Mad Prime

Hah! It looks like there's a protocol for DNA hybridization in blots using 5% Irish cream liquor! I kid you not. Here's a sample quote from the methods of Yamamoto et al. 1993:

Hybridization was carried out overnight at 65°C in a solution containing 6 × SSC, 5% Irish cream liqueur (Original Irish Cream, R & A Bailey's), 20 mM Na₂HPO₄, 20 μg/ml heat-denatured salmon sperm DNA, and 2 μCi/ml of the ³²P-labelled probe.

The original source appears to be Elbrecht, A. 1987, "Lab Hints: Irish Cream Liqueur as a Blocking Agent for DNA Dot Blots." BM Biochemica, 4:12-13. BM = Boehringer Mannheim, it appears to be a newsletter. It's too obscure for my cursory searching to turn up a copy of the original, I wonder what the motivation was! Maybe this way you can order liquor using grant money? This idea has a lot of potential...!

The New York Times has a nice article on flower evolution today.

If you enjoy looking at evolutionary trees to see how closely related different living things are, you might enjoy playing with ExploreTree. I've added features that make it a lot more fun: the zooming in and out is animated, you can search for an organism and follow a path. Plus now, with a little help from Chris, it runs on a webpage (feel free to show it to friends & family). Give it time to load, though.

Here is a snapshot of the location illustrated in the NYTimes article:

I've put off posting about the program for a while since I kept hoping to improve it a little more, but here it is. It was written in processing, you can get the code if you'd like to play with it here (or improve it!) on github.

Another social hour poster illustration:

Was kind of sad this year having a "retreat" in a slightly different building in the same city. I amused myself by constructing a genetics "buzzword bingo" list.

1. Slide showing a signaling pathway with >= 15 proteins named
2. Messing with this gene causes cancer
3. Anything involving stem cells
4. Microarray data
5. High throughput / deep sequencing
6. RNAi
7. Animal model vaguely resembling a human disease
8. GWAS
9. Messing with this gene makes this tissue/organ look funny
10. Epigenetics
11. Mass spec data
12. FACS
13. Evolution
14. A photo that makes you lose your appetite
15. Apoptosis is mentioned
16. HAIRBALL (aka. "interaction network")
17. Anything related to sex (eg. chromosomes)
18. RNA splicing
19. Bacteria
20. Yeast
21. Plant
22. Worm
23. Fly
24. Fish
25. Mammal

Although silly, I found this actually helped keep me paying attention to talks. I applied it to the last session and almost got a BINGO, but Norbert Perrimon's signaling pathway slide only had 13 proteins. So close!

This last Saturday Chris and I participated in a code jam organized by a friend using processing, a programming language oriented towards enabling interactive visualization and graphics. I used processing to create all of the graphs in the recent Nature Biotechnology paper - I came to it because I was frustrated with an inability to create exactly the graph type I wanted. In the end each of my graphs is created by a small program, but I'm happy with putting in that effort to get something that looks great.

For the code jam I had been wanting to create a browsable tree of life akin to the fractal-like tree of life comic I made a while back. To this end I created a Newick format tree, working my way back from humans. I filled in only organisms and names that were familiar to me, reasoning that obscure organisms only serve to make a tree confusing, cluttered, and unapproachable. So far I'm only as far as unikonts, you can get a copy of it here if you like. (Please consider this as licensed under CC-by-SA if you'd like to use it.)

Chris found and applied some java code for interpreting a newick format file and creating a tree data structure, and I worked out a simple recursion for drawing the tree out to a given depth from a given node. Clicking on a node redraws the tree from that location; pressing any key zooms back out by one level. Here is a screenshot of the base:

One of the nice aspects of processing is that visualizations should be portable to java applets. Although we haven't done it yet, hopefully we'll be able to do that. If you have processing installed, you can download a copy of what we wrote. (You'll need to fix the file path in the source code to point at the tree.) Other improvements I'd like to do: to make zooming smooth rather than jumping (this can be disorienting when a large change occurs) and add the ability to search and choose an organism, then color the tree according to distance from that organism so you can click "warmer" colors to get closer to it.

The theme of the event was "clocks" and although I had intended to work on this anyway, it did fit into the theme fairly well: we called the program "Evolutionary Time". We were thrilled to be awarded the "wealth" prize by processing founders Ben Fry and Casey Reas: a gift certificate to the MIT Press Bookstore, which I intend to spend on a reference or two for processing, hopefully to further improve our program. ;-)

You may have seen him before: Snowball the Dancing Cockatoo. ScienceNOW Daily News reports on a Current Biology study - a neurobiologist went to study the bird and sees dancing as a phenomenon connected to the ability to imitate sounds. A companion paper looks for dancing ability in a number of animals, but only found it in animals that were able to vocally mimic sounds.

If you haven't watched the video you definitely have have to. If you have... it's worth watching some again. :-)

The hard copy of the Nature Biotechnology with my article in finally came out, so here's a pic of me posing with it. I designed the cover too, it's an abstract representation of padlock probes capturing sites in bisulfite-treated DNA, with a color-warped photo of induced pluripotent stem cells in the background.

If you happened to stumble across this site because you're interested in the profiling methods, please feel free to contact me. Of course, the news about 5-hydroxymethyl-cytosine kind of throws a wrench into the gears of any DNA methylation profiling studies.

Today I produce things of questionable value to society. Five cheezburgers pleez, kthxbai.

moar funny pictures

Ragdoll cats are remarkably calm. Here is my cat pendulum demonstration of this, starring Zoe. I think she only started to object when I started trying to do the rotation motion.

Today I finally framed a painting of California poppies I bought on etsy a while back. You can click on it to see a more detailed photo of the painting itself. The artist retains copyright on the image, please ask her for a print if you'd like one for yourself! :-)