Yu-ichi Ozaki

Prediction and validation of the distinct dynamics of transient and sustained ERK activation

To elucidate the hidden dynamics of extracellular-signal-regulated kinase (ERK) signalling networks, we developed a simulation model of ERK signalling networks by constraining in silico dynamics based on in vivo dynamics in PC12 cells. We predicted and validated that transient ERK activation depends on rapid increases of epidermal growth factor and nerve growth factor (NGF) but not on their final concentrations, whereas sustained ERK activation depends on the final concentration of NGF but not on the temporal rate of increase. These ERK dynamics depend on Ras and Rap1 dynamics, the inactivation processes of which are growth-factor-dependent and -independent, respectively. Therefore, the Ras and Rap1 systems capture the temporal rate and concentration of growth factors, and encode these distinct physical properties into transient and sustained ERK activation, respectively.

Ca2+‐independent phospholipase A2‐dependent sustained Rho‐kinase activation exhibits all‐or‐none response

Sustained contraction of cells depends on sustained Rho‐associated kinase (Rho‐kinase) activation. We developed a computational model of the Rho‐kinase pathway to understand the systems characteristics. Thrombin‐dependent in vivo transient responses of Rho activation and Ca2+ increase could be reproduced in silico. Low and high thrombin stimulation induced transient and sustained phosphorylation, respectively, of myosin light chain (MLC) and myosin phosphatase targeting subunit 1 (MYPT1) in vivo. The transient phosphorylation of MLC and MYPT1 could be reproduced in silico, but their sustained phosphorylation could not. This discrepancy between in vivo and in silico in the sustained responses downstream of Rho‐kinase indicates that a missing pathway(s) may be responsible for the sustained Rho‐kinase activation. We found, experimentally, that the sustained phosphorylation of MLC and MYPT1 exhibit all‐or‐none responses. Bromoenol lactone, a specific inhibitor of Ca2+‐independent phospholipase A2 (iPLA2), inhibited sustained phosphorylation of MLC and MYPT1, which indicates that sustained Rho‐kinase activation requires iPLA2 activity. Thus, the systems analysis of the Rho‐kinase pathway identified a novel iPLA2‐dependent mechanism of the sustained Rho‐kinase activation, which exhibits an all‐or‐none response.

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.

Ever since reversible protein phosphorylation was discovered, it has been clear that it plays a key role in the regulation of cellular processes. Proteins often undergo double phosphorylation, which can occur through two possible mechanisms: distributive or processive. Which phosphorylation mechanism is chosen for a particular cellular regulation bears biological significance, and it is therefore in our interest to understand these mechanisms. In this paper we study dynamics of the MEK/ERK phosphorylation. We employ a model selection algorithm based on approximate Bayesian computation to elucidate phosphorylation dynamics from quantitative time course data obtained from PC12 cells in vivo. The algorithm infers the posterior distribution over four proposed models for phosphorylation and dephosphorylation dynamics, and this distribution indicates the amount of support given to each model. We evaluate the robustness of our inferential framework by systematically exploring different ways of parameterizing the models and for different prior specifications. The models with the highest inferred posterior probability are the two models employing distributive dephosphorylation, whereas we are unable to choose decisively between the processive and distributive phosphorylation mechanisms.

Optical Fiber Cable Vibrations Induced by Leakage Flow During Coating Process

Optical fiber cables constitute one the key elements supporting current information technology society. Recently, the price reduction is becoming competitive among optical fiber manufacturers. In order to meet such a need, the manufacturers are now trying to increase the operating process speed when they manufacture optical fiber cables. Under these circumstances, severe vibrations were observed on a fiber cable traveling at a high speed during coating process. This paper summarizes a case study concerning traveling optical fiber vibrations and the examination results on the mechanism of vibrations. First, we outline the characteristics of traveling cable vibrations, secondly, we explain the results of model cable vibration tests and finally, we describe the theory to clarify the mechanism of the traveling cable vibrations. In the analytical part, we start with the equation of motion of a traveling cable together with the effect of the fluid force due to the leakage flow induced in a coating dice. The effect of the leakage flow in a coating dice is formulated based on annular leakage flow theory developed by author’s group where the effect of viscosity of the coating material on the instability is taken into account. Then, the equation of a traveling cable under the effect of the leakage flow at the supporting point is successfully formulated. Based on the linearized equation of motion for the traveling cable, eigenvalue analysis was performed which leads to instability criteria selecting dice configuration and the temperature of the coating material as parameters. Finally, calculated results were compared with test experimental results and discussion on the design parameters for the stable operation is made.© 2002 ASME

Specific Features of Transient Ras and Sustained Rap1 Activation

Epidermal growth factor (EGF) and nerve growth factor (NGF) induce transient and sustained extracellular signal-regulated kinase (ERK) activation, respectively, and regulate cell growth and differentiation in PC12 cells (Fig. 1a) (Gotoh et al. 1990; Qiu and Green 1992; Traverse et al. 1992; Vaudry et al. 2002). Transient and sustained ERK activation in PC12 cells depends on transient Ras activation and sustained Rap1 activation, respectively (Fig. 1b) (Vaudry et al. 2002; York et al. 1998). We have previously modeled EGFand NGF-dependent ERK activation in PC12 cells, and found that transient Ras and consequent ERK activation depends on rapidly increasing rates of EGF and NGF, whereas sustained Rap1 and consequent ERK activation depends on the final concentration of NGF (Sasagawa et al. 2005). We here construct simple Ras and Rap1 models whose inactivation is dependent on and independent of stimulation, respectively (Fig. 1c), and summarize how the modes of inactivation of Ras and Rap1 makes the features distinct. We described the Ras model in dimensionless form as follows: