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DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute
Monthly Progress Report – July 2015
Fiscal Year: 2015
Year / Period: Year 8 / Month 10 / July 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 July 2015, tenth month of fiscal year 2015:
Item Count Highlights
Publications in Print 12 "Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment", Biotechnol Biofuels
Invention Disclosures 6 “Polyoxometalate (POM) for the Conversion of Lignocellulosic Derivatives to Renewable Platform Chemicals”
Patent Applications 3 “Synthetic Polypeptide Having A Xylose Import Activity”
Media Citations 21 Story released: Unlocking the Rice Immune System, Joint BioEnergy Institute Study Identifies Bacterial Protein that is Key to Protecting Rice against Bacterial Blight
Outreach Interactions 40 Education: 8, Public: 1 and Scientific Community: 31
On-Site Seminars 17 Prof. Morten Sommer from Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark (DTU) gave a seminar on “Developing treatment strategies that limit resistance evolution”
Industry Interactions 27 Interactions with POET - DSM Joint Venture, China Lake and Boeing.
FY15 Milestones Milestones completed: - Deconstruction: Complete characterization of lignin streams from various IL pretreatment process
configurations - Deconstruction: Establish complementary thermophilic cellulase cocktail focusing on crystalline substrates - Deconstruction: Optimize cultivation conditions for heterologous enzyme production, including temperature
and pH, and initiate ‘omic analysis of optimal vs. baseline conditions - Technology: Demonstrate microfluidic droplet platform for integration of DNA assembly, transformation of
cells, and culturing - Operations: Annual JBEI Retreat
Milestones delayed: - Feedstocks: Heterologous screening of transferases to promote in planta design of polysaccharides - Technology: Structural characterization of Fatty Acid Synthase and other large complexes by single particle
cryo electron microscopy
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Publications
In Print
Barajas, J. F., Phelan, R. M., Schaub, A. J., Kliewer, J. T., Kelly, P. J., Jackson, D. R., Luo, R., Keasling, J. D., & Tsai, S. C. (2015). "Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols". Chem Biol. doi, 10.1016/j.chembiol.2015.06.022 http://www.ncbi.nlm.nih.gov/pubmed/26235055
Beller, H. R., Lee, T. S., & Katz, L. (2015). "Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids". Nat Prod Rep. doi, 10.1039/c5np00068h http://www.ncbi.nlm.nih.gov/pubmed/26216573
Dolan, J. A., Sathitsuksanoh, N., Rodriguez, K., Simmons, B., Frazier, C., & Renneckar, S. (2015). "Biocomposite adhesion without added resin: understanding the chemistry of the direct conversion of wood into adhesives". RSC Adv., 5(82), 67267-67276. doi, 10.1039/c5ra09676f http://pubs.rsc.org/en/content/articlepdf/2015/ra/c5ra09676f
Gonzalez, T. L., Liang, Y., Nguyen, B. N., Staskawicz, B. J., Loque, D., & Hammond, M. C. (2015). "Tight regulation of plant immune responses by combining promoter and suicide exon elements". Nucleic Acids Res. doi, 10.1093/nar/gkv655 http://www.ncbi.nlm.nih.gov/pubmed/26138488
Jung, K. H., Cao, P., Sharma, R., Jain, R., & Ronald, P. C. (2015). "Phylogenomics databases for facilitating functional genomics in rice". Rice (N Y), 8(1), 60. doi, 10.1186/s12284-015-0060-7 http://www.ncbi.nlm.nih.gov/pubmed/26223238
Lupoi, J. S., Singh, S., Parthasarathi, R., Simmons, B. A., & Henry, R. J. (2015). "Recent innovations in analytical methods for the qualitative and quantitative assessment of lignin". Renewable & Sustainable Energy Reviews, 49, 871-906. doi, 10.1016/j.rser.2015.04.091
Lupoi, J. S., Smith-Moritz, A., Singh, S., McQualter, R., Scheller, H. V., Simmons, B. A., & Henry, R. J. (2015). "Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging". Biotechnol Biofuels, 8, 98. doi, 10.1186/s13068-015-0279-y http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4508826/pdf/13068_2015_Article_279.pdf
