http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&feed=atom&action=historyTeam:DTU-Denmark/Kinetic Model - Revision history2024-03-29T14:26:22ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=301341&oldid=prevVanessa: /* Results and Discussion */2013-10-04T19:37:38Z<p><span class="autocomment">Results and Discussion</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 1: Kinetic modeling of Mutant 1. Nitrite concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations. Click on the pictures to see them larger.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 1:<ins class="diffchange diffchange-inline"></b> </ins>Kinetic modeling of Mutant 1. Nitrite concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations. Click on the pictures to see them larger.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 2: Kinetic modeling of Mutant 2. Nitrous oxide concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations. Click on the pictures to see them larger.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Figure 2:<ins class="diffchange diffchange-inline"></b> </ins>Kinetic modeling of Mutant 2. Nitrous oxide concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations. Click on the pictures to see them larger.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== References ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== References ===</div></td></tr>
</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=300576&oldid=prevVanessa: /* Summary */2013-10-04T19:10:48Z<p><span class="autocomment">Summary</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Summary ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Summary ===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to determine the practicality of our solution, we are applying kinetic modeling to investigate how much time our engeneered ''E. coli'' cells will take to convert a certain amount of ammonia to nitrous oxide. For ammonia concentrations typically encountered in wastewater, our modelling shows that our transformed ''E. coli'' cells will be able to do this within less than <del class="diffchange diffchange-inline">10 </del>minutes.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to determine the practicality of our solution, we are applying kinetic modeling to investigate how much time our engeneered ''E. coli'' cells will take to convert a certain amount of ammonia to nitrous oxide. For ammonia concentrations typically encountered in wastewater, our modelling shows that our transformed ''E. coli'' cells will be able to do this within less than <ins class="diffchange diffchange-inline">15 </ins>minutes.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Methods ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Methods ===</div></td></tr>
</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=300520&oldid=prevVanessa: /* Results and Discussion */2013-10-04T19:08:53Z<p><span class="autocomment">Results and Discussion</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Results and Discussion ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Results and Discussion ===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Concentration versus time plots of ammonia and nitrous oxide are shown in Figures 1-2 for different enzyme concentrations. <del class="diffchange diffchange-inline">1000 enzymes per </del>cell <del class="diffchange diffchange-inline">seems </del>to <del class="diffchange diffchange-inline">be </del>a reasonable <del class="diffchange diffchange-inline">number and results </del>in converion times <del class="diffchange diffchange-inline">of less </del>than <del class="diffchange diffchange-inline">10 </del>minutes. The plots shown here are estimations based on literature research and will be corrected once we have experimental data.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Concentration versus time plots of ammonia and nitrous oxide are shown in Figures 1-2 for different enzyme concentrations. <ins class="diffchange diffchange-inline">There should at least be around 500 copies of each enzyme in the </ins>cell to <ins class="diffchange diffchange-inline">convert the ammonia in </ins>a reasonable <ins class="diffchange diffchange-inline">time. Especially </ins>in <ins class="diffchange diffchange-inline">Mutant 2 the conversion takes long but with 1000 enzymes per cell the </ins>converion times <ins class="diffchange diffchange-inline">is little more </ins>than <ins class="diffchange diffchange-inline">20 </ins>minutes <ins class="diffchange diffchange-inline">for an extreme concentration of 500 mg/L ammonia</ins>. The plots shown here are estimations based on literature research and will be corrected once we have experimental data.</div></td></tr>
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</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=300373&oldid=prevVanessa: /* Results and Discussion */2013-10-04T19:03:00Z<p><span class="autocomment">Results and Discussion</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 1: Kinetic modeling of Mutant 1. Nitrite concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Figure 1: Kinetic modeling of Mutant 1. Nitrite concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations<ins class="diffchange diffchange-inline">. Click on the pictures to see them larger</ins>.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Figure 2: Kinetic modeling of Mutant 2. Nitrous oxide concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Figure 2: Kinetic modeling of Mutant 2. Nitrous oxide concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations<ins class="diffchange diffchange-inline">. Click on the pictures to see them larger</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== References ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== References ===</div></td></tr>
