Team:UPF CRG Barcelona/Simulation
SIMULATION OF INTESTINE CONDITIONS
It is very important to have in mind in which environment the genetically modified bacteria are going to be working. In the intestine, there is a steep gradient for oxygen and its concentrations decrease precipitously near anoxia in the middle of the lumen (Espey, 2013). For this reason, if we want our engineered bacteria to work in the gut, it has to work under anaerobic conditions. However, LCFA are degraded via the beta-oxidation pathway, an aerobic pathway for excellence, therefore it is needed to find alternative strategies in order to metabolize LCFA without oxygen.
Moreover, when engineering a pathway in order to optimize it, it is very important to have in mind that the overall efficiency of the synthetic pathway can be reduced by the loss of metabolic intermediates by diffusion or by competent pathways (Na, Kim and Lee, 2010]. In the intestine, after diet ingest, there is going to be other energetic substrates aside of LCFA, especially sugars and amino acids. Therefore, most of the catabolic pathways of bacteria are going to be active and can interfere with beta oxidation efficiency. For this reason, it is very important to study the metabolic network as a whole instead of only focusing on the pathway that we want to modify.