Team:NYMU-Taipei/modeling/m2

From 2014.igem.org

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       <h>killing model</h>
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       <h>Competition model</h>
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       <h1>purpose & introduction</h1>
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       <h1>Purpose</h1>
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      <p>1. To quantize and prove the saying of eliminating all S. mutans would lead to the rise of other bacteria via using mathematical model.<br> 2. To predict the change of pH and ecology in oral cavity after eliminating different amount of S. mutans.</p>
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      <h1>Background</h1>
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      <p>Dental caries is defined as demineralization of tooth enamel[1]. Because tooth enamel solubility is pH dependent[2], acid production in plaque area is believed to be crucial for caries development. In 1940, Stephan has discovered that the longer time pH value of oral cavity is below “critical pH 5.5”, the more susceptible tooth enamel is. Therefore, NYMU team plans to prevent tooth caries via eliminating S. mutans, the main cariogenic bacteria that produce most of the acid[3].<br>However, studies have shown that when S. mutans no longer adapts to the environment, or the amount of S. mutans decreased to an extent, other species will become dominant instead[4]. Thus, there is concern that if we kill S. mutans excessively, other bacteria population would grow, and cause caries or do other harm to the oral cavity. Due to the limitation of our lab, we cannot do experiment in vitro or in multi-species culture to verify the saying. We then use modelling, the competition model, to demonstrate the reason why we cannot kill all S. mutans, and find the optimize amount of S. mutans elimination to prevent caries without concerning other cariogenic bacteria.<br>In our competition model, we choose to use Lotka–Volterra competition model, which based on logistic equation, for it fits very well with our experimental data on S. mutans growth curve. We choose four species that can produce acid and occupy high proportion in our oral cavity as the subjects of modeling, which are S. mutans, S. sobrinus, S. mitis[5], and Neisseria mucosa[6]. To validate our model more realistically and precisely, we use 16S rRNA gene sequencing data from a paper published in 2012, which samples from 36 human[7], to find out how bacteria compete in oral cavity. Moreover, we use experimental data from literature to know how populations shift effect oral pH value. Then we can find out the optimal S. mutans population that would maximize oral pH value, and therefore prevent caries from happening.</p>
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      <h1>Models and mathematic equations</h1>
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      <p><b>Competitive Lotka–Volterra equation</b> presents the competition between two or more species for limiting resources[8].</p>
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      <h1>Result and model validation</h1>
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      <h1>Reference</h1>
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       <p><b>How many S. mutans should we kill?</b></p>
       <p><b>How many S. mutans should we kill?</b></p>
       <p>It is bacteria’s acid production that causes caries, so we build a model to know how much S. mutans we should kill to prevent caries.</p>
       <p>It is bacteria’s acid production that causes caries, so we build a model to know how much S. mutans we should kill to prevent caries.</p>
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       <p>$$\frac{d[\text{acidic substance}]}{dt} = \sum\limits_i(\alpha_i\frac{dx_i}{dt}+\beta{x_i})$$</p>
       <p>$$\frac{d[\text{acidic substance}]}{dt} = \sum\limits_i(\alpha_i\frac{dx_i}{dt}+\beta{x_i})$$</p>
       <p>$\alpha_i,\beta_i$: related coefficient</p>
       <p>$\alpha_i,\beta_i$: related coefficient</p>
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      <h1>result</h1>
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      <h1>discussion</h1>
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Revision as of 11:18, 11 September 2014

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Competition model

Purpose

1. To quantize and prove the saying of eliminating all S. mutans would lead to the rise of other bacteria via using mathematical model.
2. To predict the change of pH and ecology in oral cavity after eliminating different amount of S. mutans.

Background

Dental caries is defined as demineralization of tooth enamel[1]. Because tooth enamel solubility is pH dependent[2], acid production in plaque area is believed to be crucial for caries development. In 1940, Stephan has discovered that the longer time pH value of oral cavity is below “critical pH 5.5”, the more susceptible tooth enamel is. Therefore, NYMU team plans to prevent tooth caries via eliminating S. mutans, the main cariogenic bacteria that produce most of the acid[3].
However, studies have shown that when S. mutans no longer adapts to the environment, or the amount of S. mutans decreased to an extent, other species will become dominant instead[4]. Thus, there is concern that if we kill S. mutans excessively, other bacteria population would grow, and cause caries or do other harm to the oral cavity. Due to the limitation of our lab, we cannot do experiment in vitro or in multi-species culture to verify the saying. We then use modelling, the competition model, to demonstrate the reason why we cannot kill all S. mutans, and find the optimize amount of S. mutans elimination to prevent caries without concerning other cariogenic bacteria.
In our competition model, we choose to use Lotka–Volterra competition model, which based on logistic equation, for it fits very well with our experimental data on S. mutans growth curve. We choose four species that can produce acid and occupy high proportion in our oral cavity as the subjects of modeling, which are S. mutans, S. sobrinus, S. mitis[5], and Neisseria mucosa[6]. To validate our model more realistically and precisely, we use 16S rRNA gene sequencing data from a paper published in 2012, which samples from 36 human[7], to find out how bacteria compete in oral cavity. Moreover, we use experimental data from literature to know how populations shift effect oral pH value. Then we can find out the optimal S. mutans population that would maximize oral pH value, and therefore prevent caries from happening.

Models and mathematic equations

Competitive Lotka–Volterra equation presents the competition between two or more species for limiting resources[8].

Result and model validation

Reference