http://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&feed=atom&action=historyTeam:Valencia/Modeling - Revision history2024-03-29T00:20:02ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=236602&oldid=prevAntropoteuthis at 03:29, 27 September 20122012-09-27T03:29:18Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of a further model on <b>export and consumption rates of sucrose</b>. This filter discards the settings where insufficient sucrose is exported to the culture to sustain the growth of the <i>A. fischeri</i> population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of a further model on <b>export and consumption rates of sucrose</b>. This filter discards the settings where insufficient sucrose is exported to the culture to sustain the growth of the <i>A. fischeri</i> population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The export of sucrose from our cyanobacteria (Ke) is: 2.07x10<sup>-11</sup> nmol/cell/s (units adapted from Ducat et al, 2012)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The export of sucrose from our cyanobacteria <ins class="diffchange diffchange-inline"><b></ins>(Ke)<ins class="diffchange diffchange-inline"></b> </ins>is: 2.07x10<sup>-11</sup> nmol/cell/s (units adapted from Ducat et al, 2012)</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The consumption of sucrose by <i>A. fischeri</i> (Kc) is: 0.00000150 nmol/cell/s (units adapted from oxygen consumption rates at maximum bioluminescent activity, at normal glycolytic route assumptions in aerobic conditions, from Makemson 1985).<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The consumption of sucrose by <i>A. fischeri</i<ins class="diffchange diffchange-inline">> <b</ins>>(Kc)<ins class="diffchange diffchange-inline"></b> </ins>is: 0.00000150 nmol/cell/s (units adapted from oxygen consumption rates at maximum bioluminescent activity, at normal glycolytic route assumptions in aerobic conditions, from Makemson 1985).<br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<i>A. fischeri</i> cell density)·(biolammp module volume) ; where only dSucrose (> or =) 0nM/s are accepted.<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<i>A. fischeri</i> cell density)·(biolammp module volume)<ins class="diffchange diffchange-inline"></b> </ins>; where only dSucrose (> or =) 0nM/s are accepted.<br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation (in a range between 0.001-10l) and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation (in a range between 0.001-10l) and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, <b>so that the energy budget is not a shortfall</b>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, <b>so that the energy budget is not a shortfall</b><ins class="diffchange diffchange-inline">.<br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The results of our model were <b>non-unimodal</b>. This means that we cannot rationally present in short the outcome of multivariate solutions we obtained as min/max limits for each variable. Our high resolution discrete outcome is an enormous multidimensional permutation. If we lower the resolution for a presentable report, the interpolation error is too high. We look forward to rationalize this by the means of analytic resolution of the differential equations system into a simpler function applicable to an easy assessment of the design parameters for the bioreactor</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><b>References</b></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><b>References</b></div></td></tr>
</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=235739&oldid=prevAntropoteuthis at 03:15, 27 September 20122012-09-27T03:15:29Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b></h2></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. 2010 and 2011. and recently adapted for <i>Synechococcus sp.</i>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In first place we adapted a metabolic model of <ins class="diffchange diffchange-inline"><i></ins>Synechococcus<ins class="diffchange diffchange-inline"></i> </ins>with the functions we included with our constructs. The model is an algorithm applied to a <ins class="diffchange diffchange-inline"><b></ins>metabolic network<ins class="diffchange diffchange-inline"></b> </ins>of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. 2010 and 2011. and recently adapted for <i>Synechococcus sp.</i>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.<ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The <ins class="diffchange diffchange-inline"><b></ins>reactions of bioluminescence<ins class="diffchange diffchange-inline"></b> </ins>expressed by the LuxAB construct were introduced <ins class="diffchange diffchange-inline">into the network </ins>as follows:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>May be noted that the luciferin (FMNH<sub>2</sub>) is reduced (regenerated) by the reaction FMN_red, which is not naturally present in <i>Synechococcus</i>, but which we added to our model to ensure light production in a persistent way. As a future aim, we plan to include luciferin regeneration gene cassettes to this wildtype. If we didn’t insert this adjustment, the model would calculate flow 0, as luminescence would extinguish in a few seconds with the scarce FMNH<sub>2</sub>, so the model has no solutions for infinite time flow. This helped us to notice (and then assured from bibliographic support) this handicap of cyanobacteria as light producers. This partly triggered the reorientation of our research towards the bispecific coculture idea. <br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>May be noted that the <ins class="diffchange diffchange-inline"><b></ins>luciferin<ins class="diffchange diffchange-inline"></b> </ins>(FMNH<sub>2</sub>) is reduced (regenerated) by the reaction FMN_red, which <ins class="diffchange diffchange-inline"><b></ins>is not naturally present in <i>Synechococcus</i<ins class="diffchange diffchange-inline">></b</ins>>, but which we added to our model to ensure light production in a persistent way. As a future aim, we plan to include luciferin regeneration gene cassettes to this wildtype. If we didn’t insert this adjustment, the model would calculate flow 0, as luminescence would extinguish in a few seconds with the scarce FMNH<sub>2</sub>, so the model has no solutions for infinite time flow. This helped us to notice (and then assured from bibliographic support) this handicap of cyanobacteria as light producers. This partly triggered the reorientation of our research towards the bispecific coculture idea. <ins class="diffchange diffchange-inline"><br></ins><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Moreover, we programmed bioluminescence functions with 3 types of fatty acid (8, 14 and 16 carbon chain length) which are most abundant in the cyanobacterial cell so could be used as ‘fuel’ with greatest probability, and lied between the operational chain-lenght limits for the luciferase.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Moreover, we programmed bioluminescence functions with <ins class="diffchange diffchange-inline"><b></ins>3 types of fatty acid<ins class="diffchange diffchange-inline"></b> </ins>(8, 14 and 16 carbon chain length) which are most abundant in the cyanobacterial cell so could be used as ‘fuel’ with greatest probability, and lied between the operational chain-lenght limits for the luciferase.