Difference between revisions of "Team:ITB Indonesia/Model"
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<h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 30px; border-bottom: 2px solid #1c2922 !important; padding-left: 30px; font-size: 100px; text-align: center; color: #1c2922">Modelling</h1> | <h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 30px; border-bottom: 2px solid #1c2922 !important; padding-left: 30px; font-size: 100px; text-align: center; color: #1c2922">Modelling</h1> | ||
| − | <h1 class="ITB_h1">Quorum Sensing</h1> | + | <h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 30px; border-bottom: 2px solid #1c2922 !important; padding-left: 30px; font-size: 30px; text-align: left; color: #1c2922">Quorum Sensing</h1> |
<p></p> | <p></p> | ||
<p>Quorum sensing mechanism was used to form biofilm of <i>E.coli</i> strain Top10, BL21 and DH5α that used in labwork. We have modeled growth curve of <i>E.coli</i> to determine when we must move <i>E.coli</i> colony from inoculum flask to reaction flask that contains PET. Besides growth curve, we have modeled some coupled ODEs to model growth curve, AI-2 production that affects signaling, and biofilm formation. AI-2 production in <i>E.coli</i> was used as colony signal of quorum sensing until it reaches specific points and finally form biofilm that affected by its quorum sensing by AI-2 signaling. We use Hill kinetics function as our approach to model AI-2 production and biofilm formation. Based on model that we built and confirmation from wetlab team, we found inoculation time until <i>E.coli</i> reaches quorum sensing condition is <b>10 hours</b>. Not only time that necessary for quorum sensing condition, we found from <b>model</b>, parameter that <b>affect significantly to biofilm formation was specific growth rate (μ) and initial amount of bacteria that will be inoculated.</b></p> | <p>Quorum sensing mechanism was used to form biofilm of <i>E.coli</i> strain Top10, BL21 and DH5α that used in labwork. We have modeled growth curve of <i>E.coli</i> to determine when we must move <i>E.coli</i> colony from inoculum flask to reaction flask that contains PET. Besides growth curve, we have modeled some coupled ODEs to model growth curve, AI-2 production that affects signaling, and biofilm formation. AI-2 production in <i>E.coli</i> was used as colony signal of quorum sensing until it reaches specific points and finally form biofilm that affected by its quorum sensing by AI-2 signaling. We use Hill kinetics function as our approach to model AI-2 production and biofilm formation. Based on model that we built and confirmation from wetlab team, we found inoculation time until <i>E.coli</i> reaches quorum sensing condition is <b>10 hours</b>. Not only time that necessary for quorum sensing condition, we found from <b>model</b>, parameter that <b>affect significantly to biofilm formation was specific growth rate (μ) and initial amount of bacteria that will be inoculated.</b></p> | ||
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<p>Growth curve</p> | <p>Growth curve</p> | ||
| − | <img src="https://static.igem.org/mediawiki/2017/8/8b/CodeCogsEqn.gif" style="width: auto; height: auto; | + | <p><img src="https://static.igem.org/mediawiki/2017/8/8b/CodeCogsEqn.gif" style="width: auto; height: auto;" /><img align="middle"> |
| + | </p> | ||
<p>AI-2 Production</p> | <p>AI-2 Production</p> | ||
| − | <img src="https://static.igem.org/mediawiki/2017/d/de/CodeCogsEqn_%281%29.gif" style="width: auto; height: auto; | + | <p><img src="https://static.igem.org/mediawiki/2017/d/de/CodeCogsEqn_%281%29.gif" style="width: auto; height: auto;" align="middle"/></p> |
<p>Biofilm Formation</p> | <p>Biofilm Formation</p> | ||
| − | <img src="https://static.igem.org/mediawiki/2017/f/f2/CodeCogsEqn_%282%29.gif" style="width: auto; height: auto; | + | <p><img src="https://static.igem.org/mediawiki/2017/f/f2/CodeCogsEqn_%282%29.gif" style="width: auto; height: auto;" align="middle"/></p> |
| − | <h1 class="ITB_h1">PETase Transcription</h1> | + | <h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 30px; border-bottom: 2px solid #1c2922 !important; padding-left: 30px; font-size: 30px; text-align: left; color: #1c2922">PETase Transcription</h1> |
<p>Paragraph apapun</p> | <p>Paragraph apapun</p> | ||
| − | <h1 class="ITB_h1">Rate of PET Degradation with Biofilm</h1> | + | <h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 30px; border-bottom: 2px solid #1c2922 !important; padding-left: 30px; font-size: 30px; text-align: left; color: #1c2922">Rate of PET Degradation with Biofilm</h1> |
<p>Paragraph apapun</p> | <p>Paragraph apapun</p> | ||
| − | <h1 class="ITB_h1">Rate of PET Degradation without Biofilm</h1> | + | <h1 class="ITB_h1" style="padding-bottom: 30px; margin-bottom: 30px; border-bottom: 2px solid #1c2922 !important; padding-left: 30px; font-size: 30px; text-align: left; color: #1c2922">Rate of PET Degradation without Biofilm</h1> |
<p>Paragraph apapun</p> | <p>Paragraph apapun</p> | ||
</div> | </div> | ||
Revision as of 07:55, 30 October 2017
Modelling
Quorum Sensing
Quorum sensing mechanism was used to form biofilm of E.coli strain Top10, BL21 and DH5α that used in labwork. We have modeled growth curve of E.coli to determine when we must move E.coli colony from inoculum flask to reaction flask that contains PET. Besides growth curve, we have modeled some coupled ODEs to model growth curve, AI-2 production that affects signaling, and biofilm formation. AI-2 production in E.coli was used as colony signal of quorum sensing until it reaches specific points and finally form biofilm that affected by its quorum sensing by AI-2 signaling. We use Hill kinetics function as our approach to model AI-2 production and biofilm formation. Based on model that we built and confirmation from wetlab team, we found inoculation time until E.coli reaches quorum sensing condition is 10 hours. Not only time that necessary for quorum sensing condition, we found from model, parameter that affect significantly to biofilm formation was specific growth rate (μ) and initial amount of bacteria that will be inoculated.
Here ODEs that we used :
Growth curve
AI-2 Production
Biofilm Formation
PETase Transcription
Paragraph apapun
Rate of PET Degradation with Biofilm
Paragraph apapun
Rate of PET Degradation without Biofilm
Paragraph apapun
