DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress Report – April 2015 Fiscal Year: 2015 Year / Period: Year 8 / Month 7 / April 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 April 2015, seventh month of fiscal year 2015: Item Count Highlights Publications in Print 6 "Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks", BioEnergy Research Invention Disclosures 3 “Method and device for tracking of droplets” Patent Applications 3 “Modified host cells having tolerance to alpha-olefins” Media Citations 3 “Liquid salt, solid science”, Berkeley Science Review Outreach Interactions 52 Education: 6, Public: 2 and Scientific Community: 44. 22 presentations were given at the 37 th Annual Symposium on Biotechnology for Fuels and Chemicals held in San Diego, April 27-30, 2015. On-Site Seminars 16 Prof. Lucy Shapiro from the Developmental Biology at the Stanford University School of Medicine gave a seminar on "Regulatory Architecture of a Bacterial Cell Cycle. Industry Interactions 16 Interactions with California Energy Commission and LanzaTech. FY15 Milestones Milestones completed: - Deconstruction: “Initiate ChIP-Seq analysis of histone modifications in A. niger aimed at identifying epigenetic determinants of high productivity” - Fuels Synthesis: “Three enzymes in S. cerevisiae glycolytic pathway replaced and impact on fatty acid- derived fuel tested” 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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DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute
Monthly Progress Report – April 2015
Fiscal Year: 2015
Year / Period: Year 8 / Month 7 / April 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 April 2015, seventh month of fiscal year 2015:
Item Count Highlights
Publications in Print 6 "Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks", BioEnergy Research
Invention Disclosures 3 “Method and device for tracking of droplets”
Patent Applications 3 “Modified host cells having tolerance to alpha-olefins”
Media Citations 3 “Liquid salt, solid science”, Berkeley Science Review
22 presentations were given at the 37th Annual Symposium on Biotechnology for Fuels and Chemicals held in San Diego, April 27-30, 2015.
On-Site Seminars 16 Prof. Lucy Shapiro from the Developmental Biology at the Stanford University School of Medicine gave a seminar on "Regulatory Architecture of a Bacterial Cell Cycle.
Industry Interactions 16 Interactions with California Energy Commission and LanzaTech.
FY15 Milestones Milestones completed:
- Deconstruction: “Initiate ChIP-Seq analysis of histone modifications in A. niger aimed at identifying epigenetic determinants of high productivity”
- Fuels Synthesis: “Three enzymes in S. cerevisiae glycolytic pathway replaced and impact on fatty acid-derived fuel tested”
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”
Baker, S. E., Schackwitz, W., Lipzen, A., Martin, J., Haridas, S., LaButti, K., Grigoriev, I. V., Simmons, B. A., & McCluskey, K. (2015). "Draft Genome Sequence of Neurospora crassa Strain FGSC 73". Genome Announc, 3(2). doi, 10.1128/genomeA.00074-15 http://www.ncbi.nlm.nih.gov/pubmed/25838471
Haushalter, R. W., Groff, D., Deutsch, S., The, L., Chavkin, T. A., Brunner, S. F., Katz, L., & Keasling, J. D. (2015). "Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production". Metab Eng. doi, 10.1016/j.ymben.2015.04.003 http://www.ncbi.nlm.nih.gov/pubmed/25887638
Li, C., Tanjore, D., He, W., Wong, J., Gardner, J. L., Thompson, V. S., Yancey, N. A., Sale, K. L., Simmons, B. A., & Singh, S. (2015). "Scale-Up of Ionic Liquid-Based Fractionation of Single and Mixed Feedstocks". BioEnergy Research, 1-10. doi, 10.1007/s12155-015-9587-0 http://dx.doi.org/10.1007/s12155-015-9587-0
Shi, J., George, K. W., Sun, N., He, W., Li, C., Stavila, V., Keasling, J. D., Simmons, B. A., Lee, T. S., & Singh, S. (2015). "Impact of Pretreatment Technologies on Saccharification and Isopentenol Fermentation of Mixed Lignocellulosic Feedstocks". BioEnergy Research, 1-10. doi, 10.1007/s12155-015-9588-z http://dx.doi.org/10.1007/s12155-015-9588-z
