DOE Genomes to Life Contractor-Grantee Workshop 2005

Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.

Welcome to Genomics:GTL Workshop III

Genomics:GTL Program Projects

Harvard Medical School

1—Metabolic Network Modeling of Prochlorococcus marinus

George M. Church* (g1m1c1@arep.med.harvard.edu), Xiaoxia Lin, Daniel Segrè, Aaron Brandes, and Jeremy Zucker

2—Quantitative Proteomics of Prochlorococcus marinus

Kyriacos C. Leptos* (leptos@fas.harvard.edu), Jacob D. Jaffe, Eric Zinser, Debbie Lindell, Sallie W. Chisholm, and George M. Church

3—Genome Sequencing from Single Cells with Ploning

Kun Zhang* (kzhang@genetics.med.harvard.edu), Adam C. Martiny, Nikkos B. Reppas, Sallie W. Chisholm, and George M. Church

Lawrence Berkeley National Laboratory

4—VIMSS Computational Microbiology Core Research on Comparative and Functional Genomics

Adam Arkin*(aparkin@lbl.gov), Eric Alm, Inna Dubchak, Mikhail Gelfand, Katherine Huang, Vijaya Natarajan, Morgan Price, and Yue Wang

5—The Virtual Institute of Microbial Stress and Survival (VIMSS): Deduction of Stress Response Pathways in Metal/Radionuclide Reducing Microbes

Carl Abulencia, Eric Alm, Gary Andersen, Adam Arkin* (APArkin@lbl.gov), Kelly Bender, Sharon Borglin, Eoin Brodie, Swapnil Chhabra, Steve van Dien, Inna Dubchak, Matthew Fields, Sara Gaucher, Jil Geller, Masood Hadi, Terry Hazen, Qiang He, Zhili He, Hoi-Ying Holman, Katherine Huang, Rick Huang, Janet Jacobsen, Dominique Joyner, Jay Keasling, Keith Keller, Martin Keller, Aindrila Mukhopadhyay, Morgan Price, Joseph A. Ringbauer, Jr., Anup Singh, David Stahl, Sergey Stolyar, Jun Sun, Dorothea Thompson, Christopher Walker, Judy Wall, Jing Wei, Denise Wolf, Denise Wyborski, Huei-che Yen, Grant Zane, Jizhong Zhou, and Beto Zuniga

6—VIMSS Applied Environmental Microbiology Core Research on Stress Response Pathways in Metal-Reducers

Terry C. Hazen* (tchazen@lbl.gov), Carl Abulencia, Gary Andersen, Sharon Borglin, Eoin Brodie, Steve van Dien, Matthew Fields, Jil Geller, Hoi-Ying Holman, Rick Huang, Janet Jacobsen,Dominique Joyner, Martin Keller, Aindrila Mukhopadhyay, David Stahl, Sergey Stolyar, Jun Sun, Dorothea Thompson, Judy Wall, Denise Wyborski, Huei-che Yen, Grant Zane, Jizhong Zhou, and Beto Zuniga

7—VIMSS Functional Genomics Core: Analysis of Stress Response Pathways in Metal-Reducin Bacteria

Aindrila Mukhopadhyay, Steven Brown, Swapnil Chhabra, Brett Emo, Weimin Gao, Sara Gaucher, Masood Hadi, Qiang He, Zhili He, Ting Li, Yongqing Liu, 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(mkeller@diversa.com), Anup Singh (aksingh@sandia.gov), Dorothea Thompson, Judy Wall (wallj@missouri.edu), Jizhong Zhou (zhouj@ornl.gov), and Jay Keasling*(keasling@socrates.berkeley.edu)

Oak Ridge National Laboratory and Pacific Northwest National Laboratory

8—Center for Molecular and Cellular Systems: High-Throughput Identification and Characterization of Protein Complexes

Michelle Buchanan, Frank Larimer, Steven Wiley, Steven Kennel, Dale Pelletier, Brian Hooker, Gregory Hurst, Robert Hettich, Hayes McDonald* (mcdonaldwh@ornl.gov), Vladimir Kery, Mitchel Doktycz, Jenny Morrell, Bob Foote, Denise Schmoyer, Manesh Shah, and Bill Cannon

9—High-Throughput Analysis of Protein Complexes in the Center for Molecular and Cellular Systems

Vladimir Kery* (vladimir.kery@pnl.gov), Dale A. Pelletier, Joshua N. Adkins, Deanna L. Auberry, FrankR. Collart, Linda J. Foote, Brian S. Hooker, Peter Hoyt, Gregory B. Hurst, Stephen J. Kennel, Trish K.Lankford, Chiann-Tso Lin, Eric A. Livesay, Tse-Yuan S. Lu, Cathy K. McKeown, Priscilla A. Moore, Ronald J.Moore, and Kristin D. Victry

