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            Modeling</h1>
 
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        <li class="active"><a href="#lA" data-toggle="tab">  biochemical model</a></li>
 
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            <p>We use the software to describe the whole idea of the experiment.Experiment was divided into three parts, and finally combined into two paths. The first part consists of copA promoter ,GFP, GshF and T7 promoter,enhancing Escherichia.coli sensitivity to copper ion. Glutathione can be synthesized by GshF, which can unifies both necessary reactions in one platform. The second part is a sgRNA-dCas9 system to enhance the efficiency of chelate cupric and cuprous by repressing the expression of copA. Finally, an automatically and efficiently copper-preventing guard are hoped to built. An overview of the biochemical process is shown in Figure 1. The figure is drawn with CellDesigner2 4.4.</p>
 
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    <h1>A model on the process of Cu<sup>2+</sup> elimination by “Copper Terminator”.</h1>
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    <h3>Abstract </h3><p>The process which this equipment “Copper Terminator” uptaking Cu<sup>2+</sup> is modeled by ordinary differential equations. Parameters in this models are both inferred from our experiments or obtained from literature. Second order Runge-Kutta method is utilized in simulation and the result shows that Cu<sup>2+</sup> is almost entirely  eliminated within 300 minutes from 1mg/L. Finally, Morris sensitivity analysis is carried out and shows that four controllable parameters are most important to the effect of elimination and this demonstrate the possibility of its application.</p>
 +
    <h1>The copper contamination.</h1>
 +
    <p>Today, from a spoon to a skyscraper, the uses of copper is extending everywhere. For meeting the increasing demand of copper in the world, the massive copper ores are mined every year [Figure 2.1.1].</p>
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    <img src="https://static.igem.org/mediawiki/2014/2/25/FH1.png" />
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    <p>And most copper is mined as copper sulfides such as chalcopyrite.Those type of mines are more likely to produce acid mine drainage (AMD) which refers to the outflow of acidic water from metal mines or coal mines [Fig 2.1.2].</p>
 +
    <img src="https://static.igem.org/mediawiki/2014/3/34/F2.png" />
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    <p>The specific process of generating AMD includes three chemical reactions:</p>
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    <p>The oxidization of pyrite which is iron-sulfide is primary contributor to AMD, the major process is:</p>
 +
    <h3>2FeS<sub>2</sub>(s) + 7O<sub>2</sub>(g) + 2H<sub>2</sub>O(l) = 2Fe<sup>2+</sup>(aq) + 4SO<sub>4</sub><sup>2−</sup>(aq) + 4H<sup>+</sup>(aq)</h3>
 +
    <p>The ferrous iron (II) generated from oxidization of pyrite is oxidized to ferric iron(III).<p>
 +
    <h3>4Fe<sup>2+</sup> (aq) + O<sub>2</sub> (g) + 4H<sup>+</sup> (aq) = 4Fe<sup>3+</sup>(aq) + 2H<sub>2</sub>O(l)</h3>
 +
    <p>And another process happens simultaneously with oxidization of pyrite and need to be catalyzed by microbes.</p>
 +
    <h3>FeS<sub>2</sub> (s) + 14Fe<sup>3+</sup> (aq) + 8H<sub>2</sub>O(l) = 15Fe<sup>2+</sup> (aq) + 2 SO<sub>4</sub><sup>2−</sup> (aq) + 16H<sup>+</sup> (aq)</h3>
 +
    <p>Those reactions jointly lower the PH of water and produce soluble ferric iron(III),and finally the acid mine drainage emerges [Figure 2.1.3].</p>
 +
    <img src="https://static.igem.org/mediawiki/2014/9/96/F3.png" />
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    <p>Associating with water and air, the metal mines where the ore is sulfide mineral or comprises pyrite can easily produce the highly acidic effusion. Usually the predominant metal ion isn’t iron but copper, zinc. The most common ore mined is chalcopyrite which is a copper-iron-sulfide and occurs with a range of other sulfides. Thus, copper mines are primary crime of AMD.</p>
 +
    <h1>Copper tolerance of <i>E.coli</i>.</h1>
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    <p>Massive mining and extensive using of copper results in serious contamination to environment, and then copper contamination threaten the balance of the whole ecosystem. Even the low concentration of copper is toxic to the organism (look at our algae experiment). But there is an exception, Escherichia coli ,which has several sophisticated and powerful systems to maintain the copper homeostasis so it can survive in skyhigh concentration(look at our MIC(minimum inhibitory concentration, MIC)experiment).Basing on this characteristic of <i>E.col</i>, we start to design an bio-machine to solve the problem of copper contamination effectively.</p>
 +
    <h3>Refrences:</h3>
 +
    <p>[1] Rensing, C., & Grass, G. (2003). Escherichia coli mechanisms of copper homeostasis in a changing environment. FEMS microbiology reviews,27(2‐3), 197-213.</p>
 +
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Revision as of 01:43, 17 October 2014