Patron, N. J., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., Raitskin, O., Leveau, A., Farre, G., Rogers, C., Smith, A., Hibberd, J., Webb, A. A., Locke, J., Schornack, S., Ajioka, J., Baulcombe, D. C., Zipfel, C., Kamoun, S., Jones, J. D., Kuhn, H., Robatzek, S., Van Esse, H. P., Sanders, D., Oldroyd, G., Martin, C., Field, R., O'Connor, S., Fox, S., Wulff, B., Miller, B., Breakspear, A., Radhakrishnan, G., Delaux, P. M., Loque, D., Granell, A., Tissier, A., Shih, P., Brutnell, T. P., Quick, W. P., Rischer, H., Fraser, P. D., Aharoni, A., Raines, C., South, P. F., Ane, J. M., Hamberger, B. R., Langdale, J., Stougaard, J., Bouwmeester, H., Udvardi, M., Murray, J. A., Ntoukakis, V., Schafer, P., Denby, K., Edwards, K. J., Osbourn, A., & Haseloff, J. (2015). "Standards for plant synthetic biology: a common syntax for exchange of DNA parts". New Phytol. doi, 10.1111/nph.13532 http://www.ncbi.nlm.nih.gov/pubmed/26171760
Scullin, C., Cruz, A. G., Chuang, Y. D., Simmons, B. A., Loque, D., & Singh, S. (2015). "Restricting lignin and enhancing sugar deposition
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Publications
In Print
in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment". Biotechnol Biofuels, 8, 95. doi, 10.1186/s13068-015-0275-2 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496950/pdf/13068_2015_Article_275.pdf
Sun, L., Singh, S., Joo, M., Vega-Sanchez, M., Ronald, P., Simmons, B. A., Adams, P., & Auer, M. (2015). "Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy". Biotechnol Bioeng. doi, 10.1002/bit.25690 http://onlinelibrary.wiley.com/store/10.1002/bit.25690/asset/bit25690.pdf?v=1&t=id0h0set&s=63925c003ec0b0b2e428650759ac900efbd56fda
Voiniciuc, C., Schmidt, M. H., Berger, A., Yang, B., Ebert, B., Scheller, H. V., North, H. M., Usadel, B., & Guenl, M. (2015). "MUCI10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage". Plant Physiol. doi, 10.1104/pp.15.00851 http://www.plantphysiol.org/content/early/2015/07/28/pp.15.00851.full.pdf
Wenz, C., Barbas, C., Lopez-Gonzalvez, A., Garcia, A., Benavente, F., Sanz-Nebot, V., Blanc, T., Freckleton, G., Britz-McKibbin, P., Shanmuganathan, M., de l'Escaille, F., Far, J., Haselberg, R., Huang, S., Huhn, C., Pattky, M., Michels, D., Mou, S., Yang, F., Neusuess, C., Tromsdorf, N., Baidoo, E. E., Keasling, J. D., & Park, S. S. (2015). "Interlaboratory study to evaluate the robustness of capillary electrophoresis with mass spectrometry for peptide mapping". J Sep Sci. doi, 10.1002/jssc.201500551 http://www.ncbi.nlm.nih.gov/pubmed/26147246
Invention Disclosures Inventor(s)
2015-138 - “Engineering Bioenergy Crops for Integrated Co-bioproduction of Fuels and Key Value Chemicals”
Aymerick Eudes, Dominique Loque, Peter Matlock and Henrik Vibe Scheller
2015-141 - “Production of omega-hydroxy and omega-1-hydroxy methyl ketones as precursors for the synthesis of macrocyclic ketones”
Jorge Alonso-Gutierrez, Ee-Been Goh, Robert Haushalter, Leonard Katz and Jay Keasling
2015-143 - “High Gravity, Fed-batch Ionic Liquid Based Process for Biomass to Fuels/Chemicals”
Blake A. Simmons, Seema Singh and Feng Xu
2015-144 - “Alkaline depolymerization of water-soluble Lignin Extracts” Chijioke Joshua, Blake A. Simmons and Steven W. Singer
2015-145 - “Novel Transporter, YbjJ, with Unknown Function, Provides Extreme Tolerance to Ionic Liquid Exposure in Model Microbial Strain Escherichia Coli”
Marijke Frederix and Aindrila Mukhopadhyay
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Media Citations
Date Article Source
July 24 Rice researchers redress retraction Nature
July 24 UC Davis researchers uncover key step in rice immune response The Sacramento Bee
July 24 What do you do after painful retractions? Q&A with Pamela Ronald and Benjamin Schwessinger
Retraction Watch
July 24 Unlocking the rice immune system (e)Science News
July 24 Unlocking the rice immune system Phys.org
July 24 Unlocking the rice immune system EurekAlert!
