Laboratory for Developmental Dynamics

A single cell, the fertilized egg, divides many times to generate many functionally different cells, each of which is brought to a specific position to produce complex multicellular structures, i.e. organs and the body. To understand the mechanism of such spatially and temporally dynamic process, we need to carry out quantitative and computational analysis, which integrates quantification, modeling and computer simulation. We develop technologies for quantitative and computational analysis on the development of multicellular organisms by integrating molecular cell biology, biophysics, genome science, computational science, mathematical science, etc. Also, we attempt to apply our technologies to mammalian embryo.

Research Subjects

• System analysis of development by using large collections of quantitative dynamic information
• Mathematical modeling of development
• Development of technology for measuring developmental dynamics
• Development of Integrated database for quantitative biology and bioimage informatics

Publications

1. Kyoda, K., Adachi, E., Masuda, E., Nagai, Y., Suzuki, Y., Oguro, T., Urai, M., Arai, R., Furukawa, M., Shimada, K., Kuramochi, J., Nagai, E., Onami, S.:
   "WDDD: worm developmental dynamics database"
   Nucleic Acids Res. 41, D732-737 (2013)
2. Fujita, M., Onami, S.:
   "Cell-to-cell heterogeneity in cortical tension specifies curvature of contact surfaces in Caenorhabditis elegans embryos"
   PLoS One 7, e30224 (2012)
3. Fujita, M., Onami, S.:
   "Estimating intercellular surface tension by laser-induced cell fusion"
   Phys. Biol. 8, 064001 (2011)
4. Kyoda, K., Baba, K., Kitano, H., Onami, S.:
   "A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks"
   Source Code Biol. Med. 6, 12 (2011)
5. Kimura, A., Onami, S.:
   "Modeling microtubuel-mediated forces and centrosome positioning in Caenorhabditis elegans embryos"
   Methods Cell Biol., 97, 437-453 (2010)
6. Hamahashi, S., Kitano, H., Onami, S.:
   "A system for measuring cell division patterns of early Caenorhabditis elegans embryos by using image processing and object tracking"
   Systems Comput. Jpn., 38(11), 12-24 (2007)
7. Kimura, A., Onami, S.:
   "Local cortical pulling force repression switches centrosomal centration and posterior displacement in C. elegans"
   J. Cell Biol., 179, 1347-1354 (2007)
8. Hamahashi, S., Onami, S., Kitano, H.:
   "Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking"
   BMC Bioinformatics 6, 125 (2005)
9. Kimura, A., Onami, S.:
   "Computer simulations and image processing reveal length-dependent pulling force as the primary mechanism for C. elegans male pronuclear migration"
   Dev. Cell 8, 765-775 (2005)