Kazuhito Shida

Hemocytes of Ciona intestinalis express multiple genes involved in innate immune host defense.

Ascidians, which are classified as urochordata, appear to employ a primitive system of host defense that is considered to be a prototype of vertebrate innate immunity. We performed a cDNA/EST study to identify the genes expressed in the hemocytes of Ciona intestinalis. We obtained 3357 one-path reads that were then grouped into 1889 independent clusters. Although two thirds of the clusters could not be assigned to any particular gene, the remaining 530 clusters had significant homology to genes with known function. Of these, 62 clusters appeared to be related to host defense mechanisms. These include transcripts whose products are probably involved in cytotoxicity, detoxification, inflammation, and apoptosis. As expected, elements of acquired immunity were not detected. Thus, Ciona hemocytes appear to express a number of host defense-related genes involved in innate immune mechanisms.

Identification of candidate genes encoding the core components of the cell death machinery in the Ciona intestinalis genome

Identification of candidate genes encoding the core components of the cell death machinery in the Ciona intestinalis genome

GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima

BackgroundComputational discovery of transcription factor binding sites (TFBS) is a challenging but important problem of bioinformatics. In this study, improvement of a Gibbs sampling based technique for TFBS discovery is attempted through an approach that is widely known, but which has never been investigated before: reduction of the effect of local optima.ResultsTo alleviate the vulnerability of Gibbs sampling to local optima trapping, we propose to combine a thermodynamic method, called simulated tempering, with Gibbs sampling. The resultant algorithm, GibbsST, is then validated using synthetic data and actual promoter sequences extracted from Saccharomyces cerevisiae. It is noteworthy that the marked improvement of the efficiency presented in this paper is attributable solely to the improvement of the search method.ConclusionSimulated tempering is a powerful solution for local optima problems found in pattern discovery. Extended application of simulated tempering for various bioinformatic problems is promising as a robust solution against local optima problems.

The cell death machinery controlled by bax and Bcl-XL is evolutionarily conserved in Ciona intestinalis

Bax and Bcl-XL are key regulators of apoptosis in mammals. Here we report the functional characterization of two Bcl-2 homologues, ciBax and ciBcl-XL, in a basal invertebrate-chordate ascidian Ciona intestinalis. CiBax is a Ciona homologue of the BH1-3 pro-apoptotic protein Bax, whereas ciBcl-XL is a Bcl-XL-like anti-apoptotic protein. Molecular modeling analysis showed that ciBax and ciBcl-XL share both sequence and structural similarities to human Bax and Bcl-XL, respectively. Like their human counterparts, ciBax could form a homodimer or oligomers as well as heterodimerize with ciBcl-XL, and overexpression of ciBax caused apoptosis that could be attenuated by ciBcl-XL. Mutagenesis studies showed that the BH3 domain of ciBax is critical for its cell death-inducing function and also for its interaction with ciBcl-XL. In Ciona embryos, ectopic expression of ciBax but not its BH3 deletion mutant resulted in cell dissociation and apoptosis after late gastrula stage of embryonic development. Moreover, not only wild type ciBcl-XL but also a mutant ciBcl-XL(F101V), which is unable to interact with ciBax, could block cell dissociation and developmental deficit in Ciona embryos induced by overexpression of ciBax. Taken together, these findings suggest that functional homologues of both the BH1-3 death effector Bax and the pro-survival Bcl-XL exist in sea squirt Ciona intestinalis, and they control the cell death machinery independent of their heterodimerization.

Automatic brain tissue extraction method using erosion-dilation treatment (BREED) from three-dimensional magnetic resonance imaging T1-weighted data

To improve the efficiency of brain image analysis, we propose a full-automatic method for extracting brain tissue from three-dimensional magnetic resonance imaging of T1-weighted data on the human head (brain tissue extraction method using erosion-dilation treatment [BREED]). The extraction processing is realized by combining signal intensity thresholding by means of the discriminant analysis method and an erosion-dilation treatment of the image. The accuracy of BREED is evaluated using both simulated and subject data. BREED can extract brain tissues with high accuracy (approximately 97%) for either simulated or subject data.

