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Biomedical subjects

T Yamane

Publications and source records attributed to T Yamane.

At least 145 records · Page 8Linked to original sources
PubMed1999

High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution.

BACKGROUND: Congerin I is a member of the galectin (animal beta-galactoside-binding lectin) family and is found in the skin mucus of conger eel. The galectin family proteins perform a variety of biological activities. Because of its histological localization and activity against marine bacteria and starfish embryos, congerin I is thought to take part in the eels' biological defense system against parasites. RESULTS: The crystal structure of congerin I has been determined in both lactose-liganded and ligand-free forms to 1. 5 A and 1.6 A resolution, respectively. The protein is a homodimer of 15 kDa subunits. Congerin I has a beta-sheet topology that is markedly different from those of known relatives. One of the beta-strands is exchanged between two identical subunits. This strand swap might increase the dimer stability. Of the known galectin complexes, congerin I forms the most extensive interaction with lactose molecules. Most of these interactions are substituted by similar interactions with water molecules, including a pi-electron hydrogen bond, in the ligand-free form. This observation indicates an increased affinity of congerin I for the ligand. CONCLUSIONS: The genes for congerin I and an isoform, congerin II, are known to have evolved under positive selection pressure. The strand swap and the modification in the carbohydrate-binding site might enhance the cross-linking activity, and should be the most apparent consequence of positive selection. The protein has been adapted to functioning in skin mucus that is in direct contact with surrounding environments by an enhancement in cross-linking activity. The structure of congerin I demonstrates the emergence of a new structure class by accelerated evolution under selection pressure.

Amino Acid Sequence↗
PubMed1999

Efficient coupled transcription/translation from PCR template by a hollow-fiber membrane bioreactor.

A novel bioreactor using a hollow-fiber membrane was developed for the coupled transcription/translation system using T7 RNA polymerase and Escherichia coli S30 extract. The large surface area per the reaction volume of the reactor assured rapid mass transfers of substrates into the reaction mixture and of wastes out from it across the membrane by their molecular diffusion. The flux was large enough to maintain nucleotide concentrations for more than 3 h, which increased the protein synthesis greatly. In addition, the T7 terminator sequence downstream from the reporter genes was found to increase the synthesized protein significantly, especially when the product of polymerase chain reaction (PCR) was used as a template. Implementation of this finding and use of the bioreactor developed multiplied the productivity of protein by the in vitro direct expression from PCR template.

Base Sequence↗
PubMed1999

Crystal structure of a protein with an artificial exon-shuffling, module M4-substituted chimera hemoglobin beta alpha, at 2.5 A resolution.

The crystal structure of the homotetramer of a chimera beta alpha-subunit of human hemoglobin was refined at 2.5 A resolution. The chimera subunit was constructed by replacing an exon-encoded module M4 of the beta-subunit with that of the alpha-subunit, simulating an exon-shuffling event. The implanted module M4 retained the native alpha-subunit structure, while module M3 was disturbed around the site where a new type of intron was recently found. Some of the residues were found in alternative conformations that avoid steric hindrance at the subunit interface. The modules are modestly rigid in their backbone structures by using side-chains to compensate for interface incompatibility.

Amino Acid Sequence↗
PubMed1999

Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus.

Phospholipase D (E.C. 3.1.4.4) from Streptomyces antibioticus has been crystallized in six crystal forms using the hanging-drop vapour-diffusion method. The type III and V crystals belong to monoclinic and hexagonal systems, respectively. All of the other crystal forms, types I, II, IV and VI, belong to orthorhombic space group P212121. Of these four types, the type VI crystals are suitable for X-ray structure determination. Crystal data for type VI crystals are: a = 50.1, b = 98.7, c = 107.6 A, V = 532100 A3, Z = 4 and Vm = 2.47 A3 Da-1. Type VI crystals diffract to at least 2.3 A resolution. A total of 11295 independent reflections to 3 A resolution have been collected from a type VI crystal using a conventional X-ray source, and its structural analysis is currently being conducted using isomorphous replacement methods.

Crystallization↗
PubMed1999

Derivation of melanocytes from embryonic stem cells in culture.

We report that embryonic stem (ES) cells were efficiently induced to differentiate to melanocytes in vitro. When undifferentiated ES cells were cocultured with a bone marrow-derived stromal cell line, a very small but significant number of melanocytes were reproducibly generated. This process was greatly enhanced by addition of dexamethasone to the culture and strictly depended on steel factor, the ligand for the c-Kit receptor tyrosine kinase. Expression of c-Kit on the precursor cells was confirmed by using SCL/tal-1-/- ES cells, which are defective for producing hematopoietic cells, which were thus ruled out as possible sources of nonmelanogenic c-Kit-expressing cells. The morphology, reactivity to growth factors, and expression of melanogenic markers of the cells generated all indicated unequivocally that these cells were melanocytes. This culture system may provide a potent tool for the study of development and function of melanocytes.

