I am excited to announce the paper “Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing” to be published in FEMS Microbiology Ecology.http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12019/abstract
This is the third paper in my “in silico series”. The other two papers in the series are:
Carrying photosynthesis genes increases ecological fitness of cyanophage in silicohttp://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01866.x/full
Resonating circadian clocks enhance fitness in cyanobacteria in silicohttp://www.sciencedirect.com/science/article/pii/S0304380010001602
Take a quick look at the model schematic in each paper (below). I think they nicely capture the spirit of the series. Specifically, all show cells with intracellular mechanisms (resolved down to the level of individual genes) [systems biology] and populations made up of individual cells [systems ecology]. This approach [systems bioecology] explicitly investigates the role of genes in the fitness of microbes.
E. coli model:
For this paper, you may also like ...
… the source code:https://www.dropbox.com/sh/mgj7glkfgohljxg/9f73m3eldl
… the movie:http://youtu.be/Dt0-YEMtTiA
… the poster:https://www.dropbox.com/sh/81tv7ozuyu6a05x/7Vfkk1l2nS/2012/ISME_Tetracycline_Resistance.pdf
The fourth paper planned for the series is the yeast bet hedging one I am presently developing.
Do you have any interesting problems that can be investigated with this approach? I am always interested in talking and collaborating. Drop me a line!