Excavated documents

Well, the big pile of documents has been excavated and the results are i) a few minor contributions to the recycling bin; ii) a smaller pile of printouts of articles; and iii) a similar pile of assorted research notes and records. Not the Perl-model manuscript drafts and notes I was looking for - they turned out to have been neatly filed in the file box labeled "Manuscripts in progress", which sits on a shelf right next to the file box labeled "Manuscripts failing to progress".

I now remember that the stuff in the pile on the floor was there for a reason. It's all sources of important ideas that I keep forgetting about - either papers I've read that tell me things I really want to remember, or notes from previous research that should someday be followed up on. Filing them would have almost the same effect as just throwing them out. This way I periodically go through the pile hoping to tidy it away but instead discovering that I need to keep these things where I'll see them now and then.

So what did I find? (Maybe if I blog about them I can decide how to use some of them?) Starting from the top of the research notes pile:

1. The table of contents of part of a former tech's lab notebook, indexing the DNA uptake experiments she had done.
2. A table listing the H. influenzae strains in a 'tiling-path' collection that a colleague had given us, with a map of the large-insert plasmid they're in. These are cloned in E. coli, and I think I was planning to use them to test whether H. influenzae competence genes work in E. coli (maybe make E. coli competent). I should mention these to the RA when we sit down on Tuesday to discuss the E. coli transformation experiments.
3. The abstract of a paper reporting that RadC (competence-induced in S. pneumoniae, H. influenzae and E. coli) does not contribute to transformation or DNA repair in S. pneumoniae. This belongs in the pile of articles, next to one showing that RadC contributes to replication-fork stabilization (highly relevant to our ideas about what else the 'competence' regulons control).
4. A very old (c. 1992?) folder containing restriction maps of some plasmids we made with the H. influenzae cya gene. I think these could be filed away.
5. A table summarizing 'Next-Generation Sequencing Informatics', printed four months ago and probably already out of date. But highly relevant to the new post-doc's research and our planned NIH proposal.
6. A list of the research questions we hoped to answer by microarray analysis of H. influenzae gene expression (also c. 1992). We've certainly answered most of these, but perhaps not all. Certainly I can't remember the answers to some.
7. An unpublished summary of research some colleagues did into the distribution of transformability in H. influenzae strains. I think it was presented as a poster about 4 years ago. They sent us the strains, and a former post-doc included some of them in her more detailed analysis of the distrobtuion of competence and transformability (now in press in Evolution).
8. Notes from my analysis of PTS genes in Pasteurellaceae, particularly the glucose and fructose transporters. Of interest because the PTS regulates cAMP which regulates competence, and the H. influenzae PTS has only the fructose transporter.
9. The reviewers' comments on a manuscript that the former post-doc is revising.
   
10. A page of notes from last summer (or the summer before last) when I was planning to test conditions that might induce E. coli sxy by assaying for expression of two lacZ fusions (to comA and ppdA). I did this and saw no induction.

That's enough for today, even though it's only about 10% of the pile.