10—Investigating Gas Phase Dissociation Pathways of Crosslinked Peptides: Application to Protein Complex Determination

Sara P. Gaucher* (spgauch@sandia.gov), Masood Z. Hadi, and Malin M. Young

11—Center for Molecular and Cellular Systems: Statistical Screens for Datasets from High- Throughput Protein Pull-Down Assays

Frank W. Larimer* (larimerfw@ornl.gov), Kenneth K. Anderson, Deanna L. Auberry, Don S. Daly, Vladimir Kery, Denise D. Schmoyer, Manesh B. Shah, and Amanda M. White

12—Center for Molecular and Cellular Systems: Analysis and Visualization of Data from a High-Throughput Protein Complex Identification Pipeline Using Modular and Automated Tools

W. Hayes McDonald (mcdonaldwh@ornl.gov), Joshua N. Adkins, Deanna L. Auberry, Kenneth J. Auberry, Gregory B. Hurst, Vladimir Kery, Frank W. Larimer, Manesh B. Shah, Denise D. Schmoyer, Eric F. Strittmatter, and Dave L. Wabb

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Sandia National Laboratories

13—Carbon Sequestration in Synechococcus: A Computational Biology Approach to Relate the Genome to Ecosystem Response

Grant S. Heffelfinger* (gsheffe@sandia.gov)

14—Integrating Heterogeneous Databases and Tools for High Throughput Microbial Analysis

Nagiza Samatva* (samatovan@ornl.gov), Al Geist, Praveen Chandramohan, and Ramya Krishnamurthy

15—Toward Comprehensive Analysis of MS/MS Data Flows

Andrey Gorin* (agor@ornl.gov), Nikita D. Arnold, Robert M. Day, and Tema Fridman

16—The Transcriptome of a Marine Cyanobacterium—Analysis Through Whole Genome Microarray Analyses

Brian Palenik* (bpalenik@ucsd.edu), Ian Paulsen* (ipaulsen@tigr.org), Bianca Brahamsha, Rob Herman, Katherine Kang, Ed Thomas, Jeri Timlin, and Dave Haaland

17—DEB: A Data Entry and Browsing Tool for Entering and Linking Synechococcus sp. WH8102 Whole Genome Microarray Metadata from Multiple Data Sources

Arie Shoshani* (Shoshani@lbl.gov), Victor Havin, Vijaya Natarajan, Tony Martino, Jerilyn A. Timlin, Katherine Kang, Ian Paulsen, Brian Palenik, and Thomas Naughton

18—Microarray Analysis using VxInsight and PAM

George S. Davidson* (GSDAVID@sandia.gov), David Hanson, Shawn Martin, Margaret Werner-Washburne, and Mark D. Rintoul

19—Mapping of Biological Pathways and Networks across Microbial Genomes

F. Mao, V. Olman, Z. Su, P. Dam, and Ying Xu* (xyn@bmb.uga.edu)

20—Proteomic Analysis of the Synechococcus WH8102 CCM with Varying CO₂ Concentrations

Arlene Gonzales, Yooli K. Light, Zhaoduo Zhang, Michael D. Leavell, Rajat Sapra, Tahera Iqbal, Todd W. Lane, and Anthony Martino* (martino@sandia.gov)

21—Predicting Protein-Protein Interactions Using Signature Products with an Application to β-Strand Ordering

Shawn Martin (smartin@sandia.gov), W. Michael Brown, Charlie Strauss, Mark D. Rintoul*, and Jean-Loup Faulon

22—In Vivo Observation of the Native Pigments in Synechocystis sp. PCC 6803 Using a New Hyperspectral Confocal Microscope

Michael B. Sinclair* (mbsincl@sandia.gov), Jerilyn A. Timlin, David M. Haaland, Sawsan Hamad, and Wim F.J. Vermaas

23—Connecting Temperature and Metabolic Rate to Population Growth Rates in Marine Picophytoplankton

Andrea Belgrano* (ab@ncgr.org) and Damian Gessler

24—Deciphering Response Networks in Microbial Genomes through Data Mining and Computational Modeling

Z. Su, P. Dam, V. Olman, F. Mao, H. Wu, X. Chen, T. Jiang, B. Palenik, and Ying Xu*(xyn@bmb.uga.edu)

25—BiLab – A New Tool that Combines the Ease-of-Use of MatLab and the Power of Multiple Computational Biology Libraries

