Team:TUDelft/Modeling Parameters

From 2009.igem.org

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Line 15: Line 15:
|5e-10
|5e-10
|maximum transcription rate (M/min)
|maximum transcription rate (M/min)
-
| [1]
+
| [[Team:TUDelft/Modeling_References|[1]]]
|-
|-
| c<sub>pTet</sub>
| c<sub>pTet</sub>
|1.5e-7
|1.5e-7
|maximum transcription rate (M/min)
|maximum transcription rate (M/min)
-
| [2]
+
| [[Team:TUDelft/Modeling_References|[2]]]
|-
|-
| c<sub>p&lambda;</sub>
| c<sub>p&lambda;</sub>
Line 30: Line 30:
|1.3e-6
|1.3e-6
|dissociation constant (M)
|dissociation constant (M)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| K<sub>50</sub><sup>LacI</sup>
| K<sub>50</sub><sup>LacI</sup>
|800e-9
|800e-9
|dissociation constant (M)
|dissociation constant (M)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| K<sub>50</sub><sup>TetR</sup>
| K<sub>50</sub><sup>TetR</sup>
|179e-12
|179e-12
|dissociation constant (M)
|dissociation constant (M)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| K<sub>50</sub><sup>CI</sup>
| K<sub>50</sub><sup>CI</sup>
|8e-12
|8e-12
|dissociation constant (M)
|dissociation constant (M)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| n<sub>IPTG</sub>
| n<sub>IPTG</sub>
|2
|2
| Hills coefficient
| Hills coefficient
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| n<sub>LacI</sub>
| n<sub>LacI</sub>
|2
|2
| Hills coefficient
| Hills coefficient
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| n<sub>TetR</sub>
| n<sub>TetR</sub>
|3
|3
| Hills coefficient
| Hills coefficient
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| n<sub>CI</sub>
| n<sub>CI</sub>
|2
|2
| Hills coefficient
| Hills coefficient
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| d<sub>LacI</sub>
| d<sub>LacI</sub>
| 0.1386
| 0.1386
| degradation rate (M/min)
| degradation rate (M/min)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| d<sub>TetR</sub>
| d<sub>TetR</sub>
| 0.1386
| 0.1386
| degradation rate (M/min)
| degradation rate (M/min)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| d<sub>CI</sub>
| d<sub>CI</sub>
| 0.042
| 0.042
| degradation rate (M/min)
| degradation rate (M/min)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| d<sub>RFP</sub>
| d<sub>RFP</sub>
| 6.3e-3
| 6.3e-3
| degradation rate (M/min)
| degradation rate (M/min)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| d<sub>GFP</sub>
| d<sub>GFP</sub>
| 6.3e-3
| 6.3e-3
| degradation rate (M/min)
| degradation rate (M/min)
-
| [3]
+
| [[Team:TUDelft/Modeling_References|[3]]]
|-
|-
| d<sub>mRNA</sub>
| d<sub>mRNA</sub>
| 0.029
| 0.029
| degradation rate (M/min)
| degradation rate (M/min)
-
| [4]
+
| [[Team:TUDelft/Modeling_References|[4]]]
|-
|-
| &alpha;
| &alpha;
| 16 - 57
| 16 - 57
| translation rate (translations/min/mRNA), depends on growth rate (a default value of 30 is used)
| translation rate (translations/min/mRNA), depends on growth rate (a default value of 30 is used)
-
| [5]
+
| [[Team:TUDelft/Modeling_References|[5]]]
|-
|-
| k<sub>IPTG</sub>
| k<sub>IPTG</sub>
| 0.92
| 0.92
| rate constant for IPTG diffusion into cell
| rate constant for IPTG diffusion into cell
-
| [6]
+
| [[Team:TUDelft/Modeling_References|[6]]]
|-
|-
|}
|}
Line 119: Line 119:
|-
|-
| A
| A
-
| 1735 mm<sup>2</sup>
+
| 1735
-
| Surface area available
+
| Surface area available (mm<sup>2</sup>)
| Area of 0.2&mu;m filter used in conjugation tests.
| Area of 0.2&mu;m filter used in conjugation tests.
|-
|-
| r<sub>0</sub>
| r<sub>0</sub>
-
| 0.8&mu;m
+
| 0.8
-
| initial colony radius
+
| initial colony radius (&mu;m)
-
| [7]
+
| [[Team:TUDelft/Modeling_References|[7]]]
|-
|-
| g<sub>n</sub>
| g<sub>n</sub>
| 0.99
| 0.99
-
| specific growth rate
+
| specific growth rate (1/hr)
| Determined experimentally for R751 containing cells.
| Determined experimentally for R751 containing cells.
|-
|-
| g<sub>r</sub>
| g<sub>r</sub>
-
| 30&mu;m/hr
+
| 30
-
| colony radial specific growth rate
+
| colony radial specific growth rate (&mu;m/hr)
-
| [8]
+
| [[Team:TUDelft/Modeling_References|[8]]]
|-
|-
| N<sub>d</sub>
| N<sub>d</sub>
Line 147: Line 147:
| initial number of donors
| initial number of donors
| Estimate
| Estimate
 +
|-
 +
| &lambda;
 +
| 5.76
 +
| intensity (CFU/mm<sup>2</sup>)
 +
| Calculated using N<sub>r</sub>/A.
|-
|-
|}
|}
<br>
<br>
-
=References=
 
