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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

All Awardee Workshops
2012 Workshop

2012 Genomic Science Awardee Meeting X

Bethesda, Maryland
February 26-29, 2012


Correct as of February 7, 2012

Sunday, February 26

5:00-8:00 pm Early Registration and Poster Setup

Monday, February 27

7:00-8:30 am Registration
7:30-8:30 am Continental Breakfast
8:30-9:00 am Welcome and Introduction to the Meeting
8:30-8:45 am Sharlene Weatherwax, Associate Director
DOE Office of Biological and Environmental Research
8:45-9:00 am Joseph Graber, Genomic Science Program Team Lead
DOE Office of Biological and Environmental Research
9:00-11:00 am Plenary Session: DOE Bioenergy Research Centers
Grand Ballroom ABCD
Moderator: Cathy Ronning, DOE BER
9:00-9:30 am Jim Tiedje, GLBRC/Michigan State University
“Metagenomics of the Prairie and Biofuel Crop Rhizospheres”
9:30-10:00 am Art Ragauskas, BESC/Georgia Institute of Technology
“Characterizing the Mechanisms of Reduced Recalcitrance of Biomass”
10:00-10:30 am Aindrila Mukhopadhyay, JBEI/Lawrence Berkeley National Laboratory
“Engineering Advanced Microbes for Biofuel Production”
10:30-11:00 am Break
11:00 am-
12:00 pm
Keynote Presentation:
Jim Collins
, Boston University
“Life Redesigned: The Emergence of Synthetic Biology”
12:00-2:00 pm Lunch
12:30-2:00 pm Lunchtime Student Oral Presentations
Grand Ballroom ABCD
Moderator: Libby White
Speakers to be Announced
Breakout Sessions
2:00-5:00 pm Breakout Session A: Plants and Their Environment: Biology, Molecular Interactions, and Homeostasis
Forest Glen Room (Lower Level)
Moderators: Cathy Ronning and Prem Srivastava, DOE BER

Description of Session: Study of plant genomics and homeostatic processes in living plants can be based on in situ chemical reactions and the environmental effects of perturbations of these chemical reactions. Molecular plant-environment (e.g. microbe) interactions and metabolism, and the use of radioactive tracers to detect and study perturbations of homeostatic reactions will be emphasized in this session.
2:00-2:10 pm Session Introduction—Cathy Ronning
2:10-2:40 pm Jean Greenberg, University of Chicago
“Tracking the Movement of Bio-Active Peptides in Arabidopsis and Poplar”
2:40-3:10 pm Richard Ferrieri, Brookhaven National Laboratory
“The Role of Radiochemistry in Systems Biology to Study the Interrelationship between Hormone Signaling and Plant Root Development”
3:10-3:30 pm Break
3:30-3:50 pm Jocelyn Rose, Cornell University
“Peeling Apart the Structural and Functional Complexity of the Cuticularized Plant Cell Wall”
3:50-4:10 pm Leland Cseke, University of Alabama, Huntsville
“Merging Bottom-Up with Top-Down Research in Symbiosis and Nutrient Cycling”
4:10-5:30 pm Roundtable Discussion—Prem Srivastava
Open Discussions on the Current State of the Art and Future Direction
2:00-5:00 pm Breakout Session B: Enabling Tools and Applications for the DOE Systems Biology
Brookside Room A/B (Lower Level)
Susan Gregurick, DOE BER

