Bodnar (2003) Valuation. The International Cost of Equity.pdf
On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at...
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![Page 1: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/1.jpg)
On-Line Research Tools for
Biology Teachers
Yaroslav (Ross) Daniel Bodnar
University of Illinois at Urbana-Champaign
GK12 Teacher Workshop
August 10, 2009
![Page 2: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/2.jpg)
Overview
● Introduction: Giving HS students research tools
● VIPERdb tutorial and exercise
● UCSC Genome Browser tutorial and exercise
● Quick introduction to nanoHUB
![Page 3: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/3.jpg)
On-Line Research Tools for Biology
Teachers● Simple, Accessible, Portable
● Science Magazine's NetWatch
– http://www.sciencemag.org/netwatch/
![Page 4: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/4.jpg)
● Comprehensive and powerful
● Designed for scientific communities to help
researchers answer difficult questions
● Relational databases and utilities
On-Line Research Tools for Biology Teachers
![Page 5: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/5.jpg)
VIPERdb: On-Line Tool Suite for
Structural and Molecular
Virology
![Page 6: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/6.jpg)
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.
![Page 7: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/7.jpg)
Viruses Are Full of Surprises!
Mutual symbiosis
between Polydnaviruses
and parasitic wasps.
Oncolytic Virotherapy:
Seneca Valley Viruses
![Page 8: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/8.jpg)
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?
![Page 9: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/9.jpg)
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.
![Page 10: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/10.jpg)
UCSC
Genome Browser
Show Them What They're Made Of
![Page 11: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/11.jpg)
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
![Page 12: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/12.jpg)
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)?
![Page 13: On-Line Research Tools for Biology Teachers Yaroslav (Ross) Daniel Bodnar University of Illinois at Urbana-Champaign GK12 Teacher Workshop August 10, 2009.](https://reader035.fdocuments.us/reader035/viewer/2022081516/5697c00d1a28abf838cc94fc/html5/thumbnails/13.jpg)
BE SURE TO CHECK OUT nanoHUB!
http://nanohub.org/
Molecular Simulations of Important Biological Systems Have Never Been
This Easy!