Tesis doctoral de Clara Prats Soler
Predictive food microbiology has become an important specific field in microbiology. Bacterial growth of a batch culture may show up to four phases: lag, exponential, stationary and death. The bacterial lag phase, which is of specific interest in the framework of predictive food microbiology, has generally been tackled with two generic approaches: at a cellular and intracellular level, which we call the microscopic scale, and at a population level, which we call the macroscopic scale. Studies at the microscopic level tackle the processes that take place inside the bacterium during its adaptation to the new conditions such as the changes in genetic expression and in metabolism. Studies at the macroscopic scale deal with the description of a population growth cycle by means of mathematical continuous modelling and experimental measurements of the variables related to cell density evolution. in this work we aimed to improve the understanding of the lag phase in bacterial cultures and the intrinsic phenomena behind it. This has been carried out from the perspective of individual-based modelling (ibm) with the simulator indisim (individual discrete simulation), which has been specifically improved for this purpose. Ibm introduces a mechanistic approach by modelling the cell as an individual unit. Ibm simulations deal with 1 to 106 cells, and allow specific study of the phenomena that emerge from the interaction among cells. These phenomena belong to the mesoscopic level. Mesoscopic approaches are essential if we are to understand the effects of cellular adaptations at an individual level in the evolution of a population. Thus, they are a bridge between individuals and population, or, to put it another way, between models at a microscopic scale and models at a macroscopic scale. first, we studied separately two of the several mechanisms that may cause a lag phase: the lag caused by the initial low mean mass of the inoculum, and the lag caused by a change in the nutrient source. The relationship among lag duration and several variables such as temperature and inoculum size were also checked. This analysis allowed identification of the biomass distribution as a very important variable to follow the evolution of the culture during the growth cycle. A mathematical tool was defined in order to assess its evolution during the different phases of growth: the distance functions. a theoretical approach to the culture lag phase through the dynamics of the growth rate allowed us to split this phase into two stages: initial and transition. A continuous mathematical model was built in order to shape the transition stage, and it was checked with indisim simulations. It was seen that the lag phase must be defined as a dynamic process rather than as a simple period of time. The distance functions were also used to discuss the balanced growth conditions. some of the reported indisim simulation results were subjected to experimental corroboration by means of flow cytometry, which allow the assessment of size distributions of a culture through time. The dynamics of biomass distribution given by indisim simulations were checked, as well as the distance function evolution during the different phases of growth. The coincidence between simulations and experiments is not trivial: the system under study is complex; therefore, the coincidence in the dynamics of the different modelled parameters is a validation of both the model and the simulation methodology. finally, we have made progress in ibm parameter estimation methods, which is essential to improve quantitative processing of indisim simulations. Classic grid search, nmta and newuoa methods were adapted and tested, the latter providing better results with regard to time spent, which maintains satisfactory precision in the parameter estimation results. above all, the validity of indisim as a useful tool to tackle transient processes such as the bacterial lag phase has been amply demonstrated.
Datos académicos de la tesis doctoral «Individual-based modelling of bacterial cultures in the study of the lag phase«
- Título de la tesis: Individual-based modelling of bacterial cultures in the study of the lag phase
- Autor: Clara Prats Soler
- Universidad: Politécnica de catalunya
- Fecha de lectura de la tesis: 13/06/2008
Dirección y tribunal
- Director de la tesis
- Daniel López Codina
- Tribunal
- Presidente del tribunal: josep Vives rego
- kristel Bernaerts (vocal)
- jan Van impe (vocal)
- Jorge Wagensberg lubinski (vocal)