http://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&feed=atom&action=historyTeam:Evry/Modeling/vf - Revision history2024-03-29T05:04:46ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=361157&oldid=prevRasend at 03:43, 29 October 20132013-10-29T03:43:49Z<p></p>
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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 a final modeling part</del>, <del class="diffchange diffchange-inline">we wanted to know if our second treatment strategy was </del>viable. <del class="diffchange diffchange-inline">We build a model that aims the same </del>type <del class="diffchange diffchange-inline">of </del>questions <del class="diffchange diffchange-inline">as the flush treatment model</del>. <del class="diffchange diffchange-inline">The assumptions are also the same</del>, <del class="diffchange diffchange-inline">but the method is really different </del>: <del class="diffchange diffchange-inline">for more precision in the process description, we used </del>a <del class="diffchange diffchange-inline">cellular automaton approach. This model showed us that the new strategy can still </del><b><del class="diffchange diffchange-inline">significantly reduce the patient</del>'<del class="diffchange diffchange-inline">s iron </del>absorption</b>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Comme partie finale de modélisation</ins>, <ins class="diffchange diffchange-inline">nous voulions savoir si notre deuxième stratégie de traitement était </ins>viable.<ins class="diffchange diffchange-inline"> Nous avons construis un modèle qui pose le même </ins>type <ins class="diffchange diffchange-inline">de </ins>questions <ins class="diffchange diffchange-inline">que le modèle de traitement « flush »</ins>.<ins class="diffchange diffchange-inline"> Les hypothèses sont également les mêmes</ins>, <ins class="diffchange diffchange-inline">mais la méthode est vraiment différente</ins>: <ins class="diffchange diffchange-inline">nous avons utilisé une approche d’automate cellulaire. Ce modèle nous </ins>a <ins class="diffchange diffchange-inline">montré que la nouvelle stratégie peut encore </ins><b><ins class="diffchange diffchange-inline">réduire de manière significative l</ins>'absorption <ins class="diffchange diffchange-inline">en fer chez les patients ayant une absorption en fer</ins></b>. </div></td></tr>
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</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=360949&oldid=prevRasend at 03:38, 29 October 20132013-10-29T03:38:25Z<p></p>
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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">We also wanted to know how much siderophore can be produced and how we can improve this</del>. <del class="diffchange diffchange-inline">We answered this with a </del><b><del class="diffchange diffchange-inline">Genome scale model</del></b>, <del class="diffchange diffchange-inline">using a flux </del>balance <del class="diffchange diffchange-inline">analysis approach</del>. <del class="diffchange diffchange-inline">We determine </del><b><del class="diffchange diffchange-inline">what are the limiting metabolites</del></b> <del class="diffchange diffchange-inline">and </del><b><del class="diffchange diffchange-inline">how we could improve our capsule</del></b>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Nous voulions aussi savoir combien de sidérophores pouvait être produit et comment nous pourrions améliorer cette technique</ins>.<ins class="diffchange diffchange-inline"> Nous avons répondu à cette question grâce à un </ins><b><ins class="diffchange diffchange-inline">modèle à l'échelle du génome</ins></b>, <ins class="diffchange diffchange-inline">en utilisant une approche d'analyse de la </ins>balance <ins class="diffchange diffchange-inline">des flux</ins>. <ins class="diffchange diffchange-inline">Nous avons étudié </ins><b><ins class="diffchange diffchange-inline">quels étaient les métabolites de limitation</ins></b><ins class="diffchange diffchange-inline"> et </ins><b><ins class="diffchange diffchange-inline">comment nous pourrions améliorer notre gélule</b>.</ins></b>.</div></td></tr>
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</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=360837&oldid=prevRasend at 03:34, 29 October 20132013-10-29T03:34:54Z<p></p>