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This yielded results as we optimized the model’s algorithm to maximize light production, by adjusting the flow rates of the other reaction of the metabolism under certain restrictions which make it a biologically reasonable maximum (principle of operation for every result we obtained from the algorithm)value of 22509mmol/g DCW/h, equivalent to 6.48x10<sup>8</sup>photons/cell/s. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This yielded results as we optimized the model’s algorithm to maximize light production, by adjusting the flow rates of the other reaction of the metabolism under certain restrictions which make it a biologically reasonable maximum (principle of operation for every result we obtained from the algorithm)value of 22509mmol/g DCW/h, equivalent to 6.48x10<sup>8</sup>photons/cell/s. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In second place, we adapted the wildtype model with the sucrose export induced by the expression of the cscB transporter gene included in the transformed strain from Harvard. Here we modeled the maximum values of sucrose export for 2 different growth restrictions, 0.09mmol Biomass/gDCW*/h (a value near to the maximum growth, similar to an averaged exponential phase culture) and 1x10<sup>-6</sup>mmol Biomass/gDCW/h (a negligible growth value which will keep all the vital reactions working but not divert a significant amount of fixed carbon to increasing biomass, as in an averaged dynamic equilibrium of a stationary phase culture).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In second place, we adapted the wildtype model with the <ins class="diffchange diffchange-inline"><b></ins>sucrose export<ins class="diffchange diffchange-inline"></b> </ins>induced by the expression of the <ins class="diffchange diffchange-inline"><b></ins>cscB transporter<ins class="diffchange diffchange-inline"></b> </ins>gene included in the transformed strain from Harvard. Here we modeled the maximum values of sucrose export for 2 different growth restrictions, 0.09mmol Biomass/gDCW*/h (a value near to the maximum growth, similar to an averaged exponential phase culture) and 1x10<sup>-6</sup>mmol Biomass/gDCW/h (a negligible growth value which will keep all the vital reactions working but not divert a significant amount of fixed carbon to increasing biomass, as in an averaged dynamic equilibrium of a stationary phase culture).</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Maximum export values yielded:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>Maximum export values yielded:<ins class="diffchange diffchange-inline"></b></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br> With minimal growth constraint: 0.3075mmol/g DCW/h</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br> With minimal growth constraint: 0.3075mmol/g DCW/h</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br> With maximal growth constraint: 0.027mmol/g DCW/h</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br> With maximal growth constraint: 0.027mmol/g DCW/h</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>As we planned to transform this cscB strain to express luxI, the protein that synthesizes AHL (autoinducer molecule), we introduced the reaction in the model as follows:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>As we planned to transform this cscB strain to express luxI, the protein that synthesizes <ins class="diffchange diffchange-inline"><b></ins>AHL (autoinducer molecule)<ins class="diffchange diffchange-inline"></b></ins>, we introduced the reaction in the model as follows:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>AHL: Hexanoyl-(acyl carrier protein) + S-adenosyl-L-methionine -> AHL + S-methyl-5'-thioadenosine + acyl-carrier protein </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>AHL: Hexanoyl-(acyl carrier protein) + S-adenosyl-L-methionine -> AHL + S-methyl-5'-thioadenosine + acyl-carrier protein </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">As we know, this </del>biomachine has 2 functions inserted, for which we have an interest of flow maximization. Unfortunately, export of sucrose and export of AHL, both carbon based molecules, sets a biochemical competition for carbon redirection. Therefore we came out with 3 modeled outputs: Parabolic curve of maximization of AHL+Sucrose (fig a), and the linear functions of AHL vs. sucrose export in both growth scenarios (fig b, c). All units are expressed in mmol/g DCW/h.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Our </ins>biomachine has 2 <ins class="diffchange diffchange-inline">synthetic </ins>functions inserted, for which we have an interest of flow maximization. Unfortunately, export of sucrose and export of AHL, both carbon based molecules, sets a <ins class="diffchange diffchange-inline"><b></ins>biochemical competition for carbon redirection<ins class="diffchange diffchange-inline"></b></ins>. Therefore we came out with 3 modeled outputs: Parabolic curve of maximization of AHL+Sucrose (fig a), and the linear functions of AHL vs. sucrose export in both growth scenarios (fig b, c). All units are expressed in mmol/g DCW/h.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We just require 1 or 2 molecules per cell of <i>Aliivibrio fischeri</i> to induce biolumminescence (Kaplan & Greenberg, 1985). In Fig c we can see the how small sucrose export values, such as our real fluxes affect very little the export of AHL. This was tested on a maximal growth restriction, as the forward idea is to keep the bioreactor in a continuous exponential phase, which corresponds to a flow of 0.00974 mmol/g DCW/h . This imposes a constant flux of sucrose and AHL, which is optimum for our system. The answer of the model to this constant export of sucrose is a flow of 0.015mmol/g DCW/h, which is a pretty high value. As you will see later, this value of AHL export is fundamental for the development of our next model.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We just require 1 or 2 molecules per cell of <i>Aliivibrio fischeri</i> to induce biolumminescence (Kaplan & Greenberg, 1985). In Fig c we can see the how small sucrose export values, such as our real fluxes affect very little the export of AHL. This was tested on a maximal growth restriction, as the forward idea is to keep the bioreactor in a continuous exponential phase, which corresponds to a flow of 0.00974 mmol/g DCW/h . This imposes a constant flux of sucrose and AHL, which is optimum for our system. The answer of the model to this constant export of sucrose is a flow of 0.015mmol <ins class="diffchange diffchange-inline">AHL</ins>/g DCW/h, which is a pretty high value. As you will see later, this value of AHL export is fundamental for the development of our next model.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2005).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2005).