PUBLICATION
Towards a digital model of zebrafish embryogenesis. Integration of cell tracking and gene expression quantification
- Authors
- Castro-Gonzalez, C., Luengo-Oroz, M.A., Douloquin, L., Savy, T., Melani, C., Desnoulez, S., Ledesma-Carbayo, M.J., Bourginey, P., Peyrieras, N., and Santos, A.
- ID
- ZDB-PUB-101201-8
- Date
- 2010
- Source
- Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 1: 5520-5523 (Journal)
- Registered Authors
- Savy, Thierry
- Keywords
- none
- MeSH Terms
-
- Animals
- Cell Lineage
- Cell Nucleus/metabolism
- Cell Tracking/methods*
- Embryo, Nonmammalian/cytology*
- Embryo, Nonmammalian/metabolism
- Embryonic Development/genetics*
- Gene Expression Regulation, Developmental*
- Goosecoid Protein/genetics
- Goosecoid Protein/metabolism
- Imaging, Three-Dimensional/methods*
- Models, Biological
- Reproducibility of Results
- Zebrafish/embryology*
- Zebrafish/genetics*
- PubMed
- 21096468 Full text @ Conf. Proc. IEEE Eng. Med. Biol. Soc.
Citation
Castro-Gonzalez, C., Luengo-Oroz, M.A., Douloquin, L., Savy, T., Melani, C., Desnoulez, S., Ledesma-Carbayo, M.J., Bourginey, P., Peyrieras, N., and Santos, A. (2010) Towards a digital model of zebrafish embryogenesis. Integration of cell tracking and gene expression quantification. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference. 1:5520-5523.
Abstract
We elaborate on a general framework composed of a set of computational tools to accurately quantificate cellular position and gene expression levels throughout early zebrafish embryogenesis captured over a time-lapse series of in vivo 3D images. Our modeling strategy involves nuclei detection, cell geometries extraction, automatic gene levels quantification and cell tracking to reconstruct cell trajectories and lineage tree which describe the animal development. Each cell in the embryo is then precisely described at each given time t by a vector composed of the cell 3D spatial coordinates (x; y; z) along with its gene expression level g. This comprehensive description of the embryo development is used to assess the general connection between genetic expression and cell movement. We also investigate genetic expression propagation between a cell and its progeny in the lineage tree. More to the point, this paper focuses on the evolution of the expression pattern of transcriptional factor goosecoid (gsc) through the gastrulation process between 6 and 9 hours post fertilization (hpf).
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping