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| | {{Paris/Header|Network Design - Part 1}} | | {{Paris/Header|Network Design - Part 1}} |
| - | =Creating an oscillating system=
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| - | == Already existing genetic oscillators and their limits ==
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| - | Designing 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.
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| - | [[Image:Oscillators.jpg|thumb|600px|center|Tab 1. Two examples of genetic oscillators. A : a simple oscillator composed of two elements. B : the repressilator. (Legend : Green arrow : Activation. Red blunt arrow : Inhibition)]]
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| - | 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'''.
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| - | == Design of our genetic oscillator : The Feed Forward Loop ==
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| - | We 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.
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| - | [[Image:Reseauoscillsimple.png|thumb|center|Network 1. Simple oscillator composed of two elements]]
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| - | Uri ALON described genetic network motifs that generate a delay. Those motifs are the type 1 coherent Feed Forward Loop (C1-FFL).
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| - | {{Paris/Toggle|More on Feed Forward Loop|Paris/FFL}}
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| - | We will use one of those network to increase the run of each period and permit more oscillations (''Network 2'').
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| - | [[Image:Reseauoscill.png|center|thumb|250 px|Network 2. Our oscillator : a C1-FFL increase the length of each period]]
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| - | == Implementation of the core system ==
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| - | [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.
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| - | A C1-FFL is present in this network.
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| - | *X is flhDC, the master regulator of the synthesis of the flagella. It is associated to its natural promoter.
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| - | *Y is fliA, another transcription factor that regulates the expression of a large amount of flagellar genes. fliA is also associated with its natural promoter.
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| - | *For Z, we need a protein that inhibits the expression of flhDC. [http://www.ncbi.nlm.nih.gov/pubmed/18193944?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Antoine Giraud ''et al.''(2008)] evidenced that EnvZ phosphorylates OmpR which becomes active. OmpR-P strongly inhibits the expression of FlhDC. We chose EnvZ for Z. For Z promoter, we chose one of the promoter controlling the expression of one of the flagellar gene that are regulated by both FliA and FlhDC. We chose the promoter of FlhB because it is the gene that is lastly activated. As a consequence, it increases the length of each cycle. Of course, to make the oscillations observable, we decided to put EnvZ and GFP under the control of the same promoter.
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| - | [[Image:Reseauoscillfinal.png|center|thumb|250 px|Network 3. Final Design of the core system.]]
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| - | == Limits of our network ==
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| - | Intuitively, it seems that there is a range of parameters that permit oscillations. However, [[Team:Paris/Network_analysis_and_design/Core_system#Oscillations|an analysis]] of the core system highlighted the fact that it could hardly have an oscillating dynamics (''Graph 1'').
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| - | Among the [[Team:Paris/Network_analysis_and_design/Core_system#System_Improvements|alternatives]] we studied, the system that could most probably oscillate is the third module that uses the quorum sensing to produce both a delay and the synchronization at the population level.
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| - | [[Team:Paris/Project|Previous step : Description of the project]]
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| - | [[Team:Paris/Network_design2|Next step : Design of the FIFO]]
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