DOE Bioenergy Research Center (BRC) - Joint BioEnergy ... · FY 2015 Dashboard For Period: October...

DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute

Monthly Progress Report – October 2014

Fiscal Year: 2015

Year / Period: Year 8 / Month 1/ October 1, 2014 – October 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 October 2014, first month of fiscal year 2015:

Item Count Highlights

Publications in Print 5 "Enhancing terpene yield from sugars via novel routes to 1-deoxy-d-xylulose 5-phosphate"

"A droplet-to-digital (D2D) microfluidic device for single cell assays"

Publications in Press 4 “Improving microbial bio-gasoline production in Escherichia coli using tolerance engineering”

“Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency”

Media Citations 19 Two stories released: “Boosting Biogasoline Production in Microbes” and “New Lab Startup Afingen Uses Precision Method to Enhance Plants”

Invention Disclosures 4 “Active Component of Cellulase Mixture from a Thermophilic Bacterial Community is a Multenzyme Complex”

Patent Applications 2 “Switchable Ionic Liquids for Biomass Pretreatment and Enzymatic Hydrolysis”

Presentations Given 9 Presentations were given at the “Frontiers in Biorefining Conference Chemicals and Products from Renewable Carbon”, The University of Tennessee, Center for Renewable Carbon, St. Simons Island, GA

On-Site Seminars 12 Prof. Michael Hahn, University of Georgia, Complex Carbohydrate Research Center, BioEnergy Science Center

Tours & Visits 11 Educational visit from PhD students from CEA Grenoble, France.

Industry Interactions 12 New interactions with Bayer, Monsanto and BASF.

Awards 1 JBEI’s CEO Jay Keasling won the The Economist 2014 Innovation Award in the Bioscience Category

FY15 Milestones 70 On track.

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

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Dashboard – October 2014 - DOE

FY 2015 Dashboard For Period: October 1 - 31

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Publications

In Print

Kirby, J., Nishimoto, M., Chow, R. W., Baidoo, E. E., Wang, G., Martin, J., Schackwitz, W., Chan, R., Fortman, J. L., & Keasling, J. D. (2014). "Enhancing terpene yield from sugars via novel routes to 1-deoxy-d-xylulose 5-phosphate". [Journal article]. Appl Environ Microbiol, 17, 02920-02914. doi, 10.1128/AEM.02920-14

Lund, C. H., Bromley, J. R., Stenbaek, A., Rasmussen, R. E., Scheller, H. V., & Sakuragi, Y. (2014). "A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus". [Journal article]. J Exp Bot, 18. doi, 10.1093/jxb/eru401

Poust, S., Yoon, I., Adams, P. D., Katz, L., Petzold, C. J., & Keasling, J. D. (2014). "Understanding the Role of Histidine in the GHSxG Acyltransferase Active Site Motif: Evidence for Histidine Stabilization of the Malonyl-Enzyme Intermediate". PLoS One, 9(10), e109421. doi, 10.1371/journal.pone.0109421

Shih, S. C., Gach, P. C., Sustarich, J., Simmons, B. A., Adams, P. D., Singh, S., & Singh, A. K. (2014). "A droplet-to-digital (D2D) microfluidic device for single cell assays". [10.1039/C4LC00794H]. Lab Chip. doi, 10.1039/c4lc00794h

Sitepu, I., Shi, S., Simmons, B. A., Singer, S. W., Boundy-Mills, K., & Simmons, C. W. (2014). "Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate". FEMS Yeast Res, n/a-n/a. doi, 10.1111/1567-1364.12224

In Press

Foo, J. L., Jensen, H. M., Dahl, R. H., George, K., Keasling, J. D., Lee, T. S., Leong, S.S.J.L & Mukhopadyay, A. (2014). “Improving microbial bio-gasoline production in Escherichia coli using tolerance engineering”. mBio

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.

Furtado, A. L., Jason; Hoang, N. V.; Healey, A.; Singh, S.; Simmons, B. A.; Henry, R. (2014). “Modifying plants for biofuel and biomaterial production”. Plant Biotechnology Journal.

