Difference between revisions of "Team:Pumas Mexico/Model"

Revision as of 01:07, 19 October 2016

Pumas_Mexico

Modeling

Chlorella vulgaris modelling by means of Flux Balance Analysis To model the growth and lipid production of Chlorella vulgaris we used the Constraint-Based Modelling, being our principal tool the kit the COBRApy library offers 1. The metabolic reconstruction we used was that of Chlorella vulgaris UTEX 395, published on July of this year 2. This reconstruction is based on Chlamydomonas reinhardii, with experimental and bioinformatic data on the literature.

It includes 843 out of 7,100 annotated genes (around 12%), delineating 1,770 metabolites and 2,294 reactions, being the amino acid and lipid metabolisms the most accurately reconstructed 2. Importantly the authors of this model report that the uptake rates were experimentally verified experimentally.

First, we analyzed which light wavelength was the best for the overall growth of the algae according to the metabolic model. When comparing different wavelengths we came to the conclusion that the best light for growing it was the ___ light, while in the literature it is reported that the best light for growing Chlorella on long periods is the blue one (wavelength of 475 nm)

Then, we analyzed the resources and nutrients for the culture. We simulated more water and carbon sources in the medium. Also we tried the effect of oxygen, given that it is present in small quantities, because we were not able to get a sealed biorreactor. For the water and oxygen simulations, we used the photoautotroph model, while for the carbon source (acetate) we used the heterotroph one. The plots of these experiments are below.

Inspiration

Here are a few examples from previous teams:

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 <br>
 <h2> Modeling</h2>
-<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
+<p> <b>Chlorella vulgaris modelling by means of Flux Balance Analysis</b>
+	To model the growth and lipid production of Chlorella vulgaris we used the Constraint-Based Modelling, being our principal tool the kit the COBRApy library offers 1. The metabolic reconstruction we used was that of Chlorella vulgaris UTEX 395, published on July of this year 2. This reconstruction is based on Chlamydomonas reinhardii, with experimental and bioinformatic data on the literature.
+</p>
+<p>It includes 843 out of 7,100 annotated genes (around 12%), delineating 1,770 metabolites and 2,294 reactions, being the amino acid and lipid metabolisms the most accurately reconstructed 2. Importantly the authors of this model report that the uptake rates were experimentally verified experimentally.</p>
+<p>First, we analyzed which light wavelength was the best for the overall growth of the algae according to the metabolic model. When comparing different wavelengths we came to the conclusion that the best light for growing it was the ___ light, while in the literature it is reported that the best light for growing Chlorella on long periods is the blue one (wavelength of 475 nm)
+</p>
+<p>Then, we analyzed the resources and nutrients for the culture. We simulated more water and carbon sources in the medium. Also we tried the effect of oxygen, given that it is present in small quantities, because we were not able to get a sealed biorreactor. For the water and oxygen simulations, we used the photoautotroph model, while for the carbon source (acetate) we used the heterotroph one. The plots of these experiments are below.
+</p>