Al Geist* (gst@ornl.gov) and David Jung

26—Microbial Cell Modeling via Reacting/Diffusing Particles

Steve Plimpton* (sjplimp@sandia.gov) and Alex Slepoy

27—Modeling RuBisCO’s Gating Mechanism Using Targeted Molecular Dynamics

Paul S. Crozier(pscrozi@sandia.gov), Steven J. Plimpton, Mark D. Rintoul*, Christian Burisch, and Jürgen Schlitter

28—Selection of Ligands by Panning of Phage Display Peptide Libraries Reveals Potential Partners for TPR Domain and rbcS in Synechococcus WH8102

Zhaoduo Zhang* (zzhang@sandia.gov), Arlene D. Gonzales, Todd W. Lane, and Anthony Martino

University of Massachusetts, Amherst

29—Progress Toward Genome-Scale Monitoring of In Situ Gene Expression During Uranium Bioremediation and Electricity Harvesting

Dawn Holmes* (dholmes@microbio.umass.edu), Kelly Nevin, Regina O’ Neil, Zhenya Shelbolina, Martin Lanthier, Jonathan Kaye, Brad Postier, and Derek Lovley

30—Integrating Phenotypic and Expression Data to Characterize Metabolism in G. sulfurreducens

R. Mahadevan, C. H. Schilling, D. Segura, B. Yan, J. Krushkal, and D. R. Lovley* (dlovley@microbio.umass.edu)

31—Novel Regulatory Systems and Adaption of Some Well-Known Systems Controlling Respiration, Growth, and Chemotaxis of Geobactor Species

Maddalena Coppi* (mcoppi@microbio.umass.edu), Byoung-Chan Kim, Laurie DiDonato, Julia Krushkal, Bin Yan, Richard Glaven, Regina O’ Neil, Suphan Bakkal, Allen Tsang, Hoa Tran, Abraham Esteve-Nunez, Cinthia Nunez, Ching Leang, Kuk-Jeong Chin, Barbara Methé, Robert Weis, Pablo Pomposiello, Kelly Nevin, and Derek Lovley

32—Nanowires, Capacitors, and Other Novel Electron Transfer Mechanisms in Geobacter Species Elucidated from Genome-Scale Investigations

Gemma Reguera* (greguera@microbio.umass.edu), Teena Mehta, Dawn E. Holmes, Abraham Esteve- Núñez, Jessica Butler, Barbara Methe, Kelly Nevin, Swades K. Chaudhuri, Richard Glaven, Tunde Mester, Raymond DiDonato, Kevin McCarthy, Mark T. Tuominen, and Derek Lovley

33—Continued Progress in the use of Microarray Technology to Predict Gene Regulation and Function in Geobacter sulfurreducens

Barbara Methé*(bmethe@tigr.org), Jennifer Webster, Kelly Nevin, and Derek Lovley

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Shewanella Federation

34—The Shewanella Federation: Functional Genomic Investigations of Dissimilatory Metal- Reducing Shewanella

James K. Fredrickson* (jim.fredrickson@pnl.gov), Carol S. Giometti, Eugene Kolker*, Kenneth H. Nealson, James M. Tiedje, Jizhong Zhou, Monica Riley, Shimon Weiss, James J. Collins, Frank Larimer, Frank Collart, Lee Ann McCue, Chip Lawrence, and Timothy S. Gardner

35—Global Profiling of Shewanella oneidensis MR-1: Expression of ‘Hypothetical’ Genes and Improved Functional Annotations

Eugene Kolker*(ekolker@biatech.org), Alex F. Picone, Michael Y. Galperin, Margaret F. Romine, Roger Higdon, Kira S. Makarova, Natali Kolker, Gordon A. Anderson, Xiaoyun Qiu, Kenneth J. Auberry, Gyorgy Babnigg, Alex S. Beliaev, Paul Edlefsen, Dwayne A. Elias, Yuri Gorby, Ted Holzman, Joel Klappenbach, Konstantinos T. Konstantinidis, Miriam L. Land, Mary S. Lipton, Lee-Ann McCue, Matthew Monroe, Ljiljana Pasa-Tolic, Grigoriy Pinchuk, Samuel Purvine, Margaret Serres, Sasha Tsapin, Brian A. Zakrajsek, Wenhong Zhu, Jizhong Zhou, Frank W. Larimer, Charles Lawrence, Monica Riley, Frank R. Collart, John R. Yates, III, Richard D. Smith, Carol Giometti, Kenneth Nealson, James K. Fredrickson, and James M. Tiedje