</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2><b>Synergic model:</b></h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2><b>Synergic model:</b></h2></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We achieved our main goal of <ins class="diffchange diffchange-inline"><b></ins>integrating and connecting all the system into a single model<ins class="diffchange diffchange-inline"></b> </ins>capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001 (source of the following figures), a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001 (source of the following figures), a hybrid model of 9 differential equations which predicts the behavior of the whole <ins class="diffchange diffchange-inline"><i>quorum sensing</i> </ins>regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a href="https://static.igem.org/mediawiki/2012/4/44/Pie-de-synergic3.png"><img src="https://static.igem.org/mediawiki/2012/4/44/Pie-de-synergic3.png" width="800" height="73"></a><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a href="https://static.igem.org/mediawiki/2012/4/44/Pie-de-synergic3.png"><img src="https://static.igem.org/mediawiki/2012/4/44/Pie-de-synergic3.png" width="800" height="73"></a><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></center></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <i>A. fischeri</i> population <del class="diffchange diffchange-inline">to </del>a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of <i>S. elongatus</i> and the extra volume from tubing and pumping systems where the medium flows.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <i>A. fischeri</i> population <ins class="diffchange diffchange-inline">into </ins>a <ins class="diffchange diffchange-inline"><b></ins>constrained volume<ins class="diffchange diffchange-inline"></b> </ins>(biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL)<ins class="diffchange diffchange-inline">, as the population cannot cross the membrane to colonize the whole of the medium</ins>. <ins class="diffchange diffchange-inline"><br></ins>Such <ins class="diffchange diffchange-inline">'dilution </ins>volume<ins class="diffchange diffchange-inline">' </ins>represents the annexing of the photobioreactor of <i>S. elongatus</i> and the extra volume from tubing and pumping systems where the medium flows <ins class="diffchange diffchange-inline">(50ml)</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We gave the system a new input of AHL derived from the <i>S. elongatus</i> population, which has a Ks (constant rate of AHL production/cell resultant from our modified <i>Synechococcus</i> metabolic network model) of 2.38x10<sup>-7</sup> nmol AHL /cell/s, multiplying the number of cells (culture density x culture volume – of the photobioreactor compartment). The model still counts with the AHL produced by the <i>A. fischeri</i> population, and the degradation half-life in the cells. As we said above, the diffusion speed of AHL is considered instantaneous (as the rate’s scale is very high compared with other variables, such as cell growth or gene expression).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We gave the system a new input of AHL derived from the <i>S. elongatus</i> population, which has a Ks (constant rate of AHL production/cell resultant from our modified <i>Synechococcus</i> metabolic network model) of <ins class="diffchange diffchange-inline"><b></ins>2.38x10<sup>-7</sup> nmol AHL /cell/s<ins class="diffchange diffchange-inline"></b></ins>, multiplying the number of cells (culture density x culture volume – of the photobioreactor compartment). The model still counts with the AHL produced by the <i>A. fischeri</i> population, and the degradation half-life in the cells. As we said above, the <ins class="diffchange diffchange-inline"><b></ins>diffusion speed of AHL is considered instantaneous<ins class="diffchange diffchange-inline"></b> </ins>(as the rate’s scale is very high compared with other variables, such as cell growth or gene expression).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The application of this model is focused in the optimization <del class="diffchange diffchange-inline">in </del>the design of the future bioreactor which may contain the system. We are looking for the values of compartment volumes, relative volume, population densities and total volume which can assure a diel control of luminescence (in 12h cycles, considering export rates and the AHL half-life of 10h) by the light induced activity of our <i>S. elongatus</i> biomachine; and, within those values, the settings with maximum luminescence values (values higher than 1000nM luciferase in the <i>A. fischeri</i> module volume).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The application of this model is focused in the <ins class="diffchange diffchange-inline"><b></ins>optimization <ins class="diffchange diffchange-inline">of </ins>the design of the future bioreactor<ins class="diffchange diffchange-inline"></b> </ins>which may contain the system. We are looking for the values of compartment volumes, relative volume, population densities and total volume which can assure a <ins class="diffchange diffchange-inline"><b></ins>diel control of luminescence<ins class="diffchange diffchange-inline"></b> </ins>(in 12h cycles, considering export rates and the AHL <ins class="diffchange diffchange-inline">degradation </ins>half-life of 10h) by the light induced activity of our <i>S. elongatus</i> biomachine; and, within those values, the settings with <ins class="diffchange diffchange-inline"><b></ins>maximum luminescence values<ins class="diffchange diffchange-inline"></b> </ins>(values higher than 1000nM luciferase in the <i>A. fischeri</i> module volume).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of <del class="diffchange diffchange-inline">our </del>further model on export and consumption rates of sucrose. This filter <del class="diffchange diffchange-inline">aims to discard </del>the settings where insufficient sucrose is exported to the culture to sustain the growth of the <i>A. fischeri</i> population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of <ins class="diffchange diffchange-inline">a </ins>further model on <ins class="diffchange diffchange-inline"><b></ins>export and consumption rates of sucrose<ins class="diffchange diffchange-inline"></b></ins>. This filter <ins class="diffchange diffchange-inline">discards </ins>the settings where insufficient sucrose is exported to the culture to sustain the growth of the <i>A. fischeri</i> population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The export of sucrose from our cyanobacteria (Ke) is: 2.07x10<sup>-11</sup> nmol/cell/s (units adapted from Ducat et al, 2012)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The export of sucrose from our cyanobacteria (Ke) is: 2.07x10<sup>-11</sup> nmol/cell/s (units adapted from Ducat et al, 2012)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The consumption of sucrose by <i>A. fischeri</i> (Kc) is: 0.00000150 nmol/cell/s (units adapted from oxygen consumption rates at maximum bioluminescent activity, at normal glycolytic route assumptions in aerobic conditions, from Makemson 1985).<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The consumption of sucrose by <i>A. fischeri</i> (Kc) is: 0.00000150 nmol/cell/s (units adapted from oxygen consumption rates at maximum bioluminescent activity, at normal glycolytic route assumptions in aerobic conditions, from Makemson 1985).<br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<i>A. fischeri</i> cell density)·(biolammp module volume)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<i>A. fischeri</i> cell density)·(biolammp module volume) <ins class="diffchange diffchange-inline">; where only dSucrose (> or =) 0nM/s are accepted.</ins><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation (in a range between 0.001-10l) and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation (in a range between 0.001-10l) and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, <ins class="diffchange diffchange-inline"><b></ins>so that the energy budget is not a shortfall<ins class="diffchange diffchange-inline"></b></ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><b>References</b></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><b>References</b></div></td></tr>
