• Tuberculosis and Respiratory Diseases
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• v.54 no.4
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• pp.367-377
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• 2003

Background : It is well known that only 10% of those infected with Mycobacterium tuberculosis actually develop clinical disease, indicating the existence of host genetic factors regulating disease expression. In this study, we investigated HLA-DRB1 and -DQB1 gene polymorphisms in Korean patients with pulmonary tuberculosis (PTB). Methods : HLA-DRB1 and -DQB1 gene polymorphisms were investigated in 67 PTB patients without previous treatment history, 38 drug-sensitive (DS) and 29 multidrug-resistant (MDR) cases, and 200 healthy controls. HLA-DRB1 typing was done using reverse SSO (sequence specific oligonucleotide) and PCR-SSCP (single strand conformational polymorphism) methods and DQB1 typing was done using PCR-RFLP (restriction fragment length polymorphism), PCR-SSCP and PCR-SSP (sequence specific primer) methods. Results : Among the PTB patients, MDR-TB cases showed frequencies of DRB1*0701 and *08032 increased by about two-fold compared to those of normal controls, and likewise for their associated DQB1 alleles, DQB1*0202 and *0601 (15.5% vs. 34.5%, p=0.01). The frequency of HLA-DQB1*0609 was significantly increased in PTB patients (4.0% vs. 14.9%, p=0.004), showing similar increases in both DS and MDR cases. There was also an association of HLA alleles with the clinical severity of the disease according to the extent of lung lesion. Significantly increased frequencies of DRB1*08032 (4.2% vs. 32.6%, p=0.007) and DQB1*0601 (12.5% vs. 34.9%, p=0.047) were observed in more advanced (moderately & far advanced/DS and far advanced/MDR), compared with less advanced (minimal/DS and moderately advanced/MDR) lung lesions. Although DRB1*0701, DQB1*0202 and DQB1*0609 showed significant increases in different subsets of the disease, these HLA alleles did not show consistent association with disease severity. Conclusion : HLA-DRB1*08032 and DQB1*0601 alleles were associated with genetic susceptibility to MDR-TB in Korean patients, and also with disease severity and progression of PTB.

• Korean Journal of Poultry Science
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• v.43 no.4
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• pp.273-279
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• 2016

Recently, it was reported that certain polymorphisms in the growth hormone secretagogue receptor gene (GHSR) are associated with the growth of chickens. However, the correlation between GHSR polymorphisms and economic traits has not been investigated in Korean native chickens (KNCs). Therefore, the objective of this study was to confirm the suitability of the GHSR gene as a candidate for genomic selection and identify a genetic marker for KNCs. A total of 220 KNCs from six breeds raised at the National Institute of Animal Science were genotyped for the c.739+726 SNP in the GHSR gene using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP), and the sequence for a subset of 30 birds was analyzed using direct sequencing. The association between the SNP genotypes and the economic traits of the KNCs was analyzed using the statistical package for the social science (SPSS) software program. The association analysis between the c.739+726T>C SNP and economic traits revealed that the SNP was significantly associated with body weight at 150 and 270 days (BW150 and BW270, respectively) in all KNCs (p<0.01), BW150 in KNC (Gary) (p<0.05), and egg production number in KNC (White, p<0.05). In addition, the SNPs discovered using direct sequencing (513A>G, 517A>T) had a significant effect on the body weight and egg production traits (p<0.05). In conclusion, these results might be useful as a basis for studies on the improvement of KNC breeds. Furthermore, these results suggest that the SNPs (c.739+726T>C, 513A>G, and 517A>T) located in the GHSR gene could be useful molecular genetic markers for KNCs.

• Clinical and Experimental Pediatrics
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• v.45 no.10
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• pp.1263-1272
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• 2002