36—Respiratory Pathways and Regulatory Networks of Shewanella oneidensis Involved in Energy Metabolism and Environmental Sensing

Alex Beliaev*, Yuri Gorby, Margie Romine, Jeff McLean, Grigoriy Pinchuk, Eric Hill, Jim Fredrickson, Jizhong Zhou, and Daad A. Saffarini

37—Functional Analysis of Shewanella, A Cross Genome Comparison

Margrethe H. Serres* (mserres@mbl.edu) and Monica Riley

38—Optical Methods for Characterization of Expression Levels and Protein-Protein Interactions in Shewanella oneidensis MR-1

Natalie R. Gassman* (ngassman@chem.ucla.edu), Xiangxu Kong, Gopal Iyer, Younggyu Kim, and Shimon Weiss

39—Reverse-Engineering Microbial Networks in Escherichia coli and Shewanella oneidensis MR-1 via Large-Scale Perturbation Studies

G. Cottarel, M.E. Driscoll, J. Faith, M.K. Kohanski, J. Wierzbowski, C.B. Cantor, J.J. Collins, and T.S. Gardner* (tgardner@bu.edu)

40—Comparative Analysis of Gene Expression Profiles of Shewanella oneidensis MR-1 Following Exposure to Ionizing Radiation and Ultraviolet Radiation

Xiaoyun Qiu*(qiuxiaoy@msu.edu), George Sundin, Michael J. Daly, Alexander Vasilenko, Marina V. Omelchenko, Jizhong Zhou, Liyou Wu, Mary S. Lipton, and James M. Tiedje

41—The Microbial Proteome Project: A Database of Microbial Protein Expression in the Context of Genome Analysis

Carol S. Giometti* (csgiometti@anl.gov), Gyorgy Babnigg, Sandra L. Tollaksen, Tripti Khare, Angela Ahrendt, Wenhong Zhu, Derek R. Lovley, James K. Fredrickson, and John R. Yates III

J. Craig Venter Institute

42—Estimation of the Minimal Mycoplasma Gene Set Using Global Transposon Mutagenesis and Comparative Genomics

John I. Glass* (JGlass@venterinstitute.org), Nina Alperovich, Nacyra Assad-Garcia, Shibu Yooseph, Mahir Maruf, Carole Lartigue, Cynthia Pfannkoch, Clyde A. Hutchison III, Hamilton O. Smith, and J. Craig Venter

43—Progress toward a Synthetic Cellular Genome

Hamilton O. Smith* (hsmith@venterinstitute.org), Cynthia Pfannkoch, Holly A. Baden-Tillson, Clyde A. Hutchison III, and J. Craig Venter

44—Development of a Deinococcus radiodurans Homologous Recombination System

Sanjay Vashee*, Ray-Yuan Chuang* (RChuang@venterinstitute.org), Christian Barnes, Hamilton O. Smith, and J. Craig Venter

45—Development of a Novel Recombinant Cyanobacterial System for Hydrogen Production from Water

Qing Xu, Shibu Yooseph, Hamilton O. Smith, and J. Craig Venter (jcventer@tcag.org)

46—Biotechnology For the Production of Ethanol and Butanol from Cellulose

Prabha P. Iyer* (piyer@venterinstitute.org), Hamilton O. Smith, and J. Craig Venter

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Communication

47—Communicating Genomics:GTL

Anne E. Adamson, Shirley H. Andrews, 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* (mansfieldbk@ornl.gov)

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Bioinformatics, Modeling, and Computation

48—SimPheny™: A Computational Infrastructure for Systems Biology

Christophe H. Schilling* (cschilling@genomatica.com), Sean Kane, Martin Roth, Jin Ruan, Kurt Stadsklev, Rajendra Thakar, Evelyn Travnik, Steve van Dien, and Sharon Wiback

49—Hybrid Bacterial Cell Models: Linking Genomics to Physiological Response

Jordan C. Atlas* (jca33@cornell.edu), Mariajose Castellanos, Anjali Dhiman, Bruce Church, and Michael L. Shuler

50—Identification of the Most Probable Biological Network Using Model Discrimination Analysis

Andrea L. Knorr and Ranjan Srivastava* (srivasta@engr.uconn.edu)

51—Rhodopseudomonas palustris Regulons Detected by a Cross-Species Analysis of the α-Proteobacteria

Sean Conlan* (sconlan@wadsworth.org), Charles E. Lawrence, and Lee Ann McCue

52—Exploring Evolutionary Space

Timothy G. Lilburn* (tlilburn@atcc.org), Yun Bai, Yuan Zhang, James R. Cole, and George M. Garrity

