Model

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     <td height="28" colspan="2" bgcolor="#03438A" id="dateformat"><br /> </td>
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     <td width="58%" rowspan="2" valign="top" bgcolor="#03438A"><img src="https://static.igem.org/mediawiki/2008/1/1d/111111.jpg" width="555" height="397" alt=""></td>
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     <td width="58%" rowspan="2" valign="top" bgcolor="#03438A"><p class="STYLE131"><img src="https://static.igem.org/mediawiki/2008/1/1d/111111.jpg" width="555" height="397" alt=""></p></td>
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     <td width="42%" valign="top" bgcolor="#03438A"><p align="center" class="STYLE9"><strong>Figure One, The concentraiton of the cells (demonstrated by the induced  expression of the antibiotic resistant genes) against time</strong></p>     </td>
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     <td width="42%" valign="top" bgcolor="#03438A"><p align="center" class="STYLE9"><strong>Figure One, The concentraiton of the cells (demonstrated by the induced  expression of the antibiotic resistant genes) against time</strong></p></td>
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     <td colspan="2" valign="top" bgcolor="#0066FF">&nbsp;</td>
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     <td colspan="2" valign="top" bgcolor="#0066FF"><p><span class="STYLE131"></span></p></td>
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     <td valign="top" bgcolor="#03438A"><img src="https://static.igem.org/mediawiki/2008/3/36/222.jpg" width="557" height="347" alt=""></td>
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     <td valign="top" bgcolor="#03438A"><p class="STYLE131"><img src="https://static.igem.org/mediawiki/2008/3/36/222.jpg" width="557" height="347" alt=""></p></td>
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     <td valign="top" bgcolor="#03438A"><p class="STYLE1"><span class="STYLE10">Figure Two,  expression of antibiotic resistant genes against time and the concentration of  AHL/BHL.</span></p>
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     <td valign="top" bgcolor="#03438A"><p class="STYLE9"><span class="STYLE10">Figure Two,  expression of antibiotic resistant genes against time and the concentration of  AHL/BHL.</span></p>
     <p class="STYLE130">The expression of the  antibiotic resistance proteins(red for chloramphenicol and green for kanamycin  resistant gene ) are infulenced by the amount of BHL/AHL added into the  culture. The curve will disply a different look when the concentration of  AHL/BHL passes the threshold of 7uM/m.</p></td>
     <p class="STYLE130">The expression of the  antibiotic resistance proteins(red for chloramphenicol and green for kanamycin  resistant gene ) are infulenced by the amount of BHL/AHL added into the  culture. The curve will disply a different look when the concentration of  AHL/BHL passes the threshold of 7uM/m.</p></td>
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     <td colspan="2" valign="top" bgcolor="#0066FF">&nbsp;</td>
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     <td colspan="2" valign="top" bgcolor="#03438A"><p class="STYLE131">&nbsp;</p>
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     <td rowspan="2" valign="top" bgcolor="#03438A"><p align="left" class="STYLE128">Assume  that the initial concentration of the two antibiotics (kanamycin and  chloramphenicol) are the same, and the amount of the antibiotic resistant  proteins comsumed per minute is [s]. When [s] is below 0.5uM, the expressions  of the two antibiotic resistant genes will be enhanced when AHL or BHL is added  into the culture, and enter to the muatualism phase where the survival of one  strain is beneficial for the other. However, when [s] passes the threshold of  0.5μL, the extinction of one strain may happen before the two enter the  muatualism stage. </p>      </td>
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    <p align="center" class="STYLE133">Figure Tree, the concentraiton of antibiotic resistant protiens against  time and its degration rate.</p>
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    <p class="STYLE132"><span class="STYLE131"><img name="" src="https://static.igem.org/mediawiki/2008/8/8e/333.jpg" width="557" height="344" alt=""></span></p>
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     <p align="left" class="STYLE128">Assume  that the initial concentration of the two antibiotics (kanamycin and  chloramphenicol) are the same, and the amount of the antibiotic resistant  proteins comsumed per minute is [s]. When [s] is below 0.5uM, the expressions  of the two antibiotic resistant genes will be enhanced when AHL or BHL is added  into the culture, and enter to the muatualism phase where the survival of one  strain is beneficial for the other. However, when [s] passes the threshold of  0.5μL, the extinction of one strain may happen before the two enter the  muatualism stage. </p></td>
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    <td height="52" valign="top" bgcolor="#03438A"><span class="STYLE10">Figure Tree, the concentraiton of antibiotic resistant protiens against  time and its degration rate.</span></td>
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     <td colspan="2" valign="top" bgcolor="#0066FF"><p align="center">&nbsp;</p>     </td>
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     <td colspan="2" valign="top" bgcolor="#03438A"><p align="center"><span class="STYLE12"><span class="STYLE13"><strong>Figure Four, the  concentration of cells against time.</strong></span></span></p>
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     <td colspan="2" valign="top" bgcolor="#03438A"><p align="center" class="STYLE131"><span class="STYLE12"><span class="STYLE13"><strong>Figure Four, the  concentration of cells against time.</strong></span></span></p>
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       <p align="center"><span class="STYLE12"><span class="STYLE13"><br>
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       <p align="left" class="STYLE131"><span class="STYLE12"><span class="STYLE13"><img name="" src="https://static.igem.org/mediawiki/2008/d/d4/444.jpg" width="476" height="295" alt=""></span></span></p>
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      </span></span><span class="STYLE1">As is  shown in the fig from the starting point to the third hour the gene circle  starts to work and finally get to a stable stage. And during this process there  is some amount of chloramphenicol resistant protein and the kanamycin resistant  protein accumulated. However the expression of the antibiotic resistant protein  has not reached the highest level. </span></p>
