Difference between revisions of "Team:HUST-China/Sort of three genes"

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Sort of three genes

1. Overview

In Rhodopseudomonas, the sequence of genes in plasmid influences them expression ability. (Shou-Chen.2012) We have three genes to transfer. So we should find out which gene is the most important, and we sort three genes by their importance.

But then we meet a problem that there are not enough references about Rhodopseudomonas for us to obtain enough parameters for our simulation, so we run the simulation in a large range of parameters for many times and use the statistical result to decide how to sort the three genes

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 references 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 find which is the most important in this parameter situation.

Income parameters	Metabolism parameters	Cross membrane parameters	Ks parameters	Gene expression
g_Pyruvate	k_2LdhA	V_max2	K_s1	K_s2
g_Acetyl-CoA	k_1LdhA		Ks_3A	[LdhA]
	V_max1		Ks_3M	Ks₅
	V_max3		K_s4
	V_max4
	V_max5

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 is not fair for each parameter situation 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 shown below:

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.

The result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes by their final scores: mles, lldp, ldhA.

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                  <div class="about-logo">
                    <h3><strong>1. <span class="red-content">Overview</span></strong></h3>
-                   <p>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.</p>
+                   <p>In Rhodopseudomonas, the sequence of genes in plasmid influences them expression ability. (Shou-Chen.2012) We have three genes to transfer. So we should find out which gene is the most important, and we sort three genes by their importance.</p>
+<p>But then we meet a problem that there are not enough references about Rhodopseudomonas for us to obtain enough parameters for our simulation, so we run the simulation in a large range of parameters for many times and use the statistical result to decide how to sort the three genes
+</p>
                    </div>
                  </div>
@@ Line 190: / Line 192: @@
                  <div class="about-logo">
                    <h3><strong>3. <span class="red-content">Parameters</span></strong></h3>
-                   <p>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.
+                   <p>There are not enough references 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 find which is the most important in this parameter situation.
                    </p>
                    <!--表格-->
@@ Line 254: / Line 256: @@
                  <div class="about-logo">
                    <h3><strong>4. <span class="red-content">Result</span></strong></h3>
-                   <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>
+                   <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 is not fair for each parameter situation 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 shown below:</p>
                       <div align="center">
                        <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>
                          <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 by following their final scores: mles, lldp, ldhA.</p>
+                       <p>The result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes by their final scores: mles, lldp, ldhA.</p>
                  </div>