Latest revision as of 10:42, 21 October 2015

House of Carbs

Manchester-Graz Collaboration

The Manchester-Graz team have developed an expression system designed to regulate single and multi-gene pathways for an intestine expression. For controlling a wide range of pathways it is designed in a flexible and modular manner. They tested the production of butyrate in the gut. The pathway was incorporated into the expression system model to observe the expression of butyrate under the control of the developed system. The model generated helped us to understand how the system is dealing with pathways that consist of several enzymes at an intestinal level.

The system consists of two quorum sensing (QS) systems EsaR/I and CepR/I. The EsaR/I system belongs to the plant pathogen Pantoea stewartii . The second QS-System, CepR/I, belongs to the opportunistic pathogen Burkholderia cenocepacia . For details about the system and the model please look into the Manchester-Graz modelling page.

Figure 1: Overview of the reduced pathway. Coenzyme A (CoA) is recycled in the pathway by the butyryl CoA-acetyl CoA-tranferase.

Butyrate is converted starting from two acetyl-CoAs over several steps to butyryl-CoA. In the last step, the coenzyme A is transferred to acetate, producing acetyl-CoA and butyrate₁. For simplicity, the pathway was reduced to some essential parts and steps in the pathway. Acetate is converted to acetyl-CoA. The steps to butyryl-CoA are reduced to one step. Coenzyme A is recycled in the last step to butyrate and can be reused to produce acetyl-CoA (Figure 1).

The pathway is controlled by three enzymes whose expression is controlled by the two quorum sensing systems.

If we simulate the model, in the first two minutes the acetate gets first converted into butyryl-CoA and then the butyrate production starts (see Figure 2). The following time is butyrate being produced constantly by the cells. The butyrate is transported out of the cells through diffusion by a rate of 207.6 µmol/h/L or 18 mg/h/L.

Figure 2: Butyrate production in the first two minutes.

Figure 3: Overview of the Simbiology model. For simplification the model was reduced to essential components.

