Saturday, November 29, 2008

Protein of the Day #14: XP_001352106

The genome of the malaria-causing Plasmodium falciparum is bizarre in a number of ways - the most striking feature being the extremely high (over 80%) A+T content. Looking on the protein level, there seem to be many proteins with long asparagine inserts. These asparagine inserts must serve some sort of purpose but it is unclear what it is. They do tend to confuse sequence-alignment and similarity searches, which is one reason so many of the proteins remain uncharacterized.
An extreme case of this is XP_001352106, which has a run of 83 asparagines in a row. It does have some similarity to a subunit of cyclin kinase but not enough to be very confident about its identity.

Sunday, November 23, 2008

Symmetric Venn Diagram

This was the start of a small industry of making symmetric Venn diagrams, which Branko Grunbaum found in 1975. I have been working on making a mathematical coloring book (first edition should be - needs to be - done by the holidays, so more details on that soon). I've been trying to making some symmetric Venn diagrams for it, this is a by-product of my first attempts:

Wednesday, November 19, 2008

Protein of the Day #13: ATP synthase, beta chain

One of my students is doing a comparative genomics study of Plasmodium falciparum (with an ultimate goal of developing better alignment algorithms for organisms with extreme genomes), and I was curious about what the most conserved protein is relative to a model organism such as yeast. Turns out its ATP synthase; not too surprising but one might guess some other things too. The wikipedia entry is pretty good, although perhaps not as good as it could be. It does have a nice cartoon of the structure:

Monday, November 17, 2008

Protein of the Day #12: V1rf3

V1rf3 vomeronasal 1 receptor, F3, as its called in mice, appears well-conserved in a variety of mammals, as shown below (sometimes under slightly different names). The vomeronasal system is distinct from the usual olfactory system for smelling, and can be sensitive to very different compounds. In mice the vomeronasal system is important for pheromones. It remains unclear whether humans have any sort of functional vomeronasal at all; my guess is that most of us do not, but perhaps a few people still do.

Friday, November 14, 2008

Permutohedron mirrors

The image below is from a viewpoint in a mirror-faced 3D permutohedron (truncated cuboctahedron). It should link to a larger (1920x1200) version. This image was produced with Sage (using the Tachyon raytracer and some new code for polytopes that I've been working on).

Thursday, November 13, 2008

Slices of the 600-cell

Over the last 6 months or so I've been doing some work on visualizing polytopes, Groebner fans, and other geometric/algebraic objects. I gave a presentation last week about some of that, which forced me to finish up some projects. One of those was a movie of the 600-cell being sliced by 3-planes.