The Sxy paper

The grad students and I sat down yesterday to go over the Results section of our rough manuscript about how the cell regulates production of the Sxy protein. Sxy acts with the broad nutritional regulator CRP to induce the other competence genes, so understanding how Sxy is regulated is the most important part of understanding how competence is regulated. We spent most of our time working out the best order for presenting results in, and the best ways to display the results in figures.

The previous version had quite a bit of important data presented numerically in two tables. We've now decided to instead present this data as bar graphs. What matters about this data is not so much the particular transformation-frequency (TF) values we've measured for the different mutants and growth conditions as the relationships between the values (e.g. that cells in late- log growth have much higher TFs than cells in early-log growth, and that the sxy-1-5 mutants have much higher TFs than the wildtype cells). Presenting the data as graphs makes it much easier for the reader to make the important comparisons and see the patterns.

Our first priority now is to get the figures in at least a rough approximation of their final form. We think we have almost all the data we want for this paper. One last experiment - asking if the sxy mutations alter how cells respond to nucleotides (see old posts on Sxy and PurR regulation - sorry I haven't figured out how to link directly to them) - will be completed this week, if all goes well. And one gel (or pair of gels) will probably need to be rerun, to get the best resolution of the bands we want to display.

Yesterday I made "place-marker" versions of the figures we don't have yet, and renumbered all the figures to fit our new plan. Today I'm making the Results-reorganization changes we decided on.