Tatsuo Shibata - Academia.edu (original) (raw)
Papers by Tatsuo Shibata
PLOS ONE, 2015
Sensory systems have mechanisms to respond to the external environment and adapt to them. Such ad... more Sensory systems have mechanisms to respond to the external environment and adapt to them. Such adaptive responses are effective for a wide dynamic range of sensing and perception of temporal change in stimulus. However, noise generated by the adaptation system itself as well as extrinsic noise in sensory inputs may impose a limit on the ability of adaptation systems. The relation between response and noise is well understood for equilibrium systems in the form of fluctuation response relation. However, the relation for nonequilibrium systems, including adaptive systems, are poorly understood. Here, we systematically explore such a relation between response and fluctuation in adaptation systems. We study the two network motifs, incoherent feedforward loops (iFFL) and negative feedback loops (nFBL), that can achieve perfect adaptation. We find that the response magnitude in adaption systems is limited by its intrinsic noise, implying that higher response would have higher noise component as well. Comparing the relation of response and noise in iFFL and nFBL, we show that whereas iFFL exhibits adaptation over a wider parameter range, nFBL offers higher response to noise ratio than iFFL. We also identify the condition that yields the upper limit of response for both network motifs. These results may explain the reason of why nFBL seems to be more abundant in nature for the implementation of adaption systems.
Single Molecule Dynamics in Life Science, 2008
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 2009
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 2005
Physical Biology, 2014
Eukaryotic chemotaxis is usually mediated by intracellular signals that tend to localize at the f... more Eukaryotic chemotaxis is usually mediated by intracellular signals that tend to localize at the front or back of the cell. Such intracellular polarities frequently require no extracellular guidance cues, indicating that spontaneous polarization occurs in the signal network. Spontaneous polarization activity is considered relevant to the persistent motions in random cell migrations and chemotaxis. In this study, we propose a theoretical model that connects spontaneous intracellular polarity and motile ability in a chemoattractant solution. We demonstrate that the intracellular polarity can enhance the accuracy of chemotaxis. Chemotactic accuracy should also depend on chemoattractant concentration through the concentration-dependent correlation time in the polarity direction. Both the polarity correlation time and the chemotactic accuracy depend on the degree of responsiveness to the chemical gradient. We show that optimally accurate chemotaxis occurs at an intermediate responsiveness of intracellular polarity. Experimentally, we find that the persistence time of randomly migrating Dictyostelium cells depends on the chemoattractant concentration, as predicted by our theory. At the optimum responsiveness, this ameboid cell can enhance its chemotactic accuracy tenfold.
ABSTRACT The signal transduction system of eukaryotic chemotaxis is one of the most well-characte... more ABSTRACT The signal transduction system of eukaryotic chemotaxis is one of the most well-characterized systems with respect to its molecular components and their interactions. Because cells are such tiny systems, the stochastic fluctuations of reactions are prominent. We first consider the noise in the chemotaxis of Dictyostelium cells. The theoretical signal-to-noise ratio can explain the accuracy of chemotaxis obtained experimentally. Then, we show self-organization in the chemotaxis signal transduction system in Dictyostelium cells. A stochastic reaction- diffusion model can reproduce the observed behavior.
We investigate nonequilibrium chemical reaction systems from the view point of steady state therm... more We investigate nonequilibrium chemical reaction systems from the view point of steady state thermodynamics proposed by Oono and Paniconi [Prog. Theor. Phys. Suppl. 130, 29 (1998)]. The concentrations of some compounds are operated by an external system, so that a transition from a steady state to other steady state takes place. We show that an analogue of Clausius inequality holds macroscopically for the operation processes. This implies that the second law of thermodynamics can be generalized, including nonequilibrium steady states. PACS numbers: 05.70.Ln, 82.60.-s, 02.50.Ga
Collective behavior is studied in globally coupled maps. Several coherent motions exist, even in ... more Collective behavior is studied in globally coupled maps. Several coherent motions exist, even in fully desynchronized state. To characterize the collective behavior, we introduce scaling transformation of parameter, and detect the tongue-like structure of collective motions in parameter space. Such collective motion is supported by the separation of time scale, given by the self-consistent relationship between the collective motion and chaotic dynamics of each element. It is shown that the change of collective motion is related with the window structure of a single one-dimensional map. Formation and collapse of regular collective motion are understood as the internal bifurcation structure. Coexistence of multiple attractors with different collective behaviors is also found in fully desynchronized state. 05.45+b,05.90+m,87.10+e
A reduced description is presented for noisy chemical reactions in small systems, such as cells. ... more A reduced description is presented for noisy chemical reactions in small systems, such as cells. We show that, even when the number of molecules of a chemical species is small, its elimination from the description is possible provided that its characteristic time scale is short. The resulting effective chemical reaction has a reaction rate which fluctuates in time. The strength of the fluctuations depends on the time scale of the eliminated species as well as its variance. We derive the master equation of the reduced system, which includes additional terms of a diffusive kind, yielding a contribution towards fluctuations from the eliminated species. The stochastic kinetic equation for the reduced system is also derived. Finally, these results are applied to some problems of gene expression.