Description of Session: The Systems Biology Knowledgebase (Kbase) will be a community-driven software framework enabling the data-driven prediction of microbial, plant, and biological community function in an environmental context. Extensible and scalable, Kbase also will feature open architecture, source code, and open development. The intent of Kbase is to provide access to a distributed, scalable computing resource for data-intensive analysis and will support a large user community with tools and services for Microbes: Reconstruction and prediction of metabolic and gene expression regulatory networks for 100 to 1,000 microbes to manipulate microbial function; Plants: Integration of phenotypic and experimental data and metadata for 10 key plants related to DOE missions to predict biomass properties from genotype and assemble regulatory data to enable analysis, cross-comparisons, and modeling; and Communities: Modeling metabolic processes within 10 to 100 microbial communities with DOE relevance and mine metagenomic data to identify unknown genes. This session will highlight some of the modeling tools and capabilities funded by DOE that could enhance the Knowledgebase.
2:00-2:30 pm Kimmen Sjolander, University of California, Berkeley
“The PhyloFacts 3.0 Phylogenomic Encyclopedia of Microbial Gene Families: New Developments and Plans”
2:30-3:00 pm Peter Karp, SRI International
“Introducing Metabolic Engineering and Atom Mapping Capabilities into Pathway Tools”
3:00-3:30 pm Chris Henry, Argonne National Laboratory
“Enhancing the SEED Framework for Curation and Analysis of Genomic Data and Genome-Scale Metabolic Models”
3:30-3:45 pm Break
3:45-4:15 pm Mark Gerstein, Yale University
“Tools and Approaches for Integrating Multiple Genetic and Cellular Networks”
4:15-4:45 pm Daniel Segre, Boston University
“From Genome-Scale to Ecosystem-Level Models of Metabolism”
4:45-5:00 pm Discussion of Gaps and Opportunities in Enabling Methods for the Knowledgebase
2:00-5:00 pm Breakout Session C: Biological Structure Research in the Genomic Science Program
Glen Echo Room (Lower Level)
Moderator: Roland Hirsch, DOE BER

Description of Session: Research in systems biology requires application of a wide range of technologies, each of which reveals aspects of the processes that occur in living cells and organisms. The DOE synchrotron light sources and neutron beam facilities provide many experimental capabilities that are being used in research projects in the Genomic Science program. The talks in this breakout session will explain how specific beamlines at those facilities are being used in GSP projects. The speakers will seek to make the technologies understandable for GSP biologists by focusing on the biological science that is enabled by the beamline experiments.
2:00-2:05 pm Session Introduction
2:05-2:40 pm Sol Gruner, Cornell University
Session Keynote: “Biomolecules Under Pressure: Why it Matters”
2:40-3:00 pm Frank Collart, Argonne National Laboratory
Representing: Argonne Structural Biology Center
“Binding Profiles and Crystal Structures of Bacterial Solute Binding Proteins for Transport of Aromatic Products of Lignin Degradation”
3:00-3:20 pm Zoe Fisher, Los Alamos National Laboratory
Representing: Los Alamos Protein Crystallography Station
“Elucidating the Proton Transfer Mechanism of Carbonic Anhydrase Using Joint Neutron/X-Ray Crystallography”
3:20-3:40 pm Break
3:40-4:00 pm George Phillips, University of Wisconsin
Representing: Berkeley Small Angle X-Ray Scattering Program
“Characterization of Cellulose Deconstruction Enzymes by Small-Angle X-Ray Scattering and X-Ray Diffraction”
4:00-4:20 pm Gang Cheng, Lawrence Berkeley National Laboratory
Representing: ORNL Center for Structural Molecular Biology
“Understanding the Effect of Ionic Liquid Treatment on the Structures of Lignins in Solutions by Small Angle Neutron Scattering”
4:20-4:40 pm Terry Hazen, University of Tennessee
Representing: Berkeley Synchrotron Infrared Structural Biology Program
“Label-Free Monitoring of Chemical Reactions in Cells During Stress-Adaptive Response”
4:40-5:00 pm Blake Simmons, Sandia National Laboratory
Representing: Berkeley National Center for X-Ray Tomography
“Understanding the Lipid Trigger in Algae using X-Ray Tomography and Spectroscopy”
5:30-8:00 pm Poster Session
Grand Ballroom EFGH