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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">At the begining of our project</del>, <del class="diffchange diffchange-inline">we aimed to enable iron chelation in the duodenum using bacteria that would flush through the duodenum and produce the siderophores</del>. <del class="diffchange diffchange-inline">Therefore we wanted to predict the minimal quantity of produced siderophores sufficient to reduce the iron intestinal </del>absorption. <del class="diffchange diffchange-inline">We first had in mind a </del>flush <del class="diffchange diffchange-inline">strategy</del>, <del class="diffchange diffchange-inline">meaning we prioritized an approach where the bacteria would start their iron sensing and siderophore </del>production <del class="diffchange diffchange-inline">before entering the duodenum</del>. <del class="diffchange diffchange-inline">This qualitative </del><b><del class="diffchange diffchange-inline">Flush treatment model</del></b> <del class="diffchange diffchange-inline">showed us that it is theoretically </del>possible <del class="diffchange diffchange-inline">to <b>significantly reduce the patient</del>'<del class="diffchange diffchange-inline">s iron </del>absorption</b>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Au début de notre projet</ins>, <ins class="diffchange diffchange-inline">nous avons cherché à permettre la chélation du fer dans le duodénum en utilisant des bactéries passeraient via le duodénum et produiraient des sidérophores </ins>.<ins class="diffchange diffchange-inline"> C'est pourquoi nous avons voulu prédire la quantité minimale de sidérophores produits suffisante pour réduire l'</ins>absorption <ins class="diffchange diffchange-inline">intestinale du fer</ins>.<ins class="diffchange diffchange-inline"> Nous avons d'abord eu à l'esprit une stratégie dynamique proche d'une chasse d'eau (</ins>flush<ins class="diffchange diffchange-inline">)</ins>, <ins class="diffchange diffchange-inline">c'est à dire que nous avons privilégié une approche où les bactéries pourraient commencer leur détection de fer et la </ins>production <ins class="diffchange diffchange-inline">de sidérophores avant d'entrer dans le duodénum</ins>.<ins class="diffchange diffchange-inline"> Ce modèle qualitatif de </ins><b><ins class="diffchange diffchange-inline">traitement «Flush»</ins></b><ins class="diffchange diffchange-inline"> nous a montré qu'il est théoriquement </ins>possible <ins class="diffchange diffchange-inline">de réduire significativement l</ins>'absorption <ins class="diffchange diffchange-inline">en fer du patient.</ins></b>. </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">The </del>conclusions <del class="diffchange diffchange-inline">were promising</del>, <del class="diffchange diffchange-inline">encouraging and comforting regarding our strategy</del>. <del class="diffchange diffchange-inline">Therefore we investigated in detail the delay in siderophore production for a given bacterial </del>production <del class="diffchange diffchange-inline">through an </del><b><del class="diffchange diffchange-inline">Enterobactin </del>production <del class="diffchange diffchange-inline">model</del></b> <del class="diffchange diffchange-inline">that integrate our sensor, invertor and chelator systems</del>. <del class="diffchange diffchange-inline">This investigation gave us more details on timings</del>. <del class="diffchange diffchange-inline">Unfortunately</del>, <del class="diffchange diffchange-inline">the </del>conclusions <del class="diffchange diffchange-inline">were in </del>contradiction <del class="diffchange diffchange-inline">with the qualitative model because the delay is too </del>important <del class="diffchange diffchange-inline">to be </del>compatible <del class="diffchange diffchange-inline">with </del>a <del class="diffchange diffchange-inline">flush strategy. <b>This finding greatly influenced the biological part</del>, <del class="diffchange diffchange-inline">especially the <a href="https://2013.igem.org/Team:Evry/Pill_design">capsule design</a></b></del>. <del class="diffchange diffchange-inline">Because iron </del>absorption <del class="diffchange diffchange-inline">is split between the duodenum </del>(60%) <del class="diffchange diffchange-inline">and the jejunum </del>(40%), <del class="diffchange diffchange-inline">we decided to retain bacteria in duodenum and the proximal area of the jejunum</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Les </ins>conclusions <ins class="diffchange diffchange-inline">ont été prometteuses</ins>, <ins class="diffchange diffchange-inline">encourageantes et rassurantes sur notre stratégie</ins>.<ins class="diffchange diffchange-inline"> Par conséquent, nous avons étudié en détail le délai dans la </ins>production <ins class="diffchange diffchange-inline">de sidérophores pour une population bactérienne donnée par un </ins><b><ins class="diffchange diffchange-inline">modèle de </ins>production <ins class="diffchange diffchange-inline">d’entérobactine</ins></b>.<ins class="diffchange diffchange-inline"> Cette enquête nous a donné plus de détails sur le temps de production</ins>.