Animals↗
PubMed1999

Enhancement of both reaction yield and rate of synthesis of structured triacylglycerol containing eicosapentaenoic acid under vacuum with water activity control.

Production of structured triacylglycerols (sTAG) containing eicosapentaenoic acid (EPA) at the sn-1 (or 3) position using Lipozyme in a solvent-free system was studied. Optimal water activity (a(w)) for the synthesis of the sTAG was investigated. Vacuum was applied to shift reaction equilibrium toward the synthesis reaction by removing by-products. During vacuum application, the water level of the reaction system was controlled at the optimal level by addition of a suitable amount of water at a predetermined interval. Intermittent periodic addition of a suitable amount of water into the reaction mixture made the reaction rate faster than that without adding water. A molar yield of 89.7% of the targeted sTAG was obtained after 16 h reaction with a(w) control during the vacuum application as compared with the yield of 87.0% after 24 h of reaction without a(w) control during the vacuum application.

Adsorption↗
PubMed1999

Nucleotide sequence of crotamine isoform precursors from a single South American rattlesnake (Crotalus durissus terrificus).

A cDNA phage library was constructed from venom glands of a single adult specimen of crotamine-plus Crotalus durissus terrificus (South American rattlesnake) captured in a known region. Fifteen crotamine positive clones were isolated using a PCR-based screening protocol and sequenced. These complete cDNAs clones were grouped for maximal alignment into six distinct nucleotide sequences. The crotamine cDNAs, with 340-360 bases, encompass open reading frame of 198 nucleotides with 5' and 3' untranslated regions of variable size, signal peptide sequence, one crotamine isoform message, and putative poly(A+) signal. Of these six different crotamine cDNA precursors, two predict the identical amino acid sequence previously described by Laure (1975), and the other four a crotamine isoform precursor where the Leucine residue at position 19 is replaced by isoleucine by a single base change. On the other hand, nucleotide variation was observed in the 5' and 3' untranslated regions, with one interesting variant containing an 18 base pair deletion at the 5' untranslated region which results in the usual ATG initiator being replaced by the rarely used GUG start codon. Comparison by Northern blot analysis of poly(A+) RNA from venom glands of a crotamine-plus specimen to total and poly(A+) RNA from a crotamine-minus snake indicated that crotamine transcripts were not expressed in the crotamine-minus specimen.

Animals↗
PubMed1999

Bronchial arterial infusion with cisplatin followed by irradiation successfully treats recurrent stage IVb thymic large cell carcinoma.

A 48-year-old female was treated with three courses of chemotherapy combined with bronchial arterial infusion (BAI) with cisplatin and intravenous drip infusion with bleomycin and vinblastine for a recurrent thymic large cell carcinoma seen 1 year after the initial operation. The patient had subsequently undergone irradiation. No sign of recurrence has been noted with a follow-up period of 6 years after the initial operation. This is the first reported case of survival from recurrence of thymic large cell carcinoma. BAI combined with irradiation should be considered as one of the treatments of choice in a recurrence like we present herein.

Antineoplastic Agents↗
PubMed1999

Modulator-mediated synthesis of active lipase of Pseudomonas sp. 109 by Escherichia coli cell-free coupled transcription/translation system.

Catalytically active lipase was synthesized using Escherichia coli S30 extract from the signal-deleted lipL gene (lipL) in the presence of its N-terminal hydrophobic fragment-truncated modulator (rLimL) that was purified from the overexpressing E. coli cells. The specific activity of the lipase thus synthesized was 125 times higher than that of the purified one from Pseudomonas sp. 109. No lipase activity was detected in the absence of rLimL, even though the lipase protein itself was synthesized. Active lipase was also produced in vitro by coexpression of rlipL and the modulator gene (rlimL), although a much smaller amount of the lipase was formed. In the absence of rLimL, aggregates of the lipase were formed during its folding process. The addition of rLimL proportionally raised both lipase solubility and enzyme activity. An unstable but high activity peak of the lipase was found during its folding process.

Journal Article↗
PubMed1999

HLA class II polymorphism in Thai patients with non-Hodgkin's lymphoma.

