Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"
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<tr> <td>\(F_\mathrm{C}\)</td> <td> Fold change between Lactate production by cancer and normal cells</td><td>2 </td> <td>4</td> <td>estimated </td> </tr> | <tr> <td>\(F_\mathrm{C}\)</td> <td> Fold change between Lactate production by cancer and normal cells</td><td>2 </td> <td>4</td> <td>estimated </td> </tr> | ||
<tr> <td>\(a_1\)</td> <td> \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)</td><td>0.05 </td> <td>1000</td> <td></td> </tr> | <tr> <td>\(a_1\)</td> <td> \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)</td><td>0.05 </td> <td>1000</td> <td></td> </tr> | ||
| − | <tr> <td>\( a_\mathrm{LacI}\)</td> <td> Maximal production rate of LacI</td><td>0.05 μM.min<SUP>-1</SUP> </td> <td> | + | <tr> <td>\( a_\mathrm{LacI}\)</td> <td> Maximal production rate of LacI</td><td>0.05 μM.min<SUP>-1</SUP> </td> <td>1 μM.min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr> |
| + | <tr> <td>\( d_\mathrm{LacI}\)</td> <td> Degradation rate of LacI</td><td>0.01 min<SUP>-1</SUP> </td> <td>0.1 min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr> | ||
| + | <tr> <td>\( K_\mathrm{R,LacI}\)</td> <td>Repression coefficient of LacI</td><td>0.1 μM </td> <td>10 μM </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr> | ||
</table> | </table> | ||
Revision as of 16:19, 20 August 2015
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Parameters
AHL module
Single cell model
| Name | Description | Value | References/Estimation |
|---|---|---|---|
| \(K_{d,\text{LuxRAHL}}\) | 100 nM | Dissociation constant between luxR and AHL | Weber, 2013 |
| \(\text{LuxR}_\text{tot}\) | 0.0025 μM | Total concentration of LuxR | estimated |
| \(a_\mathrm{LuxI}\) | 1 μM.min-1 | Maximal production rate of LuxI | Basu, 2005 |
| \(k_\mathrm{leaky}\) | 0.0005 μM-1 | Leakiness of PLuxR promoter | estimated |
| \(K_\mathrm{a,LuxRAHL}\) | 0.01 μM | Activation coefficient of LuxRAHL | estimated |
| \(d_\mathrm{LuxI}\) | 0.0167 min-1 | Degradation rate of LuxI | estimated |
| \(a_\mathrm{AHL}\) | 0.04 μM.min-1 | Production rate of AHL | Weber, 2013 |
| \(d_\mathrm{AHL}\) | 0.01 min-1 | Degradation rate of AHL | Basu, 2005 |
| \(v_\mathrm{AiiA}\) | \(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \) | Maximal conversion rate of AiiA | |
| \(k_\mathrm{cat}\) | 1.63 103min-1 | Turnover number of AiiA | Wang, 2004 |
| \(C_\mathrm{AiiA}\) | 0.05 μM | Concentration of AiiA | |
| \(K_\mathrm{M,AiiA}\) | 2.95 103 μM | of AiiA | Wang, 2004 |
| \(a_\mathrm{GFP}\) | 2 μM.min-1 | Maximal production rate of GFP | Basu, 2005 |
| \(d_\mathrm{GFP}\) | 0.01 min-1 | Degradation rate of GFP | estimated |
Lactate module
Single cell model
Assumptions
| Name | Description | Minimum Value | Maximum Value | References/Estimation |
|---|---|---|---|---|
| \(\text{B}\) | \(\frac{Lac_\mathrm{ini}^2}{K_\mathrm{d,DLL}}\) | 0.000001 | 4 | |
| \(\text{Lac}_{\text{ini}}\) | Initial concentration of lactate in the medium | 0.1 μM | 2 μM | Low concentration of lactate in the medium |
| \(K_\mathrm{d,DLL}\) | Dissociation constant between the dimer of Lldr and Lactate | 10 μM2 | 10000 μM2 | |
| \(\alpha\) | Multiplication factor between the initial concentration of Lactate and Production of normal cells | 1 | 150 | estimated |
| \(F_\mathrm{C}\) | Fold change between Lactate production by cancer and normal cells | 2 | 4 | estimated |
| \(a_1\) | \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\) | 0.05 | 1000 | |
| \( a_\mathrm{LacI}\) | Maximal production rate of LacI | 0.05 μM.min-1 | 1 μM.min-1 | Basu, 2005 |
| \( d_\mathrm{LacI}\) | Degradation rate of LacI | 0.01 min-1 | 0.1 min-1 | Basu, 2005 |
| \( K_\mathrm{R,LacI}\) | Repression coefficient of LacI | 0.1 μM | 10 μM | Basu, 2005 |