Difference between revisions of "Team:BIT-China/Model"
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<li> | <li> | ||
<a>PROJECT</a> | <a>PROJECT</a> | ||
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<li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsFeedback">Feedback</a></li> | <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsFeedback">Feedback</a></li> | ||
<li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsOutput">Output</a></li> | <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsOutput">Output</a></li> | ||
| − | <li><a href="https://2018.igem.org/Team:BIT-China/ | + | <li><a href="https://2018.igem.org/Team:BIT-China/Results">Results</a></li> |
</ul> | </ul> | ||
</li> | </li> | ||
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<ul> | <ul> | ||
<li><a href="https://2018.igem.org/Team:BIT-China/Model">Overview</a></li> | <li><a href="https://2018.igem.org/Team:BIT-China/Model">Overview</a></li> | ||
| − | <li><a href="https://2018.igem.org/Team:BIT-China/FluorescentProbesModel">Fluorescent | + | <li><a href="https://2018.igem.org/Team:BIT-China/FluorescentProbesModel">Fluorescent Probe Model </a></li> |
<li><a href="https://2018.igem.org/Team:BIT-China/H2O2DecompositionModel">H<sub>2</sub>O<sub>2</sub> | <li><a href="https://2018.igem.org/Team:BIT-China/H2O2DecompositionModel">H<sub>2</sub>O<sub>2</sub> | ||
Decomposition Model</a></li> | Decomposition Model</a></li> | ||
<li><a href="https://2018.igem.org/Team:BIT-China/roGFP2-Orp1MichaelisEquationModel">roGFP2-Orp1 | <li><a href="https://2018.igem.org/Team:BIT-China/roGFP2-Orp1MichaelisEquationModel">roGFP2-Orp1 | ||
| − | Michaelis | + | Michaelis equation Model</a></li> |
</ul> | </ul> | ||
</li> | </li> | ||
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<div id="MD-content-all" class="MD-content-container" style="margin-top:calc(25vh - 30px);"> | <div id="MD-content-all" class="MD-content-container" style="margin-top:calc(25vh - 30px);"> | ||
<div class="MD-title"> | <div class="MD-title"> | ||
| − | <a style="border-bottom-style: solid;text-decoration: none;color: #131313;"> | + | <a style="border-bottom-style: solid;text-decoration: none;color: #131313;">OVERVIEW</a> |
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<div id="MD1" class="MD-overview MD-margin-toTitle"> | <div id="MD1" class="MD-overview MD-margin-toTitle"> | ||
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<p class="MD-content-p MD-margin-toP"> | <p class="MD-content-p MD-margin-toP"> | ||
| − | To verify the functions of <i>yno1 | + | To verify the functions of <i>yno1/ndi1</i> genes and roGFP2-Orp1 fluorescent protein, DCFH-DA |
fluorescent | fluorescent | ||
probe was chosen as our output signal reference, which can detect and measure ROS concentration | probe was chosen as our output signal reference, which can detect and measure ROS concentration | ||
changes and present relative antioxidative strength. The process is indirect, so we set up <b>Fluorescent | changes and present relative antioxidative strength. The process is indirect, so we set up <b>Fluorescent | ||
| − | + | Probe Model</b> to normalize fluorescence intensities and H<sub>2</sub>O<sub>2</sub> | |
concentration, which made them comparable to each other. | concentration, which made them comparable to each other. | ||
</p> | </p> | ||
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roGFP2-Orp1 Michealis equation Model described the connection between roGFP2-Orp1 and intracellular | roGFP2-Orp1 Michealis equation Model described the connection between roGFP2-Orp1 and intracellular | ||
H<sub>2</sub>O<sub>2</sub>. | H<sub>2</sub>O<sub>2</sub>. | ||
| + | </p> | ||
| + | <p class="MD-content-p MD-margin-toP"> | ||
| + | With the three models mentioned above, we finally proved the accessibility of our roGFP2-Orp1 detecting method. | ||
</p> | </p> | ||
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<div id="MD2" class="cd-section MD-margin-title2ToUp"> | <div id="MD2" class="cd-section MD-margin-title2ToUp"> | ||
<div class="MD-title-1" style="border-left-style:solid;padding-left:10px;"> | <div class="MD-title-1" style="border-left-style:solid;padding-left:10px;"> | ||
