@biodataganache what a pretty figure behind your profile up there. What paper is that from?
— Kristen DeAngelis (@kristenobacter) March 12, 2013
Because of the fact that the paper is behind a paywall, I’m making it available as the submitted manuscript. Eventually I’ll get with the program and start releasing on ArXiv or Figshare, but for now it’s here. I’ve tried to make the version somewhat pretty (I get really tired of reading papers that are double-spaced and have the figures and tables at the end).
McDermott J.E., Oehmen C., McCue L.A., Hill H., Choi D.M., Stöckel J., Liberton M., Pakrasi H.B., Sherman L.A. (2011) A model of cyclic transcriptomic behavior in Cyanothece species ATCC 51142. Mol Biosystems 7(8):2407-2418. PMID: 21698331
*but behind a paywall at Molecular BioSystems
Cyanothece sp. 51142 is a ocean-dwelling cyanobacteria that is capable of fixing nitrogen in the dark and photosynthesizing in the light, two normally incompatible activities. Unlike some other cyanobacteria it makes this switch inside the same cell every light/dark cycle (normally about 12 hours). This makes it interesting from the standpoint of bioenergy
production but also regulation. The process of how it is able to drastically rearrange it’s machinery every 12 hours is not well understood.
What was done?
We used multiple transcriptomic datasets (measurements of levels of gene expression) taken at different times in the light/dark cycle to construct a general model of the functional processes occurring in Cyanothece. The interesting part about this was that we did not impose the circular shape on the model, it arose naturally from analysis of the data, and it really does represent a clock- with the pattern of gene expression at different times of day being located at different locations on the clock face. We then used a mathematical approach to relate the expression levels of drivers (regulators) with groups of genes that can be associated with different functions. The model allows us to plug in different starting points and predict what the state of the system will be at future times.
Why is it important?
The model we constructed can be changed and results simulated to predict what will happen in a real experiment. These kinds of models are good for focusing experimental efforts by predicting interesting behavior. An example question might be to ask what would happen to the timing of photosynthesis (as judged by gene transcription) if the levels of a key regulator are changed. The resulting prediction(s) can then be tested experimentally to discover new things about the system.
This paper took about five years to get written and accepted. That’s from the point at which I decided that a paper should be written to the point that it was published. It was from the first project I worked on at my then new position. I came up with the wreath visualization early in the process and, after having convinced myself and others that it was real, found that it was a very compelling way to think about the diurnal (day/night) cycle. The figure has been used in many different forms, mainly as eye candy. I’m amused when I see it on a poster that I had nothing to do with (from my workplace PNNL). It has even been used around the web.