Team:NTU-Taida/Modeling/Parameters

From 2012.igem.org

(Difference between revisions)
(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> \(0.8~\mu \text{M}/\text{min} \) </td>
+
           <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> \(100~\mu\text{M}/\text{min} \)</td>
+
           <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> \(1.23~\mu\text{M}/\text{min} \)</td>
+
           <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> \(0.8~\mu\text{M}/\text{min} \)</td>
+
           <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