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Saccharomyces cerevisiae to produce acrylic acid.</h4> | Saccharomyces cerevisiae to produce acrylic acid.</h4> | ||
<br> | <br> | ||
− | < | + | <div class="col-md-12"> |
− | + | <div class="col-md-6"> | |
+ | <img src="https://static.igem.org/mediawiki/2017/2/21/%E5%A4%A7%E8%82%A0%E5%8E%9F%E5%A7%8B%E4%BB%A3%E8%B0%A2.png" alt="" class="img-responsive"> | ||
+ | <h5 style="text-align:center "> Primitive metabolic path map</h5> | ||
+ | </div> | ||
+ | <div class="col-md-6"> | ||
+ | <img src="https://static.igem.org/mediawiki/2017/7/7b/%E9%85%B5%E6%AF%8D%E5%8E%9F%E5%A7%8B%E4%BB%A3%E8%B0%A2%E5%9B%BE.png" alt=" "class=" img-responsive "> | ||
+ | <h5 style="text-align:center "> Primitive metabolic path map</h5> | ||
+ | </div> | ||
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+ | </div> | ||
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<h4> | <h4> | ||
<br> We have a rational new design and transformation of the core enzyme ceaS2, at the same time, | <br> We have a rational new design and transformation of the core enzyme ceaS2, at the same time, | ||
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kinase (DAK). | kinase (DAK). | ||
<br> | <br> | ||
+ | |||
+ | |||
+ | |||
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<br> New route map | <br> New route map | ||
+ | |||
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+ | |||
<br> Before the implementation of the formal experiment, we need to model it to analyze the impact | <br> Before the implementation of the formal experiment, we need to model it to analyze the impact | ||
of the introduction of new routes on the original metabolic flow, especially the two intermediates | of the introduction of new routes on the original metabolic flow, especially the two intermediates | ||
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</h4> | </h4> | ||
<h4>The overall workflow is as follows:</h4> | <h4>The overall workflow is as follows:</h4> | ||
− | <h2 style="text-align:center">Parameter estimation</h2> | + | <h2 style="text-align:center ">Parameter estimation</h2> |
<h4>There are many parameters to be determined in the model. Most of these kinetic parameters can | <h4>There are many parameters to be determined in the model. Most of these kinetic parameters can | ||
be found in the literature or in the database, but at the same time, there are some kinetic | be found in the literature or in the database, but at the same time, there are some kinetic | ||
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we do the fitting of the probability density according to the two methods of the parameter | we do the fitting of the probability density according to the two methods of the parameter | ||
vector: 1.kernel density estimatebsp;2. Gaussian mixed model. | vector: 1.kernel density estimatebsp;2. Gaussian mixed model. | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/3/32/Model-4.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/3/32/Model-4.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
<br> | <br> | ||
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<br> | <br> | ||
<br> | <br> | ||
− | <h2 style="text-align:center">The basic workflow of parameter estimation:</h2> | + | <h2 style="text-align:center ">The basic workflow of parameter estimation:</h2> |
<h4>The Gaussian mixture model can be approximated to any real probability distribution in theory. | <h4>The Gaussian mixture model can be approximated to any real probability distribution in theory. | ||
The EM algorithm is used to estimate the parameters required for the model. And we use the | The EM algorithm is used to estimate the parameters required for the model. And we use the | ||
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parameters. | parameters. | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/f/f7/Model-5.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/f/f7/Model-5.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/b/b2/Model-6.1.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/b/b2/Model-6.1.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
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corresponding parameters when the bin reach average value. | corresponding parameters when the bin reach average value. | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/e/e5/Model-6.2.png" class="img-responsive" width="20%" height="20%"> | + | <img src="https://static.igem.org/mediawiki/2017/e/e5/Model-6.2.png " class="img-responsive |
+ | " width="20% " height="20% "> | ||
</div> | </div> | ||
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of the original PDF. The specific form and parameter values are as follows: | of the original PDF. The specific form and parameter values are as follows: | ||
<br> The reaction path of the original pathway is Gly to Gly-3-p and then to DAHP | <br> The reaction path of the original pathway is Gly to Gly-3-p and then to DAHP | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/d/da/Model-7.png" class="img-responsive" width="40%" height="40%"> | + | <img src="https://static.igem.org/mediawiki/2017/d/da/Model-7.png " class="img-responsive |
+ | " width="40% " height="40% "> | ||
</div> | </div> | ||
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</h4> | </h4> | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/9/95/Model-8.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/9/95/Model-8.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
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<br> | <br> | ||
</h4> | </h4> | ||
− | <h4 style="text-align:center">Metabolic pathways after transformation</h4> | + | <h4 style="text-align:center ">Metabolic pathways after transformation</h4> |
