Team:UT-Tokyo/Project

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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
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You <strong>MUST</strong> have all of the pages listed in the menu below with the names specified.  PLEASE keep all of your pages within your teams namespace. 
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                    <li><span class="mhead">Multicellular Analog Clock</span>
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                        <li><a href="#mSummary">Summary</a></li>
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                        <li><a href="#mBackground">Background</a></li>
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                        <li><a href="#mSystems">Systems</a></li>
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                        <li><a href="#mResults_and_Discussion">Results and Discussion</a></li>
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                    <li><span class="mhead">RNA Silencing</span>
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                        <li><a href="#rSystems">Systems</a></li>
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                        <li><a href="#rResults_and_Discussion">Results and Discussion</a></li>
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                        <li><a href="#rReferences">References</a></li>
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<h1>Multicellular Analog Clock</h1>
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            <h2 id="mSummary">Summary</h2>
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            <p class="ini"> Our concept of the multicellular analog clock is based on qualitative assumption such as how negative feedback loop behaves, how AHL diffuses, and so on. To ascertain our multicellular analog clock can function as an analogue clock, namely, to confirm the feasibility of our cell-cell communication included gene circuit, and to deepen understanding of behavior of the system, we conducted the following simulation. </p>
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            <p>Our model for multicellular analog clock consists of four parts: DDE analysis, parameter sensitivity analysis, parameter sweep, stochastic analysis. DDE analysis is to examine the feasibility of our project, and also provides the foundation for the other parts of analysis. Through parameter sensitivity analysis, we gained more insight of the relationship between input and output variables. The insight led to the third part of analysis, in which parameter sweep enabled us to grasp appropriate ranges fo the identified sensitive parameters. Finally, we conducted stochastic analysis with the sensitive parameters fixed, and simulate our device's behavior under the actual conditions.
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            <h2 id="mBackground">Background</h2>
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            <p class="ini">To simulate the cell-cell communication system, we developed a delayed differential equation model. The equation used in the model are followings. The variables are described in the following table. </p>
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            <img src="ddes.png" class="figure">
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<p> In our cell-cell communication system, the major kinetic events are: mCherry synthesis and degradation, LuxI synthesis and degradation, TetR synthesis and degradation, AHL synthesis and degradation. These kinetic events are contained in the equations. The following describes how the equations are developed.
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</p>
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<li>mCherry synthesis and degradation
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<li>LuxI synthesis and degradation</li>
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<li>TetR synthesis and degradation</li>
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<li>AHL synthesis and degradation</li>
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</ul>
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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<h2 id="mSystems">Systems</h2>
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!align="center"|[[Team:UT-Tokyo|Home]]
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<h2 id="mResults_and_Discussion">Results and Discussion</h2>
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!align="center"|[[Team:UT-Tokyo/Team|Team]]
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<h2 id="mReferences">References</h2>
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!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=UT-Tokyo Official Team Profile]
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!align="center"|[[Team:UT-Tokyo/Project|Project]]
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!align="center"|[[Team:UT-Tokyo/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:UT-Tokyo/Modeling|Modeling]]
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!align="center"|[[Team:UT-Tokyo/Notebook|Notebook]]
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!align="center"|[[Team:UT-Tokyo/Safety|Safety]]
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!align="center"|[[Team:UT-Tokyo/Attributions|Attributions]]
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            <h1>RNA Silencing</h1>
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            <h2 id="mSummary">Summary</h2>
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            <p class="ini"> Our concept of the multicellular analog clock is based on qualitative assumption such as how negative feedback loop behaves, how AHL diffuses, and so on. To ascertain our multicellular analog clock can function as an analogue clock, namely, to confirm the feasibility of our cell-cell communication included gene circuit, and to deepen understanding of behavior of the system, we conducted the following simulation. </p>
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            <p>Our model for multicellular analog clock consists of four parts: DDE analysis, parameter sensitivity analysis, parameter sweep, stochastic analysis. DDE analysis is to examine the feasibility of our project, and also provides the foundation for the other parts of analysis. Through parameter sensitivity analysis, we gained more insight of the relationship between input and output variables. The insight led to the third part of analysis, in which parameter sweep enabled us to grasp appropriate ranges fo the identified sensitive parameters. Finally, we conducted stochastic analysis with the sensitive parameters fixed, and simulate our device's behavior under the actual conditions.
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            <h2 id="mBackground">Background</h2>
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            <p class="ini">To simulate the cell-cell communication system, we developed a delayed differential equation model. The equation used in the model are followings. The variables are described in the following table. </p>
 +
            <img src="ddes.png" class="figure">
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<p> In our cell-cell communication system, the major kinetic events are: mCherry synthesis and degradation, LuxI synthesis and degradation, TetR synthesis and degradation, AHL synthesis and degradation. These kinetic events are contained in the equations. The following describes how the equations are developed.
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== '''Overall project''' ==
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<ul>
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<li>mCherry synthesis and degradation
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<li>LuxI synthesis and degradation</li>
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<li>TetR synthesis and degradation</li>
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<li>AHL synthesis and degradation</li>
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</ul>
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Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)
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<h2 id="mSystems">Systems</h2>
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<h2 id="mResults_and_Discussion">Results and Discussion</h2>
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<h2 id="mReferences">References</h2>
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== Project Details==
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=== Part 2 ===
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=== The Experiments ===
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=== Part 3 ===
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== Results ==
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Revision as of 10:04, 11 September 2013

