We noted while “pinning metabolites” that allantoin was present in the mass spec data from UCSD. This metabolite is not supposed to be present in humans; it is a breakdown product of purines in some animals, but in humans and other primates, the producing enzyme does not exist, and instead, uric acid (urate) is the final product of purine catabolism. Or at least so I thought.

It turns out that urate can spontaneously oxidize to form allantoin, and some think that this is an indicator of oxidative stress (whatever that means in this context). But there are also concerns that this is an artefact of sample handling conditions. It would be interesting to see if cells with labeled purines produce labeled allantoin …

This new Cell family journal will cater to the systems biology crowd. The first issue includes gems like network analyses of transcriptional regulation, search strategies for large biological data sets, and how to remote control mice :)

http://www.cell.com/cell-systems

Thanks Mo for the heads up!

If you haven’t seen it already, check out BioNumbers ! It’s a database of all sorts of things in biology that are measurable and can be expressed in numbers — the size of a cell, the length of a chromosome, the speed of an enzyme …  It was started by Ron Milo when he was at Harvard (now at the Weizmann Institute).

Enjoy the numbers!  :)

I’ve raved about Edward Tufte and his minimalistic approach to data visualization plenty of times before …  I just found there is an R package implementing some of his plot designs, see

http://motioninsocial.com/tufte/

I especially like the scatter plots with marginal densities indicated by “stripes” on the axes,

Of course I would like this in Mathematica instead … but better than nothing I guess  ;-)

This is a secret post (hee hee). Don’t tell anyone!

Say hello to the new web site for our lab!