DOE-OBER Workshop on New Frontiers in Characterizing Biological Systems
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Transcript of DOE-OBER Workshop on New Frontiers in Characterizing Biological Systems
DOE-OBER Workshop on New Frontiers in
Characterizing Biological Systems
Arthur M. Katz
Office of Biological & Environmental Research
September 1, 2009
Office of Science
Office of Biological and Environmental Research
Workshop Purpose
• Identify new tools and analytical approaches for characterizing cellular and multicellular level functions and processes that are essential for developing solutions for DOE missions in biofuels, carbon cycle, low dose radiation and environmental stewardship
Department of Energy • Office of Science • Biological and Environmental ResearchDepartment of Energy • Office of Science • Biological and Environmental Research2 Characterization
Workshop Scope
• What are the biological/environmental processes we need to understand?
• What are the limitations of current technology in addressing these needs?
• What technical capabilities do we need to answer these most urgent scientific questions?
Department of Energy • Office of Science • Biological and Environmental Research3 Characterization
Workshop Logistics
• May 13–14, 2009
• Bethesda, Maryland
• Agenda:
- Plenary presentations on Science Needs
- Three parallel breakout sessions
- Report Out by Breakout Co-chairs
Department of Energy • Office of Science • Biological and Environmental Research4 Characterization
Workshop Participants
Mary Helen Barcellos-Hoff New York University School of MedicineAllen Bard The University of Texas at AustinCarl Batt Cornell UniversityTalapady Bhat National Institute of Standards and TechnologyFederica Brandizzi Michigan State UniversityLiaohai Chen Argonne National LaboratoryGraham Cooks Purdue UniversityStephen Cramer University of California, DavisBrian Davison Oak Ridge National LaboratoryMitchel Doktycz Oak Ridge National LaboratoryMark Ellisman University of California, San DiegoWolfgang Fink California Institute of TechnologyBruce Fouke University of IllinoisJim Fredrickson Pacific Northwest National LaboratoryPaul Gilna University of California, San DiegoElizabeth Haswell Washington University, St. LouisLynn Hlatky Tufts University School of MedicineHoi-Ying Holman Lawrence Berkeley National LaboratoryPhil Hugenholtz Lawrence Berkeley National Laboratory / JGI
Department of Energy • Office of Science • Biological and Environmental Research5 Characterization
Workshop Participants, continued
Rob Knight University of Colorado, Boulder
Stephen Lane University of California, Davis Jan Liphardt Lawrence Berkeley National LaboratoryJohn Markley University of Wisconsin-MadisonLisa Miller Brookhaven National LaboratoryRobert Murphy Carnegie Mellon UniversityColin Murrell University of WarwickDean Myles Oak Ridge National LaboratoryGeorge Patterson National Institutes of HealthPiero Pianetta SLAC National Accelerator LaboratoryTijana Rajh Argonne National LaboratoryGary Sayler University of TennesseePatricia Sobecky University of AlabamaAlfred Spormann Stanford UniversityGary Stacey University of MissouriJonathan Sweedler University of Illinois at Urbana-ChampaignKenneth Taylor Florida State UniversityDaniel van der Lelie Brookhaven National LaboratoryTuan Vo-Dinh Duke UniversityMatthew Wallenstein Colorado State UniversitySteve Wiley Pacific Northwest National Laboratory
Department of Energy • Office of Science • Biological and Environmental Research6 Characterization
Breakout Sessions
• Cellular processes – Jonathan Sweedler/Patty Sobecky- electron transport, energy production
• Multicellular processes – Federica Brandizzi/ Mary Helen Barcellos-Hoff- biofilms, termite gut, microbial communities, tissue radiation responses
• System interface processes – Mitch Doktycz/ Phil Hugenholtz- plant/microbe, microbe/mineral, molecular machine/materials
Department of Energy • Office of Science • Biological and Environmental Research7 Characterization
Questions for the Breakouts
What are the most significant scientific challenges in your field of research,
and what information would you need to make significant advances?