Siegel, J. B., Smith, A. L., Poust, S., Wargacki, A. J., Bar-Even, A., Louw, C., Shen, B. W., Eiben, C. B., Tran, H. M., Noor, E., Gallaher, J. L., Bale, J., Yoshikuni, Y., Gelb, M. H., Keasling, J. D., Stoddard, B. L., Lidstrom, M. E., & Baker, D. (2015). "Computational protein design enables a novel one-carbon assimilation pathway". Proc Natl Acad Sci U S A, 112(12), 3704-3709. doi, 10.1073/pnas.1500545112 http://www.pnas.org/content/112/12/3704.full.pdf
Walley, J., Xiao, Y., Wang, J. Z., Baidoo, E. E., Keasling, J. D., Shen, Z., Briggs, S. P., & Dehesh, K. (2015). "Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum". Proc Natl Acad Sci U S A. doi, 10.1073/pnas.1504828112 http://www.ncbi.nlm.nih.gov/pubmed/25922532
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Media Citations
Date Article Source
April 12 3 Takeaways From My Recent Visit to Amyris Inc., Fox Business Fox Business
April 13 Proteomic Technologies Fueling Market Potential of Biofuels like Switchgrass BCC Research
April 24 Liquid salt, solid science Berkeley Science Review
Invention Disclosures Inventor(s)
2015-094 - “Strategy for fractionation and separation of constituents of non-derivatized 'native' lignin”
Chijioke Joshua, Blake A. Simmons and Steven W. Singer
2015-095 - “Method and device for tracking of droplets” Anup K Singh and Jess Sustarich
2015-096 - “Design and developmet of Acidic to basic ILs for conventional and modified hybrid Ionic liquid pretreatment process of lignocellulosic materials and lignin catalysis”
Tanmoy Dutta, Parthasarathi Ramakrishnan, Blake A. Simmons, Seema Singh and Jian Sun
Patent Applications Inventor(s)
2013-181-02, PCT/US2015/028296 “Modified host cells having tolerance to alpha-olefins”
Florence Mingardon; Angelique Chanal; Aindrila Mukhopadhyay and Camille Clement
2014-028-02, US 62/142,838 “Induction of Latex Accumulation in Rubber-Producing Shrubs” Henrik Vibe Scheller and Solomon Stonebloom
2014-028-02, US 62/147,461 “A Host Cell Modified to Produce 2-Pyrrolidone” Jay Keasling and Jingwei Zhang
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Outreach – Education
Date Presenters Audience or Presentation Title Activity Location
April 13 Amanda Reider, Shaila Kotadia
LBL Spring 2015 Interns Tour On-site
April 15 Sarah Richardson Hayward High School Other Off-site
April 23 Irina Silva, Phil Gach, Mi Yeon Lee, Clarabelle Cheng-Yue and Melissa Nhan
LBL's Daughters and Sons to Work Day Event Off-site
April 24 Peter Matlock National Visiting Committee, Bio-Link consortium
Other Off-site
April 29 Sarah Richardson Dinner with a Scientist Event Off-site
April 29 Taek Soon Lee UCSF and Stanford University Tour On-site
Outreach – Public
Date Presenters Audience or Presentation Title Activity Location
April 4 Huu Tran Nuclear Science Day 2015 for Girl Scouts and Boy Scouts
Event Off-site
April 18 Irina Silva, Yi-Lin Tsai, Leanne Chan and Virginia Tartaglio
Cal Day 2015 Event Off-site
Outreach – Scientific Community
Date Presenters Audience or Presentation Title Activity Location
April 2 Deepak Dugar California Energy Commission Tour On-site
April 3 Nathan Hillson NUS Tour On-site
April 3 Nathan Hillson, Jim Kirby LanzaTech Tour On-site
April 6 Mi Yeon Lee UCB Tour On-site
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April 7 Jeff Kimbrel and Jennifer Hiras
Coding and Big Data: Tools for solving environmental problems
Presentation Berkeley City College, STEM Careers Lunch Talks, Berkeley, CA
April 8 Jeemeng Lao Nasa Ames Research Tour On-site
April 8 Anna Lechner Max Planck Institute for Medical Research Tour On-site
April 13 Nathan Hillson Twist Biosciences Tour On-site
April 13 Seema Singh Next-gen Technologies for Enabling Future Bioeconomy
Presentation 1st Karelia Symposium - Next Generation Wood, University of Eastern Finland, Joensuu, Finland
April 12 Jay Keasling Synthetic Biology for Synthetic Chemistry, Is a PhD for Me?