</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=232068&oldid=prevAntropoteuthis at 02:04, 27 September 20122012-09-27T02:04:34Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001 <ins class="diffchange diffchange-inline">(source of the following figures)</ins>, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td></tr>
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</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=229812&oldid=prevGonzalo at 01:22, 27 September 20122012-09-27T01:22:44Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a href="https://static.igem.org/mediawiki/2012/7/76/Synergic2.png"><img src="https://static.igem.org/mediawiki/2012/7/76/Synergic2.png" width="750" height="390"></a><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a href="https://static.igem.org/mediawiki/2012/7/76/Synergic2.png"><img src="https://static.igem.org/mediawiki/2012/7/76/Synergic2.png" width="750" height="390"></a><br></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">center></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">a href="https:</ins>/<ins class="diffchange diffchange-inline">/static</ins>.<ins class="diffchange diffchange-inline">igem</ins>.<ins class="diffchange diffchange-inline">org</ins>/<ins class="diffchange diffchange-inline">mediawiki/2012/f/fc/Pie-de-synergic2</ins>.<ins class="diffchange diffchange-inline">PNG"></ins><<ins class="diffchange diffchange-inline">img src="https://static.igem.org/mediawiki/2012/f/fc/Pie-de-synergic2.PNG"</ins>><<ins class="diffchange diffchange-inline">/a</ins>><<ins class="diffchange diffchange-inline">br</ins>></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Figure 2</del>. <del class="diffchange diffchange-inline">Set of differential equations used as base model for the regulation of <i>A</del>. <del class="diffchange diffchange-inline">fischeri<</del>/<del class="diffchange diffchange-inline">i> bioluminescence in an isolated culture</del>.<<del class="diffchange diffchange-inline">br</del>><<del class="diffchange diffchange-inline">br</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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</table>Gonzalohttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=229237&oldid=prevGonzalo at 01:12, 27 September 20122012-09-27T01:12:13Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. 2010 and 2011. and recently adapted for <i>Synechococcus sp.</i>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><h2></ins><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b><ins class="diffchange diffchange-inline"></h2></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. 2010 and 2011. and recently adapted for <i>Synechococcus sp.</i>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2005).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2005).</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><h2></ins><b>Synergic model:</b><ins class="diffchange diffchange-inline"></h2></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">(</del>Hybrid<del class="diffchange diffchange-inline">)</del><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><center></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">(synergic</del>-vibrio1<del class="diffchange diffchange-inline">)</del><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2012/e/ed/</ins>Hybrid<ins class="diffchange diffchange-inline">.png"><img src="https://static.igem.org/mediawiki/2012/e/ed/Hybrid.png" width="400" height="195"></a></ins><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">(synergic2)</del><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2012/4/48/Synergic</ins>-vibrio1<ins class="diffchange diffchange-inline">.png"><img src="https://static.igem.org/mediawiki/2012/4/48/Synergic-vibrio1.png" width="800" height="397"></a></ins><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">(synergic2</del>.2<del class="diffchange diffchange-inline">)</del><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2012/7/76/Synergic2.png"><img src="https://static.igem.org/mediawiki/2012/7/76/Synergic2.png" width="750" height="390"></a></ins><br></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2012/a/ad/Synergic2</ins>.2<ins class="diffchange diffchange-inline">.png"><img src="https://static.igem.org/mediawiki/2012/a/ad/Synergic2.2.png" width="420" height="297"></a></ins><br<ins class="diffchange diffchange-inline">><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"></center</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 2. Set of differential equations used as base model for the regulation of <i>A. fischeri</i> bioluminescence in an isolated culture.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Figure 2. Set of differential equations used as base model for the regulation of <i>A. fischeri</i> bioluminescence in an isolated culture.<br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><center></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">(synergic3)</del><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2012/8/89/Synergic3.png"><img src="https://static.igem.org/mediawiki/2012/8/89/Synergic3.png" width="400" height="405"></a></ins><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">(pie</del>-de-synergic3<del class="diffchange diffchange-inline">)</del><br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><a href="https://static.igem.org/mediawiki/2012/4/44/Pie</ins>-de-synergic3<ins class="diffchange diffchange-inline">.png"><img src="https://static.igem.org/mediawiki/2012/4/44/Pie-de-synergic3.png" width="800" height="73"></a></ins><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"></center></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <i>A. fischeri</i> population to a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of <i>S. elongatus</i> and the extra volume from tubing and pumping systems where the medium flows.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <i>A. fischeri</i> population to a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of <i>S. elongatus</i> and the extra volume from tubing and pumping systems where the medium flows.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation (in a range between 0.001-10l) and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation (in a range between 0.001-10l) and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br><br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><b>References</b></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><hr><hr></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Belta, C., Schug, J., Dang, T., Kumar, V., Pappas, G.J., Rubin, H., Dunlap, P. 2001. Stability and reachability analysis of a hybrid model of luminescence in the marine bacterium Vibrio fischeri. Decis. In Cont., 1, 869-874.<br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Belta, C., Schug, J., Dang, T., Kumar, V., Pappas, G.J., Rubin, H., Dunlap, P. 2001. Stability and reachability analysis of a hybrid model of luminescence in the marine bacterium Vibrio fischeri. Decis. In Cont., 1, 869-874.<br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Ducat, D. C., Avelar-Rivas, A. J., Way, J. C. & Silver, P. A. (2012) Rerouting carbon flux to enhance photosynthetic productivity. Applied and Environmental Microbiology, 78(8):2660–2668. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Ducat, D. C., Avelar-Rivas, A. J., Way, J. C. & Silver, P. A. (2012) Rerouting carbon flux to enhance photosynthetic productivity. Applied and Environmental Microbiology, 78(8):2660–2668. <br><br></div></td></tr>
