Agenda

This is the preliminary meeting agenda. Please check back regularly for updates and changes. You may also download the agenda in PDF format. Adobe Reader is necessary to view PDF files. If you don't have the latest version of Reader, you can download a free copy at the Adobe download site.

Even-numbered posters will be presented on Monday, odd-numbered posters on Tuesday. Please set up the posters no earlier than 5:00 pm on Sunday and leave them up until noon Wednesday.

**Revised Snow Contingency Agenda posted at 11:30 p.m. on Saturday, February 6.

Sunday Evening, February 7
5:30 pm	Early Registration and Poster Setup - Early Registration CANCELLED Poster Set-Up 5:00-7:00 p.m.
6:00–8:30 pm	Reception and Scientific Mixer *Reception - CANCELLED Social 5:00-7:00 p.m.: Independence Foyer (food available and may take to lounge area for Super Bowl)**
Monday, February 8
12:00 – 12:30 pm	Welcome and State of Genomic Science Program
	12:00 – 12:15 pm	Dr. Anna Palmisano, Associate Director, Office of Biological and Environmental Research
	12:15 – 12:30 pm	Dr. Sharlene Weatherwax, Director, Biological Systems Science Division
12:30 – 2:00 pm	Lunchtime Student Oral Presentations Moderator: Libby White
2:00 - 5:00 pm	Breakout Session A: Genomic Structure and Epigenetics Moderator: Cathy Ronning Back up: Dr. Matteo Pellegrini Description of Session: Epigenetic phenomena, heritable traits that occur in both prokaryotes and eukaryotes, result from chromatin modification without DNA sequence alteration, and have been shown to contribute substantially to physiological processes such as tissue differentiation and alternative physiological states. The underlying mechanisms include DNA methylation, histone modifications, extracellular matrix composition and regulatory RNA actions however, others remain to be discovered. Epigenetic states are affected by the environmental history of a prior generation and may be passed on to subsequent generations, thus allowing for adaptation. Techniques such as ChIP-Seq, RNA-seq and BS-seq allow measurements of epigenetic states on a genome-wide scale, and provide new insights in the roles and regulation of epigenetic modifications. This breakout session will focus on current developments in chromatin modification and structure.
	Speakers:
	2:00–2:25 pm	Dr. Zhiping Wen, Department of Biochemistry and Molecular Pharmacology, UMass Medical School Title: Developmental Regulation and Individual Differences of Neuronal Epigenomes in the Prefrontal Cortex
	2:25–2:50 pm	Dr. Barbara Wold, Division of Biology, CalTech
	2:50–3:15 pm	Dr. Aleksandar Milosavljevic, Department of Molecular and Human Genetics, Baylor College of Medicine Title: Genboree Open Hosting System for Collaborative Genomic and Epigenomic Research
	3:15–3:40 pm	Dr. Matteo Pellegrini, Department of Molecular, Cell and Developmental Biology, UCLA Title: Whole Genome DNA Methylation Profiles
	3:40–4:00 pm	Coffee Break
	4:00–5:00 pm	Group Discussion
	Breakout Session B: Integrated Omics Approaches to Understand Environmental Processes Moderator: Todd Anderson Back-up: Joe Graber Description of Session:Genome-enabled techniques are revolutionizing our understanding of microbial metabolism and are poised to enable an unprecedented understanding of microbial processes in the natural environment. This session will highlight genome-based techniques and approaches that are being employed to understand microbial processes of relevance to the DOE environmental mission. The session is co-sponsored by the Climate and Environmental Sciences Division within BER and is focused on, but not limited to, microbial activities influencing the fate and transport of metal and radionuclide contaminants. A central theme of this session is not only how genome-enabled studies provide in depth knowledge of microbially-mediated processes but also how these approaches could lead to a more mechanistic integration of biology with the physical/chemical sciences in descriptions of environmental processes.
