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DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress Report June 2015 Fiscal Year: 2015 Year / Period: Year 8 / Month 9 / June 1 - 30, 2015 Department of Energy’s Joint BioEnergy Institute is supported by the US Department of Energy, Office of Science, Office of Bi ological 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 June 2015, ninth month of fiscal year 2015: Item Count Highlights Publications in Print 4 "A Versatile Microfluidic Device for Automating Synthetic Biology", ACS Synth Biol Patent Applications 2 “Rapid Discovery an screening of Enzyme Activity Using Mass Spectrometry” Agreements 3 CRADA Option with Total New Energies USA, Inc, for Biological Hydrogenation (CRADA IP) between Total Energies Nouvelles Activités USA SAS and LBNL on behalf of JBEI Media Citations 5 Why we have a Joint BioEnergy Institute: the story of ionic liquids, Biofuels Digest Outreach Interactions 35 Education: 6, Public: 3 and Scientific Community: 26. On-Site Seminars 13 Dr. Ben Harvey from Naval Air Warfare Center, China Lake gave a seminar on High Performance Renewable Fuels: A Synergistic Intersection of Biology and Chemical CatalysisIndustry Interactions 24 Interactions with Beta Renewables and Rosa / Rebecca Baillie FY15 Milestones Milestones completed: - Fuels Synthesis: Perform flux analysis of S. cerevisiae sip1 strain - Technology: Apply HT NIMS screen for fatty acids based fuel molecules (e.g. FAMK) in collaboration with the Fuels Division - Technology: Test expression of multiple GT clones in insect cell platform to produce quantities of protein for crystallization trials Milestones delayed: - Fuels Synthesis: “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” - Technology: “Structural characterization of Fatty Acid Synthase and other large complexes by single particle cryo electron microscopy”

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Page 1: DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress ... · 2019-08-16 · DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress

DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute

Monthly Progress Report – June 2015

Fiscal Year: 2015

Year / Period: Year 8 / Month 9 / June 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 June 2015, ninth month of fiscal year 2015:

Item Count Highlights

Publications in Print 4 "A Versatile Microfluidic Device for Automating Synthetic Biology", ACS Synth Biol

Patent Applications 2 “Rapid Discovery an screening of Enzyme Activity Using Mass Spectrometry”

Agreements 3 CRADA Option with Total New Energies USA, Inc, for Biological Hydrogenation (CRADA IP) between Total Energies Nouvelles Activités USA SAS and LBNL on behalf of JBEI

Media Citations 5 “Why we have a Joint BioEnergy Institute: the story of ionic liquids”, Biofuels Digest

Outreach Interactions 35 Education: 6, Public: 3 and Scientific Community: 26.

On-Site Seminars 13 Dr. Ben Harvey from Naval Air Warfare Center, China Lake gave a seminar on “High Performance Renewable Fuels: A Synergistic Intersection of Biology and Chemical Catalysis”

Industry Interactions 24 Interactions with Beta Renewables and Rosa / Rebecca Baillie

FY15 Milestones Milestones completed:

- Fuels Synthesis: Perform flux analysis of S. cerevisiae sip1 strain

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

- Technology: Test expression of multiple GT clones in insect cell platform to produce quantities of protein for crystallization trials

Milestones delayed:

- Fuels Synthesis: “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”

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

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Publications

In Print

Leverenz, R. L., Sutter, M., Wilson, A., Gupta, S., Thurotte, A., Bourcier de Carbon, C., Petzold, C. J., Ralston, C., Perreau, F., Kirilovsky, D., & Kerfeld, C. A. (2015). "A 12 Å carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection". Science, 348(6242), 1463-1466. doi, 10.1126/science.aaa7234 http://www.ncbi.nlm.nih.gov/pubmed/26113721

Schicklberger, M., Shapiro, N., Loque, D., Woyke, T., & Chakraborty, R. (2015). "Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte". Genome Announc, 3(3). doi, 10.1128/genomeA.00607-15 http://www.ncbi.nlm.nih.gov/pubmed/26067957

