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DOE Bioenergy Research Center (BRC) - Joint BioEnergy Institute

Monthly Progress Report – March 2015

Fiscal Year: 2015

Year / Period: Year 8 / Month 6 / March 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 March 2015, sixth month of fiscal year 2015:

Item Count Highlights

Publications in Print 8 "Standard flow liquid chromatography for shotgun proteomics in bioenergy research"

Publications in Press 4 "Scale-up of Ionic Liquid Based Fractionation of Single and Mixed Feedstocks"

Invention Disclosures 6 “Easy and inexpensive method for converting monomeric, oligomeric, and polymeric lignin to ionic liquid”

Patent Applications 1 “Method for production of dicarboxylic acids and dicarboxylic acid methyl esters in microbes”

Media Citations 21 One story released: Biofuel Proteomics: JBEI Researchers Use Proteomics to Profile Switchgrass

Outreach Interactions 38 Education: 8, Public: 2 and Scientific Community: 28.

On-Site Seminars 21 Prof. Akihiko Kondo, Kobe University on “Development of microbial cell factories for the production of bio-fuels and bio-based chemicals through consolidated bioprocessing”

Industry Interactions 7 Interactions with Ajinomoto and Agilent.

Honors & Awards 3 Jay Keasling was inducted as Fellow of the National Academy of Inventors.

FY15 Milestones Despite the delay, this milestones is expected to meet its deadline: “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”.

Milestones completed in March 2015:

Deconstruction: “Complete characterization of active component of JTherm”

Fuels Synthesis: “Usage of EDD, MvT and 2S-13C MFA to improve production of fatty acids in S. cerevisiae”

Fuels Synthesis: “Develop analytical method for LC-MS of MEV and DXP intermediates”

Technology: “Characterize lignin degrading enzymes in collaboration with GLBRC"

mailto:[email protected]

mailto:[email protected]

Dashboard - March 2015 - DOE

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

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Publications

In Print

Ebert, B., Rautengarten, C., Guo, X., Xiong, G., Stonebloom, S., Smith-Moritz, A.M., Herter, T., Chan, L.J.G., Adams, P.D., Petzold, C.J., Pauly, M., Willats, W.G.T., Heazlewood, J.L., Scheller, H. V., & Schievano, A. (2015). "Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis". The Plant Cell. doi, 10.1105/tpc.114.133827 http://www.plantcell.org/content/early/2015/03/24/tpc.114.133827.short?keytype=ref&ijkey=7Kz99wF4DAD1yUu

González Fernández-Niño, S. M., Smith-Moritz, A. M., Chan, L. J. G., Adams, P. D., Heazlewood, J. L., & Petzold, C. J. (2015). "Standard flow liquid chromatography for shotgun proteomics in bioenergy research". [Original Research]. Frontiers in Bioengineering and Biotechnology, 3. doi, 10.3389/fbioe.2015.00044 http://www.frontiersin.org/Journal/Abstract.aspx?s=1456&name=bioenergy_and_biofuels&ART_DOI=10.3389/fbioe.2015.00044

Konda, N. V. S. N. M., Singh, S., Simmons, B. A., & Klein-Marcuschamer, D. (2015). "An Investigation on the Economic Feasibility of Macroalgae as a Potential Feedstock for Biorefineries". BioEnergy Research. doi, 10.1007/s12155-015-9594-1 http://link.springer.com/article/10.1007/s12155-015-9594-1/fulltext.html

Lee, T., Oh, T., Yang, S., Shin, J., Hwang, S., Kim, C. Y., Kim, H., Shim, H., Shim, J. E., Ronald, P. C., & Lee, I. (2015). "RiceNet v2: an improved network prioritization server for rice genes". Nucleic Acids Res. doi, 10.1093/nar/gkv253 http://www.ncbi.nlm.nih.gov/pubmed/25813048

Poust, S., Phelan, R. M., Deng, K., Katz, L., Petzold, C. J., & Keasling, J. D. (2015). "Divergent Mechanistic Routes for the Formation of gem-Dimethyl Groups in the Biosynthesis of Complex Polyketides". [Article]. Angew Chem Int Ed Engl, 54(8), 2370-2373. doi, 10.1002/anie.201410124 http://www.ncbi.nlm.nih.gov/pubmed/25564997

Schwessinger, B., Bahar, O., Thomas, N., Holton, N., Nekrasov, V., Ruan, D., Canlas, P. E., Daudi, A., Petzold, C. J., Singan, V. R., Kuo, R., Chovatia, M., Daum, C., Heazlewood, J. L., Zipfel, C., & Ronald, P. C. (2015). "Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses". PLoS Pathog, 11(3), e1004809. doi, 10.1371/journal.ppat.1004809 http://www.plospathogens.org/article/fetchObject.action?uri=info:doi/10.1371/journal.ppat.1004809&representation=PDF

