PhD week 10: First gel

This week's milestone is pictured above. It is a picture of an agarose electrophoresis gel. These gels are made from a seaweed derivative, and are used to separate DNA of different lengths. Samples of DNA are placed into holes in the gel, and an electric current is passed through it. The DNA moves through the gel towards the positive electrode, but longer pieces move more slowly than shorter pieces. The gel is then stained with a chemical that binds to the DNA and fluoresces under UV light, allowing one to see the result. The white dashes in the picture above show where DNA has ended up. The obvious ones at either side are the DNA ladder, a mixture of DNA of known lengths, which allows one to figure out the lengths of DNA in the samples.

It so happens that this particular gel is the first one of many that I will run over the course of my PhD. It is the result of a PCR amplification of a specific fragment of DNA for a number of weevil specimens. The reason you can tell that it is genuine is that it is hideous as far as agarose gel pictures go, and the only reasons for showing anyone a picture of this quality is to point out the problems with it, or for sentimental reasons. It is shown here for both purposes. For starters, I left it running for too long, and the ladder has run off the end. Secondly, only two of eighteen samples actually worked (the ones that have been ringed). One of these is a positive control, a DNA sample that is known to have worked under the same conditions previously.

So, all in all, it's a somewhat disappointing result. However, optimising PCR protocols is a routine (though annoying) part of getting DNA sequences from a number of specimens. What this gel does show clearly is that I shall have to go through that process before I can routinely sequence DNA from my weevils.

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Read:
   Posadas P. 2012. Species composition and geographic distribution of Fuegian Curculionidae (Coleoptera: Curculionoidea). Zootaxa 3303: 1–36
   Wilson D. 2010. The People's Bible. The Remarkable History of the King James Version. Oxford: Lion
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 52–54

Websites:
Marcus Ardern's blog and website
gitHub smart HTTP support details
gitHub: Forking repositories
Geographx free downloads
Using near IR in microscopy
Setting up screensavers in Precise Pangolin
AviAtlas

Listened:
Kevin Johansen—Sur O No Sur
Color Tango—Con Estilo Para Bailar

Watched:
Wallace's standardwing (Semioptera wallacei) mating dance
National Geographic TV Profile of Jim Frazier
Star Trek: Deep Space Nine Season 3