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DOE Bioenergy Center proposalDiscussion sections
November 21, 2006
George Church and John Aach
Department of Genetics
Harvard Medical School
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Things to consider in each session
• Does this project group have a different priority than others?
• Are there synergies between these projects or with projects in other groups?
• Are there overlaps which should be resolved?
• What enabling technologies can these make use of– low cost DNA or RNA resequencing
– low cost DNA synthesis from oligos
– artificial evolution
– metagenomics
– single-cell sequencing
– membrane protein production and purification
– computational modeling
• Can specific economic benefits be assigned to any of these projects?
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Project list: Plants
2 AgrividaM. Raab (F. Ausubel)Efficient pre-harvest expression and accumulation of combinations of cell wall degrading enzymes in plants, and their post-harvest stability and effectiveness
enabling_technology
7 Brookhaven National LabC-J LiuAssess the roles of O-acylation and -deacylation enzymes in biomass formation and identify modifications that enhance lignocellulose degradation
real_step
8 Chromatin, Inc. D. PreussImprove plant biofeedstock characteristics using autonomous mini-chromosomes
enabling_technology
23 Penn State D. Braun, D. CosgroveGenetic Approaches to Improved Biomass Feedstocks [Reduced Silica, Higher Degradability
real_step
22 Penn State D. Braun, M. GuiltinanGenetic & Biochemical Analyses of Carbon Partitioning in Plants
real_step
24 Penn State D. Cosgrove, M. Buanafina, M. Tien, J. Carlson, H. Liang, K. HooverTechnologies for Generating Cellulosic Biomass for Faster Saccharification
breakthrough
25 Penn State M. Buanafina, M. Guiltinan, J. CarlsonPlant Transformation Facility enabling_technology
21 Penn State W. Curtis (P. Laible, D. Hanson)
Explore "trickle-down" bioreactor as mechanism for increasing algal biomass productivity by orders of magnitude in support of biodiesel, and for optimizing Rhodobacter-based membrane protein expression system
breakthrough
37 U. Florida, Michigan TechS. Joshi, L. IngramChanging plant cell wall composition for energy crops real_step38 U. KentuckyJ. ChappellC30-34 hydrocarbon-enhanced Plant and algae biomass breakthrough
40 U. Mass AmherstD. Schnell, (O. Parkash, T. Baskin, J. Normanly, S. Herbert, R. Prostak, Optimization of Feedstocks for Consolidated Bioprocessing to Generate Biofuels and Bioproducts
real_step
53 INL through PSUPLACEHOLDER: projects not yet defined real_step54 SC Vance RNA silencing in Arabidopsis enabling_technology30 Penn State T.L.Richard, P. Adler, G. Roth, J. Carlson, G. Caufmann, W. Curtis, A. Demirci, A. Zydney, A. Boehman, C. Song, J. Perez, J.R. Hess, C. RadtkeFields-to-Wheels Bioenergy Testbed Facility process_modeling
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Saccharification and CBP
4 Boston U. J. CollinsIdentification of efficient artificial cellulosomes using phage display
breakthrough
12 Harvard Med SchoolF. Ausubel (A. Diener, C-J Liu)Optimization of plant-pathogen derived CWDEs for biofuel feedstocks
real_step
13 Harvard Med SchoolW. ShihIdentification of efficient artificial cellulosomes using in vitro selections of very highly combinatorial libraries of DNA-display-based cellulosome mimics
breakthrough
26 Penn State P. Cirino, C.D. Maranas, S. BenkovicProtein Engineering for Biofuels: Enzyme engineering of (hemi)cellulases
real_step
32 U. FloridaL. Ingram &c.Reducing dependence on fungal cellulase (reduce cost of polymer hydrolysis): Explore use wood degrading insects
real_step
33 U. FloridaL. Ingram &c.Reducing dependence on fungal cellulase (reduce cost of polymer hydrolysis): integration & expression of glycohydrolases & uptake systems (dimers/trimers)
real_step
34 U. FloridaL. Ingram &c.Reducing dependence on fungal cellulase (reduce cost of polymer hydrolysis): B. coagulans
real_step
47 U. WisconsinT. JeffriesCharacterize and create cellulase and xylanase hypersecreting strains of fungi.
real_step
39 U. MaineH. Pendse, (S. L. Hsu, [UMass], P. Millard, A. van Heiningen, J. Genco)On-site Integration of Consolidated Bioprocessing into an Existing Industrial Facility
process_modeling
41 U. Mass AmherstJ. Blanchard, (S. Leschine, M. Henson)Optimization of C. phytofermentans for the Direct Conversion of Cellulosic Biomass to Ethanol
real_step
42 U. Mass AmherstS. Leschine, (D. Schnell, L. McLandsborough, J. Blanchard, M. Henson)A Novel Bacterial Catalyst for Consolidated Bioprocessing of Biomass to Ethanol
real_step
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BP
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Fermentation
6 Boston U. J. CollinsSystems & synthetic biology platform for reverse and forward engineering of regulatory networks for bioenergy
real_step
11 Harvard Med SchoolG. Church
Complete development of and apply High Throughput Mutation Detection - Combinatorial Variation technology to improve yield and production characteristics of a diverse set of biofuel-generating microbes
real_step
36 U. FloridaL. Ingram &c. (G. Church)Metabolic engineering for inhibitor resistance / sugar co-utilization + pretreatments
real_step
31 U. FloridaL. Ingram &c. (G. Church)Merging fermentation of hemicellulose hydrolysates (dilute acid) with cellulose hydrolysate fermentation
real_step
35 U. FloridaL. Ingram (with G. Church)Reduce water use by integrating re-utilization and production of co-products, and increasing ethanol tolerance
real_step
46 U. WisconsinT. Jeffries
Characterize and create P. stipitis with improved fermentation efficiency and production environment tolerance using combinatorial exploration of expression and effective mutation space
real_step
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Economic and process modeling; process improvement
30 Penn State T.L.Richard, P. Adler, G. Roth, J. Carlson, G. Caufmann, W. Curtis, A. Demirci, A. Zydney, A. Boehman, C. Song, J. Perez, J.R. Hess, C. RadtkeFields-to-Wheels Bioenergy Testbed Facility process_modeling
44 U. Mass AmherstM. Henson, (M. Malone, TJ Mountziaris, D. Ford)UMass Process Engineering and Design Component
process_modeling
43 U. Mass AmherstS. Auerbach, (G. Huber, Integration of Chemical Catalysis into a Biorefinery unclassified
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Alternative biofuels / paradigms
• Do we need to have a general strategy for dealing with projects which yield alternative biofuels (including non-liquid or non-transportation fuels), or different pathways (including non-biological), or different technologies? Or is it case-by-case?