July 24 Unlocking the rice immune system - Joint BioEnergy Institute study identifies bacterial protein that is key to protecting rice against bacterial blight
SeedQuest
2015-151 - “Polyoxometalate (POM) for the Conversion of Lignocellulosic Derivatives to Renewable Platform Chemicals”
Dajiang Liu, Parthasarathi Ramakrishnan, Blake A. Simmons and Seema Singh
Patent Applications
2014-020-01, 62/192,517 - “Synthetic Polypeptide Having A Xylose Import Activity” Jay Keasling, Mario Ouellet, Aindrila Mukhopadhyay and Amanda Reider Apel
2015-007-01, 62/187,767 - “Host cells and methods using a repressor polypeptide and an inducible promoter for gene expression”
Thomas L Ruegg
2015-106-01, 62/191,283 - “Producing Adipic Acid and Related Compounds Using Hybrid Polyketide Synthases”
Jay Keasling, Leonard Katz, Sean Poust and Andrew R. Hagen
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Media Citations
Date Article Source
July 24 Unlocking the Rice Immune System Newswise
July 24 Unlocking the Rice Immune System Science Springs
July 24 A Phoenix Rises from the Ashes: A new discovery emerges from the 2009 retraction The Tree of Life
July 25 New findings unlock clues to disease protection News Medical
July 25 Unlocking rice immune system will benefit humanity: Scientists Times of India
July 25 Unlocking Rice Immune System Holds Important Implications for Worldwide Supply of Rice Medindia.net
July 25 Unlocking rice immune system will benefit humanity: Scientists Sify News
July 27 Unlocking the rice immune system R&D Magazine
July 27 Trigger found for defense to rice disease (e)Science News
July 27 Scientists discover rice plant's immune system trigger UPI
July 27 Crop Attack Discovery Lets Team Bounce Back Futurity
July 27 Unlocking the Rice Immune System Lab Manager Magazine
July 28 Unlocking the rice immune system AG Professional
July 29 Rice disease-resistance find closes loop Daily Democrat
Outreach – Education
Date Presenters Audience or Presentation Title Activity Location
July 14 Peter Matlock, CJ Solano Community College, Industrial Tour On-site
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Joshua, Eva Pan and Josh Heinemann
Biotechnology Intensive Summer Program
July 14 Joseph Chen San Francisco State University Tour On-site
July 21 Irina Silva and Peter Matlock
Forsyth Tech, Winston-Salem, North Carolina Other On-site
July 23 Garima Goyal, Peter Kim and Sebastian Kolinko
National Student Leadership Conference Tour On-site
July 23 Leo d'Espaux, Marijke Frederix and Kamrun Zargar
National Student Leadership Conference Tour On-site
July 24 Alex Tsai, Matisse Roach, Morgann Reilly, Phil Gach and Veronica Benites
Self e-STEM Tour On-site
July 23 Peter Matlock Northeast Biomanufacturing Center and Collaborative (NBC2)
Meeting Off-site
July 29 Irina Silva and Peter Matlock
Delgado Community College Meeting On-site
Outreach – Public
Date Presenters Audience or Presentation Title Activity Location
July 22 Joseph Chen California Department of Public Health Tour On-site
Outreach – Scientific Community
Date Presenters Audience or Presentation Title Activity Location
July 1 Jay Keasling Engineering Microbes for Production of Presentation GRC Conference on Synthetic Biology, Newry,
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Drugs, Fuels, and Chemicals ME
July 3 Erika Yoshida Ajinomoto Co. Inc. Tour On-site
July 5-9 Joshua Heazlewood Nucleotide sugar transport: Delivering the building blocks of the plant cell wall
