North Dakota IDeA Networks of Biomedical Research Excellence

1
North Dakota IDeA Networks of Biomedical Research
Excellence

• John B. Shabb,
• University of North Dakota

2
Major goals of BRIN and INBRE

• Increase the competitiveness of biomedical
  scientists within the state
• Increase the number of undergraduates who pursue
  careers in biomedical research

3
Some North Dakota statistics

• 2003 Population 633,000
• Square miles 69,000
• Persons/sq. mi. 9

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More North Dakota statistics

• Est. no. of biomedical researchers 160
• FY2002 NIH funding 13.7 million
• FY2002 state rank in total NIH dollars 47
• 2003 PubMed publications originating from ND 265

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The IDeA program contributed 43 of total NIH
funding in North Dakota, FY 2002, 2003
Tribal Colleges 3
Other 16
Research universities 38
IDeA program 43
PUIs 0
Data from NIH Extramural Research Awards Awards
by State
6
Current ND BRIN Baccalaureate pipeline
Biological Sciences Physical Sciences Psychology 7
1
Other 919
Annual recruitment pool for graduate studies in
biomedical sciences
National Center for Education Statistics IPEDS
Degrees conferred, 2001- 2002 academic year
7
Current Tribal College pipeline
Liberal Arts 61
Annual recruitment pool for transfer to 4-year
science programs
Other 139
National Center for Education Statistics IPEDS
Associates degrees conferred, 2001- 2002
academic year
8
North Dakota BRIN 2001-2004
Building biomedical research capacity in North
Dakota by serving public universities and tribal
colleges within the state
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Participating North Dakota INBRE Institutions
Turtle Mountain Community College
Minot State University
Ft. Berthold Community College
University of North Dakota
Cankdeska Cikana Community College
Mayville State University
United Tribes Technical College
Dickinson State University
Valley City State University
North Dakota State University
WELCOME TO THE GTI ACADEMY
Sitting Bull College
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North Dakota BRIN 2001-2004

• 6.3 million budget
• 18 of the budget directly supported PUIs/tribal
  colleges

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New investigators at UND and NDSU

• 3 Department Chairs
• 2 Associate Professors
• 12 Assistant professors
• Typical ND BRIN contribution to start-up 100,000

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Research at baccalaureate institutions

• Student-oriented research projects
• Laboratory renovation
• New equipment
• Faculty development
• New contacts with scientists at research
  universities

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Tribal College Initiatives

• Conversion of Interactive Videoconferencing
  Network to internet standards
• Establishment of videoconferencing capabilities
  in science labs
• Adapting labs to distance learning

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ND BRIN Graduate Teaching Internships

• Graduate students from UND and NDSU were placed
  at tribal colleges and PUIs to provide release
  time for BRIN investigators
• 3 of 16 interns were eventually hired by their
  host institutions

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Other ND BRIN activities

• Develop the network
• Coordinate workshops, conferences and programs
• Communicate activities and accomplishments
• Evaluate

http//ndinbre.org
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North Dakota INBRE 2004-2009
Building biomedical research capacity in North
Dakota by serving public universities and tribal
colleges within the state
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North Dakota INBRE 2004-2009

• Strong emphasis on developing research programs
  at PUIs
• Thematic research focus Health and the
  Environment
• Research Universities provide mentoring, core
  facilities, administrative leadership
• Tribal Colleges receive continued outreach support

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North Dakota INBRE 2004-2009

• 16.1 million
• 56 of the budget directly supports PUIs/tribal
  colleges

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ND INBRE Scientific Network

• Health and the Environment
• Pesticides and non-mammalian biomarkers
• Genetic factors
• Nutrition, growth and development

Some of the nine ND INBRE investigators at PUIs
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Achieving competitiveness

• Expected outcomes
• Establish viable research programs
• Increase publication rate and obtain grants
• Train students in biomedical research

Some of the nine ND INBRE mentors from UND and
NDSU
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Proteomics Core Facility UND

• Services
• Protein/peptide separation by HPLC, 2D-gel
  electrophoresis
• Structural Analysis and protein identification by
  mass spectrometry
• Training

