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

Yaroslav (Ross) Daniel Bodnar

University of Illinois at Urbana-Champaign

GK12 Teacher Workshop

August 10, 2009

Overview

● Introduction: Giving HS students research tools

● VIPERdb tutorial and exercise

● UCSC Genome Browser tutorial and exercise

● Quick introduction to nanoHUB

On-Line Research Tools for Biology

Teachers● Simple, Accessible, Portable

● Science Magazine's NetWatch

– http://www.sciencemag.org/netwatch/

● Comprehensive and powerful

● Designed for scientific communities to help

researchers answer difficult questions

● Relational databases and utilities

On-Line Research Tools for Biology Teachers

VIPERdb: On-Line Tool Suite for

Structural and Molecular

Virology

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.

Viruses Are Full of Surprises!

Mutual symbiosis

between Polydnaviruses

and parasitic wasps.

Oncolytic Virotherapy:

Seneca Valley Viruses

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?

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.

UCSC

Genome Browser

Show Them What They're Made Of

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

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)?

BE SURE TO CHECK OUT nanoHUB!

http://nanohub.org/

Molecular Simulations of Important Biological Systems Have Never Been

This Easy!