-
 
-
1. M. Santillan, M.C. Mackey, E.S. Zeron, Origin of Bistability in the lac Operon, Biophysical Journal, Volume 92, Issue 11, 1 June 2007, Pages 3830-3842, ISSN 0006-3495, DOI: 10.1529/biophysj.106.101717. (http://www.sciencedirect.com/science/article/B94RW-4V9YVV6-8/2/cd4c5ba8d532a314eed932d787f56a35)
 
-
 
-
2. Thuc T. Le, Calin C. Guet, Philippe Cluzel, Protein expression enhancement in efflux-deleted mutant bacteria, Protein Expression and Purification, Volume 48, Issue 1, July 2006, Pages 28-31, ISSN 1046-5928, DOI: 10.1016/j.pep.2005.11.018.
 
-
(http://www.sciencedirect.com/science/article/B6WPJ-4HV73GJ-1/2/36f5ff80fe56e2533f1ec0699bf12a7e)
 
-
 
-
3. http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters
 
-
 
-
4. Barrio M, Burrage K, Leier A, Tian T. Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation. PLoS Comput Biol. 2006 Sep 8; 2(9): e117.
 
-
 
-
5. Liang, S.-T., Xu, Y.-C., Dennis, P., Bremer, H. mRNA Composition and Control of Bacterial Gene Expression. J. Bacteriol. 2000 182: 3037-3044.
 
-
 
-
6. Michail Stamatakis, Nikos V. Mantzaris, Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network, Biophysical Journal, Volume 96, Issue 3, 4 February 2009, Pages 887-906, ISSN 0006-3495, DOI: 10.1016/j.bpj.2008.10.028. (http://www.sciencedirect.com/science/article/B94RW-4VGGB7R-D/2/bd642ea418c1213f10259b778907a1ee)
 
-
 
-
7. E. coli Statistics http://gchelpdesk.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi
 
-
 
-
8. Julian W. T. Wimpenny. <i>CRC handbook of laboratory model systems for microbial ecosystems, Volume 2</i>. page 127. http://books.google.com/books?id=wy4WFX3_7bMC
 
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Latest revision as of 12:57, 18 October 2009

Modeling Parameters

Transcriptional Cascade


Parameter Values Description Ref
cpLac 5e-10 maximum transcription rate (M/min) [1]
cpTet 1.5e-7 maximum transcription rate (M/min) [2]
cpλ 1.5e-7 maximum transcription rate (M/min) estimate
K50IPTG 1.3e-6 dissociation constant (M) [3]
K50LacI 800e-9 dissociation constant (M) [3]
K50TetR 179e-12 dissociation constant (M) [3]
K50CI 8e-12 dissociation constant (M) [3]
nIPTG 2 Hills coefficient [3]
nLacI 2 Hills coefficient [3]
nTetR 3 Hills coefficient [3]
nCI 2 Hills coefficient [3]
dLacI 0.1386 degradation rate (M/min) [3]
dTetR 0.1386 degradation rate (M/min) [3]
dCI 0.042 degradation rate (M/min) [3]
dRFP 6.3e-3 degradation rate (M/min) [3]
dGFP 6.3e-3 degradation rate (M/min) [3]
dmRNA 0.029 degradation rate (M/min) [4]
α 16 - 57 translation rate (translations/min/mRNA), depends on growth rate (a default value of 30 is used) [5]
kIPTG 0.92 rate constant for IPTG diffusion into cell [6]


Conjugation


Parameter Values Description Ref
A 1735 Surface area available (mm2) Area of 0.2μm filter used in conjugation tests.
r0 0.8 initial colony radius (μm) [7]
gn 0.99 specific growth rate (1/hr) Determined experimentally for R751 containing cells.
gr 30 colony radial specific growth rate (μm/hr) [8]
Nd 10000 initial number of donors Estimate
Nr 10000 initial number of donors Estimate
λ 5.76 intensity (CFU/mm2) Calculated using Nr/A.



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