Purpose : Rett syndrome(RTT) is an X-linked dominant neurodevelopmental disorder affecting 1 per 10,000-15,000 female births worldwide. It was initially described by Andreas Rett in 1966. RTT involves developmental regression characterized stereotypic hand movements, tremors, gait apraxia, seizures, deceleration of head growth after the age of 6-18 months. The disease-causing gene was identified as MECP2 on chromosome Xq28. We carried out mutational analysis of MECP2 genes in RTT patients. Methods : Whole blood(5 cc) of 34 sporadic RTT patients was collected in EDTA-anticoagulated tubes. Genomic DNA was extracted from peripheral blood using the E.Z.N.A. blood DNA kit. Four exons of the MECP2 gene were amplified by PCR in 34 Korean with RTT. We carried out PCR divided the exon three into two parts and the exon four into five parts. Primer sequences designed by Amir et al. in 1999 were almost used(AF030876). Sequencing primers used were the same as PCR. DNA sequencing reactions were performed using an ABI 377 DNA sequencer and ABI PRISM dye terminator cycle sequencing reaction kit(Perkin-elmer). The results were compared with the normal DNA sequence(X99686). To confirm the change of sequence on novel mutations, RFLP analysis was performed. Results : The MECP2 mutations were detected in 23(67.6%) of the 34 patients. The mutations consisted of 12 different types including nine missense and three nonsense mutations. Of these, three (L100V, G161E and T311M) mutations were newly identified. Most of the mutations discovered are located within MBD(39.1%) and TRD(39.1%). In this study, three(T158M, R270X, R306C) mutations were identified high frequency. Conclusion : MECP2 gene was also an important cause of Korean RTT patients. MECP2 gene study is an important tool for diagnosis of Korean RTT patients.

• Tuberculosis and Respiratory Diseases
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• v.50 no.5
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• pp.568-578
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• 2001

Background : Lung cancer is frequently cited as an example of a disease caused solely by exposure to environmental carcinogens. However, there is a growing realization that the genetic constitution is also important in determining individual's susceptibility to lung cancer. This genetic susceptibility may result from functional polymorphims of the genes involved in carcinogen metabolism. In this study, the association between GSTM1 and CYP1A1 polymorphisms and the lung cancer risk in Korean males was investigated. Materials and Method : The study population consisted of 153 male lung cancer patients and 143 healthy male controls. The GSTM1 and CYP1A1 genotypes were determined by multiplex PCR and PCR-RFLP analysis. Result : There were no significant differences in the frequency of the GSTM1 null genotype between the cases and the controls. When the cases were categorized by their histologic type, the frequency of the GSTM1 null genotype in the small cell carcinoma group was higher than those of the controls(67.2% vs 55.9%), but the difference was not statistically significant(OR=1.772 ; 95% CI=0.723-4.340). The distribution of the CYP1A1 MspI genotypes among the cases were similar to those among the controls. When the cases were grouped by their histologic type, the ml/m1, ml/m2, m2/m2 genotypes frequencies among the small cell carcinomas(23.0%, 38.5%, and 38.5%, respectively) were significantly different from those of the controls(36.4%, 46.2%, and 7.4%, respectively, p<0.05). When the m1/m1 genotype was used as a reference, the ml/m2 and m2/m2 genotypes were associated with an increased risk for small cell lung cancer(ml/m2 genotype : OR=1.337, 95% CI=0.453-3.947 ; m2/m2 genotype : OR=3.374, 95% CI=1.092-10.421). Conclusion : These results suggest that the GSTM1 and CYP1A1 genotypes may be a genetic determinant of the risk for lung cancer, particlulary small cell carcinoma. Further investigation is needed to confirm these results.

• Tuberculosis and Respiratory Diseases
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• v.40 no.2
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• pp.98-103
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• 1993

Background: Inactivation of retinoblastoma gene (Rb) has been observed in a variety of human cancers. Loss of heterozygosity (LOH) of Rb which is a common mode of allelic inactivation of Rb, has been known as a frequent genetic event in small cell lung cancer but it has been detected less frequently in non-small cell lung cancer. To define the role of Rb deletion in lung cancer, we investigated the genomic DNAs of 43 non-small cell lung cancers and 1 small cell lung cancer paired with normal lung tissues obtained by thoracotomy. Methods: The genomic DNAs were obtained by the digestion with proteinase K followed by phenol-chloroform extraction method. The genomic DNAs were digested by restriction endonuclease (EcoRI), separated by agarose gel electrophoresis, transferred to nylon membrane by Southern blot transfer and then hybridized with labelled Rb 1 probe which contains. 1.4 kb sized DNA sequence containing N-terminal portion of Rb. Results: In 26 squamous cell lung cancers, 16 cases were informative after EcoRI digestion and LOH of Rb was found in 10 cases (62.5%). In 17 adenocarcinomas of lung, 11 cases were informative and LOH of Rb was found in five cases (45.4%). The analysis of clinical parameters revealed no significant differences between the two groups with or without LOH of Rb in the aspects of age, sex, degree of differentiation, stage and smoking amount. Conclusions: These results suggest that Rb inactivation is also significantly involved in the molecular pathogenesis of non-small cell lung cancer.

