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Biomedical subjects

J M Song

Publications and source records attributed to J M Song.

At least 19 recordsLinked to original sources
PubMed2001

Optimization of DNA electrophoretic behavior in poly(vinyl pyrrolidone) sieving matrix for DNA sequencing.

Poly(vinyl pyrrolidone) solution was used as a separation matrix in capillary electrophoresis for DNA sequencing. Four-label four-color detection was performed for base calling. Dye-labeled DNA showed large mobility shifts at normal conditions for DNA separation. Temporal correction of mobility shifts was achieved by normalizing with respect to pure peaks that are without spectral interference or temporal overlap at each color channel. To achieve even better performance, a DNA separation condition that does not require corrections for mobility shifts was found. Dichlororhodamine-labeled DNA fragments showed ideal electrophoretic behaviors according to DNA size in the presence of 10 M urea. The base-calling accuracy of dichlororhodamine-labeled M13mp18 and PGEM/U DNA were 99.3% for 333 bases and 99% for 315 bases, respectively. Base calling of unknown DNA samples obtained in the presence of 10 M urea showed 99.1% accuracy.

Coloring Agents↗
PubMed2001

Six-month angiographic follow-up after intravascular ultrasound-guided stenting of infarct-related artery: comparison with non-infarct-related artery.

BACKGROUND: Compared with balloon angioplasty, stenting has been established as an effective treatment modality to reduce restenosis in patients with acute myocardial infarction. However, the immediate results that predict favorable long-term outcomes in the acute infarct stenting are unknown. Therefore, we evaluated long-term outcomes of stenting for infarct-related artery (IRA) lesions by using intravascular ultrasound (IVUS) compared with that of stenting for non-IRA lesions. METHODS: IVUS-guided coronary stenting was successfully performed in 510 native coronary lesions (105 IRA vs 405 non-IRA). A 6-month follow-up angiogram was performed in 419 (82.2%) lesions: 87 (82.9%) IRA lesions and 332 (82.0%) non-IRA lesions. Coronary stenting on the IRA lesions was successfully performed within 7 to 10 days after onset of infarction in 42 patients and within 12 hours in 45 patients. Results were evaluated by clinical, angiographic, and IVUS methods. RESULTS: There were no significant differences in clinical and angiographic variables between the two groups. IVUS variables including reference vessel area and minimal stent area were also similar between the two groups. There was no significant difference in angiographic restenosis rate between the two groups in cases of minimal stent area > or = 7 mm(2): 12.8% (6 of 47) in IRA versus 19.1% (33 of 173) in non-IRA lesions (P = .315). However, the angiographic restenosis rate in cases of minimal stent area <7 mm(2) was 50% (20 of 40) in IRA lesions versus 31.5% (50 of 159) in non-IRA lesions (P = .028). CONCLUSIONS: Angiographic restenosis is significantly higher in stenting for IRA lesions compared with that for non-IRA lesions in cases of minimal stent area < 7 mm(2).

Angioplasty, Balloon, Coronary↗
PubMed2001

Effect of hypercholesterolemia on macrophage infiltration after balloon injury to rabbit iliac artery.

Both hypercholesterolemia and vascular injury have been reported to induce macrophage infiltration, but their combined effect and the mechanism by which hypercholesterolemia enhances the infiltration remain to be clarified in vivo. To evaluate the effect of hypercholesterolemia on macrophage infiltration after vascular injury, the iliac arteries of hypercholesterolemic (HC) and normocholesterolemic (NC) rabbits were examined 2h, 1 day, 3 days, 7 days, and 14 days after balloon injury using immunohistochemical staining for macrophages, intercellular adhesion molecule (ICAM)-1, and vascular cell adhesion molecule (VCAM)-1. Nuclear factor kappa-B (NF-kappaB) activation was also evaluated in fresh frozen iliac arteries using the electrophoretic mobility shift assay method. The fundamental difference between HC and NC was the amount of macrophage infiltration seen in HC from 7 days after balloon injury. Two out of 4 HC iliac arteries on the 7th day, and 3 out of 4 HC iliac arteries on the 14th day were positively stained with ICAM-1 in regenerated endothelium and neointima, whereas there were no positively stained NC iliac arteries. Neither HC nor NC tissues showed positive staining with VCAM-1. NF-kappaB was activated in HC 7 and 14 days after balloon injury, but not in NC. In conclusion, in vivo hypercholesterolemia induces macrophage infiltration after balloon injury and it is mediated by increased NF-kappaB activation promoting ICAM-1 expression.

