Emergent patterns in protein, microbial and mutualistic systems
- Autores: Alberto Pascual García
- Directores de la Tesis: Ugo Bastolla (dir. tes.)
- Lectura: En la Universidad Autónoma de Madrid ( España ) en 2015
- Idioma: inglés
- Tribunal Calificador de la Tesis: Andrés Moya Simarro (presid.), Ramón Díaz Uriarte (secret.), Bruno Contreras Moreira (voc.), Lucas Lacasa Saiz de Arce (voc.), Bartolomé Luque Serrano (voc.)
- Materias:
- Enlaces
- Tesis en acceso abierto en: Biblos-e Archivo
- Resumen
In this thesis we analyse emergent patterns in complex biological systems. We say that these patterns emerge, given that they result from behaviours of the system that are difficult to explain starting from a microscopic description.These behaviours are strongly dependent on the interactions between elements, and thus our research focuses on the identification and evaluation of interaction networks. In particular, we have analysed interactions that may reflect the response of the system to long term conditions, whose analysis may be compatible with an evolutionary interpretation.
The methodological and conceptual framework needed for the development of our research is complex. This is the reason why the first part of the thesis is devoted to clarify the epistemological approximation we have followed. In subsequent chapters, we present our research results, which have been developed around three systems with notable differences among them.
The first system considers a representative subset of all the protein structures known up to date. We develop a method that objectively demonstrates the existence of structural protein classes known as folds, defining conserved interaction patterns between amino-acids. We go deeper into the evolutionary interpretation of this result investigating the role of protein function in the structural conservation and divergence.
Second, we analyse high-throughput sequencing experiments collecting the presence of bacterial taxa in different environments. From this data we infer aggregation and segregation patterns suggesting that bacterial mutualistic interactions are very relevant, and whose functional role is explored in more detail analysing the bacterial assembly process in a group of infants during their development.
Last, we have considered mutualistic communities of plants and pollinators.
We predict the structural stability of this system defining two magnitudes: the effective interspecific competition and the propagation of perturbations. These magnitudes rationalize the relative effect of competition versus mutualism --and, in particular, of the different mutualistic networks-- in the structural stability, which we show has a main role for sustaining biodiversity.
