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Team:IIT Madras/Dry lab/Modelling/Simulations
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<h3><b><u> Simulations for Proof of Concept</a></u></b></h3><br/> | <h3><b><u> Simulations for Proof of Concept</a></u></b></h3><br/> | ||
| - | <p | + | <p><b>Concept</b>: Increase in cell growth rate due to Proteorhodopsin in Carbon stress conditions.<br/><br/> |
| - | <img src="https://static.igem.org/mediawiki/2011/e/e5/Modelin_wiki_03.jpg" | + | <b>Simulations for Proof of Concept:</b> We varied glucose uptake rates in the range 0.5-12 mmol/g-dw hr and calculated growth rates for Model_WT and Model_PR. Observing percentage increase in growth rate we could deduce the advantage given to cell due to Proteorhodopsin’s light driven proton efflux.<br/><br/> |
| - | <img src="https://static.igem.org/mediawiki/2011/9/9d/Figure-1.jpg" | + | <b>Observations:</b> As the glucose uptake rate was reduced the advantage to the cell due to Proteorhodopsin in terms of growth rate increased. Upto 30% increase in growth rate (See Figure 1 & 2) can be observed due to Proteorhodopsin at high carbon stress conditions. <br/> |
| + | <img src="https://static.igem.org/mediawiki/2011/1/10/Table-1.jpg" length="600" width="600"></p> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/e/e5/Modelin_wiki_03.jpg" height="450" width="490"> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/9/9d/Figure-1.jpg" height="450" width="490" style="float:right"> | ||
| + | <p align="center"><b><u> Figure 1 and 2 : % Increase in growth rate observed due to Proteorhodopsin (Proton efflux = 2 and 10 mmol/g-dw hr) for varying glucose uptake rates respectively.</u></b></p><br/><br/> | ||
| + | <p> <b><u>According to the model the following reactions showed major flux changes due to Proteorhodopsin :</u></b> | ||
| + | <ol><li>'adentylate kinase GTP ' </li> | ||
| + | <li>'adenosine hydrolase' </li> | ||
| + | <li>'dihydroorotic acid menaquinone 8 </li> | ||
| + | <li>'3 isopropylmalate dehydrogenase' </li> | ||
| + | <li>'psicoselysine transport via proton symport periplasm </li> | ||
| + | <li>'purine nucleoside phosphorylase Deoxyadenosine ' </li> | ||
| + | <li>'L threonine via sodium symport periplasm ' </li></ol> | ||
| + | <u>Reaction Knockout Analysis of '3 isopropylmalate dehydrogenase' was lethal and the other reactions didn’t have major effects on growth rates .</u></p><br/> | ||
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Latest revision as of 04:01, 29 October 2011
Simulations for Proof of Concept
Concept: Increase in cell growth rate due to Proteorhodopsin in Carbon stress conditions.
Simulations for Proof of Concept: We varied glucose uptake rates in the range 0.5-12 mmol/g-dw hr and calculated growth rates for Model_WT and Model_PR. Observing percentage increase in growth rate we could deduce the advantage given to cell due to Proteorhodopsin’s light driven proton efflux.
Observations: As the glucose uptake rate was reduced the advantage to the cell due to Proteorhodopsin in terms of growth rate increased. Upto 30% increase in growth rate (See Figure 1 & 2) can be observed due to Proteorhodopsin at high carbon stress conditions.
Figure 1 and 2 : % Increase in growth rate observed due to Proteorhodopsin (Proton efflux = 2 and 10 mmol/g-dw hr) for varying glucose uptake rates respectively.
According to the model the following reactions showed major flux changes due to Proteorhodopsin :
- 'adentylate kinase GTP '
- 'adenosine hydrolase'
- 'dihydroorotic acid menaquinone 8
- '3 isopropylmalate dehydrogenase'
- 'psicoselysine transport via proton symport periplasm
- 'purine nucleoside phosphorylase Deoxyadenosine '
- 'L threonine via sodium symport periplasm '