	Speakers:
	2:00–2:30 pm	Dr. Anne Summers, Microbiology Department, University of Georgia Title: The (Micro)biology of Mercury
	2:35–3:05 pm	Dr. Eoin Brodie, Lawrence Berkeley National Laboratory Title: Understanding and Predicting the Response of Soil Microbial Communities to Global Change
	3:10–3:30 pm	Coffee Break
	3:30–4:00 pm	Dr. Robert Hettich, Oak Ridge National Laboratory Title: Novel Experimental Approaches for Proteogenomic Characterizations of Microbial Soil Communities
	4:05–4:35 pm	Dr. Derek Lovley, Department of Microbiology, University of Massachusetts Title: BUGS Modeling: Predicting the Geochemical Consequences of Environmental Perturbations on Microbial Processes
	4:40–5:10 pm	Dr. Krishna Mahadevan, Department of Chemical Engineering and Applied Chemistry, University of Toronto Title: Integrated Modeling of Environmental Processes using Dynamic Genome-Based Models
	Breakout Session C: Imaging and Technology for Systems Biology Moderator: Arthur Katz Back-up: Roland Hirsch or Sharlene Weatherwax Description of Session:The Genomic Science program supports basic research aimed at achieving systems level understanding of plants, microbes, and microbial communities relevant to DOE missions in bioenergy, carbon management, and environmental stewardship. While considerable progress has been made in developing imaging and analytical technologies over the last decade, we are just at the border of achieving the temporal and spatial resolution that will support comprehensive systems level analyses. The biological challenge is to push our capabilities toward simultaneously measuring multiple chemical and biological species at multiple scales within complex, heterogonous cellular and environmental systems using the increasing temporal and spatial resolution of our technologies. This breakout session will identify and integrate the biological challenges and the technical capabilities needed to realize progress toward answering some of these pressing biological questions. The breakout will address the fundamental questions: Where do we need to go and How can we get there?
	Speakers:
	2:00–2:25 pm	Dr. Alfred Spormann, Department of Civil and Environmental Engineering, Sanford Title: NanoSIMS Analysis of Carbon and Nitrogen Partitioning in the Anabaena-Rhizobium Microbial Consortium
	2:25–2:50 pm	Dr. Bruce Fouke, Department of Geology, University of Illinois, Champaign-Urbana Title: Yellowstone Hot-Spring Systems Geobiology: Quantification and Prediction of Mineral-Water-Microbe Feedback Interactions in the Subsurface
	2:50–3:15 pm	Dr. Jan Liphardt, Lawrence Berkeley National Laboratory Title: Super-Resolution Optical Methods for the Genomic Sciences: Possibilities and Problems
	3:15–3:30 pm	Coffee Break
	3:30–3:55 pm	Dr. Jonathan Sweedler, Department of Chemistry, University of Illinois, Urbana-Champaign Title: Chemical Imaging using Mass Spectroscopy
	3:55–4:20 pm	Dr. Piero Pianetta, Stanford Synchrotron Radiation Laboratory Title: Applications of Full-Field Transmission X-Ray Microscopy to Nano- and Thick Bio-Materials
	4:20–4:45 pm	Dr. Mitch Doktycz, Oak Ridge National Laboratory Title: Micro- and Nano-technologies for Studying the Plant-Microbe Interface
	4:45–5:00 pm	Closing Comments
5:30 - 8:00 pm	Poster Session

Tuesday, February 9
8:30 - 10:00 am	Plenary Session: DOE Bioenergy Research Centers Moderator: John Houghton, Back-up: Sharlene Weatherwax
	8:30–8:50 am	Dr. Robert Landick, Department of Biochemistry, University of Wisconsin and GLBRC Title: Improving Bioenergy Microbes By Multidimensional Evolutionary and Functional Genomics
	8:50–9:15 am	Dr. Trent Northen, Lawrence Berkeley National Laboratory and JBEI Title: High Throughput Multiplexed GlycoChip Enzymatic Assays for Biofuels Development
	9:15–9:40 am	Dr. Lee Lynd, Thayer School of Engineering, Dartmouth and BESC Title: Consolidated Bioprocessing: From Science to Impact
	9:40–10:00 am	Coffee Break
10:00 - 10:45 am	Keynote Presentation: Bernhard Palsson, UCSD School of Engineering, Department of Bioengineering Title: Systems Biology of Metabolism
10:45 am - 12:00 pm	Plenary Session: Systems Biology Developments to Enable a Genomic Science Knowledgebase Moderator: Susan Gregurick, Back-up: Sharlene Weatherwax
	Speakers:
	10:45–11:10 am	Dr. Cathy Wu, Department of Biological Sciences, University of Delaware Title: Systems Integration of Omics Data for Biological Network Discovery
	11:10–11:35 am	Dr. Nitin Baliga, Institute for Systems Biology Title: A Knowledgebase for Rapid Inference and Re-engineering of Biological Circuits
	11:35 am –12:00	Dr. Harry J. Gilbert, Complex Carbohydrate Research Center, University of Georgia Title: How Easy is it to Interpret Function from CAZy Family Location?