Tuesday, February 28

8:30-10:00 am Plenary Session: Small Cogs Turn Big Wheels: Microbial Communities and the Carbon Cycle
Grand Ballroom ABCD
Moderator: Joe Graber, DOE BER
8:30-9:00 am Steve Allison, University of California, Irvine
“Linking Microbial Enzyme Genes with Community Responses to Drought and Nitrogen”
9:00-9:30 am Dave Myrold, Oregon State University
“Meta-omics Analysis of Microbial Carbon Cycling Responses to Altered Rainfall Inputs in Native Prairie Soils”
9:30-10:00 am Cheryl Kuske, Los Alamos National Laboratory
“Patterns of Soil Community Response to Elevated Atmospheric CO2 Across Terrestrial Ecosystems”
10:00-10:30 am Break
10:30 am-
12:00 pm
Plenary Session: DOE User Facilities and Community Resources
Grand Ballroom ABCD
Moderator: Dan Drell, DOE BER
10:30-11:00 am Eddy Rubin, Joint Genome Institute, Lawrence Berkeley National Laboratory
“Science at the JGI”
11:00-11:30 am Adam Arkin, Lawrence Berkeley National Laboratory
“The DOE Systems Biology Knowledgebase”
11:30 am-
12:00 pm
Keith Hodgson, SLAC National Accelerator Laboratory
“Recent Developments with the LCLS X-Ray FEL at SLAC and Prospects for Future Science”
12:00-12:15 pm DOE Report Update: “Biosystems Design: Report from the July 2011 Workshop”
Pablo Rabinowicz, DOE BER
12:15-12:30 pm DOE Report Update: “Applications of New DOE National User Facilities in Biology: Report from the May 2011 Workshop”
Roland Hirsch, DOE BER
12:30-2:00 pm Lunch
1:00-2:00 pm Lunchtime Student Oral Presentations
Grand Ballroom ABCD
Moderator: Libby White, DOE BER
Speakers to be Announced
Breakout Sessions
2:00-5:00 pm Breakout Session D: DOE Office of Basic Energy Sciences: Photosynthetic Systems
Brookside Room A/B (Lower Level)
Moderator: Gail McLean, DOE Office of Basic Energy Sciences

Description of Session: This session highlights projects in the Photosynthetic Systems program in DOE's Office of Basic Energy Sciences (BES). This program supports basic research in natural photosynthesis and brings together biology, chemistry, biochemistry, and biophysics to uncover the fundamental science of the biological capture of sunlight and its conversion to and storage as chemical energy.
2:00-2:10 pm Session Introduction
2:10-2:40 pm Kevin Redding, Arizona State University
“Routing of Electrons in the Photosynthetic Firmicute, Heliobacterium modesticaldum”
2:40-3:10 pm Christine Kirmaier, Washington University in St. Louis
“Controlling Electron Transfer Pathways in Photosynthetic Reaction Centers”
3:10-3:40 pm K.V. Lakshmi, Rensselaer Polytechnic Institute
“The Mechanism of Solar Water Oxidation in Nature: A Cross Species Comparison of the Structure of the S-State Photochemical Intermediates of Photosystem II”
3:40-4:00 pm Break
4:00-4:30 pm Ann McDermott, Columbia University
“Shifting Shapes: NMR Studies of Conformational Flexibility in Light Harvesting Complexes”
4:30-5:00 pm Robert Burnap, Oklahoma State University
“Genetic Regulatory Circuits Integrating the Light and Dark Reactions of Oxygenic Photosynthesis”
2:00-5:00 pm Breakout Session E: Integrating Societal Considerations/Impacts into BER-Funded Research
Forest Glen Room (Lower Level)
Moderator: Libby White, DOE BER

