Difference between revisions of "Team:Hong Kong HKUST/NUS"

 
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<b><em>Modelling</em></b>
 
<b><em>Modelling</em></b>
 
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<p style="color: black; font-size:1.2em;">This year, in addition to the wetlab module, we also collaborated on modelling part of our projects. To capture the dynamic of our tristable system, we built a simulation model based on chemical kinetics which assumes that the system is spatially homogenous (i.e. Diffusion of all molecules are neglected). This class of modelling approach simplifies the analysis, meanwhile being capable of capturing most of the properties of our system accurately; nonetheless, the formulation approach which considers diffusion processes as negligible may give rise to the loss of certain amount of information associated with diffusion of molecules, while these pieces  information can be critical to some special dynamic of the system.
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<p style="color: black; font-size:1.2em;">The iGEM team from the National University of Singapore offered us a model to snapshot the dynamic of our tristable system. A simulation model was built, based on chemical kinetics which assumes that the system is spatially homogenous i.e. diffusion of all molecules are neglected.
 
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To tackle this, NUS helped us in developing a diffusion framework by applying their RIOT modelling system. Building on our original chemical-kinetics-based ordinary differential equation model, NUS modeller incorporated modules which describe the diffusion of the repressors, fluorescent proteins as well as both intracellular and extracellular inducers. Thanks to their work, we are able to have a more detailed and comprehensive understanding of the system’s behaviour on molecular level.
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This class of modelling approach simplifies the analysis, which is capable of capturing most of the properties of our system accurately. Nonetheless, the formulation approach, that considers diffusion processes as negligible may give rise to the loss of certain amount of information, which associated with molecular diffusion, can be critical to some special dynamic of the system.
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<br><br>
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To tackle this, NUS helped us in developing a diffusion framework by applying their RIOT modelling system. Grounded on our original chemical-kinetics-based ODE model, NUS modeler incorporated modules, which describe the diffusion of the repressors, fluorescent proteins, and both intracellular and extracellular inducers.
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<br><br>
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Thanks to their work, we have a more detailed and comprehensive understanding of the behaviour of our system on molecular level.
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<b><em>Characterisation of a particular constructs</em></b>
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<b><em>Construct Characterisation</em></b>
 
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<p> Sharing similar experimental assay method, we collaborate in the wet-lab part by characterising four of their constructs with different strength processing a lactate responsive promoter and a sfGFP reporter gene. Repeating the assay method from the NUS Singapore iGEM team, the characterisation we did in the HKUST could act as another sets of data for further verification.<br><br>
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Unfortunately, it seemed that the bacteria was not in a good condition and the blank solution also showed very high fluorescence which were not compatible with the data obtained in the NUS. Therefore, the results could not be compared in the end. <br><br>
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In order to assist NUS to verify their characterisation data, we were characterising four of their constructs with different strengths processing a lactate responsive promoter and a sfGFP reporter gene on our end. Assay method was provided by NUS.<br><br>
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But it seemed to us that the bacteria culture did not grow well after transformation, and the blank solution also showed very high fluorescence signals, which were not compatible with the data obtained in NUS, making the results incomparable. <br><br>
 
*To learn more about the project of NUS Singapore iGEM team, please go to <a href="https://2016.igem.org/Team:NUS_Singapore" target="_blank">here</a>.
 
*To learn more about the project of NUS Singapore iGEM team, please go to <a href="https://2016.igem.org/Team:NUS_Singapore" target="_blank">here</a>.
 
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Latest revision as of 20:02, 19 October 2016

Home

Collaborations with
iGEM team NUS Singapore


Modelling


The iGEM team from the National University of Singapore offered us a model to snapshot the dynamic of our tristable system. A simulation model was built, based on chemical kinetics which assumes that the system is spatially homogenous i.e. diffusion of all molecules are neglected.

This class of modelling approach simplifies the analysis, which is capable of capturing most of the properties of our system accurately. Nonetheless, the formulation approach, that considers diffusion processes as negligible may give rise to the loss of certain amount of information, which associated with molecular diffusion, can be critical to some special dynamic of the system.

To tackle this, NUS helped us in developing a diffusion framework by applying their RIOT modelling system. Grounded on our original chemical-kinetics-based ODE model, NUS modeler incorporated modules, which describe the diffusion of the repressors, fluorescent proteins, and both intracellular and extracellular inducers.

Thanks to their work, we have a more detailed and comprehensive understanding of the behaviour of our system on molecular level.

Construct Characterisation


In order to assist NUS to verify their characterisation data, we were characterising four of their constructs with different strengths processing a lactate responsive promoter and a sfGFP reporter gene on our end. Assay method was provided by NUS.

But it seemed to us that the bacteria culture did not grow well after transformation, and the blank solution also showed very high fluorescence signals, which were not compatible with the data obtained in NUS, making the results incomparable.

*To learn more about the project of NUS Singapore iGEM team, please go to here.