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Biomedical subjects

Takashi Ikegami

Publications and source records attributed to Takashi Ikegami.

14 recordsLinked to original sources
PubMed2006

Metal ion-directed cooperative DNA binding of small molecules.

Compound (1), which consists of an oxine and a pyridinium group, was synthesized as a metal-responsive DNA binding ligand. Two 1s coordinate to a Cu(II) to form a stable dimer (1(2)-Cu), even in the presence of DNA. The binding of 1 with sonicated calf thymus DNA was enhanced by ca. 10(3) times after forming the dimer; the binding constants were estimated to be 3.2 x 10(4)M(-1) and 2.4 x 10(7)M(-1) in the absence and the presence, respectively, of a half mole of Cu(II). The enormous acceleration of the binding is partly attributed to the generation of a dicationic charge by the formation of the dimer. High cooperativity between dimers could be also responsible; dimers would gather along the duplex as a template to form 1D spiral aggregates.

Animals↗
PubMed2006

Spatial-pattern-induced evolution of a self-replicating loop network.

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

Artificial Intelligence↗
PubMed2005

Food-web formation with recursive evolutionary branching.

A reaction-diffusion model describing the evolutionary dynamics of a food-web was constructed. In this model, predator-prey relationships among organisms were determined by their position in a two-dimensional phenotype space defined by two traits: as prey and as predator. The mutation process is expressed with a diffusion process of biomass in the phenotype space. Numerical simulation of this model showed co-evolutionary dynamics of isolated phenotypic clusters, including various types of evolutionary branching, which were classified into branching as prey, branching as predators, and co-evolutionary branching of both prey and predators. A complex food-web develops with recursive evolutionary branching from a single phenotypic cluster. Biodiversity peaks at the medium strength of the predator-prey interaction, where the food-web is maintained at medium biomass by a balanced frequency between evolutionary branching and extinction.

Animals↗
PubMed2005

A new formalization of a meta-game using the lambda calculus.

This paper presents a new game system formalism. The system describes both strategies and a game master (who computes scores in a given game system) in terms of lambda-calculus. This formalism revisits the prisoner's dilemma game, to discuss how meta-strategies emerge in this classical game, even without repetition. We have also examined the evolution of meta-strategies in lambda formalism.

Computational Biology↗
PubMed2004

Inaccessibility in online learning of recurrent neural networks.

We apply nonlinear dynamical system techniques to recurrent neural networks. In particular, we numerically analyze the dynamical system characteristics of the online learning process. By introducing the notion of inaccessibility, we show that the learning process is well characterized by strong nonhyperbolicity and inaccessibility, which is a greater uncertainty than chaotic unpredictability. These results are clearly contrasted with a gradient descent dynamics, or ordinary chaos.

Artificial Intelligence↗
PubMed2004

Covalent molecular imprinting of bisphenol A using its diesters followed by the reductive cleavage with LiAlH(4).

Bisphenol A (BPA) recognition materials were synthesized by a covalent imprinting technique using BPA-dimethacrylate or BPA-diacrylate as the template monomer. Binding sites in the polymers consisted of two hydroxyl groups that are generated by reducing the ester bonds of the template monomer with lithium aluminum hydride. The polymers strongly adsorbed BPA and structurally related compounds, however, other endocrine disruptors were hardly adsorbed. The BPA-dimethacrylate-based polymer interacted with the samples more strongly than the BPA-diacrylate-based polymer.

Aluminum Compounds↗
PubMed2004

Synthetic polymers adsorbing bisphenol A and its analogues prepared by covalent molecular imprinting using bisphenol A dimethacrylate as a template molecule.

Synthetic polymers which can adsorb bisphenol A (BPA) and related compounds were prepared by a covalent molecular imprinting technique. BPA dimethacrylate, used as template molecule, was polymerized with a crosslinker, triethylene glycol dimethacrylate (TEGDMA) or trimethylol propane trimethacrylate (TRIM). After the polymerization treatment with dilute NaOH was used to cleave BPA from the polymers. For high recovery of BPA with low polymer matrix degradation, the hydrolysis conditions were determined to be treatment with 1.0 mol L(-1) NaOH for 48 h. The binding sites generated by the hydrolysis were evaluated by determination of the retentivity of BPA, BPA analogues, and other endocrine disruptors. The polymers strongly adsorbed compounds with two hydroxyl groups at the 4,4'-positions. Generally the TEGDMA-based polymers had stronger affinity than the TRIM-based polymers, although the TRIM-based polymer adsorbed steroidal hormones with two hydroxyl groups, for example 17 alpha-estradiol and 17 beta-estradiol, more strongly than the TEGDMA-based polymer, meaning that the crosslinkers affected the properties of the binding sites and, depending upon the target molecules, suitable crosslinkers should be chosen in this system.

Adsorption↗
PubMed2004

Adaptability and diversity in simulated turn-taking behavior.

Turn-taking behavior is simulated in a coupled-agents system. Each agent is modeled as a mobile robot with two wheels. A recurrent neural network is used to produce the motor outputs and to hold the internal dynamics. Agents are developed to take turns on a two-dimensional arena by causing the network structures to evolve. Turn taking is established using either regular or chaotic behavior of the agents. It is found that chaotic turn takers are more sensitive in response to inputs from the other agent. Conversely, regular turn takers are comparatively robust against noisy inputs, owing to their restricted dynamics. From many observations, including turn taking with virtual agents, we claim that there is a complementary relationship between robustness and adaptability. Furthermore, by investigating the recoupling of agents from different GA generations, we report the emergence of a new turn-taking behavior. Potential for synthesizing a new form of interaction is another characteristic of chaotic turn takers.

