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<br> Based on the points above, we get a new parametric vector after weighting.In our model, we do the | <br> Based on the points above, we get a new parametric vector after weighting.In our model, we do the | ||
fitting of the probability density according to the two methods of the parameter vector. | fitting of the probability density according to the two methods of the parameter vector. | ||
− | <br> 1.kernel density | + | <div align="center"><img src="https://static.igem.org/mediawiki/2017/3/32/Model-4.png" class="img-responsive" width="60%" height="60%" ></div> |
+ | <br> 1.kernel density estimatebsp; 2. Gaussian mixed model. | ||
</h4> | </h4> | ||
− | + | <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. The EM | <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 Gaussian mixture | algorithm is used to estimate the parameters required for the model. And we use the Gaussian mixture | ||
model to estimate the probability density of the possible distribution of parameters. | model to estimate the probability density of the possible distribution of parameters. | ||
+ | |||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/f/f7/Model-5.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/b/b2/Model-6.1.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
+ | |||
+ | |||
<br> After making the probability distribution, we select Bin randomly, which meet the conditions of | <br> After making the probability distribution, we select Bin randomly, which meet the conditions of | ||
width = len / 10.And we select the most possible bin based on the CDF, and estimate the corresponding | width = len / 10.And we select the most possible bin based on the CDF, and estimate the corresponding | ||
parameters when the bin reach average value. | parameters when the bin reach average value. | ||
+ | |||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/e/e5/Model-6.2.png" class="img-responsive" width="20%" height="20%" ></div> | ||
+ | |||
+ | |||
+ | |||
<br> Finally, we get the estimated parameter values, as well as the corresponding parameters of the original | <br> Finally, we get the estimated parameter values, as well as the corresponding parameters of the original | ||
PDF. The specific form and parameter values are as follows: | 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"><img src="https://static.igem.org/mediawiki/2017/d/da/Model-7.png" class="img-responsive" width="40%" height="40%" ></div> | ||
+ | |||
+ | |||
<br> The original pathway belongs to the reaction of a single channel, and there is a random bibi reaction | <br> The original pathway belongs to the reaction of a single channel, and there is a random bibi reaction | ||
and an irreversible Mickey equation reaction. The reaction involves two enzymes paticipating - glpk | and an irreversible Mickey equation reaction. The reaction involves two enzymes paticipating - glpk | ||
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<br> | <br> | ||
</h4> | </h4> | ||
− | < | + | |
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/9/95/Model-8.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
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<h4> | <h4> | ||
<br> We can observe that the DHAP stops growing close to 50 minutes. | <br> We can observe that the DHAP stops growing close to 50 minutes. | ||
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</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"><img src="https://static.igem.org/mediawiki/2017/3/33/Model-10.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
+ | |||
<h4> | <h4> | ||
<br> We can see that the rate of DHAP is faster after changing the metabolic pathway, which means that | <br> We can see that the rate of DHAP is faster after changing the metabolic pathway, which means that | ||
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and as a result of our experiments, GlyDH exhibited higher catalytic efficiency than glpK. Thus we | and as a result of our experiments, GlyDH exhibited higher catalytic efficiency than glpK. Thus we | ||
assume that the GlyDH enzyme and the glpK enzyme satisfy the following relationship: | assume that the GlyDH enzyme and the glpK enzyme satisfy the following relationship: | ||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/5/50/Model-11.1.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
+ | |||
<br> GlyDH enzyme activity and the Km value for gly and the Km value of the glpk enzyme to gly have been | <br> GlyDH enzyme activity and the Km value for gly and the Km value of the glpk enzyme to gly have been | ||
known in previous studies. Next we adjust the alpha coefficient to study the effect of different | known in previous studies. Next we adjust the alpha coefficient to study the effect of different | ||
ratios on the overall metabolic flow. | ratios on the overall metabolic flow. | ||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/9/9c/Model-11.2.png" class="img-responsive" width="60%" height="60%" ></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"><img src="https://static.igem.org/mediawiki/2017/8/89/Model-12.1.png" class="img-responsive" width="60%" height="60%" ></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"><img src="https://static.igem.org/mediawiki/2017/e/e9/Model-12.2.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
+ | |||
<h4> | <h4> | ||
<br> We show the highest ratio (1000) and the lowest ratio (0.001) in yellow and blue lines respectively. | <br> We show the highest ratio (1000) and the lowest ratio (0.001) in yellow and blue lines respectively. | ||
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<br> | <br> | ||
<h4 style="text-align:center">Before transformation</h4> | <h4 style="text-align:center">Before transformation</h4> | ||
+ | |||
+ | |||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/9/91/Model-14.1.png" class="img-responsive" width="60%" height="60%" ></div> | ||
<br> | <br> | ||
<h4 style="text-align:center">After trransformation</h4> | <h4 style="text-align:center">After trransformation</h4> | ||
+ | |||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/d/d8/Model-14.2.png" class="img-responsive" width="60%" height="60%" ></div> | ||
<h4> | <h4> | ||
<br> We found that the random change of ATP concentration had a significant effect on the pathway after | <br> We found that the random change of ATP concentration had a significant effect on the pathway after | ||
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<br> But when we adjust the standard deviation of the normal distribution random variable to 0.05, the | <br> But when we adjust the standard deviation of the normal distribution random variable to 0.05, the | ||
result is shown below. | result is shown below. | ||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/f/f2/Model-15.1.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2017/c/ce/Model-15.2.png" class="img-responsive" width="60%" height="60%" ></div> | ||
+ | |||
+ | |||
<br> Thus, we found that even if ATP had a greater perturbation, the overall level was relatively high | <br> Thus, we found that even if ATP had a greater perturbation, the overall level was relatively high | ||
in 0-60 min compared to the previous standard deviation of 0.02. While the transformation of the | in 0-60 min compared to the previous standard deviation of 0.02. While the transformation of the |
Revision as of 18:15, 30 October 2017