Presentation 26th International Conference on Arabidopsis Research, Paris France
July 9 Nathan Hillson FutureBio Foundry for Advanced Fuels and Chemicals Production
Presentation 5th Annual Multi-use Technology Symposium, Ridgecrest, CA
July 11-12 Rhea Stoppel A lipid-transfer protein involved in drought response and signaling from the secondary cell wall
Presentation Gordon Research Seminar - Plant Cell Walls. Waltham, MA
July 12-17 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 Gordon Research Conference on Applied and Environmental Microbiology, South Hadley, MA
July 12-17 Rhea Stoppel, Virginia Tartaglio, Berit Ebert, Henrik Vibe Scheller
A lipid-transfer protein involved in drought response and signaling from the secondary cell wall. Gordon Research Conference
Presentation Gordon Research Conference. Waltham, MA
July 12-17 Estelle Schaefer, Isabella Nielsen, Henrik Vibe Scheller
Role of TBL28 in O-acetylation of polysaccharides
Presentation Gordon Research Conference. Waltham, MA
July 12-17 Catalin Voiniciuc, Maximillian Heinrich-Wilhelm Schmidt, Adeline Berger, Bo
MUCI10 Makes Galactoglucomannan Required for Pectin and Cellulose Organization in Arabidopsis Seed Mucilage
Presentation Gordon Research Conference. Waltham, MA
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Yang, Berit Ebert, Henrik V Scheller, Helen M North, Bjorn Bjšrn Usadel, Markus Gunl
July 12-17 Lorenzo Fimognari, Majse Nafisi, Henrik Vibe Scheller, Yumiko Sakuragi
Suppressor screening of the REDUCED WALL ACETYLATION 2 reveals a complex interaction between leaf surface integrity and cell wall acetylation
Presentation Gordon Research Conference. Waltham, MA
July 12-17 Lin Fang, Ishikawa Toshiki, Emilie Rennie A, Jeemeng Lao, Taku Demura, Maki Yamada Kawai, Henrik Scheller, Jennifer C.Mortimer
Identification of a sphingolipidspecific Mannosyltransferase
Presentation Gordon Research Conference. Waltham, MA
July 12-17 Berit Ebert, Carsten Rautengarten, Lifeng Liu, Markus Pauly, Ariel Orellana, Henrik Vibe Scheller, Joshua L. Heazlewood
GFT1, the Golgi-localized GDPfucose transporter is required for development in Arabidopsis
Presentation Gordon Research Conference. Waltham, MA
July 12-17 Laura E Bartley, Matthew L Peck, Zhang Chengcheng, Steven D Karlen, Yi Lin Tsai, Sandra Thibivilliers, Berit Ebert, Robert Sykes, Erica Gjersing, Seonghee Lee, John Ralph, Henrik V. Scheller
Genetic Analysis Reveals Acyltransferases that Incorporate Hydroxycinnamates into Grass Cell Walls
Presentation Gordon Research Conference. Waltham, MA
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July 12-17 Henrik Scheller Engineering of Cell Walls in Plants for Use in Biorefineries
Presentation Gordon Research Conference. Waltham, MA
July 13 Jay Keasling Engineered Polyketide Synthases for Production of Commodity and Specialty Chemicals
Presentation ECI Biochemical Engineering Conference, Puerto Vallarta, Mexico
July 15 Nathan Hillson Update on FutureBio Foundry Progress Presentation FutureBio Insitute Planning Retreat, Berkeley, CA
July 17 Erika Yoshida Ajinomoto Co. Inc Tour On-site
July 19-24 Aymerick Eudes Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin
Presentation Gordon Conference - Plant Metabolic Engineering. Waterville Valley, NH
July 19-24 Patrick Shih A Robust Gene Stacking Method Utilizing Yeast Assembly for Plant Metabolic Engineering
Presentation Plant Metabolic Engineering. Waterville Valley, NH
July 19-24 Dominique Loque Fine-Tuning Secondary Cell Wall Engineering.
