Contents. DOE Genomes to Life Contractor-Grantee Workshop 2004

Genomes to Life Contractor-Grantee Workshop II
February 29-March 2, 2004, Washington, D.C.

Contents

Quick Links: Program Projects * Communication * Modeling / Computation * Environmental Genomics * Microbial Genomics * Technology Development * ELSI

Genomics:GTL Program Projects

Harvard Medical School

1 Flux Balance Based Whole-Cell Modeling of the Marine Cyanobacterium Prochlorococcus
George M. Church, Daniel Segre, Xiaoxia Lin, Kyriacos Leptos, Jeremy Zucker, Aaron Brandes, Dat Nguyen, and Jay MacPhee

Lawrence Berkeley National Laboratory

2 VIMSS Computational Microbiology Core Research on Comparative and Functional Genomics
Adam Arkin, Eric Alm, Inna Dubchak, Mikhail Gelfand, Katherine Huang, Kevin Keck, Frank Olken, Vijaya Natarajan, Morgan Price, and Yue Wang

3 Managing the GTL Project at Lawrence Berkeley National Laboratory
Nancy A. Slater

4 VIMSS Applied Environmental Microbiology Core Research on Stress Response Pathways in Metal-Reducers
Terry C. Hazen, Hoi-Ying Holman, Sharon E. Borglin, Dominque Joyner, Rick Huang, Jenny Lin, David Stahl, Sergey M. Stolyar, Matthew Fields, Dorothea Thompson, Jizhong Zhou, Judy Wall, H.-C. Yen, and Martin Keller

5 VIMSS Functional Genomics Core: Analysis of Stress Response Pathways in Metal-Reducing Bacteria
Jay Keasling, Steven Brown, Swapnil Chhabra, Brett Emo, Weimin Gao, Sara Gaucher, Masood Hadi, Qiang He, Zhili He, Ting Li, Yongqing Liu, Vincent Martin, Aindrila Mukhopadhyay, Alyssa Redding, Joseph Ringbauer Jr., Dawn Stanek, Jun Sun, Lianhong Sun, Jing Wei, Liyou Wu, Huei-Che Yen, Wen Yu, Grant Zane, Matthew Fields, Martin Keller, Anup Singh, Dorothea Thompson, Judy Wall, and Jizhong Zhou

Oak Ridge National Laboratory and Pacific Northwest National Laboratory

6 Establishment of Protocols for the High Throughput Analysis of Protein Complexes at the Center for Molecular and Cellular Systems
Michelle V. Buchanan, Gordon Anderson, Robert L. Hettich, Brian Hooker, Gregory B. Hurst, Steve J. Kennel, Vladimir Kery, Frank Larimer, George Michaels, Dale A. Pelletier, Manesh B. Shah, Robert Siegel, Thomas Squier, and H. Steven Wiley

7 Isolation and Characterization of Protein Complexes from Shewanella oneidensis and Rhodopseudomonas palustris
Brian S. Hooker, Robert L. Hettich, Gregory B. Hurst, Stephen J. Kennel, Patricia K. Lankford, Chiann-Tso Lin, Lye Meng Markillie, M. Uljana Mayer-Clumbridge, Dale A. Pelletier, Liang Shi, Thomas C. Squier, Michael B. Strader, and Nathan C. VerBerkmoes

8 Bioinformatics and Computing in the Genomics:GTL Center for Molecular and Cellular Systems - LIMS and Mass Spectrometric Analysis of Proteome Data
F. W. Larimer, G. A. Anderson, K. J. Auberry, G. R. Kiebel, E. S. Mendoza, D. D. Schmoyer, and M. B. Shah

9 Advanced Computational Methodologies for Protein Mass Spectral Data Analysis
Gordon Anderson, Joshua Adkins, Andrei Borziak, Robert Day, Tema Fridman, Andrey Gorin, Frank Larimer, Chandra Narasimhan, Jane Razumovskaya, Heidi Sophia, David Tabb, Edward Uberbacher, Inna Vokler, and Li Wang

10 High-Throughput Cloning, Expression and Purification of Rhodopseudomonas palustris and Shewanella oneidensis Affinity Tagged Fusion Proteins for Protein Complex Isolation
Dale A. Pelletier, Linda Foote, Brian S. Hooker, Peter Hoyt, Stephen J. Kennel, Vladimir Kery, Chiann-Tso Lin, Tse-Yuan Lu, Lye Meng Markillie, and Liang Shi

