Overview
Introduction
A mathematical model is a simulated data-generating rule for an observed object described using mathematical methods. In particular, in the natural sciences, they are often described in the form of differential equations. This is because the derivative is the rate of “change” and is very compatible with the natural sciences, which observe natural phenomena and look at “change. The mathematical models in iGEM are often related to gene expression and protein function, and help in the design and understanding of projects. the DBTL cycle is one of the most important concepts in iGEM, through which projects are refined.
Our Project and Dry Lab
Our project will use radiation from cosmic radiation and radioactive waste to create radioresistant bacteria to produce energy and useful materials. Therefore, we will first divide the project into two major parts (radiation and other) for modeling in the dry lab. Finally, these will be integrated for a deeper understanding of the project.
Model-1
Purpose
Wet experiments showed that Tyrosinase expression level is low and Melanin production is low (takes time to produce). in Dry, we thought that IPTG concentration may be the cause, so we will investigate how Tyrosinase expression level changes with IPTG concentration.
Method and Model
A schematic diagram of the reaction pathway is shown below. Based on this, we constructed an ODE model in MATLAB and performed simulations using MATLAB R2024a. Our preliminary research led us to a paper that constructs a model based on homodimerization and binding/dissociation reactions of each molecule. The parameter values were taken from this paper and the model was used as is.
Why did we use this Model?
One of the most important elements of modeling is assumptions. No matter how accurate a model is, it is useless if it is outside of the assumptions we set. We decided to use the model in this paper because it assumed the same situation we wanted to simulate
Fig.1 Title
Write caption of figure, table and/or gragh. Write caption of figure, table and/or gragh. Write caption of figure, table and/or gragh.
The lactose operon model is used. A repressor expressed from the lacI gene on the genome of E. coli DH5α forms a dimer and binds to the operator (lacO) on the plasmid to repress melA (Tyrosinase) gene expression. IPTG added to the medium forms a dimer and binds to the free lacI dimer, thereby inhibiting the binding of lacO to the repressor. Furthermore, the IPTG dimer dissociates the lacI dimer from the lacI dimer-lacO complex to form the lacI dimer-IPTG dimer complex. This removes the physical barrier of lacO and allows RNA polymerase to bind to the Promoter, thereby promoting transcription. Of the lacI dimer-IPTG dimer complex generated by the above process, only lacI is degraded and two molecules of IPTG are released and reused. In addition, the model also takes into account that even if the lacI dimer is bound to lacO, a leak can still occur that promotes transcription.
Result
It was found that Tyrosinase expression increases with increasing IPTG concentration. However, Tyrosinase expression levels at IPTG concentrations of 10 mM and 100 mM are almost the same. This indicates that the optimal is 10 mM.
Fig.2 Title
The figure shows the change in Tyrosinase expression over time. The horizontal axis represents time (minutes) and the vertical axis represents the intracellular Tyrosinase concentration (nM) at each IPTG concentration.
aaaaaaaaaaaaaaaa
Model-2
Purpose
本文
本文
本文
本文
本文
本文
aaaaaaaaaaaaaaaa
Model-3
Purpose
本文
本文
本文
本文
本文
本文
aaaaaaaaaaaaaaaa
Model-4
Purpose
本文
本文
本文
本文
本文
本文
aaaaaaaaaaaaaaaa
Model-5
Purpose
本文
本文
本文
本文
本文
本文
aaaaaaaaaaaaaaaa
