PETNICA 2016 - CAPORAL Clément
How to model colonies of Serratia marcescens on a NA Plate ?
Figure 1 : (A, Top) Screenshots of every steps of the model. The colony (red dots) are randomly spread on a 100x100 square. They grow (gray to yellow) in circle and then begin to die on their middle. The blue represents the media with nutrients. Scale : 40px = 1 cm and one image = 2h20. Read left to right. (B, Bottom) Visual comparison between the model and a real plate.)
Interesting question, but what for ?
One told me : predict is power, my son. So I wanted to model a dynamic to predict its behaviour. I choose a very pretty species called Serratia marcescens which produced a red pigment easily visible under a microscope. On a NA plate (NA means a nutrient and agar on the environment to grow), this microorganism forms colonies (big red circle). My goal is to model the development of these colonies in function of the time. The difficulties of this project are : how fast they grow and how do colonies react with each other ; compute in a programming language (I choose python) a 2D user interface to see the colonies growing on a screen. We call this model a “complex system”. Complex systems are characterized by simple rules for a little unit, with a lot of unit. So many unit that humans can’t determine in advance how the behaviour of the system will be. So I decided to dedicate 4 days on this question : How to model colonies of Serratia marcescens on a NA plate ?
How did you attempted to answer this question?
First I decided to get enough raw data (measurements) to determine :
- the growth rate of the colony in function of the time. I measured at different time different colonies measuring its diameter.In total, I provided 30 plates to do so.
- the interaction between colonies : measuring their diameter in function of the distance with others colonies. I took the distance between three different colonies to have an average.
Then, I assumed to use this data to point out rules for my model. Once my model would be similar to the real plates, I could start to imagine randomly new plates without incubating them in the lab.
First I decided to get enough raw data (measurements) to determine :
- the growth rate of the colony in function of the time. I measured at different time different colonies measuring its diameter.In total, I provided 30 plates to do so.
- the interaction between colonies : measuring their diameter in function of the distance with others colonies. I took the distance between three different colonies to have an average.
Then, I assumed to use this data to point out rules for my model. Once my model would be similar to the real plates, I could start to imagine randomly new plates without incubating them in the lab.
Did you get any results ?
I had around 270 pictures of plate of different time and concentration. I used them to collect the diameter of the colonies and its distance with the others. To homogene the distance, I created distance value which is equal to the addition of three distance between the center of the colonies.
Figure 2 : Graph presenting the size of the colony (each red dot is a colony) in function of its distance with three other colony (distance value). We can’t see a clear tendances showing us there is a correlation (a direct or indirect link) between the distance with other colonies and the diameter.
Each dots we can see on the figure 2 is a colony which is classified in function of its size and its distance value. For a same diameter, the distance value can be very different. But as there is different size in plates I observed I decided to make it random for my model rules.
With the pictures, I found that the colonies are growing in average a = 0.2cm/hours. I calculated : a = Final Siz avarage of colonye - Initial size avarage of colonyFinal time of incubation - initial time of incubation
We can see the steps of the program randomly generated on fig 1 A. The blue is the free media, and green to yellow (low to high) is the height of the colony. The model has its specific scale : 40px = 1 cm and between two images represents 2h20. The model seems to reproduce roughly the real shape of the colonies but is not very accurate.
What would I do next ? As the link between distance and size of the colony isn’t clear, I would like to look for better way to measure it. To finish I would also improve the time the model takes to calculate each steps (it’s currently very slow, it tooks around 12 minutes for fig 1)
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