this monthly progress report provides a summary of jbei’s ...€¦ · jbei contacts jay keasling,...

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DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress Report January 2015 Fiscal Year: 2015 Year / Period: Year 8 / Month 4 / January 1 - 31, 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 January 2015, fourth month of fiscal year 2015: Item Count Highlights Publications in Print 7 "Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls" Publications in Press 4 "Scale-up of Ionic Liquid Based Fractionation of Single and Mixed Feedstocks" Media Citations 10 Media highlight: U.S. Agriculture Secretary Tom Vilsack Visited JBEI Patent Applications 2 “Generation of heritable chimeric plant traits” Licenses 1 Bailment/License for invention # 2014-155 “Plasmids for Ralstonia Synthetic Biology Toolbox” Presentations Given 17 Presentations were given at the “CSU Annual Biotechnology Symposium” in San Francisco, CA and at “Lignofuels 2015” in, Madrid, Spain. On-Site Seminars 13 Prof. Anne Osbourn, Norwich Research Park Industrial Biotechnology and Bioenergy Alliance, John Innes Centre, Norwich Research Park Tours & Visits 6 California Energy Commission and U.S. Agriculture Secretary Tom Vilsack Industry Interactions 16 Interactions with Arzeda and Technology Holding LLC 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.Technology - “Structural characterization of Fatty Acid Synthase and other large complexes by single particle cryo electron microscopy”

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Page 1: This Monthly Progress Report provides a summary of JBEI’s ...€¦ · JBEI contacts Jay Keasling, Chief Executive Officer, jdkeasling@lbl.gov, 510-495-2620 Nick Everson, Chief Operating

DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute

Monthly Progress Report – January 2015

Fiscal Year: 2015

Year / Period: Year 8 / Month 4 / January 1 - 31, 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 January 2015, fourth month of fiscal year 2015:

Item Count Highlights

Publications in Print 7 "Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls"

Publications in Press 4 "Scale-up of Ionic Liquid Based Fractionation of Single and Mixed Feedstocks"

Media Citations 10 Media highlight: U.S. Agriculture Secretary Tom Vilsack Visited JBEI

Patent Applications 2 “Generation of heritable chimeric plant traits”

Licenses 1 Bailment/License for invention # 2014-155 “Plasmids for Ralstonia Synthetic Biology Toolbox”

Presentations Given 17 Presentations were given at the “CSU Annual Biotechnology Symposium” in San Francisco, CA and at “Lignofuels 2015” in, Madrid, Spain.

On-Site Seminars 13 Prof. Anne Osbourn, Norwich Research Park Industrial Biotechnology and Bioenergy Alliance, John Innes Centre, Norwich Research Park

Tours & Visits 6 California Energy Commission and U.S. Agriculture Secretary Tom Vilsack

Industry Interactions 16 Interactions with Arzeda and Technology Holding LLC

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.”

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

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Publications

In Print

Eudes, A., Sathitsuksanoh, N., Baidoo, E. E., George, A., Liang, Y., Yang, F., Singh, S., Keasling, J. D., Simmons, B. A., & Loque, D. (2015). "Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency". Plant Biotechnol J. doi, 10.1111/pbi.12310 http://www.ncbi.nlm.nih.gov/pubmed/25583257

George, K. W., Alonso-Gutierrez, J., Keasling, J. D., & Lee, T. S. (2015). “Isoprenoid Drugs, Biofuels, and Chemicals-Artemisinin, Farnesene, and Beyond”. Adv Biochem Eng Biotechnol (2015 Jan 11 ed.): Springer Berlin Heidelberg.1

Lupoi, J. S., Healey, A., Singh, S., Sykes, R., Davis, M., Lee, D. J., Shepherd, M., Simmons, B. A., & Henry, R. J. (2015). "High-Throughput Prediction of Acacia and Eucalypt Lignin Syringyl/Guaiacyl Content Using FT-Raman Spectroscopy and Partial Least Squares Modeling". BioEnergy Research. doi, 10.1007/s12155-015-9578-1 http://link.springer.com/article/10.1007/s12155-015-9578-1