53—PhyloScan: A New Tool for Identifying Statistically Significant Transcription Factor Binding Sites by Combining Cross-Species Evidence

Lee A. Newberg*, C. Steven Carmack, Lee Ann McCue(mccue@wadsworth.org), and Charles E. Lawrence

54—Predicting Protein Interactions via Docking Mesh Evaluator

Roummel F. Marcia, Susan D. Lindsey, Erick A. Butzlaff, and Julie C. Mitchell* (mitchell@math.wisc.edu)

55—UC Merced Center for Computational Biology

Michael Colvin* (mcolvin@ucmerced.edu), Arnold Kim, and Felice Lightstone

56—Biomic Approach to Predictive Cell Modeling

P. J. Ortoleva* (ortoleva@indiana.edu), L. Ensman, J. Fan, K. Hubbard, A. Sayyed-Ahmad, F. Stanley, K. Tuncay, and K. Varala

57—The BioWarehouse System for Integration of Bioinformatics Databases

Tom Lee, Valerie Wagner, Yannick Pouliot, and Peter D. Karp* (pkarp@ai.sri.com)

58—Building Large Biological Dynamic Models of Shewanella oneidensis from Incomplete Data

Ravishankar R. Vallabhajosyula* (rrao@kgi.edu), Sri Paladugu, Klaus Maier, and Herbert M. Sauro

59—A Bayesian Method for Identifying Missing Enzymes in Predicted Metabolic Pathway Databases

Michelle L. Green* (green@ai.sri.com) and Peter D. Karp

60—Does EcoCyc or KEGG Provide a Preferable Gold Standard for Training and Evaluation of Genome-Context Methods?

Peter D. Karp* (pkarp@ai.sri.com) and Michelle L. Green

61—Towards a Physics and Systems Understanding of Ion Transport in Prokaryotes

Shreedhar Natarajan, Asba Tasneem*, Sameer Varma, Lakshminarayan Iyer, L. Aravind, and Eric Jakobsson* (jake@ncsa.uiuc.edu)

62—OptStrain: A Computational Framework for Redesign Microbial Production Systems

Priti Pharkya and Costas D. Maranas* (costas@psu.edu)

63—DEMSIM: A Discrete Event Based Mechanistic Simulation Platform for Gene Expression and Regulation Dynamics

Madhukar Dasika and Costas D. Maranas* (costas@psu.edu)

64—On the Futility of Optima in Network Inferences and What Can Be Done About It

Charles (Chip) E. Lawrence* (lawrence@dam.brown.edu)

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Environmental Genomics

65—Whole Community Proteomics Study of an Acid Mine Drainage Biofilm Reveals Key Roles for “Hypothetical” Proteins in a Natural Microbial Biofilm

Jill Banfield* (jill@eps.berkeley.edu), Rachna J. Ram, Gene W. Tyson, Eric Allen, Nathan VerBerkmoes, Michael P. Thelen, Brett J. Baker, Manesh Shah, Robert Hettich, and Robert C. Blake II

66—Application of High Throughput Microcapsule Culturing to Develop a Novel Genomics Technology Platform

Martin Keller* (mkeller@diversa.com), Karsten Zengler, Marion Walcher, Carl Abulencia, Denise Wyborski, Sherman Chang, Imke Haller, Trevin Holland, Fred Brockman, Cheryl Kuske, and Susan Barns

67—Environmental Bacterial Diversity from Communities to Genomes

Janelle R. Thompson*, Silvia G. Acinas, Vanja Klepac-Ceraj, Sarah Pacocha, Chanathip Pharino, Dana E. Hunt, Luisa A. Marcelino, Jennifer Benoit, Ramahi Sarma-Rupavtarm, Daniel L. Distel, and Martin F. Polz (mpolz@mit.edu)

68—Distribution and Variation of Prochlorococcus Genotypes Across Multiple Oceanic Habitats

Adam C. Martiny* (martiny@mit.edu), P. K. Amos Tai, Anne W. Thompson, and Sallie W. Chisholm

69—From Perturbation Analysis to the Genomic Regulatory Code: the Sea Urchin Endomesoderm GRN

Paola Oliveri* (poliveri@caltech.edu), Pei-Yun Lee, Takuya Minokawa, Joel Smith, Qiang Tu, Meredith Howard, David McClay, and Eric H. Davidson

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Microbial Genomics

70—The Genome of the Ammonia Oxidizing Bacterium Nitrosomonas europaea: Iron Metabolism and Barriers to Heterotrophy

