• Korean Journal of Clinical Laboratory Science
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• v.39 no.1
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• pp.49-55
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• 2007

HCV is a single-stranded RNA virus and more than 1 million new cases are reported annually worldwide. The six major HCV genotypes and numerous subtypes vary in their geographic distribution. It is thought that genetic heterogeneity of HCV may account for some of the differences in disease outcome and response to treatment observed in HCV infected persons. In this study, we determined HCV genotypes among chronic Korean HCV patients and evaluated direct sequence PCR protocols developed. For the study, 232 chronic HCV patient sera were used. HCV RNA was extracted and two pairs of consensus PCR primers were selected in 5'UTR region for amplification of HCV RNA. Amplification products obtained from the HCV positive cases were subjected to automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. From this study, five HCV genotypes, 1b, 2a, 2b, 2c and 3a were found. HCV genotypes 4, 5 and 6 were not determined. HCV genotype 1b (53.9%, 125/232) and 2a (35.8%, 83/232) were most frequently found. This group was followed by 2b (3.9%, 9/232), 3a (3.4%, 8/232) and 2c (3.0%, 7/232). The data presented here suggest a complex distribution of HCV types and they were well correlated with other reports on Koreans and will be helpful for type-specific follow-up of Korean HCV patients. This study showed that 5'UTR direct sequence analysis is a sensitive and rapid method to identify HCV genotypes.

• Journal of Animal Science and Technology
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• v.60 no.12
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• pp.32.1-32.10
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• 2018

Background: Necdin (NDN), a member of the melanoma antigen family showing imprinted pattern of expression, has been implicated as causing Prader-Willi symptoms, and known to participate in cellular growth, cellular migration and differentiation. The region where NDN is located has been associated to QTLs affecting reproduction and early growth in cattle, but location and functional analysis of the molecular mechanisms have not been established. Methods: Here we report the sequence variation of the entire coding sequence from 72 samples of cattle, yak, buffalo, goat and sheep, and discuss its variation in Bovidae. Median-joining network analysis was used to analyze the variation found in the species. Synonymous and non-synonymous substitution rates were determined for the analysis of all the polymorphic sites. Phylogenetic analysis were carried out among the species of Bovidae to reconstruct their relationships. Results: From the phylogenetic analysis with the consensus sequences of the studied Bovidae species, we found that only 11 of the 26 nucleotide changes that differentiate them produced amino acid changes. All the SNPs found in the cattle breeds were novel and showed similar percentages of nucleotides with non-synonymous substitutions at the N-terminal, MHD and C-terminal (12.3, 12.8 and 12.5%, respectively), and were much higher than the percentage of synonymous substitutions (2.5, 2.6 and 4.9%, respectively). Three mutations in cattle and one in sheep, detected in heterozygous individuals were predicted to be deleterious. Additionally, the analysis of the biochemical characteristics in the most common form of the proteins in each species show very little difference in molecular weight, pI, net charge, instability index, aliphatic index and GRAVY (Table 4) in the Bovidae species, except for sheep, which had a higher molecular weight, instability index and GRAVY. Conclusions: There is sufficient variation in this gene within and among the studied species, and because NDN carry key functions in the organism, it can have effects in economically important traits in the production of these species. NDN sequence is phylogenetically informative in this group, thus we propose this gene as a phylogenetic marker to study the evolution and conservation in Bovidae.

• Molecules and Cells
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• v.45 no.12
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• pp.886-895
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• 2022

Malignant rhabdoid tumor (MRT) is a highly aggressive pediatric malignancy with no effective therapy. Therefore, it is necessary to identify a target for the development of novel molecule-targeting therapeutic agents. In this study, we report the importance of the runt-related transcription factor 1 (RUNX1) and RUNX1-Baculoviral IAP (inhibitor of apoptosis) Repeat-Containing 5 (BIRC5/survivin) axis in the proliferation of MRT cells, as it can be used as an ideal target for anti-tumor strategies. The mechanism of this reaction can be explained by the interaction of RUNX1 with the RUNX1-binding DNA sequence located in the survivin promoter and its positive regulation. Specific knockdown of RUNX1 led to decreased expression of survivin, which subsequently suppressed the proliferation of MRT cells in vitro and in vivo. We also found that our novel RUNX inhibitor, Chb-M, which switches off RUNX1 using alkylating agent-conjugated pyrrole-imidazole polyamides designed to specifically bind to consensus RUNX-binding sequences (5'-TGTGGT-3'), inhibited survivin expression in vivo. Taken together, we identified a novel interaction between RUNX1 and survivin in MRT. Therefore the negative regulation of RUNX1 activity may be a novel strategy for MRT treatment.

• Investigative Magnetic Resonance Imaging
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• v.12 no.2
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• pp.178-187
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• 2008