Tanger, P., 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, 1-18. doi, 10.1007/s12155-014-9573-y http://dx.doi.org/10.1007/s12155-014-9573-y

Vega-Sanchez, M. E., Loque, D., Lao, J., Catena, M., Verhertbruggen, Y., Herter, T., Yang, F., Harholt, J., Ebert, B., Baidoo, E. E., Keasling, J. D., Scheller, H. V., Heazlewood, J. L., & Ronald, P. C. (2015). "Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls". Plant Biotechnol J. doi, 10.1111/pbi.12326 http://www.ncbi.nlm.nih.gov/pubmed/25586315

Velasquez, S. M., Ricardi, M. M., Poulsen, C. P., Oikawa, A., Dilokpimol, A., Halim, A., Mangano, S., Denita Juarez, Silvina P., Marzol, E., Salgado Salter, J. D., Dorosz, J. G., Borassi, C., Möller, S. R., Buono, R., Ohsawa, Y., Matsuoka, K., Otegui, M. S., Scheller, H. V., Geshi, N., Petersen, B. L., Iusem, N. D., & Estevez, J. M. (2014). "Complex Regulation of Prolyl-4-Hydroxylases Impacts Root Hair Expansion". Molecular Plant (0). doi, 10.1016/j.molp.2014.11.017 http://www.sciencedirect.com/science/article/pii/S16742052140003802

Zuo, S., Zhou, X., Chen, M., Zhang, S., Schwessinger, B., Ruan, D., Yuan, C., Wang, J., Chen, X., & Ronald, P. C. (2014). "OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae". J Integr Plant Biol, 56(12), 1179-1192. doi, 10.1111/jipb.12290 http://www.ncbi.nlm.nih.gov/pubmed/252662703

1 Publisher does not allow for acknowledgments. 2 Publications does now acknowledge JBEI funding. Author has requested revision. 3 Idem.

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In Press

Li, C., Tanjore, D., He, W., Wong, J., Gardner, J. L., Thompson, V. S., Yancey, N. A., Sale, K., Simmons, B. A., & Singh, S. (2015). "Scale-up of Ionic Liquid Based Fractionation of Single and Mixed Feedstocks". BioEnergy Research.

Shi, J., George, K. W., Sun, S., He, W., Li, C., Stavila, V., Lee, T. S., Simmons, B. A., & Singh, S. (2015). "Impact of pretreatment technologies on saccharification and isopentenol fermentation of mixed lignocellulosic feedstocks". BioEnergy Research.

Lopez-Ortega, M. G., Chavez-Carvayar, J. A., Stavila, V., Cheng, G., Singh, S., Simmons, B. A.,& Pérez-Pimienta, J. (2015). "Characterization of agave bagasse ad a function of ionic liquid pretreatment". Biomass & Bioenergy.

Papa, G., Rodriguez, S., George, A., Schievano, A., Orzi, V., Sale, K. L., Singh, S., Adani, F., & Simmons, B. A. (2015). "Comparison of different pretreatments for the production of bioethanol and biomethane from corn stover and switchgrass". Bioresource Technology(0). doi, 10.1016/j.biortech.2015.01.121

Media Citations

Date Article Source

Jan 1 Shaking Hands With the Private Sector Innovation

Jan 9 How to Manipulate Plants to Build a Better Biofuel Scientific American

Jan 12 JBEI ready to license 4 new technologies Biofuels Digest

Jan 13 U.S. Agriculture Secretary Tom Vilsack Visits JBEI KCBS-AM

Jan 13 U.S. Agriculture Secretary Tom Vilsack Visits JBEI KQED-FM

Jan 13 U.S. Agriculture Secretary Tom Vilsack Visits JBEI KGO-AM

Jan 21 JBEI identify microbial metabolism pathway to boost terpene yields Biofuels Digest

