Team:Valencia UPV/Modelling

Link title Valencia UPV iGEM 2015

First steps

We started by figuring out how it should work in a tree diagram, keeping the idea simple:


simple circuit truth table

True table of our model


2 pulses
4 possible combinations
4 different products


Overview

dna

Our idea is to model a biological multiplexor that responds to two different light pulses.

The circuit

dna dna dna

Expression levels

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Constitutive expression

Proteins A, B, C and D, are used to control the expression of next level. As they keep being produced before light pulses are given to the organism, we will assume that their concentrations have reached their balanced values. This assumption lets us simplify several expressions from this first level, as we will demonstrate in the development of the mathemathical model.


same for B,C,D and E.

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Regulated expression: 2nd level

When A (E-PIF6), B (PhyB-VP16), C (Gal4-KDronpa) and D (NDronpa-VP16) are pro- duced, they interact with the operator binding sites OBD1 (in gE, gF and gG) and OBD2 (in gH, gI and gJ). Thus, proteins produced in previous levels, regulate the expression of the following ones. Light induced transcription, is due to the activacion of proteins B and D, whose structures change according to a certain light wavelenght. Theoretically, only if B* (activated) binds A (which is already attached to the genes), proteins E, F and G will be produced. On the other hand, it occurs similarly with D*, C and proteins H, I and J. The symbol ”+”, makes reference to those genes which can be transcripted because recombinases have not bind to them.

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