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Team:NTU-Taida/Modeling/Parameters
From 2012.igem.org
(→Single-Cell/ System analysis Model) |
(→Single-Cell/ System analysis Model) |
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<td> \(\alpha_{TetR} \) </td> | <td> \(\alpha_{TetR} \) </td> | ||
<td> TetR max. production rate </td> | <td> TetR max. production rate </td> | ||
| - | <td> \(0.8~\mu \text{M} | + | <td> \(0.8~\mu \text{M}\cdot\text{min}^{-1} \) </td> |
<td> [5] </td> | <td> [5] </td> | ||
</tr> | </tr> | ||
| Line 24: | Line 24: | ||
<td> \(\alpha_{FadR} \) </td> | <td> \(\alpha_{FadR} \) </td> | ||
<td> FadR max. production rate </td> | <td> FadR max. production rate </td> | ||
| - | <td> \(100~\mu\text{M} | + | <td> \(100~\mu\text{M}\cdot\text{min}^{-1} \)</td> |
<td> a. </td> | <td> a. </td> | ||
</tr> | </tr> | ||
| Line 30: | Line 30: | ||
<td> \(\alpha_{GLP-1} \) </td> | <td> \(\alpha_{GLP-1} \) </td> | ||
<td> GLP-1 max. production rate </td> | <td> GLP-1 max. production rate </td> | ||
| - | <td> \(1.23~\mu\text{M} | + | <td> \(1.23~\mu\text{M}\cdot\text{min}^{-1} \)</td> |
<td> a. </td> | <td> a. </td> | ||
</tr> | </tr> | ||
| Line 36: | Line 36: | ||
<td> \(\alpha_{LacI} \) </td> | <td> \(\alpha_{LacI} \) </td> | ||
<td> LacI max. production rate </td> | <td> LacI max. production rate </td> | ||
| - | <td> \(0.8~\mu\text{M} | + | <td> \(0.8~\mu\text{M}\cdot\text{min}^{-1} \)</td> |
<td> [1] </td> | <td> [1] </td> | ||
</tr> | </tr> | ||
| Line 132: | Line 132: | ||
<td> \(n_1\) </td> | <td> \(n_1\) </td> | ||
<td> FadR cooperativity coefficient </td> | <td> FadR cooperativity coefficient </td> | ||
| - | <td> 3 </td> | + | <td> \(3\) </td> |
<td> a. </td> | <td> a. </td> | ||
</tr> | </tr> | ||
| Line 138: | Line 138: | ||
<td> \(n_2\) </td> | <td> \(n_2\) </td> | ||
<td> FA cooperativity coefficient </td> | <td> FA cooperativity coefficient </td> | ||
| - | <td> 2 </td> | + | <td> \(2\) </td> |
<td> a. </td> | <td> a. </td> | ||
</tr> | </tr> | ||
| Line 144: | Line 144: | ||
<td> \(n_3\) </td> | <td> \(n_3\) </td> | ||
<td> LuxR-AHL cooperativity coefficient </td> | <td> LuxR-AHL cooperativity coefficient </td> | ||
| - | <td> 3 </td> | + | <td> \(3\) </td> |
<td> [1] </td> | <td> [1] </td> | ||
</tr> | </tr> | ||
| Line 150: | Line 150: | ||
<td> \(n_5\) </td> | <td> \(n_5\) </td> | ||
<td> TetR cooperativity coefficient </td> | <td> TetR cooperativity coefficient </td> | ||
| - | <td> 2 </td> | + | <td> \(2\) </td> |
<td> [2] </td> | <td> [2] </td> | ||
</tr> | </tr> | ||
| Line 156: | Line 156: | ||
<td> \(n_6\) </td> | <td> \(n_6\) </td> | ||
<td> LacI cooperativity coefficient </td> | <td> LacI cooperativity coefficient </td> | ||
| - | <td> 4 </td> | + | <td> \(4\) </td> |
<td> [1] </td> | <td> [1] </td> | ||
</tr> | </tr> | ||
| Line 162: | Line 162: | ||
<td> \(\eta\) </td> | <td> \(\eta\) </td> | ||
<td> AHL Diffusion rate across the cell membrane </td> | <td> AHL Diffusion rate across the cell membrane </td> | ||
| - | <td> 2 </td> | + | <td> \(2\) </td> |
<td> [2] </td> | <td> [2] </td> | ||
</tr> | </tr> | ||
| Line 168: | Line 168: | ||
<td> \(\eta\)<sub>ext</sub> </td> | <td> \(\eta\)<sub>ext</sub> </td> | ||
<td> Average diffusion rate for all cells </td> | <td> Average diffusion rate for all cells </td> | ||
| - | <td> 1 </td> | + | <td> \(1\) </td> |
<td> [2]<b></b> </td> | <td> [2]<b></b> </td> | ||
</tr> | </tr> | ||
Revision as of 18:44, 25 October 2012
Cell Population Response Model
Parameters
Contents |
Single-Cell/ System analysis Model
| Parameter | Description | Value | Reference |
| \(\alpha_{TetR} \) | TetR max. production rate | \(0.8~\mu \text{M}\cdot\text{min}^{-1} \) | [5] |
| \(\alpha_{FadR} \) | FadR max. production rate | \(100~\mu\text{M}\cdot\text{min}^{-1} \) | a. |
| \(\alpha_{GLP-1} \) | GLP-1 max. production rate | \(1.23~\mu\text{M}\cdot\text{min}^{-1} \) | a. |
