Protein of the Day #7: Enolase

Mammals have three enolases. A more descriptive name is "phosphopyruvate hydratase" - they catalyze the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate.

In Plasmodium falciparum, there is still some controversy about their enolase. It appears that at least part of it comes from a migration from the apicoplast genome into the nuclear genome, but it may be a hybrid. Here's the telltale insertion that matches up with plants (in this case rice, but the apicoplast probably came from a red algae ancestor endosymbiont):

Movie of a Groebner fan

This summer I spent some time thinking about animation and visualizing algebraic and geometric information. I have a longer to-do list than accomplishments but I have made some progress.

One of pilot project ideas was to take a 5-variable polynomial ideal and:
1) compute the Groebner fan using Sage and Gfan,
2) intersect it with a hyperplane (so now we're down to 4 dimensions)
3) slowly rotate the resulting polyhedral complex in 4 dimensions, rendering it using Tachyon/Sage
4) animate the resulting set of frames.

For step 4, I initially wanted to use Blender, but that was really overkill for what I needed and I didn't want to figure out how to get Sage and Blender using the same copy of Python (although someone should). In the end I used ffmpeg to get my movie.

Check out my current best effort.

My next goal in this direction is to do something with Sage's @interact command and JMol to highlight pieces of the fan, since the movie isn't really informative (more art than math I think).

Protein of the Day #6: CD36/Fatty acid translocase

CD36 is a great example of the complexity of biology.

After some modification, it is the same thing as "platelet glycoprotein IV", an important protein in platelets and clotting - thrombospondin binds to it. Its also important in malaria, since Plasmodium infected erythrocytes can bind to CD36, and mutations in it can result in varying severity of malaria.

But its also "fatty acid translocase" and its a receptor for low density lipoprotein (LDL). Its been associated with a number of effects on the immune system, reaction to hyperglycemia, and oxidant stress.

Both these roles make it interesing in the context of mammalian hibernation, where the clotting reactions must be suppressed and metabolism switched to using ketone bodies derived from lipid stores.

Free Stanford!

...just a little joke, no one is repressing it. But the Stanford Engineering school has done something extremely nice, namely put up entire course materials online for computer programming, AI, and some electrical engineering courses. Looks very well done. I really like the transcripts of the video lectures, since I like reading more than listening. I don't think MIT's OpenCourseWare does that, but that is another very nice open access project.

I am a little envious of today's self-motivated youth, it would be pretty easy to teach yourself almost anything these days. When I was a teenager I taught myself basic calculus from an old 1940s book (it was called something funny like Calculus for the Everyman, I can't remember exactly). It had nice line drawings but geez, being able to virtually sit in on MIT classes would have helped I think.

Protein of the Day #5: Aldehyde dehydrogenase 2

Aldehyde dehydrogenase 2, or ALHD2, is the highlight of an article in Science this week showing it is related to mechanisms for protecting the heart from ischemia (lack of blood, which results in lack of oxygen (hypoxia)). There are cytosolic and mitochondrial versions; since this protein is important in metabolizing alcohol, having both versions seems to clear alcohol faster, although I can't find a definitive reference for that fact.

Protein of the Day #4: apical membrane antigen 1 (AMA1)

In the Plasmodium species that cause malaria, the merozoite stage must invade red blood cells. It does this using the strange apicoplast organelle, which is a much-warped descendent of a chloroplast. Apicoplast:chloroplast as Gollum:Hobbit. Anyway, one of the proteins that helps this invasion is the apical membrane antigen 1, although like most Plasmodial proteins not that much is known about it.

Eloquent Javascript

Because of my interest in Sage and eventually helping more with the notebook interface, I've been trying to learn some Javascript. Recently I found a fantastic online book that's a joy to use, partly because it has an interactive Javascript console and all code examples can be run within that framework: check out Eloquent Javascript.