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A model on the process of Cu2+ elimination by “Copper Terminator”.

Abstract

The process which this equipment “Copper Terminator” uptaking Cu2+ is modeled by ordinary differential equations. Parameters in this models are both inferred from our experiments or obtained from literature. Second order Runge-Kutta method is utilized in simulation and the result shows that Cu2+ is almost entirely eliminated within 300 minutes from 1mg/L. Finally, Morris sensitivity analysis is carried out and shows that four controllable parameters are most important to the effect of elimination and this demonstrate the possibility of its application.

The copper contamination.

Today, from a spoon to a skyscraper, the uses of copper is extending everywhere. For meeting the increasing demand of copper in the world, the massive copper ores are mined every year [Figure 2.1.1].

And most copper is mined as copper sulfides such as chalcopyrite.Those type of mines are more likely to produce acid mine drainage (AMD) which refers to the outflow of acidic water from metal mines or coal mines [Fig 2.1.2].

The specific process of generating AMD includes three chemical reactions:

The oxidization of pyrite which is iron-sulfide is primary contributor to AMD, the major process is:

2FeS2(s) + 7O2(g) + 2H2O(l) = 2Fe2+(aq) + 4SO42−(aq) + 4H+(aq)

The ferrous iron (II) generated from oxidization of pyrite is oxidized to ferric iron(III).

4Fe2+ (aq) + O2 (g) + 4H+ (aq) = 4Fe3+(aq) + 2H2O(l)

And another process happens simultaneously with oxidization of pyrite and need to be catalyzed by microbes.

FeS2 (s) + 14Fe3+ (aq) + 8H2O(l) = 15Fe2+ (aq) + 2 SO42− (aq) + 16H+ (aq)

Those reactions jointly lower the PH of water and produce soluble ferric iron(III),and finally the acid mine drainage emerges [Figure 2.1.3].

Associating with water and air, the metal mines where the ore is sulfide mineral or comprises pyrite can easily produce the highly acidic effusion. Usually the predominant metal ion isn’t iron but copper, zinc. The most common ore mined is chalcopyrite which is a copper-iron-sulfide and occurs with a range of other sulfides. Thus, copper mines are primary crime of AMD.

Copper tolerance of E.coli.

Massive mining and extensive using of copper results in serious contamination to environment, and then copper contamination threaten the balance of the whole ecosystem. Even the low concentration of copper is toxic to the organism (look at our algae experiment). But there is an exception, Escherichia coli ,which has several sophisticated and powerful systems to maintain the copper homeostasis so it can survive in skyhigh concentration(look at our MIC(minimum inhibitory concentration, MIC)experiment).Basing on this characteristic of E.col, we start to design an bio-machine to solve the problem of copper contamination effectively.

Refrences:

[1] Rensing, C., & Grass, G. (2003). Escherichia coli mechanisms of copper homeostasis in a changing environment. FEMS microbiology reviews,27(2‐3), 197-213.

All Pictures come from Wikipedia.