References

1. Susan E et al (2002) The microbiology of butyrate formation in the human colon.

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      				<h1 class="title1">Manchester-Graz Collaboration</h1>
-                                         <p class="space20"> The Manchester-Graz team have developed an expression system designed to regulate single and multi-gene pathways for an intestine expression. For controlling a wide range of pathways it is designed in a flexible and modular manner. They tested the production of butyrate in the gut. The pathway was incorporated into the expression system model to observe the expression of butyrate under the control of the developed system. The model generated helped us to understand how the system is dealing with pathways that consist of several enzymes at an intestine level.  </p>
+                                         <p class="space20"> The Manchester-Graz team have developed an expression system designed to regulate single and multi-gene pathways for an intestine expression. For controlling a wide range of pathways it is designed in a flexible and modular manner. They tested the production of butyrate in the gut. The pathway was incorporated into the expression system model to observe the expression of butyrate under the control of the developed system. The model generated helped us to understand how the system is dealing with pathways that consist of several enzymes at an intestinal level.  </p>
-<p class="space20">The system consists of two quorum sensing (QS) systems EsaR/I and CepR/I. The EsaR/I system belongs to the plant pathogen Pantoea stewartii. The second QS-System, CepR/I, belongs to the opportunistic pathogen Burkholderia cenocepacia.  For details about the system and the model please look into: https://2015.igem.org/Team:Manchester-Graz/modelling.</p>
+<p class="space20">The system consists of two quorum sensing (QS) systems <i>Esa</i>R/I and <i>Cep</i>R/I. The <i>Esa</i>R/I system belongs to the plant pathogen <i> Pantoea stewartii </i>. The second QS-System, CepR/I, belongs to the opportunistic pathogen <i> Burkholderia cenocepacia </i>.  For details about the system and the model please look into <a href="https://2015.igem.org/Team:Manchester-Graz/Modeling" style = "color: #002bb8;">the Manchester-Graz modelling page</a>.</p>
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                              <img src="https://static.igem.org/mediawiki/2015/e/e2/NRP-UEA-Norwich-grazmodel1.png" href="https://static.igem.org/mediawiki/2015/e/e2/NRP-UEA-Norwich-grazmodel1.png" alt="..." class="img-responsive mautomargin fancybox" style="cursor: pointer;">
-<p><b>Figure 1:</b> Overview of the reduced pathway. Coenzyme A (Co A) is recycled in the pathway by the butyryl CoA-acetyl CoA-tranferase.
+<p><b>Figure 1:</b> Overview of the reduced pathway. Coenzyme A (CoA) is recycled in the pathway by the butyryl CoA-acetyl CoA-tranferase.
 </p>
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      			<div class="col-md-12 left">
-     					<p class="space10">Butyrate is converted starting from two Acetyl CoAs over several steps to Butyryl CoA. In the last step the Coenzyme A is transferred to Acetate, producing Acetyl CoA and Butyrate<sub><a data-id="ref" class="scroll-link" style = "color: #002bb8;">1</a></sub>.
+     					<p class="space10">Butyrate is converted starting from two acetyl-CoAs over several steps to butyryl-CoA. In the last step, the coenzyme A is transferred to acetate, producing acetyl-CoA and butyrate<sub><a data-id="ref" class="scroll-link" style = "color: #002bb8;">1</a></sub>.
-For simplicity, the pathway was reduced to some essential parts and steps in the pathway. Acetate is converted to Acetyl CoA. The steps to Butyryl CoA are reduced to one step. Coenzyme A is recycled in the last step to Butyrate and can be reused to produce Acetyl CoA (Figure 1). </p>
