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T Ueda

Publications and source records attributed to T Ueda.

At least 541 records · Page 30Linked to original sources
PubMed1997

Raman scattering tensors of adenine.

Polarized Raman scattering measurements have been made of a single crystal of adenine dihydrochloride (adenine-2H+) by the use of Raman microscope with 488.0 nm excitation. The adenine-2H+ crystal belongs to the space group Pnma (orthorhombic), and Raman intensities of Iaa, Ibb, Icc and Iac (which correspond to the aa, bb, cc and ac components of the crystal Raman tensor) have been determined for each Raman band. The depolarization ratios of Raman bands have been observed for fully random molecular orientations in an adenine 6N HCl aqueous solution. From these experimental data, and by taking the known crystal structure into account, anisotropic and isotropic molecular Raman scattering tensors have been determined for each vibrational mode of the adenine residue.

Adenine↗
PubMed1997

Raman scattering tensors of 5-iodouracil.

Polarized Raman scattering measurements have been made of a single crystal of 5-iodouracil by the use of a Raman microscope with the 488.0 nm excitation. The crystal belongs to space group P2(1) (monoclinic), and Raman scattering intensities, corresponding to the a'a', bb, cc, a'b and bc components of the crystalline Raman tensor, have been determined for each prominent Raman band, where a' is the axis perpendicular to the c axis in the ac plane. From these experimental results, the shapes and orientations of the Raman scattering tensors have been derived for 6 base vibrations in the 5-iodouracil molecule. By comparing these tensors with those for thymine and pseudouridine vibrations, discussions were made of the polarizability oscillations caused by the normal vibrations localized in the pyrimidine base.

Crystallization↗
PubMed1997

Essentially minimal sequence for substrate recognition by tRNA (guanosine-2')-methyltransferase from Thermus thermophilus HB27.

Transfer RNA (guanosine-2'-)-methyltransferase (Gm-methylase, EC.2.1.1.32) from extreme thermophile, Thermus thermophilus HB27 is one of the tRNA-ribose modification enzymes; this enzyme specifically catalyze the transfer of a methyl group from S-adenosyl-L-methionine to 2'-OH of the ribose of the guanosine at position 18 in tRNA. A broad substrate specificity of Gm-methylase was observed using natural tRNAs as methyl group acceptors, which suggests that some local stractures common in tRNAs are recognized by the enzyme. By using yeast tRNA(Phe) variants obtained by transcription of their genes with T7 RNA polymerase, it was revealed that the residues G18 and G19, as well as the D-stem structure were primarily required for the methylation reaction and that the essentially minimal sequence for the substrate was Pyrimidine17-G18-G19. The other conserved sequences and the tertiary base-pairs were not essential, but G15, G46, U55 and C56 strongly affected the methylation efficiency.

Base Composition↗
PubMed1997

Mitochondrial methionyl-tRNA transformylase from bovine liver.

Substrate specificities of mammalian mitochondrial methionyl-tRNA transformylase (MTFmt) toward tRNA substrates were characterized in vitro. The MTFmt is able to formylate E. coli initiator methionyl-tRNA (Met-tRNA(fMet)) as efficiently as mammalian mitochondrial methionyl-tRNA. Furthermore, E. coli elongator methionyl-tRNA (Met-tRNA(mMet)) also serves as a substrate for mt MTF, whereas E. coli MTF rigorously excludes E. coli Met-tRNA(mMet) from formylation reaction. Thus, mammal mt MTF is suggested to have recognition mechanism different from E. coli MTF. To pursue the relationship between protein structure and unexpected substrate specificity of mammalian MTFmt, the nucleotide sequence of MTFmt gene was determined and its amino acids sequence was compared to other MTFs of prokaryotic origin.

Animals↗
PubMed1997

5-formylcytidine (f5C) found at the wobble position of the anticodon of squid mitochondrial tRNA(Met)CAU.

In squid (Loligo breekeri) mitochondria, AUA codons are translated as methionine instead of the universal isoleucine. Here, we present the nucleotide sequence of squid mitochondrial tRNA(Met)CAU. This tRNA(Met)CAU has 5-formylcytidine (f5C) at the wobble position of the anticodon, though it is partially modified. This result indicates the common feature with bovine and nematoda mitochondrial systems in that f5C at the wobble position of the anticodon is very likely involved in translation of AUA codons as methionine in squid mitochondria.

Animals↗
PubMed1996

RNA editing in the acceptor stem of squid mitochondrial tRNA(Tyr).

