Vertebrates, especially mammals, have long been used as research models in the study of human diseases. During this research we have demonstrated the usefulness of a relatively new animal model,... Show moreVertebrates, especially mammals, have long been used as research models in the study of human diseases. During this research we have demonstrated the usefulness of a relatively new animal model, the zebrafish, in understanding human disease formation, progression and even treatment. We first analysed the impact that exposure to constant chronic hypoxia has in the zebrafish heart, both at the morphological and genetic levels. On chapters three and four we demonstrated the worth of the zebrafish larvae in understanding metastasis formation and progression. Whereas in chapter three we focused on the use of the zebrafish as a model to rapidly test the metastatic behaviour of human pancreatic cancer cell lines and primary human tumours; on chapter four we researched the role of retinoic acid receptor antagonist, and mir10-a, as a potential new anti-cancer therapy for pancreatic adenocarcinoma. Show less
Analysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and... Show moreAnalysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and is therefore of great importance in the field of genomic research. This thesis focuses on the analysis of transcriptome complexity during infectious disease and cancer. The zebrafish was applied as an immunological model organism, due to the remarkable similarities of its immune system to that of human. The studies took advantage of novel opportunities for transcriptome profiling provided by recent developments in microarray and next generation sequencing technology that have made an enormous impact on biology. In addition to studying expression of protein coding genes, the work addressed regulatory functions of microRNAs, small non-coding RNAs playing important roles in the function of the immune system and other processes. The transcriptome data provide a valuable reference set of infection-responsive genes and microRNAs in zebrafish models and have identified microRNAs conserved between human and zebrafish liver cancer. These genomic data sets provide a strong basis for future applications of zebrafish as an infection and cancer model and contribute to the understanding of pathogenesis and the development of novel strategies for disease treatment. Show less
As the zebrafish, Danio rerio, has been increasingly used as an animal model for biomedical research, we aimed to establish zebrafish cell line models for inflammation and cancer studies in this... Show moreAs the zebrafish, Danio rerio, has been increasingly used as an animal model for biomedical research, we aimed to establish zebrafish cell line models for inflammation and cancer studies in this thesis. Several zebrafish cell lines were characterized and their genetic and physiological properties were compared. We also developed a set of tool methods to investigate cellular signaling events in zebrafish cell lines. Our case studies illustrated that zebrafish cell lines are as reliable models as the widely used mammalian cell cultures. Taking advantage of the transparency of zebrafish embryos and cell implantation protocols, zebrafish cell lines can serve as a bridge platform between in vitro, in silico, ex vivo and in vivo studies in order to enhance our understanding of molecular mechanisms underlying disease progression. Show less
Bio-informatica kan omschreven worden als het toepassen van algoritmen om meerwaarde te verkrijgen uit data afkomstig van biomedisch en/of biologisch onderzoek. In bio-informatica wordt onderzoek... Show moreBio-informatica kan omschreven worden als het toepassen van algoritmen om meerwaarde te verkrijgen uit data afkomstig van biomedisch en/of biologisch onderzoek. In bio-informatica wordt onderzoek gedaan met grote gegevens verzamelingen die afkomstig zijn uit biomedisch en/of biologisch experimenten. Het doel van dit onderzoek is komen tot nieuwe inzichten vanuit de gegevens verzameling. Deze inzichten komen tot stand door de goede organisatie van de data, het linken naar en integreren met complementaire gegevens verzamelingen en ontwikkelen en toepassen van analytische methodieken. Als bio-informatica groep onderzoeken wij het inrichten en ontwikkelen van een 3D spatio-temporele data omgeving voor ontwikkelingsstudies van het zebravis model organisme. De expressie van genen in spatio-temporale patronen vormt de basis van het ontwikkelingsproces. Voor onderzoekers is een begrip van deze patronen in sam enhang met de anatomische ontwikkeling belangrijk; hoe vormen de patronen de basis voor vorm verandering en welke genen kunnen bij dergelijke veranderende patronen betrokken zijn. In deze context hebben wij een omgeving ontwikkeld voor spatio-temporele gegevens uit embryonische studies van het zebravis modelsysteem. Show less
This thesis contains the results of imaging of adult zebrafish by using different MR approaches. We present the first high resolution mMR images of adult zebrafish. To achieve high spatial... Show moreThis thesis contains the results of imaging of adult zebrafish by using different MR approaches. We present the first high resolution mMR images of adult zebrafish. To achieve high spatial resolution we used a magnetic field of 9.4T, in combination with strong magnetic field gradients (1000 mT/m) and specialized radio frequency coils. To support imaging of living fish, we designed a special flow-through setup for continuous flow of aerated water to support living zebrafish inside the magnet. Clear morphological proton images were obtained by T2-weighted RARE sequences revealing many anatomical details in the entire intact zebrafish in vivo. We successfully implemented MRS at 9.4T and obtained for the first time detailed composition of zebrafish brain in vivo. Our results in this thesis suggest that zebrafish brain has similar metabolite profile as the human brain, which proves that zebrafish is a go od model organism to study human brain disorders. This thesis demonstrates also the application of high resolution mMRI methods to track spontaneous tumors in stable transgenic zebrafish models expressing a RAS oncoprotein and lacking P53 (mitf:Ras::mitf:GFP X p53-/-). Tumors were successfully visualized at different locations in live zebrafish. Show less
Multiple processes are influenced by a protein family named the function of Mitogen Activated Protein Kinases (MAPK), where among tissue morphogenesis, cell-proliferation, cell-differentiation,... Show moreMultiple processes are influenced by a protein family named the function of Mitogen Activated Protein Kinases (MAPK), where among tissue morphogenesis, cell-proliferation, cell-differentiation, cell-survival and immune reactions. A consequence of this broad role of these proteins is that disturbed MAPK signaling possibly leads to severe affects, and could even lead to the development of a disease or disturb embryogenesis. The human genome encodes for 14 mapk genes. One of the best characterized MAPK signaling transductions pathways is the Extracellular signal Regulated Kinase 1 and 2 (ERK1/ERK2). The zebrafish is a relatively new, genetic accessible model organism, which is because of their transparency of the embryos, very suitable to study the role of the MAPKs in embryonic development. The study described in this thesis shows that the zebrafish genome encodes for the same mapk genes, which makes it possible to study the functions of these proteins, using the zebrafish. Further investigations to the roles of ERK1 and ERK2 during embryonic development led to the new insight that ERK1 and ERK2 have distinct roles during crucial developmental cell migration processes and the differentiation of tissues and cell types. In addition, it was found that ERK1 and ERK2 affect the expression of common as well as distinct target genes. Show less