Sun, N., Xu, F., Sathitsuksanoh, N., Thompson, V. S., Cafferty, K., Li, C., Tanjore, D., Narani, A., Pray, T. R., Simmons, B. A., & Singh, S. (2015). "Blending municipal solid waste with corn stover for sugar production using ionic liquid process". Bioresour Technol, 186(0), 200-206. doi, 10.1016/j.biortech.2015.02.087 http://www.ncbi.nlm.nih.gov/pubmed/25817030

Wu, Y.-W., Joshua, C., Eichorst, S. A., Gladden, J. M., Simmons, B. A., & Singer, S. W. (2015). "Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia". BioEnergy Research,



3 / 23

Publications

In Print

1-8. doi, 10.1007/s12155-015-9600-7 http://dx.doi.org/10.1007/s12155-015-9600-7

In Press

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 Announcements.

Li, C., Tanjore, D., He, W., Wong, J., Gardner, J. L., Thompson, V. S., Yancey, N. A., Sale, K., Simmons, B. A., & Singh, S. (2015). "Scale-up of Ionic Liquid Based Fractionation of Single and Mixed Feedstocks". BioEnergy Research.

Perez-Pimienta, J.A., Lopez-Ortega, M.G., Chavez-Carvayar, J.A., Varanasi, P., Stavila, V., Cheng, G., Singh, S., Simmons, B.A. (2015). "Characterization of agave bagasse as a function of ionic liquid pretreatment", Biomass and Bioenergy.

Shi, J., George, K. W., Sun, S., He, W., Li, C., Stavila, V., Lee, T. S., Simmons, B. A., & Singh, S. (2015). "Impact of pretreatment technologies on saccharification and isopentenol fermentation of mixed lignocellulosic feedstocks". BioEnergy Research.

Invention Disclosures Inventor(s)

2015-055 - “Easy and inexpensive method for converting monomeric, oligomeric, and polymeric lignin to ionic liquid”

Tanmoy Dutta, Blake A. Simmons, Seema Singh and Jian Sun

2015-057 - “Conversion of Lignin-derived Aromatics into Value-added Products by Novel Fungi and Bacteria”

John Gladden and Blake A. Simmons

2015-058 - “Microbial cell factories for the production of ionic liquids from lignocellulose-derived sugars and aromatics”

Tanmoy Dutta, John Gladden, Kenneth L. Sale, Blake A. Simmons, Steven W Singer, Seema Singh and Jian Sun

2015-059 - “Derivitization of sugars into Ionic Liquids” Tanmoy Dutta, John Gladden, Blake A. Simmons, Seema Singh and Jian Sun

2015-080 - “Low temperature Lignin dissolution and depolymerization” Tanmoy Dutta, Blake A. Simmons, Seema Singh and Jian Sun

2015-083 - “DIVA v2.0” Joanna Chen, Hector Plahar, Lisa Simirenko and Manjiri Tapaswi



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Media Citations

Date Article Source

March 3 Lygos completes first pilot-scale production of malonic acid from renewable resources at Berkeley Lab’s ABPDU

Green Car Congress

March 9 Joint BioEnergy Institute researchers use proteomics to profile switchgrass Press-News.org

March 9 Biofuel proteomics: Researchers use proteomics to profile switchgrass Science Daily

March 9 Biofuel Proteomics: Joint Bioenergy Institute Researchers Use Proteomics to Profile Switchgrass

Shale Oil News Today

March 9 Biofuel Proteomics Science Newsline Biology

March 9 Biofuel proteomics: Joint BioEnergy Institute researchers use proteomics to profile switchgrass EurekAlert!

March 9 JBEI gets results from proteomics in switchgrass varieties Biofuels Digest

March 9 Researchers use proteomics to profile switchgrass Phys.org

March 9 Biofuel Proteomics: Researchers Use Proteomics to Profile Switchgrass Scicasts

March 10 JBEI researchers use proteomics to ID 1750 unique proteins in switchgrass Anygator

March 10 Biofuel Proteomics One News Page

March 10 Proteomics May Help Manipulate Switchgrass for Increased Biofuel Production AZO Cleantech

March 11 1,750 Reasons Not To Ditch Your Old Gasmobile CleanTechnica

March 12 Using proteomics to profile switchgrass R&D Magazine

Patent Applications Inventor(s)

2014-158-01, US 62/130,971 - “Method for production of dicarboxylic acids and dicarboxylic acid methyl esters in microbes”