Presentation Gordon Conference - Plant Metabolic Engineering. Waterville Valley, NH
July 21 Jay Keasling Novo Nordisk Foundation Center for Biosustainability, DTU
Tour On-site
July 21 Nathan Hillson Introduction to the FutureBio Foundry Presentation 2015 BIO World Congress on Industrial Biotechnology, Breakout: Open Source Facilities to Scale-up Renewable Chemicals and Biobased Materials, Montreal,
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Canada
July 24 Anup Singh Autodesk Tour On-site
July 24 Erika Yoshida and Nathan Hillson
Ajinomoto Co. Inc Tour On-site
July 27 Hector Garcia Martin Metabolic Engineering Tools for biofuel Production"
Presentation Metabolomics Symposium 2015, Lexington, KY
July 28 Jay Keasling and Jenny Mortimer
Tata Power Solar Tour On-site
July 30 Jeff Kimbrel JGI Tour On-site
July 30 Jennifer Mortimer Breaking down the walls: exploring plant biomass as a feedstock for renewable fuels
Presentation Lawrence Livermore National Lab, Livermore, CA.
July 30 Nathan Hillson Synthetic Biology Informatics: Scalability and Responsible Innovation
Presentation 2015 Cold Spring Harbor Synthetic Biology Training Course, Cold Spring Harbor, NY
July 30 Nathan Hillson Introduction to the FutureBio Foundry Presentation 2015 Cold Spring Harbor Synthetic Biology Training Course, Cold Spring Harbor, NY
July 31 Sung Lee Daegu Gyeongbuk Institute of Science & Technology (DGIST)
Tour On-site
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Onsite Seminars
Date Type Presenter Title Affiliation
July 1 General Seminar
Synberc Guest
Dan Widmaier, CEO
Building Bolt Threads from Graduate School
Bolt Threads
July 1 Group Seminar Ryan Phelan Engineering polyketide synthases (PKSs) for the production of highly reduced compounds and the design of new tools to affect protein expression Streptomyces
Fuels Synthesis Division
July 1 Group Seminar Margaret Brown MicroClean: Engineering warfare agent catabolism into E. coli
Fuels Synthesis Division
July 8 Group Seminar Satoshi Yuzawa An improved design for acyltransferase domain replacements in modular polyketide synthases
Fuels Synthesis Division
July 8 Group Seminar Justin Hsia A synthetic compartmental lateral inhibition system for pattern formation.
Fuels Synthesis Division
July 15 General Seminar
Fuels Synthesis/Technology Guest
Michael Burkart Protein interactions in acetate biosynthetic pathways
University of California, San Diego
July 15 Group Seminar Heather Jensen Screening mutant library for improving expression of membrane proteins in E. coli
Fuels Synthesis Division
July 21 General Seminar
Fuels Synthesis Guest
Prof. Morten Sommer
Developing treatment strategies that limit resistance evolution
Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark (DTU)
July 22 Group Seminar Tristan de Rond Classical and modern approaches Fuels Synthesis Division
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to the discovery of enzymes involved in natural product biosynthesis
July 22 Group Seminar Daniel Sachs A Cas9-based toolkit to optimize gene expression context for yeast synthetic biology
Fuels Synthesis Division
July 29 General Seminar
Feedstocks Guest
Fanglian He Improving Experimental Reproducibility in the Life Sciences
Bio-Protocol
July 29 Group Seminar Anna Lechner Host engineering for polyketide production in S. cerevisiae
Fuels Synthesis Division
July 29 Group Seminar Aram Kang Developing screening platforms for improved activity of decarboxylases in IPP-bypassing isopentenol pathways
Fuels Synthesis Division
July 30 General Seminar
Fuels Synthesis Guest
Paul E. O’Maille, PhD.
