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/>
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<p>Concept: Increase in growth rate due to Proteorhodopsin in Carbon stress conditions
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<p><b>Concept</b>: Increase in cell growth rate due to Proteorhodopsin in Carbon stress conditions.<br/><br/>
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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.</br>
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<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/>
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Observations: 9-30% increase in growth rate was observed due to Proteorhodopsin at high carbon stress conditions.<img src="https://static.igem.org/mediawiki/2011/1/10/Table-1.jpg" length="600" width="600"></p><br/><br/>
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<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/>
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<img src="https://static.igem.org/mediawiki/2011/1/10/Table-1.jpg" length="600" width="600"></p>
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<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 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>
<p> <b><u>According to the model the following reactions showed major flux changes due to Proteorhodopsin :</u></b>

Latest revision as of 04:01, 29 October 2011

bar iGEM 2011 - Home Page Indian Institute of Technology - Madras



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 :

  1. 'adentylate kinase GTP '
  2. 'adenosine hydrolase'
  3. 'dihydroorotic acid menaquinone 8
  4. '3 isopropylmalate dehydrogenase'
  5. 'psicoselysine transport via proton symport periplasm
  6. 'purine nucleoside phosphorylase Deoxyadenosine '
  7. 'L threonine via sodium symport periplasm '
Reaction Knockout Analysis of '3 isopropylmalate dehydrogenase' was lethal and the other reactions didn’t have major effects on growth rates .