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Team:NYMU-Taipei/Modeling/Overview
From 2013.igem.org
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| - | + | ==System description== | |
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Our model can be generally divided into two sections. | Our model can be generally divided into two sections. | ||
．Circuit design | ．Circuit design | ||
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The first section of our model describes the regulation of Beecoli’s system, which mainly consists of three parts: | The first section of our model describes the regulation of Beecoli’s system, which mainly consists of three parts: | ||
| - | 1.Sensing: In this part, we describe how a constitutive promoter enhances the expressed level of activator OxyR. | + | 1. Sensing: In this part, we describe how a constitutive promoter enhances the expressed level of activator OxyR. Results are presented as a graph showing changes in OxyR concentration as time progress. |
| - | 2.Killing protein production: In this part, we describe the regulation pathway of killing protein production after AhpCp senses Nosema invasion. Results are presented as a graph showing changes in killing protein concentration as time progress after sensing promoter is triggered, which explains whether killing protein can eliminate Nosema ceranae timely. | + | 2. Killing protein production: In this part, we describe the regulation pathway of killing protein production after AhpCp senses Nosema invasion. Results are presented as a graph showing changes in killing protein concentration as time progress after sensing promoter is triggered, which explains whether killing protein can eliminate Nosema ceranae timely. |
| - | 3.Ethanol production: In this part, we describe the regulation pathway of ethanol production after AhpCp senses Nosema invasion. Results are presented as a graph showing changes in ethanol concentration as time progress after sensing promoter is triggered, which explains whether ethanol eliminates a sick bee timely when killing protein fails to kill Nosema, and that ethanol won’t kill a bee if it is cured in time. | + | 3. Ethanol production: In this part, we describe the regulation pathway of ethanol production after AhpCp senses Nosema invasion. Results are presented as a graph showing changes in ethanol concentration as time progress after sensing promoter is triggered, which explains whether ethanol eliminates a sick bee timely when killing protein fails to kill Nosema, and that ethanol won’t kill a bee if it is cured in time. |
In this system, OxyR senses changes in ROS level and regulate other circuits with promoter AhpCp, by enhancing its expression it regulates killing protein production and ethanol production more keenly. Killing protein and ethanol production effects an infected bee alternatively when the bee is in different Nosema invasion stages. | In this system, OxyR senses changes in ROS level and regulate other circuits with promoter AhpCp, by enhancing its expression it regulates killing protein production and ethanol production more keenly. Killing protein and ethanol production effects an infected bee alternatively when the bee is in different Nosema invasion stages. | ||
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==Contributions== | ==Contributions== | ||
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| - | + | 1. Our models for the circuit help the wet lab to choose biobricks for when designing the circuit. | |
| - | + | －To learn how the constitutive promoter regulating OxyR production was chosen, click here. | |
| - | + | －To learn how the regulators CI and LuxR were chosen in AMP production circuit, click here. | |
| - | 2.Our model for the synergistic effect of Nosema ceranae and Beecoli on an invaded colony provides a guideline for those who want to put our cure into practice | + | －To learn how the terminator set in ethanol producing circuit was chosen, click here. |
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| + | 2. Our model for the synergistic effect of Nosema ceranae and Beecoli on an invaded colony provides a guideline for those who want to put our cure into practice | ||
To learn about the tug of war between Nosema ceranae and Beecoli over the bees, and how many capsules should be fed to a bee colony in different infection stages, click here. | To learn about the tug of war between Nosema ceranae and Beecoli over the bees, and how many capsules should be fed to a bee colony in different infection stages, click here. | ||
==nnovations== | ==nnovations== | ||
| - | + | 1. We describe transcription and translation process separately and subsidized promoter strength with PoPS, constructing a realistic dynamic system rather than the old one described by possibilities. | |
| - | 1.We describe transcription and translation process separately and subsidized promoter strength with PoPS, constructing a realistic dynamic system rather than the old one described by possibilities. | + | |
[[To learn about this mechanism, click here.]] | [[To learn about this mechanism, click here.]] | ||
| - | 2.We describe positive and negative regulation by combining the experimental data with hill equation. | + | 2. We describe positive and negative regulation by combining the experimental data with hill equation. |
[[To learn about this mechanism, click here2.]] | [[To learn about this mechanism, click here2.]] | ||
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The promoter strengths used in our circuit model is provided by promoter testing conducted by our wet lab and partly from partregistry. | The promoter strengths used in our circuit model is provided by promoter testing conducted by our wet lab and partly from partregistry. | ||
| - | Statistics regarding how the capsules carry Beecoli into a bee’s midgut is provided by our wet lab experiment. The population growth rate is provided by previous research on Nosema ceranae influences on Apis Melifera done by the experts. | + | Statistics regarding how the capsules carry Beecoli into a bee’s midgut is provided by our wet lab experiment. The population growth rate is provided by previous research on Nosema ceranae influences on Apis Melifera done by the experts. |
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Revision as of 15:23, 27 October 2013
Contents |
System description
Our model can be generally divided into two sections.