In squid (Loligo bleekeri) mitochondria, the two 3'-terminal nucleotides (G72-G73) of the tRNA(Tyr) gene overlap with the two 5'-terminal nucleotides (G1-G2) of the downstream tRNA(Cys) gene. To elucidate the processing mechanism(s) of the tRNA molecules derived from this region, tRNAs were analyzed by sequencing cDNAs synthesized from circularized tRNAs. Nucleotides G1-G2 in tRNA(Cys) appeared to be without post-transcriptional conversion, whereas CCA was post-transcriptionally added to the 3'-terminus. In contrast, in the majority of tRNAs(Tyr), G72-G73 were found to be converted to A72-A73, accompanied by the CCA addition. These results indicate that a precursor of tRNA(Tyr) is processed at U71 and two adenosines are attached prior to the CCA addition. Thus, we suggest that 5' processing of the precursor tRNA dominates 3' processing and maturation of the tRNA is mediated by a polyadenylylation enzyme in the mitochondria, a scenario which is consistent with the editing process proposed in land snail mitochondria. We also obtained intermediates, such as a premature tRNA lacking CCA that terminated at U71 and one with a single adenosine attached at position 72, which support the suggested maturation process. However, although we failed to detect a tRNA(Cys) lacking G1-G2 at the 5'-terminus, we obtained cDNAs for tRNA(Tyr) with G72-G73 and the CCA terminus. This inconsistent result suggests the co-existence of another process(es) in the maturation of these tRNA molecules in squid mitochondria.

Animals↗
PubMed1996

Identification of the peptide region that folds native conformation in the early stage of the renaturation of reduced lysozyme.

We prepared three peptide fragments (fg.59-105, fg.63-105 and fg.64-105) by the BrCN cleavage of mutant lysozymes where Ile58, Trp62 and Trp63 were mutated to Met, respectively. From the analysis of formation of the disulfide bonds among Cys64, Cys76, Cys80 and Cys94 in the renaturation of each peptide fragment from the reduced form, Trp62 and Trp63 were required for the effective formation of two disulfide bonds. Especially, Trp62 was found to be involved in the correct formation of the disulfide bonds.

Amino Acid Sequence↗
PubMed1996

New graft-implanting method for thoracic aortic aneurysm or dissection with a stented graft.

BACKGROUND: To alleviate the invasiveness of surgical treatment for thoracic aortic aneurysm or dissection involving the distal arch, we developed a new method of implanting a graft in the distal anastomotic portion that does not require dissection, suture, or lateral thoracotomy. METHODS AND RESULTS: The tight circumferential attachment between the graft and the aortic inner wall, produced by the hoop strength of a self-expanding (Gianturco) stent that is anchored into the woven polyester graft, takes the place of the conventional anastomotic suture at the distal end of the graft. This new surgical method requires only a median sternotomy and relatively short circulatory arrest time to repair a thoracic aneurysm or dissection involving the distal arch. In a 12-month period in 1994 and 1995, we applied this new method in 10 cases (seven true aneurysms and three dissections). Complete thrombosis of the aneurysms or false lumens surrounding the grafts resulted in all 10. There were no surgical deaths, and the major complications were two cerebral infarctions due to inappropriate protection of the brain and dissecting procedure of an aortic arch, respectively. CONCLUSIONS: These preliminary results indicate that this new graft-implanting method with the stented graft should be considered one of the less-invasive surgical treatments for thoracic aneurysm and dissection involving the distal arch.

Aged↗
PubMed1996

Inactive allele-specific methylation and chromatin structure of the imprinted gene U2af1-rs1 on mouse chromosome 11.

The imprinted U2af1-rs1 gene that maps to mouse chromosome 11 is predominately expressed from the paternal allele. We examined the methylation of genomic sequences in and around the U2af1-rs1 locus to establish the extent of sequence modifications that accompanied the silencing of the maternal allele. The analysis of HapII or HhaI sites showed that the silent maternal allele was hypermethylated in a block of CpG sequences that covered more than 10 kb. By comparison, the expressed paternal allele was unmethylated from a CpG island upstream of the transcribed region through 2 kb. An analysis of DNaseI hypersensitivity of a putative promoter of U2af1-rs1 showed an open chromatin conformation only on the unmethylated, expressed paternal allele. These results suggest that allele-specific hypermethylation covering the gene and its upstream CpG island plays a role in maternal allele repression of U2af1-rs1, which is reflected in altered chromatin conformation of DNaseI hypersensitive sites.

Alleles↗
PubMed1996

Effects of modifications in the pentose moiety and conformational changes on the binding of nucleoside ligands to uridine phosphorylase from Toxoplasma gondii.

