Team:Illinois/Modelingteam

From 2009.igem.org

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We cultured cells overnight in anticipation that we will be able to perform a fluorescence reading tomorrow.
We cultured cells overnight in anticipation that we will be able to perform a fluorescence reading tomorrow.
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== June 26 ==
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== '''June 26''' ==
We were able to use a plate reader on our cells today.  Unfortunately, we learned that we did not properly culture our cells for accurate quantitative measurements, so we could only determine fluorescence to be positive or negative.  Our pXG-1 cells tested positive for fluorescence, and our other two plasmids (pXG-0 and pXG-10) tested negative.  We expected low fluorescence activity for pXG-10 but could not discern any.
We were able to use a plate reader on our cells today.  Unfortunately, we learned that we did not properly culture our cells for accurate quantitative measurements, so we could only determine fluorescence to be positive or negative.  Our pXG-1 cells tested positive for fluorescence, and our other two plasmids (pXG-0 and pXG-10) tested negative.  We expected low fluorescence activity for pXG-10 but could not discern any.
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== '''June 29''' ==
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We worked on making a model of simple transcriptional regulation by a repressor protein.  However, we encountered some problems in making the model and using SimBiology.  We will be fixing these problems soon.

Revision as of 02:46, 1 July 2009

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Contents

Modeling Team

Goals: Our team will be creating mathematical models of our bacterial decoder and of the various biological processes involved. More specifically, we will be modeling:

  • simple sRNA regulation of one gene
  • multiple sRNAs regulating one gene
  • one sRNA regulating multiple genes
  • promoter activity as a function of input concentration
  • our bacterial decoder as a whole

We will be using Matlab and SimBiology often as tools to help us model various systems. Our team will also be taking measurements and recording data in order to compare our actual decoder with the models we have constructed.


For more information, please view the Modeling page.

June 23

We made a Matlab program that models simple sRNA regulation of a single gene. The program takes a vector containing times and numbers of sRNA, mRNA, and protein molecules and outputs a vector of solutions to the differential equations used for each time.

We will be measuring fluorescence of three E. coli cultures containing cells with pXG-0, pXG-1, and pXG-10 plasmids. These plasmids contain the gene for GFP under a constitutive promoter, so these measurements will act as controls for our experiments.

June 24

We made a program in SimBiology that models simple sRNA regulation of a single gene. The equations and constant values used were taken from a paper on sRNA regulation (please see the Research page).

UI09simplesRNA.jpg

We attempted to measure fluorescence of our cells today using a plate reader, but we ran into some technical problems. We may have to use a different plate reader, or we may be able to fix the problems on the current plate reader.

June 25

We created a working program in SimBiology that roughly models our decoder. In the program, each gene is regulated by two sRNAs. The sRNA synthesis rates are assumed to be constant for now, whereas in reality these rates will depend on input concentrations and promoter activity. We verified by changing sRNA synthesis rates that combinations of two sRNAs resulted in production of the correct fluorescent protein.

UI092to4diagram.jpgUI092to4graphs.jpg

We cultured cells overnight in anticipation that we will be able to perform a fluorescence reading tomorrow.

June 26

We were able to use a plate reader on our cells today. Unfortunately, we learned that we did not properly culture our cells for accurate quantitative measurements, so we could only determine fluorescence to be positive or negative. Our pXG-1 cells tested positive for fluorescence, and our other two plasmids (pXG-0 and pXG-10) tested negative. We expected low fluorescence activity for pXG-10 but could not discern any.

June 29

We worked on making a model of simple transcriptional regulation by a repressor protein. However, we encountered some problems in making the model and using SimBiology. We will be fixing these problems soon.