ABSTRACT Stochastic fluctuations of chemical reactions are particularly prominent in small system... more ABSTRACT Stochastic fluctuations of chemical reactions are particularly prominent in small systems such as cells. Such fluctuations of cellular signal processes have been observed directly by single-molecule imaging. Recent theoretical studies have also revealed that stochastic cellular reactions generate fluctuations in the number of a molecule, which can be related to their functioning such as amplification of signals. Here, we study how large each signal reaction generates and amplifies the stochastic fluctuations. The general framework of fluctuation response relation in non-equilibrium physics throws light upon this problem. The result has been applied to the chemotactic signal processing of eukaryotic cell, such as Dictyostelium cell, revealing that the accuracy of chemotaxis is determined by the signal to noise ratio in the signal of the reaction between G-protein and G-protein coupled receptor. KeywordsFluctuations-Noise-Gain-Single molecule imaging-Gain fluctuation relation-Intrinsic noise-Extrinsic noise-Master equation-Fokker–Planck equation-Langevin equation-Gaussian white noise-Linear noise approximation-Power spectrum-Poisson process-Markov process-cAMP-cAR1-Dictyostelium push–pull reaction-Michaelis–Menten-Fokker–Planck operator-Response-fluctuation relation-Linear response-Chemotaxis-PTEN-PtdIns(3,4,5)P3-G-protein-Signal to noise ratio (SNR)-MAPK-Cascade
Progress of Theoretical Physics Supplement, 2006
ABSTRACT We provide a framework to study an effect of fluctuations in intracellular biochemical n... more ABSTRACT We provide a framework to study an effect of fluctuations in intracellular biochemical networks responsible for adaptation dynamics of bacteria. We use a 4 state chemoreceptor model, and investigate the dynamics and fluctuation. Analyzing fluctuation induced by extrinsic noise, we show a crucial relationship between the adaptation dynamics and the fluctuation; Adaptation precision of the system can be described by two quantities, normal fluctuation and irreversible circulation. This theorem means that we can predict how precisely bacteria adapt against external stimuli, by measuring state fluctuation of the chemoreceptor, without directly giving stimuli to them.
Proceedings of the National Academy of Sciences, 2005
The Monod-Wyman-Changeux (MWC) (Concerted) Model. As an example of cooperative binding reaction, ... more The Monod-Wyman-Changeux (MWC) (Concerted) Model. As an example of cooperative binding reaction, we study the MWC (concerted) model (1, 2), in which a number of identical subunits in a protein have two structural states, T and R . The state T shows a relatively low affinity for substrate, whereas the R state
Proceedings of the National Academy of Sciences, 2012
To understand complex biological systems, such as the development of multicellular organisms, it ... more To understand complex biological systems, such as the development of multicellular organisms, it is important to characterize the gene expression dynamics. However, there is currently no universal technique for targeted insertion of reporter genes and quantitative imaging in multicellular model systems. Recently, genome editing using zinc-finger nucleases (ZFNs) has been reported in several models. ZFNs consist of a zinc-finger DNA-binding array with the nuclease domain of the restriction enzyme FokI and facilitate targeted transgene insertion. In this study, we successfully inserted a GFP reporter cassette into the HpEts1 gene locus of the sea urchin, Hemicentrotus pulcherrimus. We achieved this insertion by injecting eggs with a pair of ZFNs for HpEts1 with a targeting donor construct that contained ∼1-kb homology arms and a 2Ahistone H2B-GFP cassette. We increased the efficiency of the ZFNmediated targeted transgene insertion by in situ linearization of the targeting donor construct and cointroduction of an mRNA for a dominant-negative form of HpLig4, which encodes the H. pulcherrimus homolog of DNA ligase IV required for error-prone nonhomologous end joining. We measured the fluorescence intensity of GFP at the single-cell level in living embryos during development and found that there was variation in HpEts1 expression among the primary mesenchyme cells. These findings demonstrate the feasibility of ZFN-mediated targeted transgene insertion to enable quantification of the expression levels of endogenous genes during development in living sea urchin embryos.
