A brief (I hope) loss of focus.... Now what were the main things I'm working on?
The CRP-S manuscript and the USS-2006 manuscript have both been officially accepted and proof-read. All that's left to do is pay the enormous open-access publication charges. As soon as we have the final formatted PDFs I'll replace the manuscript pdfs in the sidebar.
The sxy manuscript: Analysis of 5 hypercompetent mutants, effect of compensatory mutations, structure predicted by Mfold and confirmed by RNase mapping, effects on transcription and translation measured by lacZ fusions, real-time PCR and protein immunoblots. These experiments are all done, but the manuscript writing has stalled.
The USS-definition analysis/experiments/manuscript: 1. Characterization of genomic USS ("USS-G") by Gibbs motif searching, including effect of direction of DNA replication and of protein coding (and maybe reading frame): These experiments are partly done. 2. Re-analysis of published sequences of DNA fragments that are preferentially taken up: This is mostly not done yet. 3. Uptake experiments using DNA fragments with specific differences in USS sequence: This is mostly done. 4. Writing the manuscript: This morning the post-doc and I will sit down together to reconcile the three different versions of the Introduction. Some of it we'll move to the Discussion. The Results section is mostly not written yet - starting this will clarify what results still need to be generated. Much of the Methods is already written.
The Perl simulation: The post-doc is away for a week, leaving a simulation running on Stingray, our fast new Mac (all our computers are named for Australian animals). It's still not at equilibrium after almost a week, and the simulated sequence has accumulated a lot of USSs. The plan is to explore a range of parameter values (mutation rate, uptake bias) and then introduce some more complications (hmmm, what were they???).
The grant proposal: Create an 11-page compelling description of our past and future research. Still a long way to go, especially on the "compelling" part.
Gotta get one of these! Starry, starry bike path
52 minutes ago in The Phytophactor