The distribution of HLA-DRB1 alleles and DQB1 alleles in 100 Thai patients with non-Hodgkin's lymphoma (NHL) was analysed using the polymerase chain reaction with sequence-specific primer (PCR-SSP) method, and the association between the disease and the presence of certain HLA class II alleles was investigated. The frequencies of HLA-DRB1*1502 and DRB1*09012 were increased while those of DRB1*0404, DRB1*0803 and DRB1*1106 were decreased. On the other hand, the incidence of HLA-DQB1 alleles was similar to that in the normal population. Interestingly, only HLA-DRB1*1502 showed a significant positive association with NHL, especially in patients < or / = 45 years and in male patients. It is concluded that the DRB1*1502 allele may contribute to NHL susceptibility in the Thai population. However, further studies on the functional roles of the HLA class II alleles are necessary to elucidate NHL susceptibility.

Adult↗
PubMed1999

Purification, characterization and gene cloning of 6-hydroxynicotinate 3-monooxygenase from Pseudomonas fluorescens TN5.

6-Hydroxynicotinate 3-monooxygenase, a membrane-bound, 42-kDa monomeric enzyme from Pseudomonas fluorescens TN5 was purified and characterized. The enzyme catalyzes the oxidative decarboxylation of 6-hydroxynicotinate and depends on O2, NADH and FAD with the holoenzyme containing 1 M of FAD per 1 M of enzyme. The isolated enzyme was used for the synthesis of 2,5-dihydroxypyridine, a precursor for the chemical synthesis of 5-aminolevulinic acid, which is applied as a plant growth hormone, a herbicide and in cancer therapy. A 1.8-kbp DNA fragment, which contains the ORF encoding 6-hydroxynicotinic acid 3-monooxygenase, was cloned, sequenced and expressed in Escherichia coli. The deduced 385 amino acid sequence of the cloned ORF is in agreement with the enzyme molecular mass, amino acid sequence of an internal peptide, contains a putative FAD-binding site and is homologous to similar flavoproteins such as salicylate 1-monoxygenase.

Amino Acid Sequence↗
PubMed1999

Location of the catalytic nucleophile of phospholipase D of Streptomyces antibioticus in the C-terminal half domain.

Phospholipase D (PLD) of Streptomyces antibioticus was labelled with fluorescent-labelled substrate, 1-hexanoyl-2-{6-[(7-nitro-2-1, 3-benzoxadiazol-4-yl)-amino]hexanoyl}-sn-glycero-3-phosphocholine, when it was incubated with the substrate and the reaction followed by SDS/PAGE. Mutant enzymes lacking the catalytic activity were not labelled under the same conditions, indicating that labelling of the PLD occurred as the result of its catalytic action. This confirmed that the labelled protein was the phosphatidyl PLD intermediate. PLDs contain two copies of the highly conserved catalytic HxKxxxxD (HKD) motif. Therefore, two protein fragments were separately prepared with recombinant strains of Escherichia coli. One of the fragments was the N-terminal half of the intact PLD containing one HKD motif, and the other was the C-terminal half with the other motif. An active enzyme was reconstructed from these two fragments, and therefore designated fragmentary PLD (fPLD). When fPLD was subjected to the labelling experiment, only the C-terminal half was labelled. Therefore, it was concluded that the catalytic nucleophile that bound directly to the phosphatidyl group of the substrate was located on the C-terminal half of PLD, and that the N-terminal half did not contain such a nucleophile.

4-Chloro-7-nitrobenzofurazan↗
PubMed1999

Flow visualization analysis for evaluation of shear and recirculation in a new closed-type, monopivot centrifugal blood pump.

Flow visualization has great potential in analyzing flow patterns of centrifugal blood pumps to locate possible hemolysis and thrombus formation sites. This study focused on the said phenomena thought to correlate with areas of high shear velocity and stagnation and analyzed a new closed-type centrifugal blood pump. As a result of analyzing the flow of inlet and front gap of the impeller, flow in the front gap was approximately 30% of the external flow. Visualization in the back gap showed sufficient exchange also. Analysis in the volute area and around the washout holes revealed high shear locations and quantified the highest shear velocity. Maximum shear on the volute wall was found to be 9,000-19,000 s-1 and was located in the 0.2-mm vicinity of the wall. Based on these results, previous hemolysis tests, and small pump size, one concludes that the analyzed closed-type centrifugal pump has a relatively smooth flow suitable for a totally implantable artificial heart.

Algorithms↗
PubMed1999

A preliminary study of microcapsule suspension for hemolysis evaluation of artificial organs.

