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Model

On this page, you can find resources that could be useful for future modelisation of the characteristics of amilCP grown into yeast. This summer, we didn’t achieve to learn enough about modelling, neither had the time or materials to do enough experiments to apply this documentation to our project.

I - Observe

How to measure the growth rate?

Briggs, D.E., Hough, J.S., Stevens, R., & Tom W. Young. (1999). Malting and Brewing Science: Volume 2 Hopped Wort and Beer. (2nd ed.) Gaithersburg: Aspen Publishers, Inc. p.615 :

“A direct estimation of the biomass present may be made by determining the dry weight of a sample.” and “Cell number is most conveniently measured, after suspending cells in a suitable electrolyte, with a particle counter”

Imperial College London (2016) Proof. Retrieved from : https://2016.igem.org/Team:Imperial_College/Proof :

“We measured the growth rate of cells producing different chromoproteins by using a plate reader to measure the optical density of isolated populations over 10 hours In order to determine if different types of chromoprotein expression were influencing the growth rate differently.”

Bess Ruff. (2019). How to measure yeast growth. Retrieved from https://www.wikihow.com/Measure-Yeast-Growth:

“ When the yeast grows, it produces a gas called carbon dioxide, or CO2, which you can use measure how yeast grows over time. This experiment uses bottles and balloons to capture the CO2 from fermenting yeast and helps you to visualize how yeast uses sugar to grow.”

How to measure the intensity?

Cheng-Yi Chiang, Cheng-Yung Lin, Yen-Ting Chen, Huai-Jen Tsai, Blue fluorescent protein derived from the mutated purple chromoprotein isolated from the sea anemone Stichodactyla haddoni, Protein Engineering, Design and Selection, Volume 29, Issue 11, November 2016, Pages 523–530, https://doi.org/10.1093/protein/gzw041 :

“ Using pixel value to quantify the blue fluorescent intensity. ImageJ software “

II - Pists of systems that could model the observations

How to model the growth rate?

Zhao-gang, L. & Feng-ri, L. Journal of Forestry Research (2003) 14: 19. https://doi.org/10.1007/BF02856757

Popular model to explain the growth rate: Chapman-Richards, Schnute

How to model the intensity?

III - What could explain the observations?

Temperature, dead cells

Liljeruhm, J., Funk, S.K., Tietscher, S. et al. J Biol Eng (2018) 12: 8. https://doi.org/10.1186/s13036-018-0100-0 :

“More aeration tended to give more intense colors, consistent with knowledge that chromophore maturation in all GFP-like proteins is dependent on reaction with oxygen [1].” - And “we noticed that colored liquid cultures of certain CPs expressed from high-copy plasmids in E. coli sometimes failed to gain the same amount of color after dilution and repeated overnight liquid culturing. This indicated that certain CPs exerted a high fitness cost when highly expressed, leading to strong selection pressure for loss of expression..”

IV - Possible uses