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S Ichimura

Publications and source records attributed to S Ichimura.

At least 55 records · Page 3Linked to original sources
PubMed1993

[Cell mediated calcification in three-dimensional collagen gel culture of the osteoblast-like cells derived from rat calvaria].

Osteoblast-like cells were obtained by sequential enzymatic digestion of 19-day fetal rat calvaria and cultured within native type 1 collagen gels in alpha-MEM supplemented with 10% fetal bovine serum and 10 mM beta-glycerophosphate for 3 weeks. Cells were also cultured as monolayers in the usual manner and used as controls. The collagen gel discs contracted by one tenth in diameter after 4 days. The cells in the collagen gels seemed to proliferate at a low rate and to differentiate immediately into round cells, spindle-like cells, and adipocytes. In the monolayer cultures, calcifications were recognized after 2 weeks only in the high-density confluent areas where cells were disposed in multiple layers and alkaline phosphatase activity was high. In the collagen gels, some cells showed high alkaline phosphatase activity after 1 day of culture and calcifications were observed after 1 week around the cells with intense alkaline phosphatase activity. In collagen gel cultures, the degree of alkaline phosphatase activity and of calcification correlated with the density of the cell suspension at the time of seeding. The round cells were thought to be osteoblasts since they showed high alkaline phosphatase activity and were closely related to initial calcifications. Some of the spindle-like cells also showed high alkaline phosphatase activity and were apparently involved in the calcification process in the latter phase of culture, so that some of them seemed to be resting osteoblasts or lining cells. In electron-microscopical studies, initial calcification was related to the so-called matrix vesicles, and hydroxyapatite crystals were detected in mitochondria. Gap junctions which are specific to osteocytes were observed mainly between the round cells, but also between the round cells and the other cells. This culture system in which cells form a three-dimensional network is suitable to investigate osteoblastic functions and cell mediated calcification in vitro.

Alkaline Phosphatase↗
PubMed1992

Evolutionarily conserved structure of the 3' non-translated region of a Chinese hamster polyubiquitin gene.

From a V79 Chinese hamster genomic library, we isolated a clone containing a polyubiquitin gene (designated as CHUB1), and determined its nucleotide sequence. The coding region of the CHUB1 gene consisted of five direct repeats of the ubiquitin unit with no spacer, followed by a single tyrosine residue. Northern hybridization analysis with a synthesized probe specific to the 3' non-translated region of the CHUB1 gene revealed that it codes for a 1.8 kb mRNA. An evident homology to the human polyubiquitin gene UbB and the chicken UbI gene was observed in the region corresponding to the full extent of the mature mRNA sequence, suggesting that these three genes belong to a common polyubiquitin gene subfamily, and that the sequence in the 3' non-translated region of the CHUB1 gene is unique to this subfamily.

Amino Acid Sequence↗
PubMed1992

Essential role of duplications of short motif sequences in the genomic evolution of Bombyx mori.

The Bombyx fibroin gene has a discrete mosaic structure of various repetitive sequences, which may have evolved through various repeating arrangements. Detailed sequence analysis of the fibroin gene containing coding and noncoding regions revealed that the whole sequence could be arranged as an array of short repetitive sequences. A portion of the intron of the fibroin gene is one of interspersed repetitive elements. We cloned a 1.5-kb DNA fragment of the Bombyx genome that contains interspersed elements homologous to the intron sequence. Sequence comparison between the intron and the 1.5-kb fragment shows that partial duplication has frequently occurred in evolutionary progress, and the resultant repetitive blocks of short motif sequences are abundant in the genome. These facts suggest that tandem duplication of the short motif sequence is an important rearrangement in genomic evolution of the fibroin gene.

Animals↗
PubMed1991

Essential factors determining codon usage in ubiquitin genes.

Ubiquitin is ubiquitous in all eukaryotes and its amino acid sequence shows extreme conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences coding for 13 ubiquitin genes from 11 species reported so far have been compiled and analyzed. The G + C content of codon third base reveals a positive linear correlation with the genome G + C content of the corresponding species. The slope strongly suggests that the overall G + C content of codons of polyubiquitin genes clearly reflects the genome G + C content by AT/GC substitutions at the codon third position. The G + C content of ubiquitin codon third base also shows a positive linear correlation with the overall G + C content of coding regions of compiled genes, indicating the codon choices among synonymous codons reflect the average codon usage pattern of corresponding species. On the other hand, the monoubiquitin gene, which is different from the polyubiquitin gene in gene organization, gene expression, and function of the encoding protein, shows a different codon usage pattern compared with that of the polyubiquitin gene. From comparisons of the levels of synonymous substitutions among ubiquitin repeats and the homology of the amino acid sequence of the tail of monomeric ubiquitin genes, we propose that the molecular evolution of ubiquitin genes occurred as follows: Plural primitive ubiquitin sequences were dispersed on genome in ancestral eukaryotes. Some of them situated in a particular environment fused with the tail sequence to produce monomeric ubiquitin genes that were maintained across species. After divergence of species, polyubiquitin genes were formed by duplication of the other primitive ubiquitin sequences on different chromosomes. Differences in the environments in which ubiquitin genes are embedded reflect the differences in codon choice and in gene expression pattern between poly- and monomeric ubiquitin genes.

Amino Acid Sequence↗
PubMed1988

Specific codon usage pattern and its implications on the secondary structure of silk fibroin mRNA.

