Progress on the sxy manuscript

I've been working on the sxy manuscript, clarifying/rewriting the text and improving the figures. I'm not yet all the way through the Results but it's looking a lot better.

The Introduction wasn't too bad anyway, but now it flows better and explains the issues in a more logical order. It's also 65 words shorter, mostly because I cut out some repetition and tightened the sentences.

The Results section is a lot better now. I polished Figure 2, which shows the structure of the sxy gene's 5' end, and now point out that this untranslated region is unusually long. The correlation between Sxy protein and competence is stated rather than just being implied, and backed up with Figure 4. We have a beautiful new version of Figure 5, with all the bands clearly visible, but the text describing these results still needs work. The description of the compensatory mutation work is clearer.

I came up with a 'spin' that turns a discrepancy into a result: RNase analysis shows little difference between mutant and wild-type sxy structures, but the phenotypes are very different. I now say this means that the structure is stable in vitro but labile in vivo, probably due to dynamic effects while the mRNA is being synthesized.

My explanation of the fusions of sxy to lacZ are now much clearer, mainly because my many attempts to really understand this data finally paid off. I've inverted the order in which we discuss the normal (long) and stem-free (short) fusions. The short ones were created as a bit of an afterthought (no, that's probably unfair to the grad student who did this - these fusions we something she thought up herself, and I don't know when). Anyway, I realized that we should consider them first, and then contrast them with the fusions that have the normal structure. I think it's much easier to think about this way. And my new clarity also produced a newly-clear figure, with simple schematic drawings of the fusion structures.

And then my brain shut down for the day.