One hundred and fifty analogues of uridine, with various modifications to the uracil and pentose moieties, have been tested and compared with uridine with respect to their potency to bind to uridine phosphorylase (UrdPase, EC 2.4.2.3) from Toxoplasma gondii. The effects of the alpha- and beta-anomers, the L- and D-enantiomers, as well as restricted syn and anti rotamers, on binding were examined. Pseudo-, lyxo-, 2,3'-anhydro-2'-deoxy-, 6,5'-cyclo-, 6,3'-methano-, O5',6-methano- and carbocyclic uridines did not bind to the enzyme. Ribosides bound better than the corresponding xylosides, which were better than the deoxyribosides. The binding of deoxyribosides was in the following manner: 2',3'-dideoxynucleosides > 2',5'-dideoxynucleosides > 2'-deoxyribosides > 3'- and 5'-deoxyribosides. alpha-2'-Deoxyribosides bound to the enzyme, albeit less tightly than the corresponding beta-anomers. The acyclo- and 2,2'-anhydrouridines bound strongly, with the 2,2'-anhydro-derivatives being the better ligands. 2,5'-Anhydrouridine bound to UrdPase less effectively than 2,2'-anhydrouridine and acyclouridine. Arabinosyluracil was at best a very poor ligand, but bound better if a benzyl group was present at the 5-position of the pyrimidine ring. This binding was enhanced further by adding a 5-benzyloxybenzyl group. A similar enhancement of the binding by increased hydrophobicity at the 5-position of the pyrimidine ring was observed with ribosides, alpha- and beta-anomers of the 2'-deoxyribosides, acyclonucleosides, and 2,2'-anhydronucleosides. Among all the compounds tested, 5-(benzyloxybenzyl)-2,2'-anhydrouridine was identified as the best ligand of T. gondii UrdPase with an apparent Ki value of 60 +/- 3 nM. It is concluded that the presence of an N-glycosyl bond is a prerequisite for a nucleoside ligand to bind to T. gondii UrdPase. On the other hand, the presence of a 2'-, 3'-, or 5'-hydroxyl group, or an N-glycosyl bond in the beta-configuration, enhanced but was not essential for binding. Furthermore, the potency of the binding of 2,2'-anhydrouridines (fixed high syn isomers) in contrast to the weaker binding of the 6,1'-anhydro- or 2,5'-anhydrouridines (fixed syn isomers), and the complete lack of binding of the 6,5'-cyclo, O5',6-methano- and 6,3'-methanouridines (fixed anti isomers) to T. gondii UrdPase indicate that the binding of ligands to this enzyme is in the syn/high syn conformation around the N-glycosyl bond. The results also indicate that the parasite but not the mammalian host UrdPase can participate in hydrogen bonding with N3 of the pyrimidine ring of nucleoside ligands. T. gondii UrdPase also has a larger hydrophobic pocket adjacent to the C5 of the pyrimidine moiety than the host enzyme, and can accommodate modifications in the pentose moiety which cannot be tolerated by the host enzyme. Most prominent among these modifications is the absence and/or lack of the ribo orientation of the 3'-hydroxyl group, which is a requirement for a ligand to bind to mammalian UrdPase. These differences between the parasite and host, enzymes can be useful in designing specific inhibitors or "subversive" substrates for T. gondii UrdPase.

Animals↗
PubMed1996

Requirement of multiple DNA-protein interactions for inducible expression of RNR3 gene in Saccharomyces cerevisiae in response to DNA damage.

The RNR3 gene encodes the large subunit of ribonucleotide reductase. Transcription of this gene is induced 12-fold in response to DNA damage or by a DNA replication blocker. To investigate cis-acting regulation, deletion analysis of the promoter region of the RNR3 gene was performed and we identified two upstream-repressing sequences in the RNR3 regulatory region. An 18-base-pairs fragment, termed DNA-damage responsive element 1 (DRE1) located between -212 and -194 in this region was found to be essential for the induction of RNR3. This fragment contained a negatively acting sequence where a protein factor bound to the region during normal growth but disappeared by exposure to 4-nitroquinoline-1-oxide. The other repressive element homologue to DRE1 was located at -263 to -254. One possible upstream-activating sequence which regulates the basal expression of RNR3 was also found. These results show that at least three potential cis-elements are necessary for the inducible expression of yeast expression of yeast RNR3 in response to DNA damage.

4-Nitroquinoline-1-oxide↗
PubMed1996

Prognostic significance of Ki67 (MIB1) proliferation index and p53 over-expression in chondrosarcomas.

To investigate the prognostic significance of the Ki67 (MIBI)-proliferation index and p53 over-expression in chondrosarcomas, we retrospectively analyzed a cohort of 29 patients with chondrosarcomas using immunohistochemical assays with MIBI and p53 monoclonal antibodies on formalin-fixed, paraffinembedded tissue samples with microwave preparation. We also assessed 19 patients with benign cartilaginous tumors as a control group. There was a significant positive correlation between MIBI index and tumor grade in chondrosarcomas, while there was no significant difference in the MIBI index between the grade-1 chondrosarcomas and the benign cartilaginous tumors. Patients categorized in the high-MIBI-index group had a significantly lower survival rate than those in the low-index group. Moreover, in analyzing the sub-set of the patients with grade-II chondrosarcomas, it was found that they could be prognostically sub-divided according to MIBI index. The p53 index also significantly correlated with patient survival, and there was significant correlation between the MIBI index and the p53 index. However, in multivariate analysis, only the MIBI index and tumor grade proved to be independent prognostic indicators of chondrosarcomas. These results demonstrate that the MIBI index can be a useful procedure for assessing tumor grade in chondrosarcomas, especially for determining the prognosis of patients with grade-II chondrosarcoma.

