Saturday, February 20, 2010

Welcome to my job

I've been at work for three hours so far today.  That's right: not only have I been at work since 8:25 am this morning, but it's fucking SATURDAY.

There's actually a good reason why I'm here today.  We've got all these mice whose genotypes (that is, their particular genes) we aren't sure off.  Their parents were heterozygous for our gene of interest--heterozygous means that of the two copies of this particular gene, the parents have two different alleles (forms of the gene).  For us, that means they have one "wild-type" or "normal" copy of the gene, and one non-functioning version.  When we breed these mice, they give, randomly, one of their alleles to each of their off-spring.  We don't know which.  So, for all of these baby mice we got, we know about 25% of them are probably completely wild-type (two copies of the wild-type allele), 50% of them are probably heterozygous or "het" (one copy of the wild-type allele and one copy of the non-functioning allele), and the last 25% are probably "knock-outs" (two copies of the non-functioning allele, which means the gene has been effectively "knocked out").

I hope you enjoyed this biology lesson.

So, we have tails samples of about 24 different mice.  We have their retinas and their retinal RNA, too, but in order for us to make sense of the information we can get from those samples, we need to know their genotypes.  In order to find the genotypes, I have to dissolve the tails to get the DNA out of them, and then I have to make lots and lots of copies of the DNA.  When I use PCR, I use these DNA templates called primers; the primers make it so that only the gene I'm interested in will show up in my PCR results.  If the DNA sample doesn't have the gene that the primer works for, it'll come up negative in the results.  I've got primers for the wild-type and the knock-out versions of the gene (and a generic primer that should work for all samples, and if it doesn't, it means I made a mistake).

When I get the PCR results, none of the samples should come back completely negative.  If it comes back negative for wild-type, but positive for knock-out, the mouse is a complete knock-out.  If it's the opposite, it's a complete wild-type.  If it has both, it's heterozygous.
So, what the fuck have I been doing at work since 8:30 in the morning?  I prepared the tail samples, and I just put in my first PCR plate about 15 minutes ago.  It'll be done in about 2.25 hours.  Then I'll put in the second one, and then later the third one.

Our PCR machine can only run one plate at a time, and you can't even use the computer while a run is in progress.  Since a lot of people need to use the machine, you have to sign up for it.  There are three time slots per day: 9:00am-1:00pm, 1:00pm-5:00pm, and 5:00pm-overnight.  I'm signed up for all three time slots today, something I would never do if it weren't a weekend.  I'll probably be done by about 6:30, I'm guessing.  I could leave the last plate overnight, and I might do that, depending on what else is going on.  I also have to do some other stuff today, like feed cells.

And that is why I'm here so early on a Saturday.  The end.

PS: Kicked the GRE's ass.

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