</table>Gonzalohttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=226856&oldid=prevAntropoteuthis at 00:25, 27 September 20122012-09-27T00:25:48Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 00:25, 27 September 2012</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We just require 1 or 2 molecules per cell of <i>Aliivibrio fischeri</i> to induce biolumminescence (Kaplan & Greenberg, 1985). In Fig c we can see the how small sucrose export values, such as our real fluxes affect very little the export of AHL. This was tested on a maximal growth restriction, as the forward idea is to keep the bioreactor in a continuous exponential phase, which corresponds to a flow of 0.00974 mmol/g DCW/h . This imposes a constant flux of sucrose and AHL, which is optimum for our system. The answer of the model to this constant export of sucrose is a flow of 0.015mmol/g DCW/h, which is a pretty high value. As you will see later, this value of AHL export is fundamental for the development of our next model.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We just require 1 or 2 molecules per cell of <i>Aliivibrio fischeri</i> to induce biolumminescence (Kaplan & Greenberg, 1985). In Fig c we can see the how small sucrose export values, such as our real fluxes affect very little the export of AHL. This was tested on a maximal growth restriction, as the forward idea is to keep the bioreactor in a continuous exponential phase, which corresponds to a flow of 0.00974 mmol/g DCW/h . This imposes a constant flux of sucrose and AHL, which is optimum for our system. The answer of the model to this constant export of sucrose is a flow of 0.015mmol/g DCW/h, which is a pretty high value. As you will see later, this value of AHL export is fundamental for the development of our next model.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. <del class="diffchange diffchange-inline">2004</del>).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. <ins class="diffchange diffchange-inline">2005</ins>).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <i>S. elongatus</i> and <i>A. fischeri</i> modules.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Belta, C., Schug, J., Dang, T., Kumar, V., Pappas, G.J., Rubin, H., Dunlap, P. 2001. Stability and reachability analysis of a hybrid model of luminescence in the marine bacterium Vibrio fischeri. Decis. In Cont., 1, 869-874.<br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Ducat, D. C., Avelar-Rivas, A. J., Way, J. C. & Silver, P. A. (2012) Rerouting carbon flux to enhance photosynthetic productivity. Applied and Environmental Microbiology, 78(8):2660–2668. <br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Kaplan H., Greenberg, E.B. 2004. Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system. Journ. Of Bacteriol. 1210-1214.<br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Makemson J., 1985. Luciferase-dependent oxygen consumption by bioluminescent Vibrios. Amer. Soc. for Microb.165(2): 465-466.<br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Montagud, A., Navarro E., Fernández de Córdoba, P., Urchueguía, J.F., Patil, K.R. (2010). Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Syst. Biol. 4:156.<br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Montagud, A., Zelezniak, A., Navarro E., Fernández de Córdoba, P., Urchueguía, J.F., Patil, K.R. (2011). Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803. Biotechnol. J. 6(3):330-42.<br><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Rosales, N., Ortega, J., Mora, R., Morales, E. 2005. Influence of salinity on the growth and biochemical composition of the cyanobacterium Synechococcus sp. Ciencias Marinas, 31(2): 349–355.<br><br></ins></div></td></tr>
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</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=226577&oldid=prevAntropoteuthis at 00:21, 27 September 20122012-09-27T00:21:05Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. <del class="diffchange diffchange-inline">2009 </del>and 2011. and recently adapted for <i>Synechococcus sp.</i>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. <ins class="diffchange diffchange-inline">2010 </ins>and 2011. and recently adapted for <i>Synechococcus sp.</i>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td></tr>
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</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=223674&oldid=prevAntropoteuthis at 23:24, 26 September 20122012-09-26T23:24:39Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. 2009 and 2011. and recently adapted for Synechococcus sp., where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <i>Synechococcus elongatus</i>:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <i>Synechocystis sp.</i> by Montagud et al. 2009 and 2011. and recently adapted for <ins class="diffchange diffchange-inline"><i></ins>Synechococcus sp.<ins class="diffchange diffchange-inline"></i></ins>, where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype <i>S. elongatus</i> with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>May be noted that the luciferin (FMNH<sub>2</sub>) is reduced (regenerated) by the reaction FMN_red, which is not naturally present in Synechococcus, but which we added to our model to ensure light production in a persistent way. As a future aim, we plan to include luciferin regeneration gene cassettes to this wildtype. If we didn’t insert this adjustment, the model would calculate flow 0, as luminescence would extinguish in a few seconds with the scarce FMNH<sub>2</sub>, so the model has no solutions for infinite time flow. This helped us to notice (and then assured from bibliographic support) this handicap of cyanobacteria as light producers. This partly triggered the reorientation of our research towards the bispecific coculture idea. <br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>May be noted that the luciferin (FMNH<sub>2</sub>) is reduced (regenerated) by the reaction FMN_red, which is not naturally present in <ins class="diffchange diffchange-inline"><i></ins>Synechococcus<ins class="diffchange diffchange-inline"></i></ins>, but which we added to our model to ensure light production in a persistent way. As a future aim, we plan to include luciferin regeneration gene cassettes to this wildtype. If we didn’t insert this adjustment, the model would calculate flow 0, as luminescence would extinguish in a few seconds with the scarce FMNH<sub>2</sub>, so the model has no solutions for infinite time flow. This helped us to notice (and then assured from bibliographic support) this handicap of cyanobacteria as light producers. This partly triggered the reorientation of our research towards the bispecific coculture idea. <br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Moreover, we programmed bioluminescence functions with 3 types of fatty acid (8, 14 and 16 carbon chain length) which are most abundant in the cyanobacterial cell so could be used as ‘fuel’ with greatest probability, and lied between the operational chain-lenght limits for the luciferase.