DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute …€¦ · DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress Report ... Industry Interactions

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

mailto:[email protected]

mailto:[email protected]

Dashboard - July 2015 - DOE

FY 2015 Dashboard For Period: July 1 - 31, 2015

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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



4 / 25

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



5 / 25

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


July 22 Joseph Chen California Department of Public Health Tour On-site

Outreach – Scientific Community


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


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




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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


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


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


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




9 / 25

July 12-17 Henrik Scheller Engineering of Cell Walls in Plants for Use in Biorefineries


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


July 8 Group Seminar Satoshi Yuzawa An improved design for acyltransferase domain replacements in modular polyketide synthases


July 8 Group Seminar Justin Hsia A synthetic compartmental lateral inhibition system for pattern formation.



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 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



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


July 29 Group Seminar Aram Kang Developing screening platforms for improved activity of decarboxylases in IPP-bypassing isopentenol pathways




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



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


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


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



15 / 25

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)


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


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)


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



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)


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


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



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Milestones

Technology Division (continued)


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



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Milestones

Operations Management Division


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



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Milestones

Operations Management Division (continued)


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

Documents

DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute …€¦ · DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute Monthly Progress Report ... Industry Interactions