FY 2015 - Dashboard September 2015 DOE - JBEI ·...

DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress Report – September 2015 Fiscal Year: 2015 Year / Period: Year 8 / Month 12 / September 1 - 30, 2015

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 September 2015, twelfth month of fiscal year 2015:

Item Count Highlights

Publications in Print 11 "Development of a High Throughput Platform for Screening Glycoside Hydrolases based on Oxime-NIMS"

Invention Disclosures 1 “Multi-Omics Viewing Tool (MVT)”

Media Citations 5 Article by EMSL on creating sustainable bioproducts from lignin in which JBEI is quoted was covered by EurekAlert, Newswise, Enjeux Energies, Science Daily and AZoCleantech.com

Awards 2 2015 Eden Area ROP “Business Person of the Year” award for contribution to East Bay schools

Outreach Interactions 17 Education: 4, Public: 3 and Scientific Community: 10

On-Site Seminars 28 Nils J. H. Averesch from the Centre for Microbial Electrochemical Systems (CEMES), Advanced Water Management Centre, The University of Queensland (UQ) gave a seminar on “Model guided metabolic engineering for production of aromatics in S. cerevisiae”.

Industry Interactions 27 Interactions with Chevron, Total, Ajinomoto, & DuPont.

FY15 Milestones Milestones completed: -‐ Feedstocks: Novel acetyl and feruloyltransferase activities characterized (CWB) -‐ Feedstocks: Genetic characterization of mutant candidates from rice stem saccharification screen (GG) -‐ Feedstocks: Correlation between cell wall modification and environmental interactions investigated (GG) -‐ Feedstocks: Characterization of novel GT activities (SB). -‐ Feedstocks: Evaluation of engineered plants with new lignin traits (including analysis with the Deconstruction

and Technology Divisions) (CWE) -‐ Feedstocks: Nucleotide sugar transporters used for cell wall engineering (CWB) -‐ Feedstocks: Optimization of translation control technologies to improve tissue-specific expression (CWE) -‐ Feedstocks: Cell wall related genes in switchgrass functionally annotated, integrated into phylogenomics

databases, and integrated with Kbase (GG) -‐ Feedstocks: Resequencing of Kitaake mutants (with JGI) and a database set up for hi throughput




-‐ Feedstocks: Translation of best technologies developed in Arabidopsis to other plant species (CWE) -‐ Deconstruction: Use multi-scale simulations strategies (from first principle quantum mechanics to force field

based) to understand interactions between biomass derived ILs and lignocellulosic biomass -‐ Deconstruction: Demonstrate using directed evolution to engineer enhanced stability and activity of a -

glucosidase in up to 20% [C2mim][OAc]. -‐ Deconstruction: Validate candidate genes for hyperproduction phenotypes through gene deletion and/or

overexpression -‐ Fuels Synthesis: In vitro, anaerobic testing of toluene biosynthesis candidates -‐ Fuels Synthesis: In vitro, anaerobic testing of ladderane biosynthesis candidates -‐ Fuels Synthesis: Improve methyl ketone production in E. coli with NIMS-aided HT screening and metabolic

modeling -‐ Fuels Synthesis: E. coli pathway engineering for isopentenol production both in aerobic and anaerobic

conditions -‐ Fuels Synthesis: Genes encoding isoprenoid pathway integrated into E. coli chromosome -‐ Fuels Synthesis: Codon optimization tool (GeneDesign) integrated into the DIVA platform. -‐ Fuels Synthesis: Clonal sequence validation (Sanger and/or MiSeq) pipeline implemented and integrated

with DIVA/ICE -‐ Fuels Synthesis: Implement interactive metabolic engineering on MvT -‐ Technology: SEM and TEM analysis of genetically altered feedstock biomass (including lignin and protein

mapping) with Feedstocks and Deconstruction Divisions -‐ Technology: Electron tomographic analysis of plant cell walls of engineered feedstocks, and CAD model

generation for mechanical properties simulation. -‐ Technology: Structural characterization of Fatty Acid Synthase and other large complexes by single particle

cryo electron microscopy -‐ Technology: EDD further developed to support enzyme characterization data and workflows, with

