Team:Stockholm/Modelling/Suitable model

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Revision as of 12:07, 25 October 2010

Choosing proper model for LacI/allolactose dynamics

With the mentioned details, first step should be about preparing a proper model for allolactose/lactose dynamics. The reason to this is the binding of allolactose to LacI and inhibiting it from binding to operator, which will result in gene expression. Yildirim N et al 2002 proposed a mathematical model for lac operon induction in E. Coli. The details that they considered in the model are what we are looking for: external lactose, internal lactose, conversion of lactose to allolactose and glucose, interaction of allolactose with LacI (Lac Repressor) and mRNA. Since on the plasmid that we are using to express our genes in bacteria, LacI also acts as repressor, it is reasonable to use the same model as Yildirim N et al 2002.

We start slowly by talking a little about Lac operon in E. Coli. Lac operon is responsible for transport and metabolism of lactose in e coli. It has a promoter site and three structural genes (LacZ, LacY and LacA). Availability of external Lactose and Glucose regulates this operon. In the absence of Lactose the LacI gene - which is always expressed, codes for the repressor and represses the expression the of Lac operon. When Lactose is available again for the bacteria in the absence of glucose, Allolactose (a β-galactosidase side reaction) binds to repressor and makes it impossible for the repressor to bind the operator on Lac operon. This will result in production of high levels of LacZ (β-galactosidase) , LacY (β-galactoside permease) and LacA; the latter is not interesting for our case. Lacz and LacY expression will lead to more production of Allolactose(a metabolite of lactose).

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 === Choosing proper model for LacI/allolactose dynamics ===
-With the above mentioned details, first step should be preparing a proper model for allolactose production, degradation and possible dilution. The reason to this is the binding of allolactose to LacI and inhibiting it from binding to operator, which will result in gene expression.
+<div align="justify">With the mentioned details, first step should be about preparing a proper model for allolactose/lactose dynamics. The reason to this is the binding of allolactose to LacI and inhibiting it from binding to operator, which will result in gene expression. [http://www.ncbi.nlm.nih.gov/pubmed/12719218 Yildirim N et al 2002] proposed a mathematical model for lac operon induction in E. Coli. The details that they considered in the model are what we are looking for: external lactose, internal lactose, conversion of lactose to allolactose and glucose, interaction of allolactose with LacI (Lac Repressor) and mRNA. Since on the plasmid that we are using to express our genes in bacteria, LacI also acts as repressor, it is reasonable to use the same model as [http://www.ncbi.nlm.nih.gov/pubmed/12719218 Yildirim N et al 2002].
-[http://www.ncbi.nlm.nih.gov/pubmed/12719218 Yildirim N et al 2002] proposed a mathematical model for lac operon induction in E. Coli. The details that they considered in the model are what we are looking for: external lactose, internal lactose, conversion of lactose to allolactose and glucose, interaction of allolactose with LacI (Lac Repressor) and mRNA. Since the plasmid(?) that we are using to express our genes in bacteria have LacI as repressor, it is reasonable to use the same model as [http://www.ncbi.nlm.nih.gov/pubmed/12719218 Yildirim N et al 2002].
+We start slowly by talking a little about Lac operon in E. Coli. Lac operon is responsible for transport and metabolism of lactose in e coli. It has a promoter site and three structural genes (LacZ, LacY and LacA). Availability of external Lactose and Glucose regulates this operon. In the absence of Lactose the LacI gene - which is always expressed, codes for the repressor and represses the expression the of Lac operon. When Lactose is available again for the bacteria in the absence of glucose, Allolactose (a β-galactosidase side reaction) binds to repressor and makes it impossible for the repressor to bind the operator on Lac operon. This will result in production of high levels of LacZ (β-galactosidase) , LacY (β-galactoside permease) and LacA; the latter is not interesting for our case. Lacz and LacY expression will lead to more production of Allolactose(a metabolite of lactose).
+</div>
-Lac operon is responsible for transport and metabolism of lactose in e coli. It has a promoter site and three structural genes (LacZ, LacY and LacA). Availability of external Lactose and Glucose regulates this operon. In the absence of Lactose, the LacI gene (always expressed) ,which codes for the repressor , represses the expression the of Lac operon. When Lactose is available again for the bacteria, Allolactose (a β-galactosidase side reaction) binds to repressor and makes it impossible for the repressor to bind the operator on Lac operon. This will result in production of high levels of LacZ (β-galactosidase) , LacY (β-galactoside permease) and LacA, and these will lead to more production of Allolactose. Until this point we have the same assumption as [http://www.ncbi.nlm.nih.gov/pubmed/12719218 Yildirim N et al 2002]. Here we will introduce the model proposed by [http://www.ncbi.nlm.nih.gov/pubmed/12719218 Yildirim N et al 2002] a brief introduction to their model, then we will try to simplify it and continue with our gene expression model in bacteria as final stage.