Woo, H. L., Ballor, N., Hazen, T.C., Fortney, J. L., Simmons, B. A., Davenport, K. W., Goodwin, L., Ivanova, N., Kyrpides, N., Mavromatis, K., Woyke, T., Jansson, J., Kimbrel, J., and DeAngelis, K. (2014). “Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2”. Standards in Genomic Sciences



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News Citations

Date Article Source

Oct 1 Sifting Through Metagenomes With MaxBin Design & Trend

Oct 1 TeselaGen Receives $750k NSF SBIR Phase II Award IT Business Net

Oct 1 TeselaGen Receives $750k NSF SBIR Phase II Award ABC2 WBay

Oct 27 Boosting biogasoline production in microbes Science Codex

Oct 27 Boosting biogasoline production in microbes Press-News.org

Oct 27 Boosting Biogasoline Production in Microbes Science Newsline - Biology

Oct 28 Boosting biogasoline production in microbes Phys.org

Oct 28 JBEI identifies microbial genes to boost biogasoline production Biofuels Digest

Oct 28 Boosting biogasoline production in microbes R&D Magazine

Oct 28 JBEI Researchers Identify Microbial Genes That Can Improve Biogasoline Production in E. coli AZoCleantech.com

Oct 28 Lygos Inc. receives two grants for microbial technology projects Biomass Magazine

Oct 29 New Lab Startup Afingen Uses Precision Method to Enhance Plants EIN Presswire

Oct 30 New Startup Afingen Uses Precision Method To Enhance Plants Technology.org

Oct 30 Afingen uses precision method to enhance plants R&D Magazine

Oct 30 JBEI researchers boost biogasoline production in microbes Biomass Magazine

Oct 30 Lab breakthrough can lead to cheaper biofuels, improved crops, and new products from plants Phys.org

Oct 31 Research Finds Key to Cheaper Biofuels, Improved Crops Laboratory Equipment

Oct 31 Engineering Boosts Biogas Production in Microbes Laboratory Equipment



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News Citations

Date Article Source

Oct 31 Lab Breakthrough Paves Way for Improved Crops, Cheaper Biofuels China Topix

Inventions Disclosed Inventor(s)

2015-006 “Thermotoloerant mixture of a Glucoside hydrolase family 1 beta-glucosidase and a glucoside hydrolase family 16 laminarinase for algal biomass deconstruction”

John Cunha, Richard Heins, Kenneth L. Sale, Chessa Scullin, Blake A. Simmons and Seema Singh

2015-007 “Jungle Express – inducible Eil-promoters for gene expression” Thomas L Ruegg

2015-010 “Active Component of Cellulase Mixture from a Thermophilic Bacterial Community is a Multenzyme Complex”

Evelyn Denzel, John Gladden, Jennifer Hiras and Steven W Singer.

2015-012 “The Unexpected Importance of Actinobacterial GH12 in Hydrolysis of Crystalline Cellulose”

Jennifer Hiras, Steven W Singer and Yu-Wei Wu.

Patent Applications Inventor(s)

2013-128-01US62/068,595 “Method and device for manipulation of a droplet” Anup Singh, Jess Sustarich, and Chao Chung Shih

2014-064-01US62/073,802 “Switchable Ionic Liquids for Biomass Pretreatment and Enzymatic Hydrolysis”

Blake Simmons, Kenneth L. Sake, and Michael J. Liszka



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Presentations

Date Division Presenter(s) Title Presentation Location

Oct 2 Fuels Synthesis

Keasling, J. D. Synthetic Biology for Synthetic Chemistry

University of Virginia, Charlottesville, VA

Oct 5-8 Feedstocks Mann, G.W., Joshi, H. J., Petzold, C. J., Heazlewood, J.L.

Mining post translational modifications in Arabidopsis using the ModHunter

Human Proteome Organization World Congress, Madrid, Spain

Oct 8 Deconstruction Thelen, M. P. Microbial-Enabled Bioenergy Sonoma State University Biology Colloquium, Sonoma, CA


Hillson, N. J. Synthetic Biology Informatics: Scalability and Responsible Innovation

Novo Nordisk Center for Biosustainability, Copenhagen, Denmark

Oct 21-24 Deconstruction Singh, S. Development and Demonstration of an Integrated Biomass Sugar Production Platform based on Ionic Liquids

Frontiers in Biorefining Conference Chemicals and Products from Renewable Carbon, The University of Tennessee, Center for Renewable Carbon, St. Simons Island, GA

Oct 21-24 Deconstruction Parthasarathi, R., Simmons, B. A., and Singh, S.