Animals↗
PubMed2000

Alternative base-calling algorithm for DNA sequencing based on four-label multicolor detection.

A simple base-calling scheme based on four-label multicolor detection is suggested for DNA sequencing. The entire spectra of the dye labels were used for identification. Specifically, the maxima of the emission spectra rather than the intensity ratios at selected wavelengths are used to provide excellent discrimination. Capillary gel electrophoresis was used for the separation of DNA fragments. Data acquisition and analysis compatible with fast and high-throughput imaging detection was accomplished. The accuracy of base calling of PGEM/U DNA from the raw data obtained with 5 nm and 7 nm spectroscopic resolution were 98.4% for 386 bases and 98.4% for 385 bases. Base calling of M13mp18 DNA showed 98.3% accuracy for 420 bases.

Algorithms↗
PubMed1999

Mitral annulus velocity in the evaluation of left ventricular diastolic function in atrial fibrillation.

This study assessed the clinical utility of mitral annulus velocity in the evaluation of left ventricular diastolic function in patients with atrial fibrillation. Atrial fibrillation is the most common sustained arrhythmia encountered in clinical practice. The clinical usefulness of conventional Doppler indexes is limited in atrial fibrillation because of the altered left atrial pressure and loss of synchronized atrial contraction. Mitral inflow and mitral annulus velocities were measured simultaneously with tau in 27 patients with nonrheumatic atrial fibrillation at the cardiac catheterization laboratory. Among deceleration time of mitral inflow, peak mitral inflow velocity (E), and peak diastolic mitral annulus velocity (E), only E correlated with tau (r = 0.51, P =.007). Prolonged tau (>/=50 ms) could be predicted by E <8 cm/s with a sensitivity of 73% (16 of 22) and a specificity of 100% (5 of 5). The E/E ratio correlated with left ventricular filling pressure (r = 0.79, P <.001). The E/E ratio of >/=11 could predict elevated left ventricular filling pressure (>/=15 mm Hg) with a sensitivity of 75% (9 of 12) and a specificity of 93% (14 of 15). Mitral annulus velocity is useful in the detection of impaired left ventricular relaxation and estimation of filling pressure even in patients with atrial fibrillation.

Adult↗
PubMed1999

Variant angina is not associated with angiotensin I converting enzyme gene polymorphism but rather with smoking.

BACKGROUND: Angiotensin converting enzyme (ACE) perhaps plays roles in regulating coronary vasomotor tone by producing angiotensin II and degrading bradykinin. OBJECTIVES: We sought to investigate the role of ACE gene polymorphism in the pathogenesis of variant angina and to compare it with that of other clinical risk factors for male patients with variant angina and age-matched and sex-matched control subjects. METHODS: We studied 78 male patients with variant angina who exhibited spontaneous or provoked coronary spasms during coronary angiography and compared prevalences of ACE gene genotype (deletion D and insertion I) and other risk factors between this group of patients with variant angina and age-matched and sex-matched control subjects whose angiograms were normal and in whom the ergonovine test did not cause spasms (n = 80). RESULTS: Smokers were more prevalent in the group of patients with variant angina (P < 0.05). Genotype and allele prevalences of the group of patients with variant angina (0.14, 0.53 and 0.33 for DD, DI and II and 0.41 and 0.59 for D and I, respectively) were no different from those of the control group (0.16, 0.49 and 0.35 for DD, DI and II and 0.40 and 0.60 for D and I). Multiple logistic regression analysis showed that smoking was a significant risk factor for variant angina (odds ratio 2.61, 95% confidence interval 1.03-6.66) whereas ACE genotype was not. CONCLUSIONS: Variant angina is associated with an environmental factor, such as smoking, rather than a genetic factor, such as ACE gene polymorphism.

Aged↗
PubMed1997

Evidence of genetic progression in human gastric carcinomas with microsatellite instability.