Jan 21 Enhancing microbial pathways for biofuel production Phys.org

Jan 21 Enhancing microbial pathways for biofuel production (e) Science News

Jan 26 Breaking Down the Wall Bioenergy Connection

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Patent Applications Inventor(s)

2013-171-02, US 14/598,599 “Generation of heritable chimeric plant traits” Dominique Loque and Yan Liang

3293-03, US 14/606,976 “Yeast artificial positive feedback loop as tool to enhance multigenes metabolic pathways”

Dominique Loque

Licenses Inventor(s)

Bailment/License – Nonexclusive Agreement # 2014-0490, Kiverdi Inc., Joint BioEnergy Institute (JBEI), Lawrence Berkeley National Laboratory for invention # 2014-155 “Plasmids for Ralstonia Synthetic Biology Toolbox”

Changhao Bi, Yung Hsu Tang and Peter Su

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Presentations

Date Division Presenter(s) Title Presentation Location

Jan 5 Feedstocks Loque, D. Use of synthetic biology to improve bioenergy crops.

Glasgow University, Glasgow, UK

Jan 8-10 Fuels Synthesis

King, S.; Chen, J. C.; Hillson, N. J.; Garcia Martin, H.; Goh, E.-B.; and Beller, H. R.

Assessing strategic chromosomal knockouts to enhance methyl ketone synthesis in E. coli for biofuel production

CSU Annual Biotechnology Symposium, San Francisco, CA

Jan 9 Fuels Synthesis

Keasling, J.D. Translating Academic Innovation to Biotechnology Development,

Center for Emerging and Neglected Diseases, University of California, Berkeley, CA

Jan 20 Feedstocks Scheller, H. V. Optimizing plant cell walls for biorefinery applications - using rice and Arabidopsis as model plants

International Rice Research Institute, Los Baños, Philippines

Jan 20-22 Deconstruction Singh, S. Enabling Bio-Economy through Biofuels & Chemicals

Lignofuels 2015, Madrid, Spain

Jan 23 Deconstruction Singh, S. Development & Demonstration of an Integrated Sugar Production Platform based on Ionic Liquids,

Abengoa, Seville, Spain

Jan 23 Feedstocks Ronald, P. The rice immune receptor XA21 recognizes a tyrosine sulfated peptide from aGram-negative bacterium

Carnegie Institution for Science, Department of Plant Biology, Stanford, CA

Jan 24 Fuels Synthesis

Keasling, J. D. Engineering Microbes to Produce our Stuff

UC Emeritus Association, Berkeley, CA

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Jan 27 Deconstruction Singh, S. Enabling Advanced Biofuels & Chemicals

Institute of Catalysis, CSIS, Madrid, Spain

Jan 27 Fuels Synthesis

Keasling, J. D. Engineering Microbes for Production of Chemicals and Fuels

National University of Singapore, Singapore

Jan 29 Fuels Synthesis

Garcia Martin, H. Quantitative metabolic modeling for biofuel synthesis

Joint Genome Institute, Walnut Creek, CA

Jan 29 Deconstruction Singh, S. Green Chemistry in USA La Bioeconomy as Key for the Future Development, Milan, Italy

Jan 29 Fuels Synthesis

Beller, H. R. Exploring microbial metabolic potential of natural systems

LBNL BioSciences Expert Advisory Committee, Berkeley, CA

Jan 29 Feedstocks Mortimer, J. Synthesis and Function of Glycans in Plants

LBNL Biosciences Review, Berkeley

Jan 29-30 Feedstocks Loque, D. Use of Synthetic Biology to Develop Novel Technologies to Improve Crops

LBNL Biosciences Review, Berkeley,

Jan 30 Fuels Synthesis

Hillson, N. J. Enhancing the Design-Build-Test-Learn Cycle for Metabolic Engineering

