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Biomedical subjects

Kouichi Takahashi

Publications and source records attributed to Kouichi Takahashi.

5 recordsLinked to original sources

Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.

How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists to elucidate the implications of space in signaling pathways. We argue that intracellular macromolecular crowding is an important modeling issue, and describe how recent simulation methods can reproduce this phenomenon in either implicit, semi-explicit or fully explicit representation.

Algorithms↗

Chiral phosphinooxazolidine ligands for palladium- and platinum-catalyzed asymmetric Diels-Alder reactions.

Cationic palladium (Pd)- and platinum (Pt)-phosphinooxazolidine catalysts 13a-c, 15a-d, 17a-c, and 19a-c were prepared from phosphinooxazolidine ligands 1-3, MCl(2) (M = Pd and Pt), and counterions, and the activities of the catalysts in the asymmetric Diels-Alder (DA) reactions of cyclic or acyclic dienes with imide dienophiles were investigated. These catalysts demonstrated high levels of catalytic activity. The cationic Pd-POZ complex 13c provided particularly excellent enantioselectivity (98% ee) in the DA reactions of cyclopentadiene with acryloyl-, crotonyl-, and fumaroyl-1,3-oxazolidin-2-ones (20a-c).

Journal Article↗

A multi-algorithm, multi-timescale method for cell simulation.

MOTIVATION: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models. RESULTS: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a 'composite' heat-shock response model that combines the Gillespie-Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown.

Algorithms↗

A method to accurately inject tumor cells into the caudate/putamen nuclei of the mouse brain.

OBJECTIVE: To improve currently used techniques to implant tumor cells into the parenchyma of the mouse brain. MATERIALS AND METHODS: The stereotactic injection of 0.5 to 5 microl of indigo carmine over 5 to 40 minutes into the caudate/putamen nuclei of the mouse was done followed by sacrifice and examination of the brain injection site. 1 microl containing 10(5) U87MG glioma cells were stereotactically implanted into the caudate/ putamen nuclei over 20 minutes. The animals were sacrificed from one hour to 63 days after implantation and the brain examined and tumor size measured. RESULTS: An injection of 1 microl of indigo carmine over 20 minutes produced a spherical deposit of dye within the caudate/putamen nuclei. Larger volumes of indigo carmine or shorter injection times resulted in dye spreading along the injection tract or into the ventricles or subarachnoid space. Using the results of the dye studies, the same parameters were used to successfully inject and confine the glioma cells to the caudate/putamen nuclei in 30 of 32 mice. No tumor was found in 2 animals and appears to be explained by obstruction of the injection cannula. The tumor cells appeared viable an hour after injection. However by day three, considerable necrosis of tumor cells were noted, the effects of which resolved by day five. On day six, the injection site was comparable to that at one hour. In the early phase, until the fifth week, tumor volume doubling time was ten days while afterward it was only five days. CONCLUSION: The technique described allows the highly accurate and reproducible introduction of a given number of cells into a specific area of the mouse brain. This should reduce the intragroup variability, be it control or therapeutic, allowing better assessment of outcome with fewer number of mice.

Animals↗