Adolescent↗
PubMed1996

Surfactant protein B metabolism in newborn rabbits.

Surfactant protein B (SP-B) is critical to the biophysical function of surfactant. To characterize its metabolism in vivo in the newborn, we administered [35S]methionine and [3H]palmitate to newborn rabbits intravascularly. Three groups of 4 rabbits per group were killed at each of 4 time points followed by isolation of SP-B from alveolar wash and lamellar bodies. The labeling kinetics for alveolar wash associated SP-B and saturated phosphatidylcholine (Sat PC) had similar patterns. To characterize SP-B clearance from the airspace, rabbit SP-B was iodinated, mixed with [14C]dipalmitoylphosphatidylcholine and given by intratracheal injection. Alveolar washes and lamellar bodies were recovered from 4 animals at each of 7 time points. Both SP-B and Sat PC were cleared slowly from the total lung (half-life values approximately 25 h). However, SP-B was cleared more rapidly from the airspaces than was Sat PC. The ratio of [125I]SP-B to [14C]Sat PC in lamellar bodies increased 2-fold by 8 h. These results support the concept of linked secretion and clearance pathways for SP-B and Sat PC, although small differences in reuptake were detected.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1996

A new sensitive method for determination of intracellular 1-beta-D-arabinofuranosylcytosine 5'-triphosphate content in human materials in vivo.

A new sensitive method for the measurement of 1-beta-D-arabinofuranosyl-CTP (ara-CTP), an intracellular active metabolite of 1-beta-D-arabinofuranosylcytosine (ara-C), in human materials in vivo has been established. An acid-soluble fraction containing ara-CTP was extracted from blastic cells by ara-C treatment with trichloroacetic acid (final concentration, 0.3 M) neutralized with an equal volume of cold freon containing 0.5 M tri-n-octylamine. The ara-CTP fraction was separated from the acid -soluble fraction by high-performance liquid chromatography (TSK gel diethylaminoethyl-2 SW column) eluted with 0.05 M phosphate buffer (pH 6.9) and 20% acetonitrile. ara-CTP was lyophilized, dephosphorylated to ara-C by incubation with 10 units alkaline phosphatase for 12 h at 55 degrees C, and measured by RIA using anti-ara-C serum. Recovery through the whole procedure was 92%. In the human chronic myelogenous leukemia cell line K562, the intracellular ara-CTP levels produced when the cells were incubated with ara-c were assayed as above, and they showed a linear increase depending on Ara-C concentrations from 0.01 to 10 microns, demonstrating a very close correlation with the labeled ara CTP levels yielded by cells on incubation with radiolabeled ara-C (r2 = 0.99). The detection limit was 0.1 pmol/5 x 10(6) cells, and a sample amount of only 5 x 10(6) cells was enough for each assay. In the clinical applications, our method proved capable of detecting a wide concentration range of ara-CTP produced when patients were treated with ara-C or its derivatives from very low to intermediate doses. No radiolabeled drug was necessary. The method was very useful for in vivo pharmacodynamic studies of ara-C therapy.

Alkaline Phosphatase↗
PubMed1996

Phase switching of oscillatory contraction in relation to the regulation of amoeboid behavior by the plasmodium of Physarum polycephalum.

The plasmodium of the true slime mould Physarum polycephalum is a large aggregate of protoplasm and behaves like an amoeboid cell, exhibiting rhythmic contraction everywhere within the organism. Phase dynamics of these oscillations were studied in relation to the global organization of amoeboid behavior, by analysing the thickness oscillation, isotonic tension and the motive force of the streaming. Usually the plasmodium showed synchrony, the phase of the oscillation being the same everywhere excepting the peripheral part. We found several situations where this in-phase relationship switched to anti-phase. This occurred either at the early stages of the plasmodial coalescence, or when a single plasmodium was nearly separated by partition, or when the streaming of the protoplasm was hindered by applying the hydrostatic pressure. Furthermore, the motive force of the protoplasmic streaming increased once the anti-phase relationship was established. In this way, the weak interactions among plasmodial parts induce the switching of phase relationship from in-phase to anti-phase, and this transition in turn acts to increase the interaction by promoting a rapid mixing of the protoplasm. This global feedback mechanism by phase switching should help maintain a large single plasmodium without separating into parts. The possible mechanism of phase switching is discussed in terms of coupled nonlinear oscillators.

Animals↗