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Search Results: 1 - 10 of 1267 matches for " Kunihiko Kaneko "
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Evolution of Robustness to Noise and Mutation in Gene Expression Dynamics
Kunihiko Kaneko
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000434
Abstract: Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external origins that are encountered during growth and development. Is there a relationship between these two types of robustness, one during a single generation and the other during evolution? Could stochasticity in gene expression have any relevance to the evolution of these types of robustness? Robustness can be defined by the sharpness of the distribution of phenotype; the variance of phenotype distribution due to genetic variation gives a measure of ‘genetic robustness’, while that of isogenic individuals gives a measure of ‘developmental robustness’. Through simulations of a simple stochastic gene expression network that undergoes mutation and selection, we show that in order for the network to acquire both types of robustness, the phenotypic variance induced by mutations must be smaller than that observed in an isogenic population. As the latter originates from noise in gene expression, this signifies that the genetic robustness evolves only when the noise strength in gene expression is larger than some threshold. In such a case, the two variances decrease throughout the evolutionary time course, indicating increase in robustness. The results reveal how noise that cells encounter during growth and development shapes networks' robustness to stochasticity in gene expression, which in turn shapes networks' robustness to mutation. The necessary condition for evolution of robustness, as well as the relationship between genetic and developmental robustness, is derived quantitatively through the variance of phenotypic fluctuations, which are directly measurable experimentally.
Proportionality between variances in gene expression induced by noise and mutation: consequence of evolutionary robustness
Kunihiko Kaneko
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-27
Abstract: Using numerical models simulating the evolutionary changes in the gene regulation network required to achieve a particular expression pattern, we first confirmed that gene expression dynamics robust to mutation evolved in the presence of a sufficient level of transcriptional noise. Under such conditions, the two types of variances in the gene expression levels, i.e. those due to mutations to the gene regulation network and those due to noise in gene expression dynamics were found to be proportional over a number of genes. The fraction of such genes with a common proportionality coefficient increased with an increase in the robustness of the evolved network. This proportionality was generally confirmed, also under the presence of environmental fluctuations and sexual recombination in diploids, and was explained from an evolutionary robustness hypothesis, in which an evolved robust system suppresses the so-called error catastrophe - the destabilization of the single-peaked distribution in gene expression levels. Experimental evidences for the proportionality of the variances over genes are also discussed.The proportionality between the genetic and epigenetic variances of phenotypes implies the correlation between the robustness (or plasticity) against genetic changes and against noise in development, and also suggests that phenotypic traits that are more variable epigenetically have a higher evolutionary potential.Plasticity and robustness are basic concepts in evolutionary and developmental biology. Plasticity refers to the changeability of phenotypes in response to external environmental perturbations. Indeed many important concepts in biology are concerned with the changeability in the system. This changeability depends on each phenotype: some phenotypes are more variable than others. How is such degree of changeability characterized quantitatively?On the other hand, robustness is another basic concept in evolutionary and developmental biology. Here, phenotypic rob
Correction: Proportionality between variances in gene expression induced by noise and mutation: consequence of evolutionary robustness
Kaneko Kunihiko
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-240
Abstract:
Relevance of Dynamic Clustering to Biological Networks
Kunihiko Kaneko
Physics , 1993, DOI: 10.1016/0167-2789(94)90274-7
Abstract: Network of nonlinear dynamical elements often show clustering of synchronization by chaotic instability. Relevance of the clustering to ecological, immune, neural, and cellular networks is discussed, with the emphasis of partially ordered states with chaotic itinerancy. First, clustering with bit structures in a hypercubic lattice is studied. Spontaneous formation and destruction of relevant bits are found, which give self-organizing, and chaotic genetic algorithms. When spontaneous changes of effective couplings are introduced, chaotic itinerancy of clusterings is widely seen through a feedback mechanism, which supports dynamic stability allowing for complexity and diversity, known as homeochaos. Second, synaptic dynamics of couplings is studied in relation with neural dynamics. The clustering structure is formed with a balance between external inputs and internal dynamics. Last, an extension allowing for the growth of the number of elements is given, in connection with cell differentiation. Effective time sharing system of resources is formed in partially ordered states.
