Model Systems for Neuroproteomics

United States

NIDA Organizer(s): The Workshop was organized by Karen Skinner, Ph.D. under the auspices of the NIDA Emerging Technologies   Workgroup. Christine Colvis, Ph.D. served as co-chair at the meeting. 

Purpose & Intent

• To bring together scientists from a variety of disciplines (including neuroscience, computation, informatics, and systems biology) to discuss how the study of proteomes and proteins (alone and combined with other studies, such as gene expression, lipidomics, etc.) can aid in understanding the classification and function of neuronal cells based on the properties of their intracellular networks.
• To discuss and explore the relevance of systems biology at the cellular level for understanding the actions of drugs, and endogenous molecules stimulated by exogenous factors (such as behavior, stress, diet, time, the environment, etc) on different neuronal cell types.
• To identify possible model cells, tissues, sub-proteomes,   and metabolic, genetic, or signaling molecular networks which may form the basis of a research strategy for undertaking studies of neuronal systems at the cellular level, and which would benefit from studies of their proteomes.
• To discuss strategies and tools for acquiring, managing and integrating information from proteomic and other systems research relevant to understanding neuronal cellular networks, and the research paradigms necessary to implement these strategies.
• To identify research goals which may be accomplished over the next 10-15 years in terms of understanding protein and other networks comprising neuronal cells, and their potential relevance to biomedical translational applications.
• To identify research gaps and opportunities which, if addressed, may enhance and accelerate understanding of the properties and actions of networks constituting neuronal cell types.

To explore how applications of systems biology in other areas may relate to neuroscience and drug abuse research, and to foster new research collaborations.

Meeting Outcome

The following points were emphasized during the presentations and collective discussions during the workshop:

• Current efforts should work towards systems biology and think beyond current uses of data.   Good systems analyses may be five years in the future because of critical quantitative data needs, but standardization in terms of data gathering and storage is needed now to enable future analyses.
• Improved   technologies   which encourage quantitative approaches and provide better quantitative data are needed
• Standards are important in defining biological time constants and frequency of measures
• Rather than limiting systems studies to standards of particular cell or tissue types, flexibility should be exercised in terms of biological systems studied. . Simpler model systems may be particularly useful when developing   technologies.
• Many specific functional biological questions remain which are best addressed through the efforts of individual laboratories, rather than high-throughput means. .
• Modelers and technologists should work together to develop quantitative technologies and models.
• Biological "modules," rather than whole systems, should be studied initially. The study of cellular subcompartments and their function -- for example neuronal terminals, spines or growth cones, and subcellular proteomes, such as the mitochondria --appear particularly manageable and attractive. Modules could also include particular functions such as signal transduction or endocytosis.
• A need exists for cell maps which incorporate modular and subcompartment data
• Biological studies should be at various levels of organization to fill the need for layered descriptions of networks
• An enormous need exists for desktop and PC tools which capture experimental conditions. Most existing laboratory management systems capture clinical type data, not data for basic research.
• A vision is needed of how biologists will interact with the grid; to provide interfaces for them, and provide a means for informing basic scientists of tools which are available
• A need exists for molecular tools which enable correlations with phenotypes

Expected Follow-up

The workshop is expected to continue to provide important insights into the planning and programmatic directions for NIDA's future initiatives and efforts in the application of systems approaches to the study of substance abuse, and in proteomics, and in NIDA's coordination with other NIH programs and activities in these areas. (Note: On April 28, 2003, NIDA issued RFA DA-04-004, "NIDA NEUROPROTEOMICS RESEARCH CENTERS")

Brief Description of Resulting Publications:

A formal meeting report was not published; however, a summary of the workshop's discussions was provided to the NIH RoadMap working group on Networks and Pathways. The workshop also was included as among those whose discussions and outcomes were considered by the Interagency Modeling and Analysis Group (IMAG) in shaping a new initiative just released: NSF Program Solicitation 04-067, " Interagency Opportunities in Multi-Scale Modeling in Biomedical, Biological, and Behavioral Systems." The workshop also served as one of the sources of background information which aided the planning of the first NIH symposium on "Digital Biology," including the associated NSF satellite event: "Information Processing in the Biological Organism (A Systems Biology Approach)"

Participants

Ben A. Barres, M.D., Ph.D.
Professor, Department of Neurobiology
Stanford University School of Medicine
Fairchild, D 235
299 Campus Drive
Stanford, CA 94305-5125
Phone: 650-723-3231
Fax: 605-725-3958
E-mail: barres@stanford.edu

James Eberwine, Ph.D.
Professor, Departments of Pharmacology and Psychiatry
University of Pennsylvania Medical Center
36th and Hamilton Walk
Philadelphia, PA 19104
Phone: 215-898-0420
Fax: 215-573-2236
eberwine@pharm.med.upenn.edu

Fabien Campagne, Ph.D.
Bioinformatics Officer
Institute for Computational Biomedicine
Department of Physiology and Biophysics
Mount Sinai School of Medicine
One Gustave L. Levy Place
Box 1218
New York, NY 10029
Phone: 212-241-0860
Fax: 212-860-3369
fabien.campagne@mssm.edu

