Friday, February 5, 2010

Mayonnaise for Science

This isn't what you're thinking. I'm not talking about some kind of microbiology experiment with mayo or anything. I'm talking about Emulsion PCR. Obscure phrase, I know, but I think its pretty neat, so I wanted to introduce it here. First a little background.

PCR (for those not familiar with it) is an acronym for Polymerase Chain Reaction. That wikipedia page has a pretty good overview (if you are young, and looking for references for you're science class, unless your teacher has said otherwise, wikipedia is not a good reference), but for those who don't want to link, a PCR reaction is a method for making thousand and thousands of copies of a piece of DNA. It can by any piece you want really (with some provisions), and its one step to getting those neat pictures that everyone sees on the crime shows.

In the last few months I've been learning a lot about Next Generation sequencing (NGS), and one of the steps in the process is Emusion PCR. This method is key to how NGS works. In NGS, you fragment your genome into millions of pieces, each one of these pieces is then chemically attached to a microbead. But, you need to keep your beads separate, so that each bead only amplifies one sequence, this is important, because it relates to how you will be able to assemble your sequences later. If more than one sequence amplifies, the sequencing machine may misread or combine the sequences on that bead, which, since they attach randomly, would lead to an error when the sequence is assemble. So how do you keep the beads separate? Emulsion.

In an emulsion, say, between water and oil, the oil is separated into smaller and smaller units, surrounded by water through agitation. Think of shaking up a bottle of italian salad dressing. If you agitate vigorously enough for long enough, the droplets of oil will get smaller and smaller, and mix with the water more and more, making the solution thicker. This (with some other additives) is how mayonnaise is made. Emulsion PCR is the same process, but with your reagents and some oil. You mix up your beads and sample, suspend some oil with them and vortex them until and emulsion is formed. It even looks like mayonnaise!

image courtesy of genefish flickr pool

Why would you want to do this? In making the emulsion, a single bead, with a single sequence attached, is separated out into each tiny droplet of oil, allowing separation and amplification of your samples, without cross contamination.

Mayonnaise for science, Pretty neat!

Tuesday, January 19, 2010

A disturbing forum post

So, currently I am working on a lot of next generation sequencing stuff. I'll do a post later on the details of that, but one good resource for this technology is a forum called Today there is a disturbing thread about possible contamination. I'll be watching this a bit. Getting literally millions of contamination sequences would be a total bummer.

Tuesday, January 12, 2010


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