| − | Fluorescent | + | Fluorescent Probe Model <a href="https://2018.igem.org/Team:BIT-China/FluorescentProbesModel" style="color:#131313;text-decoration:none;font-size: 16px;"> |
(Chick | (Chick | ||
here for details)</a> | here for details)</a> | ||
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<div class="MD-content MD-margin-toTitle1"> | <div class="MD-content MD-margin-toTitle1"> | ||
<p class="MD-content-p"> | <p class="MD-content-p"> | ||
| − | we fitted the relationship between | + | In our experiment, we found it was hard to measure the intracellular H<sub>2</sub>O<sub>2</sub> concentration, so we controlled the external H<sub>2</sub>O<sub>2</sub> concentration in culture to confirm our system's function because the H<sub>2</sub>O<sub>2</sub> can entry the cell quickly through simple diffusion. So we fitted the relationship between two kinds of H<sub>2</sub>O<sub>2</sub> concentration, through experimental data and ordinary differential equation based on the processes of H<sub>2</sub>O<sub>2</sub> diffusion and decomposition in yeast cells. In this way, the mutual translation of external and intracellular H<sub>2</sub>O<sub>2</sub> concentrations can be achieved. |
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Latest revision as of 00:40, 18 October 2018
Modeling is significant for supporting and improving the meaning of our project. Generally speaking, we hope to use mathematics methods to verify the feasibility and validity of our project. In this modeling, four core variables were introduced: fluorescence intensity of DFCH-DA probe, fluorescence intensity of roGFP2-Orp1 protein, external H2O2 concentration and intracellular H2O2 concentration.
roGFP2-Orp1 protein expression cassette is our core manner for detecting and measuring ROS level. In the further application of our device, users can calculate antioxidative ability by collecting roGFP2-Orp1fluoresecent intensities data. The whole modeling goes with the goal that making roGFP2-Orp1 realize it's proper functions.
To verify the functions of yno1/ndi1 genes and roGFP2-Orp1 fluorescent protein, DCFH-DA fluorescent probe was chosen as our output signal reference, which can detect and measure ROS concentration changes and present relative antioxidative strength. The process is indirect, so we set up Fluorescent Probe Model to normalize fluorescence intensities and H2O2 concentration, which made them comparable to each other.
To simulate the accumulation of intracellular H2O2 and set a relationship with external H2O2(the external H2O2 is the H2O2 we added in media), H2O2 Decomposition Model was induced.
With simulating the process that how roGFP2-Orp1 generates, reacts and degrades inside cells, roGFP2-Orp1 Michealis equation Model described the connection between roGFP2-Orp1 and intracellular H2O2.
With the three models mentioned above, we finally proved the accessibility of our roGFP2-Orp1 detecting method.
The model was established based on the mechanism of the fluorescence probe and we revised it according to the experimental results. From this model we can realize the conversion between fluorescence intensity of the probe and intracellular H2O2 concentration from overexpression of genes.
In our experiment, we found it was hard to measure the intracellular H2O2 concentration, so we controlled the external H2O2 concentration in culture to confirm our system's function because the H2O2 can entry the cell quickly through simple diffusion. So we fitted the relationship between two kinds of H2O2 concentration, through experimental data and ordinary differential equation based on the processes of H2O2 diffusion and decomposition in yeast cells. In this way, the mutual translation of external and intracellular H2O2 concentrations can be achieved.
The model was established based on the mechanism of the Michealis equation to describe the relationship between intracellular H2O2 concentrations and the roGFP2 fluorescence intensity changing. We simplified the process of the reaction between roGFP2-Orp1 and intracellular H2O2 as a classic Michealis equation, which helped us understanding this process better.