12:00 - 12:30 pm	Lunch Pickup
12:30 - 2:00 pm	Lunchtime Student Oral Presentations Moderator: Libby White
2:00 - 5:00 pm	Breakout Session D: Systems Biology Knowledgebase Workshop for Genomic Sciences Applications Moderator: Susan Gregurick, Back-up: Bob Cottingham Description of Session: This workshop will bring together researchers from the Genomic Sciences Community in microbial systems biology, computational biology and bioinformatics. The goal of this workshop is to outline the near, mid and long term trajectory of microbial sciences for energy and the environment. A second scientific objective is to map the associated workflows and data integration methods that can inform the specifications and requirements for the future development of the DOE Systems Biology Knowledgebase.
	Chairs:
	2:00–2:20 pm	Dr. Robert Cottingham, Oak Ridge National Laboratory Title: Microbial Systems Biology Knowledgebase: Scientific Objectives and Current Prospects
	2:20–2:50 pm	Open Panel Discussion
	2:50–3:00 pm	Coffee Break
	3:00–3:30 pm	Dr. Robert Kelly, Department of Chemical and Biomolecular Engineering, North Carolina State University Title: Near-Term Prospects for Functional Microbial Genomics: Moving Beyond the Monoculture Paradigm
	3:30–4:00 pm	Open Panel Discussion
	4:00–4:30 pm	Dr. Adam Arkin, Lawrence Berkeley National Laboratory Title: From Pathways to Populations and Back Again: Long Term Prospects for the Microbial Systems Biology Knowledgebase
	4:30–5:00 pm	Open Panel Discussions
	Breakout Session E: Synthetic Biology Moderators: Marvin Stodolsky and Dan Drell Description of Session: The Genomic Science program supports basic research aimed at achieving systems level understanding of plants, microbes, and microbial communities relevant to DOE missions in bioenergy, carbon management, and environmental stewardship. The first result of genome sequencing efforts is the determination of the potential ‘parts list’ for an organism and can range from as few as 580 ‘parts’ in a simple Mycoplasm to many thousands in eukaryotes. The promise of synthetic biology is to treat these biological parts as building blocks and to assemble functional units from them. In addition to the opportunity to explore how nature has built functions from natural parts, synthetic biology offers a tool kit for the construction of new functions. This breakout session will explore current work using biological parts to build mission-relevant functions, to showcase student-initiated efforts to build novel biological activities and to consider some of the social implications of this new technology.
