20 Chapter 1 the output layer129. They rely on big data sets and can be used to automatize analyses and quantification of different parameters. In the context of this thesis, I will present an application of DL for the analysis of organoid number and size from brightfield microscopy images. AIMS AND OUTLINE OF THIS THESIS The aim of this thesis is to develop and characterize in vitro and computational translational models to study two diseases affecting fatty acid metabolism. In both diseases, peroxisomal and mitochondrial homeostasis are known or hypothesized to be disrupted. In the case of malnutrition, it has been proposed that peroxisomal loss precedes the mitochondrial phenotype56. In the case of MCADD, peroxisomes have been hypothesized to play a compensatory role in the disease. Experimental and computational tools to study these two diseases largely overlap. Studying two different diseases, in which the interplay between mitochondria and peroxisomes is affected, will provide deeper insight into the underlying mechanisms. In part I, I focus on the development and characterization of two in vitro malnutrition models from mouse primary tissue (both liver and intestine), based on growth media lacking amino acids. In part II, I first make use of this newly characterized malnutrition hepatic organoid model to understand the underlying causes for peroxisomal loss under low amino acid conditions. Secondly, I test different pharmacological approaches to prevent peroxisomal loss in the liver. Moreover, I also develop a detailed kinetic model of the peroxisomal β-oxidation to understand the effects of malnutrition and the different treatments on the pathway. In part III, I focus on the study of MCADD. To do so, I develop and characterize an MCADD in vitro model making use of patient specific iPSC-derived hepatic organoids and asses the role peroxisomes play in the disease. Finally, in part IV I focus on contextualizing the results presented throughout the thesis and discuss the literature on the topic. I also discuss the limitations and possibilities of these new translational models (both from the technical and the biological point of view) and highlight and potential ways to improve in the future. Part I – Malnutrition in vitro In chapter 2, I develop and characterize an organoid in vitro model to study malnutrition both in the liver and the intestine. These 3D systems replicate many of the organ-specific malnutrition phenotypes of both organs. In the case
RkJQdWJsaXNoZXIy MTk4NDMw