Sandia National Laboratories

11 Modeling Cellular Response
Mark D. Rintoul, Steve Plimpton, Alex Slepoy, and Shawn Means

12 The Synechococcus Encyclopedia
Nagiza F. Samatova, Al Geist, Praveen Chandramohan, Ramya Krishnamurthy, Gong-Xin Yu, and Grant Heffelfinger

13 Carbon Sequestration in Synechococcus: A Computational Biology Approach to Relate the Genome to Ecosystem Response
Grant S. Heffelfinger

14 Improving Microarray Analysis with Hyperspectral Imaging, Experimental Design, and Multivariate Data Analysis
David M. Haaland, Jerilyn A. Timlin, Michael B. Sinclair, Mark H. Van Benthem, Michael R. Keenan, Edward V. Thomas, M. Juanita Martinez, Margaret Werner-Washburne, Brian Palenik, and Ian Paulsen

15 Multi-Resolution Functional Characterization of Synechococcus WH810
Nagiza F. Samatova, Andrea Belgrano, Praveen Chandramohan, Pan Chongle, Paul S. Crozier, Al Geist, Damian Gessler, Andrey Gorin, Jean-Loup Faulon, Hashim M. Al-Hashimi, Eric Jakobbson, Elebeoba May, Anthony Martino, Shawn Means, Rajesh Munavalli, George Ostrouchov, Brian Palenik, Byung-Hoon Park, Susan Rempe, Mark D. Rintoul, Diana Roe, Peter Steadman, Charlie E. M. Strauss, Jerilyn Timlin, Gong-Xin Yu, Maggie Werner-Washburne, Dong Xu, Ying Xu, and Grant Heffelfinger

16 Computational Inference of Regulatory Networks in Synechococcus sp WH8102
Zhengchang Su, Phuongan Dam, Hanchuan Peng, Ying Xu, Xin Chen, Tao Jiang, Dong Xu, Xuefeng Wan, and Brian Palenik

University of Massachusetts, Amherst

17 Analysis of Predominant Genome Sequences and Gene Expression During In Situ Uranium Bioremediation and Harvesting Electricity from Waste Organic Matter
Stacy Ciufo, Dawn Holmes, Zhenya Shelbolina, Barbara Methé, Kelly Nevin, and Derek Lovley

18 Functional Analysis of Genes Involved in Electron Transport to Metals in Geobacter sulfurreducens
Maddalena Coppi, Eman Afkar, Tunde Mester, Daniel Bond, Laurie DiDonato, Byoung-Chan Kim, Richard Glaven, Ching Leang, Winston Lin, Jessica Butler, Teena Mehta, Susan Childers, Barbara Methé, Kelly Nevin, and Derek Lovley

19 Adapting Regulatory Strategies for Life in the Subsurface: Regulatory Systems in Geobacter sulfurreducens
Gemma Reguera, Cinthia Nunez, Richard Glaven, Regina O'Neil, Maddalena Coppi, Laurie DiDonato, Abraham Esteve-Nunez, Barbara Methé, Kelly Nevin, and Derek Lovley

Shewanella Federation

20 Global and Physiological Responses to Substrate Shifts in Continuous and Controlled Batch Cultures of Shewanella oneidensis MR-1
Jim Fredrickson, Alex Beliaev, Bill Cannon, Yuri Gorby, Mary Lipton, Peter Liu, Margie Romine, Richard Smith, and Harold Trease

21 Integrated Analysis of Gene Functions and Regulatory Networks Involved in Anaerobic Energy Metabolism of Shewanella oneidensis MR-1
Jizhong Zhou, Dorothea K. Thompson, Matthew W. Fields, Timothy Palzkill, James M. Tiedje, Kenneth H. Nealson, Alex S. Beliaev, Ting Li, Xiufeng Wan, Steven Brown, Dawn Stanek, Weimin Gao, Feng Luo, Jianxin Zhong, Liyou Wu, Barua Soumitra, Crystal B. McAlvin, David Yang, Robert Hettich, Nathan VerBerkmoes, Yuri Gorby, Richard Smith, Mary Lipton, and James Cole

