Wednesday, March 23, 2016
"Miniprep" methodology for extracellular vesicles
Ever spent time around genetics people working? Its all "miniprep" this, "maxiprep" that. For over a year I thought that a coworker had an odd speech mannerism or defect of some kind, then I realized there is also a "miDiprep" and he just couldn't say the "N" sound in that particular word.
The subject of this really nice paper from Jaco Knol et al., is a miniprep isolation of extracellular vesicles (EVs). Why? Cause EVs are super important and great places to find biomarkers. Unfortunately, the prep protocols out there are pretty terrible. You ultracentrifuge some huge amounts of samples forever and:
1) Maybe it works (probably doesn't)
2) It takes forever
3) If yours does work and somebody else tries to reproduce it -- it doesn't work. Then you assume they're dumb and you don't want to go out for drinks after work with and that's a slippery slope of seeming snobby and/or just antisocial and you eventually have no friends and just end up writing a blog or getting a bunch of small animals or something else in some desperate effort to fill that lonely void in your life. ;)
To save themselves from this fate, these authors go through a previously described protocol that has been shown by various inferior methods to be 1) Fast 2) Scalable 3) Reproducible! and show that the darned thing works for proteomics!!!
Check out the time savings summarized in the pic above. Normal method on left! Almost 4 hours of just centrifugation. Versus...wait...I cut the timing off the right. Its 32 minutes! You'll have to believe me, I'm not taking another screenshot. I've got to go to work this morning. Way better!
Not only does this method work, but the coverage is awesome. They show something along the line of 3,000 protein IDs with their method which is on par with the much longer method and pretty solid levels of reproduction.
This is a great little method that is going to make the days of some people I know a good bit shorter. It also highlights the power of looking at EVs ,and the dangers of overlooking them. That is a big section of the proteome floating around there!