Atsuko Takamatsu

Two rotating cilia in the node cavity are sufficient to break left–right symmetry in the mouse embryo

Determination of left-right asymmetry in mouse embryos is achieved by a leftward fluid flow (nodal flow) in the node cavity that is generated by clockwise rotational movement of 200-300 cilia in the node. The precise action of nodal flow and how much flow input is required for the robust read-out of left-right determination remains unknown. Here we show that a local leftward flow generated by as few as two rotating cilia is sufficient to break left-right symmetry. Quantitative analysis of fluid flow and ciliary rotation in the node of mouse embryos shows that left-right asymmetry is already established within a few hours after the onset of rotation by a subset of nodal cilia. Examination of various ciliary mutant mice shows that two rotating cilia are sufficient to initiate left-right asymmetric gene expression. Our results suggest the existence of a highly sensitive system in the node that is able to sense an extremely weak unidirectional flow, and may favour a model in which the flow is sensed as a mechanical force.

Environment-dependent morphology in plasmodium of true slime mold Physarum polycephalum and a network growth model

Branching network growth patterns, depending on environmental conditions, in plasmodium of true slime mold Physarum polycephalum were investigated. Surprisingly, the patterns resemble those in bacterial colonies even though the biological mechanisms differ greatly. Bacterial colonies are collectives of microorganisms in which individual organisms have motility and interact through nutritious and chemical fields. In contrast, the plasmodium is a giant amoeba-like multinucleated unicellular organism that forms a network of tubular structures through which protoplasm streams. The cell motility of the plasmodium is generated by oscillation phenomena observed in the partial bodies, which interact through the tubular structures. First, we analyze characteristics of the morphology quantitatively, then we abstract local rules governing the growing process to construct a simple network growth model. This model is independent of specific systems, in which only two rules are applied. Finally, we discuss the mechanism of commonly observed biological pattern formations through comparison with the system of bacterial colonies.

Traffic optimization in railroad networks using an algorithm mimicking an amoeba-like organism, Physarum plasmodium

Traffic optimization of railroad networks was considered using an algorithm that was biologically inspired by an amoeba-like organism, plasmodium of the true slime mold, Physarum polycephalum. The organism developed a transportation network consisting of a tubular structure to transport protoplasm. It was reported that plasmodium can find the shortest path interconnecting multiple food sites during an adaptation process (Nakagaki et al., 2001. Biophys. Chem. 92, 47-52). By mimicking the adaptation process a path finding algorithm was developed by Tero et al. (2007). In this paper, the algorithm is newly modified for applications of traffic distribution optimization in transportation networks of infrastructure such as railroads under the constraint that the network topology is given. Application of the algorithm to a railroad in metropolitan Tokyo, Japan is demonstrated. The results are evaluated using three performance functions related to cost, traveling efficiency, and network weakness. The traffic distribution suggests that the modified Physarum algorithm balances the performances under a certain parameter range, indicating a biological process.

Control of interaction strength in a network of the true slime mold by a microfabricated structure

The plasmodium of the true slime mold, Physarum polycephalum, which shows various nonlinear oscillatory phenomena, for example, in its thickness, protoplasmic streaming and concentration of intracellular chemicals, can be regarded as a collective of nonlinear oscillators. The plasmodial oscillators are interconnected by microscale tubes whose dimensions can be closely related to the strength of interaction between the oscillators. Investigation of the collective behavior of the oscillators under the conditions in which the interaction strength can be systematically controlled gives significant information on the characteristics of the system. In this study, we proposed a living model system of a coupled oscillator system in the Physarum plasmodium. We patterned the geometry and dimensions of the microscale tube structure in the plasmodium by a microfabricated structure (microstructure). As the first step, we constructed a two-oscillator system for the plasmodium that has two wells (oscillator part) and a channel (coupling part). We investigated the oscillation behavior by monitoring the thickness oscillation of the plasmodium in the microstructure with various channel widths. It was found that the oscillation behavior of two oscillators dynamically changed depending on the channel width. Based on the results of measurements of the tube dimensions and the velocity of the protoplasmic streaming in the tube, we discuss how the channel width relates to the interaction strength of the coupled oscillator system.

Emergence of traveling waves in the zebrafish segmentation clock.

The spatial and temporal periodicity of somite formation is controlled by the segmentation clock, in which numerous cells cyclically express hairy-related transcriptional repressors with a posterior-to-anterior phase delay, creating ‘traveling waves’ of her1 expression. In zebrafish, the first traveling wave buds off from the synchronous oscillation zone in the blastoderm margin. Here we show that the emergence of a traveling wave coincides with the anterior expansion of Fgf signaling and that transplanted Fgf8b-soaked beads induce ectopic traveling waves. We thus propose that as development proceeds, the activity of Fgf signaling gradually expands anteriorly, starting from the margin, so that cells initiate her1 oscillation with a posterior-to-anterior phase delay. Furthermore, we suggest that Fgf has an essential role in establishing the period gradient that is required for the her1 spatial oscillation pattern at the emergence of the traveling wave.

Frequency Coupling Model for Dynamics of Responses to Stimuli in Plasmodium of Physarum Polycephalum

Gathering or escaping behavior in the plasmodium of Physarum polycephalum is considered to relate to an entrainment of the coupled nonlinear oscillators. The behavior has been explained to be caused by the formation of phase gradient between those oscillators, which results from the local frequency modulation at the stimulated site. However, it has not yet been elucidated how the formation process relates to the migration of the plasmodium. In this paper, we have introduced a model with frequency coupling besides the phase coupling in the system of coupled oscillators. By the simulation, we have shown that not only the phase gradient but also the concentration gradient of substances such as Ca 2+ and ATP are self-organized and their reverse by the stimulus results in the migration of plasmodium.

Controlling the geometry and the coupling strength of the oscillator system in plasmodium of Physarum polycephalum by microfabricated structure

SummaryThe plasmodium of the true slime moldPhysarum polycephalum, which shows various oscillatory phenomena, can be regarded as a collective of nonlinear oscillators. Partial bodies in the plasmodium, which are assumed to be nonlinear oscillators, are mutually connected by microscale tubes named plasmodial strand. The interactions among the oscillators can be strongly affected by the geometry and the dimension of the tube network. Investigation of the collective behavior under the condition that the configuration of the network can be manipulated gives significant information on the characteristics of the plasmodium from the viewpoint of nonlinear dynamics. In this study, we have developed a new method to control the geometry and the tube dimension of the plasmodium with a microfabricated structure. It is shown that the geometry of the plasmodium can be manipulated with a microstructure which is fabricated of ultrathick photoresist resin by photolithographic processes. In order to confirm that not only the geometry but also the dimension of the tubes can be controlled with the microstructure, we observed the cross section of the patterned plasmodium with a three-dimensional internal-structure microscope. By observing the oscillatory behavior of the partial bodies of the patterned plasmodium, it was confirmed that the coupling strength between two oscillators, which corresponds to the dimension of the plasmodial strand, can be controlled by the microstructure. It is concluded that the present method is suitable for further studies of the network of Physarum plasmodium as a collective nonlinear oscillator system.

Characterization of Adaptation by Morphology in a Planar Biological Network of Plasmodial Slime Mold

Growth processes of a planar biological network of plasmodium of a true slime mold, Physarum polycephalum , were analyzed quantitatively. The plasmodium forms a transportation network through which protoplasm conveys nutrients, oxygen, and cellular organelles similarly to blood in a mammalian vascular network. To analyze the network structure, vertices were defined at tube bifurcation points. Then edges were defined for the tubes connecting both end vertices. Morphological analysis was attempted along with conventional topological analysis, revealing that the growth process of the plasmodial network structure depends on environmental conditions. In an attractive condition, the network is a polygonal lattice with more than six edges per vertex at the early stage and the hexagonal lattice at a later stage. Through all growing stages, the tube structure was not highly developed but an unstructured protoplasmic thin sheet was dominantly formed. The network size is small. In contrast, in the repulsive conditio...

Asymmetric rotational stroke in mouse node cilia during left-right determination.

Rotational movement of isolated single cilia in mice embryo was investigated, which generates leftward fluid flow in the node cavity and plays an important role in left-right determination. The leftward unidirectional flow results from tilting of the rotational axis of the cilium to the posterior side. By combining computational fluid dynamics with experimental observations, we demonstrate that the leftward stroke can be more effective than expected for cases in which cilia tilting alone is considered with the no-slip condition under constant driving torque. Our results suggest that the driving torque is asymmetric.

Ca2+ effect on protoplasmic streaming in Nitella internodal cell

Ca(2+) ion effect on protoplasmic streaming in an internodal cell of Nitella has been investigated for various temperatures. We have found that the protoplasmic streaming at low temperature is remarkably affected by the Ca(2+) ions in the internodal cell but larger concentrations of the Ca(2+) ions are needed to suppress the streaming velocity at higher temperatures. These streaming behaviors of the protoplasm, furthermore, have been elucidated on the basis of the reaction equations which take into account ATP hydrolysis due to actin-myosin molecules and inactivity of the molecules due to the Ca(2+) ions.