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Team:Evry/Modeling
From 2013.igem.org
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| - | We also wanted to know how much siderophore can be produced and how we can improve this. We answered this with a <b>Genome scale model</b>, using a flux balance analysis approach. | + | We also wanted to know how much siderophore can be produced and how we can improve this. We answered this with a <b>Genome scale model</b>, using a flux balance analysis approach. We determine <b>what are the limiting metabolites</b> and <b>how we could improve our capsule</b>. |
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Revision as of 02:25, 29 October 2013
Modeling Overview
Following the different remarks made by the team, judges, and other people, we reworked entirely the modeling section :
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On the structure:
- Each header section presents the methods used in the model, and could be compared to a "Material and Methods" section of an article;
- Each subsequence page presents the different simulations and answers obtained with the model; as in the "Result" section of an article;
- This page is now an entry point to our work, presenting out modeling philosophy, main results and pointers to the relevant models.
- The description of each model is now more precise, the equations better explained and the results analyzed in depths.
- We highlighted more carefuly the each assumption of the models and each parameter's value, giving sources when possible.
- Finally, our efforts focused on better describing the links between the biology part of our projet and our models and between the different models.
Modeling Parts
| Flush treatment model | |
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At the begining of our project, we aimed to enable iron chelation in the duodenum using bacteria that would flush through the duodenum and produce the siderophores. Therefore we wanted to predict the minimal quantity of produced siderophores sufficient to reduce the iron intestinal absorption. We first had in mind a flush strategy, meaning we prioritized an approach where the bacteria would start their iron sensing and siderophore production before entering the duodenum. This qualitative Flush treatment model showed us that it is theoretically possible to significantly reduce the patient's iron absorption. |
| Enterobactin production model | |
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The conclusions were promising, encouraging and comforting regarding our strategy. Therefore we investigated in detail the delay in siderophore production for a given bacterial production through an Enterobactin production model that integrate our sensor, invertor and chelator systems. This investigation gave us more details on timings. Unfortunately, the conclusions were in contradiction with the qualitative model because the delay is too important to be compatible with a flush strategy. This finding greatly influenced the biological part, especially the capsule design. Because iron absorption is split between the duodenum (60%) and the jejunum (40%), we decided to retain bacteria in duodenum and the proximal area of the jejunum. |
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| Genome scale model | |
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We also wanted to know how much siderophore can be produced and how we can improve this. We answered this with a Genome scale model, using a flux balance analysis approach. We determine what are the limiting metabolites and how we could improve our capsule. |
| Population scale model | |
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Tools:
When working on a scientific project, it is always good to properly define and clarify the tools being used. These pages contain the theorical background for our models:
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| Logistic functions | Chemical reasoning |