+For simplicity, the pathway was reduced to some essential parts and steps in the pathway. Acetate is converted to acetyl-CoA. The steps to butyryl-CoA are reduced to one step. Coenzyme A is recycled in the last step to butyrate and can be reused to produce acetyl-CoA (Figure 1). </p>
 <div class="space10"></div>
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 </p>
-<p class ="space20">If we simulate the model, in the first two minutes the acetate gets first converted into Butyryl CoA and then the Butyrate production starts (Figure. 2). The following time butyrate gets produced constantly by the cells. The butyrate is transported out of the cells through diffusion by a rate of 207,6 µmol/h/L or 18 mg/h/L.</p>
+<p class ="space20">If we simulate the model, in the first two minutes the acetate gets first converted into butyryl-CoA and then the butyrate production starts (see Figure 2). The following time is butyrate being produced constantly by the cells. The butyrate is transported out of the cells through diffusion by a rate of 207.6 µmol/h/L or 18 mg/h/L.</p>
-<img src="https://static.igem.org/mediawiki/2015/8/83/NRP-UEA-Norwich-manchester3.png" href="https://static.igem.org/mediawiki/2015/8/83/NRP-UEA-Norwich-manchester3.png" alt="..." class="img-responsive mautomargin fancybox" style="cursor: pointer;">
+<img src="https://static.igem.org/mediawiki/2015/8/83/NRP-UEA-Norwich-manchester3.png" href="https://static.igem.org/mediawiki/2015/8/83/NRP-UEA-Norwich-manchester3.png" alt="..." class="img-responsive mautomargin fancybox space10" style="cursor: pointer;">
 <p><b>Figure 2:</b> Butyrate production in the first two minutes.</p>
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 </section>
-<div class="row">
-    			<div class="col-md-6 left">
-    				<h4 class="title2">Differential equations</h4>
-<script type="text/x-mathjax-config">
-  MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}});
-</script>
-<script type="text/javascript"
-  src="https://2015.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
-$$
-\begin{array}{ccl}
-\frac {\mathrm{d}\left( {{\mathrm{[G6P]}} \,  } \right) }  {\mathrm{d}{t} }  \; &=& \;  { \, - \,  \, \left(\frac {\frac {{\mathrm{Vf}}_{\mathrm{(Pgm)}} \, \cdot \, {\mathrm{[G6P]}} } {{\mathrm{Kms}}_{\mathrm{(Pgm)}} } \, - \, \frac {{\mathrm{Vr}}_{\mathrm{(Pgm)}} \, \cdot \, {\mathrm{[G1P]}} } {{\mathrm{Kmp}}_{\mathrm{(Pgm)}} } }  { {{1} \, + \, \frac{\mathrm{[G6P]}}{{\mathrm{Kms}}_{\mathrm{(Pgm)}} } }  \, + \, \frac{\mathrm{[G1P]}}{{\mathrm{Kmp}}_{\mathrm{(Pgm)}} } } \right) } \\
- && \\
-\frac {\mathrm{d}\left( {{\mathrm{[G1P]}} \,  } \right) }  {\mathrm{d}{t} }  \; &=& \;  { \, + \,  \,  \left(\frac {\frac {{\mathrm{Vf}}_{\mathrm{(Pgm)}} \, \cdot \, {\mathrm{[G6P]}} } {{\mathrm{Kms}}_{\mathrm{(Pgm)}} } \, - \, \frac {{\mathrm{Vr}}_{\mathrm{(Pgm)}} \, \cdot \, {\mathrm{[G1P]}} } {{\mathrm{Kmp}}_{\mathrm{(Pgm)}} } }  { {{1} \, + \, \frac{\mathrm{[G6P]}}{{\mathrm{Kms}}_{\mathrm{(Pgm)}} } }  \, + \, \frac{\mathrm{[G1P]}}{{\mathrm{Kmp}}_{\mathrm{(Pgm)}} } } \right) } \\
- && \\
- \; && \;  { \, - \,  \, \left(\frac { {{\mathrm{Vmax}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{[G1P]}} }  \, \cdot \, {\mathrm{[ATP]}} }  { { { {{\mathrm{KmB}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{KmA}}_{\mathrm{(GlgC)}} }  \, + \,  {{\mathrm{KmB}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{[G1P]}} }  }  \, + \,  {{\mathrm{KmA}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{[ATP]}} }  }  \, + \,  {{\mathrm{[G1P]}} \, \cdot \, {\mathrm{[ATP]}} }  } \right) } \\
- && \\
- \; && \;  { \, + \,  \,  \left(\frac {{V}_{\mathrm{("GlgX-GlgP")}} \,  {\mathrm{[Glycogen]}} }  {{\mathrm{Km}}_{\mathrm{("GlgX-GlgP")}} \, + \, {\mathrm{[Glycogen]}} } \right) } \\
- && \\