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Moreover, we programmed bioluminescence functions with 3 types of fatty acid (8, 14 and 16 carbon chain length) which are most abundant in the cyanobacterial cell so could be used as ‘fuel’ with greatest probability, and lied between the operational chain-lenght limits for the luciferase.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br> With maximal growth constraint: 0.027mmol/g DCW/h</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br> With maximal growth constraint: 0.027mmol/g DCW/h</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>As we planned to transform this cscB strain to express luxI, the protein that synthesizes AHL (<del class="diffchange diffchange-inline">Vibrio </del>autoinducer molecule), we introduced the reaction in the model as follows:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>As we planned to transform this cscB strain to express luxI, the protein that synthesizes AHL (autoinducer molecule), we introduced the reaction in the model as follows:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">ahl</del>: Hexanoyl-(acyl carrier protein) + S-adenosyl-L-methionine -> <del class="diffchange diffchange-inline">ahl </del>+ S-methyl-5'-thioadenosine + <del class="diffchange diffchange-inline">an </del>acyl-carrier protein </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">AHL</ins>: Hexanoyl-(acyl carrier protein) + S-adenosyl-L-methionine -> <ins class="diffchange diffchange-inline">AHL </ins>+ S-methyl-5'-thioadenosine + acyl-carrier protein </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As we know, this biomachine has 2 functions inserted, for which we have an interest of flow maximization. Unfortunately, export of sucrose and export of AHL, both carbon based molecules, sets a biochemical competition for carbon redirection. Therefore we came out with 3 modeled outputs: Parabolic curve of maximization of AHL+Sucrose (fig a), and the linear functions of AHL vs. sucrose export in both growth scenarios (fig b, c). All units are expressed in mmol/g DCW/h.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As we know, this biomachine has 2 functions inserted, for which we have an interest of flow maximization. Unfortunately, export of sucrose and export of AHL, both carbon based molecules, sets a biochemical competition for carbon redirection. Therefore we came out with 3 modeled outputs: Parabolic curve of maximization of AHL+Sucrose (fig a), and the linear functions of AHL vs. sucrose export in both growth scenarios (fig b, c). All units are expressed in mmol/g DCW/h.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2004).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2004).</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <del class="diffchange diffchange-inline">Synechococcus </del>and <i>A. fischeri</i> modules.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both <ins class="diffchange diffchange-inline"><i>S. elongatus</i> </ins>and <i>A. fischeri</i> modules.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <i>A. fischeri</i>.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <i>A. fischeri</i> population to a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of <del class="diffchange diffchange-inline">Synechococcus </del>and the extra volume from tubing and pumping systems where the medium flows.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <i>A. fischeri</i> population to a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of <ins class="diffchange diffchange-inline"><i>S. elongatus</i> </ins>and the extra volume from tubing and pumping systems where the medium flows.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We gave the system a new input of AHL derived from the <del class="diffchange diffchange-inline">Synechococcus </del>population, which has a Ks (constant rate of AHL production/cell resultant from our modified <del class="diffchange diffchange-inline">Syenchococcus </del>metabolic network model) of 2.38x10<sup>-7</sup> nmol AHL /cell/s, multiplying the number of cells (culture density x culture volume – of the photobioreactor compartment). The model still counts with the AHL produced by the <i>A. fischeri</i> population, and the degradation half-life in the cells. As we said above, the diffusion speed of AHL is considered instantaneous (as the rate’s scale is very high compared with other variables, such as cell growth or gene expression).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We gave the system a new input of AHL derived from the <ins class="diffchange diffchange-inline"><i>S. elongatus</i> </ins>population, which has a Ks (constant rate of AHL production/cell resultant from our modified <ins class="diffchange diffchange-inline"><i>Synechococcus</i> </ins>metabolic network model) of 2.38x10<sup>-7</sup> nmol AHL /cell/s, multiplying the number of cells (culture density x culture volume – of the photobioreactor compartment). The model still counts with the AHL produced by the <i>A. fischeri</i> population, and the degradation half-life in the cells. As we said above, the diffusion speed of AHL is considered instantaneous (as the rate’s scale is very high compared with other variables, such as cell growth or gene expression).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The application of this model is focused in the optimization in the design of the future bioreactor which may contain the system. We are looking for the values of compartment volumes, relative volume, population densities and total volume which can assure a diel control of luminescence (in 12h cycles, considering export rates and the AHL half-life of 10h) by the light induced activity of our <del class="diffchange diffchange-inline">Synechococcus </del>biomachine; and, within those values, the settings with maximum luminescence values.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The application of this model is focused in the optimization in the design of the future bioreactor which may contain the system. We are looking for the values of compartment volumes, relative volume, population densities and total volume which can assure a diel control of luminescence (in 12h cycles, considering export rates and the AHL half-life of 10h) by the light induced activity of our <ins class="diffchange diffchange-inline"><i>S. elongatus</i> </ins>biomachine; and, within those values, the settings with maximum luminescence values <ins class="diffchange diffchange-inline">(values higher than 1000nM luciferase in the <i>A. fischeri</i> module volume)</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of our further model on export and consumption rates of sucrose. This filter aims to discard the settings where insufficient sucrose is exported to the culture to sustain the growth of the <i>A. fischeri</i> population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of our further model on export and consumption rates of sucrose. This filter aims to discard the settings where insufficient sucrose is exported to the culture to sustain the growth of the <i>A. fischeri</i> population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<i>A. fischeri</i> cell density)·(biolammp module volume)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<i>A. fischeri</i> cell density)·(biolammp module volume)</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (<del class="diffchange diffchange-inline">cell densities </del>in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation <ins class="diffchange diffchange-inline">(in a range between 0.001-10l) </ins>and the cell densities for S. elongatus cscB and for <i>A. fischeri</i> (in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td></tr>
