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Biomedical subjects

S Shin

Publications and source records attributed to S Shin.

At least 127 records · Page 7Linked to original sources
PubMed1995

Separation and size determination of circular and linear single-stranded DNAs by alkaline agarose gel electrophoresis.

The electrophoretic mobility of single-stranded DNA (ssDNA) through agarose gels depends on size (number of bases; molecular weight), topology (linear or circular), and conformation (secondary and tertiary folding through base pairing and stacking), as well as on gel concentration and field strength. Under alkaline conditions that disrupt secondary and tertiary structures, the linear and circular forms of a given single-stranded DNA can be easily resolved. The mobility ratios, mulinear/mucircular, depend strongly on gel concentration and less strongly on DNA size. Protocols have been developed to determine conveniently the size within 2% and the fractions of circular and linear forms for ssDNA sizes on the order of 10 kb.

DNA, Circular↗
PubMed1995

C2, and unusual filamentous bacterial virus: protein sequence and conformation, DNA size and conformation, and nucleotide/subunit ratio.

Inovirus C2 is 1295 nm long and 6.8 nm in diameter, and its mass is 24 million Da. Its genome is a topologically circular, single-stranded DNA molecule of 8100 nucleotides. The DNA is packed in the virion as two antiparallel strands, with a rise per nucleotide in each strand of 3.2 A; it can be assigned spectroscopic properties like those of base-stacked, right-handed, double-stranded DNA. The stoichiometric ratio (n/s) of nucleotides to subunits of the major coat protein is close to 2. The protein subunit contains 52 amino acids, and the DNA sequence of its gene does not encode a signal peptide. The protein conformation in the virion is helical, mostly alpha-helix with perhaps some 3(10)-helix. The amino acid sequence of the DNA interaction domain of the subunit is unique among Inovirus species. On the basis of its coat protein sequence and available theories of helical symmetry in such structures, C2 appears to be either an unusual member of filamentous virus symmetry class II or the defining member of a new symmetry class.

Amino Acid Sequence↗
PubMed1995

Analysis of seven pedigrees of childhood Wilson's disease characterized by abdominal symptoms.

In a survey of childhood Wilson's disease (WD) characterized by abdominal symptoms, three patients with high levels of immunologically detectable ceruloplasmin (CP) in serum were found. These three cases were compared with typical cases of WD in which serum CP level was low. In order to clarify the cause of WD, serum CP levels were quantified by two methods, an immunological protein assay and an oxidase activity assay. Using the results of these two assays, WD cases were classified into three groups on the basis of CP content; the first group consisted of patients with low enzyme activity and low CP protein content, the second group consisted of patients with low enzyme activity and normal CP protein content, and the third group, those patients with normal enzyme activity and normal CP protein content. No significant difference in symptoms was observed between these three groups. Since relatively high levels of CP were detected in some WD patients, genetic variation in CP in WD patients was examined by restriction enzyme fragment length polymorphism analysis using CP cDNA. However, no large deletion in the CP gene was detected. Using four types of gene probes for chromosome 13 known to be related to WD, the DNA of WD patients was examined in a similar fashion, but no significant difference was observed between the groups.

Abdomen↗
PubMed1995

Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR.

During the search for unknown factors involved in motility, we have found that expression of the flagellar master operon flhDC is affected by mutations of the pta and ackA genes, encoding phosphotransacetylase and acetate kinase, respectively (S. Shin, J. Sheen, and C. Park, Korean J. Microbiol. 31:504-511, 1993). Here we describe results showing that this effect is modulated by externally added acetate, except when both pta and ackA are mutated, suggesting the role of acetyl phosphate, an intermediate of acetate metabolism, as a regulatory effector. Furthermore, the following evidence indicates that the phosphorylation of OmpR, a trans factor for osmoregulation, regulates flagellar expression. First, in a strain lacking ompR, the expression of flhDC is no longer responsive to a change in the level of acetyl phosphate. Second, an increase in medium osmolarity does not decrease flhDC expression in an ompR mutant. It is known that such an increase normally enhances OmpR phosphorylation. Third, OmpR protein binds to the DNA fragment containing the flhDC promoter, and its affinity is increased with phosphorylation by acetyl phosphate. DNase I footprinting revealed the regions of the flhDC promoter protected by OmpR in the presence or absence of phosphorylation. Therefore, we propose that the phosphorylated OmpR, generated by either osmolarity change or the internal level of acetyl phosphate, negatively regulates the expression of flagella.

