"
Team:Imperial College London/Drylab/Genome deletion
From 2009.igem.org
(→Our goals) |
(→Our goals) |
||
| Line 35: | Line 35: | ||
*Explore how temperature correlates to restriction enzyme concentration, and see how it affects the population of live cells, so as to characterise the effects of temperature on cell death. | *Explore how temperature correlates to restriction enzyme concentration, and see how it affects the population of live cells, so as to characterise the effects of temperature on cell death. | ||
| + | |||
| + | --[[User:Mabult|Mabult]] 18:14, 17 October 2009 (UTC) illustrate not explore since will not have any data... | ||
*Develop a model of the number of dead cells as this correlates to our live and dead cells assay. (hyperlink to assay). From this, we can monitor the rate of killing and perform data analysis. | *Develop a model of the number of dead cells as this correlates to our live and dead cells assay. (hyperlink to assay). From this, we can monitor the rate of killing and perform data analysis. | ||
| + | |||
| + | --[[User:Mabult|Mabult]] 18:14, 17 October 2009 (UTC) Rewrite: model has two components: dead cells and live cells | ||
<html><a href="https://2009.igem.org/Team:Imperial_College_London/Drylab/Genome_Deletion/Analysis"><img style="vertical-align:bottom;" width=50px align="left" src="http://i691.photobucket.com/albums/vv271/dk806/II09_Learnmore.png"></a></html> about the model assumptions and predictions! | <html><a href="https://2009.igem.org/Team:Imperial_College_London/Drylab/Genome_Deletion/Analysis"><img style="vertical-align:bottom;" width=50px align="left" src="http://i691.photobucket.com/albums/vv271/dk806/II09_Learnmore.png"></a></html> about the model assumptions and predictions! | ||
| Line 46: | Line 50: | ||
*In a separate model, model for the effects of Dam methylase in protection against cell death. We want to know how much Dam methylase will be necessary to prevent cell death for basal production of restriction enzymes. | *In a separate model, model for the effects of Dam methylase in protection against cell death. We want to know how much Dam methylase will be necessary to prevent cell death for basal production of restriction enzymes. | ||
| + | --~~~~ Have we done this? | ||
In summary, our model will allow us to characterise the effects of temperature on the parallel production of restriction enzymes DpnII and TaqI, that are required to kill E. coli. We can also characterise the extent Dam methylase can protect E. coli against cell death. (not yet done) | In summary, our model will allow us to characterise the effects of temperature on the parallel production of restriction enzymes DpnII and TaqI, that are required to kill E. coli. We can also characterise the extent Dam methylase can protect E. coli against cell death. (not yet done) | ||
| + | |||
| + | --~~~~ Get rid of this!! We are not going to do it | ||
--> | --> | ||
<!--<biblio> | <!--<biblio> | ||
Revision as of 18:14, 17 October 2009
Genome Deletion
Based on the genetic circuit, we know that
- The lambda cI promoter is repressed by the protein cI that is produced constitutively under the strong promoter J23114.
- At 28°C, functional protein cI will bind to the lambda cI promoter to repress it. Restriction enzymes DpnII and TaqI will not be produced.
- When there is an increase in temperature (from 28°C to 42°C [http://www.ncbi.nlm.nih.gov/pubmed/15652426?ordinalpos=13&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum [1]][http://www.ncbi.nlm.nih.gov/pubmed/10235623 [2]]), there will be a de-repression of lambda cI promoter, causing restriction enzymes DpnII and TaqI to be produced.
Contents |
Our goals
We aim to:
- Explore how temperature correlates to restriction enzyme concentration, and see how it affects the population of live cells, so as to characterise the effects of temperature on cell death.
--Mabult 18:14, 17 October 2009 (UTC) illustrate not explore since will not have any data...
- Develop a model of the number of dead cells as this correlates to our live and dead cells assay. (hyperlink to assay). From this, we can monitor the rate of killing and perform data analysis.
--Mabult 18:14, 17 October 2009 (UTC) Rewrite: model has two components: dead cells and live cells
about the model assumptions and predictions!
--Mabult 18:08, 17 October 2009 (UTC) Redo image please
The system
The system is made up of 6 ODEs based on the Module 3: Genome deletion genetic circuit. ODEs are also used in modelling the population of E. coli.
about the equations and what they mean!
Summary of Simulation results
Temperature above threshold – Cell population goes to zero
- If the temperatures are above threshold, the population growth of live cells will be constrained by the concentration of restriction enzyme.
- The maximum live cell population at a given temperature will also be lower for higher temperatures
- If the lambda cI promoter is strong, there will be a higher rate of cell death than cell growth; we will see a decrease in live cell population. However, if lambda cI promoter is weak, there might not be enough killing, so we will only see a reduction in growth of cell population, ie: a slower increase in population.
about the simulations!
Conclusions
- A decrease in live cell population means that cell death is greater than cell growth, due to the killing by restriction enzyme. This is when M3 has fully kicked in.
- At the threshold temperature, cell death balances cell reproduction, and we would notice a straight line in the live cell curve. Above this temperature, cell death dominates, and a decrease in cell population will be observed.
References
[1] Jechlinger W, Glocker J, Haidinger W, Matis A, Szostak MP, and Lubitz W. Modulation of gene expression by promoter mutants of the lambdacI857/pRM/pR system. J Biotechnol 2005 Mar 2; 116(1) 11-20. doi:10.1016/j.jbiotec.2004.10.002 pmid:15652426.
[2]Jana NK, Roy S, Bhattacharyya B, and Mandal NC. Amino acid changes in the repressor of bacteriophage lambda due to temperature-sensitive mutations in its cI gene and the structure of a highly temperature-sensitive mutant repressor. Protein Eng 1999 Mar; 12(3) 225-33.
[3] Alon, U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits - Chapman & Hall/Crc Mathematical and Computational Biology
