June 23, 2011
Mo MAGIC high school student demonstration
Outline for 15 minute Chimera HIV demonstration.
Data files for this demonstration for Chimera 1.5.3 or more recent version.
What we do. My lab writes computer software to look at the molecules that make up living things.
Why? Understanding all the molecules that make your body function helps develop drugs. All drugs work by sticking to specific molecules in your body and interfering with those molecules.
Example: HIV virus. Let's look some of the molecules that make the HIV virus. HIV virus causes AIDS.
Show segmented HIV particle EM data. Hand out stereo glasses.
The virus is round and the other blue shell has been cut in half. Turn off per-model clipping to show whole shell, then back on.
This is a view of the virus through a million dollar electron microscope. The virus is too small to see in a microscope that uses light.
Space Navigator. We always look at 3-dimensional shapes. To move those around we can use a joy-stick designed for moving 3-dimensional objects.
Demonstrate. Pushing down moves molecule down. Pulling up moves it up. Rotating the knob rotates the virus. Pushing away moves it away. Have students try it about 10 seconds each.
Molecule size. Zoom in on a tiny blob -- this is the size of a typical molecule the virus is built from. The electron microscope is not powerful enough to see the thousands of individual molecules.
Ice-cream cone. Other methods using x-rays can see the molecules and atoms. Let's look at a more detailed version of the red ice cream cone.
AIDS epidemic: Which country has the highest HIV infection rate? Swaziland (bordering on South Africa, population 1 million). Half of 20-29 year olds are infected. Life expectancy is 32 years (2009).
Close segmented hiv session. Show hivcapsid.py session.
Cage. Notice blue rings are hexagons 6 sides, orange rings are pentagons sides. This is basically a soccer ball deformed by adding a bunch of extra hexagons.
The cage is not the actual virus molecules. It is just a diagram showing the pattern of the construction.
Molecules. Use Model Panel to show other 4 models depicting the molecules. Each yellow or purple blob is one molecule.
Atoms. Zoom in on hexamer shown as atoms.
What's inside? Move front clip plane into cone at big end. Nothing. In the real virus the instructions for how to create the virus are inside.
AIDS epidemic: How many AIDS patients have been cured? One. The "Berlin patient" had their immune system completely replaced by a bone marrow transplant for leukemia (bone marrow and blood cancer). Transplant had very rare mutant cells that cannot be invaded by HIV. Bone marrow transplant kills patient in 30% of cases.
Plastic print out. Hand around printed plastic model. Printed on a 3-dimensional plastic printer downstairs about the size of a mini-refrigerator.
Instructions. This is inside. Show RNA paper tape. Show 4 different color bands. Hand one end to a student, untangle, and hand parts to other students to see how long it is.
18 different HIV molecules are encoded in these instructions.
Your DNA. This HIV RNA is the equivalent of your DNA which encodes about 30,000 molecules and would fill this room in paper tape form.
Opportunity. AIDS will still need a solution when you get out of school. Study biology, work hard, and you can get paid well to solve an important problem. 16 million kids, mostly in Africa, have no parents because of AIDS. This matters.