Shih, S. C., Goyal, G., Kim, P. W., Koutsoubelis, N., Keasling, J. D., Adams, P. D., Hillson, N. J., & Singh, A. K. (2015). "A Versatile Microfluidic Device for Automating Synthetic Biology". ACS Synth Biol. doi, 10.1021/acssynbio.5b00062 http://www.ncbi.nlm.nih.gov/pubmed/26075958

Yang, Y. R., Song, Y. Y., Scheller, H. V., Ghosh, A., Ban, Y. H., Chen, H., & Tang, M. (2015). "Community structure of arbuscular mycorrhizal fungi associated with Robinia pseudoacacia in uncontaminated and heavy metal contaminated soils". [Article]. Soil Biology & Biochemistry, 86, 146-158. doi, DOI 10.1016/j.soilbio.2015.03.018 http://www.sciencedirect.com/science/article/pii/S0038071715001194

Patent Applications Inventor(s)

3262-05, US14/651546 “Rapid Discovery an screening of Enzyme Activity Using Mass Spectrometry”, inventors

Trent R Northen, Kai Deng, Tristan de Rond, Pamela Patricia Peralta-Yahya, Xiaoliang Cheng and Jay Keasling

3265-03, US14/650,506 “Renewable Aromatics from Lignocellulosic Lignin” Blake A. Simmons, Seema Singh and Patanjali Varanasi

Agreements

2015-0156, CRADA Option with Total New Energies USA, Inc, for Biological Hydrogenation (CRADA IP) between Total Energies Nouvelles Activites USA SAS and LBNL on behalf of JBEI (option)

2015-0380, MTA / Option with Riffyn, Inc. for Development and Evaluation (partnership agreement and option)

2015-0493, Beta Test Site Agreement with Agilent, for Evaluation. (partnership agreement, not a license or option)

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Media Citations

Date Article Source

June 15 Why we have a Joint BioEnergy Institute: the story of ionic liquids Biofuels Digest

June 16 Scientists hit the sweet spot on sugar conversion for biofuels Bio Buzz

June 26 Microfluidic Device Mixes And Matches DNA For Synthetic Biology Chemical & Engineering News

June 26 Magnetic Attraction EMSL

June 29 Magnetic Attraction Newswise

Outreach – Education

Date Presenters Audience or Presentation Title Activity Location

June 3 Peter Matlock, Margaret Brown, Victor Chubukov and Jennifer Hiras

Annual Bio-Link Fellows Forum Tour On-site

June 4 Irina Silva Annual Bio-Link Fellows Forum Gala Dinner Networking Off-site

June 9 Irina Silva and Peter Matlock

Ellyn Daugherty, Biotechnology Educator Meeting On-site

June 26 Chris Petzold, Dominique Loque, Garima Goyal, Kamrun Zargar, Peter Matlock and Sarah Richardson

Ellyn Daugherty, Biotechnology Educator Meeting/Interviews On-site

June 30 Jenny Mortimer and Irina Silva

Synberc Community College Tour On-site

June 30 Jennifer Hiras, Irina Silva and Peter Matlock

Berkeley City College, Biotech Dept. Tour/Meeting On-site

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Outreach – Public

Date Presenters Audience or Presentation Title Activity Location

June 12 Nurgul Kaplan and Tim Lease

LBNL, OCFO, Procurement & Property Group

Tour On-site

June 19 Blake Simmons Congressman Desaulnier Presentation LBNL

June 23 Aindrila Mukhopadhyay, Chris Petzold, Diane Pierotti, Dominique Loqué, Nathan Hillson and Nick Everson

Lawrence Hall of Science Meeting On-site

Outreach – Scientific Community

Date Presenters Audience or Presentation Title Activity Location

June 1-5 Henrik Scheller Nucleotide Sugar Transporters And Their Role In Cell Wall Biosynthesis

Presentation The 5th Pan-American Plant Membrane Biology Workshop, San Pedro de Atacama, Chile

June 1-5 Jennifer Mortimer GIPC biosysnthesis and function Presentation The 5th Pan-American Plant Membrane Biology Workshop, San Pedro de Atacama, Chile

June 1-5 Taek Soon Lee, Aram Kang, et al.

