Difference between revisions of "Team:HUST-China/Sort of three genes"
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<h3><strong>4. <span class="red-content">Result</span></strong></h3> | <h3><strong>4. <span class="red-content">Result</span></strong></h3> | ||
| − | <p>We generate each group ’s value | + | <p>We generate each group ’s value from 〖10〗^(-5) to 〖10〗^5，and run the simulation. At the beginning, we simply sum the concentration of Lactate outside. But it’s not fair for every parameter situations because in some cases the value of final result is much lower than others. So we use the SOFTMAX function to turn the concentration result into scores from 0 to 1. The function is:</p> |
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<img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074349%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" ></div> | <img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074349%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" ></div> | ||
<p>If the gene expression parameter is lower than 1，we take the negative value of score. Then we sum all scores together, and get the final result.</p> | <p>If the gene expression parameter is lower than 1，we take the negative value of score. Then we sum all scores together, and get the final result.</p> | ||
<img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074548%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" > | <img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074548%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" > | ||
| − | <p>Result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes | + | <p>Result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes by following their final scores: mles, lldp, ldhA.</p> |
</div> | </div> | ||
Revision as of 08:43, 15 October 2018
Sort of three genes
1. Overview
Safe strains and safe gene products were selected to complete our project design. The products of the genes transferred into the microorganisms are all determined and do not cause any known diseases to humans, animals and plants. Any microorganisms involved in our project is encapsulate in electricity generation device. So far, the devise can recharge the phone, and in the future, electricity generation based on microbial co-culture may become a new choice of electricity production.
2. Function
(We skip some reactions in tricarboxylic acid cycle, and let Isocitrate come to Malate in one reaction.)
3. Parameters
There are not enough studies for us to get exact parameters. So we assort parameters into several groups. And change one group’s value each time. At the same time, we change the expression abilities of three genes to see which is most important in this parameter situation.
| Income parameters | Metabolism parameters | Cross membrane parameters | Ks parameters | Gene expression |
|---|---|---|---|---|
| gPyruvate | k2LdhA | Vmax2 | Ks1 | Ks2 |
| gAcetyl-CoA | k1LdhA | Ks3A | [LdhA] | |
| Vmax1 | Ks3M | Ks5 | ||
| Vmax3 | Ks4 | |||
| Vmax4 | ||||
| Vmax5 |
4. Result
We generate each group ’s value from 〖10〗^(-5) to 〖10〗^5，and run the simulation. At the beginning, we simply sum the concentration of Lactate outside. But it’s not fair for every parameter situations because in some cases the value of final result is much lower than others. So we use the SOFTMAX function to turn the concentration result into scores from 0 to 1. The function is:
If the gene expression parameter is lower than 1，we take the negative value of score. Then we sum all scores together, and get the final result.
Result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes by following their final scores: mles, lldp, ldhA.