LBNL BioSciences Expert Advisory Committee, Berkeley, CA,

Jan 31 Feedstocks Jing, B. GONST1 and GONST2 are GIPC-specific GDP-sugar Transporters

Gordon Research Seminar on Plant Lipids, Galveston TX

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Onsite Seminars

Date Type Presenter Title Affiliation

Jan 13 General Seminar Deconstruction Guest

Jing Ke Progress towards Biological Pretreatment – Understanding Varied Lignin Modifying Mechanisms in Natural Systems

Postdoc Interview Candidate

Jan 14 JBEI Seminar Series Deepak Dugar Bio-based processes for high performance polymers: Development and commercialization

Cyclotron Road, LBL

Jan 14 Group Seminar Victor Chubukov Thermodynamics of Cofactor Engineering

Fuels Synthesis Division

Jan 14 Group Seminar Lara Rajeev Regulatory systems in D. vulgaris: nitrite-sensing and tungstate-sensing factors

Fuels Synthesis Division

Jan 16 General Seminar Fuels Synthesis Guest

Prof. Anne Osbourn Unlocking plant metabolic diversity Director, Norwich Research Park Industrial Biotechnology and Bioenergy Alliance, John Innes Centre, Norwich Research Park

Jan 21 Group Seminar Justin Hsia Design and Engineering of Pattern Formation in Gene Expression in E. coli

Fuels Synthesis Division

Jan 21 Group Seminar Sean Poust Fuels Synthesis Division

Jan 22 General Seminar Fuels Synthesis Guest

Professor Dong-Yup Lee Integrated multi-omics profiling and systems modeling for characterizing and designing microbial, plant and mammalian

Department of Chemical and Biomolecular Engineering, National University of Singapore (NUS)

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cells

Jan 22 General Seminar Deconstruction Guest

Timo Schuerg A cell biology and genetics approach to uncover the machinery and mechanisms of cellulase secretion in the model filamentous fungus Neurospora crassa.

Postdoc Interview Candidate

Jan 23 General Seminar Deconstruction Guest

Sara Saedinia Laminated Microfluidic Coupon Systems for Biological Applications

Postdoc Interview Candidate

Jan 28 Group Seminar Anna Lechner Engineering bacterial polyketide synthases in S. cerevisiae

Fuels Synthesis Division

Jan 28 Group Seminar Chris Petzold New developments in JBEI Proteomics

Technology Division

Jan 28 JBEI Seminar Series Nat Echols Automating biological crystallography data analysis for high-throughput applications in Phenix

Fuels Synthesis Division

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Tours and VIP Visits at JBEI

Date Company Attendees

Jan 7 California Energy Commission Commissioner Janea Scott, Jim Bartridge, Michelle Chester and O'Shea Bennett

Jan 13 USDA Tom Vilsack, Sec. of Agrictulture; Matthew McKenna, Special Advisor and Matt Paul, Director of Communications

Jan 16 Zhongguancun Science Park, China Xiaofeng Sun and Administrative Committee Delegation

Jan 16 Norwich Research Park Industrial Biotechnology and Bioenergy Alliance, John Innes Centre, Norwich Research Park, UK

Anne Osbourn, Director

Jan 16 La Ka Shing Foundation Solina Chau, Director

Jan 27 Piedmont High 32 students

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Industry Interactions

Date Company / Contact

Jan 12 ALS Biosciences / Sebastián Scaparro

Area of interest: ABPDU

Jan 13 Monsanto Growth Ventures / John Hamer

Area of interest: IAC and BOB

Jan 13 Cooley LLC / Fred Dorey

Jan 15 Futuragene / Daniel Siegel

Area of interest: Reporting, potential new technology areas

Jan 16 Norwich Research Park Industrial Biotechnology & Bioenergy Alliance / Prof. Anne Osbourn