Biomass Pretreatment Using Designer Ionic Liquids

Frontiers in Biorefining Conference Chemicals and Products from Renewable Carbon, The University of Tennessee, Center for Renewable Carbon, St. Simons Island, GA


Hillson, N. J. Synthetic Biology Informatics: Scalability and Responsible

University of Edinburgh, Edinburgh, Scotland



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Innovation

Oct 27-29 Feedstocks Heazlewood, J. L. Beyond the Golgi proteome. ARC Centre of Excellence in Plant Cell Walls

Annual Retreat. Yarra Valley, Victoria, Australia


Hillson, N. J. Berkeley Open BioFoundry (BOB) Update

LBNL BioSciences Retreat, Berkeley, CA



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Onsite Seminars

Date Type Presenter Title Affiliation

Oct 1 JBEI Seminar Series Nathan Hillson Berkeley Open Biofoundry (BOB): Overall Vision and a Day in the Life

Director, Synthetic Biology, Fuels Synthesis Division

Oct 1 Group Seminar Kevin George Characterizing IPP toxicity in E. coli DH1

Fuels Synthesis Division

Oct 8 General Seminar Deconstruction Guest

Prof. Michael Hahn Analysis of Biomass Structure and Processing using Antibody Probes

Professor of Plant Biology, Adjunct Professor of Biochemistry and Molecular Biology, and Plant Pathology; University of Georgia, Complex Carbohydrate Research Center, BioEnergy Science Center

Oct 8 Group Seminar Clara Eng Engineering the β-Ketoreductase Domain of Polyketide Synthases


Oct 15 General Seminar Todd Pray, Program Head Process Development and Scale-up for Feedstock Flexibility and Bio-based Product Diversification

Advanced Biofuels (and Bioproducts) Process Demonstration Unit (ABPDU)

Oct 15 Group Seminar Gabriela Guzman Model-driven discovery of underground metabolic functions in Escherichia coli


Oct 15 Group Seminar Elizabeth Brunk Application of Genome-Scale Metabolic Models in Metabolic Engineering


Oct 22 General Seminar Deconstruction Guest

Dr. Huaming Wang Fungal system biology towards fungus enzymes for food and feed

Principal Investigator; Tianjing Institute of Industrial Biotechnology, Chinese Academy of Science;



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applications Chief Scientist, Qingdao Vland Biotech Group, P.R. China

Oct 22 Group Seminar Jeff Wong Identifying novel genes involved in phorbol biosynthesis in Jatropha curcas


Oct 22 Group Seminar Nicolas Koutsoubelis Precursor pathway engineering in Saccharomyces cerevisiae for PKS expression


Oct 29 Group Seminar Kamrun Zargar Discovery of genes associated with bacterial toluene biosynthesis


Oct 29 Group Seminar Margaret Brown Engineering chemical warfare agent catabolism into E. coli




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Tours and VIP Visits at JBEI

Date Company Attendees

Oct 1 CTO of COFCO Dr. Ping Chen

Oct 3 R&D Planning Dept. Ajinomoto Co., Inc. (Tokyo) Kazuya Onomichi, Nobuhisa Shimba

Oct 6 Calif. Inst. of Technology Professor Harry Atwater

Oct 6 New Fuel and Vehicle Systems Optima (NFVSO) Andrew Sutton, Art Pontau, Brad Ziegler, Jennifer Dunn, John Farrell, John Holladay, Matt McNenly, Paul Miles, Richard Boardman, Robert Wagner, Sam Saxena and Tom Foust

Oct 8 Jülich Research Center Wolfgang Marquardt, Svenja Kruse, Thorsten Voss, Rainer Waser

Oct 10 Die Zeit (German Newspaper) Christiane Grefe

Oct 13 University of Queensland Anton Middelberg

Oct 15 Idaho National Laboratory Visit Vicki Thompson & Darryl Reed

Oct 16 Riffyn Tim Gardner

Oct 22 DOE Chicago real estate team Rick Chapman, Kevin Hartnett, Laura Troche, Roger Doole, Susan Bourgart

Oct 29 CEA Grenoble 15 PhD Students



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Industry Interactions

Date Company / Contact

Oct 1 COFCO / Dr. Ping Chen

Oct 1 Tehnology Holding Co. / Jessica Elwell and Mukund Karanjikar

Area of interest: Methyl Butanols SBIR/STTR Request for Information

Oct /3 Ajinomoto / Dr. Kazuya Onomichi

Oct 14 Reliance Industries Limited / Makarand Phadke and Vidhya Rangaswamy

Oct 14 Total / Angelique Chanal and Shital Tripathi

Oct 15 COFCO / Bo Chen (LBL)