Are there promising tools and technologies to address these information
gaps? What approaches or technologies would represent breakthroughs?
Are there specific questions that require information developed at more than
one scale (subcellular, cellular, multicellular, organism) in order to provide
adequate understanding? What types of approaches are available or needed to
connect information across the various scales?
Department of Energy • Office of Science • Biological and Environmental Research8 Characterization
Department of Energy • Office of Science • Biological and Environmental Research9 Characterization
• High-throughput genomic approaches for rapid single-cell characterization
• Super-resolution optical spectroscopy at the nanometer scale
• New nongenomic fluorescence probes
• Electrochemical imaging
• Novel isotope technologies including subcellular tracer studies
• Nuclear magnetic resonance
• Synchrotron-based approaches including X-ray fluorescence and tomography
• Electron microscopy
• Atomic force microscopy at the molecular scale
• Secondary ion mass spectrometry on the nanoscale
• Mass spectrometric metabolomics and proteomic approaches for global characterization
Representative Technologies
Outcome: Four Major Technology Needs for Understanding Biological Function
1. Adding dimensions to biological measurements
- Measuring simultaneously multiple chemical species/biological components and fluxes with appropriate temporal and spatial resolution
- Creating multi modal measurements with spatial and temporal registration
- Linking molecular to cellular to multi-cellular to environmental scales
10 Characterization Department of Energy • Office of Science • Biological and Environmental Research
11 Characterization Department of Energy • Office of Science • Biological and Environmental Research
Current Capabilities and Future Achievement
Currently we can localize in the microbe target molecular species with high resolution.
What we need:
• The physical location of the target microbe in its biological and abotic environment
• Flux measurements of molecules in and out of the target cell • Quantified levels of specific proteins, RNA transcripts and metabolites
in the target microbe at several time points
Outcome: Four major technology needs for understanding biological function
1. Adding dimensions to biological measurements
- Measuring simultaneously multiple chemical species/biological components and fluxes with appropriate temporal and spatial resolution
- Creating multi modal measurements with spatial and temporal registration
- Linking molecular to cellular to multi-cellular to environmental scales
2. Identifying important events in heterogeneous environments- Measuring and associating rare events or minority components to functional outcomes.
- Identifying and detecting single or small populations of molecules or cells amidst complex heterogeneous backgrounds
Department of Energy • Office of Science • Biological and Environmental Research12 Characterization
Outcome: Four major technology needs for understanding biological function, continued
3. Completing the “parts-list”—Seeing it all - Capturing of cellular components, e.g. metabolites and carbohydrates, that are currently invisible or poorly characterized
- Manipulating the activity of these poorly characterized components to understand their functional significance
4. Integrating information for predictive understanding- Creating tools for the integration and interpretation of complex data sets
- Developing databases and computational approaches for integrating measurements and models at multiple scales.
- Constructing iterative feedback systems between experiment and modeling
Department of Energy • Office of Science • Biological and Environmental Research13 Characterization
Workshop Report
Currently completing the workshop report and executive summary– Substantial written materials produced by the working
groups have been organized and integrated
– Co-Chairs and other participants have had regular telephone conferences to review drafts of sections of report
– Final version of the report is under way.
Department of Energy • Office of Science • Biological and Environmental Research14 Characterization
Report schedule
• Target date for completion of final draft of the report is September 30, 2009
• Report is expected to be posted by October 15, 2009 on http://www.sc.doe.gov/ober/BER_workshops.html
Department of Energy • Office of Science • Biological and Environmental Research15 Characterization
Workshop leadership
• External co-chairs– Jonathan Sweedler, University of Illinois at
Urbana-Champaign
– Patricia Sobecky, University of Alabama
– Federica Brandizzi, Michigan State University
– Mary Helen Barcellos-Hoff, New York University
– Mitch Doktycz, Oak Ridge National Laboratory
– Phil Hugenholtz, Joint Genome Institute
• BSSD Division– Drs Arthur Katz and Dean Cole
Department of Energy • Office of Science • Biological and Environmental Research16 Characterization