Advanced pathways for microbial production of branched C5 alcohols

Presentation Terpnet 2015, Vancouver, Canada

June 8 Henrik Scheller Optimizing plant polysaccharide biosynthesis for biofuel production

Presentation University Andres Bello, Santiago, Chile

June 8 Jennifer Mortimer Xylan biosysnthesis Presentation University Andres Bello, Santiago, Chile

June 9 Nathan Hillson FutureBio Foundry for Advanced Fuels and Chemicals Production

Presentation 5th Annual Multi-use Technology Symposium,

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Ridgecrest, CA

June 11-12 Hector Garcia Martin, Jennifer Gin, Chris Shymansky, Amit Ghosh, Garrett Birkel, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, and Jay Keasling

Quantitative Metabolic Modeling at Fuel Synthesis Division (JBEI)

Presentation SEED 2015, Boston, MA

June 11-12 Garima Goyal, Jorge Alonso-Gutierrez, Aram Kang, Taek Soon Lee, Jay Keasling, and Nathan Hillson

PIACE: Parallel Integration and Chromosomal Expansion of Biofuels Pathways in E. coli

Presentation SEED 2015, Boston, MA

June 11-12 Lisa Simirenko, Miranda Harmon-Smith, Axel Visel, Edward M. Rubin and Nathan Hillson

The Joint Genome Institute’s Synthetic Biology Internal Review Process

Presentation SEED 2015, Boston, MA

June 11-12 Lisa Simirenko and Nathan Hillson

BLiSS: Black List Sequence Screening pipeline

Presentation SEED 2015, Boston, MA

June 11-12 Ernst Oberortner, Jan-Fang Cheng, Nathan Hillson and Samuel Deutsch

In silico Preparation of DNA Sequences for Synthesis

Presentation SEED 2015, Boston, MA

June 11-12 Hector A. Plahar, Lisa Simirenko, Garima Goyal, Joanna Chen, Manjiri Tapaswi, Nina Stawski, Jacob Coble, Paul D. Adams, Jay

DIVA: More Science, Less DNA Construction Presentation SEED 2015, Boston, MA

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Keasling and Nathan Hillson

June 11-12 Jacqueline Quinn, Robert Sidney Cox III, Aaron Adler, Jacob Beal, Swapnil Bhatia, Yizhi Cai, Joanna Chen, Kevin Clancy, Michal Galdzicki, Nathan J. Hillson, Nicolas Le Novere, Akshay Maheshwari, James Alastair McLaughlin, Chris Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Larisa Soldatova, Guy-Bart Stan, Neil Swanston, Anil Wipat and Herbert M. Sauro

SBOL Visual aids rapid communication of variant synthetic DNA designs

Presentation SEED 2015, Boston, MA

June 11-12 Sangeeta Nath, Cindi Hoover, Katherine Louie, Ben Bowen, Eddy Rubin, Jay Keasling, Chris Petzold, Trent Northen, Jeffrey Kim, Nathan Hillson and Samuel Deutsch

Construction and characterization of a fully refactored Actinorhodin biosynthetic cluster

Presentation SEED 2015, Boston, MA

June 11-12 Brian Olson, Sam Deutsch, Chris J. Petzold, Hector Garcia-Martin, Vivek K. Mutalik, Blake A.

Automated Statistical Design of Experiments for Metabolic Engineering

Presentation SEED 2015, Boston, MA

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Simmons, Trent R. Northen, Paul D. Adams, Eddy M. Rubin, Jay D. Keasling, Adam Arkin, Nathan Hillson, and Paramvir S. Dehal

June 11-12 Brian Olson, Sam Deutsch, Chris J. Petzold, Hector Garcia-Martin, Vivek K. Mutalik, Blake A. Simmons, Trent R. Northen, Paul D. Adams, Eddy M. Rubin, Jay D. Keasling, Adam Arkin, Nathan Hillson, and Paramvir S. Dehal