• Tuberculosis and Respiratory Diseases
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• v.52 no.1
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• pp.5-13
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• 2002

Background: DNA repair plays a crucial role in protecting the genome from cancer-causing agents. Therefore, a reduced DNA repair capacity can increase the susceptibility to cancer. The human OGG1 (hOGG1) gene encodes DNA glycosylase/apurinic lyase and excise 8-hydroxyguanine, one of the major premutagenic DNA lesions, which is produced by oxygen radical forming agents including smoking. Recently several polymorphisms in the hOGG1 gene were identified, and it is possible that these polymorphism') may affect the DNA repair capacity and thus modulate cancer susceptibility. The relationship between the codon 326 polymorphism (Ser to Cys) in the hOGG1 gene and lung cancer risk was investigated. Materials and Method: The Ser326Cys genotypes were determined using PCR-RFLP analysis in 299 primary lung cancer patients and 186 healthy controls who were frequency (case:control=3:2) matched according to age and sex. Result: The frequencies of the Ser326Cys genotypes (Ser/Ser, Ser/Cys and Cys/Cys) among cases (23.4%, 51.8%, and 24.7%, respectively) were not significantly different from those among the controls (22.6%,52.1% and 25.3%, respectively). When the analyses were stratified according to age, sex, smoking status and packyears of smoking, no significant association between this polymorphism and lung cancer risk was found. Moreover, the Ser326Cys genotype showed no apparent relationship with any of the histological types of lung cancer. Conclusion: These result suggest that the hOGG1 Ser326Cys polymorphism is not a major contributor to individual lung cancer susceptibility in Koreans.

• Tuberculosis and Respiratory Diseases
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• v.58 no.4
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• pp.359-366
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• 2005

Background : IGFBP-3 inhibits the mitogenic and anti-apoptotic activity of IGF by blocking the binding of IGF to its receptor. However, under certain circumstances, IGFBP-3 can enhance the activity of IGF by protecting IGF from its degradation. More than half of the interindividual variations in IGFBP-3 levels are known to be genetically determined by the polymorphism at -202 locus of IGFBP-3 gene. Method : We attempted to ascertain whether A-202C polymorphic variation of IGFBP-3 gene constitutes a risk factor for non-small cell lung cancer (NSCLC), using PCR-restriction fragment length polymorphism (RFLP). Our study included 104 NSCLC patients and 104 age-, gender-, and smoking status-matched control subjects. Result : In the 104 NSCLC subjects, the genotypic frequencies at the -202 site were as follows: AA = 67 (64.4%), AC = 35 (33.7%), and CC = 2 (1.9%). We did detect significant differences in the genotypic distribution between the NSCLC and the control subjects (p<0.05), and the NSCLC risk correlated significantly with AA genotype at the -202 locus (AA>AC>CC). Using CC genotype as a reference, the odds ratio (OR) for the subjects with AC genotype was 2.60 (95% CI: 0.89 - 8.60), and the OR associated with AA genotype was 5.89 (95% CI: 1.92 - 21.16). Conclusion : These results indicate that the dysregulation of IGF axis should now be considered as another important risk factor for NSCLC, and a potential target for novel antineoplastic therapies and/or preventative strategies in high-risk groups.

• Radiation Oncology Journal
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• v.24 no.1
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• pp.30-36
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• 2006

Purpose: It is well known from clinical experience that acute complications of chemoradiation therapy vary from patients to patients. However, there are no known factors to predict these acute complications before treatment starts. The human XRCC1 gene is known as a DNA base excision repair gene. We investigated the possibilities of XRCC1 gene polymorphisms as a predictor for the acute complications of chemoradiation therapy in colorectal cancer patients. Materials and Methods: From July 1997 to June 2003, 86 colorectal cancer patients (71 rectal cancer, 13 sigmoid colon cancer and 2 colon cancer patients) were treated with chemoradiation therapy at the Department of Radiation Oncology, Inha University Hospital. Twenty-two patients were in stage B, 50 were in stage C, 8 were in stage D and 6 patients were unresectable cases. External radiation therapy was delivered with 10MV X-ray at a 1.8 Gy fraction per day for a total dose of radiation of $30.6{\sim}59.4 Gy$ (median: 54 Gy). All the patients received 5-FU based chemotherapy regimen. We analyzed the acute complications of upper and lower gastrointestinal tract based on the RTOG complication scale. The initial and lowest WBC and platelet count were recorded during both the RT period and the whole treatment period. Allelic variants of the XRCC1 gene at codons 194, 280 and 399 were analyzed in the lymphocyte DNA by performing PCR-RFLP. Statistical analyses were carried out with the SAS (version 6.12) statistical package. Results: When all the variables were assessed on the multivariate analysis, recurrent disease revealed the factors that significantly correlated with upper gastrointestinal acute complications. Arg399Gln polymorph isms of the XRCC1 gene, the radiation dose and the frequencies of chemotherapy during radiation therapy were significantly correlated with lower gastrointestinal complications. Arg399Gln polymorph isms also affected the decrease of the WBC and platelet count during radiation therapy. Conclusion: Although the present sample size was too small for fully evaluating this hypothesis, this study suggests that Arg399Gln polymorph isms of the XRCC1 genes may be used as one of the predictors for acute complications of chemoradiation therapy in colorectal cancer patients.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.116-124
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• 2006

