Cooperation with Wetlab
The entire summer, the UIUC software team and wetlab, worked in conjunction as we met every week to update each other on our progress and to collaborate on many issues. Collaboration included administrative tasks, recruitment for the next year, and community outreach.
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 micromoles 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: Biomass Formation of E. coli with additional constraints over time
This figure shows the biomass formation of the E. coli cells given that they contain the additional reactions of ArsB, ArsR and LamB which aid in the removal of arsenic from the internal compartment of the cell.
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.
T, et al. “The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.” Bacteriol, 2008 Apr.
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.
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.