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Team:Illinois/Modelingteam
From 2009.igem.org
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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. | 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. | ||
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| + | == '''July 3''' == | ||
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| + | We have begun work on characterizing various promoters from the Parts Registry. We transformed the Biobricks for GFP (BBa_E0240) and for our reference standard promoter that we will measure fluorescence against (BBa_J23101) into DH5α cells and cultured them overnight. | ||
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| + | == '''July 6''' == | ||
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| + | Transformations of GFP and the reference standard promoter were successful. We successfully miniprepped the DNA for both Biobricks. | ||
== '''July 10''' == | == '''July 10''' == | ||
Revision as of 20:18, 13 July 2009
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).
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.
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.
July 3
We have begun work on characterizing various promoters from the Parts Registry. We transformed the Biobricks for GFP (BBa_E0240) and for our reference standard promoter that we will measure fluorescence against (BBa_J23101) into DH5α cells and cultured them overnight.
July 6
Transformations of GFP and the reference standard promoter were successful. We successfully miniprepped the DNA for both Biobricks.
July 10
Our team has begun work to characterize various promoters via fluorescence readings. We transformed two different arabinose promoters from the Parts Registry (BBa_I0500 and BBa_K113009) into competent DH5α cells and cultured them overnight.
July 13
The transformation of BBa_K113009 yielded colonies, whereas the transformation of BBa_I0500 did not. We will have to redo the transformation of BBa_I0500.
We ran a PCR to amplify the pSB3K3 plasmid backbone for testing our promoters. For some reason, the gel we ran indicated a 6kbp band when it should have been 2.75kbp.