Acetates↗
PubMed1995

Molecular cloning, characterization, and chromosomal mapping of a novel human gene (GTF3A) that is highly homologous to Xenopus transcription factor IIIA.

We have isolated a novel human cDNA that is highly related to Xenopus transcription factor IIIA (TFIIIA). This clone contains an open reading frame of 1,269 nucleotides encoding 423 amino acids, including nine repeats of the Cys2His2-type of zinc-finger domain. A comparison of its sequence with Xenopus TFIIIA revealed 63% identity in nucleic acids and 58% identity in amino acids over a large portion of the gene and predicted peptide, indicating that the human homologue is likely to function as a transcription factor. The zinc-finger domains of the predicted protein also showed homology with those of human genes such as WT1, transcriptional repressor YY1, and MYC-associated zinc-finger protein (MAZ). Northern analysis showed expression in various tissues examined. The human TFIIIA gene (GTF3A) was localized to chromosome band 13q12.3-->q13.1 by fluorescent in situ hybridization (FISH).

Amino Acid Sequence↗
PubMed1995

Adhalin gene mutations in patients with autosomal recessive childhood onset muscular dystrophy with adhalin deficiency.

Homozygous adhalin gene mutations were found in three patients from two consanguineous families with autosomal recessive childhood onset muscular dystrophy. Muscle biopsies from patients in each family showed complete absence of adhalin. Sequencing of adhalin cDNA prepared from skeletal muscle by reverse transcription PCR demonstrated a cytosine to thymidine substitution at nt 229 in the patient in family 1 and an adenine to guanine substitution at nt 410 and a 15-base insertion between nt 408 and 409 in the two patients in family 2. Sequencing of genomic DNA prepared from peripheral blood leukocytes by PCR confirmed these mutations. The parents in each family were found to be heterozygous for the respective mutations. These adhalin gene mutations are presumed to be responsible for the absence of adhalin in the skeletal muscle. Adhalin deficiency likely causes disruption of the muscle cell membrane, resulting in dystrophic changes in the skeletal muscle similar to dystrophin deficiency in Duchenne muscular dystrophy.

Adult↗
PubMed1995

Recurrent Cushing's disease associated with nephrotic syndrome.

A case of recurrent Cushing's disease with nephrotic syndrome due to membranoproliferative glomerulonephritis (MPGN) is presented. Functional pituitary adenoma recurred 6 years after transsphenoidal pituitary adenomectomy. Due to infiltration into the surrounding tissues, transcranial surgery was performed. However, this failed to induce a remission and thus gamma knife therapy was applied. Histopathological evaluation revealed that the glomerular lesions had progressed to a rather advanced stage of MPGN. Although this association could be coincidental, the recurrence of pituitary macroadenoma might be induced by the cessation of steroid treatment for the nephrotic syndrome.

Adult↗
PubMed1995

[Laser-TURP with a lateral firing fiber for contact irradiation].

We have operated 25 BPH patients with transurethral Nd-YAG laser ablation for prostate from June of 1993 till December of 1993. We used UltraLine fiber for contact laser irradiation of the prostate. This is a lateral firing quartz fiber with high density laser energy output, and so made it possible for us to vaporize prostatic tissue rapidly and deeply. We used 60 Watts of power for all cases. For the prostates larger than 50 cm3, limited resection after laser ablation allowed early relief of patients' symptoms. Two months after the treatment, average flow rate improved from 3.7 ml/sec to 7.8 ml/sec. Volume of residual urine decreased from 48.4 ml to 17.0 ml. Twenty-four percent decrease of prostatic volume was also recognized with transrectal sonography. Only 4 patients complained of transient urinary retention, although another 3 or 5 days catheter placement relieved their symptoms. Bleeding was negligible and the other postoperative complications were not recognized at all. Laser-TURP is a new treatment that is effective, less morbid and economical, compared with the ordinary TUR-P. So it will soon become an alternative method to electrocautery TUR-P.