Purpose : To evaluate and compare the diagnostic accuracy of MRI and ultrasound(US) for estimation of invasion depth of gastric carcinoma by correlation with histopathologic findings in vitro and to find out the best MR pulse sequence for detection and accurate delineation of tumor. Materials and Methods : Resected specimen of total or subtotal gastrectomy from 53 patients with gastric carcinoma were done of imaging studies of MRI and US. And US was examined by using high frequency linear transducer for tumor invasion depth by a radiologist. In each case, both imaging findings of MRI and US were evaluated independently for tumor detection and invasion depth by consensus of two radiologists and were compared the diagnostic accuracy between two imaging modalities according to the histopathologic findings. MR imaging with five MR pulse sequences, spin echo T1 and in- and out-of phase gradient echo T1 weighted images, FSE and SSFSE T2 weighted images, were performed. Five MR pulse sequences were evaluated and compared on the point of detection and accurate distinction of tumor from surrounding normal tissue. Results : In EGC, diagnostic accuracy of US(77%) was superior than that of MRI(59%) but no statistically significant difference was noted between two imaging modalities(p=0.096). In AGC, both imaging modalities of MRI and US showed relatively high diagnostic accuracy as 97% and 84% respectively. Diagnostic accuracy of MRI was statistically better than that of US at the significant level(p<0.001). The best MR pulse sequence among five in each specimen was FSE T2WI(75.5%, 40/53) in both EGC and AGC. In AGC, FSE T2WI showed excellent imaging quality by showing very high ratio (93.5%, 29/31) of accurate delineation of tumor. Conclusion : MRI and US show relatively high diagnostic accuracy in the evaluation of tumor invasion depth of resected specimen in AGC. The most excellent pulse sequence of MRI for the evaluation of tumor invasion depth is FSE T2WI on the point of detection and accurate delineation of tumor in both EGC and AGC.

• Horticultural Science & Technology
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• v.34 no.2
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• pp.305-313
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• 2016

Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U's triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety 'Blackgat' was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.

• Investigative Magnetic Resonance Imaging
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• v.18 no.3
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• pp.200-207
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• 2014

Purpose : We evaluated the diagnostic value of susceptibility-weighted imaging (SWI) for the detection of developmental venous anomaly (DVA). Materials and Methods: Retrospective review of 1068 brain MR examinations found 28 DVAs in 28 patients (2.6%) on contrast-enhanced T1-weighted images. SWI, T2, and FLAIR images of 28 patients with DVA and 28 sex- and age-matched control patients without DVA were analyzed by blinded readers on each type of sequences. All images were independently reviewed by two radiologists who were blinded to other MR imaging finding. In cases of discrepancy, two reviewers reached a consensus later. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of each MR sequence for the detection of DVA were determined. Statistical analysis was performed by using the Mcnemar test. The significance level was p < 0.05. Results: The sensitivity, specificity, PPV, and NPV of SWI for the detection of DVA were 85.7%, 92.9%, 92.3%, and 86.7%, respectively. T2 and FLAIR images showed sensitivity of 35.7% and 35.7%, specificity of 92.9% and 96.4%, PPV of 83.3% and 90.9%, and NPV of 59.1% and 60.0%, respectively. On SWI, the sensitivity and NPV for the detection of DVAs were significantly higher than those of T2 and FLAIR images (p < 0.05). Conclusion: SWI was sensitive and specific for the detection of DVA.

• Journal of Life Science
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• v.17 no.2 s.82
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• pp.167-173
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• 2007

To study the transcriptional mechanisms by which expression of the murine glial cell-derived neurotrophic factor inducible transcription factor (mGIF) gene is regulated, a murine genomic clone was iso-lated using a mGIF cDNA as probe. A 13-kb genomic fragment, which comprises 4-kb upstream of the transcription initiation site was sequenced. The promoter region lacks a TATA box and CAAT box, is rich in G+C content, and has multiple putative binding sites for the transcription factor Spl. The mGIF gene also has consensus sequences for AP2 binding sites. The transcriptional activity of five deletion mutants of a 2.1-kb fragment was analyzed by modulating transcription of the heterologous luciferase gene in the promoterless plasmid pGL2-Basic. All mutants showed significant transcriptional activity in the murine neuroblastoma cell line NB41A3. Transient expression assays suggested the presence of a positive regulator between -213 and -129 while a negative regulator was found in the region between -806 and -214. Relatively strong transcriptional activity was observed in neuronal NB41A3, glial C6 cells and hepatic HepG2, but very weak activity in skeletal muscle C2C12 cells. These findings confirm the tissue-specific activity of the mGIF promoter and suggest that this gene shares structural and functional similarities with the dopamine receptor genes that it regulates.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.2
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• pp.99-104
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• 2006

Human Papilloma viruses (HPVs) are etiological agents for cervical cancer and are classified into low- and high-risk categories. The aim of this study was to determine the frequency of the HPV genotype in the HPV screening test of Korean women using PCR-direct sequencing. Consensus primers of L1 legion were used for the amplification of HPV DNA and the PCR products (450 bps) obtained were analyzed by automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. Cervical swab samples of 3,978 women (20-73 years) were tested and the average age was 37.6 years. In this study, 1,174 samples were HPV positive out of 3,978 cervical swab samples screened (29.5%) and 136 samples (11.6%) showed a double infection. A total of 1,310 HPV genotypes were analyzed. The HPV positive rate was the lowest in the 20 years group (69.5%) and most of the samples of the > 60 years group were found HPV positive. Among thirty seven different HPV types identified by sequencing, 21 were HPV high risk types and 16 HPV low risk types were 69.8% (914/1,310) and 26.0% (340/1,310), respectively. In HPV high-risk types, 16 (13.21%), was the most frequently found. HPV 53 (9.62%) and 58 (9.24%) were also frequently found. This group was followed by HPV types 70 (5.50%), 33 (4.73%), 66 (4.20%), 18 (4.05%), 52 (4.05%), 31 (3.97%) and 56 (3.51%) in descending order of frequency. Among HPV low-risk types, 62 (4.20%), 6 (3.59%), 81 (3.59%), 84 (3.51%), and 11 (2.6%) were frequently found. In conclusion, PCR-direct sequencing could be used for quick and reliable typing of known and novel HPVs from clinical specimens. This data could be useful for epidemiological study of HPV and it also allows type-specific follow-up of women who have been treated for cervical intraepithelial neoplasia.