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</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=222784&oldid=prevAntropoteuthis at 23:07, 26 September 20122012-09-26T23:07:10Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <del class="diffchange diffchange-inline">S. </del>elongatus:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for Synechocystis sp. by Montagud et al. 2009 and 2011. and recently adapted for Synechococcus sp.,where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in <ins class="diffchange diffchange-inline"><i>Synechococcus </ins>elongatus<ins class="diffchange diffchange-inline"></i></ins>:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for <ins class="diffchange diffchange-inline"><i></ins>Synechocystis sp.<ins class="diffchange diffchange-inline"></i> </ins>by Montagud et al. 2009 and 2011. and recently adapted for Synechococcus sp., where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We transformed a wildtype <del class="diffchange diffchange-inline">Synechococcus </del>elongatus with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We transformed a wildtype <ins class="diffchange diffchange-inline"><i>S. </ins>elongatus<ins class="diffchange diffchange-inline"></i> </ins>with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This yielded results as we optimized the model’s algorithm to maximize light production, by adjusting the flow rates of the other reaction of the metabolism under certain restrictions which make it a biologically reasonable maximum (principle of operation for every result we obtained from the algorithm)value of 22509mmol/g DCW/h, equivalent to 6.48x10<sup>8</sup>photons/cell/s. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This yielded results as we optimized the model’s algorithm to maximize light production, by adjusting the flow rates of the other reaction of the metabolism under certain restrictions which make it a biologically reasonable maximum (principle of operation for every result we obtained from the algorithm)value of 22509mmol/g DCW/h, equivalent to 6.48x10<sup>8</sup>photons/cell/s. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In second place, we adapted the wildtype model with the sucrose export induced by the expression of the cscB transporter gene included in the transformed strain from Harvard. Here we modeled the maximum values of sucrose export for 2 different growth restrictions, 0.09mmol Biomass/gDCW*/h (a value near to the maximum growth, similar to an averaged exponential phase culture) and 1x10<sup>-6</sup>mmol Biomass/gDCW/h (a negligible growth value which will keep all the vital reactions working but not divert a significant amount of fixed carbon to increasing biomass, as in an averaged dynamic equilibrium of a stationary phase culture).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In second place, we adapted the wildtype model with the sucrose export induced by the expression of the cscB transporter gene included in the transformed strain from Harvard. Here we modeled the maximum values of sucrose export for 2 different growth restrictions, 0.09mmol Biomass/gDCW*/h (a value near to the maximum growth, similar to an averaged exponential phase culture) and 1x10<sup>-6</sup>mmol Biomass/gDCW/h (a negligible growth value which will keep all the vital reactions working but not divert a significant amount of fixed carbon to increasing biomass, as in an averaged dynamic equilibrium of a stationary phase culture).</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We just require 1 or 2 molecules per cell of <i>Aliivibrio fischeri</i> to induce <del class="diffchange diffchange-inline">the system </del>(Kaplan & Greenberg, 1985). In Fig c we can see the how small sucrose export values, such as our real fluxes affect very little the export of AHL. This was tested on a maximal growth restriction, as the forward idea is to keep the bioreactor in a continuous exponential phase, which corresponds to a flow of 0.00974 mmol/g DCW/h . This imposes a constant flux of sucrose and AHL, which is optimum for our system. The answer of the model to this constant export of sucrose is a flow of 0.015mmol/g DCW/h, which is a pretty high value. As you will see later, this value of AHL export is fundamental for the development of our next model.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We just require 1 or 2 molecules per cell of <i>Aliivibrio fischeri</i> to induce <ins class="diffchange diffchange-inline">biolumminescence </ins>(Kaplan & Greenberg, 1985). In Fig c we can see the how small sucrose export values, such as our real fluxes affect very little the export of AHL. This was tested on a maximal growth restriction, as the forward idea is to keep the bioreactor in a continuous exponential phase, which corresponds to a flow of 0.00974 mmol/g DCW/h . This imposes a constant flux of sucrose and AHL, which is optimum for our system. The answer of the model to this constant export of sucrose is a flow of 0.015mmol/g DCW/h, which is a pretty high value. As you will see later, this value of AHL export is fundamental for the development of our next model.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2004).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>-*: DCW=Dry Cell Weight, where an average <i>Synechococcus</i> cell has a dry weight of 3.87ng (Rosales et al. 2004).</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both Synechococcus and <del class="diffchange diffchange-inline">Aliivibrio </del>modules.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Synergic model:</b> We achieved our main goal of integrating and connecting all the system into a single model capable of predicting the luminescence of the consortium system in different bioreactor setting scenarios, assuming fast diffusion mechanisms of substances in the medium with a pump system and a pump-filter-return control of population density in both Synechococcus and <ins class="diffchange diffchange-inline"><i>A. fischeri</i> </ins>modules.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <del class="diffchange diffchange-inline">Aliivibrio </del>fischeri.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The main part is based on the model of bioluminescence regulation developed by Belta et al. 2001, a hybrid model of 9 differential equations which predicts the behavior of the whole regulatory mechanism of luciferase expression (including cAMP, AHL, LuxR and LuxI expression) in <ins class="diffchange diffchange-inline"><i>A. </ins>fischeri<ins class="diffchange diffchange-inline"></i></ins>.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <del class="diffchange diffchange-inline">Aliivibrio </del>population to a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of Synechococcus and the extra volume from tubing and pumping systems where the medium flows.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We modified this model to restrict the growth of the <ins class="diffchange diffchange-inline"><i>A. fischeri</i> </ins>population to a constrained volume (biolamp compartment) meanwhile we adopted a greater volume for the dilution of the autoinducer (AHL). Such volume represents the annexing of the photobioreactor of Synechococcus and the extra volume from tubing and pumping systems where the medium flows.