Mutator phenotype tumors provide unique opportunities to unravel malignant progression because of various gene alterations acquired during clonal tumor evolution. Gastric carcinomas, which have been known to show frequent genetic instability, would be composed of initial gene alterations shared by most tumor areas and subsequent alterations restricted to particular tumor sites. To analyse the timing of genetic events, we examined separate sites of tumor tissue obtained from a given gastric carcinoma patient with microsatellite instability (MSI). Our study included 95 normal/tumor area pairs from 25 patients. Six of the 25 patients (24%) demonstrated various levels of MSI ranging from 7% (two of 30) to 97% (28 of 29) of markers tested in multiple tumor sites. Of the six patients, five manifested frameshift mutations in a tract of ten deoxyadenosines within transforming growth factor beta receptor type II and four demonstrated frameshift mutations in a tract of eight deoxyguanosines within BAX. These mutations were common to all tumor sites regardless of the various level of MSI phenotype, indicating initial events. Two of the six patients exhibited frameshift mutations in mononucleotide repeats of mismatch repair genes, hMSH3 and hMSH6, and the insulin-like growth factor II receptor in restricted tumor areas, indicating additional alterations. Insulin-like growth factor II receptor mutations appear to be caused by hMSH3 and hMSH6 mutations because the former mutations were confined to tumor portions with the latter two mismatch repair lesions. These results provide genetic progression evidence for gastric carcinomas of the mutator pathway. In this pathway, mismatch repair insufficiency initially targets mononucleotide tracts of transforming growth factor beta receptor type II and BAX. During tumorigenesis, primary mismatch repair failure may give rise to the secondary mismatch repair lesions, frameshift mutations of hMSH3 and hMSH6, which result in another tumorigenic mutation in the insulin-like growth factor II receptor.

Adult↗
PubMed1996

Microsatellite instability-associated mutations associate preferentially with the intestinal type of primary gastric carcinomas in a high-risk population.

Most colon cancers exhibiting microsatellite instability (MI), a mutator phenotype of mismatch repair failure, are associated with mutations of the transforming growth factor-beta receptor type II genes (TGF-beta RII). Of intestinal- and diffuse-type gastric carcinomas, the former have been thought to arise from intestinal metaplasia in which gastric mucosa resembles intestinal mucosa. To evaluate the preferential histological type of MI-associated mutations in the development of gastric carcinoma, mutations of TGF-beta RII, p53, and p16 were analyzed for the two types of primary gastric carcinomas showing MI. Of 50 primary gastric carcinomas, including 33 intestinal types and 17 diffuse types, 15 cases (30%) demonstrated MI at 1 or more of the 11 microsatellite markers tested. The 15 MI cases were classified into two groups, widespread MI and low-level MI, based on the number of markers exhibiting the instability. Eleven were widespread MIs, and the remaining four cases were low-level MIs. Ten of the 11 (91%) widespread MIs were of the intestinal type, and 1 case (9%) was of the diffuse type. Of the 11 widespread MIs, 10 cases (91%) demonstrated frameshift mutations within the polyadenylate tract of the TGF-beta RII. The frameshift mutation was rarely detected at p53 and p16 (1 of 11, 9%). In contrast, the four low-level MI cases had no frameshift mutations within the repeat sequences of TGF-beta RII, p53, and p16, but two of the four cases demonstrated base substitution mutations within p53. Our results suggest that mismatch repair failure can mutate the TGF-beta RII and may provide one of the pathways for the development of the intestinal-type gastric carcinoma in high-risk populations.

Adenocarcinoma↗
PubMed1996

Organization and characterization of the two yeast ribosomal protein YL19 genes.

A second copy of the Saccharomyces cerevisiae ribosomal protein YL19 gene was isolated through the use of the RPL19A gene as a probe. The nucleotide sequence of the gene, RPL19B, was determined. RPL19B contains an intron of 384 nucleotides located near its 5'-end. The coding regions of the two yeast genes, RPL19A and RPL19B, differ in only 34 nucleotides, none of which lead to changes in the amino-acid sequences of the predicted protein of 189 amino acids. RPL19B is also closely linked to a mitochondrial ADP/ATP carrier protein gene AAC2. Yeast cells containing disruption of either RPL19A or RPL19B formed smaller colonies than wild-type strains; however, simultaneous deletion of both genes is lethal.

Amino Acid Sequence↗
PubMed1995

The N-terminal, dehydrogenase/cyclohydrolase domain of yeast cytoplasmic trifunctional C1-tetrahydrofolate synthase requires the C-terminal, synthetase domain for the catalytic activity in vitro.

The yeast ADE3(1-333) gene which encodes a truncated protein containing the N-terminal 5,10-methylene-tetrahydrofolate (THF) dehydrogenase (D)/5,10-methyl-THF cyclohydrolase (C) domain of cytoplasmic trifunctional C1-THF synthase is able to complement all the phenotypes associated with ade3 mutations in vivo. However, expression of the ADE3(1-333) gene in an ade3 strain does not retain any D activity in vitro. Expression in a yeast ade3 strain of the ADE3(1-333) fused to the Escherichia coli lacZ gene or to the yeast SER2 gene allows detection of D and C activities in vitro. These results indicate that the N-terminal D/C domain of C1-THF synthase requires the C-terminal 10-formyl-THF synthetase domain for stable catalytic activity in vitro.