22 Profiling Shewanella oneidensis Strain MR-1: Converting Hypothetical Genes into Real, Functional Proteins
Eugene Kolker, Samuel Purvine, Alex F. Picone, Natali Kolker, and Tim Cherny

23 Systems Biology of Shewanella oneidensis MR-1: Physiology and Genomics of Nitrate Reduction, the Radiation Stress Response, and Bioinformatics Applications
James M. Tiedje, James R. Cole, Claribel Cruz-Garcia, Joel A. Klappenbach, and Xiaoyun Qiu

24 Development and Application of Optical Methods for Characterization of Protein-Protein Interactions in Shewanella oneidensis MR-1
Natalie R. Gassman, Achillefs N. Kapanidis, Nam Ki Lee, Ted A. Laurence, Xiangxu Kong, and Shimon Weiss

25 Annotation of Genes and Metabolism of Shewanella oneidensis MR-1
Margrethe Serres and Monica Riley

Institute for Biological Energy Alternatives

26 Estimation of the Minimal Mycoplasma Gene Set Using Global Transposon Mutagenesis and Comparative Genomics
John I. Glass, Nina Alperovich, Nacyra Assad-Garcia, Holly Baden-Tillson, Hoda Khouri, Matt Lewis, William C. Nierman, William C. Nelson, Cynthia Pfannkoch, Karin Remington, Shibu Yooseph, Hamilton O. Smith, and J. Craig Venter

27 Whole Genome Assembly of Infectious fX174 Bacteriophage from Synthetic Oligonucleotides.
Hamilton O. Smith, Clyde A. Hutchison III, Cynthia Pfannkoch, and J. Craig Venter

28 Development of a Deinococcus radiodurans Homologous Recombination System
Sanjay Vashee, Ray-Yuan Chuang, Christian Barnes, Hamilton O. Smith, and J. Craig Venter

29 Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter, Karin Remington, Jeff Hoffman, Holly Baden-Tillson, Cynthia Pfannkoch, and Hamilton O. Smith

GTL Communication

30 Communicating Genomics:GTL
Anne E. Adamson, Jennifer L. Bownas, Denise K. Casey, Sherry A. Estes, Sheryl A. Martin, Marissa D. Mills, Kim Nylander, Judy M.Wyrick, Anita J. Alton, and Betty K. Mansfield

Modeling/Computation

31 Global Organization of Metabolic Fluxes in the Bacterium, Escherichia coli
E. Almaas, B. Kovács, T. Vicsek, Z. N. Oltvai and A.-L. Barabási

32 SimPheny™: Establishing a Computational Infrastructure for Systems Biology
Christophe H. Schilling, Sean Kane, Martin Roth, Jin Ruan, Kurt Stadsklev, Rajendra Thakar, Evelyn Travnik, and Sharon Wiback

33 Analysis and Design of Genome-Scale Metabolic Networks
Costas D. Maranas, Anthony P. Burgard, Evgeni V. Nikolaev, Priti Pharkya, and Christophe H. Schilling

34 Development and Industrial Bioprocessing Application of a Genome-Scale Metabolic Model for Pseudomonas fluorescens
Sung M. Park, Christophe H. Schilling, Tom Ramseier, and Charles Squires

35 Parallel Scaling in Amber Molecular Dynamics Simulations
Michael Crowley, Scott Brozell, and David A. Case

36 Bioinformatics Methods for Tandem Mass Spectrometry
Andrey Gorin, Tema Fridman, Robert M. Day, Jane Razumovskaya, Andrei Borziak, and Edward Uberbacher

37 The Use of Microarray Technology and Data Mining Techniques to Predict Gene Regulation and Function in Geobacter sulfurreducens
Barbara Methé, Kelly Nevin, Jennifer Webster, and Derek Lovley

38 In Silico Elucidation of Transcription Regulons and Prediction of Transcription Factor Binding Sites in Geobacter Species Using Comparative Genomics and Microarray Clustering
Julia Krushkal, Bin Yan, Daniel Bond, Maddalena Coppi, Kelly Nevin, Cinthia Nunez, Regina O'Neil, Barbara Methé, and Derek Lovley

