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On-Line Research Tools for Biology Teachers

Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009. On-Line Research Tools for Biology Teachers. Overview. Introduction: Giving HS students research tools VIPERdb tutorial and exercise UCSC Genome Browser tutorial and exercise

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On-Line Research Tools for Biology Teachers

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  1. Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009 On-LineResearch Tools for Biology Teachers

  2. Overview • Introduction: Giving HS students research tools • VIPERdb tutorial and exercise • UCSC Genome Browser tutorial and exercise • Quick introduction to nanoHUB

  3. On-Line Research Tools for Biology Teachers • Simple, Accessible, Portable • Science Magazine's NetWatch • http://www.sciencemag.org/netwatch/

  4. On-Line Research Tools for Biology Teachers • Comprehensive and powerful • Designed for scientific communities to help researchers answer difficult questions • Relational databases and utilities

  5. VIPERdb: On-Line Tool Suite for Structural and Molecular Virology

  6. Viruses: Microcosms of Contemporary Cell & Molecular Biology • Physical principles impose constraints on biological systems. • Structure-Dynamics-Function relationships. • A systems perspective: Understanding of complex function by looking at its components. • Self-assembly gives rise to complex forms in biological systems. • Using a simplified model system to understand a broad range of more complex phenomena. • Viruses are one of nature's most successful bio-engineers.

  7. Viruses Are Full of Surprises! • Mutual symbiosis between Polydnaviruses and parasitic wasps. • Oncolytic Virotherapy: Seneca Valley Viruses

  8. VIPERdb Exercise 1 • Browse VIPERdb. Try to view a variety of viruses (both in virus family and T-number). • As you surf, keep track of the T-number, excess surface charge, and average radius of each virus. • Is there a relationship between the T-number and the size (average radius) of a virus capsid? Why may this be? • Clue: most virus capsid proteins are approximately the same size. • Do you notice a trend in the charge of virus capsids (do they tend to be positively or negatively charged)? Why does this make sense? • Clue: remember that viral capsids are essentially “molecular containers.” What do they contain? What is the charge of the contents?

  9. VIPERdb Exercise 2 • Now it's time for STRAP. • Load 6 to 10 viruses from the same family into STRAP and perform a multi-sequence alignment. • Choose one of the viruses from above and list several of the most highly conserved regions. • Why do you think these highly conserved regions are important? What do they do? Use structural information and other information available on VIPERdb to support your hypotheses. • Suppose you want to identify regions of your virus that interact with antibodies. How can you use VIPERdb to do this? • Clue: Different strains (or serotypes) of a virus are characterized by which antibodies bind to them. This means that strains of the same virus will differ in the regions you're interested in.

  10. UCSC Genome Browser Show Them What They're Made Of

  11. Organization of Human Genome • 3 billion base pairs, 25 thousand genes...so what? • This is huge! • 99% of the genome doesn't code for proteins • About 30% of the human genome is junk • Lots of highly conserved non-coding regions • Our genome is very similar to that of other mammals

  12. UCSC GB Exercise • Browse the genome. • Look for gene deserts (regions that don't have genes). • What is the largest gene desert that you find? • Are there highly conserved regions in your largest desert? What could these regions be? • Look for gene rich regions. • What is the most gene dense region that you find? • What is something interesting that you discovered or that came to mind while browsing (an observation or a question)?

  13. BE SURE TO CHECK OUT nanoHUB!http://nanohub.org/ Molecular Simulations of Important Biological Systems Have Never Been This Easy!

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