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NanoToxicology and Bioinformatics. 2006 Arkansas NSF EPSCoR Thematic Proposal. Bioinformatics at UALR. Steve Jennings Professor Applied Science/EIT SFJennings@UALR.Edu (501) 569-8216/ETAS 505 http://Bioinformatics.UALR.Edu. Intersection of Interests. Nanotechnology Biosciences

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NanoToxicology and Bioinformatics

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nanotoxicology and bioinformatics

NanoToxicology and Bioinformatics

2006 Arkansas NSF EPSCoR

Thematic Proposal

NSF EPSCoR Thematic Proposals

bioinformatics at ualr
Bioinformatics at UALR

Steve Jennings


Applied Science/EIT


(501) 569-8216/ETAS 505


NSF EPSCoR Thematic Proposals

intersection of interests
Intersection of Interests
  • Nanotechnology
  • Biosciences
  • Computational Sciences

NSF EPSCoR Thematic Proposals

thematic structure
Thematic Structure
  • Regional interests and strengths
  • National/ international impacts
  • Local economic impact

NSF EPSCoR Thematic Proposals

theme suggestion nanobioinfo
Theme Suggestion: NanoBioInfo
  • Toxicology of Nanoparticles
    • Understanding mechanisms
    • Abatement strategies
  • Strengths
    • Clear opportunity for combining three cores
    • In addition to involving UAF, ASU and UALR, it’s possible to draw upon the research capabilities of NCTR, UAMS and a number of UGIs
    • Major funding opportunities over the long term – not just EPSCoR

NSF EPSCoR Thematic Proposals

thematic guidelines
Thematic Guidelines
  • Problem solution in overlapping cores
  • Build upon the strengths of each core
  • All efforts should be in support of the overall theme
  • Important to focus upon the common objectives

NSF EPSCoR Thematic Proposals

participation potential
Participation Potential

NSF EPSCoR Thematic Proposals

nanotechnology grows up science 6 18 04
Nanotechnology Grows UpScience 6/18/04

“Carbon nanotubes, quantum dots …, and nanoparticles have enticing electrical and optical properties, but toxicologists worry that they might harm organisms.”

NSF EPSCoR Thematic Proposals

nano hazards exposure to minute particles harms lungs circulatory system science news 3 19 05
Nano Hazards: Exposure to minute particles harms lungs, circulatory systemScience News 3/19/05

“… new animal studies indicate that inhaling these microscopic spheres and tubes could cause big trouble, especially for workers who manufacture and handle them.”

NSF EPSCoR Thematic Proposals

special treatment tiny technology tackles mega messes science news 4 23 05
Special Treatment: Tiny Technology Tackles Mega MessesScience News 4/23/05

“Unfortunately, risk assessments lag far behind the pace of new developments in nanotechnology.”

NSF EPSCoR Thematic Proposals

nanotechnology grows up science 6 18 0411
Nanotechnology Grows UpScience 6/18/04

“As funding for nanotech skyrockets, the U.S. National Nanotechnology Initiative devotes 11% of its budget to health and environmental issues.”

NSF EPSCoR Thematic Proposals

  • Collaboration with NCTR instantly gives us the scientific credibility to compete internationally
    • This is a new area of great interest to NCTR
  • NCTR has major animal study capabilities
  • ASU and UAPB have established capabilities in undertaking toxicology studies
    • Other UGIs and UAMS may also be contributors as well

NSF EPSCoR Thematic Proposals

toxicology research areas
Toxicology Research Areas
  • Assessing potential toxic effects of nanoparticles
  • Abatement strategies for reducing harmful effects
  • Manufacturing and disposal strategies
  • Understanding basic mechanisms
  • Appropriate use

NSF EPSCoR Thematic Proposals

  • UAF and UALR have major investments in the nanosciences including the unique capability of producing high-quality nanoparticles (i.e., of uniform characteristics)
    • This is critical for undertaking toxicology studies
  • ASU has interest in collaborating in this area

NSF EPSCoR Thematic Proposals

nanotechnology research areas
Nanotechnology Research Areas
  • Production of high-quality nanoparticles for toxicology testing
  • Experimental strategies for producing particles with less toxic effects
    • Structural changes
    • Size changes
    • Encapsulation strategies
    • Delivery strategies

NSF EPSCoR Thematic Proposals

nanotechnology collaborators
Nanotechnology Collaborators
  • UAF
    • Greg Salamo and colleagues
  • UALR
    • Abhijit Bhattacharyya
    • Alex Biris
    • Malay Mazumder
    • Karin Pruessner
  • ASU
    • Robert Engelken

NSF EPSCoR Thematic Proposals

  • All three universities have major bioscience capabilities
    • Biology
    • Chemistry
    • Biochemistry

NSF EPSCoR Thematic Proposals

biosciences research areas
Biosciences Research Areas
  • Understanding basic mechanisms
  • Developing appropriate biological models