Kenneth J. Kauffman,
Assistant Professor, Chemical and Environmental Engineering
University of California
Riverside, CA 92521
kkauffma@engr.ucr.edu

Christine Colvis, Ph.D.
Research Branch, Division of Neuroscience and Behavioral Research
National Institute on Drug Abuse
National Institutes of Health
6001 Executive Boulevard
Bethesda, MD 20892-9645
Phone: 301-443-6300
Fax: 301-594-6043
cc432a@nih.gov

Deborah K. Gracio
Associate Division Director
Computational Sciences and Mathematics
Pacific Northwest National Laboratory
P.O. Box 999, MS K1-85
Richland, WA 99352
Phone: 509-375-6362
Fax: 509-375-6631
debbie.gracio@pnl.gov

Todd C. Holmes, Ph.D.
Assistant Professor, Department of Biology
New York University
1009 Silver Center
100 Washington Square East
New York, NY 10003
Phone: 212-998-8275
Fax: 212-995-4015
todd.holmes@nyu.edu

Peter S. McPherson, Ph.D.
Associate Professor, Department of Neurology and Neurosurgery
Montreal Neurological Institute
McGill University
3801 University Street
Montreal, Quebec
Canada H38 2B4
Phone: 514-398-7355
Fax: 514-398-8106
peter.mc ph erson@mcgill.ca

Michael F. Huerta, Ph.D.
Director, Office of Translational Research and Scientific Technology
Associate Director, Division of Neuroscience and Basic Behavioral Research
National Institute of Mental Health
National Institutes of Health
6001 Executive Boulevard
Room 7202, MSC 9645
Bethesda, MD 20892-9645
Phone:301-443-3563
Fax: 301-443-1731
mhuerta@helix.nih.gov

David G. Myszka, Ph.D.
Director, Center for Biomolecular Interaction Analysis
University of Utah School of Medicine
50 North Medical Drive, #4A417
Salt Lake City, UT 84132
Phone: 810-585-5358
Fax: 801-585-2978
E-mail: dmyszka@cores.utah.edu

Ravi Iyengar, Ph.D.
Professor, Department of Pharmacology
Mount Sinai School of Medicine
One Gustave L. Levy Place
Box 1215
New York, NY 10029
Phone:212-659-1707
Fax: 212-831-0114
ravi.iyengar@mssm.edu

Eric Neumann, Ph.D.
Vice President of Informatics
Beyond Genomics, Inc.
40 Bear Hill Road
Waltham, MA 02451
Phone: 781-890-1199
Fax: 781-895-1119
eneumann@beyondgenomics.com

Grace C. Peng, Ph.D.
Program Director, Division of Bioengineering
National Institute of Biomedical Imaging and Bioengineering
National Institutes of Health
6707 Democracy Boulevard, Suite 200
Bethesda, MD 20892-5469
Phone: 301-496-9178
Fax: 301-480-0679
penggr@mail.nih.gov

Karen Skinner, Ph.D.
Deputy Director, Science and Technology Development
Division of Neuroscience and Behavioral Research
National Institute on Drug Abuse
National Institutes of Health
6001 Executive Boulevard
Bethesda, MD 20892-9645
Phone:301-435-0886
Fax: 301-594-6043
kskinner@nida.nih.gov

William R. Schafer, Ph.D.
Associate Professor, Department of Biology
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0349
Phone:858-827-0508
Fax: 858-822-2003
wschafer@ucsd.edu

Joel R. Stiles, M.D., Ph.D.
Senior Scientific Specialist, Biomedical Supercomputing Initiative
Pittsburgh Supercomputing Center
4400 Fifth Avenue, Room 220A
Pittsburgh, PA 15213
Phone: 412-268-4786
Fax: 412-268-8200
stiles@psc.edu

James S. Schwaber, Ph.D.
Director, Daniel Baugh Institute of Functional Genomics/Computational Biology
Thomas Jefferson University Medical College
1020 Locust Street, Room 520JAH
Philadelphia, PA 19107
Phone:215-503-7823
Fax: 215-923-3808
james.schwaber@mail.tju.edu

Mark E. VonZastrow, M.D., Ph.D.
Associate Professor, Department of Psychiatry and Pharmacology
University of California, San Francisco
401 Parnassus Avenue
San Francisco, CA 94143-0984
Phone:415-476-7855
Fax: 415-476-7884
zastrow@itsa.ucsf.edu

John Whitmarsh, Ph.D.
Program Director, Cell Biology and Biophysics
National Institute of General Medical Sciences
National Institutes of Health
Building 45, Room 2AS/19E
45 Center Drive
Bethesda, MD 20892
Phone:301-402-6272
Fax: 301-480-2004
whitmarj@nigms.nih.gov

Steven Wiley, Ph.D.
Director, Biomolecular Systems Initiative
Department of Biological Sciences
Pacific Northwest National Laboratory
P.O. Box 999, MS P7-53
Richland, WA 99352
Phone:509-373-6218
Fax: 509-376-1494
steven.wiley@pnl.gov