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view/download model file: logical_promoter.nlogo
WHAT IS IT?
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This is a model that demonstrates possible ways that two genes could bind and influence expression of a third, either turning it off or on. The conditions modelled here are not an exhaustive range of the possiblities available in biological systems, but each condition represents an important class of control mechanisms.
HOW IT WORKS
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In this system, there are three genes: A, B and C. Genes A and B produce transcription factors. Gene C has two promoters that the transcription factors can bind to. Depending on the settings of the system, these are either enhancers (turning on transcription of C) or silencers (turning off transcription of C).
HOW TO USE IT
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Click "setup" to create the genes and ribosomes.
Click "go" to start the model.
Switches allow the user to turn genes A and B on and off.
A pop-up menu allows the user to select which logical gate to emulate.
A plot shows levels of A, B, and C.
THINGS TO NOTICE
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Even when C is turned off, you may notice it occasionally being transcribed. Why might this be? Are some gates "leakier" than others? Why? You can use the counters to put
the system in equilibrium and then reset the counters and experiment with which configurations are most effective.
THINGS TO TRY
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For each gate, determine what role the promoter is playing in the system (enhancer or silencer).
Consider constructing a "truth table" that lists possible states of "A", "B", and "C" under each condition to help disinguish among conditions that otherwise may appear to be identical.
EXTENDING THE MODEL
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To simplify this model, a number of factors have been de-paramaterized, including the rates of each gene (dA, dB, dC) and the coefficients of binding and dissociation (KB and Kd). By adding sliders, you could extend this model and explore the behavior of the system with different values. By changing these values you can try to decrease the leakiness of the system and increase the speed of the system turning on or off.
CREDITS AND REFERENCES
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This model was created as part of the 2004 BioQUEST Curriculum Consortium
Summer Workshop.
Copyright 2004 by Steven Brewer. All rights reserved.
This model was inspired by many of the sample Netlogo models and parts were based on functions from the Enzyme Kinetics model. (Wilensky, U. (2001). NetLogo Enzyme Kinetics model. http://ccl.northwestern.edu/netlogo/models/EnzymeKinetics. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.)
Permission to use, modify or redistribute this model is hereby granted,
provided that both of the following requirements are followed:
a) this copyright notice is included.
b) this model will not be redistributed for profit without permission
from the authors.
Contact the authors for appropriate licenses for redistribution for
profit.
To refer to this model in academic publications, please use:
Brewer, S.D. (2004). Logical Promoter: Simulating Logical Gates Using
a Model of Gene Expression. http://bcrc.bio.umass.edu/netlogo/models/LogicalPromoter
Biology Computer Resource Center
In other publications, please use:
Copyright 2004 by Steven Brewer. All rights reserved. See
http://bcrc.bio.umass.edu/netlogo/models/LogicalPromoter
for terms of use.