Difference between revisions of "Team:Bielefeld-CeBiTec/Model"

Revision as of 16:26, 29 July 2018

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Modelling

„Any modeling project should be tempered by the morality of laziness.“ (Barnes et. al., 2010) This phrase illustrates that lab results can be predicted before actually working in the lab, saving precious time. Our project revolves around new discovered or theoretical biological systems like for example RNAi in prokaryotes or newly discovered copper transport porins. For those we will program following models beside the standard calculations for growth rates and reaction kinetics.

siRNA promoter model

First the most fitting siRNAs for our project has to be calculated. A program will be written which returns a selection of compatible siRNAs for a gene you want to silence. Possible secondary structures should also be considered (Mathews, 1999) because they could prevent the silencing mechanism of siRNAs.

Figure 1: The siRNA with the compatible secondary structure binds to the mRNA and enables its digestion and blocks the translation of the sequence (A). The wrong secondary structure can’t bind and that way the mRNA can be translated and won’t be digested (B).

We assume that the rate of silencing by siRNAs depends in the first place on the promoter region in front of the RNAi gene. By gathering expression rates of the most popular promoters in the iGEM parts registry valuable information for modelling will be acquired. Furthermore additional factors like secondary structures, diffusion rates and degradation rates of RNA fragments. With that a model of the actual expression rate of proteins can be modeled with a given sequence that shall be silenced. The other way round this model should tell which is the best fitting promoter for a specific protein concentration. Combining both applications in one will result in a useful tool for the iGEM community.

Nanoparticle growth rates

Another big application we try to realise is the formation of nanoparticles inside the cell. For that a growing 3D model will be programmed with the Unity engine which illustrates the growth rate of different nanoparticle shapes. The growth rate depends on the existence of capping agents. The growth kinetic can be described like a chemical reaction kinetic (Phan, 2017).

References

Barnes, D. J., & Chu, D. (2010). Introduction to modeling for biosciences. Springer Science & Business Media.
Delihas, N., & Forst, S. (2001). MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors1. Journal of molecular biology, 313(1), 1-12.
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure1. Journal of molecular biology, 288(5), 911-940.
Phan, C. M., & Nguyen, H. M. (2017). Role of capping agent in wet synthesis of nanoparticles. The Journal of Physical Chemistry A, 121(17), 3213-3219.
Stach, J. E., & Good, L. (2011). Synthetic RNA silencing in bacteria–antimicrobial discovery and resistance breaking. Frontiers in microbiology, 2, 185.

@@ Line 48: / Line 48: @@
 Our project revolves around new discovered or theoretical biological systems like for example RNAi in prokaryotes or newly discovered copper transport porins. For those we will program following models beside the standard calculations for growth rates and reaction kinetics.
-   <h2>siRNA promoter model</h2> <br/>
+   <br/><h2>siRNA promoter model</h2>
@@ Line 60: / Line 60: @@
 We assume that the rate of silencing by siRNAs depends in the first place on the promoter region in front of the RNAi gene. By gathering expression rates of the most popular promoters in the iGEM parts registry valuable information for modelling will be acquired. Furthermore additional  factors like secondary structures, diffusion rates and degradation rates of RNA fragments. With that a model of the actual expression rate of proteins can be modeled with a given sequence that shall be silenced. The other way round this model should tell which is the best fitting promoter for a specific protein concentration. Combining both applications in one will result in a useful tool for the iGEM community.
-     <h2>Nanoparticle growth rates</h2> <br/>
+     <br/><h2>Nanoparticle growth rates</h2>
 Another big application we try to realise is the formation of nanoparticles inside the cell. For that a growing 3D model will be programmed with the Unity engine which illustrates the growth rate of different nanoparticle shapes. The growth rate depends on the existence of capping agents.  The growth kinetic can be described like a chemical reaction kinetic (Phan, 2017).