NSF EPSCoR Thematic Proposals

toxicology and bioscience collaborators

John Bush

Jerry Darsey

QingFang He

Maurice Kleve

David Lindquist

XiaoDong Ma

Gary Thompson

HongLi Wang


Andy Goodwin

Steve Lochmann


Dan Buzatu

Yvonne Dragan

Paul Howard

Dwight Miller


Roger Buchanan

Carole Cramer

Maureen Dolan

Jerry Farris

Robyn Hannigan

Beth Hood

Malathi Srivatsan

Toxicology and Bioscience Collaborators

NSF EPSCoR Thematic Proposals

  • UALR/UAMS Joint Graduate Program in Bioinformatics
    • 40+ participating faculty
      • Including many NCTR adjunct faculty
    • 10 current graduate students
      • Could double in next six months
      • Does not count UALR Applied Science graduate students doing bioinformatics-related projects
  • NCTR Center for Toxicoinformatics

NSF EPSCoR Thematic Proposals

bioinformatics research areas
Bioinformatics Research Areas
  • Data management and data mining
    • Strong and active research programs at UALR
    • Leverage ties with Acxiom
  • Modeling and simulation of biosystems and nanoparticles
    • Strong collaborations between UALR and NCTR (and UAMS) in model development
  • Visualization of models and mechanisms
    • Major capabilities and investments in these areas at UALR

NSF EPSCoR Thematic Proposals

bioinformatics collaborators
Weida Tong and colleagues (NCTR)

UALR Bioinformatics Collaborators

Al Adams – Swaminadham Midturi

Coskun Bayrak – Fani Milanova

Yupo Chan – Jennifer Perkins

Chia-Chu Chiang – Peiyi Tang

Sean Geoghegan – Edi Tudoreanu

Kamran Iqbal – Xiaowei Xu

Steve Jennings – Kenji Yoshigoe

Bioinformatics Collaborators

NSF EPSCoR Thematic Proposals

bioinformatics resources
Bioinformatics Resources
  • UALR MidSouth Bioinformatics Center
    • Bioinformatics Computing Facility
  • NCTR Center for Toxicoinformatics
  • UAMS Bioinformatics Centre
  • UALR Virtual Reality Center
  • Access Grids

NSF EPSCoR Thematic Proposals

bioinformatics computing facility
Bioinformatics Computing Facility
  • SunFire Servers
    • V880
      • Eight 900MHz UltraSPARC-III processors
      • 32G memory with 438G disk space
    • Two 280Rs
      • Dual 1.2GHz UltraSPARC-III processors
      • 8G memory, Fiber Channel Disk Array, SCSI tape drive
  • Free, open source software
    • bioPerl, EMBOSS, NCTR’s ArrayTrack
  • Commercial software packages as required
    • Oracle and S+/ArrayAnalyzer

NSF EPSCoR Thematic Proposals

ualr s virtual reality center
UALR’s Virtual Reality Center

NSF EPSCoR Thematic Proposals

visualizing aphid attacks on plant cells
Visualizing Aphid Attacks on Plant Cells

3D Fungus Attack

Cell wall

Traditional View: microscopy

Interactive selection and navigation

Immersed:seeing 3D frominside the cell

NSF EPSCoR Thematic Proposals


Access Grid Conferencing

University of Arkansas at Little Rock

Funded through CyberCollege start-up

University of Arkansas at Little Rock

Funded by AR BRIN

University of Arkansas for Medical Sciences

Housed in the UAMS Library, 3rd floor

University of Arkansas at Fayetteville

Housed at Mullins Library

Arkansas State University

Housed at Dean B. Ellis Library

University of Arkansas for Medical Sciences

University of Arkansas at Little Rock

NSF EPSCoR Thematic Proposals

arkansas brin inbre programs
Arkansas BRIN/INBRE Programs
  • In the midst of nine years of major funding for UAMS, UAF, UALR and seven UGIs to participate in biomedical research infrastructure development
  • Funded initial bioinformatics efforts
  • Enabled strong working relationships between these ten institutions
    • Intend to leverage these relationships in this expanded program area of nanotoxicology

NSF EPSCoR Thematic Proposals

midsouth nanotoxicology and bioinformatics summit
MidSouth Nanotoxicology and Bioinformatics Summit
  • Statewide meeting to be held on Monday/Tuesday, September 19/20
  • Monday afternoon (NCTR): Welcome and tours of NCTR facilities
  • Tuesday 8-5 (UALR): Keynote speaker, Disciplinary working sessions, Action plan for NSF EPSCoR white paper
  • Sponsored by NCTR, UALR Graduate School and UALR CyberCollege

NSF EPSCoR Thematic Proposals

dr anna shvedova national institute for occupational safety and health
Dr. Anna ShvedovaNational Institute forOccupational Safety and Health

NSF EPSCoR Thematic Proposals

nanotox 2006
NanoTox 2006

NSF EPSCoR Thematic Proposals

advisory board
Advisory Board
  • Board made up of senior scientific/ administrative representatives from:
    • ASU – UALR
    • NCTR – UAMS
    • UAF – UGIs
  • Responsible for overall project oversight, inter-institutional coordination, and assuring cohesiveness of sub-projects
  • Assist with long-term funding (post-EPSCoR submission)

NSF EPSCoR Thematic Proposals

about epscor
About EPSCoR

“EPSCoR’s goal is to maximize the potential inherent in a state’s S&T resources and use those resources as a foundation for economic growth.”

NSF EPSCoR Thematic Proposals