UNL 2017

Helping reduce methane emissions from livestock

MODELING

Introduction

Due to the unknown nature of some of the turnover rates of enzymes and structures in the cell, the model was mainly used for explaining some of the poor results received from characterization of our nitrite reductase BioBrick. The specific structure and reactant explored in the modeling was heme. Heme is toxic in large quantities to E coli, but is also very useful to the metabolic functions of the cell (Anzaldi & Skaar, 2010). This interaction causes heme to become highly regulated and the average concentration of free heme to decrease. The coding sequence in our plasmid design is being constantly produced and codes for a multiheme enzyme.

The refectory period for the enzyme after it reacts with the nitrite was modeled using a loop with a degradation rate.

The key reactant, nitrite, is a charged molecule and does not pass the membrane of the cell easily. Therefore, the model starts will 100 molecules of nitrite. For the purposes of this model, diffusion of nitrite into the cell is not expressed. It can be assumed that if the rate of diffusion is greater than the rate of reduction to ammonia, there will be an excess of nitrite and the cell will likely die.

Gold Medal Criterion #3

To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your judging form. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.

Please see the 2017 Medals Page for more information.

Best Model Special Prize

To compete for the Best Model prize, please describe your work on this page and also fill out the description on the judging form. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.

You must also delete the message box on the top of this page to be eligible for the Best Model Prize.

Inspiration

Here are a few examples from previous teams:

Works Cited

Anzaldi, L. L., and Skaar, E. P. (2010) Overcoming the Heme Paradox: Heme Toxicity and Tolerance in Bacterial Pathogens. Infection and Immunity 78, 4977–4989.
Bremer, H., and Dennis, P. P. (2008) Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates. EcoSal Plus 3.
Einsle, O., and Kroneck, P. (2007) Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound substrate nitrite.
Hagen, S. J., Hofrichter, J., and Eaton, W. A. (1997) Rate of Intrachain Diffusion of Unfolded Cytochromec. The Journal of Physical Chemistry B 101, 2352–2365.
Janecky, L. R. (2013) Quantification of protein half-lives in the budding yeast proteome. Front Cell Infect Microbiol 3.
Kubitschek, H. E. (1990) Cell volume increase in Escherichia coli after shifts to richer media. Journal of Bacteriology 172, 94–101.
Liu, Y., and Montellano, P. R. O. D. (2000) Reaction Intermediates and Single Turnover Rate Constants for the Oxidation of Heme by Human Heme Oxygenase-1. Journal of Biological Chemistry 275, 5297–5307.
Runyen-Janecky, L. J. (2013) Role and regulation of heme iron acquisition in gram-negative pathogens. Frontiers in Cellular and Infection Microbiology 3.
Vogel, U., and Jensen, K. F. (1994) The RNA chain elongation rate in Escherichia coli depends on the growth rate. Journal of Bacteriology 176, 2807–2813.

Team:UNebraska-Lincoln/Model