just freaking great

A little disclaimer: the following post will be mostly technobabble if you aren't familiar with the process of making a knockout mouse. Still, I just have to spill it all out. Mainly because I still am struggling with this result (hence the hour of this posting...).

Today I genotyped 36 pups from 6 different het-het mating litters. Some of the litters were quite small (3-5 pups), but for first-time mothers you never know what to expect.

What I didn't expect, however, was the results that I got...of the 36 (live) pups, exactly 12 were wild-type, 24 were heterozygotes. Just what you'd expect if the homozygous mutants are embryonic lethal.

Now, I will rerun a few of the PCRs just to be sure, but I'm quite convinced that I'll get the same results. All of these pups were around 2 weeks old. I have a couple more litters I will be able to tail early next week, and of course I'm working on getting those 6 moms pregnant again (left the dads in the mating cages so that they'll get pregnant again ASAP), so I'll have to see what happens with a second set of pregnancies.

I've been turning over in my head all sorts of other potential explanations, apart from 1) embryonic lethality and 2) just the odds, given 1st time pregnancies and some small litter sizes. One is that in knocking out PKal I've screwed up something else. If you recall, one of the cytochrome P450 genes is upstream of PKal (though its LAST coding exon is about 10 kb upstream of the PKal ATG), and Factor XI is just downstream (about 8 kb between PKal's end and FXI's start). FXI KOs have been made and they're fine, so that can't be it; I will have to redo some serious digging but I saw no mention of any downstream regulatory elements for cytochrome P450 when I was planning this strategy before. But somehow I think that this possibility of an unforseen effect on another gene is pretty small.

I'll have to see how the next couple of litters turn out, and until then, I will have to do some refresher reading up on mouse embryology. Just in case. I will also write Dave to see what sort of litter sizes he got in his F2 generation of gene trap mice; if 50:50 Bl/6:129 litters usually give 8 or 9 pups then maybe it's just an odds thing; however, if they are usually more robust, yielding 12-14 pups, then I'll know I'm on to something.

What vexes me the most is that I didn't flox the gene because it wasn't supposed to be freaking embryonic lethal! Aaargh! Now I know how I'm going to spend my Thanksgiving break...refreshing myself on mouse embryology.