Manuscripts progress

Last week I finally submitted our manuscript about how CRP acts at CRP-S sites in H. influenzae and E. coli. The most interesting result in it was obtained by the gsnpiw just before he left for Belize. He showed that CRP-S sites contain regulatory sequences just upstream of the FCRP-S site that are needed for transcriptional activation; these sequences aren't typically present in CRP-N promoters.
Still to resubmit is our manuscript about Sxy. It too has been enhanced by a new result from the gsnpiw. The experiments are described here). He only had time to do it once before he left, so we're not treating them as part of the paper's Results section, but the results are sufficiently good to be briefly described in the Discussion section. They show directly that mutations in sxy do alter the ability of the sxy mRNA to be translated. Two of the reviewers had suggested we do a different experiment ("toeprinting") which would have tested whether the mutant mRNAs differ in their ability to serve as templates for a polymerase. In my cover letter to the editor of our manuscript I'll explain why we think our new experiments are more informative than toeprinting would have been. I'll also explain that they're not ready to be part of the Results, and that, if the editor thinks that the experiments need to be completed and included in the Results, we'd like a two-month extension of our revisions deadline so they can be completed after the gsnpiw returns from Belize.

I spent much of yesterday making changes to the manuscript and figures and writing responses to the many points raised by the reviewers. A downside of getting four thorough reviews of a manuscript is the very large number of issues they raised. I'm not complaining, as almost all of of these issues lead to improvements; either the reviewer is right, and we make the suggested change, or the reviewer misunderstood what we meant, and we clarify our writing to prevent the misunderstanding.

Only a few points remain to be dealt with. We used lacZ fusions to examine the effect of sxy secondary structure, and one reviewer wants more background information about the behaviour of the reference fusion. This data is in the PhD thesis of a former grad student (an author on the paper), so we may be able to simply refer to it there rather than adding the data to the manuscript's Results.