| \(\alpha_{LacI} \) | LacI max. production rate | \(0.8~\mu\text{M}\cdot\text{min}^{-1} \) | [1] |
| \(k_{s1} \) | AHL i production rate | \(0.01~\text{min}^{-1} \) | [2] |
| \(\rho_R \) | LuxR-AHL dimerization rate | \(0.5~\mu\text{M}^{-3}\cdot min^{-1} \) | [1] |
| \(\beta_{TetR} \) | TetR repression coefficient | \(0.13~\mu\text{M} \) | a. |
| \(\beta_{FA} \) | FA repression coefficient | \(10~\mu\text{M} \) | [1] |
| \(\beta_{FadR} \) | FadR repression coefficient | \(0.13~\mu\text{M} \) | [1] |
| \(\beta_{LacI} \) | LacI repression coefficient | \(0.8~\mu\text{M} \) | [1] |
| \(\beta_R \) | LuxR-AHL repression coefficient | \(0.01~\mu\text{M} \) | [1] |
| \(\gamma_{TetR} \) | TetR degradation rate | \(0.0692~\text{min}^{-1} \) | a. |
| \(\gamma_{LacI} \) | LacI degradation rate | \(0.0231~\text{min}^{-1} \) | [1] |
| \(\gamma_{GLP-1} \) | GLP-1 degradation rate | \(0.0731~\text{min}^{-1} \) | [1] |
| \(\gamma_{LuxI} \) | LuxI degradation rate | \(0.0167~\text{min}^{-1} \) | [3] |
| \(k_{s0} \) | AHLi degradation rate | \(1~\text{min}^{-1} \) | [2] |
| \(k_{se} \) | AHLe degradation rate | \(1~\text{min}^{-1} \) | [2] |
| \(\gamma_R \) | LuxR-AHL degradation rate | \(0.0231~\text{min}^{-1} \) | [1] |
| \(\gamma_{RFP} \) | RFP degradation rate | \(0.0041~\text{min}^{-1} \) | [4] |
| \(n_1\) | FadR cooperativity coefficient | \(3\) | a. |
| \(n_2\) | FA cooperativity coefficient | \(2\) | a. |
| \(n_3\) | LuxR-AHL cooperativity coefficient | \(3\) | [1] |
| \(n_5\) | TetR cooperativity coefficient | \(2\) | [2] |
| \(n_6\) | LacI cooperativity coefficient | \(4\) | [1] |
| \(\eta\) | AHL Diffusion rate across the cell membrane | \(2\) | [2] |
| \(\eta\)ext | Average diffusion rate for all cells | \(1\) | [2] |
Fatty Acid Reaction Absorption Model Model
|
Parameter |
Description |
Value |
Reference |
|
[E]t |
Total active enzyme |
50 uM |
[8] |
|
Km |
Reaction rate constant |
47.9 |
[6][7] |
|
DFA |
FA Diffusion Constant |
6.46*10-10m2/s |
|
|
d |
Thickness of the unstirred water layer |
190 um |
[9] |
|
Kcat/ molecular weight |
Catalytic Rate constant |
1.8*10^-3 |
[6][7] |
Cell-Cell Communication Model
|
Parameter |
Description |
Value |
Reference |
|
cd |
E.
coli Cell Density |
0.1 |
|
|
DFA |
FA Diffusion Constant |
6.46* 10^-10m^2 /s |
|
|
DAHL |
AHL Diffusion Constant |
4.9e-6 cm2/s |
[9] |
|
γAHL,ext |
AHL cell-external degradation |
8.0225e-006/s |
Derived from 1 day half-life at pH 7 [7] |
Reference
|
Source |
|
|
[1] |
Subhayu Basu, Yoram
Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A
synthetic multicellular system for programmed pattern formation, Nature
Vol. 434, 2005 |
|
[2] |
Garcia-Ojalvo, Michael B. Elowitz,
and Steven H. Strogatz. Modeling a synthetic multicellular clock:
Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004 |
|
[3] |
MIT igem 2010 |
|
[4] |
Michael Halter, Alex Tona,
Kiran Bhadriraju, Anne L. Plant, John T. Elliott, Automated Live Cell
Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,
Cytometry Part A, Volume 71A Issue 10, 2007 |
|
[5] |
Wilfried Weber, Markus
Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique
Aubel, Cornelia C Weber & Martin Fussenegger, Gas-inducible
transgene expression in mammalian cells and mice, Nature Biotechnology, volume
22, number 11, 2004 |
|
[6] |
Sulaiman Al-Zuhair,
Masitah Hasan, K.B. Ramachandran, Kinetics of the enzymatic hydrolysis of
palm oil by lipase, Process Biochemistry Volume 38, Issue 8, 2003 |
|
[7] |
Ho-Shing Wu, Ming-Ju Tsai,
Kinetics of tributyrin hydrolysis by
lipase, Enzyme and Microbial Technology, Volume 35, Issues 6–7, 2004 |
|
[8] |
Bengt Borgstrom, Luminal Digestion of Fats, Handbook
of Physiology, The Gastrointestinal System, Intestinal Absorption and
Secretion, 1991 |
|
[9] |
Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake
of short- and medium-chain fatty acids and alcohols, Journal of Lipid
Research, 1973 |