A microcapsule suspension, a substitute for animal blood in hemolysis tests, has been developed for evaluation of the absolute hemolytic properties of circulatory artificial organs. The microcapsule suspension was made by dispersing microcapsule slurry into an ethylene glycol sodium chloride solution. The microcapsule slurry was composed of a leuco dye solution and polyurethane membrane made by the reaction between aliphatic poly-isocyanate and polyamine by interfacial polycondensation. The microcapsule was a small particle containing dye inside. The microcapsule suspension was white; the diameter of the microcapsules was from 5 to 100 microns. The specific gravity of the suspension was 1.024, and the membrane was elastic. The fluid showed Newtonian characteristics, different from animal blood, and its viscosity was approximately 5.8 mPa.s. After the microcapsules were destroyed, the leuco dye was extracted with n-hexane from the suspension and was measured by spectroscopy after being colored with acid ethanol. Hemolysis can be regarded as a fatigue fracture of cell membranes rather than a static fracture. The destruction of microcapsules by a Potter type tissue grinder was observed at a low stroke number region and was compared to rat blood. Moreover, hemolysis tests of a commercially available centrifugal blood pump and the prototype of our centrifugal pump for mechanism checks were carried out with bovine blood. The hemolysis level of the prototype pump increased with time while the hemolysis level of the commercial blood pump did not change as much as that of the control when both pumps were tested with the microcapsule suspension. These results are similar to tests utilizing bovine blood. Therefore, hemolysis tests of circulatory artificial organs completed with microcapsule suspension are expected to provide results similar to tests with animal blood.

Animals↗
PubMed1999

Flow visualization study to improve hemocompatibility of a centrifugal blood pump.

A correlation study was conducted among quantitative flow visualization analysis, computational fluid dynamic analysis, and hemolysis tests regarding the flow in a centrifugal blood pump to prevent hemolysis. Particular attention was paid to the effect of the impeller/casing gap widths on the flow in the volute and in the outlet. Flow vector maps were obtained for 250% scaled-up models with various geometries, using an argon ion laser light sheet, a high speed video camera, and particle tracking velocimetry. In terms of the results, in the small radial gap model, high shear occurred near the inside wall of the outlet and stagnation near the outside wall of the outlet whereas the standard model maintained smooth flow and low shear. The small radial gap model showed a lower head and greater hemolysis than the standard model. This head decrease could be partly restored by relocating the outlet position; however, the hemolysis level hardly decreased. From these results, it was found that the small radial gap itself is important. It was also confirmed by detailed flow visualization and simple laminar shear analysis near the wall that the small radial gap caused a wider high shear layer (110-120 microm) than the standard model (approximately 80 microm). In the small radial gap model, the high shear layer in the outlet (approximately 50 microm) is much narrower than that in the volute. Flow visualization together with the aid of computational fluid dynamic analysis would be useful to eliminate the causes of hemolysis.

Blood Flow Velocity↗
PubMed1999

Development of design methods for a centrifugal blood pump with a fluid dynamic approach: results in hemolysis tests.

The purpose of this study was to examine the relationship between local flow conditions and the hemolysis level by integrating hemolysis tests, flow visualization, and computational fluid dynamics to establish practical design criteria for centrifugal blood pumps with lower levels of hemolysis. The Nikkiso centrifugal blood pump was used as a standard model, and pumps with different values of 3 geometrical parameters were tested. The studied parameters were the radial gap between the outer edge of the impeller vane and the casing wall, the position of the outlet port, and the discharge angle of the impeller vane. The effect of a narrow radial gap on hemolysis was consistent with no evidence that the outlet port position or the vane discharge angle affected blood trauma in so far as the Nikkiso centrifugal blood pump was concerned. The radial gap should be considered as a design parameter of a centrifugal blood pump to reduce blood trauma.

Animals↗
PubMed1999

Computational fluid dynamics analysis to establish the design process of a centrifugal blood pump: second report.

To establish an efficient design process for centrifugal blood pumps, the results of computational fluid dynamics (CFD) analysis were compared to the results of flow visualization tests and hemolysis tests, using the Nikkiso centrifugal blood pump. CFD analysis revealed that the radial gap greatly affected the shear stress in the outlet diffuser. The hemolysis study also indicated a similar tendency. To see the flow behind the impeller, we conducted a comparative study between models with and without washout holes using the CFD technique. CFD analysis indicated that flow and pressure distributions behind the impeller were different between both models, and a particle was observed to remain longer behind the impeller in the model without washout holes. In the future, CFD analysis could be a useful tool for developing blood pumps in comparison to flow visualization tests and hemolysis tests.

Computer Simulation↗