Oct 16 Riffyn / Tim Gardner and Claude Calegari

Oct 17 Monsanto / Ginni Ursin

Area of interest: EIB-3144, golgi nucleotide sugar transporters, Engineering tolerance to drought/submergence by over expression of a grass specific protein: 2014-108

Oct 17 Bayer / Garth Hodges

Area of interest: Improved Crops with Increased Galactan Content: EIB-3144, Engineering Competitive Pathways for Tissue-Specific Lignin Reduction: EIB-3266

Oct 17 BASF / Burkhard Ernst and Lahoucine Achnine

Area of interest: Improved Crops with Increased Galactan Content: EIB-3144, Engineering Competitive Pathways for Tissue-Specific Lignin Reduction: EIB-3267



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Awards

Name Award

Jay Keasling The Economist 2014 Innovation Awards – Bioscience Category

Oct 21 Virdia / Robert Jansen

Oct 22 Agilent / Steve Royce

Area of interest: Proposed and onsite meeting at JBEI



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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 10

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

Sept. 2015 8

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

Sept. 2015 8

Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 5

Characterization of novel GT activities (SB) Sept. 2015 5

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 10

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

Sept. 2015 9

Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 9

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

Sept. 2015 15

Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 0

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

Sept. 2015 0



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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 8

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

Sept. 2015 8

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

Sept. 2015 9



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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 10

Complete characterization of lignin streams from various IL pretreatment process configurations

July 2015 8

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

Aug. 2015 7

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 7

Enzyme Optimization

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

Feb. 2015 15

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 10

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 7

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

Sept. 2015 7



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Milestones

Deconstruction Division (continued)


Microbial Communities

Complete characterization of active component of JTherm March 2015 15

Establish complementary thermophilic cellulase cocktail focusing on crystalline substrates

July 2015 10

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

Sept. 2015 7

Fungal Biotechnology

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

Feb. 2015 13

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

April 2015 10

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

July 2015 10

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

Sept. 2015 7



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Milestones



Discovery of Novel Hydrocarbon Biochemistries

In vitro, anaerobic testing of toluene biosynthesis candidates Sept. 2015 8

In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 8

Optimization of Hydrocarbon Biosynthetic Pathways

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

Sept. 2015 8

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

Sept. 2015 8

Genes encoding isoprenoid pathway integrated into E. coli chromosome

Sept. 2015 8

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

Sept. 2015 8

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 30

Host Engineering S. cerevisiae: Consolidate xylose utilizing production strains with production pathways.

Sept. 2015 0

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 30



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Milestones

Fuels Synthesis Division (continued)


Synthetic Biology

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

Sept. 2015 8

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

Sept. 2015 8

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 30

Perform flux analysis of S. cerevisiae sip1 strain June 2015 60

Implement interactive metabolic engineering on MvT Sept. 2015 7



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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 12

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

Sept. 2015 10

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

Sept. 2015 8

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

July 2015 10

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

Sept. 2014 10

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

Sept. 2015 15

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

Sept. 2015 15



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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 8

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

Sept. 2015 8

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

Sept. 2015 30

Characterize lignin degrading enzymes in collaboration with GLBRC Sept. 2015 25

Informatics Implemented an updated, refactored version of the EDD to support JBEI’s future data needs

Sept. 2015 20

Integrate EDD with data and workflows for characterizing biological parts, with Fuels Synthesis

Sept. 2015 5

Integrate EDD with data and workflows for characterizing enzymes, with Deconstruction Division

Sept. 2015 5



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Milestones

Operations Management Division


Intellectual Property Management

Generate >10 inventions Sept. 2015 60

Educate researchers about the tech transfer process Sept. 2015 10

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 9

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 8

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

Sept. 2015 8

Business Development Outreach

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

Sept. 2015 9

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

Sept. 2015 10

Industry Advisory Committee

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

Sept. 2015 5

Industry Partnership Program

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

Sept. 2015 9



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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 8

Annual JBEI Conference

Annual JBEI Retreat Sept. 2015 11

Human Resources Staffing for year 8 complete Sept. 2015 8

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