Alleles↗
PubMed1995

Nucleotide sequence and characterization of the Saccharomyces cerevisiae RPL19A gene encoding a homolog of the mammalian ribosomal protein L19.

A gene designated RPL19A has been identified in the region downstream from the 3'-end of the Saccharomyces cerevisiae MIS1 gene encoding the mitochondrial C1-tetrahydrofolate synthase. The gene codes for the yeast ribosomal protein YL19 which exhibits 57.5% identify with the mammalian ribosomal protein L19. RPL19A is one of two functional copies of the YL19 gene located on chromosome II. The disruption of RPL19A has no effect on the growth of the yeast. The RPL19A gene contains an intron located near the 5'-end. The 5'-flanking region contains one similar and one complete UASrpg upstream activating sequence. RPL19A was also found to be adjacent to the chromosome II AAC3 gene, encoding the mitochondrial ADP/ATP carrier protein.

Amino Acid Sequence↗
PubMed1993

Single-stranded DNA binding activity of C1-tetrahydrofolate synthase enzymes.

In eukaryotes C1-5,6,7,8-tetrahydrofolate (THF) synthase is a trifunctional enzyme that catalyzes the interconversion of reduced forms of folate to supply activated one-carbon units required for a variety of metabolic pathways. The enzymatic activities include 10-formyl-THF synthetase (EC 6.3.4.3), 5,10-methenyl-THF cyclohydrolase (EC 3.5.4.9), and 5,10-methylene-THF dehydrogenase (EC 1.5.1.5). In bacteria separate, monofunctional or bifunctional polypeptides catalyze the same reactions. We have purified C1-THF synthase from the fission yeast Schizosaccharomyces pombe and found its physical and enzymatic properties similar to those of other eukaryotic C1-THF synthase enzymes. Unexpectedly, the S. pombe enzyme bound strongly (Keq = 100 pM) to single-stranded DNA, but not to double-stranded DNA or to RNA. The binding was sequence-independent, apparently not cooperative, and not detectably inhibited by C1-THF synthase substrates or cofactors. Trifunctional cytoplasmic enzyme from Saccharomyces cerevisiae and monofunctional (synthetase) enzyme from Clostridium acidiurici also bound tightly to single-stranded DNA, while bifunctional (dehydrogenase and cyclohydrolase) enzyme from Escherichia coli did not, suggesting that single-stranded DNA binding is a conserved function of the synthetase domain of C1-THF synthase enzymes.

Aminohydrolases↗
PubMed1993

Function of yeast cytoplasmic C1-tetrahydrofolate synthase.

The protein product of the ADE3 gene of the yeast Saccharomyces cerevisiae has been identified as the cytoplasmic trifunctional C1-tetrahydrofolate (THF) synthase, which possesses 10-formyl-THF synthetase (EC 6.3.4.3), 5,10-methenyl-THF cyclohydrolase (EC 3.5.4.9), and 5,10-methylene-THF dehydrogenase (EC 1.5.1.5) activities. However, it has been suggested that the ADE3-encoded C1-THF synthase does not play a role in providing the enzymes involved in the generation of one-carbon intermediates in the biosynthesis of the purine bases but functions in maintaining the structural integrity of the enzyme complex involved in purine biosynthesis [Barlowe, C. K. & Appling, D. A. (1990) Mol. Cell. Biol. 10, 5679-5687]. This hypothesis is based on their finding that the presence of the full-length ADE3 C1-THF synthase, whether catalytically active or not, is correlated with the Ade+ phenotype. In contrast to their results, our deletion analysis of the ADE3 gene indicates that the presence of either the synthetase or dehydrogenase/cyclohydrolase domains of C1-THF synthase is enough to complement the adenine requirement in ade3 strains. These results are also consistent with those obtained in heterologous expression of spinach and Clostridium acidiurici monofunctional synthetases in ade3 strains. Heterologous expression studies show that the high synthetase activity may be correlated with the increased growth in medium lacking adenine. These results suggest that the catalytic activity of the C1-THF synthase is involved in purine biosynthesis.

Aminohydrolases↗
PubMed1992

The prognostic significance of DNA ploidy pattern in transitional cell cancer of the renal pelvis and ureter: continuing follow-up.