Algorithms↗
PubMed2003

Chaotic itinerancy in coupled dynamical recognizers.

We argue that chaotic itinerancy in interaction between humans originates in the fluctuation of predictions provided by the nonconvergent nature of learning dynamics. A simple simulation model called the coupled dynamical recognizer is proposed to study this phenomenon. Daily cognitive phenomena provide many examples of chaotic itinerancy, such as turn taking in conversation. It is therefore an interesting problem to bridge two chaotic itinerant phenomena. A clue to solving this is the fluctuation of prediction, which can be translated as "hot prediction" in the context of cognitive theory. Hot prediction is simply defined as a prediction based on an unstable model. If this approach is correct, the present simulation will reveal some dynamic characteristics of cognitive interactions.

Cognition↗
PubMed2003

Metal ion-directed outside binding of small DNA ligand.

DNA binding of the ligand bearing an oxine and a pyridinium group was regulated by coexisting Cu2+ over the binding constant range of three orders of magnitude. The ligands coordinated to Cu2+ to form a dimer and then cooperatively bound outside of DNA duplex to give the well-regulated 1-D structure along the DNA backbone.

DNA↗
PubMed2002

Model mice for tissue-specific deletion of the manganese superoxide dismutase (MnSOD) gene.

Manganese superoxide dismutase (MnSOD) is the enzyme that converts toxic O(2)(-) to H(2)O(2) in mitochondria. Previous reports showed that a deficiency of MnSOD in mice was neonatal lethal. Therefore, a model mouse was not available for the analysis of the pathological role of O(2)(-) injuries in adult tissues. To explore an adult-type model mouse, we designed tissue-specific MnSOD conditional knockout mice using a Cre-loxp system. First, we crossbred MnSOD flox mice with transgenic mice expressing Cre recombinase under the control of the chicken actin promoter (CAG). We confirmed that CAG MnSOD knockout mice were completely deficient in MnSOD and died as neonates, validating the use of the Cre-loxp system. Next, we generated liver-specific MnSOD-deficient mice by crossbreeding with Alb-Cre transgenic mice. MnSOD activity and protein were both significantly downregulated in the liver of liver-specific MnSOD knockout mice. However, no obvious morphological abnormality was observed in the liver when biochemical alterations such as lipid peroxidation were not detectable, suggesting a redundant or less important physiological role for MnSOD in the liver than previously thought. In the present study, we successfully generated tissue-specific MnSOD conditional knockout mice that would provide a useful tool for the analysis of various age-associated diseases such as diabetes mellitus, Parkinson's disease, stroke, and heart disease, when crossbred with tissue-specific transgenic Cre mice.

Actins↗
PubMed2002

Transgenic expression of the protein-L-isoaspartyl methyltransferase (PIMT) gene in the brain rescues mice from the fatal epilepsy of PIMT deficiency.

Protein-L-isoaspartyl methyltransfearase (PIMT) plays a physiological role in the repair of damaged proteins containing isoaspartyl residues. In previous studies, we showed that PIMT-deficient mice developed a fatal epileptic seizure associated with the accumulation of damaged proteins in the brain. The mutant mice also showed a neurodegenerative pathology in hippocampi and impaired spatial memory. Still undefined, however, is how the accumulation of isoaspartates leads to the death of PIMT-deficient mice. In the present study, we generated PIMT transgenic (Tg) mice to investigate whether the exogenous expression of PIMT could improve the symptoms associated with PIMT deficiency. Rescue experiments showed that Tg expression of PIMT driven by a prion promoter effectively cured the PIMT-deficient mice. Biochemically, a higher expression level of transgene led to the effective repair of damaged proteins in vivo. Although a lower level of expression caused an accumulation of damaged proteins in a partially rescued line, the mice survived. Interestingly, synapsin I, which was extensively modified posttranslationally in PIMT-deficient mice, was specifically repaired in a partially rescued, but symptom-improved, Tg line. Our results suggest that an overall accumulation of damaged proteins does not necessarily lead to a fatal epileptic seizure, whereas certain modifications, such as changes in synapsin I, may play a pivotal pathological role in epilepsy.

Animals↗
PubMed1992

Evolution of host-parasitoid network through homeochaotic dynamics.

Host-parasitoid systems with evolving mutation rates are studied. By increasing the growth rate of hosts, the diversity of both species is maintained dynamically. For the lower growth rate, diversity is brought about by mere parasitism. The average mutation rate for parasites is elevated to a high value, while that for hosts is suppressed at a low level. For the higher growth rate, the mutation rates for both hosts and parasites are elevated to form a symbiotic cluster connected by on-going mutation. This symbiotic state is sustained through a chaotic oscillation keeping some coherency among species. For a flat landscape for hosts, dynamical clustering of oscillation is observed. Lyapunov spectra of such oscillations show that high dimensional chaos with small positive exponents underlies in the symbiotic state. This weak high dimensional chaos, termed "homeochaos," is essential to the maintenance of symbiosis in ecosystems.

Journal Article↗