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Team:KULeuven/Modeling
From 2011.igem.org
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<p id="references">References</p> | <p id="references">References</p> | ||
<ol> | <ol> | ||
| - | <li><i>J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702. </i | + | <li><i>J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702. </i> |
| - | + | <li><i>"Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004</i> | |
| - | <li><i>"Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004</i | + | <li><i>Tuttle L.M., Salis H., Tomshine J., and Kaznessis Y.N., "Model-Driven Designs of an Oscillating Gene Network", Biophysical Journal, vol. 89, no. 6, pp. 3873--3883, 2005.</i> |
| - | <li><i>Tuttle L.M., Salis H., Tomshine J., and Kaznessis Y.N., "Model-Driven Designs of an Oscillating Gene Network", Biophysical Journal, vol. 89, no. 6, pp. 3873--3883, 2005.</i | + | <li><i>Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” Appl. Environ. Microbiol., vol. 71, Mar. 2005, pp. 1291-1299. </i> |
| - | <li><i>Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” Appl. Environ. Microbiol., vol. 71, Mar. 2005, pp. 1291-1299. </i | + | <li><i>N. Qin et al., “Analysis of LuxR Regulon Gene Expression during Quorum Sensing in Vibrio fischeri,” J. Bacteriol., vol. 189, Jun. 2007, pp. 4127-4134.</i> |
| - | <li><i>N. Qin et al., “Analysis of LuxR Regulon Gene Expression during Quorum Sensing in Vibrio fischeri,” J. Bacteriol., vol. 189, Jun. 2007, pp. 4127-4134.</i | + | <li><i>L. Wang et al., “Specificity and enzyme kinetics of the quorum-quenching AHL-lactonase,” J. Biol. Chem., Jan. 2004, p. M311194200.</i> |
| - | <li><i>L. Wang et al., “Specificity and enzyme kinetics of the quorum-quenching AHL-lactonase,” J. Biol. Chem., Jan. 2004, p. M311194200.</i | + | |
<li><i>http://partsregistry.org/Part:BBa_B0032</i> accessible<a href="example"> here</a></li> | <li><i>http://partsregistry.org/Part:BBa_B0032</i> accessible<a href="example"> here</a></li> | ||
| - | <li><i>Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005</i | + | <li><i>Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005</i> |
| - | <li><i>https://2008.igem.org/Team:KULeuven/Model/CellDeath</i | + | <li><i>https://2008.igem.org/Team:KULeuven/Model/CellDeath</i> |
<ol> | <ol> | ||
</div> | </div> | ||
Revision as of 09:30, 16 September 2011
Modeling Overview
1. Description of the whole system
To make predictions for are plasmid transformed E.coli, a structured segregated model is designed in Simbiology. A graphical representation of the model was build in the block diagram editor . Afterwards reaction equations and parameters were added. We designed one model for the whole system and 3 models for 3 subsystems. The 3 subsystems are antifreeze, freeze and cell death. For more information about these 3 subsystems, we refer to the extended project description and the 3 modelling pages: freeze, antifreeze and cell death.2. Full Model
There are in total 5 different kinetic equations we used in the model Transcription equation For most promoters, hill kinetics is used, it is a way of quantitatively describing cooperative binding processes, it was developed for hemoglobin in 1913. A Hill coefficient (n) is a measure for the cooperativity. Translation equation RNA degradation Protein degration Assimiliation3. Simulation tests
In the table below the parameters for our full model are displayed. However it was hard to find accurate parameters, because databases for kinetic parameters are limiting.The parameters used in this model are:
| Parameter | Value | Description | Reference |
|---|---|---|---|
 |
0 | NA | Notation convention |
 |
0 | NA | Notation convention |
 |
0 | HIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII | BioNumbers with an approximation: all our contructs are around 1-2kb |
References
- J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702.
- "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
- Tuttle L.M., Salis H., Tomshine J., and Kaznessis Y.N., "Model-Driven Designs of an Oscillating Gene Network", Biophysical Journal, vol. 89, no. 6, pp. 3873--3883, 2005.
- Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” Appl. Environ. Microbiol., vol. 71, Mar. 2005, pp. 1291-1299.
- N. Qin et al., “Analysis of LuxR Regulon Gene Expression during Quorum Sensing in Vibrio fischeri,” J. Bacteriol., vol. 189, Jun. 2007, pp. 4127-4134.
- L. Wang et al., “Specificity and enzyme kinetics of the quorum-quenching AHL-lactonase,” J. Biol. Chem., Jan. 2004, p. M311194200.
- http://partsregistry.org/Part:BBa_B0032 accessible here
- Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
- https://2008.igem.org/Team:KULeuven/Model/CellDeath
