Yesterday one of the post-docs and I discussed whether we should submit a proposal to NIH. Yes, we did just get one proposal funded, to work on the regulation of competence genes in H. influenzae and E. coli. But her project is completely different, and some parts of it are going to be expensive.
She's studying when, how and why different lineages of H. influenzae lose (or maybe gain) the ability to take up DNA and recombine it into the chromosome. We already knew that this occurs in various bacteria, and she's now completing a thorough analysis of the variation in DNA uptake and recombination ability in a broad selection of H. influenzae strains.
Some of these strains were chosen because their genomes have been or are in the process of being completely sequenced (one of the benefits of working on a sometime pathogen), and her next goal is to analyze these sequences for differences that could explain their different phenotypes. This bioinformatics work won't cost much except her time; we've already bought a nice fast computer for it. And her time doesn't cost the lab anything, because she's supported by a lovely post-doctoral fellowship from NIH.
But the next steps will be expensive. She wants to use the bioinformatics information to design investigations into the genetic differences of strains that haven't been sequenced. Her original plan was to develop a microarray chip containing all the genes and alleles that the bioinformatics and other work suggested might be involved. This still seems like a good approach, but the field is changing so fast that better ways to survey genomes are becoming available faster than we can keep up. One thing they have in common is that they'll all cost a bundle.
Subsequent work will also be pricey. We'll probably want to follow up the H. influenzae findings with investigation into related bacteria. This will be beyond the scope of the present post-doc, so we'll need new post-docs or grad students or technicians, as well as money for the tools and techniques.
The other reason to write a proposal to NIH is that proposal-writing is the best framework I know of for clear thinking about research plans.
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