Deconstruction Division -‐ Technology: EDD further developed to support genetic expression tool data and workflows, with Fuels

Synthesis -‐ Technology: BioCad tools enabled to query ICE and EDD for enzymes and expression tools satisfying

specified performance characteristics -‐ Tech Transfer: Educate researchers about the tech transfer process -‐ Tech Transfer: Increase number of patent applications or inventions licensed or optioned and/or licensing

agreements executed relative to the average of years 1 - 7. -‐ Tech Transfer: 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. -‐ Tech Transfer: Maintain regular JBEI on-site office hours for the Berkeley Lab entrepreneur adviser. -‐ Tech Transfer: Promote each JBEI invention to at least 700 contacts in the biofuels industry. -‐ Tech Transfer: Conduct meetings with at least fifteen companies each year, at least one-third of which are

new to JBEI -‐ Tech Transfer: Strengthen relationships with current partners and pursue collaborations with new industry

partners in areas of complementary research. -‐ Operations: Staffing for year 8 complete

Milestone delayed:

-‐ Feedstocks: Heterologous screening of transferases to promote in planta design of polysaccharides (SB).

Dashboard - September 2015 - DOE

FY 2015 Dashboard For Period: September 1 - 30, 2015

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Publications In Print

Chiu, T. Y., Lao, J., Manalansan, B., Loque, D., Roux, S. J., & Heazlewood, J. L. (2015). "Biochemical characterization of Arabidopsis APYRASE family reveals their roles in regulating endomembrane NDP/NMP homeostasis". Biochem J. doi, 10.1042/bj20150235 http://www.biochemj.org/content/ppbiochemj/early/2015/09/03/BJ20150235.full.pdf

Deng, K., Guenther, J. M., Gao, J., Bowen, B. P., Tran, H., Reyes-Ortiz, V., Cheng, X., Sathitsuksanoh, N., Heins, R., Takasuka, T. E., Bergeman, L., Geertz-Hansen, H., Deutsch, S., Loqué, D., Sale, K., Simmons, B., Adam, P. D., Singh, A. K., Fox, B. G., & Northen, T. R. (2015). "Development of a High Throughput Platform for Screening Glycoside Hydrolases based on Oxime-NIMS". [Methods]. Frontiers in Bioengineering and Biotechnology, 3. doi, 10.3389/fbioe.2015.00153 http://www.frontiersin.org/Journal/Abstract.aspx?s=1456&name=bioenergy_and_biofuels&ART_DOI=10.3389/fbioe.2015.00153 Ford, K. L., Zeng, W., Heazlewood, J. L., & Bacic, A. (2015). "Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques". Front Plant Sci, 6, 674. doi, 10.3389/fpls.2015.00674 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551829/pdf/fpls-06-00674.pdfhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551829/pdf/fpls-06-00674.pdf

Garcia Martin, H., Kumar, V. S., Weaver, D., Ghosh, A., Chubukov, V., Mukhopadhyay, A., Arkin, A., & Keasling, J. D. (2015). "A Method to Constrain Genome-Scale Models with 13C Labeling Data". PLoS Comput Biol, 11(9), e1004363. doi, 10.1371/journal.pcbi.1004363 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574858/pdf/pcbi.1004363.pdfhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574858/pdf/pcbi.1004363.pdf

Gardner, J. L., He, W., Li, C. L., Wong, J., Sale, K. L., Simmons, B. A., Singh, S., & Tanjore, D. (2015). "Calorimetric evaluation indicates that lignin conversion to advanced biofuels is vital to improving energy yields". [10.1039/C5RA01503K]. Rsc Advances, 5(63), 51092-51101. doi, 10.1039/c5ra01503k http://pubs.rsc.org/en/content/articlepdf/2015/ra/c5ra01503k

