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Team:Wisconsin/Modeling
From 2008.igem.org
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| - | |Our modeling adventure started with a brief introduction to programming using GAMS software and an E. coli database developed by Dr. Jennie Reed at the University of Wisconsin College of Engineering. Dr. Reed’s database works in conjunction with the GAMS software to measure metabolic fluxes in E. coli. Using this as a base point we were able to computationally manipulate metabolites, genes, and the growth environment to determine the most optimal conditions to grow and hopefully produce sorbitol. Glycerol is currently produced at a rate of one pound for every ten pounds of biodiesel produced. Consequently, our team felt it would be interesting if we could find a novel use for glycerol in our pursuit of sorbitol producing E. coli. As such we decided to utilize glycerol as our growth media carbon source. After many hours spent running simulations we discovered that the greatest metabolic flux towards sorbitol was observed when the gene encoding _____ was knocked out. This enzyme catalyzes the conversion of _____ to _____. Our team has theories as to why this knockout increases flux towards sorbtiol but we cannot say for sure. Currently we are working with the modeling software to map different gene knockouts and their metabolic fluxes onto metabolic maps.. | + | |Our modeling adventure started with a brief introduction to programming using GAMS software and an ''E. coli'' database developed by Dr. Jennie Reed at the University of Wisconsin College of Engineering. Dr. Reed’s database works in conjunction with the GAMS software to measure metabolic fluxes in ''E. coli''. Using this as a base point we were able to computationally manipulate metabolites, genes, and the growth environment to determine the most optimal conditions to grow and hopefully produce sorbitol. Glycerol is currently produced at a rate of one pound for every ten pounds of biodiesel produced. Consequently, our team felt it would be interesting if we could find a novel use for glycerol in our pursuit of sorbitol producing ''E. coli''. As such we decided to utilize glycerol as our growth media carbon source. After many hours spent running simulations we discovered that the greatest metabolic flux towards sorbitol was observed when the gene encoding _____ was knocked out. This enzyme catalyzes the conversion of _____ to _____. Our team has theories as to why this knockout increases flux towards sorbtiol but we cannot say for sure. Currently we are working with the modeling software to map different gene knockouts and their metabolic fluxes onto metabolic maps.. |
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Revision as of 16:28, 1 August 2008
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| Our modeling adventure started with a brief introduction to programming using GAMS software and an E. coli database developed by Dr. Jennie Reed at the University of Wisconsin College of Engineering. Dr. Reed’s database works in conjunction with the GAMS software to measure metabolic fluxes in E. coli. Using this as a base point we were able to computationally manipulate metabolites, genes, and the growth environment to determine the most optimal conditions to grow and hopefully produce sorbitol. Glycerol is currently produced at a rate of one pound for every ten pounds of biodiesel produced. Consequently, our team felt it would be interesting if we could find a novel use for glycerol in our pursuit of sorbitol producing E. coli. As such we decided to utilize glycerol as our growth media carbon source. After many hours spent running simulations we discovered that the greatest metabolic flux towards sorbitol was observed when the gene encoding _____ was knocked out. This enzyme catalyzes the conversion of _____ to _____. Our team has theories as to why this knockout increases flux towards sorbtiol but we cannot say for sure. Currently we are working with the modeling software to map different gene knockouts and their metabolic fluxes onto metabolic maps.. |
