In this thesis, we presented three main types of analyses of metabolism, most of which involved symbiosis: metabolic dialogue between a trypanosomatid and its symbiont, comparative analyses of metabolic networks and exploration of metabolomics data. All of them were essentially based on genomics data where metabolic capabilities were predicted from the annotated genes of the target organism, and were further refined with other types of data depending on the aim and scope of each investigation. The metabolic dialogue between a trypanosomatid and its symbiont was explored with functional and evolutionary goals which included analysing the classically defined pathways for the synthesis of essential amino acids and vitamins, exploring the genome-scale metabolic networks and searching for potential horizontal gene transfers from bacteria to the trypanosomatids. The comparative analyses performed focused on the common metabolic capabilities of different lifestyle groups of bacteria and we proposed a method to automatically establish the common and the group-specific activities. The application of our method on metabolic stories enumeration to the yeast response to cadmium exposure was a validation of this approach on a well-studied biological response to stress. We showed that the method captured well the underlying knowledge as it extracted stories allowing for further interpretations of the metabolomics data mapped into the genome-scale metabolic model of yeast
| Identifer | oai:union.ndltd.org:CCSD/oai:tel.archives-ouvertes.fr:tel-01050338 |
| Date | 12 November 2013 |
| Creators | Coimbra Klein, Cecilia |
| Publisher | Université Claude Bernard - Lyon I |
| Source Sets | CCSD theses-EN-ligne, France |
| Language | English |
| Detected Language | English |
| Type | PhD thesis |
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