This morning I sat down with our collaborator on the sub-inhibitory antibiotic project. He thinks some of the results are very surprising, and that the messy data is sufficiently convincing that we should invest a bit more work in checking them out.
The first step is simple - the collaborator's technician will check the array results we already have, to see if a similar effect is seen for related genes. If it's not, we stop. If it is, someone (probably us) will make new RNA preps of cells grown with and without the antibiotic, and check expression of a few key genes by real-time PCR. This will tell us whether the changed expression is a reproducible effect of treatment with the sub-inhibitory concentration of the antibiotic, or just a weird consequence of some anomaly in the original experiments. If it's not reproducible, we stop. If it is, we decide whether or not to go on.
Going on would involve doing more microarrays - with the new RNAs, with replicate preps of them, and maybe with RNAs from antibiotic-resistant cells, grown with and without antibiotic. More real-time PCR assays would probably also be needed. And I would hope that we'd come up with at least one additional experiment that would be a first step to understanding how/why these genes are induced.
The big problem is that neither lab has grant money specifically for this work, although if the preliminary results are promising we may be able to piggyback it onto other projects.
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