Targets of Opportunity: Hypergraph Analysis of the Retrosynthetic Design Space

Presentation SEED 2015, Boston, MA

June 11-12 Hector A. Plahar, Oge Nnadi, Joanna Chen, Timothy Ham, Zinovii Dmytriv, Paul D. Adams, Jay D. Keasling and Nathan Hillson

ICE: A Distributed and Interconnected Biological Part Registry

Presentation SEED 2015, Boston, MA

June 11-12 Philip C. Gach, Steve C.C. Shih, Jess Sustarich, Jay D. Keasling, Paul D. Adams, Nathan J. Hillson and Anup K. Singh

Towards Synthetic Biology in a Chip: An Integrated Digital Microfluidic Platform for Transformation, Culture and Expression

Presentation SEED 2015, Boston, MA

June 11-12 William Morrell, Nathaniel Echols, Garrett Birkel, Ian

The JBEI Experiment Data Depot Presentation SEED 2015, Boston, MA

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Vaino, Nathan J. Hillson, and Hector Garcia-Martin

June 16 Henrik Scheller Biofuels and biomass - biosynthesis of plant cell wall polysaccharides

Presentation Technical University of Denmark, Lyngby, Denmark

June 17 Jay Keasling Carbon-neutral Transportation Fuels from Plant Biomass

Presentation Legislative Committee Presentation, State Capitol, Sacramento, CA

June 22-24 Jennifer Hiras, Yu-Wei Wu, Susannah G. Tringe, Carrie Nicora, Joshua Aldrich, Errol Robinson, Jon Jacobs, Blake Simmons and Steven Singer

The unexpected importance of actinobacterial GH12 in hydrolysis of crystalline cellulose

Presentation 16th Annual UC Systemwide Bioengineering Symposium, University of California - Santa Cruz, CA

June 23 Ben Wu, Blake Simmons

Sandia Govt. Relations Tour On-site

June 23 Jay Keasling Engineering Microbial Metabolism for Production of Chemicals

Presentation Enabling Technologies for Eukaryotic Synthetic Biology Conference, Heidelberg, Germany

June 24 Jay Keasling Synthetic Biology for Synthetic Chemistry Presentation RWTH-ERS Synthetic Biology Workshop, Aachen, Germany

June 25 Jay Keasling Engineering Microbial Metabolism for Synthesis of Advanced Biofuels

Presentation Tailor-Made Fuels from Biomass Conference, RWTH - Aachen University, Aachen, Germany

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Onsite Seminars

Date Type Presenter Title Affiliation

June 3 Group Seminar Itay Budin Functional roles for membrane fluidity in JBEI model organisms

Fuels Synthesis Division

June 3 General Seminar Deconstruction Guest

Prof. Steve Hallam

From Microbiomes to BioRefineries: A microbial community paradigm for energy and materials innovation

University of British Columbia, Department of Microbiology & Immunology, Life Sciences Institute

June 10 Group Seminar Jingwei Zhang Microbial lactam biosynthesis and high through-out screening for improving lactam production

Fuels Synthesis Division

June 10 General Seminar Technology/Commercialization Guest

Prof. Toby Freedman

Careers in the Life Sciences -Finding Your Way

Synapsis Search

June 11 Group Seminar Chris Shymansky Progress on the application of two-scale 13C metabolic flux analysis in yeast

Fuels Synthesis Division

June 11 Group Seminar Jeff Wong Recent advancements in elucidating prostratin biosynthesis

Fuels Synthesis Division

June 16 General Seminar Deconstruction Guest

Jamie Meadows Carnitine and O-acylcarnitines in Pseudomonas aeruginosa: transport, metabolism, and regulation

Univ. of Vermont, College of Medicine

June 17 JBEI Seminar Ee-Been Goh Development of a JBEI fuel: Engineering E. coli for methyl ketone overproduction

Fuels Synthesis Division

June 17 General Seminar Deconstruction Guest

Shivani Garg Towards bio-based chemicals using novel 3-Ketoacyl-ACP

Iowa State University

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Synthase III (KASIII) enzymes