Monte Carlo calculation of second and third virial coefficients of linear and star polymers on lattice

An efficient algorithm for counting contributing terms in the calculation of second and third virial coefficients of the lattice polymer model was proposed. The algorithm was applied to linear and three-arm star polymers. The algorithm’s efficiency was demonstrated, and the obtained results were compared to both experimental and computational results already reported. To the authors’ best knowledge, the estimation of the third virial coefficient of the three-arm star polymer is the first reported.

First-principles analysis of structural and opto-electronic properties of indium tin oxide

Density functional theory (DFT) and DFT + U (DFT with on-site Coulomb repulsion corrections) calculations have been carried out to study the structural and opto-electronic properties of indium tin oxide (ITO) for both the oxidized and reduced environment conditions. Some of the results obtained by DFT calculations differ from the experimental observations, such as uncertain indication for the site preference of tin atom to replace indium atom at b-site or d-site, underestimation of local inward relaxation in the first oxygen polyhedra around tin atom, and also the improper estimation of electronic density of states and hence resulting in an inappropriate optical spectra of ITO. These discrepancies of theoretical outcomes with experimental observations in ITO arise mainly due to the underestimation of the cationic 4d levels within standard DFT calculations. Henceforth, the inclusion of on-site corrections within DFT + U framework significantly modifies the theoretical results in better agreement to the exp...

An improved chain extension algorithm and its application for various branched polymers

Statistical properties of flexible polymers with controlled molecular weights (length of arms) and branching patterns (topology) has been attracting strong interest. Basically, the lattice enrichment algorithms are suitable for simulating this kind of subject because they allow direct estimation of the total configuration number. However, it is difficult to apply this kind of algorithm for polymers with highly complicated structures, namely the comb-polymers. One of the difficulties is that the efficiency of simulation is severely limited. In this paper, a previously reported improvement technique is revisited, enhanced, and combined with several new ideas for developing a modified algorithm, which can solve such a situation. The validation and performance evaluation of the modified algorithm is presented. The algorithm is then applied to small scale polymer combs. In particular, the value of the critical exponent related to the configuration number is estimated on these combs. The result obtained for an H-shaped polymer is in accordance with previous simulations and a theoretical prediction formula already proposed. Possibilities for the future extension of the algorithm are briefly discussed.

Large scale Monte Carlo simulations of center‐adsorbed star polymers

A star‐shaped polymer whose center unit is adsorbed on a surface offers a peculiar example of surface‐grafted polymers. When it is isolated in a good solvent, it has been conjectured that several distinct scaling relations hold for the monomer and end‐point density profiles. Especially, the density decay in a direction parallel to the surface is described by a new critical exponent λ(f) as ρ(r,z=0)∼r−d+λ(f). However, the precise values of the exponent as a function of the number of arms were still unclear. Another interesting quantity is the total number of configurations behaving as N∼lγs(f)−1μfl. Here, l is the length of the arm, μ the effective coordination number for a single chain, and λs(f) a new surface critical exponent yet to be known. We perform large scale Monte Carlo simulations of such an adsorbed star with the number of arms, f, ranging from 2 to 15, to verify the predicted scaling theory and to calculate various static properties and exponents. Estimates of γs(f ) are presented. The validit...

Monte Carlo analysis of the osmotic pressure of athermal polymer solutions in dilute and semi-dilute regimes

Abstract The enrichment Monte Carlo algorithm is applied here, for the first time, to calculate the osmotic pressure of an athermal solution of linear chains on a lattice, in dilute and semi-dilute regimes. Complementarily to the Widoms test particle insertion method, the algorithm enables one to estimate directly the free energy and the osmotic pressure of the solution. The result shows that there is a large deviation in the free energy from the Flory–Huggins theory which may be attributed to the chain internal entropy. Moreover, the osmotic pressure shows des Cloizeauxs c9/4 behavior clearly when the concentration, c, is greater than the estimated overlap concentration. We estimate also the second and third virial coefficients that are compared with experimental values.