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      <p class="STYLE9"><span class="STYLE9">As is  shown in the fig from the starting point to the third hour the gene circle  starts to work and finally get to a stable stage. And during this process there  is some amount of chloramphenicol resistant protein and the kanamycin resistant  protein accumulated. However the expression of the antibiotic resistant protein  has not reached the highest level.</span></p>
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      <p align="center"><span class="STYLE12"><span class="STYLE13"><img name="" src="https://static.igem.org/mediawiki/2008/d/d4/444.jpg" width="476" height="295" alt=""></span></span></p>
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       <p class="STYLE9">The  third hour is the critical point for the AHL for the concentration of AHL will  get down to the same level as the BHL within 24 minutes and keep on this  cooperation. When the plux and prhl promoters have been activate to their  greatest capacity there will be a small peak because of the leakiness of the  PBad/araC promoter. And in this situation the expression of the antibiotic resistant  protein get to the highest level.</p>
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       <p class="STYLE1">The  third hour is the critical point for the AHL for the concentration of AHL will  get down to the same level as the BHL within 24 minutes and keep on this  cooperation. When the plux and prhl promoters have been activate to their  greatest capacity there will be a small peak because of the leakiness of the  PBad/araC promoter. And in this situation the expression of the antibiotic resistant  protein get to the highest level.</p>
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       <p class="STYLE9">By  adding arabinose or IPTG at the eighth hour there still will be a small peak.  However both of them will fall until the restarting of the PBad/araC promoter.</p>
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       <p class="STYLE1">By  adding arabinose or IPTG at the eighth hour there still will be a small peak.  However both of them will fall until the restarting of the PBad/araC promoter.</p>
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       <p class="STYLE9">From  the starting point to the twelfth hour the whole mechanism can be seen as a  completely regulating process which shows the shifting from the competent state  to the mutualism state.</p>
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       <p class="STYLE1">From  the starting point to the twelfth hour the whole mechanism can be seen as a  completely regulating process which shows the shifting from the competent state  to the mutualism state.</p>
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       <p class="STYLE9">The  robustness of the whole system depend on several key factors listed below: </p>     <ol class="STYLE131">
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       <p class="STYLE1">The  robustness of the whole system depend on several key factors listed below: </p>
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           <li class="STYLE1">The different inherent  behaviors of the promoters determines the performance of the toggle switch. </li>
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           <li class="STYLE1">
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           <li class="STYLE1">The degradation rates of the  AHL(BHL)and arabinose(IPTG) will have some impact  in the next control.</li>
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            <p class="STYLE9">The different inherent  behaviors of the promoters determines the performance of the toggle switch. </p>
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          </li>
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            <p><span class="STYLE9">The degradation rates of the  AHL(BHL)and arabinose(IPTG) will have some impact  in the next control.</span></p>
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       <p class="STYLE9"><strong>The assumptions of the model </strong><br>
       <p class="STYLE9"><strong>The assumptions of the model </strong><br>
         1 The  concentration of the signal molecules is even in all regions of the culture,  as well as within the cells. <br>
         1 The  concentration of the signal molecules is even in all regions of the culture,  as well as within the cells. <br>
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         2 The  amounts of the antibiotic resistant proteins are enough to make sure the cells’  survival. <br></p>
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         2 The  amounts of the antibiotic resistant proteins are enough to make sure the cells’  survival. <br>
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      </p>
       <p class="STYLE9">3 The amount of  antibiotics resistant proteins consumed per minute [s] is a constant when the  concentration of antibiotics is stable, and will vary with the variance of the  concentration of antibiotics. A strain is assumed to be extinguished when the  amount of antibiotic resistant protein expressed is negative. </p>
       <p class="STYLE9">3 The amount of  antibiotics resistant proteins consumed per minute [s] is a constant when the  concentration of antibiotics is stable, and will vary with the variance of the  concentration of antibiotics. A strain is assumed to be extinguished when the  amount of antibiotic resistant protein expressed is negative. </p>
       <p class="STYLE9">&nbsp;</p>
       <p class="STYLE9">&nbsp;</p>
       <p class="STYLE9">4 The  inducers IPTG or arobinose will function for long, and their concentration  won’t be affected significantly when they combine the repressors. </p>
       <p class="STYLE9">4 The  inducers IPTG or arobinose will function for long, and their concentration  won’t be affected significantly when they combine the repressors. </p>
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       <p class="STYLE9">5 The survival  ability of a cell is demonstrated by the amount of antibiotic resistant  proteins expressed. </p>   </td>
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       <p class="STYLE9">5 The survival  ability of a cell is demonstrated by the amount of antibiotic resistant  proteins expressed. </p></td>
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Revision as of 04:04, 30 October 2008

