Very recently I got into a discussion in which I was being super negative about our tendency as scientists to seek to do "one more experiment," and the feeling that it is possible to increase the impact of work by doing more of it. Frankly, if you look at papers in "top tier" journals we see papers that appear to be a collection of somewhat unrelated results bundled up into a massive effort. So it definitely feels like a necessary evil to survive in academia, and even in our lab you'll hear folks complaining about how "thin" such-and-such paper is. The painful part is that the drive to avoid a "thin" paper often ends up in inconclusive or negative results which are never published.
This morning I woke up thinking that instead of being so damn negative (which is depressing for morale of all involved), we could do something positive and actually put some of that stuff up on the web, something Arjun's been encouraging since he set up the blog but we haven't really followed up with in the group. That way the work wasn't for nothing and even though its not in a journal, maybe google will find it when someone makes a search.
This is the first of a few short posts on experiments that we did in relation to our paper on the relationship between cell division times and gene expression onsets in early development of C. elegans embryos. The core of that paper was completed rather quickly, but we spent quite some time trying to add stuff to it. Here is some of the stuff that didn't make the cut.
Expression dynamics in C. elegans mes-2 mutant embryos
In the midst of working on the project that resulted in the paper I went to a talk by Prof. Susan Mango describing their work on mes-2 mutants (Yuzyuk et al. Dev Cell 2009). MES-2 is a component of Polycomb and its mutation was reported to change the window of developmental plasticity in the embryo. I thought it would be interesting to measure the dynamics of the genes to be featured in our wormpaper in this mutant background, since the paper was all about timing of expression of lineage-specification genes. Perhaps there would be something interesting.
Methods: mes-2(bn11) was the mutant studied by Yuzyuk et al. We got it in strain SS186 from the C. Elegans Genetics Center. mes-2 mutants have a very peculiar phenotype: Progeny of mes-2 homozygous mothers are sterile. We switched the balancer with a GFP balancer by mating with strain MT20110, constructed by Erik Andersen, a friend and collaborator of Arjun's from his postdoc time. I wanted to avoid using a fluorescent worm-sorter, so I ended up manually removing all GFP(+) worms from a small synchronized plate. The remaining worms are either fertile mes-2 first-generation homozygotes or their sterile progeny. Very carefully, we ran those ~1000 worms through a micro-scale version of our worm embryo preparation (which usually works with >10x the amount of worms). We then conducted RNA-FISH as usual.
Results: In the developmental window we were interested in there were no changes at all in the RNA level dynamics of genes we tested compared to wild type (N2 strain). Below is a figure for our favorite genes: end-1, end-3, and elt-2.
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| y-axis: Number of RNA counted by RNA-FISH. x-axis: number of nuclei (cells) in the embryo. |
Similarly, in our hands, the expression dynamics of elt-7, hlh-1, and elt-1, were nearly identical to N2.
Discussion: Seeing no effect was disappointing, but it doesn't necessarily contradict the Yuzyuk report, since most of its statements on expression level effects deal with 8E or later stages in development. That is right about where our window of interest ended.
Perspective: I did these experiments on the common rationale that Perhaps there would be something interesting. That is a good reason to do an experiment. In fact, that is how all experiments get started.
However, it was a bad reason to withhold developing the manuscript for the actual paper, because this experiment, no matter what the outcome would have been, does not have all that much to do with the question of how cell divisions and expression timing are coordinated. So that should have continued as a parallel rather than an in-series effort. What is very telling is that this result is not in the paper because it was a negative result, but we would have probably found a way to put it in if it was positive. Very few experiments of that sort are related in an honest way to the paper that they are being bundled with. Its just fluff.
But we waited because of that feeling that bundling cool stuff together makes for a more compelling and publishable paper. And because, currently, there is no home for "thin" results, like this little blurb on mes-2.
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