Team:UIUC-Illinois/Modeling

From 2010.igem.org

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== Cell Survivability ==
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We have collaborated with the UIUC Software Tools team to analyze the ability of cells to survive when under the slight strain of overexpressing ArsB, ArsR, and LamB for the Arsenic Bioremediation system. Below is a summary of the work that Meagan Musselman and Anna Kropornica have compiled to demonstrate that indeed, ''E. coli'' cells will be well able to survive while over-expressing the aforementioned proteins.<br><br>
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'''Modeling for UIUC Bioware'''
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The Illinois Bioware team’s project was to develop bacteria able to facilitate the removal of heavy metals, a process known as bioremediation. The metal that was focused on was Arsenic. To test the program as well as to aid the Illinois Software team in their experimental procedure, we utilized the Constraint-based reconstruction analysis software1 through MATLAB to provide a prediction of growth for the Escherichia coli cells with the proteins implemented. In this modeling, we made the assumptions that the primary protein additions are the Arsenite/antimonite transporter (ArsB), DNA-binding transcriptional repressor (ArsR) and maltose outer membrane porin (LamB) proteins are the most influential components of the team’s Escherichia coli strain when in a medium containing the heavy metal, arsenic. The ArsB protein functions as a membrane transporting pump of arsenate, arsenite and antimonite outside of the cell while utilizing ATP4. The ArsR transcriptional repressor functions within a cell by regulating the expression of the arsRBC that is directly involved in creating resistance to arsenic4. Finally, the LamB protein functions as a maltoporin-like protein by transporting maltodextrins across the membrane2. <br>
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The uptake rate of arsenic by ArsB was determined by Meng, et al. (2004). The dynamic flux balance analysis result (Figure 1) was determined with a initial concentration of 10-3 μmol and a initial biomass of 0.1 milligrams of Dry Weight Liter-1, a time of one hour and maximum number of steps at 20. In Figure 1, the plot shows changes in biomass concentration as a function of time on the left side, given the additional components. <br><br>
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'''Figure 1'''<br>
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[[Image:UIUC-IllinoisCellSurvivability.jpg]]
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'''References'''
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1. Becker, Scott; et al.”Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.” Department of Bioengineering, University of California San Diego.Nature Protocols Vol.2 No.3. March 2007.<br>
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2. Durfee T, et al. “The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.” Bacteriol, 2008 Apr. <br>
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3. Meng, Y., et al. “As(III) and Sb(III) Uptake by GlpF and Efflux by ArsB in Escherichia coli.” The Journal of Biological Chemistry, 2004 Apr 30.<br>
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4. Ogura Y, et al. “Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli.” Ogura Y, et al. Proc Natl Acad Sci U S A, 2009 Oct 20. <br>

Revision as of 23:48, 27 October 2010

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Cell Survivability

We have collaborated with the UIUC Software Tools team to analyze the ability of cells to survive when under the slight strain of overexpressing ArsB, ArsR, and LamB for the Arsenic Bioremediation system. Below is a summary of the work that Meagan Musselman and Anna Kropornica have compiled to demonstrate that indeed, E. coli cells will be well able to survive while over-expressing the aforementioned proteins.

Modeling for UIUC Bioware

The Illinois Bioware team’s project was to develop bacteria able to facilitate the removal of heavy metals, a process known as bioremediation. The metal that was focused on was Arsenic. To test the program as well as to aid the Illinois Software team in their experimental procedure, we utilized the Constraint-based reconstruction analysis software1 through MATLAB to provide a prediction of growth for the Escherichia coli cells with the proteins implemented. In this modeling, we made the assumptions that the primary protein additions are the Arsenite/antimonite transporter (ArsB), DNA-binding transcriptional repressor (ArsR) and maltose outer membrane porin (LamB) proteins are the most influential components of the team’s Escherichia coli strain when in a medium containing the heavy metal, arsenic. The ArsB protein functions as a membrane transporting pump of arsenate, arsenite and antimonite outside of the cell while utilizing ATP4. The ArsR transcriptional repressor functions within a cell by regulating the expression of the arsRBC that is directly involved in creating resistance to arsenic4. Finally, the LamB protein functions as a maltoporin-like protein by transporting maltodextrins across the membrane2.
The uptake rate of arsenic by ArsB was determined by Meng, et al. (2004). The dynamic flux balance analysis result (Figure 1) was determined with a initial concentration of 10-3 μmol and a initial biomass of 0.1 milligrams of Dry Weight Liter-1, a time of one hour and maximum number of steps at 20. In Figure 1, the plot shows changes in biomass concentration as a function of time on the left side, given the additional components.

Figure 1
File:UIUC-IllinoisCellSurvivability.jpg

References 1. Becker, Scott; et al.”Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.” Department of Bioengineering, University of California San Diego.Nature Protocols Vol.2 No.3. March 2007.
2. Durfee T, et al. “The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.” Bacteriol, 2008 Apr.
3. Meng, Y., et al. “As(III) and Sb(III) Uptake by GlpF and Efflux by ArsB in Escherichia coli.” The Journal of Biological Chemistry, 2004 Apr 30.
4. Ogura Y, et al. “Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli.” Ogura Y, et al. Proc Natl Acad Sci U S A, 2009 Oct 20.



Asfree + AsMT + Ascell = Astotal
Aufree + AuMT + Aucell = Autotal
ṁin = ṁefflux
... !!!!

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