Presentation University of California, Berkeley. Berkeley, CA
April 13 Jay Keasling Microbial Production of Artemisinin Presentation Universities Allied for Essential Medicines, University of California Berkeley, Berkeley, CA
April 15 Jay Keasling Life 2.0: Engineering Biology for Sustainable Development
Presentation Abbott Lecture, Rensselaer Polytechnic Institute, Troy, New York
April 16 Jay Keasling Advanced Fuels from Advanced Plants Presentation Abbott Lecture, Rensselaer Polytechnic Institute, Troy, New York
April 16 Anthe George Total Tour On-site
April 20 Nathan Hillson Mills College Tour On-site
April 21 Jennifer Hiras. Climate Change: Effects on microbial biodiversity and society
Presentation Berkeley City College, STEM Careers Lunch Talks, Berkeley, CA
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April 22 Michael Thelen LLNL/UCB Seminar On-site
April 23 Jay Keasling Total Tour On-site
April 24-May 1
Aindrila Mukhopadhyay Engineering Microbial Solvent Tolerance using efflux pumps
Presentation Gordon research Conference, Lucca, Italy
April 27-28
Henrik Scheller Engineering plants for improved biofuels production
Presentation The Berkeley – Tel Aviv Workshop on Bioeconomy, Tel Aviv, Israel
April 27-30
Chijioke J. Joshua, Blake Simmons and Steven W. Singer
Elucidating the effect of aggregation of lignin particles on aqueous characteristics of lignin
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Weihua Wu, William Tran, Craig A, Taatjes and John M. Gladden
Functional characterization of terpene synthases from four endophytic xylariaceae
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
N.V.S.N. Murthy Konda, Gabriella Papa, Blake Simmons, Daniel Klein-Marcuschamer
Integrated biorefinery for the production of biofuels and terpenes from loblolly pine: A technoeconomic assessment
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Ziyu Dai, Shuang Deng, David E. Culley, Kenneth S. Bruno and Jon K. Magnuson
Agrobacterium tumefaciens-mediated transformation of the oleaginous yeast genus Lipomyces
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Joshua T. Claypool, Blake Simmons, Steve W. Singer, Christopher W. Simmons and Jean VanderGheynst
Time-course transcriptome of Bacillus coagulans in the presence of 1-ethyl-3-methylimidazolium acetate
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Douglas A. Higgins, Trey K. Sato, Thomas L. Ruegg, Blake Simmons, Steven Singer and Michael P. Thelen
Ionic liquid tolerance in microbes Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
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April 27-30
David W. Reed, Taya Feldman, Dayna L. Daubaras, Abdul A. N. Saqib, Kenneth L. Sale, E. Tim Davies and Vicki S. Thompson
Development of a high temperature biological process for efficient butanol production
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Anne Ware, Gabriella Papa, James Kirby, Robert Sykes, Blake Simmons, Gary Peter and Mark Davis
Advancements towards the production of biofuels from loblolly pine: Increases in terpenoid content and development of innovative and high-throughput extractions and analysis of terpenoids
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Scott Baker, Kevin McCluskey, Blake Simmons, Jed Lynn, John M. Gladden, and Jon Magnuson
Genomics and regulation of fungal enzyme secretion
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
James R Collett, Aye Meyer, Yunhua Zhu, Erik R. Hawley, Ziyu Dai, Mark G. Butcher, Susanne Jones and Jon K. Magnuson
Bioreactor performance data and preliminary biorefinery techno-economics for the production of distillate fuels via bioconversion of pretreated corn stover by Lipomyces starkeyi,
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Sara Pace, Shannon Ceballos, Duff Harrold, Whitney Trower, Blake A. Simmons, Steven W. Singer, Michael P. Thelen and Jean VanderGheynst