Description of Session: As BER's Genomic Science program's research progresses, DOE will continue to incorporate into such research a component that addresses societal considerations/impacts. This session will focus on ongoing efforts at DOE and other organizations to look at societal considerations/impacts, as well as gaps/potential future ELSI research needs.
2:00-2:05 pm Session Introduction
Libby White
2:05-2:25 pm Amy Wolfe, Oak Ridge National Laboratory
“Societal Implications of Science and Technology Research and Development Undertaken at U.S. DOE Research Centers”
2:25-2:45 pm Sarah Carter, Venter Institute
“Managing the Risks of Synthetic Biology Assessing the U.S. Regulatory System”
2:45-3:05 pm Nathan Hillson, Lawrence Berkeley National Laboratory
“Assessing and Mitigating the Risks of Large-Scale Metabolic Engineering”
3:05-3:20 pm Break
3:20-3:40 pm Paula Olsiewski, Sloan Foundation
“Overview of Sloan Foundation's Synbio-ELSI Program”
3:40-4:00 pm Dave Rejeski, Wilson Center
“Summary of Fall 2010 Workshop and Other Related Wilson Center Efforts”
4:00-4:30 pm Tom Murray, The Hastings Center
“The Evolution of ELSI: Where it is Today and How it Could Respond to Synthetic Biology”
4:30-5:00 pm Wrap-up Discussion/Panel Discussion of Previous Speakers
2:00-5:00 pm Breakout Session F: Innovative Analytical and Imaging Technology for Plants and Microbes
Glen Echo Room (Lower Level)
Moderators: Arthur Katz and Dean Cole, DOE BER

Description of Session: The Genomic Science program supports basic research that includes the application and development of a variety of imaging and analytical technologies. The biological challenge for these technologies remains extending their capabilities in order to simultaneously measure multiple chemical and biological species at multiple scales within complex, heterogeneous cellular and environmental systems. One critical step will be increasing temporal and spatial resolution. This breakout session will introduce current capabilities of key technologies and relate how they can be used to address significant biological problems of interest to the BER community.
2:00-2:30 pm Mitch Doktycz, Oak Ridge National Laboratory
“Microfluidic Technologies for Characterizing Plant-Microbe Interfaces”
2:30-3:00 pm Haw Yang, Princeton University
“Visualizing Molecular Reactivity in Context”
3:00-3:30 pm Paul Bohn, Notre Dame University
“Applications of In Situ Raman Microscopy and Spectroscopy to Spatially and Temporally Distributed Processes in Complex Multi-Organismal Systems”
3:30-3:45 pm Break
3:45-4:15 pm Kenneth Hammel, University of Wisconsin
“Fungal Biodegradative Oxidants in Lignocellulose: Fluorescence Mapping and Correlation with Gene Expression”
4:15-4:45 pm Drew Weisenberger, Jefferson Laboratory
“PET Radiotracer Imaging in Plant Biology”
4:45-5:00 pm Observations and Comments
5:30-8:00 pm Poster Session
Grand Ballroom EFGH

Wednesday, February 29

8:30-10:00 am Plenary Session: Extending Systems Biology to the Community Scale
Grand Ballroom ABCD
Moderator: Roland Hirsch, DOE BER
8:30-9:00 am Margie Romine, Pacific Northwest National Laboratory
“Genome Sequence-Enabled Investigations of Microbial Interactions in Mat Communities”
9:00-9:30 am Chris Marx, Harvard University
“Evolution of Cooperation in Synthetic, Multi-Species Microbial Consortia”
9:30-10:00 am Dave Stahl, University of Washington
“Adaptive and Evolutionary Dimensions of Microbial Communities”
10:00-10:30 am Break
10:30-11:50 am Plenary Session: DOE Early Career Research Program
Grand Ballroom ABCD
Moderator: John Houghton, DOE BER
10:30-10:50 am Susannah Tringe, Lawrence Berkeley National Laboratory
“Microbial Communities in Restored Freshwater Wetlands”
10:50-11:10 am Sam Hazen, University of Massachusetts
“Optimizing Plant-Microbial Systems for Energy—Mapping Feedstock Quality Genes in Brachypodium distachyon”
11:10-11:30 am Yongqin Jiao, Lawrence Livermore National Laboratory
“Understanding Uranium Resistance and Mineralization by Caulobacter crescentus”
11:30-11:50 am Mary Dunlop, University of Vermont
“Engineering Robust Hosts for Microbial Biofuel Production”
12:00 pm Closeout and Adjournment

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