PLOS ONE, 2015
Sensory systems have mechanisms to respond to the external environment and adapt to them. Such ad... more Sensory systems have mechanisms to respond to the external environment and adapt to them. Such adaptive responses are effective for a wide dynamic range of sensing and perception of temporal change in stimulus. However, noise generated by the adaptation system itself as well as extrinsic noise in sensory inputs may impose a limit on the ability of adaptation systems. The relation between response and noise is well understood for equilibrium systems in the form of fluctuation response relation. However, the relation for nonequilibrium systems, including adaptive systems, are poorly understood. Here, we systematically explore such a relation between response and fluctuation in adaptation systems. We study the two network motifs, incoherent feedforward loops (iFFL) and negative feedback loops (nFBL), that can achieve perfect adaptation. We find that the response magnitude in adaption systems is limited by its intrinsic noise, implying that higher response would have higher noise component as well. Comparing the relation of response and noise in iFFL and nFBL, we show that whereas iFFL exhibits adaptation over a wider parameter range, nFBL offers higher response to noise ratio than iFFL. We also identify the condition that yields the upper limit of response for both network motifs. These results may explain the reason of why nFBL seems to be more abundant in nature for the implementation of adaption systems.
Single Molecule Dynamics in Life Science, 2008
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 2009
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 2005
Physical Biology, 2014
Eukaryotic chemotaxis is usually mediated by intracellular signals that tend to localize at the f... more Eukaryotic chemotaxis is usually mediated by intracellular signals that tend to localize at the front or back of the cell. Such intracellular polarities frequently require no extracellular guidance cues, indicating that spontaneous polarization occurs in the signal network. Spontaneous polarization activity is considered relevant to the persistent motions in random cell migrations and chemotaxis. In this study, we propose a theoretical model that connects spontaneous intracellular polarity and motile ability in a chemoattractant solution. We demonstrate that the intracellular polarity can enhance the accuracy of chemotaxis. Chemotactic accuracy should also depend on chemoattractant concentration through the concentration-dependent correlation time in the polarity direction. Both the polarity correlation time and the chemotactic accuracy depend on the degree of responsiveness to the chemical gradient. We show that optimally accurate chemotaxis occurs at an intermediate responsiveness of intracellular polarity. Experimentally, we find that the persistence time of randomly migrating Dictyostelium cells depends on the chemoattractant concentration, as predicted by our theory. At the optimum responsiveness, this ameboid cell can enhance its chemotactic accuracy tenfold.
ABSTRACT The signal transduction system of eukaryotic chemotaxis is one of the most well-characte... more ABSTRACT The signal transduction system of eukaryotic chemotaxis is one of the most well-characterized systems with respect to its molecular components and their interactions. Because cells are such tiny systems, the stochastic fluctuations of reactions are prominent. We first consider the noise in the chemotaxis of Dictyostelium cells. The theoretical signal-to-noise ratio can explain the accuracy of chemotaxis obtained experimentally. Then, we show self-organization in the chemotaxis signal transduction system in Dictyostelium cells. A stochastic reaction- diffusion model can reproduce the observed behavior.
We investigate nonequilibrium chemical reaction systems from the view point of steady state therm... more We investigate nonequilibrium chemical reaction systems from the view point of steady state thermodynamics proposed by Oono and Paniconi [Prog. Theor. Phys. Suppl. 130, 29 (1998)]. The concentrations of some compounds are operated by an external system, so that a transition from a steady state to other steady state takes place. We show that an analogue of Clausius inequality holds macroscopically for the operation processes. This implies that the second law of thermodynamics can be generalized, including nonequilibrium steady states. PACS numbers: 05.70.Ln, 82.60.-s, 02.50.Ga
Collective behavior is studied in globally coupled maps. Several coherent motions exist, even in ... more Collective behavior is studied in globally coupled maps. Several coherent motions exist, even in fully desynchronized state. To characterize the collective behavior, we introduce scaling transformation of parameter, and detect the tongue-like structure of collective motions in parameter space. Such collective motion is supported by the separation of time scale, given by the self-consistent relationship between the collective motion and chaotic dynamics of each element. It is shown that the change of collective motion is related with the window structure of a single one-dimensional map. Formation and collapse of regular collective motion are understood as the internal bifurcation structure. Coexistence of multiple attractors with different collective behaviors is also found in fully desynchronized state. 05.45+b,05.90+m,87.10+e
A reduced description is presented for noisy chemical reactions in small systems, such as cells. ... more A reduced description is presented for noisy chemical reactions in small systems, such as cells. We show that, even when the number of molecules of a chemical species is small, its elimination from the description is possible provided that its characteristic time scale is short. The resulting effective chemical reaction has a reaction rate which fluctuates in time. The strength of the fluctuations depends on the time scale of the eliminated species as well as its variance. We derive the master equation of the reduced system, which includes additional terms of a diffusive kind, yielding a contribution towards fluctuations from the eliminated species. The stochastic kinetic equation for the reduced system is also derived. Finally, these results are applied to some problems of gene expression.