	Speakers:
	2:00–2:30 pm	Dr. John Glass, J. Craig Venter Institute Title: Synthetic Genomics: Progress on Construction of a Synthetic Bacterial Cell
	2:30–3:00 pm	Dr. Nathan Hilson, Lawrence Berkely National Laboratory Title: Integration of BioCAD tools, Parts Registries, and Automated- Assembly
	3:00–3:30 pm	Dr. George M. Church,Genetics Department, Harvard Medical School Title: Genome Engineering, Multi-Virus Resistance, & Accelerated Evolution for Industrial Chemicals
	3:30–3:50 pm	Coffee Break
	3:50–4:10 pm	iGEM, Cornell Team, Alyssa Henning Title: Engineering the Bacillus Subtilis Metal Ion Homeostasis System to Serve as a Cadmium-responsive Biosensor
	4:10–4:30 pm	iGEM Utah Team, Libbie Linton and faculty advisor Dr. Charles Miller, Biological and Irrigation, Utah State University Title: BioBricks Without Borders: Investigating a Multi-host BioBrick Vector and Secretion of Cellular Products
	4:30–5:00 pm	Dr. Lori Knowles, Health Law Institute, University of Alberta Title: Synthetic Genomics: Oxymorons and Communication Bloopers–Why Researchers’ Enthusiasm for “Tinkering with Life” Might Not be Contagious
	Breakout Session F: Structural Biology Applications in Genomic Science Moderator: Roland Hirsch Description of Session: This session will provide examples of how the Department of Energy’s synchrotron light sources and neutron facilities are of value for Genomic Science research projects. Each talk will focus on a biological problem within the scope of the Genomic Science program. The speakers will define the problem, then explain the selection of the particular structural biology technique, and finally discuss how the technique has helped advance the research project. The emphasis will be on the biology rather than the technology. The techniques to be included in the talks in this session are macromolecular crystallography with x-rays and neutrons, small-angle x-ray and neutron scattering and infrared and x-ray imaging.
	Speakers:
	2:00–2:25 pm	Dr. Marianne Schiffer, Argonne National Laboratory Title: Structural Studies of Heme Containing Proteins from Geobacter Sulfurreducens using the Structural Biology Center Beam Lines at the Advanced Photon Source
	2:25–2:50 pm	Dr. Paul Langan, Los Alamos National Laboratory Title: Using Neutron Crystallography to Reveal the Mechanism of Enzymes for Renewable Energy and the Environment
	2:50–3:15 pm	Dr. Greg Hura, Lawrence Berkeley National Laboratory Title: Developed Proteomics Scale Solution X-ray Scattering (SAXS) Tools Applied to Metabolic Networks of Interest from the ENIGMA Program Project
	3:15–3:30 pm	Coffee Break
	3:30–3:55 pm	Dr. Blake Simmons, Lawrence Berkeley National Laboratory Title: Novel Insights into the Structural Mechanism of Lipid Accumulation within Algae using Soft X-ray Tomography
	3:55–4:20 pm	Dr. Hoi-Ying Holman, Lawrence Berkeley National Laboratory Title: Real-Time Monitoring of Chemical Environment in Cells During Stress-Adaptive Response
	4:20–4:45 pm	Dr. Barbara Evans, Oak Ridge National Laboratory Title: Changes in Switchgrass Structure during Acid Pretreatment Examined with Small-angle Neutron Scattering and Wide-angle X-ray Diffraction
	4:45–5:00 pm	Closing remarks and discussion
5:30 - 8:00 pm	Poster Session

Wednesday, February 10
8:30 - 9:00 am	Imaging Workshop Report Arthur Katz
9:00 - 9:30 am	Dr. Jennifer Lippincott-Schwartz, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health Title: Insights into Organelle Biogenesis and Near Molecule Protein Distribution Using Photoactivatable Fluorescent Protein Technology
9:30 - 10:00 am	Break
10:00 - 12:00 pm	Plenary Session: Systems Biology for H₂ Production Moderator: Joe Graber
	Speakers:
	10:00–10:40 am	Dr. Josh Rabinowitz, Lewis-Sigler Institute for Integrative Genomics, Princeton University Title: Metabolomic Data Reveals Pathways and Regulatory Principles
	10:40–11:20 am	Dr. Caroline Harwood, Department of Microbiology, University of Washington Title: Protons as Electron Acceptors: What Can This Teach Us About Bioenergy Generation?
	11:20–12:00 pm	Dr. Judy Wall, Department of Biochemistry, University of Missouri Title: Pathway of Fermentative Hydrogen Production by Sulfate-Reducing Bacteria
12:00 pm	Close-out and Adjournment