Jay Keasling and Robert Haushalter



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Media Citations

Date Article Source

March 12 JBEI researchers use proteomics to profile switchgrass Biomass Magazine

March 12 JBEI researchers use proteomics to profile switchgrass Ethanol Producer Magazine

March 17 Proteomika biopaliw Laboratoria.net (Polish website)

March 17 Researchers Profile Switchgrass Proteome as Part of Biofuel Development Efforts Genomeweb

March 23 Switchgrass proteomics for improved next generation biofuel crops Human Frontier Science Program

March 23 Lygos Demonstrates Biology’s Advantage Over Petroleum Synbiobeta

March 30 How Genetics Can Help Solve World Hunger BioTechNow

Outreach – Education

Date Presenters Audience or Presentation Title Activity Location

March 3 Jennifer Hiras Berkeley City College - STEM Careers Lunch Talks: "Biofuels: Sustainable Energy from Natural Resources"

Seminar Berkeley, CA

March 12 Aindrila Mukhopadhyay, Jenny Mortimer

National Defense University Tour On-site

March 13 Victor Chubukov, Saori Campen

Galileo High School Biotech Academy Tour On-site

March 16 Dominique Loque, Aymerique Eudes

Mines Paris Tech University Tour On-site

March 16 Sarah Richardson UC Berkeley - Woymn in Science & Engineering Seminar Off-site

March 17 Jennifer Hiras Berkeley City College - STEM Careers Lunch Seminar Berkeley, CA



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Talks: "Bioremediation: Using microbes to treat our waste"

March 19 Sarah Richardson Beacon Day School Workshop Oakland, CA

March 31 Dominique Loque BioTech Partners Tour On-site

Outreach – Public


March 12 Nathan Hillson Times of India Group Tour On-site

March 18 Pam Ronald TED2015 Talk, Pam Ronald "How genetic engineering creates food security"

Seminar Vancouver, Canada

Outreach – Scientific Community


March 1-6

Henrik Scheller Nucleotide Sugar Transporters in Plants and Their Role in Glycan Biosynthesis’

Presentation Gordon Research Conference on Glycobiology, Lucca, Italy

March 2 Nathan Hillson Keio University / Kobe University / University of Tokyo

Tour On-site

March 4 Nathan Hillson (via video conference)

DIVA: More Science, Less DNA construction Presentation Novo Nordisk Center for Biosustainability, Copenhagen, Denmark

March 5 Dominique Loque Heising Simons Foundation Tour On-site

March 6 Erika Yoshida Ajinomoto Co., Inc Tour On-site

March 9 Erika Yoshida Ajinomoto Co., Inc Tour On-site

March 9 Jay Keasling Engineering Microbes to Solve Global Challenges

Presentation Miller Institute for Basic Research in Science, Berkeley, CA.

March 15 Jay Keasling Engineering Microbes to Solve Global Presentation American Institute for



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Challenges Medical and Biological Engineering (AIMBE) Annual Meeting, Arlington, VA

March 20 Hector Garcia Martin Quantitative metabolic modeling for biofuel synthesis

Presentation Genomatica , San Diego, CA

March 22-26

Taek Soon Lee Advanced pathways for microbial production of branched C5 alcohols

Presentation 249th ACS National Meeting & Exposition, Denver, CO

March 22-26

Beibei Jing, T. Ishikawa, N. Inada, X. Yu, Jeemeng Lao, T. Demura, Kawai-Yamada M., Paul Dupree, Jennifer Mortimer

GONST1 and 2 are GIPC specific GDP-Mannose transporters

Presentation British Council/FAPESP Workshop on Plant Development. Campinas, Brazil

March 22-26

Jennifer Mortimer Synthesis and Function of Glycans in Plants Presentation British Council/FAPESP Workshop on Plant Development. Campinas, Brazil

March 22-26

Henrik Scheller Use of Synthetic Biology to Improve Bioenergy Crops

Presentation 249th ACS National Meeting, Denver, CO

March 22-26

Michael S. Kent, Isaac C. Avina, Nadeya Rader, Michael L. Busse, Anthe George, Noppandon Sathitsuksanoh, Edward Baidoo, Jerilyn Timlin, Nicholas H. Giron, Mathias C. Celina, Laura E. Martin, Ronen Polsky, Victor H. Chavez, Dale L. Huber, Blake A. Simmons, Kenneth L. Sale

New Multiplexed Assay for Lignin Depolymerization

Presentation 249th ACS National Meeting, Denver Colorado



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March 24 Dominique Loque Use of Synthetic Biology to Improve Crops Presentation Colorado State University, Fort Collins, CO

