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Bioinformatics Vol. 19 no. 6 2003
Pages 704-716
© 2003 Oxford University Press

Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans

Atsushi Kajita 1,1, Masayuki Yamamura 2 and Yuji Kohara 1

1 Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540
2 Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8502, Japan

Received on September 10, 2002 ; revised on December 2, 2002 ; accepted on December 6, 2002

Motivation: The ultimate goal of bioinformatics is to reconstruct biological systems in the computer. Since biological systems have many levels, it is important to focus on an appropriate level. In our first application of computer modeling to the early development of the nematode Caenorhabditis elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell–cell interaction, and is regarded as a system, one level higher than the system of gene regulation within cells. It is largely restricted by physical conditions that seemed feasible to model by computer.

Results: We constructed a computer model of the C.elegans embryo, currently up to the 4-cell stage, using a deformable and dividable triangulated network. The model is based solely on cellular-level dynamics. We found that the optimal ranges of three parameters that affect the elongation of dividing cells led, in computer simulations, to almost the same cellular arrangements as in real embryos. The nature of the model and the relationship with real embryos are discussed.

Availability: The software is available upon request.

Contact: akajita{at}lab.nig.ac.jp

* To whom correspondence should be addressed.


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