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Biology Core Facilities NDSU

• Services
• DNA analysis
• DNA sequencing
• Cell Biology/histology
• Laser cytometry
• Cell culture/bioassays
• Training

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Bioinformatics An essential part of ND BRIN and
ND INBRE

• Increase access to electronic resources
• Enhance computing capabilities at the research
  institutions

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Electronic resources

• Form a consortium of research libraries to
  negotiate competitive subscription rates
• Seek cost-effective ways of providing expanded
  access to PUIs and Tribal Colleges
• Educate potential users about new resources

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Electronic resources education and outreach

• Host NCBI, PubMed workshops
• Offer tutorials for proprietary databases and
  software
• Raise awareness of new resources

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BRIN-supported Electronic Resources

• Statewide access
• Vector NTI nucleic acid sequence analysis
• Nature Press
• Cell Press
• Annual Reviews
• BioMed Central
• Limited Access
• SciFinder chemical fragment database
• American Society of Microbiology journals
• Current Protocols

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Vector NTI sequence analysis software usage
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SciFinder Scholar chemical fragment database usage
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Electronic Resources the next five years

• Institutionalize BRIN phase I subscriptions
• Acquire additional resources to support
  biomedical research
• Continue education/awareness

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The CCBN State-of-the-Art Molecular Modeling

• Shared computational resources (UND/NDSU)
• High-end software
• Computing power
• Training
• Comprehensive systems administration

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CCBN hardware (purchased 2002)

• SGI Origin 300 server (2)
• 8 R14000 processors, 8 GB memory
• SGI Fuel workstations (12)
• 600 MHz R14000A/4 MB cache
• 512 MB memory
• 18 GB system disk
• 21 monitor

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CCBN locations

• NDSU (6 workstations, 1 server)
• UND (6 workstations, 1 server)
• Other INBRE institutions remote access

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CCBN shared software Accelrys

• Multiple Insight II licenses for biomolecular
  modeling
• Specialized modules for energy calculations,
  homology modeling, NMR analysis, and others

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CCBN shared software Tripos

• Multiple licenses of Sybyl for small molecule
  modeling
• Specialized modules for dynamics, molecular
  mechanics, CoMFA, QSAR, conformational analysis,
  pharmacophore generation, and others

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CCBN integrated systems administration

• SGI IRIX expertise
• Server and workstation maintenance
• Software installation and upgrades
• Account management
• Useage statistics
• Scheduling
• backups

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CCBN Training

• On-site tutorials by local experts
• Simultaneous training at remote sites using
  collaboration software
• Recruitment of new users

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CCBN mean monthly usage statistics

• unique users 18
• CPU min 560,000
• of sessions 2,400

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Research using the CCBN human matrix
metalloproteinases

• Advance computational demonstration of low
  selectivity of MMP inhibitors
• Implication more efficient lead optimization
  for novel MMP drugs

Lukocova et al., J. Biol. Chem. 27914194-14200,
2004
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CCBN the next five years

• Support computational needs of INBRE
  investigators
• Broaden user base through continued training
• Convert to LINUX platform
• Shift to UND and NDSU high performance computing
  clusters
• Achieve sustainability

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Summary

• ND BRIN emphasizes human resource development to
  enhance biomedical research capacity
• Programs are diverse and responsive to the unique
  needs at each participating institution
• Bioinformatics efforts include
• Increasing access to electronic resources
• Establishing and developing a computational
  chemistry and biology network
• Impact on biomedical research competitiveness in
  North Dakota is anticipated to be positive and
  long-term

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Acknowledgements

• John Shabb Principal Investigator
• Donald Schwert Program Coordinator
• Kathy Sukalski Dir. of Evaluation
• Kim Hansen Administrative Officer
• Pat Miller Public Information
• Wendy McQuay Administrative Assistant
• Judy Rieke Electronic resources Coordinator
• Stefan Balaz CCBN Site Coordinator
• Kathryn Thomasson CCBN Site Coordinator
• Other core directors, coordinators,
  investigators, mentors, advisors

made possible by NIH grant number P20 RR016741
from the INBRE program of the National Center
for Research Resources.