Jan 16 Arzeda / Andrew Ban and Daniela Grabs

Area of interest: DOE TTO SBIR Grant

Jan 21 Technology Holding LLC / Mukund Karanjikar

Area of interest: STTR

Jan 26 Mass Insight / Tom Gilman

Area of interest: License negotiation

Jan 27 Ajinomoto / Erika Yoshida

Area of interest: Preparation for Ajinomotoo visit

Jan 27 Riffyn / Timothy Gardner

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Area of interest: Negotiating procurement agreement

Jan 28 DSM Venturing / Greg McParland

Jan 29 Virdia / Robert Jansen and Maya Skubatch

Area of interest: License agreement

Jan 31 Kiverdi / Lisa Dyson

Area of interest: Bailment agreement

Jan (multiple)

Total / Florence Mingardon, Angelique Chanal, Olivier-A. Pernet, Hubert Le-Gallic and Renaud Maillard

Area of interest: Option negotiation

Jan (multiple)

Afingen / Ai Oikawa and Henrik Scheller

Area of interest: Option agreements

Jan (multiple)

Technology Holding LLC / Mukund Karanjikar

Area of interest: STTR

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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 32

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

Sept. 2015 32

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

Sept. 2015 32

Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 40

Characterization of novel GT activities (SB) Sept. 2015 40

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 40

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

Sept. 2015 28

Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 34

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

Sept. 2015 33

Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 30

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

Sept. 2015 10

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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 32

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

Sept. 2015 32

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

Sept. 2015 35

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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 50

Complete characterization of lignin streams from various IL pretreatment process configurations

July 2015 40

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

Aug. 2015 40

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 30

Enzyme Optimization

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

Feb. 2015 90

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 70

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 35

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

Sept. 2015 40

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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 80

Establish complementary thermophilic cellulase cocktail focusing on crystalline substrates

July 2015 50

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

Sept. 2015 50

Fungal Biotechnology

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

Feb. 2015 90

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

April 2015 55

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

July 2015 45

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

Sept. 2015 40

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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 33

In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 33

Optimization of Hydrocarbon Biosynthetic Pathways

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

Sept. 2015 33

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

Sept. 2015 35

Genes encoding isoprenoid pathway integrated into E. coli chromosome

Sept. 2015 33

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

Sept. 2015 33

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 60

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

Sept. 2015 20

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 39

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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 34

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

Sept. 2015 34

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 80

Perform flux analysis of S. cerevisiae sip1 strain June 2015 90

Implement interactive metabolic engineering on MvT Sept. 2015 65

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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 35

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

Sept. 2015 35

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

Sept. 2015 33

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

July 2015 40

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

Sept. 2015 40

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

Sept. 2015 40

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

Sept. 2015 50

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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 33

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

Sept. 2015 33

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

Sept. 2015 50

Characterize lignin degrading enzymes in collaboration with GLBRC Sept. 2015 85

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

Sept. 2015 20

Synthetic Bio Informatics

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

Sept. 2015 34

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

Sept. 2015 34

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

Sept. 2015 34

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Dashboard – January 2015 - DOE

FY 2015 Dashboard For Period: January 1 – 31, 2015

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Milestones

Operations Management Division

Area Initiatives Milestone/Deliverables Due % Complete

Intellectual Property Management

Generate >10 inventions Sept. 2015 71

Educate researchers about the tech transfer process Sept. 2015 35

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 34

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 33

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

Sept. 2015 33

Business Development Outreach

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

Sept. 2015 34

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

Sept. 2015 35

Industry Advisory Committee

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

Sept. 2015 26

Industry Partnership Program

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

Sept. 2015 34

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Dashboard – January 2015 - DOE

FY 2015 Dashboard For Period: January 1 – 31, 2015

21 / 21

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 33

Annual JBEI Conference

Annual JBEI Retreat Sept. 2015 44

Human Resources Staffing for year 8 complete Sept. 2015 33