We have identified two distinctive regions of the repetitive unit nucleotide sequence of fibroin mRNA of Bombyx mori. The codon usage for the major amino acids, glycine, alanine and serine is distinctly different in these two regions, indicating that it is determined by the fibroin mRNA or gene structure but not by the tRNA population. Comparative computer analyses of nucleotide substitutions in the unit sequence suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the fibroin mRNA.

Amino Acid Sequence↗
PubMed1988

Interparticle interactions and structural changes of nucleosome core particles in low-salt solution.

The structural behavior of the nucleosome core particles in the range of solvent Na+ concentration from 10.45 to 0.45 mM has been studied by small-angle neutron and synchroton radiation X-ray scattering, sedimentation, atomic absorption spectroscopy, density measurements, and circular dichroism. With decreasing salt concentration, the appearance of a scattering peak that is assignable to interparticle interactions, an intraparticle structural transition, a decrease in the sedimentation velocity of the particle, and a release of bound Na+ ions from the particle are all observed concurrently when the ratio of solvent Na+ ions per particle is below approximately 1000. These observations are interpreted to indicate that a release of bound Na+ ions from the particle brings about structural rearrangements and weakens the electrostatic shielding of the particle, and this introduces long-range repulsive ordering of the particle in low-salt solution. Analyses of the scattering data indicate that the rearrangement within the core particle in low-salt solution is slight, changing the particle's shape slightly from cylindrical to a more spherical form by moving the center of the mass of the DNA somewhat inward with accompanying small decreases in the radii of gyration of both the DNA and the histones.

Animals↗
PubMed1984

Conformation of the HMG17-nucleosome complex.

The nucleosome core binds more than two molecules of HMG17 at low ionic strength (8.9 mM Tris-HCl/8.9 mM boric acid/0.25 mM Na2EDTA, pH 8.3). Circular dichroism of the complexes showed only minor conformational changes of the nucleosome core DNA on binding of HMG17, with no detectable change in the histone secondary structure. The fluorescence of N-(3-pyrene) maleimide bound to -SH groups at Cys-110 of H3 histones in the core particle suggested that the structure of the histone octamer assembly changed little upon binding of HMG17 to the nucleosome. These observations support the idea that even a high level of HMG17 binding, e.g., four HMGs per nucleosome, alone, does not open up the core particle.

Animals↗
PubMed1983

Isolation of deuterated histones from yeast grown on media dissolved in 2H2O.

We have succeeded in growing Saccharomyces cerevisiae (baker's yeast) on media containing 2H2O and isolating the core histones highly deuterated in the non-exchangeable positions. The deuterated histones obtained here are of great value for their possible widespread use for structural studies of chromatin.

Deuterium↗
PubMed1982

Essential role of arginine residues in the folding of deoxyribonucleic acid into nucleosome cores.

The kinetic studies of chemical modifications of the lysine and arginine residues of the nucleosome core particle from chicken erythrocytes with large molar excesses of 2,4,6-trinitrobenzenesulfonic acid and 2,3-butanedione, respectively, were performed over 20 mM-2.0 M NaCl. Each modification reaction was divided into the two, a rapid and an extremely slow, pseudo-first-order processes, and the numbers of the exposed and buried residues of the respective amino acids were determined. At very low ionic strength (20 mM boric buffer) all residues were inaccessible to the reagents. Between 0.3 and 0.6 M NaCl the basic amino acid residues in a nucleosome core particle were classified into the following three groups: (1) 42 arginine and 78 lysine residues in the N-terminal and C-terminal regions of the histones that are exposed to solvent, (2) a small number of arginine residues (approximately less than 14 Arg) that are strongly bound to the DNA phosphates, and (3) 48 arginine and 38 lysine residues buried in the globular region of the histone octamer. The results suggest that a small number of arginine residues play an essential role in the folding of DNA into a nucleosome core particle.

Animals↗
PubMed1982

Small angle neutron scattering studies of the structure of nucleosome cores at low ionic strength.

Nucleosome core particles from chicken erythrocytes have been studied by small angle neutron scattering over the range from 10 to 0.04 mM Na+ at 65 and 100% D2O, and the radii of gyration of the particle were determined. A single transition in the radius of gyration was observed at either D2O concentration. With decreasing the ionic strength from 10 mM, the radius of gyration of the histones obtained at 65% D2O increased from 35 to 40A at about 1 mM ionic strength, whereas at 100% D2O the radius of gyration decreased from 39 to 36A also near 1 mM ionic strength. No loss of the secondary structure of the histones was observed by circular dichroism over the range of the ionic strength examined. These results suggest that at low ionic strength (less than or equal to 1 mM) the histones may locate outside of the nucleosome core particle accompanied by an alteration of the tertiary and/or the quaternary structure of the histone octamer.

Animals↗
PubMed1980

Esophageal carcinoma in rats induced by N-amyl-N-methylnitrosamine.

N-Amyl-N-methylnitrosamine (AMN) induced esophageal carcinoma in Donryu strain rats when given in drinking water. The incidence of carcinomas was high when AMN was given as 0.0015% solution for 90 days or 0.003% solution for 60 days. There was no difference in the incidence in males and females. Sequential studies showed that 4-week administration was necessary to induce esophageal papillomas, and 8-week administration to induce esophageal carcinomas. Whole-body autoradiography after intravenous injection of N-amyl-N-methyl[14C]-nitrosamine (14C-AMN) indicated that AMN accumulated preferentially in the esophagus.

Age Factors↗