1. 1 Plan for group integration and response to RFA November 21, 2006 John Aach, PhD, Lecturer Church Lab Department of Genetics Harvard Medical School aach@receptor.med.harvard.edu CONFIDENTIAL

2. 2 What we are now Fantastic -- great science, stature, experience! We are a major force now. Not completely familiar with each other Projects unintegrated. Many individuals/groups with independent projects should connect and synergize Budget a bit too big with items still coming in. Need for prioritization and adjustments –Currently ~$30.4M / year vs. $30M / year ( = $25 GTL-BRC + $5 GTL-SB)

3. 3 Objectives for this meeting Operate as a Center –Establish climate of open discussion Start process of Center-wide integration –Look for opportunities for improvement and integration –Understand our strengths & strengths of competing teams Establish focus on what it will take to have a winning proposal –Bring merger and budget considerations within that focus –Discuss how to align project repertoire with DOE expectations –Provide food for thought on what projects, people, and groups need to do to fit into winning proposal Call for preliminary management team; identify next steps

4. 4 Things we will not do Completely resolve project integration or budget considerations –Much will be left to preliminary management team Things we need to do Disclose contacts / collaborations with other proposal groups and BP effort

5. 5 Purpose of this talk Describe on-going thinking about how to structure Center / proposal Identify key themes and issues that we need to think and talk about in today’s area-specific sessions Identify some of the next steps

6. 6 Plugging in + some next steps for everyone Contact me to get on Center email distribution list and to get access to the Center proposal wiki wiki address: http://karma.med.harvard.edu/gclab-gtl my email: aach@receptor.med.harvard.eduhttp://karma.med.harvard.edu/gclab-gtlaach@receptor.med.harvard.edu wiki GTL_grant_sections page has project write-up examples and standards. Get me information sufficient to render your project into this format by the end of November. –~60-65 pages for “project narrative”, currently >50 projects –Deliverables, Time Line, Project Summary that is clear concerning proposed project activities We consider the wiki, this meeting, and all associated materials to be confidential.

7. 7 DOE says a BRC must … Basic attributes be a Center be a Genomics:GTL BRC have short, intermediate, and long term vision respond to shifting research directions / promising opportunities Activities conduct basic, genomics-based research; fundamental science develop basic research to point of easy transition to applied science – “real steps to real solutions” support range of “high-risk, high-return” approaches (“high-payoff breakthroughs”) top priority: improve production of liquid transportation fuels; cellulosic ethanol = “most plausible near-term candidate” Other “vertical integration” (?? – two perspectives) –develop & integrate needed core capabilities (Center) –complete, integrated strategy for improving biofuel production (Process) understand current industry roadblocks; aim to resolve them quality assurance / information management strategy component collaborate with National Labs / companies

8. 8 Resources relevant to DOE expectations for BRCs RFA 8/2006 6/2006 White Paper 8/2006

9. 9 Resources relevant to DOE expectations for Genomics:GTL Centers NAS Report 3/2006 DOE Roadmap: 4 Centers which are “user facilities”, each dedicated to single capability –Protein production, “molecular machines”, proteomics, modeling Centers to support microbial research for 3 long-term goals –Bioenergy, environmental remediation, carbon cycling/climate NAS: Better to have these capabilities “vertically integrated” in each Center & dedicate Centers to specific goals (Bioenergy = #1) DOE: accepted NAS recommendations (embodied in the RFA) 2005

10. 10 Two DOE offices have had input … Office of Biomass Program Office of Science RFA comes from OBER Harvard/MIT GTL Center = Genomics:GTL Center

11. 11 What we need to have for a winning RFA response Centerhood Integrated project portfolio that addresses DOEs expectations Other attributes –Short, intermediate, long term goals –Required components (QAIMS) Draft Center Vision / Letter of Intent statement http://karma.med.harvard.edu/gclab-gtl/ Go to GTL_Grant_Sections and look at Center Vision item

12. 12 Centerhood Geographical vs. “conceptual” No DOE requirement for geographical Centers but DOE makes allowances for them, suggesting possible preference We claim that ‘conceptual center’ with ‘best + most experienced minds’ is better than a geographical Center How to achieve Centerhood Unified vision, integrated plan, integrated management (see wiki) We need to start today by setting up a preliminary management team Center composition Very desirable to include National Labs, companies

13. 13 Project portfolio implicit in DOE documents Improve current practice Move mainstream research directions closer to practice “real steps to real solutions” Explore alternative paradigms (e.g., biodiesel / alkanes..) Explore new organisms, capabilities “high-payoff breakthroughs” systems biology enabling basic science and technology GTL:Genomics approach Process and economic modeling, policy analysis environmental + ELSI ‘Understand industry roadblocks’

14. 14 “real step to real solution” vs. “high-payoff breakthrough” Distinction

15. 15 “real step to real solutions” vs. “high-payoff breakthrough” Fermentation Organisms that take lignocellulose hydrolysates  EtOH on par/+ with organisms taking starch  EtOH –C5+C6  EtOH >95% theory yield –Final EtOH titers 10-15% –2-5 g/L-h productivity –Resistant to hydrolysate toxins Genomes and sys.bio on engineered, evolved, wt yeast, coli Additional engineering, evolutions Process improvements: SSCF, less severe pretreatments, CBP Microbial communities vs. monocultures Predictive systems models of metabolism and regulation Direct production of alkanes, long chain alcohols, fatty acids Final EtOH titers of 40% Biocatalysts taking syngas  EtOH “real steps to real solutions”“high-payoff breakthrough”