           PROJECT

Multicellular Analog Clock

Summary

Our concept of the multicellular analog clock is based on qualitative assumption such as how negative feedback loop behaves, how AHL diffuses, and so on. To ascertain our multicellular analog clock can function as an analogue clock, namely, to confirm the feasibility of our cell-cell communication included gene circuit, and to deepen understanding of behavior of the system, we conducted the following simulation.

Our model for multicellular analog clock consists of four parts: DDE analysis, parameter sensitivity analysis, parameter sweep, stochastic analysis. DDE analysis is to examine the feasibility of our project, and also provides the foundation for the other parts of analysis. Through parameter sensitivity analysis, we gained more insight of the relationship between input and output variables. The insight led to the third part of analysis, in which parameter sweep enabled us to grasp appropriate ranges fo the identified sensitive parameters. Finally, we conducted stochastic analysis with the sensitive parameters fixed, and simulate our device's behavior under the actual conditions.

Background

To simulate the cell-cell communication system, we developed a delayed differential equation model. The equation used in the model are followings. The variables are described in the following table.

In our cell-cell communication system, the major kinetic events are: mCherry synthesis and degradation, LuxI synthesis and degradation, TetR synthesis and degradation, AHL synthesis and degradation. These kinetic events are contained in the equations. The following describes how the equations are developed.

  • mCherry synthesis and degradation
  • LuxI synthesis and degradation
  • TetR synthesis and degradation
  • AHL synthesis and degradation

Systems

Results and Discussion

References

RNA Silencing

Summary

Our concept of the multicellular analog clock is based on qualitative assumption such as how negative feedback loop behaves, how AHL diffuses, and so on. To ascertain our multicellular analog clock can function as an analogue clock, namely, to confirm the feasibility of our cell-cell communication included gene circuit, and to deepen understanding of behavior of the system, we conducted the following simulation.

Our model for multicellular analog clock consists of four parts: DDE analysis, parameter sensitivity analysis, parameter sweep, stochastic analysis. DDE analysis is to examine the feasibility of our project, and also provides the foundation for the other parts of analysis. Through parameter sensitivity analysis, we gained more insight of the relationship between input and output variables. The insight led to the third part of analysis, in which parameter sweep enabled us to grasp appropriate ranges fo the identified sensitive parameters. Finally, we conducted stochastic analysis with the sensitive parameters fixed, and simulate our device's behavior under the actual conditions.

Background

To simulate the cell-cell communication system, we developed a delayed differential equation model. The equation used in the model are followings. The variables are described in the following table.

In our cell-cell communication system, the major kinetic events are: mCherry synthesis and degradation, LuxI synthesis and degradation, TetR synthesis and degradation, AHL synthesis and degradation. These kinetic events are contained in the equations. The following describes how the equations are developed.

  • mCherry synthesis and degradation
  • LuxI synthesis and degradation
  • TetR synthesis and degradation
  • AHL synthesis and degradation

Systems

Results and Discussion

References

Retrieved from "http://2013.igem.org/Team:UT-Tokyo/Project"