Gupta, S., Guttman, M., Leverenz, R. L., Zhumadilova, K., Pawlowski, E. G., Petzold, C. J., Lee, K. K., Ralston, C. Y., & Kerfeld, C. A. (2015). "Local and global structural drivers for the photoactivation of the orange carotenoid protein". Proc Natl Acad Sci U S A. doi, 10.1073/pnas.1512240112 http://www.ncbi.nlm.nih.gov/pubmed/26385969http://www.ncbi.nlm.nih.gov/pubmed/26385969

Hiras, J., Wu, Y.-W., Eichorst, S. A., Simmons, B. A., & Singer, S. W. (2015). "Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage". [Original Article]. ISME J. doi, 10.1038/ismej.2015.158 http://www.nature.com/ismej/journal/vaop/ncurrent/pdf/ismej2015158a.pdf

Kent, M. S., Avina, I. C., Rader, N., Busse, M. L., George, A., Sathitsuksanoh, N., Baidoo, E., Timlin, J., Giron, N. H., Celina, M. C., Martin, L. E., Polsky, R., Chavez, V. H., Huber, D. L., Keasling, J. D., Singh, S., Simmons, B. A., & Sale, K. L. (2015). "Assay for lignin breakdown based on lignin films: insights into the Fenton reaction with insoluble lignin". [10.1039/C5GC01083G]. Green Chem. doi,



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Publications In Print 10.1039/c5gc01083g http://pubs.rsc.org/en/content/articlepdf/2015/gc/c5gc01083g

Parthasarathi, R., Balamurugan, K., Shi, J., Subramanian, V., Simmons, B. A., & Singh, S. (2015). "Theoretical Insights into the Role of Water in the Dissolution of Cellulose using IL/Water Mixed Solvent Systems". J Phys Chem B. doi, 10.1021/acs.jpcb.5b02680 http://pubs.acs.org/doi/pdfplus/10.1021/acs.jpcb.5b02680http://pubs.acs.org/doi/pdfplus/10.1021/acs.jpcb.5b02680

Petzold, C. J., Chan, L. J., Nhan, M., & Adams, P. D. (2015). "Analytics for Metabolic Engineering". [Review]. Front Bioeng Biotechnol, 3, 135. doi, 10.3389/fbioe.2015.00135 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561385/pdf/fbioe-‐03-‐00135.pdfhttp://pubs.acs.org/doi/pdfplus/10.1021/acs.jpcb.5b02680

Torr, K. M., Love, K. T., Simmons, B. A., & Hill, S. J. (2015). "Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids". Biotechnol Bioeng. doi, 10.1002/bit.25831 http://onlinelibrary.wiley.com/store/10.1002/bit.25831/asset/bit25831.pdf?v=1&t=if5nb8g6&s=bafdd94f8da66903359a054a3ac06c53ad557370http://onlinelibrary.wiley.com/store/10.1002/bit.25831/asset/bit25831.pdf?v=1&t=if5nb8g6&s=bafdd94f8da66903359a054a3ac06c53ad557370

Media Citations Date Article Source

Sept 8 Making the most from carbon in plants EurekAlert

Sept 8 Making the Most From Carbon in Plants Newswise

Sept 9 Making the most from carbon in plants Enjeux Energies

Sept 9 Making the most from carbon in plants Science Daily

Sept 11 EMSL User Program Projects Aim to Create Sustainable Carbon Sources from Biomass AZoCleantech.com

Invention Disclosures Inventor(s) 2015-181 “Multi-Omics Viewing Tool (MVT)” Garrett Birkel, Hector Garcia Martin and

William Morrell



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Awards Name Award

Harry Beller Member of the Scientific Advisory Committee (SAC) for the Biosciences Division of the SLAC National Accelerator Laboratory (Menlo Park, CA)

Sarah Richardson 2015 Eden Area ROP “Business Person of the Year” award for contribution to East Bay schools

Outreach – Education Date Presenters Audience or Presentation Title Activity Location

