Difference between revisions of "Team:HUST-China/Model/model-app"

Line 222: Line 222:
 
                 <p>Since our loop has a filtering effect, for the sake of convenience we will set the rate for most of the following models to constant.</p>
 
                 <p>Since our loop has a filtering effect, for the sake of convenience we will set the rate for most of the following models to constant.</p>
 
                 <h2>Lactose absorption</h2>
 
                 <h2>Lactose absorption</h2>
−
                 <p>Assuming that there is one engineered bacteria in each matrix, lactose flows through the matrix. We want to see the change in lactose concentration over time in the matrix to see if our engineering bacteria can consume a significant amount of lactose and reduce lactose absorption by other flora .</p>
+
                 <p>Assuming that there is one engineered bacteria in each matrix, lactose flows through the matrix. We want to see the change in lactose concentration over time in the matrix to see if our engineering bacteria can consume a significant amount of lactose and reduce lactose absorption by other flora.</p>
 
                 <img src="https://static.igem.org/mediawiki/2016/6/63/T--HUST-China--application_lac_flow.png" alt="">
 
                 <img src="https://static.igem.org/mediawiki/2016/6/63/T--HUST-China--application_lac_flow.png" alt="">
 
                 <p style="text-align:center">(To simulate the flow of lactose in the intestine)</p>
 
                 <p style="text-align:center">(To simulate the flow of lactose in the intestine)</p>
−
                 <p>It is a pity that we have found that even if we adjust the lactose absorption rate of our engineered bacteria to a considerable value, we can not prevent the spread of lactose, even the impact of the surrounding lactose concentration is not as large as we thought, which means that Our ability to compete for lactose is not strong, but if we increase the number of flora and may cause other problems of the human body. This means that in our next step we will use secretory enzymes to help break down the lactose.</p>
+
                 <p>It is a pity that we have found that even if we adjust the lactose absorption rate of our engineered bacteria to a considerable value, we cannot prevent the spread of lactose, even the impact of the surrounding lactose concentration is not as large as we thought, which means that Our ability to compete for lactose is not strong, but if we increase the number of flora, it may cause other problems of the human body. This means that in our next step we will use secretory enzymes to help break down the lactose.</p>
 
                 <h2>Decomposition of lactic acid</h2>
 
                 <h2>Decomposition of lactic acid</h2>
−
                 <p>We assume that there is one engineering bacterium (center) in each matrix and four other bacteria (random positions). Assuming that the other bacteria consistently produce lactic acid after absorbing lactose, our engineered bacteria are experiencing a ph transition due to lactic acid buildup (ph &lt 7)and then began to secrete lactate dehydrogenase. Secretory lacta te dehydrogenase can break down lactic acid and reduce gastrointestinal irritation.</p>
+
                 <p>We assume that there is one engineering bacterium (center) in each matrix and four other bacteria (random positions). Assuming that the other bacteria consistently produce lactic acid after absorbing lactose, our engineered bacteria are experiencing a pH transition due to lactic acid buildup (pH<7) and then began to secrete lactate dehydrogenase. Secretory lactate dehydrogenase can break down lactic acid and reduce gastrointestinal irritation.</p>
 
                 <p>We need to confirm the change in lactic acid concentration by diffusion model to determine whether our engineered bacteria play a corresponding role.</p>
 
                 <p>We need to confirm the change in lactic acid concentration by diffusion model to determine whether our engineered bacteria play a corresponding role.</p>
 
                 <img src="https://static.igem.org/mediawiki/2016/5/59/T--HUST-China--modeling-application-LA_decomposition.png" alt="">
 
                 <img src="https://static.igem.org/mediawiki/2016/5/59/T--HUST-China--modeling-application-LA_decomposition.png" alt="">
Line 237: Line 237:
 
                 <img src="https://static.igem.org/mediawiki/2016/f/f4/T--HUST-China--modeling-application-LA_diffuse-last.png" alt="">
 