Thermophilic enrichment of microbial communities in the presence of tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate ionic liquids
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Michael Kent, Isaac Avina, Noppandon Sathitsuksanoh, Nadeya Rader, Jerilyn A. Timlin, Ronan Polsky, Bryce Ricken, Kenneth L. Sale and Blake Simmons
New assay for lignin depolymerization based on lignin films
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
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April 27-30
Jose A. Perez-Pimienta, Carlos A. Flores-Gomez, Héctor A. Ruiz, Noppadon Sathitsuksanoh, Venkatesh Balan, Leonardo Sousa, Bruce Dale, Seema Singh and Blake Simmons
A comparative evaluation of agave bagasse in function of autohydrolysis, AFEX and ionic liquid pretreatment
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
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 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Feng Xu, Ning Sun, Noppadon Sathitsuksanoh, Vicki S. Thompson, Chenlin Li, Deepti Tanjore, Todd Pray, Blake Simmons and Seema Singh
Impact of municipal solid waste paper mix as a blending agent on enzymatic hydrolysis and acidolysis
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Steven Singer, Blake Simmons, John M. Gladden, Jennifer Hiras, Evelyn Denzel, Firehiwot Tachea, Todd Pray, Jeff Kimbrel, Saori Campen and Jon Magnuson
Development of a versatile multicomponent glycoside hydrolase mixture from thermophilic bacteria for high temperature biomass saccharification
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Ning Sun, Feng Xu, Noppadon Sathitsuksanoh, Vicki S. Thompson, Kara Cafferty, Chenlin Li, Deepti Tanjore, Akash Narani, Todd Pray, Blake Simmons and Seema Singh
Blending municipal solid waste with corn stover for sugar production using ionic liquid process
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
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April 27-30
Akash Narani, Phillip Coffman, James Gardner, N.V.S.N. Murthy Konda, Kevin L. Kenney, Vicki Thompson, Garold L. Gresham, Chenlin Li, Blake Simmons, Daniel Klein-Marcuschamer, Todd Pray and Deepti Tanjore
Predictive modeling can de-risk bio-based production
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Chenlin Li, Ling Liang, Ning Sun, Feng Xu, Vicki S. Thompson, Akash Narani, Qian He, Tina Luong, Deepti Tanjore, Todd Pray, Blake Simmons and Seema Singh
Scale-up and process integration of sugar production by acidolysis of single and mixed feedstocks in ionic liquids
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Parthasarathi Ramakrishnan, Tanmoy Datta, Blake Simmons and Seema Singh
Lignocellulosic biomass dissolution and depolymerization in ionic liquids
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Thales Costa, Aymerick Eudes, Henrik Scheller, Adriane Milagres, Andre Ferraz
Estimating the lignin composition of sugarcane hybrids with varied lignin content by pyrolysis-GC/MS
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 27-30
Dominique Loque Use of Synthetic Biology to Improve BioEnergy Crops
Presentation 37th Symposium on Biotechnology for Fuels and Chemicals, San Diego, CA
April 30 Andrew Brandon, Henrik Scheller
Engineering plants for improved biofuels production
Presentation Futuragene, Rehovot, Israel
April 30 Deepak Dugar Entropy Resins Tour On-site
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Onsite Seminars
Date Type Presenter Title Affiliation
April 1 JBEI Seminar Series Kai Deng High-throughput Carbohydrate-active Enzyme Assay Development Based on Synthetic Organic Chemistry and Nanostructure Initiator Mass Spectrometry (NIMS)
Technology Division
April 1 Group Seminar Kamrun Zargar Discovery of genes associated with bacterial toluene biosynthesis
Fuels Synthesis Division
April 1 Group Seminar Chris Eiben Production of Novel Terpenes via the Lepidopteron Mevalonate Pathway
