So today is March 15th, one of my favorite days for no discernible reason other than that I can call it the ides of March. I know there are ides for all months, not just March, but if I said to you, “Beware the ides of September!” would you care? I’m guessing not.

Of course, you might not care if I said to beware the ides of any month…I know how you are.

It’s been a busy past few days, so I’ve been a slacker on my blogging. I’ve put in a goodly number of hours the past three days and have gotten a lot of low-level stuff accomplished. Lots of PCR and cloning, which correlates to lots of minipreps, digestions, and gels. Man, I love minipreps…there’s something so relaxing about them to me. I get into a nice zone of mindlessness. It’s almost but not completely unlike meditation.

The rest of my time has been spent preparing for my committee meeting tomorrow, which should be short. Hopefully. I just had a meeting in December, so I don’t have a lot of new data to present to them. I have decided, though, that rather than spend the next eighteen years doing an analysis of the long-range interactions in the entire domain in multiple tissues, I’m going to focus on one gene in particular. It’s not a terribly interesting gene in and of itself — there’s no phenotype to the knockout — and it’s not conserved between humans and rodents (it appears to have retrotransposed into the domain sometime after our ancestors split), but it is imprinted and I’ve found varying levels of expression in a few different tissues, nicely paralleling what other genes in the domain do. High expression in brain, low expression in fibroblasts, etc.

My plan is to do a complete epigenetic profile of the gene’s promoter in a few different tissues. As of right now, we’re thinking newborn brain (high expression), adult spleen (no expression of the other genes…I haven’t checked this one yet), newborn or adult liver (moderate expression) and fibroblasts (low expression). I’ll do a DNase I hypersensitivity analysis in the tissues at the promoter and ChIP for a variety of histone modifications. H3K4 and H3K27 methlyation, for instance. We also have a model for the involvement of a few specific transcription factors, so I think I’m going to ChIP blindly for those factors. I have to wait on an antibody for one of them, but for the rest we have good antibodies. I’m also going to do an in vivo footprinting analysis of the promoter (and probably the early body of the gene, based on predicted transcription factor binding sites). I think we’re going to start with the fibroblasts and cross our fingers. Expression is relatively low in the fibroblasts which may correlate to weak footprints, but Jixiu has found absolutely blazing footprints at another gene which is expressed in a similar fashion.

Nothing else terribly exciting to report at the moment. I’ve recently (as in yesterday) been in touch with a Heggestad in Norway and we’re exploring to see if we have any common ancestors. Emma and I are going to go to the beach this weekend and relax. This is her first weekend completely off in months (and the last for at least many weeks), so we’re going to seize the opportunity to catch a few rays.

The chickencam is today facing the woods around our hammock (visible in the lower right corner of the picture). I think the cats mess with it during the day, because I’m convinced that the picture shifts between the time I set it up in the morning and the time I get home. I could try to figure out how to keep an archive of each picture, but that’d just be clever. Better to guess, right? Okay…back to work. Those 30 minipreps aren’t going to prep themselves!