Drug origin and action: systems and biochemical basis of synergy (epistasis)
The John Innes Centre, Department of Metabolic Biology and The Institute of Food Research, Food & Health Programme
July 30 General Seminar
Fuels Synthesis Guest
Mohammad Tajparast
Storage Metabolism during Feast-Famine Cycles of Activated Sludge Wastewater Treatment and during a Sudden Nutrient Limitation Studied in Rhodococcus jostii RHA1 Using a Genome-Scale Metabolic Modeling Approach
Dept. of Physiology, McGill University, Montreal, Canada
July 31 General Seminar
Technology Guest
Hyun Soo Kim High-throughput microfluidic microalgae screening platforms for
Department of Electrical and Computer Engineering, Texas A&M
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growth and oil production analysis University
July 31 General Seminar
Technology Guest
Manasi Raje Automation of Serial Dilution by Microfluidic Digital Logic
M.S. Biomedical Engineering, University of California - Irvine, CA
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Industry Interactions
Date Company / Contact
July 2 InSITE Fellows / Richard Nespola
July 6 ADM / Mitchell Schutlz
July 6 Bolt Threads / Gustavo Pesce
July 7 Ceres / Roger Penell
July 7 Dow / Steve Hahn
July 14 Novozymes / Sarah Teeter
July 14 Bio-Amber / Jim Millis
July 14 Ceres / Roger Pennell
July 15 Mass Insight / Tom Gilman
July 16 DuPont / Luis Cascao-Pereira
July 16 DowAgro / Nigel Mouncey, Steve Evans
July 20 Agilent / Jens Trafkowski, Klaus Witt, Steffen Mueller, Stephan Buckenmaier and Ulrich Eberhardinger
July 21 DSM Ventures / Greg McParland
July 21 Genomatica / Chrisoph Schilling, Mark Burk
July 21 Mass Insight / Tom Gilman
July 22 China Lake / Bill Hogan
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July 23 Ceres / Roger Penell
July 23 Boeing / James Kinder
July 23 FedEx / Michael Fulton
July 24 Autodesk / Andrew Hessel
July 24 Ajinomoto / Hiroyuki Kojima, Nobuhisa Shimba, Kazuo Nakanishiyuri Nagai, Susan Hao
July 24 Monsanto / Ginni Ursin
July 24 Medicago / Marc-Andre D'Aoust
July 30 POET - DSM Joint Venture / Daniel Cummings
July 31 Bewnson Hill Biosciences / Ben Gray
Several LanzaTech / Sean Simpson
Several Technology Holding / Mukund Karanjikar
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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 90
Genetic characterization of mutant candidates from rice stem saccharification screen (GG)
Sept. 2015 85
Correlation between cell wall modification and environmental interactions investigated (GG)
Sept. 2015 85
Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 85
Characterization of novel GT activities (SB) Sept. 2015 87
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 95
Transgenic plants with dominant repressors of hemicellulose biosynthesis characterized (CWB)
Sept. 2015 77
Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 90
Optimization of translation control technologies to improve tissue-specific expression (CWE)
Sept. 2015 82
Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 83
Heterologous screening of transferases to promote in planta design of polysaccharides (SB).
Sept. 2015 70
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Milestones
Feedstocks Division (continued)
Area Initiatives Milestone/Deliverables Due % Complete
Engineering of Modifications in Different Plant Species
Cell wall related genes in switchgrass functionally annotated, integrated into phylogenomics databases, and integrated with Kbase (GG)
Sept. 2015 85
Resequencing of Kitaake mutants (with JGI) and a database set up for hi throughput in silico screening (GG).
Sept. 2015 87
Translation of best technologies developed in Arabidopsis to other plant species (CWE)
Sept. 2015 83
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Milestones
Deconstruction Division
Area Initiatives Milestone/Deliverables Due % Complete
Biomass Pretreatment
Predict and develop task specific ILs for selective lignin or cellulose dissolution and low temperature pretreatment
May 2015 100
Complete characterization of lignin streams from various IL pretreatment process configurations
July 2015 100
Design, synthesis and assessment of lignin and hemicellulose derived IL mixtures for mixed and engineered feedstock pretreatment
Aug. 2015 90
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 88
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 act -glucosidase in up to 20% [C2mim][OAc].
