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BIOMD0000000438 - Saeidi2012 - Quorum sensing device that produces GFP

 

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Reference Publication
Publication ID: 10.1016/j.ces.2012.1...
Nazanin Saeidi, Mohamed Arshath, Matthew Wook Chang, and Chueh Loo Poh
Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation
Chemical Engineering Science 2012; 0009-2509
School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459  [more]
Model
Original Model: BIOMD0000000438.xml.origin
Submitter: Nazanin Saeidi
Submission ID: MODEL1301110000
Submission Date: 11 Jan 2013 06:13:20 UTC
Last Modification Date: 06 Jun 2013 11:55:21 UTC
Creation Date: 27 Feb 2013 13:22:55 UTC
Encoders:  Vijayalakshmi Chelliah
   Nazanin Saeidi
set #1
bqbiol:isVersionOf Gene Ontology quorum sensing
set #2
bqmodel:is Taxonomy cellular organisms
Notes
Saeidi2012 - Quorum sensing device that produces GFP

Saeidi et al. (2012) has modelled a quorum sensing device that produces green fluorescent protein (GFP) as reporter in the presence of Acyl Homoserine Lactone (AHL).

This model is described in the article:

Nazanin Saeidi, Mohamed Arshath, Matthew Wook Chang, Chueh Loo Poh
Chemical Engineering Science. December 2012.

Abstract:

Modeling of biological parts is of crucial importance as it enables the in silico study of synthetic biological systems prior to the actual construction of genetic circuits, which can be time consuming and costly. Because standard biological parts are utilized to build the synthetic systems, it is important that each of these standard parts is well characterized and has a corresponding mathematical model that could simulate the characteristics of the part. These models could be used in computer aided design (CAD) tools during the design stage to facilitate the building of the model of biological systems. This paper describes the development of a mathematical model that is able to simulate both the dynamic and static performance of a biological device created using standard parts. We modeled an example quorum sensing device that produces green fluorescent protein (GFP) as reporter in the presence of Acyl Homoserine Lactone (AHL). The parameters of the model were estimated using experimental results. The simulation results show that the model was able to simulate behavior similar to experimental results. Since it is important that these models and the content in the models can be searchable and readable by machines, standard SBML (system biology markup language) format was used to store the models. All parts and reactions are fully annotated to enable easy searching, and the models follow the Minimum Information Requested In the Annotation of Models (MIRIAM) compliance as well as the Minimum Information About a Simulation Experiment (MIASE).

Figure 4a of the reference publication has been reproduced as curation figure. The plot shows the performance of the model at different concentrations of the inducer (3OC12HSL=5E-10, 5E-07, 5E-07).

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 10.1016/j.ces.2012.1... Submission Date: 11 Jan 2013 06:13:20 UTC Last Modification Date: 06 Jun 2013 11:55:21 UTC Creation Date: 27 Feb 2013 13:22:55 UTC
Mathematical expressions
Reactions
re3 re2 re4 re5
re8 re1 re14  
Physical entities
Compartments Species
default Ptet-LasR LasR sa3_degraded
3OC12HSL pLuxR A pLux
sa6_degraded LasR/AHL mRNA(LasR)
GFP    
Reactions (7)
 
 re3 [LasR] → [sa3_degraded];   {LasR}
 
 re2 [mRNA(LasR)] → [LasR];   {mRNA(LasR)}
 
 re4 [LasR] + [3OC12HSL] → [LasR/AHL];   {LasR} , {3OC12HSL} , {LasR/AHL}
 
 re5 [LasR/AHL] + [pLuxR] → [A pLux];   {pLuxR} , {LasR/AHL} , {A pLux}
 
 re8 [3OC12HSL] → [sa6_degraded];   {3OC12HSL}
 
 re1 [Ptet-LasR] → [mRNA(LasR)];   {Ptet-LasR} , {mRNA(LasR)}
 
 re14 [A pLux] → [GFP];   {A pLux} , {GFP}
 
   Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
   Ptet-LasR
Compartment: default
Initial amount: 1.0E-5
 
 LasR
Compartment: default
Initial amount: 1.0E-6
 
   sa3_degraded
Compartment: default
Initial amount: 0.0
 
 3OC12HSL
Compartment: default
Initial concentration: 5.0E-6
 
   pLuxR
Compartment: default
Initial amount: 1.0E-5
 
 A pLux
Compartment: default
Initial amount: 0.0
 
   sa6_degraded
Compartment: default
Initial amount: 0.0
 
 LasR/AHL
Compartment: default
Initial amount: 0.0
 
 mRNA(LasR)
Compartment: default
Initial amount: 0.0
 
 GFP
Compartment: default
Initial amount: 0.0
 
re3 (1)
 
   degradation rate of LasR
Value: 0.0696   (Units: substance)
Constant
 
re2 (1)
 
   k2
Value: 35.7   (Units: substance)
Constant
 
re4 (2)
 
   k3
Value: 9600000.0   (Units: substance)
Constant
 
   k4
Constant
 
re5 (2)
 
   k5
Value: 1960000.0   (Units: substance)
Constant
 
   k6
Value: 10.2   (Units: substance)
Constant
 
re8 (1)
 
   Y3
Value: 2.832E-4   (Units: substance)
Constant
 
re1 (2)
 
   k1
Value: 3.734   (Units: substance)
Constant
 
   Y1
Value: 0.348   (Units: substance)
Constant
 
re14 (8)
 
   K7
Value: 0.004051   (Units: substance)
Constant
 
   K8
Value: 0.009567   (Units: substance)
Constant
 
   K9
Value: 9.742E-8   (Units: substance)
Constant
 
   K10
Value: 6.5E-16   (Units: substance)
Constant
 
   K11
Value: 1.0E-14   (Units: substance)
Constant
 
   K12
Value: 2.4E-7   (Units: substance)
Constant
 
   n1
Value: 2.0   (Units: substance)
Constant
 
   n2
Value: 2.0   (Units: substance)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000438

Curator's comment: (updated: 27 Feb 2013 13:21:32 GMT)

Figure 4a of the reference publication has been reproduced as curation figure. The obtain the plot the concentrations of the inducer (3OC12HSL=5E-10, 5E-07, 5E-07) should be changed.
The data were obtained by simulating the model using Copasi v4.8 (Build 35). The plot was generated using Gnuplot.

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