Sept 8 Irina Silva Gyeonggibuk Science High School, Korea Tour On-site

Sept 17 Daisuke Koma, Erika Yoshida and Saori Campen

Kagoshima University Tour On-site

Sept 25 Solomon Stonebloom and Thea Pick

Bishop O'Dowd High School Tour On-site

Sept 28 Blake Simmons National Autonomous University of Mexico Tour On-site

Outreach – Public Date Presenters Audience or Presentation Title Activity Location

Sept 13 Belle Smith, Irina Silva, Leanne Chan, Mi Yeon Lee and Phil Gach

41st Annual Solano Avenue Stroll Event Berkeley, CA

Sept 15 Blake Simmons, Jenny Mortimer, Peter Matlock and Steve Singer

USPTO hosted delegation from China Tour On-site



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Sept 29 Lin Fang, Peter Matlock and Yan Liang

Wuhan investors Tour On-site

Outreach – Scientific Community Date Presenters Audience or Presentation Title Activity Location

Sept 3 Nathan Hillson DIVA, SynBio Internal Review Process, and Biosecurity DNA Sequence Screening Pipeline

Presentation Synbio UK

Sept 8 Ben Wu Sandia National Laboratories Tour On-site

Sept 8-11 Dominique Loque Gene Stacking and Metabolic Engineering in Plants

Presentation Joint 7th Conference of the Polish Society for Experimental Plant Biology and the Intercollegiate Faculty of Biotechnology UG & MUG. Gdańsk, Poland

Sept 14-15 Henrik Scheller Engineering of plant cell walls for improved biofuel production

Presentation Plant Genomics Congress USA, St. Louis, MO

Sept 15 Jennifer Mortimer Futuragene Tour On-site

Sept 19 Hector A. Plahar, Lisa Simirenko, Garima Goyal, Joanna Chen, Manjiri Tapaswi, Nina Stawski, Jacob Coble, Paul D. Adams, Jay D. Keasling, and Nathan J. Hillson

DIVA: More Science, Less DNA Construction Presentation Synberc Fall Retreat 2015, Boston, MA

Sept 20 Garrett Birkel The Multi-Omics Viewing Software Project Presentation Synberc Fall Retreat 2015,



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Boston, MA

Sept 23 Blake Simmons (invited)

Building the link between advanced biofuels and engines

Presentation CRC Annual Meeting, Albuquerque, NM

Sept 29 Jay D. Keasling Engineering Microbes for Production of Chemicals and Fuels

Presentation National University of Singapore, Singapore

Sept 30 Jay D. Keasling Life 2.0: Engineering Biology for Sustainable Development

Presentation SynCTI Symposium, National University of Singapore, Singapore



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Onsite Seminars Date Type Presenter Title Affiliation

Sept 2 General Seminar Fuels/Tech Guest

Erik Jensen An end-to-end microfluidic platform for engineering life supporting microbes in space exploration missions

HJ Science & Technology, Inc.

Sept 2 Group Seminar Chris Petzold JBEI 'omic analytics and the Experiment Data Depot (EDD)

Technology Division

Sept 9 JBEI Seminar Nathan Hillson Synthetic Biology: Responsible Innovation and FutureBio Foundry update

Synthetic Biology Informatics

Sept 9 Group Seminar Erik Hanko Metabolic Engineering Yarrowia lipolytica for the Production of Methyl ketones

Fuels Synthesis Division

Sept 9 Group Seminar James Kirby Taking a Closer Look at Biofuel Pathway Yields


Sept 16 General Seminar Technology Guest

Joshua K. Michel Process Development for Industrial Enzyme Manufacturing

Dupont

Sept 16 Group Seminar Sarah Richardson

CRISPR design and unusual uses for CRISPR associated proteins


Sept 16 Group Seminar Ankita Kothari Studying the Alkane Hydroxylases from Acinetobacter venetianus ATCC 31012 for Dodecane Degradation


Sept 17 General Seminar Nils J. H. Model guided metabolic engineering for production of

Centre for Microbial Electrochemical Systems



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Fuels Guest Averesch aromatics in S. cerevisiae (CEMES), Advanced Water Management Centre, The University of Queensland (UQ)

