Team:Michigan/Modeling

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HOME THE TEAM THE PROJECT MODELING REGISTRY PARTS NOTEBOOK SAFETY

The Toluene Terminator Model

Kill switch topology for modeling.jpg


Arabinose Inducible Suicide Mechanism Cell Growth/Death

Cell Lysis happens when holin creates pores in membrane and lysozyme enters Assume rate of cell death ∝[holin](# cells), rate of cell growth in exponential phase

Equation1.jpg

Transcription of Repressor:

Equation2.jpg 𝑓([𝑇]) is a function of toluene concentration

Use Hill Equation to describe binding affinity of toluene to Pu promoter.

Equation3.jpg

Transcription of Lysozyme and Holin:

Assume transcription rate is proportional to # of free operator sites (which should be the same for both lysozyme and holin, since they are downstream of the same promoter)

Equation4.jpg

Assume transcription rates for H and L are the same

Repression of Lysozyme and Holin Transcription

Repressor binds with free operator site, preventing transcription of lysozyme and holin. Use a model invoking law of mass action.

Equation5.jpg

Assuming that fops and Rfops do not undergo spontaneous degradation.

Production of Repressor

Using the translation rate for R and taking into consideration the binding of R with fops,

Equation6.jpg

Production of Proteins

Production of antiholin, under constitutive promoter, is at a constant rate γA, which depends on the promoter that is used

Dimerization: Since holin and antiholin form a complex

Equation7.jpg

Using the translation rates and incorporating dimerization using the law of mass action,

Equation8.jpg

Assumptions

Can set γA equal to rate of production of holin in the case that all operating sites are free

  • This is in order to balance antiholin and holin levels without repression
  • This can be tuned so that timing of cell death works out
  • Set antiholin production rate to that of holin in the absence of repression
  • Put this through the transcription and translation equations to obtain production rate

Assume degradation rates of all mRNAs are the same

  • Can directly search for these rates in literature
  • Can use half life to calculate rate Equation9.jpg

For protein degradation rate:

Case 1: Proteins are stable:

  • Degradation rates equal reproduction rate of cell
  • This is due to dilution of proteins across daughter cells

Case 2: Proteins are unstable

  • If not other degradation rate information is provided, can possibly assume that the degradation rates are a few orders of magnitude above the reproduction rate of cell
  • Will have to look into this further

Variables and Parameters

VariablesParameters.jpg