Spatiotemporal pattern in somitogenesis: a non-Turing scenario with wave propagation.

Living organisms maintain their lives under far-from-equilibrium conditions by creating a rich variety of spatiotemporal structures in a self-organized manner, such as temporal rhythms, switching phenomena, and development of the body. In this paper, we focus on the dynamical process of morphogens in somitogenesis in mice where propagation of the gene expression level plays an essential role in creating the spatially periodic patterns of the vertebral columns. We present a simple discrete reaction-diffusion model which includes neighboring interaction through an activator, but not diffusion of an inhibitor.

Large-scale on-off switching of genetic activity mediated by the folding-unfolding transition in a giant DNA molecule: an hypothesis.

We present a model to describe the on-off switching of transcriptional activity in a genetic assembly by considering the intrinsic characteristics of a giant genomic DNA molecule which can undergo a discrete structural transition between coiled and compact states. We propose a model in which the transition in the higher-order structure of DNA plays an essential role in regulating stable on-off switching and/or the oscillation of a large number of genes under the fluctuations in a living cell, where such a structural transition is caused by environmental factors. This model explains the rapid and broad transcriptional response in a genetic assembly as well as its robustness against fluctuations.

Survival versus collapse: abrupt drop of excitability kills the traveling pulse, while gradual change results in adaptation.

Excitable media show changes in their basic characteristics that reflect temporal changes in the environment. In the photosensitive Belousov-Zhabotinsky (BZ) reaction, excitability is decreased by illumination. We found that a traveling pulse failed to propagate when a certain level of light intensity was switched on abruptly, but the pulse continued propagating when the light intensity reached the same level gradually.

Ultradian oscillations of Stat, Smad, and Hes1 expression in response to serum.

Serum response has been used as a model for studying signaling transduction for many biological events such as cell proliferation and survival. Although expression of many genes is up- or down-regulated after serum stimulation, the Notch effector Hes1 displays oscillatory response. However, the precise mechanism and biological significance of this oscillation remain to be determined.

Real-time imaging of the somite segmentation clock: revelation of unstable oscillators in the individual presomitic mesoderm cells.

Notch signaling components such as the basic helix-loop-helix gene Hes1 are cyclically expressed by negative feedback in the presomitic mesoderm (PSM) and constitute the somite segmentation clock. Because Hes1 oscillation occurs in many cell types, this clock may regulate the timing in many biological systems. Although the Hes1 oscillator is stable in the PSM, it damps rapidly in other cells, suggesting that the oscillators in the former and the latter could be intrinsically different.

Direction detector on an excitable field: field computation with coincidence detection.

Living organisms process information without any central control unit and without any ruling clock. We have been studying a novel computational strategy that uses a geometrically arranged excitable field, i.e.