Biocurious is a weblog about biology, quantified.

Pain In the USS

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.

  Textile help