Team:Warwick/Parts/IRES

From 2014.igem.org

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             <h1> MODELLING </h1> <br> <br>
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             <h1> IRES </h1> <br> <br>
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<p> Our modelling in this project has several aims: </p>
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<p>This
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<ul type="circle">
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<li>To find the amount of DPP-IV reduction reached when the system reaches equilibrium</li>
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<li>To find a way to control the level of DPP-IV reduction</li>
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<li>To find the minimum number of RdRps, replicons, etc to be initially transfected into the cell, which are required to achieve a steady state for the system</li>
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<li>To find out how long does it take for the system to reach equilibrium</li>
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<li>To find out the level of reduction we need to treat diabetes</li>
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<li>To find out how stable the system is (i.e. will the system only work in very specific situations, or in lots of different systems?)
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</ul>
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<p> We are currently using Simbiology in Matlab and Copasi to model the system. We are currently adapting several different models, which come from research into HCV replicons, to our system. If our models can be made to fit our experiments well, we may extend our project to try and find a way to control the level of DPP-IV which is reduced. In addition modelling the system will allow it to be better optimised in the future, and optimum values for constants such as the strength of the ribosome binding sites, and the number of siRNAs produced by each degradation, so that the effect of our biobrick can be optimised. </p>
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<p> We are currently using Simbiology in Matlab and Copasi to model the system. We are currently adapting several different models, which come from research into HCV replicons, to our system. If our models can be made to fit our experiments well, we may extend our project to try and find a way to control the level of DPP-IV which is reduced. In addition modelling the system will allow it to be better optimised in the future, and optimum values for constants such as the strength of the ribosome binding sites, and the number of siRNAs produced by each degradation, so that the effect of our biobrick can be optimised. </p>
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<p> Initially we determined that our system should reach some equilibrium after a certain amount of time. This is because firstly, HCV is a successful virus, so the replicons should not completely degrade away as time goes to infinity.  Secondly, since there are only a finite amount of resources within the cell, the number of replicons in the system cannot keep increasing forever. This means either the number of replicons must tend towards a certain constant (constant with respect to time), or the number of replicons should tend towards oscillations. </p>
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acts as an initiation for eukaryotic
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<p>
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ribosomes and begins translation of the
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        \begin{eqnarray}
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\label{system1}
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following protein sequence. We
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\frac{dm}{dt} &amp;=&amp; \alpha_m - \beta_m m - k_s ms
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\\ \label{system2}
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compared two different IRESs: the
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\frac{ds}{dt} &amp;=&amp; \alpha_s - \beta_s s - p_s k_s ms - k_r sr
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\\ \label{system3}
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classical EMCV IRES used in many papers,which has been shown to be compatible
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\frac{dr}{dt} &amp;=&amp; \alpha_r - \beta_r r - p_r k_r sr
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\end{eqnarray}
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with replicons and the NKRF IRES derived from the 3’UTR of
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</p>
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the mammalian NF-kappaB repressing
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factor, which we also chose to test because during
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investigation regarding the efficacy and
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strength of the EMCV IRES, the NKRF derived
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IRES was shown to be 30-fold more
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efficient however had never been previously used in Huh7.</p>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442023">here</a> to learn about our EMCV IRES. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442024">here</a> to learn about our NKRF IRES. </h2>  
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</div>

Revision as of 23:33, 16 October 2014

IRES



This acts as an initiation for eukaryotic ribosomes and begins translation of the following protein sequence. We compared two different IRESs: the classical EMCV IRES used in many papers,which has been shown to be compatible with replicons and the NKRF IRES derived from the 3’UTR of the mammalian NF-kappaB repressing factor, which we also chose to test because during investigation regarding the efficacy and strength of the EMCV IRES, the NKRF derived IRES was shown to be 30-fold more efficient however had never been previously used in Huh7.

Click here to learn about our EMCV IRES.

Click here to learn about our NKRF IRES.

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