19 Harvard Med SchoolP. SilverIncorporate pathways into S. cerevisiae that support bio-hydrogen generation
breakthrough
28 Penn State D. A. Bryant, J. H. GolbeckEngineering Novel Metabolic Capabilities in Cyanobacteria for Bioenergy
breakthrough
27 Penn State J.G. Ferry, P. Cirino, J.J. ReganMethane and Syngas Fermentation breakthrough
29 Penn State J.M. Regan and B.E. LoganMicrobial Fuel Cells for Coupled Energy Recovery and Water Reuse
breakthrough
48 UCLA A. DienerLipid accumulation in Fusarium breakthrough
21 Penn State W. Curtis (P. Laible, D. Hanson)
Explore "trickle-down" bioreactor as mechanism for increasing algal biomass productivity by orders of magnitude in support of biodiesel, and for optimizing Rhodobacter-based membrane protein expression system
breakthrough
43 U. Mass AmherstS. Auerbach, (G. Huber, Integration of Chemical Catalysis into a Biorefinery unclassified
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38 U. KentuckyJ. ChappellC30-34 hydrocarbon-enhanced Plant and algae biomass
breakthrough
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Pretreatment, Extraction, Use
• These areas are not well represented. Only projects are:
• Instead, many projects attempt to deal with them via upstream or downstream modifications, e.g., – Modify plants to reduce pretreatment– Modify microbes to be tolerant to inhibitors and conditions
generated by pretreatment– Reduce extraction costs by increasing EtOH tolerance
• Is this acceptable, or do we want more projects specifically addressed to them?
43 U. Mass AmherstS. Auerbach, (G. Huber, Integration of Chemical Catalysis into a Biorefinery unclassified
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56 Penn State T. RichardPLACEHOLDER: Biological pretreatment via silage real_step
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Enabling science and technology3 Argonne National LabP. Laible, D. Hanson
Improved production of membrane proteins relevant to biomass to biofuels processing
enabling_technology
5 Boston U. D. SegreBioenergy-relevant extensions of Flux Balance Analysis models and their applications to Center organisms
enabling_technology
9 HarvardC. MarxEvolving tradeoffs: role of selective regime on specialization and adaptation
enabling_technology
10 HarvardC. MarxThe origin of cooperation and coevolution: selection of increased metabolite production in spatially-structured, cross-feeding microbial consortia
enabling_technology
14 Harvard Med SchoolG. ChurchGeneration of Flux Balance Analysis models for Center organisms
real_step
15 Harvard Med SchoolG. ChurchImproved and multiplex single cell genome sequencing on environmental samples
enabling_technology
17 Harvard Med SchoolG. ChurchDevelopment of engineered RNA molecules to control gene expression, sense metabolites and optimize the properties of metabolic pathways
enabling_technology
18 Harvard Med SchoolG. ChurchGenome re-engineering (rEcoli) enabling_technology
16 Harvard Med SchoolW. ShihStructures of transporters using DNA-nanotube liquid crystals
enabling_technology
20 MIT P. Chisholm, M. Polz, E. AlmGenomic structure, metagenomics, horizontal gene transfer, and natural diversity of Prochlorococcus and Vibrio (GTL Systems Biology project)
enabling_technology
45 U. MichiganN. Lin Development of alternative modeling techniques enabling_technology
49 Harvard Med SchoolSarracino, KucherlapatiPLACEHOLDER: service cost referred to by Marx but not quantified
enabling_technology
50 MIT Endy, Knight, RettbergPLACEHOLDER: Synthetic Biology enabling_technology51 MIT JacobsonPLACEHOLDER: Genome Engineering enabling_technology52 UCSD Palsson PLACEHOLDER: Flux balance modeling enabling_technology
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Open discussion
• ???
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Budget
We intend the preliminary management team to work out the budget.
Here we want input on:• Should some project areas / pathway steps get more
/ less priority?• In what way should we accommodate companies in
the budget?• How should we manage the budget process going
forward?
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Next steps
Preliminary management team • Needs to be defined ASAP• First duties of PMT: letter of intent, review / reorganize
budget
Everyone else• Get ‘plugged in’ (email distribution list, wiki access)• Flesh out, reformat project write-ups by November 30.• Disclose contacts / collaborations with other BRC
groups / BP
Up and coming• Review of integrated proposal
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Thank you for coming &
Enjoy your Thanksgiving holiday!
George and John
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