Fuels Synthesis Division
April 8 Group Seminar Erika Yoshida Hydroxytyrosol production in E. coli
Fuels Synthesis Division
April 8 Group Seminar Aram Kang A modified mevalonate pathway for isopentenol production
Fuels Synthesis Division
April 15 JBEI Seminar Series Joel Guenther jSALSA — Robotic workflows for high-throughput engineering of enzymes and feedstocks
Technology Division
April 15 Group Seminar Hector Plahar ICE Software Platform Fuels Synthesis Division
April 15 Group Seminar Sung Lee MAGE-based genome editing and its applications in Escherichia coli
Fuels Synthesis Division
April 22 General Seminar Fuels Synthesis Guest
Prof. Lucy Shapiro Regulatory Architecture of a Bacterial Cell Cycle
Developmental Biology at the Stanford University School of Medicine
April 22 Group Seminar Kamrun Zargar Discovery of genes associated with bacterial toluene biosynthesis
Fuels Synthesis Division
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April 22 Group Seminar Sam Curran Measuring active-site acylation to understand an iterative polyketide synthase
Fuels Synthesis Division
April 29 Group Seminar Jorge Alonzo Gutierrez CRISPR / MAGE mediated metabolic engineering in E. coli
Fuels Synthesis Division
April 29 Group Seminar Charles Denby Incorporating an ATP:Citrate lyase into Saccharomyces cerevisiae for energy efficient production of value-added chemicals
Fuels Synthesis Division
April 29 General Seminar Technology/Commercialization Guest
David Andrew Mills Microbial Landscapes within Wine and Beer Production
Dept of Food Science & Technology Dept of Viticulture & Enology Univ. of California
April 29 General Seminar Deconstruction Guest
Ricardo Alamillo Carbohydrate conversion mechanisms for production of chemicals and fuels
Decon Interview Candidate
April 30 General Seminar Deconstruction Guest
Long Chen HDO catalysis for fine chemicals from lignin
Decon Interview Candidate
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Industry Interactions
Date Company / Contact
April 1 LanzaTech / Alex Juminaga, Ryan Tappel, Arthur Shockley
April 1 DSM / Roel A.L. Bovenberg
April 1 Dow Agrosciences / Steven Evans, Nigel Mouncey
April 1 Monsanto / Philip Eppard, Ginnin Ursin
April 2 California Energy Commission
April 2 Agilent / Steven Royce
April 3 Evolva / Stephan Herrera
April 8 Ryffin / Tim Gardner
April 9 Afingen / Ai Oikawa
April 9 MassInsight / Tom Gilman
April 10 Ajinomoto / Erika Yoshida
April 14 Teselagen / Michael Fero
April 14 COFCO / Bo Chen
April 16 Total / Florence Mingardon and Vineet Rajgarhia
April 22 Novozymes / Sarah Teter, Brian Scott, Hui Xu, Claus Crone Fuglsang
April 30 TekHolding / Mukund Karanjikar and Robert Price
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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 66
Genetic characterization of mutant candidates from rice stem saccharification screen (GG)
Sept. 2015 58
Correlation between cell wall modification and environmental interactions investigated (GG)
Sept. 2015 58
Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 65
Characterization of novel GT activities (SB) Sept. 2015 70
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 68
Transgenic plants with dominant repressors of hemicellulose biosynthesis characterized (CWB)
Sept. 2015 56
Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 65
Optimization of translation control technologies to improve tissue-specific expression (CWE)
Sept. 2015 55
Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 58
Heterologous screening of transferases to promote in planta design of polysaccharides (SB).
Sept. 2015 50
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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 58
Resequencing of Kitaake mutants (with JGI) and a database set up for hi throughput in silico screening (GG).