Xueming Wei, Neeraja Vajrala, Norman Hommes, Luis Sayavedra-Soto*, and Daniel Arp (arpd@science.oregonstate.edu)

71—Pelagibacter ubique: A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium

Stephen J. Giovannoni* (steve.giovannoni@oregonstate.edu), Lisa Bibbs, James Tripp, Scott Givan, Jang-Cheon Cho, Martha D. Stapels, Russell Desiderio, Mercha Podar, Kevin L. Vergin, Mick Noordeweir, Michael S. Rappé, Samuel Laney, Douglas F. Barofsky, and Eric Mathur

72—Does the Three Dimensional Organization of the Nucleoid of the Deinococcaceae Contribute to their Ionizing Radiation Resistance?

J. M. Zimmerman and J. R. Battista* (jbattis@lsu.edu)

73—Large Scale Genomic Analysis for Understanding Hydrogen Metabolism in Chlamydomonas reinhardtii

Michael Seibert*(mike_seibert@nrel.gov), Arthur R. Grossman, Maria L. Ghirardi, and Matthew C. Posewitz

74—Exploring the Genome and Proteome of Desulfitobacterium hafniense DCB2 for its Protein Complexes Involved in Metal Reduction and Dechlorination

James M. Tiedje*, Sang-Hoon Kim, Christina Harzman, John Davis, Brett Phinney, Michael Ngowe, Washington Mutatu, William Broderick, David DeWitt, Joan Broderick, and Terence L. Marsh (marsht@msu.edu)

75—An Integrative Approach to Energy, Carbon, and Redox Metabolism in the Cyanobacterium Synechocystis sp. PCC 6803

Wim Vermaas* (wim@asu.edu), Robert Roberson, Allison van de Meene, Bing Wang, Sawsan Hamad, Zhi Cai, Julian Whitelegge, Kym Faull, Sveta Gerdes, Andrei Osterman, and Ross Overbeek

76—Role of Cellulose Binding Modules in Cellulose Hydrolysis

David B. Wilson* (dbw3@cornell.edu) and Shaolin Chen

77—Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretation

Matthew B. Sullivan*(mbsulli@mit.edu), Maureen Coleman, Peter Weigele, Forest Rohwer, and Sallie W. Chisholm

78—The Alternative Sigma Factor RpoN Regulon of Rhodopseudomonas palustris

Yasuhiro Oda* (yasuhiro-oda@uiowa.edu), Sudip K. Samanta, Frank W. Larimer, and Caroline S. Harwood

79—Integrative Control of Key Metabolic Processes in Rhodopseudomonas palustris for the Enhancement of Carbon Sequestration and Biohydrogen Production

F. Robert Tabita* (Tabita.1@osu.edu), Janet L. Gibson, Caroline S. Harwood, Frank Larimer, J. Thomas Beatty, James C. Liao, and Jizhong (Joe) Zhou

80—Whole Genome Transcriptional Analysis of Toxic Metal Stresses in Caulobacter crescentus

Gary L. Andersen* (GLAndersen@lbl.gov), Ping Hu, Eoin L. Brodie, and Harley H. McAdams

81—Systematic Analysis of Two-Component Signal Transduction Systems Regulating Cell Cycle Progression in Caulobacter crescentus

Michael Laub* (Laub@CGR.Harvard.edu)

82—The U.S. DOE Joint Genome Institute Microbial Program

David Bruce* (dbruce@lanl.gov), Alla Lapidus, Patrick Chain, Jeremy Schmutz, Frank Larimer, Nikos Kyrpides, Paul Gilna, Eddy Rubin and Paul Richardson

83—Identification of Genes that are Required for Recycling Reducing Power during Photosynthetic Growth

Christine L. Tavano, Angela M. Podevels, and Timothy J. Donohue* (tdonohue@bact.wisc.edu)

84—A Tightly-Regulated Oscillatory Circuit Formed by Conserved Master Regulator Proteins Controls the Caulobacter Cell Cycle

Harley McAdams* (hmcadams@stanford.edu) and Lucy Shapiro

85—Dynamics and Control of Biofilms of the Oligotrophic Bacterium Caulobacter crescentus

Alfred M. Spormann (spormann@stanford.edu) and Plamena Entcheva-Dimitrov

86—Widespread and Abundant CelM Endoglucanases of Marine Cytophaga-like Bacteria Revealed by Whole Genome Shotgun Sequencing and Fosmid Cloning

Matthew T. Cottrell and David L. Kirchman* (kirchman@cms.udel.edu)

