Team:Grenoble/Modeling/Amplification/Sensitivity
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Once the production of Arac has been activated, we have: | Once the production of Arac has been activated, we have: | ||
</br> | </br> | ||
- | <center><img src="https://static.igem.org/mediawiki/2012/f/f6/Eq_sens_1.png" alt="" /></center> | + | <table> |
- | <center><img src="https://static.igem.org/mediawiki/2012/1/11/Eq_sens_2.png" alt="" /></center> | + | <tr> |
+ | <th>Parameter Name</th> | ||
+ | <th>Value</th> | ||
+ | <th>Unit</th> | ||
+ | <th>Source</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>AraC synthesis rate <i>v<span class="indice">mAraC</span></i></td> | ||
+ | <td>12*10<span class="exposant">-8</span></td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span>.min<span class="exposant">-1</span></i></td> | ||
+ | <td>Yes [1] and explanation 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ca synthesis rate <i>v<span class="indice">mAraC</span></i></td> | ||
+ | <td>2*10<span class="exposant">-9</span></td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span>.min<span class="exposant">-1</span></i></td> | ||
+ | <td>No, explanation 2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>AraC threshold <i>K<span class="indice">AraC</span></i></td> | ||
+ | <td>0.3*10<span class="exposant">-6</span></td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span></i></td> | ||
+ | <td>No, explanation 3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ca threshold <i>K<span class="indice">Ca</span></i> (for (CRP-cAMP) activation)</td> | ||
+ | <td>0.6*10<span class="exposant">-6</td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span></i></td> | ||
+ | <td>No, explanation 3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ca threshold <i>K'<span class="indice">Ca</span></i> (for AraC* activation)</td> | ||
+ | <td></td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span></i></td> | ||
+ | <td>No, explanation 3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span></i></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | <td></td> | ||
+ | <td><i>mol.L<span class="exposant">-1</span></i></td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <!--<center><img src="https://static.igem.org/mediawiki/2012/f/f6/Eq_sens_1.png" alt="" /></center> | ||
+ | <center><img src="https://static.igem.org/mediawiki/2012/1/11/Eq_sens_2.png" alt="" /></center>--> | ||
</br> | </br> | ||
In addition, we assume that p_Arac ≪v_mArac thus, we get: | In addition, we assume that p_Arac ≪v_mArac thus, we get: |
Revision as of 23:32, 24 September 2012
Classic Odes Parameters
Explanation 1
- Arac and Ca:
Parameter Name | Value | Unit | Source |
---|---|---|---|
AraC synthesis rate vmAraC | 12*10-8 | mol.L-1.min-1 | Yes [1] and explanation 1 |
Ca synthesis rate vmAraC | 2*10-9 | mol.L-1.min-1 | No, explanation 2 |
AraC threshold KAraC | 0.3*10-6 | mol.L-1 | No, explanation 3 |
Ca threshold KCa (for (CRP-cAMP) activation) | 0.6*10-6 | mol.L-1 | No, explanation 3 |
Ca threshold K'Ca (for AraC* activation) | mol.L-1 | No, explanation 3 | |
mol.L-1 | |||
mol.L-1 |
- CRP:
Explanation 2
We don’t know the value of the synthesis rate of adenylate cyclase, but we assume that there is less adenylate cyclase, because if there is a huge amont of adenylate cyclase, there will too much cAMP, and then cAMP will repress the adenylate cyclase production (see reference [6]). For the basal production, we make the same assumption as for Arac.Explanation 3
- Activations by (CRP-cAMP):
- Activation by Arac*:
Explanation 4
Inspired from Arac. By discussing with the biologists we concluded that Ca is also a stable protein.Explanation 5
By discussing with the biologists, we assumed that there is around 10 times more cAMP out of the cell than inside the cell.Explanation 6
In the reference [6], we have kcat=100 min-1 in vitro. However, by discussing with the biologists, we assumed that in vivo this value was higher.Quorum sensing parameters
Explanation 1
We assumed that they wouldn’t be glued together, but not too far at the same time.Explanation 2
We work above the threshold, because we want to know the speed of the diffusion when we have a detection.References
- [1] Bionumbers. http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=arac&org=
- [2] Purification of and properties of the cyclic adenosine 2' ,5'-monophosphate receptor which mediates cyclic adenosine 3',5'-monophosphate dependent gene transcription in E. Coli. W.B. Aderson, A. B. Schneider, M. Emmer, R.L. Perlman, and I. Pasta
- [3] AraC protein, regulation of the L-arabinose operon inEscherichiacoli, and the light switch mechanism of AraC action. Robert Schleif Biology Department, Johns Hopkins University, Baltimore, MD, USA.
- [4] Epstein et Hesse 1975.
- [5] Transcriptional regulation shapes the organization of genes on bacterial chromosomes.Sarath Chandra Janga, Heladia Salgado, Augustino Martinez. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699516/
- [6] Regulation of adenylate cyclase in E. coli. Edith Gstrein-Reider and Manfred Schweiger, Institut fur Biochemie (nat. Fak.), UniversitAt Innsbruck, A-6020 Innsbruck, Austria.
- [7] Purification and characterization of adenylate cyclase from E. coli K12. Yang and Epstein 1983.
- [8] Solubility and diffusion coefficient of adenosine 3’ :5’ – monophosphate. Martin Dworkin and Kenneth H. Keller, 1976.