Joint Meeting - Genomics - U.S. Department of Energy

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2 The following table is a summation of how GTL science and DOE missions align (DOE Genomics:GTL Roadmap: Systems Biology for Energy and Environment; October 2005, p. 40). (GenomicsGTL.energy.gov) Summary Table. GTL Science Roadmap for DOE Missions A capsule summary of systems being studied, mission goals that drive the analysis, generalized science roadmaps, and outputs to DOE missions. To elucidate design principles, each of these goals entails the examination of thousands of natural primary and ancillary pathways, variants, and functions, as well as large numbers of experimental mutations.
Systems Biology for DOE Energy and Environmental Missions Bioenergy Biofuels > Bioenergy Research Centers 1 Great Lakes Bioenergy Research Center Timothy Donohue, 1 * Kenneth Keegstra, 2 Richard Amasino, 1 Bruce Dale, 2 Robert Landick, 1 John Ohlrogge, 1 George Phillips, 2 Phillip Robertson, 2 and Michael Sussman 1 1 University of Wisconsin, Madison, Wisconsin and 2 Michigan State University, East Lansing, Michigan Project Goals: Remove the bottlenecks in converting biomass into biofuels. GTL The Great Lakes Bioenergy Research Center (GLBRC) is led by the University of Wisconsin-Madison, in close partnership with Michigan State University (www.greatlakesbioenergy.org). Additional scientific partners include the Pacific Northwest National Laboratory, Oak Ridge National Laboratory, University of Florida, Illinois State University, Iowa State University, and Lucigen Corporation. Located in the world’s most productive agricultural region, the GLBRC is taking scientifically diverse approaches to converting sunlight and diverse plant feedstocks (agricultural residues, wood chips, grasses) into fuels. GLBRC programs are organized in the following areas: Improving Plant Biomass: In addition to studying how genes affect cell-wall assembly, GLBRC will be breeding plants to produce hemicellulose, starches and oils that are more easily processed into fuels. GLBRC researchers aim to increase the energy density of grasses and other nontraditional oil crops by understanding and manipulating the metabolic and genetic circuits that control accumulation of oils and other easily digestible polymers in plant tissues. Improving Biomass Processing: New and improved catalysts created by the GLBRC protein-production pipeline will be used with a range of plant materials and pretreatment conditions to identify the best mix of enzymes, chemicals, and physical processing for enhanced digestibility and increased fuel production from specific biomass sources. To decrease the costs of producing and using enzymes to breakdown plant cellulose, researchers are working to express biomass-degrading catalysts in the stems and leaves of plants—essentially designing crops that “self-destruct” on cue in the biofuel-production facility. Improving Biomass Conversion to Energy Compounds: GLBRC biomass-conversion research is driven by the need to increase the quantity, diversity, and efficiency of energy products derived from plant biomass. Cellulosic ethanol is a major focus of GLBRC research, but the center will also improve biological and chemical methods for converting plant material into hydrogen, electricity, or other chemicals that can replace fossil fuels. Fostering Sustainable Bioenergy Practices: For a bioeconomy to positively impact the energy grid, complex issues in agricultural, industrial, and behavioral systems must be addressed. To create a better understanding of what will ultimately influence the direction and acceptance of new bioenery technologies, GLBRC scientists will examine the environmental and socioeconomic dimensions of converting biomass to biofuel. To determine the best practices for biofuel production, GLBRC researchers will study how to minimize energy and chemical inputs for bioenergy crop production, reduce greenhouse gas emissions from the biofuel production life cycle, and predict environmental impacts of removing stalks, stems, and leaves from food crops. GLBRC scientists also will study the social and/or financial incentives needed to adopt these best practices. Creating Technologies to Enable Advanced Bioenergy Research: Core GLBRC activities will provide cutting-edge, genome-based technologies to enable the innovative discoveries and creative solutions needed to advance bioenergy research. GLBRC researchers will deploy high-throughput, automated screens for genes and proteins in plants and microbes that affect biomass and * Presenting author 3
Page 1: Joint Meeting Genomics:GTL Awardee
Page 5 and 6: Contents Welcome ..................
