Thursday, November 15, 2012

New paper: 3rd in the “in silico series”

Hello People!

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 silico
http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01866.x/full

and

Resonating circadian clocks enhance fitness in cyanobacteria in silico
http://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.

Prochlorococcus model:



Synechococcus model: 


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!

Best regards,
Ferdi

2 comments:

  1. I really enjoyed the movie. This is a nice example of linking intracellular biological mechanisms to a process of interest for environmental pollution monitoring.

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    Replies
    1. Dear Ben:

      Thanks for your comment! I am glad to hear you see the connection with environmental/pollution. Bringing modern biology into environmental engineering models is an important goal of my research.

      Related to antibiotic resistance, here are two papers that are more applied:
      http://www.mdpi.com/1660-4601/8/2/480/pdf
      http://iris.lib.neu.edu/aes/vol5/iss1/8/
      And there is a third one currently under review...

      Sincerely,
      Ferdi

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