Team:BOKU-Vienna/Model

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Project Inspiration Design

Modeling Overview

Introduction

Since mathematical models are a very important part to help figuring out if our idea is theoretically possible, we started very early to dive into this topic. After considering Matlab we decided to do our model in Copasi which is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.[1]
In the first weeks of July, we started to build the whole system in Copasi. From the binding of Mycolactone to the riboswitch over the production of AHL and the amplification of it to the production of blue Chromoprotein.

This is our general Idea:

T--BOKU-Vienna--_Ecoli_modeling_grafik.png

Here are the Constructs as we have put them together.

Constructs

Modeling Reactions

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Species Overview

Species Description
Mycolactone Is a polyketide-derived macrolide produced and secreted by a group of very closly related pathogenic Mycobacteria.
Theophyllin A inducer molecule for a specific Aptamer.
Aptamer An oligonucleotide or peptide molecule that binds to a specific target molecule.
T7-Polymerase is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' direction.
T7-Promotor Specific T7 bacteriophage derived sequence for binding and initiation of the transcription.
mRNA-LuxI mRNA of the LuxI-Enzyme being transcribed by the Lux Promotor and by the T7-Promotor
LuxI Ezyme that catalyses the Reaktion from Precursors to AHL
AHL 30C6-HSL is an acyl homoserine lactone which diffuses into the cell and mainly binds to LuxR.[2]
LuxR Constitutively expressed regulator protein that can bind LuxAHL and stimulate transcription of Bxb1.[2]
AHL/LuxR-Komplex Komplex formed by 2 AHL and 2 LuxR
mRNA-amilCP mRNA of the amilCP-protein being transcribed by the Lux Promotor
amilCP The blue Chromoprotein we used.
T7-Promotor Promoter for the Lux-System

Parameter Overview

Parameter Description value
k0 Transcription rate of LuxI 2,5 1/min Literature value [4]
k1 Translation rate of LuxI 0,868 1/min Literature value [4]
k2 Rate of AHL-synthese 0,04 1/min Literature value [4]
k3 Rate of Komplexassociation 10-5 mL3/(mmol3*min) Estimated by our self
k4 rate of Promoter activation 0,16 mL/(mmol*min) Estimated by our self
k5 Transcription rate of mRNA- AmilCP 4300 1/min Estimated by our self
k6 Translation rate of mRNA-AmilCP 1075 1/min Estimated by our self
r1 Diffusionrate of AHL outside of the cell 13,24 mL/min Literature value [3]
r2 Diffusionrate of AHL into the cell 11,04 mL/min Estimated by our self
c1 Constant flux of LuxR 0,0005 mmol/(mL*min) Estimated by our self
c2 Constant flux of pAHL 0,01 mmol/(mL*min) Estimated by our self
d1 Degradation rate of LuxR 0,0231 1/min Literature value [3]
d2 Degradation rate of AHL inside the cell 0,004 1/min Literature value [5]
d3 Degradation rate of AHL in the media 0,0004 1/min Literature value [5]
d4 Mycolacton degradation rate 3,33*10-7 1/min Estimated by our self

Modellation Results:

Our main goal concerning the system was to determine after what time the production of blue Chromoprotein will start.

T--BOKU-Vienna--Modelling-Diagramm1
Diagramm1: Results of the blue Chromoprotein production start.

According to the Diagram the blue Chromoprotein production will start at about 50 minutes and will reach a peak after 100 minutes.

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