Sept. 2015 87
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Milestones
Deconstruction Division (continued)
Area Initiatives Milestone/Deliverables Due % Complete
Microbial Communities
Complete characterization of active component of JTherm March 2015 100
Establish complementary thermophilic cellulase cocktail focusing on crystalline substrates
July 2015 100
Identify five bacterial strains capable of metabolizing mixtures of aromatics from pretreatment-derived lignin streams
Sept. 2015 98
Fungal Biotechnology
Design new expression systems based on recent “omics” discoveries in regard to promoters and assess heterologous GH expression
Feb. 2015 100
Initiate ChIP-Seq analysis of histone modifications in A. niger aimed at identifying epigenetic determinants of high productivity
April 2015 100
Optimize cultivation conditions for heterologous enzyme production, including temperature and pH, and initiate ‘omic analysis of optimal vs. baseline conditions
July 2015 100
Validate candidate genes for hyperproduction phenotypes through gene deletion and/or overexpression
Sept. 2015 85
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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 84
In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 84
Optimization of Hydrocarbon Biosynthetic Pathways
Improve methyl ketone production in E. coli with NIMS-aided HT screening and metabolic modeling
Sept. 2015 84
E. coli pathway engineering for isopentenol production both in aerobic and anaerobic conditions
Sept. 2015 92
Genes encoding isoprenoid pathway integrated into E. coli chromosome
Sept. 2015 85
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 90
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 90
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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 84
Clonal sequence validation (Sanger and/or MiSeq) pipeline implemented and integrated with DIVA/ICE
Sept. 2015 84
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 90
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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 94
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 82
Demonstrate microfluidic droplet platform for integration of DNA assembly, transformation of cells, and culturing
July 2015 100
Proteomics Develop rapid untargeted proteomics methods for relative quantification of >800 E. coli and S. cerevisiae proteins
Sept. 2015 95
Develop absolute quantification targeted proteomic assays for 150 S. cerevisiae proteins
Sept. 2015 90
Implement membrane proteomics assays to enable E. coli membrane editing with Fuels Synthesis Division
Sept. 2015 90
Dashboard - July 2015 - DOE
FY 2015 Dashboard For Period: July 1 - 31, 2015
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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 88
Electron tomographic analysis of plant cell walls of engineered feedstocks, and CAD model generation for mechanical properties simulation.
Sept. 2015 88
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 60
Synthetic Bio Informatics
EDD further developed to support enzyme characterization data and workflows, with Deconstruction Division
Sept. 2015 84
EDD further developed to support genetic expression tool data and workflows, with Fuels Synthesis
Sept. 2015 84
BioCad tools enabled to query ICE and EDD for enzymes and expression tools satisfying specified performance characteristics
Sept. 2015 84
Dashboard - July 2015 - DOE
FY 2015 Dashboard For Period: July 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 98
Educate researchers about the tech transfer process Sept. 2015 95
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 83
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 92
Maintain regular JBEI on-site office hours for the Berkeley Lab entrepreneur adviser.
Sept. 2015 90
Business Development Outreach
Promote each JBEI invention to at least 700 contacts in the biofuels industry.
Sept. 2015 94
Conduct meetings with at least fifteen companies each year, at least one-third of which are new to JBEI
Sept. 2015 86
Industry Advisory Committee
Hold an annual meeting of the IAC to inform JBEI research of industry concerns and technology bottlenecks.
Sept. 2015 98
Industry Partnership Program
Strengthen relationships with current partners and pursue collaborations with new industry partners in areas of complementary research.
Sept. 2015 97
Dashboard - July 2015 - DOE
FY 2015 Dashboard For Period: July 1 - 31, 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 83
Annual JBEI Conference
Annual JBEI Retreat Sept. 2015 100
Human Resources Staffing for year 8 complete Sept. 2015 83