87—Data Analysis and Protein Identification Strategy for the Systems-Level Protein-Protein Interaction Networks of Shewanella oneidensis MR-1

Gordon A. Anderson* (gordon@pnl.gov), James E. Bruce, Xiaoting Tang, Gerhard Munske, and Nikola Tolic

88—A Protein Interaction Reporter Strategy for Systems-Level Protein Interaction Networks of Shewanella oneidensis MR-1

James E. Bruce* (james_bruce@wsu.edu), Xiaoting Tang, Harry Zhu, Saiful Chowdhury, Devi Adhikari, Gerhard Munske, Gordon A. Anderson, and Nikola Tolic

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Technology Development and Use

Imaging, Molecular, and Cellular Analysis

89—Probing Single Microbial Proteins and Multi-Protein Complexes with Bioconjugated Quantum Dots

Gang Bao* (gang.bao@bme.gatech.edu), Grant Jensen, Shuming Nie, and Phil LeDuc

90—Single-Molecule Imaging of Macromolecular Dynamics in a Cell

Jamie H. D. Cate (jcate@lbl.gov) and Haw Yang*(hawyang@berkeley.edu)

91—Developing a High Resolution Method for Protein Localization in Whole Bacterium

Huilin Li* (hli@bnl.gov) and James Hainfeld (hainfeld@bnl.gov)

92—Novel Vibrational Nanoprobes for Microbiology at the Single Cell Level

Thomas Huser* (huser1@llnl.gov), Chad E. Talley, James W. Chan, Heiko Winhold, Ted Laurence, Anthony Esposito, Christopher W. Hollars, Christine A. Hara, Allen T. Christian, Michele H. Corzett, Rod Balhorn, and Stephen M. Lane

93—Instrumented Cell for Characterization of Mammalian and Microbial Cells

Jane Bearinger* (bearinger1@llnl.gov), Graham Bench, Jackie Crawford, Lawrence Dugan, Amy Hiddessen, Angela Hinz, Thomas Huser, Robin Miles, Magnus Palmblad, Chad Talley, Elizabeth Wheeler, and Allen Christian

94—Chemical Imaging of Biological Materials by NanoSIMS

Peter K. Weber* (weber21@llnl.gov), Ian D. Hutcheon, Radu Popa, and Ken Nealson

95—Direct Determination of Affnity in Individual Protein-Protein Complexes in Mono and Multivalent Configurations Using Dynamic Force Spectroscopy

Todd A. Sulchek, Kevin Langry, Raymond W. Friddle, Timothy V. Ratto, Sally DeNardo, Huguette Albrecht, Michael Colvin, and Aleksandr Noy*(noy1@llnl.gov)

96—Electron Tomography of Intact and Sectioned Microbial Cells

Kenneth H. Downing* (khdowning@lbl.gov), Luis Comolli, Haixin Sui, Hoi-Ying Holman, Ellen Judd, and Harley McAdams

97—Probing the High-Resolution Architecture and Environmental Dynamics of Microbial Surfaces by in vitro Atomic Force Microscopy

Alexander J. Malkin*(malkin1@llnl.gov), Marco Plomp, Terrance J. Leighton, and Katherine E. Wheeler

98—Real-Time Gene Expression Profiling of Single Live Cells of Shewanella oneidensis

X. Sunney Xie*, Jie Xiao, Ji Yu, Long Cai, Paul Choi*, Nir Friedman, Xiajia Ren, and Luying Xun*

99—High Throughput Fermentation and Cell Culture Device

David Klein (dklein@gener8.net), David Laidlaw, Gregory Andronaco, and Stephen Boyer

100—Immobilized Enzymes in Nanoporous Materials Exhibit Enhanced Stability and Activity

Chenghong Lei, Yongsoon Shin, Jun Liu, and Eric J. Ackerman* (eric.ackerman@pnl.gov)

Protein Production and Molecular Tags

101—Towards High Throughput Selection of Binding Ligands: Using Flow Cytometry

Peter Pavlik, Milan Ovecka, Nileena Velappan, and Andrew Bradbury* (amb@lanl.gov)

102—Effcient Chemical Methods for the Total Synthesis of Small Proteins: The First Crystallographic Structure of a Protein Diastereomer, [D-Gln35]-ubiquitin

Duhee Bang* (duhee@uchicago.edu), George I. Makhatadze, and Stephen B. Kent (skent@uchicago.edu)

103—Development and Application of Multipurpose Affnity Probes to Isolate Intact Protein Complexes Associated with Metal Reduction from Shewanella oneidensis MR-1