</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=300345&oldid=prevVanessa: /* Methods */2013-10-04T19:01:51Z<p><span class="autocomment">Methods</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It is necessary to know or estimate the enzyme concentration if k<sub>cat</sub> values are used. Based on a paper we found that gives typical protein concentrations in ''E. coli'' [4] we chose to use four different enzyme concentrations in our model: 100, 500, 1000 and 100 000 enzymes per cell corresponding to low, medium, high and very high concentrations of enzyme. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It is necessary to know or estimate the enzyme concentration if k<sub>cat</sub> values are used. Based on a paper we found that gives typical protein concentrations in ''E. coli'' [4] we chose to use four different enzyme concentrations in our model: 100, 500, 1000 and 100 000 enzymes per cell corresponding to low, medium, high and very high concentrations of enzyme. </div></td></tr>
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</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=300220&oldid=prevVanessa: /* Results and Discussion */2013-10-04T18:56:12Z<p><span class="autocomment">Results and Discussion</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 2: Kinetic modeling of Mutant 2. Nitrous oxide concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 2: Kinetic modeling of Mutant 2. Nitrous oxide concentration over time based on kinetic parameters found in literature and for different enzyme and substrate (here NO<sub>2</sub>) concentrations.</div></td></tr>
</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=298946&oldid=prevNataliaP: /* Methods */2013-10-04T18:00:38Z<p><span class="autocomment">Methods</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in aquatic cultures, 10 mg/L for municipal waste water and more than 100 mg/L for</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in aquatic cultures, 10 mg/L for municipal waste water and more than 100 mg/L for</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>industrial waste water. So the concentrations we want to look at in our model are: 1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>industrial waste water. So the concentrations we want to look at in our model are: 1</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>mg/L (58.72μM), 10 mg/L (587.2μM), 100 mg/L(5.872 mM) and 500 mg/L (29.358</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>mg/L (58.72μM), 10 mg/L (587.2μM), 100 mg/L (5.872 mM) and 500 mg/L (29.358</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>mM) ammonia.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>mM) ammonia.</div></td></tr>
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</table>NataliaPhttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=298937&oldid=prevNataliaP: /* Methods */2013-10-04T18:00:16Z<p><span class="autocomment">Methods</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>weight of 472 kDa corresponding to 7.838 · 10<sup>−16</sup> mg. With this number we convert</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>weight of 472 kDa corresponding to 7.838 · 10<sup>−16</sup> mg. With this number we convert</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>the vmax to 3.116 · 10<sup>−14</sup> μmol min<sup>−1</sup> . Then using the Avogadro number we derive a</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>the vmax to 3.116 · 10<sup>−14</sup> μmol min<sup>−1</sup> . Then using the Avogadro number we derive a</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>k<<del class="diffchange diffchange-inline">sup</del>>cat</<del class="diffchange diffchange-inline">sup</del>> value of 18765 min<sup>−1</sup>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>k<<ins class="diffchange diffchange-inline">sub</ins>>cat</<ins class="diffchange diffchange-inline">sub</ins>> value of 18765 min<sup>−1</sup>.</div></td></tr>
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</table>NataliaPhttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=294317&oldid=prevVanessa: /* Methods */2013-10-04T14:51:51Z<p><span class="autocomment">Methods</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:1a.png|400px|center]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:1a.png|400px|center]]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">The </del>iGEM team from [https://2012.igem.org/Team:NYMU-Taipei Taipei in 2012] was <del class="diffchange diffchange-inline">using </del>Nir and Nos <del class="diffchange diffchange-inline">in their project as well and did some kinetic modeling based on literature research. To describe product formation by the enzymes they used the Michaelis-Menten approach</del>:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">We constructed a kinetic model of our transformants based on literature research. To describe product formation by the enzymes we used the Michaelis-Menten approach (also the </ins>iGEM team from [https://2012.igem.org/Team:NYMU-Taipei Taipei in 2012] was <ins class="diffchange diffchange-inline">looking into kinetic modelling of </ins>Nir and Nos<ins class="diffchange diffchange-inline">)</ins>:</div></td></tr>
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</table>Vanessahttp://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Kinetic_Model&diff=294032&oldid=prevVanessa: /* Scripts */2013-10-04T14:38:50Z<p><span class="autocomment">Scripts</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Scripts===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Scripts===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Model of Mutant 1</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[https://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/model_mutant1 </ins>Model of Mutant 1<ins class="diffchange diffchange-inline">]</ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Plot time series Mutant 1</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[https://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/plot_mutant1 </ins>Plot time series Mutant 1<ins class="diffchange diffchange-inline">]</ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Plot time series of Mutant 2</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[https://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/plot_mutant2 </ins>Plot time series of Mutant 2<ins class="diffchange diffchange-inline">]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:DTU-Denmark/Templates/EndPage}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:DTU-Denmark/Templates/EndPage}}</div></td></tr>
</table>Vanessa