．Circuit design The first section of our model describes the regulation of Beecoli’s system, which mainly consists of three parts:
1. Sensing: In this part, we describe how a constitutive promoter enhances the expressed level of activator OxyR. Results are presented as a graph showing changes in OxyR concentration as time progress.
2. Killing protein production: In this part, we describe the regulation pathway of killing protein production after AhpCp senses Nosema invasion. Results are presented as a graph showing changes in killing protein concentration as time progress after sensing promoter is triggered, which explains whether killing protein can eliminate Nosema ceranae timely.
3. Ethanol production: In this part, we describe the regulation pathway of ethanol production after AhpCp senses Nosema invasion. Results are presented as a graph showing changes in ethanol concentration as time progress after sensing promoter is triggered, which explains whether ethanol eliminates a sick bee timely when killing protein fails to kill Nosema, and that ethanol won’t kill a bee if it is cured in time.
In this system, OxyR senses changes in ROS level and regulate other circuits with promoter AhpCp, by enhancing its expression it regulates killing protein production and ethanol production more keenly. Killing protein and ethanol production effects an infected bee alternatively when the bee is in different Nosema invasion stages.
．Effect of Beecoli on the bee colony The second section of our model describes the system in which Nosema ceranae and Beecoli infect the subjected colony by an epidemic model. Results are presented as graphs showing population changes as time progress. In addition, there is a graph showing what capsule dosage and infection severity will result in which survival rate of the bee colony eventually for practical purpose.
This part of the model is based on the circuit’s efficiency discussed on the first section of our model.
Contributions
1. Our models for the circuit help the wet lab to choose biobricks for when designing the circuit.
－To learn how the constitutive promoter regulating OxyR production was chosen, click here.
－To learn how the regulators CI and LuxR were chosen in AMP production circuit, click here.
－To learn how the terminator set in ethanol producing circuit was chosen, click here.
2. Our model for the synergistic effect of Nosema ceranae and Beecoli on an invaded colony provides a guideline for those who want to put our cure into practice
To learn about the tug of war between Nosema ceranae and Beecoli over the bees, and how many capsules should be fed to a bee colony in different infection stages, click here.
nnovations
1. We describe transcription and translation process separately and subsidized promoter strength with PoPS, constructing a realistic dynamic system rather than the old one described by possibilities.
To learn about this mechanism, click here.
2. We describe positive and negative regulation by combining the experimental data with hill equation.
To learn about this mechanism, click here2.
Parameters and Reference
The promoter strengths used in our circuit model is provided by promoter testing conducted by our wet lab and partly from partregistry.
Statistics regarding how the capsules carry Beecoli into a bee’s midgut is provided by our wet lab experiment. The population growth rate is provided by previous research on Nosema ceranae influences on Apis Melifera done by the experts.
