by PhilipJ on 24 April 2006
Alex is complaining about the naming scheme they use for yeast strains in his lab, particularly because for him it will spell out a woman’s name—AMY. I think I’d be kind of annoyed if all my strains had names that could be people too, but thankfully I don’t do enough work with cells to require naming them anything special. I do, however, have a fun naming story about a plasmid I was working on last semester.
Plasmids are closed loops of DNA, usually containing specific genes you wish to express in a cell, often E. coli. While many plasmids have strange or boring names, the general scheme always seems to follow pXYZ#, where the leading p denotes that it is a plasmid, XYZ are some (usually cryptic) letters, and # is the “version” of the plasmid, not entirely unlike software versions.
In an optical tweezers instrument, it is often easier to use DNA that is a few microns long upon full extension, and so I was happy to find out my advisor was able to get the plasmid she used to use as a post-doc for our lab. It was cryptically named pPIA2-6, and at 15071 bp (x 0.0338 nm/bp = 5.09 microns), it was more or less the perfect length for our instrument (I’ve actually mentioned it before, here). I already had another plasmid I needed to use, called pUSS1, which contained something called an Uptake Signaling Sequence, but it was unfortunately much too short for our purposes at only about a micron in length.
So, I spent a fair amount of time cutting both pieces of DNA with the same two restriction enzymes and, after getting rid of the pieces I didn’t want anymore, ligating the remaining two back together to form a single new plasmid. Now it came time to name it.
It turned out that pPIA2-6 was rather hard to clone (perhaps this should be obvious by its rather high version number of 2-6), and I was eventually told it was so named because it was a Pain In the Ass to work with. Even though I didn’t have a large amount of trouble working with the plasmid, I decided to keep the scheme, and since I joined pPIA2-6 and pUSS1 together, I’m the proud creator of pPIU1, for Pain In the USS.