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We gave the system a new input of AHL derived from the Synechococcus population, which has a Ks (constant rate of AHL production/cell resultant from our modified Syenchococcus metabolic network model) of 2.38x10<sup>-7</sup> multiplying the number of cells (culture density x culture volume – of the photobioreactor compartment). The model still counts with the AHL produced by the <del class="diffchange diffchange-inline">Aliivibrio </del>population, and the degradation half-life in the cells. As we said above, the diffusion speed of AHL is considered instantaneous (as the rate’s scale is very high compared with other variables, such as cell growth or gene expression).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We gave the system a new input of AHL derived from the Synechococcus population, which has a Ks (constant rate of AHL production/cell resultant from our modified Syenchococcus metabolic network model) of 2.38x10<sup>-7</sup> <ins class="diffchange diffchange-inline">nmol AHL /cell/s, </ins>multiplying the number of cells (culture density x culture volume – of the photobioreactor compartment). The model still counts with the AHL produced by the <ins class="diffchange diffchange-inline"><i>A. fischeri</i> </ins>population, and the degradation half-life in the cells. As we said above, the diffusion speed of AHL is considered instantaneous (as the rate’s scale is very high compared with other variables, such as cell growth or gene expression).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The application of this model is focused in the optimization in the design of the future bioreactor which may contain the system. We are looking for the values of compartment volumes, relative volume, population densities and total volume which can assure a diel control of luminescence (in 12h cycles, considering export rates and the AHL half-life of 10h) by the light induced activity of our Synechococcus biomachine; and, within those values, the settings with maximum luminescence values.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The application of this model is focused in the optimization in the design of the future bioreactor which may contain the system. We are looking for the values of compartment volumes, relative volume, population densities and total volume which can assure a diel control of luminescence (in 12h cycles, considering export rates and the AHL half-life of 10h) by the light induced activity of our Synechococcus biomachine; and, within those values, the settings with maximum luminescence values.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of our further model on export and consumption rates of sucrose. This filter aims to discard the settings where insufficient sucrose is exported to the culture to sustain the growth of the <del class="diffchange diffchange-inline">Aliivibrio </del>population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>A second filter is be applied to the group of solutions obtained from these premises, with the result of our further model on export and consumption rates of sucrose. This filter aims to discard the settings where insufficient sucrose is exported to the culture to sustain the growth of the <ins class="diffchange diffchange-inline"><i>A. fischeri</i> </ins>population. We managed to adapt some experimental values of sucrose export and consumption from the literature:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The export of sucrose from our cyanobacteria (Ke) is: 2.07x10<sup>-11</sup> nmol/cell/s (units adapted from Ducat et al, 2012)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The export of sucrose from our cyanobacteria (Ke) is: 2.07x10<sup>-11</sup> nmol/cell/s (units adapted from Ducat et al, 2012)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The consumption of sucrose by <del class="diffchange diffchange-inline">Aliivibrio </del>fischeri (Kc) is: 0.00000150 nmol/cell/s (units adapted from oxygen consumption rates at maximum bioluminescent activity, at normal glycolytic route assumptions in aerobic conditions, from Makemson 1985).<br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The consumption of sucrose by <ins class="diffchange diffchange-inline"><i>A. </ins>fischeri<ins class="diffchange diffchange-inline"></i> </ins>(Kc) is: 0.00000150 nmol/cell/s (units adapted from oxygen consumption rates at maximum bioluminescent activity, at normal glycolytic route assumptions in aerobic conditions, from Makemson 1985).<br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(A. fischeri cell density)·(biolammp module volume)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>dSucrose=Ke·(S. elongatus cell density).(photobioreactor module volume) - Kc·(<ins class="diffchange diffchange-inline"><i></ins>A. fischeri<ins class="diffchange diffchange-inline"></i> </ins>cell density)·(biolammp module volume)</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation and the cell densities for S. elongatus cscB and for A. fischeri (cell densities in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This amendment model sets the total volume of dilution, the compartmental volumes of occupation and the cell densities for S. elongatus cscB and for <ins class="diffchange diffchange-inline"><i></ins>A. fischeri<ins class="diffchange diffchange-inline"></i> </ins>(cell densities in a range between 0 and 10<sup>9</sup> cell/ml) as controlled variables.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br>The output gives the multivariate scenarios where the rate of change of sucrose concentration in the common broth is 0 or positive, so that the energy budget is not a shortfall.</div></td></tr>
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</table>Antropoteuthishttp://2012.igem.org/wiki/index.php?title=Team:Valencia/Modeling&diff=221963&oldid=prevAntropoteuthis at 22:49, 26 September 20122012-09-26T22:49:21Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in S. elongatus:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for Synechocystis sp. by <del class="diffchange diffchange-inline">Lopo </del>et al <del class="diffchange diffchange-inline">2012 </del>and recently adapted for Synechococcus sp.,where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b>Light, sucrose and AHL yield in S. elongatus:</b> In first place we adapted a metabolic model of Synechococcus with the functions we included with our constructs. The model is an algorithm applied to a metabolic network of reactions, originally designed for Synechocystis sp. by <ins class="diffchange diffchange-inline">Montagud </ins>et al<ins class="diffchange diffchange-inline">. 2009 and 2011. </ins>and recently adapted for Synechococcus sp.,where optimization of determined fluxes with constraints on certain reactions which make it behave like a living cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype Synechococcus elongatus with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We transformed a wildtype Synechococcus elongatus with the luciferase genes (luxAB) regulated by the promoter psbA. The reactions of bioluminescence expressed by the LuxAB construct were introduced as follows:</div></td></tr>
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</table>Antropoteuthis