- \; && \;  { \, + \,  \,  \left(\frac {{V}_{\mathrm{(AspP)}} \, \cdot \, {\mathrm{[ADPG]}} }  {{\mathrm{Km}}_{\mathrm{(AspP)}} \, + \, {\mathrm{[ADPG]}} } \right) } \\
- && \\
-\frac {\mathrm{d}\left( {{\mathrm{[ADPG]}} \,   } \right) }  {\mathrm{d}{t} }  \; &=& \;  { \, - \,  \,  \left(\frac {{V}_{\mathrm{(GlgA)}} \, \cdot \, {\mathrm{[ADPG]}} }  {{\mathrm{Km}}_{\mathrm{(GlgA)}} \, + \, {\mathrm{[ADPG]}} } \right) } \\
- && \\
- \; && \;  { \, + \,  \,  \left(\frac { {{\mathrm{Vmax}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{[G1P]}} }  \, \cdot \, {\mathrm{[ATP]}} }  { { { {{\mathrm{KmB}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{KmA}}_{\mathrm{(GlgC)}} }  \, + \,  {{\mathrm{KmB}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{[G1P]}} }  }  \, + \,  {{\mathrm{KmA}}_{\mathrm{(GlgC)}} \, \cdot \, {\mathrm{[ATP]}} }  }  \, + \,  {{\mathrm{[G1P]}} \, \cdot \, {\mathrm{[ATP]}} }  } \right) } \\
- && \\
- \; && \;  { \, - \,  \,  \left(\frac {{V}_{\mathrm{(AspP)}} \, \cdot \, {\mathrm{[ADPG]}} }  {{\mathrm{Km}}_{\mathrm{(AspP)}} \, + \, {\mathrm{[ADPG]}} } \right) } \\
- && \\
-\frac {\mathrm{d}\left( {{\mathrm{[1,4glucan]}} \,  } \right) }  {\mathrm{d}{t} }  \; &=& \;  { \, + \, \left(\frac {{V}_{\mathrm{(GlgA)}} \, \cdot \, {\mathrm{[ADPG]}} }  {{\mathrm{Km}}_{\mathrm{(GlgA)}} \, + \, {\mathrm{[ADPG]}} } \right) } \\
- && \\
- \; && \;  { \, - \,  \left(\frac {{V}_{\mathrm{(GlgB)}} \, \cdot \, {\mathrm{[1,4glucan]}} }  {{\mathrm{Km}}_{\mathrm{(GlgB)}} \, + \, {\mathrm{[1,4glucan]}} } \right) } \\
- && \\
-\frac {\mathrm{d}\left( {{\mathrm{[Glycogen]}} \,  } \right) }  {\mathrm{d}{t} }  \; &=& \;  { \, + \,  \, \left(\frac {{V}_{\mathrm{(GlgB)}} \, \cdot \, {\mathrm{[1,4glucan]}} }  {{\mathrm{Km}}_{\mathrm{(GlgB)}} \, + \, {\mathrm{[1,4glucan]}} } \right) } \\
- && \\
- \; && \;  { \, - \,  \, \left(\frac {{V}_{\mathrm{("GlgX-GlgP")}} \,\cdot \, {\mathrm{[Glycogen]}} }  {{\mathrm{Km}}_{\mathrm{("GlgX-GlgP")}} \, + \, {\mathrm{[Glycogen]}} } \right) } \\
- && \\
-\end{array}
-$$
-    			</div>
-    		</div>
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      <li><img src="https://static.igem.org/mediawiki/2015/9/9c/NRP-UEA-Norwich-Ibcarb_logo.png" width="200" height="100" class="img-grey mautomargin"></a></li>
      <li><img src="https://static.igem.org/mediawiki/2015/8/8b/NRP-UEA-Norwich-TSL-logo.png" width="200" height="100" class="img-grey mautomargin"></a></li>
-     <li><img src="https://static.igem.org/mediawiki/2015/f/f0/NRP-UEA-Norwich-Biochemsociety.png" width="225" height="100" class="img-grey mautomargin"></a></li>
+     <li><img src="https://static.igem.org/mediawiki/2015/7/7d/NRP-UEA-Norwich-SEB-Logo.png" width="225" height="100" class="img-grey mautomargin"></a></li>
      <li><img src="https://static.igem.org/mediawiki/2015/d/d3/NRP-UEA-Norwich-JIC.png" width="200" height="100" class="img-grey mautomargin" width="200" height="100"></a></li>
      <li><img src="https://static.igem.org/mediawiki/2015/c/c5/NRP-UEA-Norwich-Bbsrc.png" width="200" height="100" class="img-grey mautomargin"></a></li>
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      <li><img src="https://static.igem.org/mediawiki/2015/e/e3/NRP-UEA-Norwich-Wellcome_Trust_logo.png" width="250" height="100" class="img-grey mautomargin"></a></li>
      <li><img src="https://static.igem.org/mediawiki/2015/7/74/NRP-UEA-Norwich-IBBA_logo.png" width="125" height="125" class="img-grey mautomargin"></a></li>
+     <li><img src="https://static.igem.org/mediawiki/2015/d/d0/NRP-UEA-Norwich-SfAM-Logo.png" width="220" height="100" class="img-grey mautomargin" width="200" height="100"></a></li>

Difference between revisions of "Team:NRP-UEA-Norwich/Collaborations/Manchester"

Latest revision as of 10:42, 21 October 2015

Manchester-Graz Collaboration

References

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