ABSTRACT Stochastic fluctuations of chemical reactions are particularly prominent in small system... more ABSTRACT Stochastic fluctuations of chemical reactions are particularly prominent in small systems such as cells. Such fluctuations of cellular signal processes have been observed directly by single-molecule imaging. Recent theoretical studies have also revealed that stochastic cellular reactions generate fluctuations in the number of a molecule, which can be related to their functioning such as amplification of signals. Here, we study how large each signal reaction generates and amplifies the stochastic fluctuations. The general framework of fluctuation response relation in non-equilibrium physics throws light upon this problem. The result has been applied to the chemotactic signal processing of eukaryotic cell, such as Dictyostelium cell, revealing that the accuracy of chemotaxis is determined by the signal to noise ratio in the signal of the reaction between G-protein and G-protein coupled receptor. KeywordsFluctuations-Noise-Gain-Single molecule imaging-Gain fluctuation relation-Intrinsic noise-Extrinsic noise-Master equation-Fokker–Planck equation-Langevin equation-Gaussian white noise-Linear noise approximation-Power spectrum-Poisson process-Markov process-cAMP-cAR1-Dictyostelium push–pull reaction-Michaelis–Menten-Fokker–Planck operator-Response-fluctuation relation-Linear response-Chemotaxis-PTEN-PtdIns(3,4,5)P3-G-protein-Signal to noise ratio (SNR)-MAPK-Cascade
Progress of Theoretical Physics Supplement, 2006
ABSTRACT We provide a framework to study an effect of fluctuations in intracellular biochemical n... more ABSTRACT We provide a framework to study an effect of fluctuations in intracellular biochemical networks responsible for adaptation dynamics of bacteria. We use a 4 state chemoreceptor model, and investigate the dynamics and fluctuation. Analyzing fluctuation induced by extrinsic noise, we show a crucial relationship between the adaptation dynamics and the fluctuation; Adaptation precision of the system can be described by two quantities, normal fluctuation and irreversible circulation. This theorem means that we can predict how precisely bacteria adapt against external stimuli, by measuring state fluctuation of the chemoreceptor, without directly giving stimuli to them.
Proceedings of the National Academy of Sciences, 2005
The Monod-Wyman-Changeux (MWC) (Concerted) Model. As an example of cooperative binding reaction, ... more The Monod-Wyman-Changeux (MWC) (Concerted) Model. As an example of cooperative binding reaction, we study the MWC (concerted) model (1, 2), in which a number of identical subunits in a protein have two structural states, T and R . The state T shows a relatively low affinity for substrate, whereas the R state
Proceedings of the National Academy of Sciences, 2012
To understand complex biological systems, such as the development of multicellular organisms, it ... more To understand complex biological systems, such as the development of multicellular organisms, it is important to characterize the gene expression dynamics. However, there is currently no universal technique for targeted insertion of reporter genes and quantitative imaging in multicellular model systems. Recently, genome editing using zinc-finger nucleases (ZFNs) has been reported in several models. ZFNs consist of a zinc-finger DNA-binding array with the nuclease domain of the restriction enzyme FokI and facilitate targeted transgene insertion. In this study, we successfully inserted a GFP reporter cassette into the HpEts1 gene locus of the sea urchin, Hemicentrotus pulcherrimus. We achieved this insertion by injecting eggs with a pair of ZFNs for HpEts1 with a targeting donor construct that contained ∼1-kb homology arms and a 2Ahistone H2B-GFP cassette. We increased the efficiency of the ZFNmediated targeted transgene insertion by in situ linearization of the targeting donor construct and cointroduction of an mRNA for a dominant-negative form of HpLig4, which encodes the H. pulcherrimus homolog of DNA ligase IV required for error-prone nonhomologous end joining. We measured the fluorescence intensity of GFP at the single-cell level in living embryos during development and found that there was variation in HpEts1 expression among the primary mesenchyme cells. These findings demonstrate the feasibility of ZFN-mediated targeted transgene insertion to enable quantification of the expression levels of endogenous genes during development in living sea urchin embryos.