Tuesday, May 12, 2015

Global proteomics of starving nemotodes

I feel like this paper was almost written to give me the best start to a Tuesday ever!    Before I go further the paper is from Mark Larance et al., out of the University of Dundee.

Why am I so happy about this paper?
1)  I very easily could find a Sponge Bob clip with hungry nemotodes
2) The starvation stress response is one of the most interesting things that happens in multicellular organisms and we don't know nearly enough about it, particularly how this weird system seems to play into the whole awful aging process thing.
3) This paper is just awesome.  It reads like a Cell paper.  The model is awesome. The experiment is set out in a very elegant way. The stats look rock solid. The observations are well validated....

Okay!  How'd this go?  They SILAC labeled nemotodes (wild-type and mutants!) then put them through a thoroughly used starvation modeling system.  They used a combination of SAX fractionation and organelle specific fractionation and did the proteomics with a (50cm EasySpray, FTW!) Q Exactive. They deposited the RAW files where they can be easily found. They processed the data with MaxQuant using sensible settings. Then all the stuff coming out was checked for statistical significance in R.  GO was generated by DAVID.  Cool stuff that was significant was tested with qRT-PCR.  A huge matrix of data was generated and the discussion on the results is clear and broken into the major observations including changes in the metabolic pathways and in histone composition (cool....).  The processed data appears to be available through the Encyclopedia of Proteome Dynamics, but I'm about out of time this morning.  Excited to check it out.

This paper is just a great study that just happened to generate an awesome new resource for the biological community!  Kudos to this group for doing just a superb job.

1 comment: