Team:TUDelft/Modeling Parameters

From 2009.igem.org

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==Transcriptional Cascade==
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|'''Parameter'''
|'''Parameter'''
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| rate constant for IPTG diffusion into cell
| rate constant for IPTG diffusion into cell
| [6]
| [6]
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==Conjugation==
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<br>
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{| align="center" border="1"
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|'''Parameter'''
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|'''Values'''
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|'''Description'''
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|'''Ref'''
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|-
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| A
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| 1735 mm<sup>2</sup>
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| Surface area available
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| Area of 0.2&mu;m filter used in conjugation tests
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|-
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| r<sub>0</sub>
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| 0.8&mu;m
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| initial colony radius
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| [7]
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|-
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| g<sub>n</sub>
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| 0.99
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| specific growth rate
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| Determined experimentally for R751 containing cells.
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|-
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| g<sub>r</sub>
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| 30&mu;m/hr
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| colony radial specific growth rate
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| [8]
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|-
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| N<sub>d</sub>
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| 10000
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| initial number of donors
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| Estimate
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|-
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| N<sub>r</sub>
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| 10000
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| initial number of donors
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| Estimate
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Revision as of 17:08, 17 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 mm2 Surface area available Area of 0.2μm filter used in conjugation tests
r0 0.8μm initial colony radius [7]
gn 0.99 specific growth rate Determined experimentally for R751 containing cells.
gr 30μm/hr colony radial specific growth rate [8]
Nd 10000 initial number of donors Estimate
Nr 10000 initial number of donors Estimate

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)


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