Difference between revisions of "Team:UCSC/Model"
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To predict theoretical acetaminophen production, we calculated the amount of a precursor, chorismate, by quantifying its main products, the aromatic amino acids phenylalanine, tyrosine, and tryptophan. | To predict theoretical acetaminophen production, we calculated the amount of a precursor, chorismate, by quantifying its main products, the aromatic amino acids phenylalanine, tyrosine, and tryptophan. | ||
Since no amino acid composition data was available for Synechococcus, we started by using literature data for similar cyanobacteria species Spirulina and Synechocystis and found that between one and 13.6 percent of amino acids were aromatics by mass, or between XX and YY molar percent. | Since no amino acid composition data was available for Synechococcus, we started by using literature data for similar cyanobacteria species Spirulina and Synechocystis and found that between one and 13.6 percent of amino acids were aromatics by mass, or between XX and YY molar percent. | ||
| − | To further verify our | + | To further verify our organism's amount of acetaminophen precursor, we ran both the genome and ribosomal protein sequences through a custom Python program converting codons to amino acids and calculating aromatic amino acid molar percentages which resulted in 9.3% and 5.14% respectively. |
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(Equation/ table summing amino acids converting to molar percentage) | (Equation/ table summing amino acids converting to molar percentage) | ||
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Revision as of 20:04, 19 September 2017
Modelling
Estimate and optimize yield.
Acetaminophen
To predict theoretical acetaminophen production, we calculated the amount of a precursor, chorismate, by quantifying its main products, the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Since no amino acid composition data was available for Synechococcus, we started by using literature data for similar cyanobacteria species Spirulina and Synechocystis and found that between one and 13.6 percent of amino acids were aromatics by mass, or between XX and YY molar percent. To further verify our organism's amount of acetaminophen precursor, we ran both the genome and ribosomal protein sequences through a custom Python program converting codons to amino acids and calculating aromatic amino acid molar percentages which resulted in 9.3% and 5.14% respectively. (Equation/ table summing amino acids converting to molar percentage) Using our sequence generated median chorismate value of 9.3% and the assumption that our enzymes would take a third of the chorismate precursor, we got an estimate for acetaminophen concentration of between 17.5mg and 1.29 mg per gram dried biomass. These numbers show that there is likely enough precursor and that acetaminophen production should be within a measurable range. (Equation producing acetaminophen)Biomass
Timescale: days Light Intensity: μE m-2 s-1 Temperature: ℃ Starting Density: g biomass/ LReferences
Growth optimization of Synechococcus elongatus PCC7942 in lab flasks and a 2-D photobioreactor Carbon metabolism and energy conversion of Synechococcus sp. PCC 7942 under mixotrophic conditions.
Jack Baskin School of Engineering
University of California, Santa Cruz
1156 High Street
Santa Cruz, California, 95064
Contact Us: UCSC iGEM
