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GTL PI Meeting 2007 Abstracts DOE/SC-0098 Joint Meeting Genomics:GTL Awardee Workshop V and Metabolic Engineering Working Group Interagency Conference on Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop 2007 Bethesda, Maryland February 11–14, 2007 Prepared for the Prepared by U.S. Department of Energy Genome Management Information System Office of Science Oak Ridge National Laboratory Office of Biological and Environmental Research Oak Ridge, TN 37830 Office of Advanced Scientific Computing Research Managed by UT-Battelle, LLC Germantown, MD 20874-1290 For the U.S. Department of Energy Under contract DE-AC05-00OR22725 http://genomicsgtl.energy.gov Welcome elcome to the 2007 Joint Genomics:GTL fundamental research addressing DOE mission Awardee Workshop, Metabolic Engineer- needs, including bioenergy. DOE embraced this Wing Interagency Working Group Conference ,and recommendation, and review of proposals for GTL the USDA-DOE Plant Feedstock Genomics for Bioenergy Research Centers is under way. Bioenergy Joint Program Meeting. Attendees of this year’s joint meeting represent a broad cross sec- This year’s meeting features sessions that will be of tion of cutting-edge research disciplines, including broad interest to scientists funded by all three of the microbiology, plant biology, genomics, proteomics, participating research programs—the Genomics: physiology, structural biology, metabolic engineering, GTL program, the Metabolic Engineering Work- ecology, evolutionary biology, bioinformatics, and ing Group, and the USDA-DOE Plant Feedstock computational biology. Uniting this diverse com- Genomics for Bioenergy Joint Program. The goal of munity of researchers is the shared goal to understand the Metabolic Engineering Working Group is the the complex genetic and metabolic systems supporting targeted and purposeful alteration of an organism’s the life of microbes, plants, and biological communi- metabolic pathways to better understand and use ties. This approach is by definition integrative and cellular pathways for chemical transformation, multidisciplinary, and we applaud the collaborative energy transduction, and supramolecular assembly. spirit that brings you to this meeting and informs The USDA-DOE Plant Feedstock Genomics for your research. This joint meeting provides unique op- Bioenergy joint program focuses on genomics-based portunities to enhance collaboration and advance sci- research leading to the improved use of biomass and ence beyond the boundaries of any of these individual plant feedstocks for the production of such fuels as research programs. ethanol or renewable chemical feedstocks. By bring- ing together these distinct but complementary re- In May of 2006, the National Research Council of search communities, we hope to foster the exchange the National Academies completed an independent of ideas, sharing of expertise, and formation of new review of the Genomics:GTL program. The review partnerships among researchers. committee enthusiastically endorsed the systems biol- ogy focus of the program, lauded the general excel- We look forward to an exciting and productive meet- lence of research conducted by its grantees, and re- ing and encourage you to participate in discussions emphasized the critical importance of the program’s and build new relationships. We wish to thank the core mission—to advance fundamental research on organizers of this year’s meeting, especially members bioenergy solutions, bioremediation of environmental of the research community who have generously contaminants, and global carbon cycling and seques- agreed to play a larger role in organizing this year’s tration. The review also recommended that, in place breakout sessions. Finally, we thank you for lending of the previously proposed technology-oriented user your knowledge, creativity, and vision to the repre- facilities, the Genomics:GTL program should form sented research programs and wish you continued interdisciplinary research centers focused on success in the coming year. Jerry Elwood Michael Strayer Fred Heineken Anna Palmisano Acting Associate Director Associate Director of Chair of the Interagency Deputy Administrator of of Science for Biological and Science for Advanced Metabolic Engineering Competitive Programs Environmental Research Scientific Computing Working Group Cooperative State Research, Office of Science Research National Science Foundation Education, & Extension U.S. Department of Energy Office of Science Service U.S. Department of Energy U.S. Department of Agriculture Agenda Sunday Evening, February 11th 2:00-4:30 Breakout Session A USDA-DOE Plant Feedstock Genomics for Bioenergy Joint Program 5:00-8:00 Registration and Poster Setup Meeting Moderators: Ed Kaleikau (USDA) & Sharlene Weatherwax (DOE) 6:00-8:00 Mixer 2:00-2:15 Program Overview: Chavonda Jacobs-Young - USDA 2:15-2:30 Vincent Chiang – North Carolina State University th Monday, February 12 2:30-2:45 Clint Chapple – Purdue University 2:45-3:00 Chang-Jun Liu – Brookhaven National Laboratory 7:00-8:00 Continental Breakfast 3:00-3:15 Bikram Gill – Kansas State University 3:15-3:30 Richard Dixon – The Nobel Foundation 8:00-8:45 Welcome 3:30-4:00 Break State of Genomics:GTL Program, Vision for the Future 4:00-4:15 William Rooney – Texas A&M University Mike Viola, David Thomassen, and Jim Fredrickson 4:15-4:30 Charles Brummer – University of Georgia 8:45-9:15 Systems Biology: An Overview 4:30-4:45 John Ralph - USDA-ARS, University of Wisconsin 4:45-5:00 Chris Somerville – Carnegie Institute of Timothy Donohue – University of Wisconsin, Madison Washington “Systems Analysis of Solar Energy Stress Responses” 2:00-5:00 Breakout Session B 9:15-12:00 Plenary Session Data Management & Sharing Tutorial Carbon Processing at Organismal, Community, & Global Scales Organizers: Ed Uberbacher – Oak Ridge National Laboratory Moderator: Dan Drell Jeff Grethe – University of California, San Diego Session Objectives: This session will examine the global carbon Moderator: John Houghton cycle at various levels of resolution and from a variety of differ- 2:00-3:30 Panel Discussion (Participants To Be Announced) ent research perspectives. The goal of the session is to promote 3:30-4:00 Break discussion of potential contributions of GTL research towards more 4:00-5:00 Group Discussion effectively modeling the global carbon budget and understanding the role of microbes and microbial communities in planetary scale 2:00-5:00 Breakout Session C processing and sequestration of carbon. Cultivation Methodology Tutorial 9:15-9:45 Jae Edmonds – Pacific Northwest National Moderator: Joe Graber Laboratory Organizers: Slava Epstein & Hans Scholten “Biotech, Energy, and a Climate-Constrained World” 2:00-2:20 Slava Epstein – Northeastern University 9:45-10:15 Bruce Hungate – Northern Arizona University 2:20-2:40 Hans Scholten – Pacific Northwest National Title To Be Announced Laboratory 2:40-2:55 Martin Keller – Oak Ridge National Laboratory 10:15-10:30 Break 2:55-3:10 Chris Belnap – University of California, Berkeley 10:30-11:00 Mary Lidstrom – University of Washington 3:10-3:25 Judy Wall – University of Missouri, Columbia “Integrated Metabolism Studies of Methylotrophy” 3:30-4:00 Break 11:00-11:30 Ramon Gonzalez – Rice University 4:00-5:00 Group Discussion “The Role of Metabolic Engineering and Systems 5:00-8:00 Poster Session Biology in Biofuel Production” 12:00-2:00 Lunch Tuesday, February 13th 2:00-5:00 Breakout Session D Metabolic Engineering Interagency Working Group Conference: 7:00-8:00 Continental Breakfast Methods to Examine Biochemical & Metabolic Networks Organizers: Gail McLean (USDA) & Sharlene Weatherwax (DOE) 8:00-10:00 Plenary Session Moderators: Mark Segal (EPA) & Fred Heineken (NSF) Environmental Sensing & Response In Contaminated Habitats 2:00-3:30 Presentations: Moderator: Joe Graber Bernhard Palsson – University of California, Session Objectives: This session will examine the means by which San Diego microorganisms sense environmental conditions and process the George Bennett – Rice University acquired information to form an adaptive response. Emphasis will James Liao – University of California, Los Angeles be placed on the role of GTL research in understanding organismal Jackie Shanks – Iowa State University and community dynamics in relevant habitats and how this 3:30-4:00 Break information can be integrated into the study of contaminant fate 4:00-5:00 Group Discussion and transport. 2:00-5:00 Breakout Session E 8:00-8:30 Derek Lovley – University of Massachusetts, Tools for the Prediction & Validation of Gene Function Amherst Organizers: Margaret Romine – Pacific Northwest National “Adaptive Evolution and Adaptive Responses Laboratory in Gene Expression of Geobacter Species During Andrei Osterman – The Burnham Institute Uranium Bioremediation and in Microbial Moderator: Marvin Stodolsky Fuel Cells” 8:30-9:00 Tim Gardner, Boston University 2:00-3:30 Panel Discussion: “Genome-scale mapping of transcription networks Scott Lesley - Scripps Research Institute in Shewanella oneidensis: identification of carbon Tom Squier - Pacific Northwest National Laboratory and metal-respiratory regulation” Tim Gardner - Boston University 9:00-9:30 Jill Banfield - University of California, Berkeley 3:30-4:00 Break Title To Be Announced 4:00-5:00 Group Discussion 9:30-10:00 Adam Arkin – Lawrence Berkely National Laboratory 2:00-5:00 Breakout Session F Title To Be Announced Imaging Techniques Tutorial Organizers: Eva Nogales - University of California, Berkeley 10:00-10:15
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