Team:Warwick/Parts/3promoter

From 2014.igem.org

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             <h1> MODELLING </h1> <br> <br>
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             <h1> 5' Promoter </h1> <br> <br>
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<p> Our modelling in this project has several aims: </p>
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<p>This is derived from the 5i UTR of the HCV virus strain 1b isolate Con1. The secondary structure of this sequence acts as a binding site and initiates replication of the system by RdRp. It also includes the first 16 amino acids of the first gene of HCV as this has been shown to increase the efficacy of binding of the RdRp to the 5' promoter.</p>
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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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<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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<h2> Click <a href="http://parts.igem.org/Part:BBa_K1442118">here</a> to learn about our 5' Promoter. </h2>  
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<p>
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<h1> 3' Promoter </h1> <br> <br>
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        \begin{eqnarray}
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<p>Each unique RNA dependent RNA polymerase (RdRP) initiates de novo replication of a RNA strand by interacting with RdRP-specific RNA sequences, henceforth called RdRP/RNA promoters. The RdRP chosen for our project is taken from the Hepatitis C virus (HCV) and it recognizes a limited set of such sequences. All of them possess a few common characteristics: an initiation cytidylate at the 3’ end, where the replication starts; and a stable secondary structure – single stranded tail and a stem of various length. For our project in addition to the indigenous to HCV RdRP promoters, we designed alternative promoter sequences previously identified by Heinz et. Al. as templates for replication by the HCV RdRP. The list below illustrates all the 3' promoters we considered as part of our system.</p>
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\label{system1}
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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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\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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\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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</p>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442033">here</a> to learn about our C2. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442034">here</a> to learn about our 3' HCV. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442103">here</a> to learn about our Reverse 5' HCV. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442115">here</a> to learn about our B2. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442116">here</a> to learn about our SLC8. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442117">here</a> to learn about our Sldel+8. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442304">here</a> to learn about our SD3. </h2>
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<h2> Click <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1442108">here</a> to learn about our C2HP. </h2>
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Revision as of 00:13, 17 October 2014

5' Promoter



This is derived from the 5i UTR of the HCV virus strain 1b isolate Con1. The secondary structure of this sequence acts as a binding site and initiates replication of the system by RdRp. It also includes the first 16 amino acids of the first gene of HCV as this has been shown to increase the efficacy of binding of the RdRp to the 5' promoter.

Click here to learn about our 5' Promoter.

3' Promoter



Each unique RNA dependent RNA polymerase (RdRP) initiates de novo replication of a RNA strand by interacting with RdRP-specific RNA sequences, henceforth called RdRP/RNA promoters. The RdRP chosen for our project is taken from the Hepatitis C virus (HCV) and it recognizes a limited set of such sequences. All of them possess a few common characteristics: an initiation cytidylate at the 3’ end, where the replication starts; and a stable secondary structure – single stranded tail and a stem of various length. For our project in addition to the indigenous to HCV RdRP promoters, we designed alternative promoter sequences previously identified by Heinz et. Al. as templates for replication by the HCV RdRP. The list below illustrates all the 3' promoters we considered as part of our system.

Click here to learn about our C2.

Click here to learn about our 3' HCV.

Click here to learn about our Reverse 5' HCV.

Click here to learn about our B2.

Click here to learn about our SLC8.

Click here to learn about our Sldel+8.

Click here to learn about our SD3.

Click here to learn about our C2HP.

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