Field of Science

Where was I?

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.


  1. And somehow you will need to find the time to eat and sleep too!

  2. all our computers are named for Australian animals
    This is an excellent naming strategy :)
    What are the others called?

    By the way, have you got around to installing Bioperl on any of your machines? Reading some of your posts makes me thing you'd really benefit from some Bioperl goodness.


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