System level analysis of the metabolic robustness in bacteria.
The whole is other than the sum of its parts. With this sentence, the German psychologist Kurt Koffka summarized the Gestalt theory which argue about the own entity, independent of its elemental components, of any whole. The primary responsible of these higher attributes of a whole with respect to the sum of its components is the so-called emergence. The emergence is defined as: “The arising of novel and coherent structures, patterns and properties during the process of self-organization in complex systems” . In biology, the Gestalt principles also can be applied if we consider as the whole any biological system and as the parts, its essential components from atoms to molecules, cells, even complete organisms. Accepting this premise, inevitably leads to accept that any biological system cannot be completely understood by studying its components, but the full comprehension of its emergence is mandatory. RobDcode represents a novel integrative biology approach to study and break down the complexity of the biological robustness, one of the more ubiquitous system-level emergent properties of living systems. Through the construction of genome-scale models including metabolic modules likely involved in robustness, and the further analysis and molecular characterization of such modules, it will be possible to address for the first time, and with enough garanties, the study of the molecular mechanisms leading to biological robustness. The decifering and de-composition of biological robustness will allow not only a better understanding of life, but the application of this new knowledge in fields as diverse as biomedicine and biotechnology. RobDcode is therefore proposed as the initial step towards a more ambitious framework aiming to Systems Robustness Engineering for green biotechnology.
As basic objectives RobDcode is focus on:
1.- The development of a suitable computational framework for systematic analyzing of biological robustness in bacteria under genetic and (un)predictable environmental changes.
2.- The experimental validation and system level contextualization of the robustness modules contributing to increase robustness in bacteria.
Overview of RobDcode: Robustness can be understood as that layer of biological processes dispensable for growth but assisting to biological core processes in optimal fitness. RobDcode proposes the identification of metabolic modules driving robustness in bacteria and decoding the complex biological robustness of P. putida into condition-specific robustness cycles through three highly iterative steps, modeling, validation and analysis. Such approach will allow the system understanding of such cycles at molecular level.
Researchers in charge: J. Nogales