Sept. 2015 59
Translation of best technologies developed in Arabidopsis to other plant species (CWE)
Sept. 2015 58
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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 95
Complete characterization of lignin streams from various IL pretreatment process configurations
July 2015 75
Design, synthesis and assessment of lignin and hemicellulose derived IL mixtures for mixed and engineered feedstock pretreatment
Aug. 2015 70
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 70
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 95
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 55
Demonstrate using directed evolution to engineer enhanced stability -glucosidase in up to 20% [C2mim][OAc].
Sept. 2015 65
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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 95
Identify five bacterial strains capable of metabolizing mixtures of aromatics from pretreatment-derived lignin streams
Sept. 2015 55
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 70
Validate candidate genes for hyperproduction phenotypes through gene deletion and/or overexpression
Sept. 2015 60
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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 58
In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 58
Optimization of Hydrocarbon Biosynthetic Pathways
Improve methyl ketone production in E. coli with NIMS-aided HT screening and metabolic modeling
Sept. 2015 58
E. coli pathway engineering for isopentenol production both in aerobic and anaerobic conditions
Sept. 2015 65
Genes encoding isoprenoid pathway integrated into E. coli chromosome
Sept. 2015 58
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 60
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 45
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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 58
Clonal sequence validation (Sanger and/or MiSeq) pipeline implemented and integrated with DIVA/ICE
Sept. 2015 58
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 93
Implement interactive metabolic engineering on MvT Sept. 2015 80
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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 65
Apply HT NIMS screen for fatty acids based fuel molecules (e.g. FAMK) in collaboration with the Fuels Division.
Sept. 2015 60
Implement software to automate unit operations (e.g., droplet dispensing, routing, merger, and sorting) on an integrated droplet chip
Sept. 2015 58
Demonstrate microfluidic droplet platform for integration of DNA assembly, transformation of cells, and culturing
July 2015 70
Proteomics Develop rapid untargeted proteomics methods for relative quantification of >800 E. coli and S. cerevisiae proteins
Sept. 2015 75
Develop absolute quantification targeted proteomic assays for 150 S. cerevisiae proteins
Sept. 2015 80
Implement membrane proteomics assays to enable E. coli membrane editing with Fuels Synthesis Division
Sept. 2015 75
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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 58
Electron tomographic analysis of plant cell walls of engineered feedstocks, and CAD model generation for mechanical properties simulation.
Sept. 2015 58
Structural Biology Test expression of multiple GT clones in insect cell platform to produce quantities of protein for crystallization trials
Sept. 2015 70
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 45
Synthetic Bio Informatics
EDD further developed to support enzyme characterization data and workflows, with Deconstruction Division
Sept. 2015 58
EDD further developed to support genetic expression tool data and workflows, with Fuels Synthesis
Sept. 2015 58
BioCad tools enabled to query ICE and EDD for enzymes and expression tools satisfying specified performance characteristics
Sept. 2015 58
Dashboard - April 2015 - DOE
FY 2015 Dashboard For Period: April 1 - 30, 2015
21 / 22
Milestones
Operations Management Division
Area Initiatives Milestone/Deliverables Due % Complete
Intellectual Property Management
Generate >10 inventions Sept. 2015 90
Educate researchers about the tech transfer process Sept. 2015 61
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 59
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 64
Maintain regular JBEI on-site office hours for the Berkeley Lab entrepreneur adviser.
Sept. 2015 61
Business Development Outreach
Promote each JBEI invention to at least 700 contacts in the biofuels industry.
Sept. 2015 61
Conduct meetings with at least fifteen companies each year, at least one-third of which are new to JBEI
Sept. 2015 59
Industry Advisory Committee
Hold an annual meeting of the IAC to inform JBEI research of industry concerns and technology bottlenecks.
Sept. 2015 61
Industry Partnership Program
Strengthen relationships with current partners and pursue collaborations with new industry partners in areas of complementary research.
Sept. 2015 61
Dashboard - April 2015 - DOE
FY 2015 Dashboard For Period: April 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 59
Annual JBEI Conference
Annual JBEI Retreat Sept. 2015 78
Human Resources Staffing for year 8 complete Sept. 2015 59