Chaos as a Source of Complexity and Diversity in Evolution
Kunihiko Kaneko
Physics , 1993,
Abstract: The relevance of chaos to evolution is discussed in the context of the origin and maintenance of diversity and complexity. Evolution to the edge of chaos is demonstrated in an imitation game. As an origin of diversity, dynamic clustering of identical chaotic elements, globally coupled each to other, is briefly reviewed. The clustering is extended to nonlinear dynamics on hypercubic lattices, which enables us to construct a self-organizing genetic algorithm. A mechanism of maintenance of diversity, ``homeochaos", is given in an ecological system with interaction among many species. Homeochaos provides a dynamic stability sustained by high-dimensional weak chaos. A novel mechanism of cell differentiation is presented, based on dynamic clustering. Here, a new concept -- ``open chaos" -- is proposed for the instability in a dynamical system with growing degrees of freedom. It is suggested that studies based on interacting chaotic elements can replace both top-down and bottom-up approaches.
Coupled Maps with Growth and Death: An Approach to Cell Differentiation
Kunihiko Kaneko
Physics , 1996, DOI: 10.1016/S0167-2789(96)00282-5
Abstract: An extension of coupled maps is given which allows for the growth of the number of elements, and is inspired by the cell differentiation problem. The growth of elements is made possible first by clustering the phases, and then by differentiating roles. The former leads to the time sharing of resources, while the latter leads to the separation of roles for the growth. The mechanism of the differentiation of elements is studied. An extension to a model with several internal phase variables is given, which shows differentiation of internal states. The relevance of interacting dynamics with internal states (``intra-inter" dynamics) to biological problems is discussed with an emphasis on heterogeneity by clustering, macroscopic robustness by partial synchronization and recursivity with the selection of initial conditions and digitalization.
Chaotic Traveling Waves in a Coupled Map Lattice
Kunihiko Kaneko
Physics , 1993, DOI: 10.1016/0167-2789(93)90126-L
Abstract: Traveling waves triggered by a phase slip in coupled map lattices are studied. A local phase slip affects globally the system, which is in strong contrast with kink propagation. Attractors with different velocities coexist, and form quantized bands determined by the number of phase slips. The mechanism and statistical and dynamical characters are studied with the use of spatial asymmetry, basin volume ratio, Lyapunov spectra, and mutual information. If the system size is not far from an integer multiple of the selected wavelength, attractors are tori, while weak chaos remains otherwise, which induces chaotic modulation of waves or a chaotic itinerancy of traveling states. In the itinerancy, the residence time distribution obeys the power law distribution, implying the existence of a long-ranged correlation. Supertransients before the formation of traveling waves are noted in the high nonlinearity regime. In the weaker nonlinearity regime corresponding to the frozen random pattern, we have found fluctuation of domain sizes and Brownian-like motion of domains. Propagation of chaotic domains by phase slips is also found. Relevance of our discoveries to B\'{e}nard convection experiments and possible applications to information processing are briefly discussed.
Recursiveness, Switching, and Fluctuations in a Replicating Catalytic Network
Kunihiko Kaneko
Physics , 2003, DOI: 10.1103/PhysRevE.68.031909
Abstract: A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers of molecules and species, three phases are found: fast switching state without recursive production, recursive production, and itinerancy between the above two states. The number distributions of the molecules in the recursive states are shown to be log-normal except for those species that form a core hypercycle, and are explained with the help of a heuristic argument.
Prevalence of Milnor Attractors and Chaotic Itinerancy in 'High'-dimensional Dynamical Systems
Kunihiko Kaneko
Physics , 2003,
Abstract: Dominance of Milnor attractors in high-dimensional dynamical systems is reviewed, with the use of globally coupled maps. From numerical simulations, the threshold number of degrees of freedom for such prevalence of Milnor attractors is suggested to be $5 \sim 10$, which is also estimated from an argument of combinatorial explosion of basin boundaries. Chaotic itinerancy is revisited from the viewpoint of Milnor attractors. Relevance to neural networks is discussed.
Shaping Robust System through Evolution
Kunihiko Kaneko
Physics , 2008, DOI: 10.1063/1.2912458
Abstract: Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness of the phenotype. Here we study how this dynamical system is robust to noise during development and to genetic change by mutation. We adopt a simplified transcription regulation network model to govern gene expression, which gives a fitness function. Through simulations of the network that undergoes mutation and selection, we show that a certain level of noise in gene expression is required for the network to acquire both types of robustness. The results reveal how the noise that cells encounter during development shapes any network's robustness, not only to noise but also to mutations. We also establish a relationship between developmental and mutational robustness through phenotypic variances caused by genetic variation and epigenetic noise. A universal relationship between the two variances is derived, akin to the fluctuation-dissipation relationship known in physics.
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