Team:UNOTT/Modelling

Modeling

The central aim for the modeling would be to write a simulation for the wet lab to aid construction of the bacteria.

Download our source code from our gitHub page

  • Predicting Fluoresce Intensity and Wavelengths
  • Absorption and Emission Wavelengths
  • Gene Transcription Regulation by Repressors (CRISPR)
  • MISSION: LIGATING BRICKS
  • MISSION: CONTROL PLASMID TRANSFORMATION

  • Predicting Fluoresce Intensity and Wavelengths Given Parameters





    Constitutive Gene Expression For Protein and mRNA Expression over Time

    Assuming the gene expression was unregulated and the gene is always on, the constitutive gene expression model was used to guide the model.
        $$ sfGFP \underset{Transcriptin}{\rightarrow} mRNA \underset{Translation}{\rightarrow} sfGFP $$ $$ mRNA \underset{Degradation}{\rightarrow} \oslash $$ $$ sfGFP \underset{Degradation}{\rightarrow} \oslash $$
    Using the Law of Mass Action, this model can be described as:
    $$ mRNA = k_{1} -d _{1 } mRNA $$ $$ Protein = k_{2} \cdot mRNA - d_{2} \cdot Protein $$  
    Using this, we can calculate the concentration of proteins we can expect over time. This was useful because it allowed us to see how much protein was made which were emitting the light so we could make an accurate prediction of how much intensity there was at a certain amount of time.






  • Absorption and Emission Wavelengths From Given Concentrations of sfGFP, mRFP & ECFP

    Using Shemrock's online fluorescence graph maker, I generated the expected Absorption and Emission wavelengths that are taken in and produced by sfGFP (green), mRFP (red) and ECFP (blue) proteins. This was done through the web app on the website.
    This graph tells us the emitted light is expected to be at a higher wavelength than when absorbed. This must be considered in the model as there is overlap between emitted and absorbed wavelengths so some emitted light may be absorbed and re-emitted at a higher wavelength.
    This model is important as it guides us when using wavelengths as parameters so we know which wavelengths to use, especially when trying to create a specific color








  • Gene Transcription Regulation by Repressors (CRISPR) - Concentration over Time

    To calculate our Protein concentration at any given time when using CRISPR, the expanded mRNA and Protein concentration models from the Constitutive Gene Expression Model were used and an element of repression was added to the model as we were using CRISPR as a repressor.
    $ Gene \overset{Repressor}{\rightarrow} mRNA \rightarrow Protein $$ $$ mRNA \underset{Degradation}{\rightarrow} \oslash $$ $$ sfGFP \underset{Degradation}{\rightarrow} \oslash $$
    This change can be applied using the Law of Mass Action:
    $$ m = k_{1} \cdot \frac{k^{n}}{k^{n} + R^{n}}- d_{1}m $$ $$ p = k_{2} m - d_{2}p $$

    Where...

    • < m = mRNA concentration
    • p = Protein concentration
    • R = Repressor
    • k1 = Max Transcription Rate
    • k = Repression Coefficient
    • n = Hill Coefficient (number of repressors that need to cooperatively bind the promoter to trigger the inhibition of gene expression)
    • R = Repressor
    • d1 = mRNA degradation rate
    • d2 = Protein degradation rate
    When visually modeled using Python:

  • MISSION: LIGATING BRICKS

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  • MISSION: CONTROL PLASMID TRANSFORMATION

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