Revision as of 13:14, 25 October 2008 by David.bikard (Talk | contribs)



Our project aims at biologically devising a “oscillating FIFO behaviour, synchronized at population level”. Such a setup will trigger periodic events and,therefore, can be considered as a “biological clock”. To completely deserve this appellation, the system has to fulfill the following specifications :

  • Oscillatory system : It will consist in providing a periodic output for the duration of the experiment. To do so, we will use a genetic cascade, initiated by a specific inducer which last step will inhibit the previously mentioned inducer.
  • FIFO System : The period of the oscillation is even more interesting if fit allows the sequential switching on and off of several genes. Our setup involves three genes which will get activated and desactivated successively as a “FIFO : First In, First Out”. This sequence is monitored by a logic structure called Feed-Forward Loop (FFL).
  • Synchronization : Yet, being able to control this sequential activation within a single cell can be seen as a “first step” in biological clock devising. In order to amplify this phenomenon (to observe it in an easier way or even to find future applications), it has to be extended to a whole population of bacteria. Here comes the synchronization issue: we will use methods based on the “quorum sensing” phenomenon.

We will base our project on an already existing structure, partly fulfilling the evoked specifications: the system that leads to the production of E. coli flagella.



First In First Out (FIFO) systems are present everywhere in nature from flux management or electronics to genetic networks. It is interesting in any process that requires several steps in a defined order. FIFO behaviour indeed prevents from needlessly performing the first steps while the last ones are OFF.

If you want to make French fries you need to produce potatoes before you can cut them and you need to cut them before frying them. But it would be a waste to continue producing potatoes if you've already turned off the fryer :-) You would accumulate unprocessed intermediates!

The same goes for the bacterium flagella. To be efficient they naturally need to produce the proteins of the base first. But when you stop making flagella, the base proteins are also the first thing you need to stop producing. It has been proposed (Alon, ...) that the gene network controlling the production of E.coli flagellum behaves as a FIFO. We thus decided to use this regulatory network to implement our FIFO.

For a detailed description of E.Coli flagellum regulatory network, please go here


Oscillating FIFO

More details [PDF]

The 3 Modules