NanoToxicology and Bioinformatics

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NanoToxicology and Bioinformatics

• 2006 Arkansas NSF EPSCoR
• Thematic Proposal

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Bioinformatics at UALR

• Steve Jennings
• Professor
• Applied Science/EIT
• SFJennings_at_UALR.Edu
• [phone]/ETAS 505
• http//Bioinformatics.UALR.Edu

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Intersection of Interests

• Nanotechnology
• Biosciences
• Computational Sciences

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Thematic Structure

• Regional interests and strengths
• National/ international impacts
• Local economic impact

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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, its
  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

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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

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Participation Potential
NCTR UALR UAF ASU UGIs
Toxicology X X X X
Nanosciences X X X
Biosciences X X X X X
Bioinformatics X X
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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.

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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.

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Special Treatment Tiny Technology Tackles Mega
MessesScience News 4/23/05

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

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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.

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Toxicology

• 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

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Toxicology Research Areas

• Assessing potential toxic effects of
  nanoparticles
• Abatement strategies for reducing harmful effects
• Manufacturing and disposal strategies
• Understanding basic mechanisms
• Appropriate use

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Nanosciences

• 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

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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

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Nanotechnology Collaborators

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

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Biosciences

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

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Biosciences Research Areas

• Understanding basic mechanisms
• Developing appropriate biological models

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Toxicology and Bioscience Collaborators

• UALR
• John Bush
• Jerry Darsey
• QingFang He
• Maurice Kleve
• David Lindquist
• XiaoDong Ma
• Gary Thompson
• HongLi Wang
• UAPB
• Andy Goodwin
• Steve Lochmann

• NCTR
• Dan Buzatu
• Yvonne Dragan
• Paul Howard
• Dwight Miller
• ASU
• Roger Buchanan
• Carole Cramer
• Maureen Dolan
• Jerry Farris
• Robyn Hannigan
• Beth Hood
• Malathi Srivatsan

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Bioinformatics

• 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

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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

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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

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Bioinformatics Resources

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

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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, NCTRs ArrayTrack
• Commercial software packages as required
• Oracle and S/ArrayAnalyzer

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UALRs Virtual Reality Center
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Visualizing Aphid Attacks on Plant Cells
3D Fungus Attack
Cell wall
Traditional View microscopy
Interactive selection and navigation
Immersedseeing 3D frominside the cell
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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
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INBRE Funding Access Grid Executive Stations for
Seven AR UGIs
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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

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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
• REGISTER AT http//bioinformatics.ualr.edu/nanotox
  

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Dr. Anna ShvedovaNational Institute
forOccupational Safety and Health
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NanoTox 2006
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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)

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About EPSCoR

• EPSCoRs goal is to maximize the potential
  inherent in a states ST resources and use those
  resources as a foundation for economic growth.