March 24 Nathan Hillson Synthetic Biology Internal Review Process and Biosecurity Screening

Presentation Tenth Annual DOE Joint Genome Institute User Meeting, Walnut Creek, CA

March 24-26

Blake Simmons Genomics-enabled Development of Ionic Liquid Tolerant Enzymes and Microbial Biofuel Hosts


March 24-26

Alan Kuo, Robert W. Riley, Alicia Clum, Asaf Salamov, Scott Baker, Blake Simmons, Mikael Andersen, and Igor Grigoriev

Whole-Genus Sequencing: 300 Aspergilli Presentation Tenth Annual DOE Joint Genome Institute User Meeting, Walnut Creek, CA

March 24-26

Yu-Wei Wu, Blake Simmons, and Steven Singer

MaxBin 2.0: Integrating multiple metagenomic datasets to recover more high quality individual genomes


March 24-26

Nasim Mansoori Zangir, Carlos Hernandez-Garcia, Patrick Shih, Charlee Vuu, Garima Goyal, Sangeeta Nath, Nathan J. Hillson, Samuel Deutsch, Dominique Loqué

Universal expression tools to improve nutrient acquisition of energy crops


March 24-26

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

Synthetic Biology in a Chip: A digital microfluidic platform for cell transformation, culture and expression


March 24-26

Tania L. González, Yan Liang, Bao N. Nguyen,

Tight, inducible gene expression in plants with alternatively spliced suicide exons

Presentation Tenth Annual DOE Joint Genome Institute User



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Geoffrey Liou, Brian J. Staskawicz, Dominique Loqué, and Ming C. Hammond

Meeting, Walnut Creek, CA

March 25 Mi Yeon Lee University of California - Riverside Tour On-site

March 27 Mi Yeon Lee SANDIA Tour On-site

March 27 Florence Mingardon TOTAL Tour On-site

March 27 Sung Lee Kwangwoon University - Korea Tour On-site

March 27 Jay Keasling Engineering Microbes for Production of Chemicals and Fuels

Presentation Directing Biosynthesis IV, Norwich, United Kingdom

March 30 Nathan Hillson Motley Fool Tour On-site



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Onsite Seminars

Date Type Presenter Title Affiliation

March 2 General Seminar Fuels Synthesis Guest

Prof. Akihiko Kondo Development of microbial cell factories for the production of bio-fuels and bio-based chemicals through consolidated bioprocessing

Dept. of Chemical Science & Engineering, Kobe University

March 2 General Seminar Deconstruction Guest

Kwang Kim Understanding the thermochemical conversion of biomass to overcome biomass recalcitrance

Iowa State University


Gautami Newalkar High-pressure pyrolysis and gasification of biomass

Georgia Institute of Technology

March 4 Group Seminar Elizabeth Brunk A workflow to systematically integrate polyomic data and metabolic modeling

Fuels Synthesis Division


Prof. Hiroshi Nikaido Multidrug Efflux by E. coli AcrB: Substrates, Inhibitors, and Stimulators.

Graduate School Division of Biochemistry, Biophysics and Structural Biology

March 4 Group Seminar Sarah Richardson Making genetic toolkits: Wrangling up Streptomyces venezuelae et al


March 4 Group Seminar Elizabeth Brunk A workflow to systematically integrate polyomic data and metabolic modeling



Prof. Bernhard Palsson Workflows for genome-scale model deployment in metabolic engineering

Department of Bioengineering, & Pediatrics at the University of California, San Diego

March 11 JBEI Seminar Series Chris Petzold Proteomics for Biomanufacturing Technology Division



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Research

March 11 Group Seminar Andrew Hagen Understanding and engineering an atypical polyketide synthase for chemical production


March 11 Group Seminar Clara Eng Altering Polyketide Stereochemistry Using Domain Swapping


March 13 General Seminar Technology Guest

Eric W. Lam, Ph.D Design & application of a continuous flow microcalorimeter using off-the-shelf components

Electrical Engineering and Computer Science, Massachusetts Institute of Technology


Cynthia M. Cipolla Analytical Techniques for Evaluating Function in Islets of Langerhans

Analytical Chemistry


Yinjie Tang 13C-metabolism analysis of microbial cell factories: a touch of revelation

University of Michigan

March 18 Group Seminar Bob Haushalter Expanding the chemical diversity of E. coli-derived products


March 18 Group Seminar Tristan De Rond High-throughput mass-spectrometric enzyme activity determination with PECAN



Prof. Peter Punt Approaches for engineering of fungi and yeasts towards production of building Block chemicals

TNO, Microbiology & Systems Biology

March 25 Group Seminar Dan Arlow Single-molecule DNA Construction: toward rapid de novo synthesis of multi-kilobase DNA




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March 25 JBEI Seminar Series Peter Matlock JBEI IP management, issues, opportunities, policies, etc.