Sept 21 General Seminar Deconstruction Guest

Juan VillaRomero Novel microbes, novel applications: where to look and how to find them

UC Berkeley - Interview Candidate

Sept 23 Group Seminar Leo D'Espaux Metabolic Engineering of Saccharomyces cerevisiae for Fatty Chemical Production


Sept 23 Group Seminar Rachel Li Taxol biosynthesis: a search for a tree and struggles with S. cerevisiae



Binod Neupane Integrated Sustainability Assessment of Forest-Based Drop-in

School of Economics/Ecology and Environmental Sciences Program University of Maine, Orono


Cecily Ryan Anaerobic Degradation of PHBV/Wood Flour Biocomposites

Stanford University


Eric Shiue, Ph.D. Metabolic Engineering of E. coli for Improved

Massachusetts Institute of Technology

Sept 28 General Seminar Feedstocks Guest

Nadav Sorek New Insights into Cobra EBI

Sept 28 General Feedstocks Seminar William Moore Arabinogalactan Proteins are Involved in Beneficial Plant-Microbe Interactions

Feedstocks Division

Sept 28 General Seminar Feedstocks Vicente Ramirez Characterization of A Suppressor EBI



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Guest of TBL29

Sept 28 General Feedstocks Seminar Lin Fang Loss of a Sphingolipid Specific Mannosyltransferase Induces Plant Immune Responses and Deficiency in Cellulose Production

Feedstocks Division


Yunjun Zhao Sorghum as a Feedstock for Biofuels

EBI

Sept 28 General Feedstocks Seminar Guotian Li Use a Sequence-Indexed Mutant Collection in Cell Wall Studies in Rice

Feedstocks Division


Markus Pauly Agave as a Feedstock for Biofuels EBI

Sept 28 General Feedstocks Seminar Yan Liang Transcript Repression Switch for Fine-Tuning of Transgene Expression

Feedstocks Division


Heidi Szemenyei Characterization of Suppressors of PMR5/TBL44

EBI

Sept 28 General Feedstocks Seminar Aymerick Eudes Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase (HCT) to Reduce Lignin

Feedstocks Division

Sept 30 General Seminar Fuels /Commercialization Guest

Dr. Sergey Mashko, Research Head

D-Glucaric Acid Production Feedstocks Division

Sept 30 Group Seminar Clara Eng Altering polyketide stereochemisty by ketoreductase domain




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swapping

Sept 30 Group Seminar Chris Eibeen Production of Novel Terpenes via the Lepidopteron Mevalonate Pathway




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Industry Interactions Date Company / Contact

Sept. 14 Lanzatech/Alex Juminaga, Sean Simpson

Sept. 21 Ecovia/Jeremy Minty

Sept. 22 Alignment Polymers/Frank Adamsky

Sept. 23 Tencent/Kyle Kupinski

Sept. 24 Technology Holding/Mukund Kajanikar

Sept. 24 iCultiver/Raj Khanna

Sept. 24 China Lake/Bill Hogan

Sept. 25 Benson Hill Biosystems/Ben Gray

Sept. 22 Geneshifters/Kulvinder Gill

Sept. 14 Cargill/Gary Folkert

Sept. 14 BioAmber/Jim Millis

Sept. 14 MMI/Pat Smith, Tom Gregory

Sept. 15 Henton Consulting/Dave Henton

Sept. 15 China Lake/Ben Harvey

Sept. 21 Cummins, Inc./John Wall

Sept. 21 Innosense/Anamika Ray



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Sept. 21 Intact Genomics/Brian Villa

Sept. 21 Chevron/Jeffrey Jacobs

Sept. 21 Agilent/Steffen Mueller

Sept. 21 Genesys/Goutham Vemuri

Sept. 16 Ceres/Roger Pennell

Sept. 17 Zeachem/Nick Bilotti

Sept. 18 Evodia/Bob Haushalter, Ee-Been Goh

Sept. 21 Total/Florence Mingardon, etc.

