2015 20



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Milestones

Technology Division


High Throughput Screening

Support the optimization of T and IL tolerant cellulose/hemicellulase cocktail using HT-NIMS

Sept. 2015 25

Apply HT NIMS screen for fatty acids based fuel molecules (e.g. FAMK) in collaboration with the Fuels Division.

Sept. 2015 25

Implement software to automate unit operations (e.g., droplet dispensing, routing, merger, and sorting) on an integrated droplet chip

Sept. 2015 25

Demonstrate microfluidic droplet platform for integration of DNA assembly, transformation of cells, and culturing

July 2015 28

Proteomics Develop rapid untargeted proteomics methods for relative quantification of >800 E. coli and S. cerevisiae proteins

Sept. 2014 25

Develop absolute quantification targeted proteomic assays for 150 S. cerevisiae proteins

Sept. 2015 30

Implement membrane proteomics assays to enable E. coli membrane editing with Fuels Synthesis Division

Sept. 2015 40



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Milestones

Technology Division (continued)


Physical Characterization

SEM and TEM analysis of genetically altered feedstock biomass (including lignin and protein mapping) with Feedstocks and Deconstruction Divisions

Sept. 2015 25

Electron tomographic analysis of plant cell walls of engineered feedstocks, and CAD model generation for mechanical properties simulation.

Sept. 2015 25

Structural Biology Test expression of multiple GT clones in insect cell platform to produce quantities of protein for crystallization trials

Sept. 2015 40

Characterize lignin degrading enzymes in collaboration with GLBRC Sept. 2015 45

Structural characterization of Fatty Acid Synthase and other large complexes by single particle cryo electron microscopy

Sept. 2015 15

Synthetic Bio Informatics

EDD further developed to support enzyme characterization data and workflows, with Deconstruction Division

Sept. 2015 25

EDD further developed to support genetic expression tool data and workflows, with Fuels Synthesis

Sept. 2015 25

BioCad tools enabled to query ICE and EDD for enzymes and expression tools satisfying specified performance characteristics

Sept. 2015 25



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Milestones

Operations Management Division


Intellectual Property Management

Generate >10 inventions Sept. 2015 71

Educate researchers about the tech transfer process Sept. 2015 27

Licensing Increase number of patent applications or inventions licensed or optioned and/or licensing agreements executed relative to the average of years 1 - 7.

Sept. 2015 26

Start-up Company Creation

Identify any IP or portfolios of IP that could lead to a start-up company and create an internal commercialization team to develop an initial go-to-market plan around that IP.

Sept. 2015 25

Maintain regular JBEI on-site office hours for the Berkeley Lab entrepreneur adviser.

Sept. 2015 25

Business Development Outreach

Promote each JBEI invention to at least 700 contacts in the biofuels industry.

Sept. 2015 26

Conduct meetings with at least fifteen companies each year, at least one-third of which are new to JBEI

Sept. 2015 27

Industry Advisory Committee

Hold an annual meeting of the IAC to inform JBEI research of industry concerns and technology bottlenecks.

Sept. 2015 18

Industry Partnership Program

Strengthen relationships with current partners and pursue collaborations with new industry partners in areas of complementary research.

Sept. 2015 26



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Milestones

Operations Management Division (continued)


Annual Scientific Advisory Meeting

Hold the annual meeting and report to DOE on the findings of the committee

Sept. 2015 25

Annual JBEI Conference

Annual JBEI Retreat Sept. 2015 33

Human Resources Staffing for year 8 complete Sept. 2015 25

DOE Bioenergy Research Center (BRC) - jbei.org · JBEI contacts Jay Keasling, Chief Executive...

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