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Figure One, The concentraiton of the cells (demonstrated by the induced expression of the antibiotic resistant genes) against time

The viability of mutuallism and competition varies in different conditions, as is shown in the graph above, the adding of AHL,after a short time of perturbation lead to a mutualism phase, where both strains' growth increased to a higher level, while the adding of arabinose resulted in the significant decrease of one strain.

Figure Two, expression of antibiotic resistant genes against time and the concentration of AHL/BHL.

The expression of the antibiotic resistance proteins(red for chloramphenicol and green for kanamycin resistant gene ) are infulenced by the amount of BHL/AHL added into the culture. The curve will disply a different look when the concentration of AHL/BHL passes the threshold of 7uM/m.

 

Figure Tree, the concentraiton of antibiotic resistant protiens against time and its degration rate.

Assume that the initial concentration of the two antibiotics (kanamycin and chloramphenicol) are the same, and the amount of the antibiotic resistant proteins comsumed per minute is [s]. When [s] is below 0.5uM, the expressions of the two antibiotic resistant genes will be enhanced when AHL or BHL is added into the culture, and enter to the muatualism phase where the survival of one strain is beneficial for the other. However, when [s] passes the threshold of 0.5μL, the extinction of one strain may happen before the two enter the muatualism stage.

Figure Four, the concentration of cells against time.

As is shown in the fig from the starting point to the third hour the gene circle starts to work and finally get to a stable stage. And during this process there is some amount of chloramphenicol resistant protein and the kanamycin resistant protein accumulated. However the expression of the antibiotic resistant protein has not reached the highest level.

The third hour is the critical point for the AHL for the concentration of AHL will get down to the same level as the BHL within 24 minutes and keep on this cooperation. When the plux and prhl promoters have been activate to their greatest capacity there will be a small peak because of the leakiness of the PBad/araC promoter. And in this situation the expression of the antibiotic resistant protein get to the highest level.

By adding arabinose or IPTG at the eighth hour there still will be a small peak. However both of them will fall until the restarting of the PBad/araC promoter.

From the starting point to the twelfth hour the whole mechanism can be seen as a completely regulating process which shows the shifting from the competent state to the mutualism state.

The robustness of the whole system depend on several key factors listed below:

    • The different inherent behaviors of the promoters determines the performance of the toggle switch.

    • The degradation rates of the AHL(BHL)and arabinose(IPTG) will have some impact in the next control.

Figure Five, The expression of kanamycin resistant genes against time and Hill coefficient(Xm) of the promoter Plux and Prhi.

As is shown, the graph takes a look of Figure 1 only when Xm is within the range of 2.6-2.84.
The result of this model, indicates that the capacity of promoters affect the viability of the system to a great extent, thus provide a powerful tool for the optimization of the design in terms of the choice promoters.

 

The assumptions of the model
1 The concentration of the signal molecules is even in all regions of the culture, as well as within the cells.
2 The amounts of the antibiotic resistant proteins are enough to make sure the cells’ survival.

3 The amount of antibiotics resistant proteins consumed per minute [s] is a constant when the concentration of antibiotics is stable, and will vary with the variance of the concentration of antibiotics. A strain is assumed to be extinguished when the amount of antibiotic resistant protein expressed is negative.

 

4 The inducers IPTG or arobinose will function for long, and their concentration won’t be affected significantly when they combine the repressors.

5 The survival ability of a cell is demonstrated by the amount of antibiotic resistant proteins expressed.

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