16. 16 “real step to real solutions” vs. “high-payoff breakthrough” Feedstock deconstruction Structure / chemistry analysis of cell walls Better ligninases, hemicellulases Better understanding / improvement of cellulases, cellulosomes Discovery of new enzymes / systems via metagenomics High-throughput characterization of cell walls Express cell wall deconstruction enzymes in plants “real steps to real solutions”“high-payoff breakthrough”

17. 17 “real step to real solutions” vs. “high-payoff breakthrough” Biofeedstocks Understand, optimize cell wall structure and composition (e.g., control lignin) Understand “type II” (energy only) plants such as perennial grasses Understand / modify poplar Stress tolerance, productivity High-productivity biodiesel crops (“other” opportunity) “real steps to real solutions”“high-payoff breakthrough”

18. 18 “real step to real solutions” vs. “high-payoff breakthrough” Bottom line “real steps to real solutions” –Improve current practice –mainstream research directions that have demonstrated at least a small improvement –current systems biology / genomic / analytic tools on principal organisms, features, enzymes / structures –extend modifications in one system to another similar one –certain well-argued good ideas that have not been demonstrated “high-payoff breakthrough” –Good idea that has been tried / theoretically feasible but for which there is uncertainty regarding successful development –Understand, develop, exploit currently uncharacterized phenomenon found in nature relevant to bioenergy

19. 19 Enabling technology

20. 20 Enabling technologies & expertise available in Center Low cost genome DNA resequencing –e.g., for strains optimized by artificial evolution low cost DNA or RNA tag sequencing low cost DNA synthesis from oligos –e.g., synthesis of libraries of gene or promoter variants metagenomics artificial evolution single-cell sequencing membrane protein production and purification computational modeling –e.g., reverse engineering of regulatory networks, –metabolic network modeling –forward engineering of artificial circuits (switches, counters, etc.)?Low- cost resequencing

21. 21 Process modeling and economic and policy analysis p. 181

22. 22 Some of your answers

23. 23 Project universe by pathway steps AGRICULTURE Separate vs. CBP Enabling Tech: Modeling, Synthesis, Evolution, Sequencing, … Plants Pretreat  Trichoderma, Clostridia, Aspergillus, new … x (soluble vs. cellulosome) Ferment Pichia, Klebsiella, new, communities … x (sequential vs. cofermentation)  Zea,Miscanthus,Poplar, Crambe, Algae  silage x (acid, NH4) Saccharify  Saccharomyces, Escherichia, Zymomonas, Extract  distill, gas strip, phase Process  crack, blend, zeolite, … Uses  transportation, chemicals, power

24. 24 Process and economic modeling combined with field testing as a kind of high-level systems biology PROJECTS AGRICULTURE Plants Pretreat Ferment Saccharify Extract Process Uses AGRICULTURE Plants Pretreat Ferment Saccharify Extract Process Uses Process and economic modeling AGRICULTURE Plants Pretreat Ferment Saccharify Extract Process Uses Field testing (Fields-to- Wheels?) CENTER INDUSTRY

25. 25 Our current project mix Project category Pathway step

26. 26 Project category and pathway steps as management tools Should we set targets for fraction of budget or project number for project categories? How about pathway steps?

27. 27 Other attributes “Short, intermediate, long term vision” required by DOE, but time frames are not identified in RFA –Cellulosic ethanol report: 5, 10, 15 year time frames –GTL:Genomics Roadmap: 1-8, 9-15, >15 year time frames (1.3.6.1) –Center is funded for 5 years, so could be 1-2, 2-4, 5 years. Quality Assurance and Information Management Strategy –Assumption is that there will need to be a bioinformatics ‘czar’ in the Center to help coordinate data and computational resources and guide them towards accepted standards

28. 28 Questions to ask yourself for rest of day Where does my project fit into the DOE scheme of things? What are the “real steps” vs “breakthrough” directions for each process category? (Is DOE right?) What is the likely economic benefit of my project? What are reasonable targets and priorities for project categories and pathway steps? How can my project synergize with others I am hearing about? What enabling technologies will help my project? Have we interpreted DOE expectations correctly? Should we argue with them vs. accept them? Budget issues –Can the project category / pathway step framework help guide budget adjustments? –Should there be special provisions for companies in the budget? Do we have a reasonable approach to Centerhood? What is a good name for our Center?

29. 29 “Next steps” that will follow this meeting Settle on preliminary management team Develop priorities and implement in project portfolio and budget Finalize Letter of Intent Get on the Center proposal mailing list Look at Center proposal wiki and revise, supplement your project write-ups by end of November. List of core services at your institution

30. 30 Thank you! John Aach aach@receptor.med.harvard.edu 617-432-0061 http://karma.med.harvard.edu/gclab-gtl/

31. 31 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? CONFIDENTIAL

32. 32 Thank you for coming & Enjoy your Thanksgiving holiday! George and John