Cardiac arrhythmias are a common cause of sudden death worldwide. However, despite decades of thorough investigation the underlying biophysical mechanisms of cardiac arrhythmias are still... Show moreCardiac arrhythmias are a common cause of sudden death worldwide. However, despite decades of thorough investigation the underlying biophysical mechanisms of cardiac arrhythmias are still insufficiently understood due to incomplete theories and the lack of precise spatiotemporal control in experiments. In the last decade, the problem of insufficient spatiotemporal control has started to be tackled by means of a new technique, called optogenetics. This technique employs expression of light-activated proteins, which are activated or deactivated in time and space by switching on/off light (in the near-ultraviolet to near-infrared wavelength range) in specific patterns thus realizing fully biological spatiotemporal control. However, with a few notable exceptions, cardiac optogenetic studies have only confirmed previously known mechanisms and yielded no or little novel mechanistic insights. In this thesis, to fill this gap, we combined nonlinear dynamics theory, numerical simulations and optogenetic experiments with unique spatiotemporal control to theoretically predict and demonstrate novel arrhythmogenic phenomena in cardiac tissue. Thanks to the robustness of the optogenetics methods and generality of the applied theories and computations, this thesis uncovered novel mechanisms for the biophysics of cardiac tissue that are applicable to the functioning of excitable systems in general. Show less
A complex community of microbes develops in the infant gut shortly after birth. We call this community the infant gut microbiota. The microbiota influences the health of the infant, which makes the... Show moreA complex community of microbes develops in the infant gut shortly after birth. We call this community the infant gut microbiota. The microbiota influences the health of the infant, which makes the composition and function of the infant gut microbiota an important topic to study. It’s not possible to directly study the development of the microbiota inside the infant, so we are limited to information from fecal samples and laboratory experiments. Because it is so difficult to study, the processes and mechanisms that shape the microbiota also remain unclear. Mathematical models can generate hypotheses and predictions about the unseen inner workings of a system such as the infant gut microbiota.In this thesis we develop a mathematical model that makes predictions both on how bacteria are influenced by the environment and on how they influence the environment. By applying this influence to the environment and repeating the technique, the model can make predictions for how the whole system changes over time. We use this model to make predictions on how changes to the environment, such as the presence of oxygen, antibiotic disturbances, or in particular the presence of oligosaccharides, influence the infant gut microbiota, their metabolism, and ultimately the infant. Show less
Rozendaal, Y.J.W.; Wang, Y.N.; Hilbers, P.A.J.; Riel, N.A.W. van 2019
BackgroundA positive energy balance is considered to be the primary cause of the development of obesity-related diseases. Treatment often consists of a combination of reducing energy intake and... Show moreBackgroundA positive energy balance is considered to be the primary cause of the development of obesity-related diseases. Treatment often consists of a combination of reducing energy intake and increasing energy expenditure. Here we use an existing computational modelling framework describing the long-term development of Metabolic Syndrome (MetS) in APOE3L.CETP mice fed a high-fat diet containing cholesterol with a human-like metabolic system. This model was used to analyze energy expenditure and energy balance in a large set of individual model realizations.ResultsWe developed and applied a strategy to select specific individual models for a detailed analysis of heterogeneity in energy metabolism. Models were stratified based on energy expenditure. A substantial surplus of energy was found to be present during MetS development, which explains the weight gain during MetS development. In the majority of the models, energy was mainly expended in the peripheral tissues, but also distinctly different subgroups were identified.In silico perturbation of the system to induce increased peripheral energy expenditure implied changes in lipid metabolism, but not in carbohydrate metabolism. In silico analysis provided predictions for which individual models increase of peripheral energy expenditure would be an effective treatment.ConclusionThe computational analysis confirmed that the energy imbalance plays an important role in the development of obesity. Furthermore, the model is capable to predict whether an increase in peripheral energy expenditure - for instance by cold exposure to activate brown adipose tissue (BAT) - could resolve MetS symptoms. Show less
Many studies in developmental biology rely on the construction and analysis of models. This research presents a broad view of modelling approaches for developmental biology, with a focus on... Show moreMany studies in developmental biology rely on the construction and analysis of models. This research presents a broad view of modelling approaches for developmental biology, with a focus on computational methods. An overview of modelling techniques is given, followed by several case studies. Using 3D reconstructions, the heart development of the turtle is examined, with special attention to heart looping and the development of the outflow tract. Subsequently, an ontology system is presented in which anatomical, developmental and physiological information on the vertebrate heart is modelled. Finally, two Petri net models are discussed, which model the developmental process of gradient formation, both in a qualitative and quantitative manner. Show less
