Spatio-temporal gene expression analysis from 3D in situ hybridization images

Welten, M.C.M. (2007)

Doctoral Thesis

In developmental biology, the expression of genes is studied to understand development, phenotypes and to construct models to understand disease. In this thesis, we explore and validate biological as well as computerized tools, to address research questions in developmental biology. Based on these techniques, we developed a workflow to generate a large number of 3D spatio-temporal patterns of gene expression. Though several techniques for gene expression analysis are available, most spatial gene expression data are only in 2D. In order to study gene expression and differentiation of structures during development at the same time, both spatial 3D information, and temporal data are essential. These spatio-temporal patterns of gene expression have to be generated. To that end, we have developed a workflow based on fluorescent in situ hybridization (FISH) (ZebraFISH;), confocal laser scanning microscopy (CLSM) and subsequent three-dimensional modeling with, in our case, TDR-3Dbase software- resulting in a large amount of 3D spatio-temporal patterns of gene expression, obtained in a straightforward and non-destructive manner. In the work described in this thesis, we applied the workflow to 30 genes in 5 developmental processes. 3D modeling and data mining software are used to analyse gene expression patterns in zebrafish embryos and across species

• 3D imaging
• 3D reconstruction
• data mining algorithm
• Embryonic development
• Fluorescent in situ hybridization
• Gene expression
• Spatio-temporal

• All authors: Welten, M.C.M.
• Supervisor: Verduyn Lumel, S.M.; Spaink, H.P.
• Co-supervisor: Verbeek, F.J.
• Qualification: Doctor (dr.)
• Awarding Institution: Faculty of Science, Leiden University
• Date: 2007-11-27
• Publisher: Leiden Institute of Advanced Computer Science, group Imaging and Bio-informatics, Faculty of Science, Leiden University
• Sponsorship: ZF Screens B.V.