Upload
others
View
4
Download
0
Embed Size (px)
Citation preview
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”
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
2 / 22
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)
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
3 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
4 / 22
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,
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
5 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
6 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
7 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
8 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
9 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
10 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
11 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
12 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
13 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
14 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
15 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
16 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
17 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
18 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
19 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
20 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
21 / 22
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
Dashboard - June 2015 - DOE
FY 2015 Dashboard For Period: June 1 - 30, 2015
22 / 22
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