<ins class="diffchange diffchange-inline"> Malheureusement</ins>, <ins class="diffchange diffchange-inline">les </ins>conclusions <ins class="diffchange diffchange-inline">sont en </ins>contradiction <ins class="diffchange diffchange-inline">avec le modèle qualitatif car le délai est trop </ins>important <ins class="diffchange diffchange-inline">pour être </ins>compatible <ins class="diffchange diffchange-inline">avec une stratégie « Flush ». Ce constat </ins>a <ins class="diffchange diffchange-inline">grandement influencé la partie biologique</ins>, <ins class="diffchange diffchange-inline">en particulier la conception de la gélule </ins>.<ins class="diffchange diffchange-inline"> En effet l'</ins>absorption <ins class="diffchange diffchange-inline">du fer est divisée entre le duodénum </ins>(60%) <ins class="diffchange diffchange-inline">et le jéjunum </ins>(40%), <ins class="diffchange diffchange-inline">nous avons donc décidé de retenir les bactéries dans le duodénum et la zone proximale du jéjunum</ins>.</div></td></tr>
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</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=360300&oldid=prevRasend at 03:20, 29 October 20132013-10-29T03:20:39Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1>Aperçu de la partie modélisation</h1></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h1>Aperçu de la partie modélisation</h1></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">p</del>> <del class="diffchange diffchange-inline">La partie modélisation s'organise autour de 3 axes principaux:</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">h2>Modeling Parts</h2</ins>></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"> </del><<del class="diffchange diffchange-inline">li</del>><del class="diffchange diffchange-inline">La cartographie de l</del>'<del class="diffchange diffchange-inline">intestin et des interactions</del>: <span style="<del class="diffchange diffchange-inline">font-style</del>:<del class="diffchange diffchange-inline">italic;</del>"><del class="diffchange diffchange-inline">Quels seraient les effets du traitement ?</del></span></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">tr width="100%"</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"> </del><<del class="diffchange diffchange-inline">li</del>><del class="diffchange diffchange-inline">La croissance de la population de bactéries chélatant le fer </del>: <span style="<del class="diffchange diffchange-inline">font-style</del>:<del class="diffchange diffchange-inline">italic;</del>"><del class="diffchange diffchange-inline">Nos bactéries peuvent-elles coloniser le duodénum ? </del></span></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><td align="center"><span style="color:#7B0000"><b>Flush treatment model</b></span></td></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"> </del><<del class="diffchange diffchange-inline">li</del>><del class="diffchange diffchange-inline">Evaluation des risques </del>: <span style="<del class="diffchange diffchange-inline">font-style</del>:<del class="diffchange diffchange-inline">italic;</del>"><del class="diffchange diffchange-inline">prévision</del>, <del class="diffchange diffchange-inline">contrôle</del>, ...</<del class="diffchange diffchange-inline">span</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><td align="center"></td></ins></div></td></tr>
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<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"><td align="center"><a href="https://2013.igem.org/Team:Evry/flush_model"><img height="300px" src="https://static.igem.org/mediawiki/2013/1/1e/OverviewDuodenum.png"/></a></ins></div></td></tr>
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<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">At the begining of our project, we aimed to enable iron chelation in the duodenum using bacteria that would flush through the duodenum and produce the siderophores. Therefore we wanted to predict the minimal quantity of produced siderophores sufficient to reduce the iron intestinal absorption. We first had in mind a flush strategy, meaning we prioritized an approach where the bacteria would start their iron sensing and siderophore production before entering the duodenum. This qualitative <b>Flush treatment model</b> showed us that it is theoretically possible to <b>significantly reduce the patient</ins>'<ins class="diffchange diffchange-inline">s iron absorption</b>. </ins></div></td></tr>
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<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"><td align="center"></ins><span style="<ins class="diffchange diffchange-inline">color</ins>:<ins class="diffchange diffchange-inline">#7B0000</ins>"><ins class="diffchange diffchange-inline"><b>Enterobactin production model</b></ins></span<ins class="diffchange diffchange-inline">></td</ins>></div></td></tr>