39 In Silico Modeling to Improve Uranium Bioremediation and Energy Harvesting by Geobacter species
R. Mahadevan, B. O. Palsson, C. H. Schilling, D. R. Bond, J. E. Butler, M. V. Coppi, A. Esteve-Nunez, and D. R. Lovley

40 Continued Studies on Improved Methods of Visualizing Large Sequence Data Sets
George M. Garrity, Timothy G. Lilburn, and Yuan Zheng

41 PQuad for the Visualization of Mass Spectrometry Peptide Data
Bobbie-Jo Webb-Robertson, Susan L. Havre, Deborah A. Payne, and Mudita Singhal

42 Computational Framework for Microbial Cell Simulations
Haluk Resat, Linyong Mao, Heidi Sofia, Harold Trease, Samuel Kaplan, and Christopher Mackenzie

43 Optimization Modules for SBW and BioSPICE
Vijay Chickarmane, Herbert M. Sauro, and Cameron Wellock

44 The Docking Mesh Evaluator
Roummel Marcia, Susan D. Lindsey, J. Ben Rosen, and Julie C. Mitchell

45 Functional Analysis and Discovery of Microbial Genes Transforming Metallic and Organic Pollutants: Database and Experimental Tools
Lawrence P. Wackett and Lynda B. M. Ellis

46 Comparative Genomics Approaches to Elucidate Transcription Regulatory Networks
Lee Ann McCue, Thomas M. Smith, William Thompson, C. Steven Carmack, and Charles E. Lawrence

47 Elucidating and Evaluating Patterns of Lateral Gene Transfer in Prokaryotic Genomes: Phylogenomic Analyses using GeneMarkS Gene Predictions
John Besemer, Mark Borodovsky, and John M. Logsdon, Jr.

48 Cell Modeling and the Biogeochemical Challenge
P. J. Ortoleva

49 Rapid Reverse-Engineering of Genetic Networks via Systematic Transcriptional Perturbations
J. J. Collins, T. S. Gardner, and C. R. Cantor

50 Computational Hypothesis Testing: Integrating Heterogeneous Data and Large-Scale Simulation to Generate Pathway Hypotheses
Mike Shuler

51 Bacterial Annotation Tools
Owen White

52 RELIC - A Bioinformatics Server for Combinatorial Peptide Analysis and Identification of Protein-Ligand Interaction Sites
Suneeta Mandava, Lee Makowski, Satish Devarapalli, Joseph Uzubell, and Diane J. Rodi

53 On Truth, Pathways and Interactions
Andrey Rzhetsky

In Search of Complexity: Bioinformatics and Molecular Tools in the Search for Protein Recoding
Norma Wills, Barry Moore, Andy Hammer, Mike Howard, Clark Henderson, Jason Simmons, John Atkins, and Ray Gesteland

Environmental Genomics

54 Identification and Isolation of Active, Non-Cultured Bacteria from Radionuclide and Metal Contaminated Environments for Genome Analysis
Susan M. Barns, Elizabeth C. Cain, Leslie E. Sommerville, and Cheryl R. Kuske

55 Metagenomic Analysis of Uncultured Cytophaga and Other Microbes in Marine and Freshwater Consortia
David L. Kirchman, Matthew T. Cottrell, and Lisa Waidner

56 Approaches for Obtaining Genomic Information from Contaminated Sediments Beneath a Leaking High-Level Radioactive Waste Tank
Fred Brockman, S. Li, M. Romine, J. Shutthanandan, K. Zengler, G. Toledo, M. Walcher, M. Keller, and Paul Richardson

57 Application of High Throughput Microcapsules Culturing to Develop a Novel Genomics Technology Platform
Karsten Zengler, Marion Walcher, Imke Haller, Carl Abulencia, Denise Wyborski, Fred Brockman, Cheryl Kuske, Susan Barns, and Martin Keller

58 Insights into Community Structure and Metabolism Obtained by Reconstruction of Microbial Genomes from the Environment
Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, Paul Richardson, Victor Solovyev, Edward Rubin, Daniel Rokhsar, and Jillian F. Banfield

