Team:Paris/Analysis/Design1
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Theoretically, there exist a range of parameters that permit oscillations. According to our bibliographic studies and models based on those studies (link), our system should not oscillate (Graph 1.). | Theoretically, there exist a range of parameters that permit oscillations. According to our bibliographic studies and models based on those studies (link), our system should not oscillate (Graph 1.). | ||
A simple study on the parameters lead us to the conclusion that an augmentation of the length of the period should lead to better oscillations. | A simple study on the parameters lead us to the conclusion that an augmentation of the length of the period should lead to better oscillations. | ||
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One of the consequence of the last module of our system, the synchronization, is an increasing of the period. According to the simulations, this increasing is sufficient to observe oscillations. | One of the consequence of the last module of our system, the synchronization, is an increasing of the period. According to the simulations, this increasing is sufficient to observe oscillations. |
Revision as of 19:14, 26 October 2008
Network Design - Part 1
Creating an oscillatory systemAlready existing genetic oscillators and their limitsDesigning a simple genetic network that presents an oscillatory behavior is one of the first challenge synthetic biology overcame. More or less successfully. We can count more than ten synthetic genetic oscillators that have varied period and mechanisms. [http://www.ncbi.nlm.nih.gov/pubmed/16604190?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Raúl GUANTES and Juan F. POYATOS (2006)] studied the most simple oscillators composed of two elements while [http://www.ncbi.nlm.nih.gov/pubmed/10659856?ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Michael B. ELOWITZ and Stanislas LEIBLER (2000)] designed the more complex "repressilator" (Table 1), to quote only the best known. Both oscillators work : we can observe oscillations but only a limited number of cycles. Actually, they always reach a steady-state because the degradation/dilution rate is often too low : at the end of each cycle, the conditions are not exactly the initial conditions. Experimentally, the longer is the period the more cycles we can observe. Design of our genetic oscillator : The Feed Forward LoopWe want to design a simple oscillator that oscillates during as many cycles as possible. We propose a system based on an oscillator composed of two elements (Network 1) on which we added a delay at the end of each cycle. Uri ALON described genetic network motifs that generate a delay. Those motifs are the type 1 coherent Feed Forward Loop (C1-FFL). ↓ More on Feed Forward Loop ↑
We will use one of those network to increase the run of each period and permit more oscillations (Network 2). Implementation of the core system[http://www.ncbi.nlm.nih.gov/pubmed/16729041?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Shiraz Kalir et al. (2004)] studied the complex network of gene that lead to the synthesis of E. coli flagella. A C1-FFL is present in this network.
Limits of our networkTheoretically, there exist a range of parameters that permit oscillations. According to our bibliographic studies and models based on those studies (link), our system should not oscillate (Graph 1.). A simple study on the parameters lead us to the conclusion that an augmentation of the length of the period should lead to better oscillations. One of the consequence of the last module of our system, the synchronization, is an increasing of the period. According to the simulations, this increasing is sufficient to observe oscillations. |