In this study was performed to analyze quantitatively the number of viable but non-culturable bacteria in the Pine and Quercus forest soil by improved direct viable count (DVC) and plate count (PC) methods. The number of living bacteria of Pine and Quercus forest soil by PC method were less then 1% of DVC method. This result showed that viable but non-culturable (VBNC) bacteria existed in the forest soil with high percentage. Diversity and structure of VBNC bacterial populations in forest soil were analyzed by direct extracting of DNA and 16S rDNA-ARDRA from Pine and Quercus forest soil. Each of them obtained 111 clones and 108 clones from Pine and Quercus forest soil. Thirty different RFLP types were detected from Pine forest soil and twenty-six different RFLP types were detected from Quercus forest soil by HeaIII. From ARDRA groups, dominant clones were selected for determining their phylogenetic characteristics based on 16S rDNA sequence. Based on the 16S rDNA sequences, dominant clones from ARDRA groups of Pine forest soil were classified into 7 major phylogenetic groups ${\alpha}$-proteobacteria (12 clones), ${\gamma}$-proteobacteria (3 clones), ${\delta}$-proteobacteria (1 clone), Flexibacter/Cytophaga (1 clone), Actinobacteria (4 clones), Acidobacteria (4 clones), Planctomycetes (5 clones). Also, dominant clones from ARDRA groups of Quercus forest soil were classified into 6 major phylogenetic groups : ${\alpha}$-proteobacte,ia (4clones), ${\gamma}$-proteobacteria (2 clones), Actinobacteria (10 clones), Acidobacteria (8 clones), Planctomycetes (1 clone), and Verrucomicobia (1 clone). Result of phylogeneric analysis of microbial community from Pine and Quercus forest soils were mostly confirmed at uncultured or unidentified bacteria, VBNC bacteria of over 99% existent in forest soil were confirmed variable composition of unknown micro-organism.

• Journal of Life Science
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• v.17 no.3 s.83
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• pp.386-395
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• 2007

A total of 27 strains of Vibrio parahaemolyticus (18 strains isolated from Korea and 9 strains from Japan) were serotyped and examined for biochemical characteristics, antimicrobial susceptibility patterns, cytotoxicity assay, thermostable direct hemolysin (TDH) production and molecular epidemiology. Using polymerase chain reaction (PCR) method and DNA probe hybridization method, the strains were tested for toxR, tdh, trh and ORF 8 genes. The V. parahaemolyticus isolated from patients were belonged to 8 different serotypes : O3:K6, O1:K38, O3:K57, O4:K9, O4:Kl2, O4:K68, O5:Kl5 and O6:K46. Urease-positive strain possessed the trh gene, and conversely, urease-negative strains lacked the gene, indicating that urease production by V. parahemolyticus strains strongly correlates with the possession of the trh gene. Most strains showed multiple resistant to more than three antibiotics and the antibiogram could be classified into 6 group (I to VI). All of the O3:K6 strains isolated in South Korea and Japan producted TDH at high levels. The TDH titers ranged between 256 and 2.048, and the average titer was 1009. To distinguish the new and increasingly common V. parahaemolyticus strains from clinical isolates, ORF 8 is a useful genetic marker. After Southern hybridization, the HindIII restriction fragment patterns of the tdh gene were grouped one type, respectively. One type showed two bands one of which was 4.3kb and the other was 11.5kb in size. Variation between the O3:K6 serotype are minor when compared to the differences seen with the non O3:K6 strains. The migration patterns of Not I -digested of the total DNA of the O3:K6 strains were similar, and only slight variations were observed between the serotypes. By contrast, the O3:K6 strains and non O3:K6 had markedly different profiles. In conclusion, Random amplified polymorphic DNA (RAPD) profile using appropriate primers was an effective epidemiological marker.