Saturday, March 21, 2009

Rotation #3 Diary: Week 1

A new rotation brings a new series of blog posts! I finished my first week today, and I think things went well. I started off pretty helpless, as is the case with any new lab position. It's interesting to see how different labs perform common tasks like PCR and westerns, because everyone has their own favorite reagents, special protocols, and secret tricks for optimizing the results. Once I learned some of this lab's quirks, I was set free to start doing my experiments.

I started off genotyping mice. Woo, thrilling. But, I'm actually quite interested in what the results will be (I should know on Monday, when my sequencing data comes in). The lab is generating a new line of mice, and I'm testing the first litters born to a couple of chimeras. When making genetically engineered mice, you have to start with regular mice and make these blended embryos from normal mouse cells and mouse cells that you have messed with. If these embryos survive, they grow up to be chimeras (usually you choose mice of two different colors, so that the chimeras will be obvious because they come out all patchy). Then you have to hope that at least some of the germ cells (eggs or sperm -- the chimeras are normally male, but we have one female, who is probably XO rather than the normal XX due to some quirks of the mouse-making process) from those chimeras are mutant cells, so that they will produce offspring that contain your desired genetic modification. If you don't get any germ-line chimeras, you have to make more chimeras, which quickly gets expensive. So, we have a vested interest in seeing if these baby mice are mutants or not.

Thus, I did some PCRs, then purified my PCR product and sent it off for sequencing. Apparently this is easier, more reliable, and perhaps even cheaper than doing an enzyme digest to see whether my mice are mutants or not. (The mutant gene contains a restriction site that isn't found in the normal gene, thus if you digest the DNA with a restriction enzyme, the mutant DNA is cut into two pieces while the wild-type DNA remains whole. You can see the different sized pieces of DNA if you run them out on a gel.) It costs about $8/sample, which seems ridiculously cheap to me. Of course, I'm only sequencing an amplified piece of DNA that's around 300 base pairs long. For reference, your genome is a million times bigger than that -- that's three billion base pairs. And I would not pay $8 million to have my genome sequenced. So, it might not be such a great deal, after all...

In between my genotyping experiments, I got to learn some new mouse-related skillz. This lab identifies individual mice with numbered ear tags, which I have not used before. To tag the mice you use a little pliers-type thing that punches a small metal tab through the ear flap and puts the tag in place. It's basically like getting your ears pierced by the piercing gun at a Claire's in the mall. I had never done this before (previous labs used toe-cutting -- which is pretty barbaric, but it's the only way to ID very small newborn mice -- and ear punches). So, I got to practice tagging a few mice. I have to say, they seem much more upset about being picked up and gently restrained than they do about having their ears pierced.

The lab also does a fair number of behavioral assays, which I have no experience with. On Friday, my labmates were testing a drug treatment on some of the mice, so I got to watch them administer the drug and give the mice a behavioral score reflecting the severity of the drug's effects every 10 minutes. It was pretty interesting, but I can see how it would get old after doing it over many trials. Since you're observing every 10 minutes, it would be hard to get anything else done during the trial, and staring at mice is not the most fun thing in the world. A video recording system would allow the experimenter to walk away during the trial and review the film later (with the added benefit of blinding the experimenter to the amount of time elapsed since drug administration, if the film could be chopped up into segments and rearranged), but since this system is intended to be high-throughput, they just suck it up and spend a few boring hours running lots of mice as needed.

So far, so good. Everyone in the lab has been really friendly to me, and they seem like a fun bunch of people. Plus, we get free lunch at lab meetings! (This is a crucial point to consider when choosing a lab.) Mouse work is not my favorite thing, as maintaining a mouse colony gets tedious (not to mention smelly), but the mouse is a pretty good model system if you want to do clinically relevant research. I may have to just resign myself to the task.

More updates next week!

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