                 <img src="https://static.igem.org/mediawiki/2016/f/f4/T--HUST-China--modeling-application-LA_diffuse-last.png" alt="">
 
                 <p style="text-align:center">(Lactic acid final time concentration [without engineered bacteria])</p>
 
                 <p style="text-align:center">(Lactic acid final time concentration [without engineered bacteria])</p>
−
                 <p>We can clearly see that lactate dehydrogenase produced by our engineering bacteria can effectively reduce the lactate concentration in the whole matrix through the comparison of the dynamic state and the final state. According to our summation of lactic acid concentration in the matrix, Of the engineered bacteria reduced the overall lactic acid concentration by 20% and could reduce irritation to the gastrointestinal tract.</p>
+
                 <p>We can clearly see that lactate dehydrogenase produced by our engineering bacteria can effectively reduce the lactate concentration in the whole matrix through the comparison of the dynamic state and the final state. According to our summation of lactic acid concentration in the matrix, the engineered bacteria reduce the overall lactic acid concentration by 20% and could reduce irritation to the gastrointestinal tract.</p>
  
  

Revision as of 11:54, 18 October 2016

Modeling

Application

Overview

We designed our protocol for lactose intolerance based on prokaryotic pathways, which continue to secrete β-galactosidase at high pH, and lactate dehydrogenase when ph decreases due to elevated lactate concentrations.

Gastrointestinal diffusion model

- For the treatment of lactose intolerance

Through previous modeling and modeling of our prokaryotic pathways, we learned some of the necessary data to aid our application. The pathways we use to treat lactose intolerance are the same as our prokaryotic pathways.

To further model our application we created a model based on the diffusion equation. We modeled a portion of the intestinal tract with a 20 x 20 x 20 three-dimensional matrix and used it to model the state of our engineered bacteria in the stomach.

We hope that this part of the simulation model to test our loop in the treatment of lactose intolerance of the feasibility and make more improvements.

Since our loop has a filtering effect, for the sake of convenience we will set the rate for most of the following models to constant.

Lactose absorption

Assuming that there is one engineered bacteria in each matrix, lactose flows through the matrix. We want to see the change in lactose concentration over time in the matrix to see if our engineering bacteria can consume a significant amount of lactose and reduce lactose absorption by other flora.

(To simulate the flow of lactose in the intestine)

It is a pity that we have found that even if we adjust the lactose absorption rate of our engineered bacteria to a considerable value, we cannot prevent the spread of lactose, even the impact of the surrounding lactose concentration is not as large as we thought, which means that Our ability to compete for lactose is not strong, but if we increase the number of flora, it may cause other problems of the human body. This means that in our next step we will use secretory enzymes to help break down the lactose.

Decomposition of lactic acid

We assume that there is one engineering bacterium (center) in each matrix and four other bacteria (random positions). Assuming that the other bacteria consistently produce lactic acid after absorbing lactose, our engineered bacteria are experiencing a pH transition due to lactic acid buildup (pH<7) and then began to secrete lactate dehydrogenase. Secretory lactate dehydrogenase can break down lactic acid and reduce gastrointestinal irritation.

We need to confirm the change in lactic acid concentration by diffusion model to determine whether our engineered bacteria play a corresponding role.

(Lactic acid diffusion [with engineered bacteria])

(Lactic acid diffusion [without engineered bacteria])

(Lactic acid final time concentration [with engineered bacteria])

(Lactic acid final time concentration [without engineered bacteria])

We can clearly see that lactate dehydrogenase produced by our engineering bacteria can effectively reduce the lactate concentration in the whole matrix through the comparison of the dynamic state and the final state. According to our summation of lactic acid concentration in the matrix, the engineered bacteria reduce the overall lactic acid concentration by 20% and could reduce irritation to the gastrointestinal tract.

Summary

We have obtained some useful results by simulating the intestinal tract. It is concluded that although the ability of our engineered bacteria to compete for lactose needs to be enhanced, it has some effect on inhibiting the increase of lactic acid concentration, which can relieve lactose intolerance to a certain extent.