59 Growing Unculturable Microorganisms from Soil Communities
Kim Lewis, Slava S. Epstein, and Anthony V. Palumbo

Microbial Genomics

60 Gene Expression Profiles of Rhodopseudomonas palustris Nitrogenases by Whole Genome Microarray
Y. Oda, S. K. Samanta, L. Wu, X.-D. Liu, T.-F. Yan, J. Zhou, and C. S. Harwood

61 Harnessing the Integrative Control of C, N, H, S and Light Energy Metabolism in Rhodopseudomonas palustris to Enhance Carbon Sequestration and Biohydrogen Production
F. Robert Tabita, Janet L. Gibson, Caroline S. Harwood, Frank Larimer, J. Thomas Beatty, James C. Liao, and Jizhong (Joe) Zhou

62 Gene Expression Profiles of Nitrosomonas europaea During Active Growth, Starvation and Iron Limitation
Xueming Wei, Tingfen Yan, Norman Hommes, Crystal McAlvin, Luis Sayavedra-Soto, Jizhong Zhou, and Daniel Arp

63 Photosynthesis Genes in Prochlorococcus Cyanophage
Debbie Lindell, Matthew B. Sullivan, Zackary I. Johnson, Andrew C. Tolonen, Forest Rohwer, and Sallie W. Chisholm

64 Metabolomic Functional Analysis of Bacterial Genomes
Pat J. Unkefer, Rodolfo A. Martinez, Clifford J. Unkefer, and Daniel J. Arp

65 Genomics of T. fusca Plant Cell Wall Degradation
David B. Wilson, Shaolin Chen, and Jeong H. Kim

66 Proteomic Analyses of a Hydrogen Metabolism Mutant of Methanococcus maripaludis
M. Hackett, J. Amster, B. A. Parks, J. Wolff, Q. Xia, T. Wang, Y. Zhang, W. B. Whitman, W. Kim, I. Porat, J. Leigh, and E. Hendrickson

67 Gene Transfer in Hyperthermophiles: Thermotoga and Pyrococcus as Model Systems
Emmanuel F. Mongodin, Ioana Hance, Bruce Weaver, Robert T. Deboy, Steven R. Gill, Tanya Marushak, Wei Xianying, Patricia Escobar-Paramo, Sulagna Gosh, Jocelyne DiRuggiero, Karl Stetter, Robert Huber, and Karen E. Nelson

68 Novel Proteins Help Mediate the Ionizing Radiation Resistance of Deinococcus radiodurans R1
John R. Battista, Masashi Tanaka, L. Alice Simmons, Edmond Jolivét, and Ashlee M. Earl

69 The Microbial Proteome Project: A Database of Microbial Protein Expression in the Context of Genome Analysis
Carol S. Giometti, Gyorgy Babnigg, Sandra L. Tollaksen, Tripti Khare, George Johnson, Derek R. Lovley, James K. Fredrickson, Wenhong Zhu, and John R. Yates III

70 The Molecular Basis for Aerobic Energy Generation by the Facultative Bacterium Rhodobacter sphaeroides
Christine Tavano, Daniel Smith, Matthew Riley, Zi Tan, Samuel Kaplan, Jonathan Hosler, and Timothy Donohue

71 Rhodobacter sphaeroides Gene Expression; Analysis of the Transcriptome and Proteome
Jung Hyeob Roh, Jesus Eraso, Miguel Dominguez, Christine Tavano, Carrie Goddard, Matthew Monroe, Mary Lipton, Samuel Kaplan, and Timothy Donohue

72 The Respiratory Enzyme Flavocytochrome c₃ Fumarate Reductase of Shewanella frigidimarina
T. P. Straatsma, E. R. Vorpagel, M. Dupuis, and D. M. A. Smith

73 The Cyanobacterium Synechocystis sp. PCC 6803: Integration of Structure, Function, and Genome
Wim Vermaas, Robert Roberson, Julian Whitelegge, Kym Faull, and Ross Overbeek

74 Transport and Its Regulation in Marine Cyanobacteria
Brian Palenik, Bianca Brahamsha, Jay McCarren, Ian Paulsen, and Kathy Kang