Sept. 25 Afingen/Ai Oikawa

Sept. 30 Ajinomoto/Dr. Sergey Mashko, Dr. Kojima

Sept. 16 DuPont/Josh Michel



15 / 18

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 100

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

Sept. 2015 100

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

Sept. 2015 100

Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 100

Characterization of novel GT activities (SB) Sept. 2015 100

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 100

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

March 2016 82

Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 100

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

Sept. 2015 100

Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 100

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

Nov. 2015 70



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Milestones Feedstocks Division (continued) Area Initiatives Milestone/Deliverables Due % Complete

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 100

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

Sept. 2015 100

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

Sept. 2015 100



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Milestones Deconstruction Division

Area Initiatives Milestone/Deliverables Due % Complete

Biomass Pretreatment

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

May 2015 100

Complete characterization of lignin streams from various IL pretreatment process configurations

July 2015 100

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

Aug. 2015 100

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 100

Enzyme Optimization

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

Feb. 2015 100

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 100

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.

Dec. 2015 75

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

Sept. 2015 100



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Milestones Deconstruction Division (continued)

Area Initiatives Milestone/Deliverables Due % Complete

Microbial Communities

Complete characterization of active component of JTherm March 2015 100

Establish complementary thermophilic cellulase cocktail focusing on crystalline substrates

July 2015 100

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

Sept. 2015 100

Fungal Biotechnology

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

Feb. 2015 100

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

April 2015 100

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

July 2015 100

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

Sept. 2015 100



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Milestones Fuels Synthesis Division Area Initiatives Milestone/Deliverables Due % Complete

Discovery of Novel Hydrocarbon Biochemistries

In vitro, anaerobic testing of toluene biosynthesis candidates Sept. 2015 100

In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 100

Optimization of Hydrocarbon Biosynthetic Pathways

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

Sept. 2015 100

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

Sept. 2015 100

Genes encoding isoprenoid pathway integrated into E. coli chromosome

Sept. 2015 100

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

Sept. 2015 100

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 100

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

Sept. 2015 100

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 100



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Milestones Fuels Synthesis Division (continued) Area Initiatives Milestone/Deliverables Due % Complete

Synthetic Bio Informatics

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

Sept. 2015 100

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

Sept. 2015 100

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 100

Perform flux analysis of S. cerevisiae Δsip1 strain June 2015 100

Implement interactive metabolic engineering on MvT Sept. 2015 100



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Milestones Technology Division Area Initiatives Milestone/Deliverables Due % Complete

High Throughput Screening

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

Sept. 2015 100

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

Sept. 2015 100

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

Sept. 2015 100

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

July 2015 100

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

Sept. 2015 100

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

Sept. 2015 100

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

Sept. 2015 100



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Milestones Technology Division (continued) Area Initiatives Milestone/Deliverables Due % Complete

Physical Characterization

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

Sept. 2015 100

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

Sept. 2015 100

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

Sept. 2015 100

Characterize lignin degrading enzymes in collaboration with GLBRC Sept. 2015 100

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

Sept. 2015 100

Synthetic Bio Informatics

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

Sept. 2015 100

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

Sept. 2015 100

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

Sept. 2015 100



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Milestones Operations Management Division Area Initiatives Milestone/Deliverables Due % Complete

Intellectual Property Management

Generate >10 inventions Sept. 2015 100

Educate researchers about the tech transfer process Sept. 2015 100

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 100

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 100

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

Sept. 2015 100

Business Development Outreach

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

Sept. 2015 100

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

Sept. 2015 100

Industry Advisory Committee

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

Sept. 2015 100

Industry Partnership Program

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

Sept. 2015 100



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Milestones Operations Management Division (continued) Area Initiatives Milestone/Deliverables Due % Complete

Annual Scientific Advisory Meeting

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

Sept. 2015 100

Annual JBEI Conference

Annual JBEI Retreat Sept. 2015 100

Human Resources Staffing for year 8 complete Sept. 2015 100

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