DOEOBER Workshop on New Frontiers in Characterizing Biological Systems

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DOE-OBER Workshop on New Frontiers in
Characterizing Biological Systems

• Arthur M. Katz
• Office of Biological Environmental Research
• September 1, 2009
• arthur.katz_at_science.doe.gov

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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 Research
Department of Energy Office of Science
Biological and Environmental Research
2 Characterization
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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 Research
3 Characterization
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Workshop Logistics

• May 1314, 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 Research
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Workshop Participants
Mary Helen Barcellos-Hoff New York University
School of Medicine Allen Bard The University of
Texas at Austin Carl Batt Cornell
University Talapady Bhat National Institute of
Standards and Technology Federica
Brandizzi Michigan State University Liaohai
Chen Argonne National Laboratory Graham
Cooks Purdue University Stephen
Cramer University of California, Davis Brian
Davison Oak Ridge National Laboratory Mitchel
Doktycz Oak Ridge National Laboratory Mark
Ellisman University of California, San
Diego Wolfgang Fink California Institute of
Technology Bruce Fouke University of
Illinois Jim Fredrickson Pacific Northwest
National Laboratory Paul Gilna University of
California, San Diego Elizabeth
Haswell Washington University, St. Louis Lynn
Hlatky Tufts University School of
Medicine Hoi-Ying Holman Lawrence Berkeley
National Laboratory Phil Hugenholtz Lawrence
Berkeley National Laboratory / JGI
Department of Energy Office of Science
Biological and Environmental Research
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Workshop Participants, continued
Rob Knight University of Colorado,
Boulder Stephen Lane University of California,
Davis Jan Liphardt Lawrence Berkeley National
Laboratory John Markley University of
Wisconsin-Madison Lisa Miller Brookhaven
National Laboratory Robert Murphy Carnegie
Mellon University Colin Murrell University of
Warwick Dean Myles Oak Ridge National
Laboratory George Patterson National Institutes
of Health Piero Pianetta SLAC National
Accelerator Laboratory Tijana Rajh Argonne
National Laboratory Gary Sayler University of
Tennessee Patricia Sobecky University of
Alabama Alfred Spormann Stanford University Gary
Stacey University of Missouri Jonathan
Sweedler University of Illinois at
Urbana-Champaign Kenneth Taylor Florida State
University Daniel van der Lelie Brookhaven
National Laboratory Tuan Vo-Dinh Duke
University Matthew Wallenstein Colorado State
University Steve Wiley Pacific Northwest
National Laboratory
Department of Energy Office of Science
Biological and Environmental Research
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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 Research
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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 Research
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Representative Technologies

• 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

Department of Energy Office of Science
Biological and Environmental Research
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Outcome Four Major Technology Needs for
Understanding Biological Function

• 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
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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

11 Characterization
Department of Energy Office of Science
Biological and Environmental Research
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Outcome Four major technology needs for
understanding biological function

• 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
• 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 Research
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Outcome Four major technology needs for
understanding biological function, continued

• Completing the parts-listSeeing 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
• 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 Research
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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 Research
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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.h
  tml

Department of Energy Office of Science
Biological and Environmental Research
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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 Research
16 Characterization