Liang Shi*, Thomas C. Squier* (thomas.squier@pnl.gov), M. Uljana Mayer*, Haishi Cao, Baowei Chen, Yuri A. Gorby, David F. Lowry, Jeff Mclean, Seema Verma, and Ping Yan

104—A Combined Informatics and Experimental Strategy for Improving Protein Expression

Osnat Herzberg, John Moult* (moult@umbi.umd.edu), Fred Schwarz, and Harold Smith

105—High-Throughput Production and Analyses of Purified Proteins

F. William Studier* (studier@bnl.gov), John C. Sutherland, Lisa M. Miller, and Lin Yang

106—Development of Genome-Scale Expression Methods

Sarah Fey, Elizabeth Landorf, Yuri Londer, Terese Peppler, and Frank Collart* (fcollart@anl.gov)

107—Plate-Based Methods for Expression of Cytoplasmic Proteins from Shewanella oneidensis

Elizabeth Landorf, Terese Peppler, Sarah Fey, Alexander Iakounine, Eugene Kolker, and Frank Collart* (fcollart@anl.gov)

108—Generating scFv and Protein Scaffolds to Protein Targets

Brian K. Kay* (bkay@anl.gov), Michael Scholle, Ushma Kriplani, John Kehoe, and Frank Collart

109—Cell Free Approaches for Protein Production

Gerald W. Becker*, Pavel Shiyanov, Yifei Wu, Sarah Fey, Elizabeth Landorf, Terese Peppler, and Frank Collart (fcollart@anl.gov)

110—Rapid Synthesis of Peptidic and Peptidomimetic Ligands for High-Throughput Protein Purification and Labeling

Jeffrey B.-H. Tok* (tok2@llnl.gov), Priscilla Chan, David Smithson, Ted Tarasow, and Rod Balhorn

Proteomics and Metabolomics

111—Development and Application of New Technologies for Comprehensive and Quantitative High Throughput Microbial Proteomics

Richard D. Smith* (rds@pnl.gov), Mary S. Lipton, James K. Fredrickson, Matthew Monroe, Eric Livesay, Konstantinos Petritis, Joshua Adkins, Gordon A. Anderson, Kim Hixson, Ruihua Fang, Rui Zhao, Ronald J. Moore, and Yufeng Shen

112—Characterization of Rhodobacter sphaeroides by High Resolution Proteomic Measurements

Mary S. Lipton* (Mary.Lipton@pnl.gov), Timothy Donohue* (tdonohue@bact.wisc.edu), Samuel Kaplan* (Samuel.Kaplan@uth.tmc.edu), Stephen Callister, Matthew E. Monroe, Margie F. Romine, Ruihua Fang, Carrie D. Goddard, Nikola Tolic, Gordon A. Anderson, Richard D. Smith, Jim K. Fredrickson, Miguel Dominguez, Christine Tavano, Xiaihua Zeng, and Jung Hyeob Roh

113—Quantitative Metalloproteomics

Patrick G. Grant* (pggrant@llnl.gov), Sharon Shields, Magnus Palmblad, and Graham Bench

114—New Technologies for Metabolomics

Jay D. Keasling* (jdkeasling@lbl.gov), Carolyn Bertozzi, Julie Leary, Michael Marletta, and David Wemmer

115—Characterization of Metal Reducing Microbial Systems by High Resolution Proteomic Measurements

Mary S. Lipton* (Mary.Lipton@pnl.gov), Ruihua Fang, Dwayne A. Elias, Margie F. Romine, Alex Beliaev, Matthew E. Monroe, Kim K. Hixson, Yuri A. Gorby, Ljiljana Pasa-Tolic, Heather M. Mottaz, Gordon A. Anderson, Richard D. Smith, Jim K. Fredrickson, Derek Lovley, and Yanhuai R. Ding

116—Protein Complexes and Pathways

David Eisenberg* (david@mbiucla.edu), Peter Bowers, Michael Strong, Huiying Li, Lukasz Salwinski, Robert Riley, Richard Llwellyn, Einat Sprinzak, Debnath Pal, and Todd Yeates

117—Metabolomic Functional Analysis of Bacterial Genomes

Clifford J. Unkefer* (cju@lanl.gov)

118—Dynameomics: Mass Annotation of Protein Dynamics through Molecular Dynamics Simulations of Fold-Space Representatives

David A. C. Beck* (dacb@u.washington.edu), Ryan Day, Kathryn A. Scott, R. Dustin Schaeffer, Robert E. Steward, Amanda L. Jonsson, Darwin O. V. Alonso, and Valerie Daggett

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