Aged↗
PubMed1995

Efficacy of interferon alfa therapy in chronic hepatitis C patients depends primarily on hepatitis C virus RNA level.

To clarify the viral factors that may predict the therapeutic effect of interferon (IFN) in chronic hepatitis C (CHC) patients, we investigated the quantitative serum hepatitis C virus (HCV) RNA level, genotype, and liver biopsy histological features in 60 patients who were treated with 360 x 10(6) U of natural IFN-alpha for 36 to 48 weeks and for more than 12 months after therapy. A branched DNA (bDNA) assay was used to measure HCV RNA levels. All responders, defined as those individuals with normal alanine transaminase (ALT) levels at 48 weeks after therapy, had less than 2 x 10(6) HCV RNA Eq/mL before administration of IFN. Of 39 patients with RNA levels (less than 2 x 10(6) Eq/L) 23 (59.0%) were responders. The genotype was determined for each patient using type-specific polymerase chain reaction (PCR) primers. There was a significant difference in rate of response between subtype 1b and subtypes 2a and 2b (P < .0002); however, all responders had less than 2 x 10(6) Eq/L independent of genotype. In a multivariate analysis, RNA level was the most statistically significant factor affecting response to IFN. Although disease severity, as defined by histological features, was not statistically correlated with nonresponse, patients that responded to IFN tended to have less severe disease.

Adult↗
PubMed1995

[Detection of loss of heterozygosity by microsatellite probe and DNA content analysis].

We examined replication error (RER) and loss of heterozygosity (LOH) in the region of microsatellites in 60 cases of resected lung cancer. We used microsatellite probes for the short arm of the 2nd chromosome (D2S123, D2S136), the short arm of the 3rd chromosome (D3S1067), and the short arm of the 17th chromosome (TP53). According to stage, the frequency of LOH was 25% in stage I, 33% in stage II, 44% in stage IIIA, 11% in stage III B, and 63% in stage IV. According to histological classification, the frequency of LOH was 41% for squamous cell carcinoma, 24% for adenocarcinoma, and 100% for small cell carcinoma. According to microsatellite probe results, the frequency of LOH was 6.7% for D2S123, 5.0% for D2S136, 16.7% for D3S1067, and 18.3% for TP53. Two of the 60 cases showed RER. One case was stage I squamous cell carcinoma, and the other was stage IV adenocarcinoma. Except for stage III B,LOH in the microsatellite region increases with the stage. LOH is often detected in the order of small cell carcinoma, squamous cell carcinoma, and adenocarcinoma. According to the chromosome number, LOH is detected more often in the 3rd and 17th chromosomes than in the 2nd chromosome. In 20 cases with LOH, only two showed DNA diploidy. Compared to LOH of the microsatellite region, DNA content analysis by flow cytometry has accuracy problems.

Aneuploidy↗
PubMed1995

[Detection of K-ras mutation from malignant cells in sputum with mutant-allele specific amplification (MASA) method].

Sputum cells from 44 lung cancer patients (22 adenocarcinoma, 19 squamous cell carcinoma and 3 small cell carcinoma cases) were examined to contain mutant K-ras genes. The mutant-allele-specific amplification (MASA) method was used for detection of K-ras point mutations. The reaction was designed to amplify only mutant codons with polymerase chain reaction (PCR). Codons 12, 13 and 61 were studied with synthesized primers. Two cases (primary adenocarcinoma of the lung and pancreas adenocarcinoma with lung metastasis) were positive for point mutations at codon 12. The mutation of GGT to GTT was found in the first case and to GAT in the second one. Further experiments with colony hybridization revealed the mutations were found in 1% of alleles in both cases. There were no point mutations found at codon 13 nor 61. Our experiments showed it is possible to detect K-ras mutation in sputum cells from lung cancer patients, with MASA method.

Adenocarcinoma↗
PubMed1994

Molecular cloning and expression of a novel human gene that is highly homologous to human FK506-binding protein 12kDa (hFKBP-12) and characterization of two alternatively spliced transcripts.

