Team:Paris/Analysis/Design1
From 2008.igem.org
Network Design - Part 1
Generating a FIFO sequential order of expressionA clock that would only indicate one hour, would not be very useful. The same goes for our BacteriO'clock. It is necessary that we add several distinct events in each cycle. We want to use three genes activated successively. The easiest way to control a sequential expression of genes : the LIFO order
This order poses a real problem to us : several states of the system are redundant (Table 1). We can not accept a clock that would display twice the same hour !
The rules to generate a FIFO temporal orderIn the contrary, in a FIFO order, there is no confusion possible between different states : they are all distincts. To generate this complex behavior, there are two major possibilities. The simplest way to generate a FIFO : a simple cascade of genes
This network is really simple to implement but presents several problems that makes it incompatible with our project. First of all, the cascade is not resistant to mutations : when one gene is mutated, the cascade is definitely broken. Secondly, the time scale if far too long. Each activation step would take approximately one hour. One full cycle would last almost six hours. Last but not least, the cascade is probably not very resistant to intracellular noise, it is not robust enough. The more sophisticated way to generate a FIFO behavior : a particular Multiple Output Feed-Forward LoopImplementation of our FIFOIn the FIFO you could start by saying we were looking for a FIFO and rather than designing it from scratch we decided to look in nature where we found and adopted the flagella which then inspired us further |