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Notebook Calendar Thermosensor Lactate Sensor Cre Lox

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Contents 1 Introduction 2 Our Circuit 3 The Model 3.1 Mass-Action Equations 3.2 System of ODEs 3.3 Temperature Dependence 3.4 Parameter Estimation 4 Experimental Data from Lab Work 5 Analysis 5.1 Bifurcation Analysis 5.2 Steady State Analysis 6 Modeling our Thermosensor 6.1 Smith-Waterman Algorithm 6.2 Our Revised Algorithm 6.3 Results

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 system designed to detect higher than normal levels of all three, producing two separate outputs.

Insert picture of model here

In order to model our system, we have undertaken 3 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 Model

Mass-Action Equations

System of ODEs

Temperature Dependence

Parameter Estimation

Experimental Data from Lab Work

Analysis

Bifurcation Analysis

Steady State Analysis

Modeling our Thermosensor

Smith-Waterman Algorithm

Our Revised Algorithm

Results