Team:KULeuven/Model/Inverter

From 2008.igem.org

(Difference between revisions)
m (Matlab (SBML file))
(Simulations)
Line 179: Line 179:
=== Simulations ===
=== Simulations ===
 +
 +
{| class="wikitable"
 +
|-
 +
! Time span
 +
! Input (TetR)
 +
! Results
 +
|-
 +
| A
 +
| 0.0125
 +
| The amount LacI increases from state zero to state one because both mRNA_RIBOKEY and pT7_tag are present. This results in a repression of LuxI which decreases to zero.
 +
|-
 +
| B
 +
| 5E-5
 +
|
 +
|-
 +
| C
 +
| 5E-5
 +
|
 +
|-
 +
| D
 +
| 5E-5
 +
|
 +
|-
 +
| E
 +
| 0.0125
 +
|
 +
|-
 +
| F
 +
| 5E-5
 +
|
 +
|-
 +
| G
 +
| 5E-5
 +
|
 +
|-
 +
| H
 +
| 5E-5
 +
|
 +
|}
 +
 +
 +
Remark: simulation is not from latest version.
Remark: simulation is not from latest version.

Revision as of 13:12, 8 September 2008

  dock/undock dropdown  

Pictogram inverter.png

Contents

Invertimer

Position in the system

The invertimer subsystem receives its input from the filter, T7. The invertimer's function is to produce HSL when no input is present, so a low T7 input gives rise to a high HSL output and vice versa. The production of HSL means that the cell will start a timer that eventually will be used in the celldeath-subsystem to produce ccdB. In this way the cell will die off if no desease remains present.

Describing the system

see also: Project:Invertimer

Inverter BioBrick.jpg

ODE's

Parameters

Parameter values (Inverter)
Name Value Comments Reference
Degradation Rates
dLuxI dLVA = 2.814E-4 s-1 LVA-tag reduces lifetime to 40 minutes [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
dRNA_LuxI 0.0025 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dLuxI_antimRNA 0.0045303737 s-1 estimate: because this RNA isn't translated, it degrades faster
dLacI dLVA = 2.814E-4 s-1 LVA-tag reduces lifetime to 40 minutes [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=106306 link]
dclosed mRNA LacI 0.0046209812 s-1 estimate: because this mRNA isn't translated, it degrades faster
dopen mRNA LacI 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen mRNA LacI complex 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dHSL 1.02E-6 s-1 very stable in the medium, lifetime around 185h [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
LuxI catalysis
kcat 0.0166666667 s-1 Estimated to be about 90% of Vmax in LB medium. [http://www.pnas.org/content/93/18/9505 link]
T7 Transcription
KT7 421 dissociation constant, recalculated to remove units [http://www.jbc.org/cgi/content/full/279/5/3239 link]
kmax 0.044 s-1 maximal T7 transcription rate [http://www.jbc.org/cgi/content/full/279/5/3239 link]
Key-Lock constants
Keq 1 0,015 [M] between closed and open T7 mRNA, experimental [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
Keq 2 0.0212 [M] between closed T7 mRNA and key unlocked mRNA complex, experimental [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
kdis2 0.00416 s-1 derived from experimental values [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
kcomplex2 0.00237 s-1 derived from experimental values [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
kclosed 500 s-1 derived from experimental values [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
kopen 7.5 s-1 derived from experimental values [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link]
LacI repression
KLacI 1.0E-10 M-1 Dissociation constant
nLacI 2.0 Hill coefficient for LacI [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
k_trans_LacI 0.0025 s-1 Estimated maximal transcription rate from R0011 [http://partsregistry.org/Part:BBa_R0011 link]
Antisense LuxI
k_complex3 0.00237 s-1 rate constant for formation of asRNA - LuxI mRNA duplex
KmRNA_LuxI:antisense_mRNA 4.22E14 Complex of LuxI mRNA with antisense mRNA
Translation Rates
ktransl LuxI 0.167 s-1 translation rate for B0032 RBS (0.3 relative efficiency) [http://partsregistry.org/Part:BBa_B0032 link]
ktransl LacI 0.167 s-1 lock defined translation rate for LacI

Models

CellDesigner (SBML file)

Inverter

Matlab (SBML file)

Inverter

Simulations

Time span Input (TetR) Results
A 0.0125 The amount LacI increases from state zero to state one because both mRNA_RIBOKEY and pT7_tag are present. This results in a repression of LuxI which decreases to zero.
B 5E-5
C 5E-5
D 5E-5
E 0.0125
F 5E-5
G 5E-5
H 5E-5


Remark: simulation is not from latest version.

filter

Sensitivity Analysis

Sens Inverter.png