June 24 JBEI Seminar Corinne Scown Closing the gap between basic research, techno-economic analysis, and life-cycle assessment for bio-based fuels and products

Deconstruction Division

June 24 Group Seminar Jacquelyn Blake-Hedges

Toward understanding the region-specificity of methylation in polyketide synthase-derived branched fatty acids

Fuels Synthesis Division

June 24 Group Seminar Victor Chubukov Decoupling growth and metabolism under nitrogen limitation in E. coli

Fuels Synthesis Division

June 30 General Seminar Technology/Commercialization Guest

Dr. Ben Harvey High Performance Renewable Fuels: A Synergistic Intersection of Biology and Chemical Catalysis

Alternative Fuels Lead Chemistry Branch, Naval Air Warfare Center, Weapons Division, China Lake

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Industry Interactions

Date Company / Contact

June 4 Seed Central / Francois Korn

June 5 Naval Air Warfare Center, China Lake

June 5 BioKimika (spin-off of Technology Holding) / Mukund Karanjikar

June 10 Genomatica / Mark Burk

June 11 Technology Holding Co. / Mukund Karanjikar

June 11 Agilent / Fred Ernani, Leo Bonilla and Steffen Mueller

June 11 BioKimika (spin-off of Technology Holding) / Mukund Karanjikar

June 11 Cooley LLP / Fred Dorey

June 15 Innovation Assoc. / D. Palmintera

June 16 Rosa & Co. / Rebecca Baillie

June 17 Verdezyne / Brian Conn

June 18 Lanzatech / Sean Simpson

June 19 Bill Hogan

June 19 USDA, regarding Bridgestone / Colleen McMahan

June 22 Firmenich / Laurent Daviet

June 23 ADM / Mitchell Schultz

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June 23 Calysta / Lori Giver

June 23 USDA / H. Baumes and Todd Campbell

June 23 Beta Renewables / Michele Rubino

June 23 Poet / Dan Cummings

June 23 Total / Florence Mingardon

June 23 Rosa / Ron Beaver

June 29 Naval Air Warfare Center, China Lake / Ben Harvey

Multiple Visolis / Deepak Dugar and Brian Lee

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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 82

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

Sept. 2015 75

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

Sept. 2015 75

Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 77

Characterization of novel GT activities (SB) Sept. 2015 82

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 85

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

Sept. 2015 73

Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 82

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

Sept. 2015 75

Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 75

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

Sept. 2015 68

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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 75

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

Sept. 2015 77

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

Sept. 2015 75

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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 90

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

Aug. 2015 85

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 80

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 60

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

Sept. 2015 80

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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 98

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

Sept. 2015 96

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 88

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

Sept. 2015 75

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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 75

In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 75

Optimization of Hydrocarbon Biosynthetic Pathways

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

Sept. 2015 75

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

Sept. 2015 84

Genes encoding isoprenoid pathway integrated into E. coli chromosome

Sept. 2015 77

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 80

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 60

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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 75

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

Sept. 2015 75

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 sip1 strain June 2015 100

Implement interactive metabolic engineering on MvT Sept. 2015 87

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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 87

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 74

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

July 2015 90

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

Sept. 2015 90

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

Sept. 2015 85

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

Sept. 2015 85

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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 80

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

Sept. 2015 80

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 55

Synthetic Bio Informatics

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

Sept. 2015 75

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

Sept. 2015 75

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

Sept. 2015 75

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Dashboard - June 2015 - DOE

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

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Milestones

Operations Management Division

Area Initiatives Milestone/Deliverables Due % Complete

Intellectual Property Management

Generate >10 inventions Sept. 2015 96

Educate researchers about the tech transfer process Sept. 2015 87

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 74

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 82

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

Sept. 2015 80

Business Development Outreach

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

Sept. 2015 87

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

Sept. 2015 77

Industry Advisory Committee

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

Sept. 2015 95

Industry Partnership Program

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

Sept. 2015 87

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Dashboard - June 2015 - DOE

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

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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 75

Annual JBEI Conference

Annual JBEI Retreat Sept. 2015 95

Human Resources Staffing for year 8 complete Sept. 2015 75