Page 7 and 8: Poster Page 20 Thermophilic Electri
Page 9 and 10: Poster Page 39 Growth Rate and Prod
Page 11 and 12: Poster Page 60 MicroCOSM: Phylogene
Page 13 and 14: Poster Page 83 Experimental Mapping
Page 15 and 16: Poster Page 102 High Throughput Com
Page 17 and 18: Poster Page 120 Protein Complex Ana
Page 19 and 20: Poster Page 139 Phylogenomics-Guide
Page 21: Introduction to Workshop Abstracts
Page 25 and 26: to improve deconstruction, BESC wit
Page 27 and 28: isms for development of this CPB pr
Page 29 and 30: ticularly, those focused on issues
Page 31 and 32: • Visualization of structural cha
Page 33 and 34: esolution, three-dimensional images
Page 35 and 36: 14 Single-Molecule Studies of Cellu
Page 37 and 38: while minimizing the expression of
Page 39 and 40: 7. Sokolova, T.G. et al. Thermincol
Page 41 and 42: 23 High-Throughput Screening Assay
Page 43 and 44: New Haven, Connecticut; and 3Depart
Page 45 and 46: 30 Towards Experimental Verificatio
Page 47 and 48: espect to parameters (in our case e
Page 49 and 50: photosynthetic bacteria. We will va
Page 51 and 52: Systems Environmental Microbiology
Page 53 and 54: Washington; 7 Montana State Univers
Page 55 and 56: transcriptomic data, a mutant was g
Page 57 and 58: favored Methanococcus. These result
Page 59 and 60: hydrogenotrophic methanogens for co
Page 61 and 62: at a chemical level how the obligat
Page 63 and 64: the shorter-term ESPP2 project goal
Page 65 and 66: GTL 51 Applications of GeoChip to E
Page 67 and 68: GTL 53 Comparative Metagenomics of
Page 69 and 70: To complement this research, a requ
Page 71 and 72: ties survive in uncertain environme
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use only of reliable non-transferre
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64 Towards Genomic Encyclopedia of
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genome sequences, it is now possibl
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MR1 provided via ongoing efforts of
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strains ranges from 95.76% (S. balt
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transcriptional profiling data from
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educer Wolinella succinogenes. The
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Under O 2 -limited conditions, pyru
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dynamically generated using Java Se
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applications as well as develop a b
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tions is now underway. This computa
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simulations with randomized paramet
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experimental determination of an im
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tein. Cytochromes appear to be unde
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Therefore, it is important to under
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structures, and the functional inte
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91 Transcriptome Structure of Halob
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version with the advantages of HPF,
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(D) GmpA self-assembles into a stru
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98 New Methods for Whole-Genome Ana
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Systems Biology Research Strategy a
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communities found in coastal areas.
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challenges. For example, microbial
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oad implication for conducting prot
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variation in the AMD system, there
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scaffolds were identified by proteo
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109 Development of Mass Spectrometr
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silico from the CRISPR loci were us
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Molecular Interactions and Protein
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for high throughput characterizatio
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polyamine produced as a key interme
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Tagless purification of water solub
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characterized complexes from other
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known for homologous proteins from
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GTL 124 Protein Complex Analysis Pr
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and subjected to mass spectrometry
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of electrons to nitrogenase. Subseq
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Validation of Genome Sequence Annot
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134 Characterization of Sensor Prot
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than methods that treat functional
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Of the many functions undertaken by
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Computing Resources and Databases 1
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143 The Ribosomal Database Project
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2. It predicts which genes fill hol
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146 Genome Management Information S
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Ethical, Legal, and Societal Issues
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employment base. A key policy issue
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5. 6. McDougall, R. and Golub, A. (
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Program Websites • • • •
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A Abraham, Paul 100 Abulencia, Carl
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Fichtenholtz, Alex 20 Field, Lori 1
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Lu, Vincent 127 Lynd, L. 6 Lyons, C
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Shirodkar, Sheetal 57 Shukla, Anil
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American Type Culture Collection 93
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The complimentary use of small angl
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The reduced genomic content of M. g
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Discovery of Novel Machinery for La
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Creating a Pathway for the Biosynth
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AGENDA Sunday Evening, February 10,
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2:50-3:15 Gary Siuzdak - Scripps Re
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Paramvir Dehal, Lawrence Berkeley N
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Joint Meeting - Genomics - U.S. Department of Energy

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