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

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Poster Page xviii 128 Characterization of a Stress Response Pathway in the Anoxygenic Phototrophic Bacterium Rhodopseudomonas palustris ........................................................................................................................................... 124 Michael S. Allen* (allenms@ornl.gov), Dale A. Pelletier, Gregory B. Hurst, Linda J. Foote, Trish K. Lankford, Catherine K. McKeown, Tse-Yuan S. Lu, Elizabeth T. Owens, Denise D. Schmoyer, Jennifer L. Morrell-Falvey, W. Hayes McDonald, Mitchel J. Doktycz, Brian S. Hooker, William R. Cannon, and Michelle V. Buchanan 129 Protein-Protein Interactions Involved in Electron Transfer to Nitrogenase for Hydrogen Production in Rhodopseudomonas palustris ............................................................................................................. 124 Dale A. Pelletier* (pelletierda@ornl.gov), Erin Heiniger, Gregory B. Hurst, Trish K. Lankford, Catherine K. McKeown, Tse-Yuan S. Lu, Elizabeth T. Owens, Denise D. Schmoyer, Jennifer L. Morrell-Falvey, Brian S. Hooker, W. Hayes McDonald, Mitchel J. Doktycz, William R. Cannon, Caroline S. Harwood, and Michelle V. Buchanan 130 Application and Optimization of a Multi-Use Affinity Probe (MAP) Toolkit for Systems Biology....................................................................................................................................................................................125 M. Uljana Mayer, Baowei Chen, Yijia Xiong, and Thomas C. Squier* (thomas.squier@pnl.gov) 131 Development of Highly Efficient Bacterial Hosts for High Throughput Recombinant Membrane Protein Production ................................................................................................................................... 126 Hiep-Hoa T. Nguyen* (hiephoa@its.caltech.edu), Sanjay Jayachandran, and Randall M. Story Validation of Genome Sequence Annotation 132 A High Thoughput Proteomic and Protein Expression Strategy for Annotation of Fungal Glycosyl Hydrolases ......................................................................................................................................................... 127 Scott E. Baker* (scott.baker@pnl.gov), Jon K. Magnuson, Ellen A. Panisko, Adrian Tsang, and Frank Collart 133 Assignment of Enzymatic Function for Core Metabolic Enzymes ............................................................ 127 Vincent Lu,* Gopi Podila, Michael Proudfoot, Alexander Yakunin, and Frank Collart (fcollart@anl.gov) 134 Characterization of Sensor Proteins and Domains ............................................................................................ 129 Sarah Giuliani,* Lori Field, F. William Studier, Lisa M. Miller, and Frank Collart (fcollart@anl.gov) 135 Protein Annotation from Interaction Networks using Zorch and Bayesian Functional Linkages ................................................................................................................................................................................130 Richard Llewellyn* and David Eisenberg (david@mbi.ucla.edu) 136 Annotation of Novel Enzymatic Functions in Methanogens ....................................................................... 131 Ethel Apolinario, Zvi Kelman, Jing Li, Basil J. Nikolau, Kevin Sowers, and John Orban* (orban@umbi.umd. edu) 137 Genemap-MS: High Throughput Mass Spectrometry Methods for Functional Genomics ........... 132 Trent R. Northen* (trnorthen@lbl.gov), Linh Hoang, Steven M. Yannone, Jason Raymond, Jill Fuss, Jinq- Chyi Lee, Der-Ren Hwang, Chi-Huey Wong, John Tainer, and Gary Siuzdak 138 The Application of Phage Display to Advanced Genome Annotation: C. Thermocellum as an Example ................................................................................................................................................................................. 132 Andrew Bradbury* (amb@lanl.gov) * Presenting author
Poster Page 139 Phylogenomics-Guided Validation of Function for Conserved Unknown Genes ............................... 133 * Presenting author Valérie de Crécy-Lagard* (vcrecy@ufl.edu), Basma El Yacoubi, Crysten Haas, Valeria Naponelli, Alexandre Noiriel, Jeffrey C. Waller, and Andrew D. Hanson 140 Prodigal: A New Prokaryotic Gene Identification Program with Enhanced Translation Initiation Site (TIS) Prediction ..................................................................................................................................134 Doug Hyatt, Loren Hauser* (hauserlj@ornl.gov), Frank Larimer, and Miriam Land Computing Resources and Databases 141 Further Refinement and Deployment of the SOSCC Algorithm as a Web Service for Automated Classification and Identification of Bacteria and Archaea ....................................................... 135 J. Fish, Q. Wang, S.H. Harrison, T.G. Lilburn, P.R. Saxman, J.R. Cole, and G.M. Garrity* (garrity@msu.edu) 142 NamesforLife Resolution Services for the Life Sciences .................................................................................136 George M. Garrity* (garrity@msu.edu), Catherine M. Lyons, and James R. Cole 143 The Ribosomal Database Project................................................................................................................................ 137 J.R. Cole* (colej@msu.edu), Q. Wang, B. Chai, E. Cardenas, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, J.A. Fish, G.M. Garrity, and J.M. Tiedje 144 The MetaCyc and BioCyc Pathway Databases, and the Pathway Tools Software ................................138 Ron Caspi, Carol Fulcher, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, Lukas Mueller, Anuradha Pujar, Peifen Zhang, Sue Rhee, and Peter D. Karp* (pkarp@ai.sri.com) 145 Global Credibility of Sequence Alignments ......................................................................................................... 139 Bobbie-Jo M. Webb-Robertson (bj@pnl.gov), Lee Ann McCue* (leeann.mccue@pnl.gov), and Charles E. Lawrence (Charles_Lawrence@brown.edu) Communication ...........................................................................................................................................................................141 146 Genome Management Information System: A Multifaceted Approach to DOE Genome Research Facilitation and Communication ........................................................................................................... 141 Anne E. Adamson, Shirley H. Andrews, Jennifer L. Bownas, Kris Christen, Sheryl A. Martin, Marissa D. Mills, Kimberly McGrew, Suzanne Parete-Koon, Judy M. Wyrick, Anita J. Alton, and Betty K. Mansfield* (mansfieldbk@ornl.gov) Ethical, Legal, and Societal Issues ..........................................................................................................................143 147 Meeting the Demand for Biofuels: Impact on Land Use and Carbon Mitigation ............................... 143 Madhu Khanna (khanna1@uiuc.edu), Atul Jain,* Hayri Onal, and Jurgen Scheffran 148 The Biofuels Revolution: Understanding the Social, Cultural, and Economic Impacts of Biofuels Development on Rural Communities ....................................................................................................144 Theresa Selfa* (tselfa@ksu.edu), Richard Goe, Laszlo Kulcsar, Gerad Middendorf, and Carmen Bain xix
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: Poster Page 120 Protein Complex Ana
Page 21 and 22: Introduction to Workshop Abstracts
Page 23 and 24: Systems Biology for DOE Energy and
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
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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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