Among 190 patients operated on for transitional cell cancer of the renal pelvis and/or ureter from 1976 to 1990, 95 had their tumor studied by flow cytometry. Of these, the prognostic significance of the DNA ploidy pattern with respect to the standard pathologic features was assessed in a retrospective analysis, where survival information were updated to October 1991 and the mean follow-up of patients exceeded 5.5 years (longest follow-up: 15.5 years). Five and ten-year survival probabilities for the whole group were, respectively, 65.5 and 51%. Patients with a diploid tumor had significantly better survival rates than patients with tetraploid/aneuploid cancer (p less than 0.00001). The impact of the DNA ploidy on survival was confirmed by a multivariate analysis of prognostic factors, where only tumor grade (p less than 0.0001), tumor stage (p less than 0.0001), number of neoplastic foci (p = 0.022) and nuclear DNA pattern (p less than 0.068) had a significant influence on survival. In the group of patients with low-stage (pTa-pT1) and low-grade (G1-G2) transitional cell cancer of the upper urinary tract, the DNA analysis was unable to identify any subset of patients at higher risk for disease progression.

Carcinoma, Transitional Cell↗
PubMed1991

Transitional cell carcinoma of the upper urinary tract: evaluation of prognostic factors by histopathology and flow cytometric analysis.

Prognostic factors in transitional cell carcinoma of the upper urinary tract were assessed with histopathological examination and flow cytometric analysis in a series of 127 patients operated upon between 1976 and 1988. In particular, we evaluated the usefulness of flow cytometry to identify patients who require adjuvant treatment among those with low grade and low stage disease (51% in this series). A multivariate analysis was done on 92 cases, considering patient age and sex, stage, grade and number of lesions (unifocal versus multifocal), site (renal pelvis versus ureter), presence of vesical tumors, recurrences along the urinary tract or in the bladder, type of operation and nuclear deoxyribonucleic acid (DNA) ploidy (diploid versus tetraploid/aneuploid tumors). Only the stage (p = 0.001), grade (p = 0.001) and, to a lesser extent, the DNA pattern (p = 0.031), as well as the number of lesions (p = 0.061) were determinant for prognosis. In regard to the subgroup of 41 patients with grade 2 or less, stage P1 or less tumors, no significant difference in survival was demonstrated between diploid and nondiploid tumor patients. However, 7 of 10 patients from the latter group are still under observation. Therefore, our conclusions may have to be modified in the future.

Adult↗
PubMed1990

Effects of multiple yeast rad3 mutant alleles on UV sensitivity, mutability, and mitotic recombination.

A yeast strain was constructed that had a disruption of the chromosomal RAD3 gene and carried a series of centromeric plasmids with defined mutations in this gene. Using this isogenic collection, we examined sensitivity to UV radiation, spontaneous and UV radiation-induced mutagenesis, and mitotic recombination. Several alleles resulted in a marked increase in UV sensitivity. Most of these alleles were found to carry mutations located in consensus motifs for DNA helicases. Other alleles caused a modest or no increase in UV sensitivity and carried mutations in regions of the Rad3 polypeptide that are apparently not conserved. This correlation suggests that the DNA helicase activity of Rad3 protein is required for nucleotide excision repair of DNA. Some rad3 alleles conferred a marked increase in the frequency of spontaneous mutagenesis, including nonsuppressor reversion of the lys2-1 ochre mutation. These alleles also showed a good correlation with conserved DNA helicase domains, suggesting that the Rad3 DNA helicase also plays a role in the fidelity of DNA synthesis or postreplicative mismatch correction. Several rad3 mutator alleles also resulted in increased levels of mitotic recombination. Increased spontaneous mutagenesis and mitotic recombination are characteristic features of the Rem- phenotype. However, in contrast to the prototypic Rem- phenotype, the rad3 mutator alleles identified in this study did not confer inviability in the presence of mutations in the RAD50 or RAD52 gene required for strand break repair of DNA.

Alleles↗
PubMed1989

Mutations in ADE3 reduce the efficiency of the omnipotent suppressor sup45-2.

Mutations in a known yeast gene, ADE3, were shown to act as an antisuppressor, reducing the efficiency of the omnipotent suppressor, sup45-2. The ADE3 locus encodes the trifunctional enzyme C1-tetrahydrofolate synthase, which is required for the biosynthesis of purines, thymidylate, methionine, histidine, pantothenic acid and formylmethionyl-tRNA(fMet. The role of this enzyme in translational fidelity had not previously been suspected.

Aminohydrolases↗