JBEI - Technology & Commercialization


Michael S. Bono, Jr. Dielectic measurement of algal lipid content for biodiesel production

Sandia Post Doc Interview Candidate (Technology Division)


Todd Duncombe Microfluidic Bioanalytical Device & Assay Development for High-Throughput Electrophoretic Protein Analysis

Sandia Post Doc Interview Candidate (Technology Division)



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Honors & Awards

Name Award

Harry Beller Named as an Associate Editor at BMC Biotechnology

Jay Keasling Honorary doctorate from Chalmers University of Technology for his significant contributions in metabolic engineering

Jay Keasling Inducted as National Academy of Inventors Fellow

Industry Interactions

Date Company / Contact

March 9 Ajinomoto Co., Inc / Ito Hisao, Yuri Uehara Nagai, Keita Fukui and Kazuo Nakanishi

March 9 POET / Wade Robey

Area of interest: Invitation to visit JBEI.

March 10 Agilent / Steve Royce


March 23 Monsanto / John Edward Hamer, Michael Lopez and Kiersten Stead


March 25 Kinkead Reiling

Area of interest: Discuss business development

March 19 Technology Holding / Mukund Karanjikar

Area of interest: Discuss potential NSF SBIR application.

March 23 Total / Florence Mingardon

Area of interest: Discuss option agreement



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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 52

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

Sept. 2015 50

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

Sept. 2015 50

Characterization of novel nucleotide sugar transporters (SB) Sept. 2015 60

Characterization of novel GT activities (SB) Sept. 2015 65

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 60

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

Sept. 2015 47

Nucleotide sugar transporters used for cell wall engineering (CWB) Sept. 2015 57

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

Sept. 2015 45

Analysis of stacked traits in Arabidopsis (CWE) Sept. 2015 50

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

Sept. 2015 40



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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 50

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

Sept. 2015 50

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

Sept. 2015 50



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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 90

Complete characterization of lignin streams from various IL pretreatment process configurations

July 2015 60

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

Aug. 2015 60

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 60

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 90

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 50

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

Sept. 2015 60



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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 70

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

Sept. 2015 80

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 75

Optimize cultivation conditions for heterologous enzyme production, including temperature and pH, and initiate ‘omic analysis of optimal vs. baseline conditions

July 2015 60

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

Sept. 2015 50



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Milestones



Discovery of Novel Hydrocarbon Biochemistries

In vitro, anaerobic testing of toluene biosynthesis candidates Sept. 2015 50

In vitro, anaerobic testing of ladderane biosynthesis candidates Sept. 2015 50

Optimization of Hydrocarbon Biosynthetic Pathways

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

Sept. 2015 50

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

Sept. 2015 55

Genes encoding isoprenoid pathway integrated into E. coli chromosome

Sept. 2015 50

Three enzymes in S. cerevisiae glycolytic pathway replaced and impact on fatty acid-derived fuel tested

Sept. 2015 50

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 50

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 55



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Milestones

Fuels Synthesis Division (continued)


Synthetic Bio Informatics

Codon optimization tool (GeneDesign) integrated into the DIVA platform.

Sept. 2015 50

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

Sept. 2015 50

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 75



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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 45

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

Sept. 2015 56

Implement software to automate unit operations (e.g., droplet dispensing, routing, merger, and sorting) on an integrated droplet chip

Sept. 2015 50

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

July 2015 60

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

Sept. 2015 70

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

Sept. 2015 75

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

Sept. 2015 70



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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 50

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

Sept. 2015 50

Structural Biology Test expression of multiple GT clones in insect cell platform to produce quantities of protein for crystallization trials

Sept. 2015 65

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 40

Synthetic Bio Informatics

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

Sept. 2015 50

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

Sept. 2015 50

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

Sept. 2015 50



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Milestones

Operations Management Division


Intellectual Property Management

Generate >10 inventions Sept. 2015 85

Educate researchers about the tech transfer process Sept. 2015 52

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 50

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 55

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

Sept. 2015 50

Business Development Outreach

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

Sept. 2015 52

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

Sept. 2015 50

Industry Advisory Committee

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

Sept. 2015 50

Industry Partnership Program

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

Sept. 2015 52



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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 50

Annual JBEI Conference

Annual JBEI Retreat Sept. 2015 67

Human Resources Staffing for year 8 complete Sept. 2015 50

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