75 Whole Genome Optical Mappings of Two Eukaryotic Phytoplanktons Thalasiosira pseudonana and Emiliana huxleyi
Shiguo Zhou, Michael Bechner, Mike Place, Andrew Kile, Erika Kvikstad, Louise Pape, Rod Runnheim, Jessica Severin, Dan Forrest, Casey Lamers, Gus Potamousis, Steve Goldstein, Mark Hildbrand, Ginger Armbrust, Betsy Read, Diego Martinez, Nicholas Putnam, Daniel S. Rokhsar, Thomas S. Anantharaman, and David C. Schwartz

76 Whole Genome Transcriptional Analysis of Toxic Metal Stresses in Caulobacter crescentus
Gary L. Andersen, Ping Hu, and Harley McAdams

Technology Development

Imaging

77 Electron Tomography of Intact Microbes
Kenneth H. Downing

78 Probing Single Microbial Proteins and Multi-Protein Complexes with Bioconjugated Quantum Dots
Gang Bao

79 Single Molecule Imaging of Macromolecular Dynamics in a Cell
Jamie H. D. Cate, Jennifer Blough, Hauyee Chang, Raj Pai, Abbas Rizvi, Chung M. Wong, Wen Zhou, and Haw Yang

80 Developing a Hybrid Electron Cryo-Tomography Scheme for High Throughput Protein Mapping in Whole Bacteria
Huilin Li and James Hainfeld

81 Probing Gene Expression in Living Bacterial Cells One Molecule at a Time
X. Sunney Xie, Jie Xiao, Long Cai, and Joseph S. Markson

Protein Production and Molecular Tags

82 Developing a High Throughput Lox Based Recombinatorial Cloning System
Robert Siegel, Nileena Velappan, Peter Pavlik, Leslie Chasteen, and Andrew Bradbury

83 Methods for Efficient Production of Proteins and High-Affinity Aptamer Probes
Michael Murphy, Paul Richardson, and Sharon A. Doyle

84 Development of Multipurpose Tags and Affinity Reagents for Rapid Isolation and Visualization of Protein Complexes
M. Uljana Mayer, Liang Shi, Yuri A. Gorby, David F. Lowry, David A. Dixon, Joel G. Pounds, and Thomas C. Squier

85 Development of Genome-Scale Expression Methods
Frank Collart, Gerald W. Becker, Brian Hollaway, Yuri Londer, Marianne Schiffer, and Fred Stevens

86 Chemical Methods for the Production of Proteins
Stephen Kent

87 A Combined Informatics and Experimental Strategy for Improving Protein Expression
John Moult, Osnat Herzberg, Frederick Schwarz, and Harold Smith

88 High-Throughput Production and Analyses of Purified Proteins
F. William Studier, John C. Sutherland, Lisa M. Miller, and Lin Yang

Proteomics

89 Ultrasensitive Proteome Analysis of Deinococcus radiodurans
Norman J. Dovichi

90 Pilot Proteomics Production Pipeline
Gordon A. Anderson, Mary S. Lipton, Gary R. Kiebel, David A. Clark, Ken J. Auberry, Eric A. Livesay, Vladimir Kery, Brian S. Hooker, Elena S. Mendoza, Ljiljana Pasa-Tolic, Matthew Monroe, Margie Romine, Jim Fredrickson, Yuri Gorby, Nikola Tolic, George S. Michaels, and Richard D. Smith

91 Characterization of Microbial Systems by High Resolution Proteomic Measurements
Mary S. Lipton, Ljiljana Pasa-Tolic, Matthew E. Monroe, Kim K. Hixson, Dwayne A. Elias, Margie F. Romine, Yuri A. Gorby, Ruihua Fang, Heather M. Mottaz, Carrie D. Goddard, Nikola Tolic, Gordon A. Anderson, Richard D. Smith, and Jim K. Fredrickson

92 Advanced Technologies and Their Applications for Comprehensive and Quantitative Microbial Proteomics
Richard D. Smith, Mary S. Lipton, Ljiljana Pasa-Tolic, Gordon A. Anderson, Yufeng Shen, Matthew Monroe, Christophe Masselon, Eric Livesay, Ethan Johnson, Keqi Tang, Harold R. Udseth, and David Camp

93 New Developments in Peptide Identification from Tandem Mass Spectrometry Data
William R. Cannon, Kristin H. Jarman, Alejandro Heredia-Langner, Douglas J. Baxter, Joel Malard, Kenneth J. Auberry, and Gordon A. Anderson