Moneil5 Week 6

Helpful Links

Margaret J. ONeil

Assignment Pages:

• Week 1 Assignment
• Week 2 Assignment
• Week 3 Assignment
• Week 4 Assignment
• Week 5 Assignment
• Week 6 Assignment
• Week 7 Assignment
• Week 9 Assignment
• Week 10 Assignment
• Week 11 Assignment
• Week 12 Assignment
• Week 14/15 Assignment

Personal Journal Entries:

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 7 Re-visited
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14/15

Shared Journal Entries:

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14/15

Purpose

The purpose of this assignment is to delve deeper in modeling to better understand the processes occurring in the chemostat. This is meant to be done through further investigating and researching the relationship of different state variables and parameters on the population growth rate in yeast (project 1).

Methods/Workflow

• I started this assignment by reading through both top articles for the two categories of study
• After reading both I concluded that I wanted my subject to focus on "Gaining a Better Understanding of the Respiration/Fermentation Switch" because I find the challenge of modeling fermentation and respiration in the same model to be appealing
• In deciding to focus on subject 1, I began taking notes on the various papers which can be found at the following links:
  • Albertin et al. (2011) Notes
  • van den Brink et al. (2008) Notes
  • Brauer et al. (2005) Notes
• After reading the papers in depth, concluded that there needs to be a series of equations similar to the equations used in the Week 5 assignment, however some of the parameters must be re-written as state variables
• The assumption is also being made from this point forward that the system being modeled is in a chemostat

Results

Hypothesis

Based on the readings, I feel like the ammonia feed rate when it switches from becoming the limiting agent to being the agent in excess leads to making the glucose a limiting agent, which causes a metabolic shift in the yeast from undergoing fermentation (glucose in excess) to aerobic respiration (glucose is depleted/limiting)

System of Differential Equations

My system of differential equations is based on the Model 2 Week 5 Assignment with some changes made to account for fermentation and aerobic respiration shifts. While possibly not accurate, based on my current understanding, this is my beast guess of how the system might work

Best attempt at the system of differential equations can be found here

References

Albertin, W., Marullo, P., Aigle, M., Dillmann, C., de Vienne, D., Bely, M., & Sicard, D. (2011). Population Size Drives Industrial Saccharomyces cerevisiae Alcoholic Fermentation and Is under Genetic Control . Applied and Environmental Microbiology, 77(8), 2772–2784. http://doi.org/10.1128/AEM.02547-10

Brauer, M. J., Saldanha, A. J., Dolinski, K., & Botstein, D. (2005). Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures. Molecular Biology of the Cell, 16(5), 2503–2517. http://doi.org/10.1091/mbc.E04-11-0968

Dahlquist, Kam D. (2017) BIOL398-05/S17:Week 6. Retrieved from http://www.openwetware.org/wiki/BIOL398-05/S17:Week_6 on 22 February 2017.

Fitzpatrick, Ben G. (2017) Biol 398/Math 388 Week 5 Assignment: Multiple Nutrients in the Chemostat Retrieved from http://www.openwetware.org/images/5/5f/Chemostat_multiple_nutrient_modeling.pdf on 22 February 2017

Van den Brink, J., Canelas, A. B., van Gulik, W. M., Pronk, J. T., Heijnen, J. J., de Winde, J. H., & Daran-Lapujade, P. (2008). Dynamics of Glycolytic Regulation during Adaptation of Saccharomyces cerevisiae to Fermentative Metabolism . Applied and Environmental Microbiology, 74(18), 5710–5723. http://doi.org/10.1128/AEM.01121-08