We isolated a novel gene encoding a protein highly homologous to human FK506-binding protein 12kDa (hFKBP-12) from a human fetal brain cDNA library and determined the full-length cDNA sequence. The cDNA clone contained the open reading frame of 324 nucleotides encoding 108 amino acid and revealed 76% identity in DNA sequence and 88% identity in predicted amino acid sequence with hFKBP-12. The DNA and amino-acid sequence of this gene, designated OTK4, also had homology with other FKBPs in species ranging from humans to prokaryotes. Recombinant protein, produced in E.coli transformed by a pGEX2T expression vector containing the OTK4 cDNA and purified, showed peptidyl-prolyl cis-trans isomerase activity like other FKBP proteins. An alternatively spliced form of the transcript found in the cDNA library contained a 45-bp insertion which included a stop codon. Although the biological function of the truncated version of OTK4 is unknown, both transcripts were ubiquitously expressed in human tissues examined by the reverse-transcriptase PCR (RT-PCR) method.

Alternative Splicing↗
PubMed1994

Immunoreactive hepatocyte growth factor is a strong and independent predictor of recurrence and survival in human breast cancer.

Hepatocyte growth factor (HGF) is a stromally derived modulator of epithelial cell proliferation and motility. In the present study, we have measured immunoreactive (ir)-HGF concentration in tumor extracts of 258 primary human breast cancers using an enzyme-linked immunosorbent assay and have evaluated its association with disease-free and overall survival. The median value of ir-HGF concentration was 11.0 ng/100 mg protein (range, 1.4-566.7 ng/100 mg protein). Correlation analyses between ir-HGF concentration and clinicopathological factors showed that the ir-HGF level was correlated only with tumor size (P = 0.05). No significant associations were found between ir-HGF content and age, menopausal status, nodal status, histological type, histological grade, vessel involvement, estrogen receptor, progesterone receptor, type of surgery, or postoperative adjuvant therapy. Breast cancer patients with high ir-HGF concentration had a significantly shorter relapse-free (P = 0.001) and overall survival (P = 0.001) rate when compared to those with low ir-HGF concentration at the cutoff point of 21.7 ng/100 mg protein, which was determined in another group of 82 patients. In multivariate analysis, ir-HGF level was found to be the most important independent factor in predicting relapse-free and overall survival, of greater import than lymph node involvement. The putative role of HGF in breast cancer growth and metastasis is hereby strengthened.

Adult↗
PubMed1994

Relationship between plasma adenosine concentration and breathing movements in growth-retarded fetuses.

OBJECTIVE: The purpose of this study was to investigate the relationship between plasma adenosine concentration and breathing movements in growth-retarded fetuses. STUDY DESIGN: We measured the incidence of fetal breathing movements and breathing rate immediately before cordocentesis in 26 growth-retarded fetuses at 31 to 38 weeks' gestation. Blood retrieved by cordocentesis was then analyzed for umbilical venous plasma adenosine concentration, blood gases, and pH. RESULTS: In growth-retarded fetuses with hypoxia and acidosis plasma adenosine concentration was elevated and the incidence of fetal breathing movements was reduced. The change in plasma adenosine concentration correlated inversely and significantly with the incidence of fetal breathing movements. CONCLUSION: Decreased breathing movements correlate with elevated plasma adenosine concentration in fetuses. We postulate that the enhanced adenosine formation in growth-retarded fetuses may modulate the inhibition of fetal breathing movements.

Adenosine↗
PubMed1994

A detection method for point mutation in the precore region of human hepatitis B virus (HBV)-DNA using mutation-site-specific assay.

In the natural progression of acute active hepatitis and chronic active hepatitis in human hepatitis B virus (HBV)-infected patients, inactive hepatitis develops by seroconversion, which can be explained by the disappearance of HBe antigen. However, it has been found that in some patients with hepatitis, alanine aminotransferase levels undergo fluctuation even though their serum is negative for HBe antigen. In these patients, HBV-DNA has been detected in the serum and the HBV-DNA so detected has been considered a cause of worsening liver function. Most HBV-DNA detected in these cases has a point mutation from G to A at the 83rd base in the precore region. As a result of this point mutation, HBV is unable to produce HBe antigen. We have devised a sensitive polymerase chain reaction (PCR) method, a mutation-site-specific assay, for the detection of point mutations at the 83rd base in the precore region using a specific mutation-trapped oligonucleotide primer for the mutant HBV genome.

Base Sequence↗