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/3/33/Model-10.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/3/33/Model-10.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
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than glpK. Thus we assume that the GlyDH enzyme and the glpK enzyme satisfy the following | than glpK. Thus we assume that the GlyDH enzyme and the glpK enzyme satisfy the following | ||
relationship: | relationship: | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/5/50/Model-11.1.png" class="img-responsive" width="30%" height="30%"> | + | <img src="https://static.igem.org/mediawiki/2017/5/50/Model-11.1.png " class="img-responsive |
+ | " width="30% " height="30% "> | ||
</div> | </div> | ||
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have been known in previous studies. Next we adjust the alpha coefficient to study the effect | have been known in previous studies. Next we adjust the alpha coefficient to study the effect | ||
of different ratios on the overall metabolic flow. | of different ratios on the overall metabolic flow. | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/9/9c/Model-11.2.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/9/9c/Model-11.2.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
</h4> | </h4> | ||
<br> | <br> | ||
− | <h4 style="text-align:center">KATA Sensitivity Test before Modification</h4> | + | <h4 style="text-align:center ">KATA Sensitivity Test before Modification</h4> |
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/8/89/Model-12.1.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/8/89/Model-12.1.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
<br> | <br> | ||
− | <h4 style="text-align:center">KATA Sensitivity Test after Modification</h4> | + | <h4 style="text-align:center ">KATA Sensitivity Test after Modification</h4> |
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/e/e9/Model-12.2.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/e/e9/Model-12.2.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
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<br> | <br> | ||
<br> | <br> | ||
− | <h4 style="text-align:center">Before transformation</h4> | + | <h4 style="text-align:center ">Before transformation</h4> |
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/9/91/Model-14.1.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/9/91/Model-14.1.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
<br> | <br> | ||
− | <h4 style="text-align:center">After trransformation</h4> | + | <h4 style="text-align:center ">After trransformation</h4> |
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/d/d8/Model-14.2.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/d/d8/Model-14.2.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
<h4> | <h4> | ||
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<br> But when we adjust the standard deviation of the normal distribution random variable to | <br> But when we adjust the standard deviation of the normal distribution random variable to | ||
0.05, the result is shown below. | 0.05, the result is shown below. | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/f/f2/Model-15.1.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/f/f2/Model-15.1.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
− | <div align="center"> | + | <div align="center "> |
− | <img src="https://static.igem.org/mediawiki/2017/c/ce/Model-15.2.png" class="img-responsive" width="60%" height="60%"> | + | <img src="https://static.igem.org/mediawiki/2017/c/ce/Model-15.2.png " class="img-responsive |
+ | " width="60% " height="60% "> | ||
</div> | </div> | ||
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</div> | </div> | ||
− | <div class="tab-pane fade" id="service-two"> | + | <div class="tab-pane fade " id="service-two "> |
− | <h3 style="text-align: center;">Abstract</h3> | + | <h3 style="text-align: center; ">Abstract</h3> |
<br> | <br> | ||
<h4>Engineering for the desired enzyme catalytic properties plays an important role in the biosynthesis | <h4>Engineering for the desired enzyme catalytic properties plays an important role in the biosynthesis | ||
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<br> | <br> | ||
</h4> | </h4> | ||
− | <h3 style="text-align: center;">Introduction</h3> | + | <h3 style="text-align: center; ">Introduction</h3> |
<h4> | <h4> | ||
<br> Enzyme engineering has been extensively used to optimize biocatalysts in industrial biotechnology | <br> Enzyme engineering has been extensively used to optimize biocatalysts in industrial biotechnology | ||
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<br> | <br> | ||
</h4> | </h4> | ||
− | <h3 style="text-align: center;">What is AEMD?</h3> | + | <h3 style="text-align: center; ">What is AEMD?</h3> |
<h4> | <h4> | ||
<br> AEMD is a web-based pipeline, which integrates several approaches together for enzyme stability, | <br> AEMD is a web-based pipeline, which integrates several approaches together for enzyme stability, | ||
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<br> | <br> | ||
</h4> | </h4> | ||
− | <h3 style="text-align: center;">Process</h3> | + | <h3 style="text-align: center; ">Process</h3> |
<h4> | <h4> | ||
<br> AEMD is a web-based pipeline, which integrates several approaches together for enzyme stability, | <br> AEMD is a web-based pipeline, which integrates several approaches together for enzyme stability, | ||
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</div> | </div> | ||
− | <img src="https://static.igem.org/mediawiki/2017/0/0c/Jz.png" class="img-responsive"> | + | <img src="https://static.igem.org/mediawiki/2017/0/0c/Jz.png " class="img-responsive "> |
</div> | </div> | ||
</div> | </div> |
Revision as of 20:20, 31 October 2017