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<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 conclusions were promising, encouraging and comforting regarding our strategy. Therefore we investigated in detail the delay in siderophore production for a given bacterial production through an <b>Enterobactin production model</b> that integrate our sensor, invertor and chelator systems. This investigation gave us more details on timings. Unfortunately, the conclusions were in contradiction with the qualitative model because the delay is too important to be compatible with a flush strategy. <b>This finding greatly influenced the biological part, especially the <a href="https</ins>:<ins class="diffchange diffchange-inline">//2013.igem.org/Team:Evry/Pill_design">capsule design</a></b>. Because iron absorption is split between the duodenum (60%) and the jejunum (40%), we decided to retain bacteria in duodenum and the proximal area of the jejunum.</ins></div></td></tr>
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<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://2013.igem.org/Team:Evry/ent_prod"><img height="300px" src="https://static.igem.org/mediawiki/2013/c/c8/OverviewMetabolic.png"/></a></ins></div></td></tr>
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<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"><td align="center"></ins><span style="<ins class="diffchange diffchange-inline">color</ins>:<ins class="diffchange diffchange-inline">#7B0000</ins>"><ins class="diffchange diffchange-inline"><b>Genome scale model</b></ins></span<ins class="diffchange diffchange-inline">></td</ins>></div></td></tr>
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<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"><td align="center"><a href="https</ins>:<ins class="diffchange diffchange-inline">//2013.igem.org/Team:Evry/Metabolism_model"><img height="300px" src="https://static.igem.org/mediawiki/2013/6/65/OverviewFBA.png"/></a></ins></div></td></tr>
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<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">We also wanted to know how much siderophore can be produced and how we can improve this. We answered this with a <b>Genome scale model</b>, using a flux balance analysis approach. We determine <b>what are the limiting metabolites</b> and <b>how we could improve our capsule</b>.</ins></div></td></tr>
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<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">As a final modeling part</ins>, <ins class="diffchange diffchange-inline">we wanted to know if our second treatment strategy was viable. We build a model that aims the same type of questions as the flush treatment model. The assumptions are also the same</ins>, <ins class="diffchange diffchange-inline">but the method is really different : for more precision in the process description, we used a cellular automaton approach</ins>. <ins class="diffchange diffchange-inline">This model showed us that the new strategy can still <b>significantly reduce the patient's iron absorption</b></ins>. </div></td></tr>
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</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=110607&oldid=prevRasend at 09:10, 9 September 20132013-09-09T09:10:12Z<p></p>
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</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=110602&oldid=prevRasend at 09:09, 9 September 20132013-09-09T09:09:12Z<p></p>
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</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=66564&oldid=prevRasend at 21:18, 11 August 20132013-08-11T21:18:39Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> La partie modélisation s'organise autour de 3 axes principaux:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> La partie modélisation s'organise autour de 3 axes principaux:</div></td></tr>
</table>Rasendhttp://2013.igem.org/wiki/index.php?title=Team:Evry/Modeling/vf&diff=66563&oldid=prevRasend: Created page with "{{:Team:Evry/vf/template_model}} <html> <div id="mainTextcontainer"> <h1>Aperçu de la partie modélisation</h1> <h2 align='center'> <a href="https://2013.igem.org/Team:Evry/M..."2013-08-11T21:18:26Z<p>Created page with "{{:Team:Evry/vf/template_model}} <html> <div id="mainTextcontainer"> <h1>Aperçu de la partie modélisation</h1> <h2 align='center'> <a href="https://2013.igem.org/Team:Evry/M..."</p>
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<p> La partie modélisation s'organise autour de 3 axes principaux:<br />
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<li>La cartographie de l'intestin et des interactions: <span style="font-style:italic;">Quels seraient les effets du traitement ?</span><br />
<li>La croissance de la population de bactéries chélatant le fer : <span style="font-style:italic;">Nos bactéries peuvent-elles coloniser le duodénum ? </span><br />
<li>Evaluation des risques : <span style="font-style:italic;">prévision, contrôle, ...</span><br />
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