Time to do some experiments

I did something at my bench yesterday, for the first time in more than two months. It wasn't a proper experiment - I was only growing up and checking some cells that another researcher has requested from us. But it reminded me of how long it's been since I did any benchwork (more than two months).

I realized several years ago that the pleasure of doing "real" experiments was worth the time away from my desk. This time could productively be spent working on manuscripts and advising other lab members on their experiments, maybe more productively than by doing experiments. But doing experiments is where the best fun is, and I'm not going to let an obsession with productivity deny me the pleasure of doing them.

But first I need to decide what to do. I could take up the "Can E. coli be made competent?" work I left off a couple of months ago. (I had found that the reporter genes I was testing were not suitable for the analysis I wanted to do.) Or I could go back farther and continue the preparations for laser-tweezers analysis of DNA uptake. (I had all the components in place to test the system, and stopped only because other work became more urgent.)

One of the post-docs has just blogged on the role of nucleotides in regulating competence, reminding me that this poorly understood regulation is the critical evidence that bacteria take up DNA as food (that the evolutionary function of DNA uptake is nutrient acquisition). What are the important questions?

First (simplest), does the PurR repressor regulate the rec2 gene? This gene's product plays an essential role in bringing DNA across the inner membrane, and its promoter has what looks like a strong binding site for PurR. We also have preliminary evidence that PurR does repress rec2, from one microarray of cells whose purR gene had been knocked out.

I just searched my previous posts and those of another lab member for "PurR" and found a lot of analyses and information I'd forgotten. So I think I need to get together with the two post-docs that are also thinking about this, and pool our memories and ideas.