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Team:BYUProvo/Modeling
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= Introduction = | = Introduction = | ||
| - | Colon cancer polyps produce high amounts of reactive oxygen species (ROS) and lactate. The high metabolic activity also causes an increase in temperature. Sensors for any one of these inputs alone would be confounded by normal physiological variation in temperature, lactate concentration, and ROS concentration. We propose a genetic circuit designed to detect higher than normal levels of all three, producing two separate outputs. There are two parts to the | + | Colon cancer polyps produce high amounts of reactive oxygen species (ROS) and lactate. The high metabolic activity also causes an increase in temperature. Sensors for any one of these inputs alone would be confounded by normal physiological variation in temperature, lactate concentration, and ROS concentration. We propose a genetic circuit designed to detect higher than normal levels of all three, producing two separate outputs. There are two parts to the circuit: The first is a dual input system, using temperature and ROS as inputs to produce an output (LacZ). The second is a single input system, using lactate to produce GFP. |
Insert picture of model here | Insert picture of model here | ||
| - | In order to model our system, we have undertaken | + | In order to model our system, we have undertaken three main tasks: |
1) Create a model using Mass-Action Enzyme Kinematics | 1) Create a model using Mass-Action Enzyme Kinematics | ||
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Insert picture of circuit here. | Insert picture of circuit here. | ||
| - | The diagram above depicts the inner workings of our circuit created within ''E. Coli''. | + | The diagram above depicts the inner workings of our circuit created within ''E. Coli''. The following chemical equations depict the pathway: |
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| + | Insert chemical equations here. | ||
= The Model = | = The Model = | ||
== Mass-Action Equations == | == Mass-Action Equations == | ||
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| + | Using mass-action kinetics, we write these chemical equations as a system of differential equations. | ||
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| + | <math>Insert formula here</math> | ||
== System of ODEs == | == System of ODEs == | ||
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| + | As it is, the system is too complicated for us to analyze, so we hereby make a few assumptions to simplify. | ||
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| + | Quasi Steady-State Assumption | ||
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| + | Forward Reaction Assumption | ||
== Temperature Dependence == | == Temperature Dependence == | ||
Revision as of 16:02, 1 October 2012
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Contents |
Introduction
Colon cancer polyps produce high amounts of reactive oxygen species (ROS) and lactate. The high metabolic activity also causes an increase in temperature. Sensors for any one of these inputs alone would be confounded by normal physiological variation in temperature, lactate concentration, and ROS concentration. We propose a genetic circuit designed to detect higher than normal levels of all three, producing two separate outputs. There are two parts to the circuit: The first is a dual input system, using temperature and ROS as inputs to produce an output (LacZ). The second is a single input system, using lactate to produce GFP.
Insert picture of model here
In order to model our system, we have undertaken three main tasks:
1) Create a model using Mass-Action Enzyme Kinematics
2) Analyze this model using computational methods
3) Create an algorithm to predict the structure of our RNA thermosensors
We start first, creating a system of differential equations from our reaction sequence.
Our Circuit
Insert picture of circuit here.
The diagram above depicts the inner workings of our circuit created within E. Coli. The following chemical equations depict the pathway:
Insert chemical equations here.
The Model
Mass-Action Equations
Using mass-action kinetics, we write these chemical equations as a system of differential equations.
<math>Insert formula here</math>
System of ODEs
As it is, the system is too complicated for us to analyze, so we hereby make a few assumptions to simplify.
Quasi Steady-State Assumption
Forward Reaction Assumption
