• Journal of Periodontal and Implant Science
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• v.39 no.sup2
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• pp.269-278
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• 2009

Purpose: The aim of this study was to investigate matrix metalloproteinase 1 (MMP-1) gene polymorphism (1G/2G at -1607 and A/G at -519) in Korean subject and to assess the association between polymorphism and periodontal status. Methods: Forty nine generalized aggressive periodontitis (GAP) patients and 57 periodontally healthy children were recruited and genomic DNA was extracted from buccal swab. The polymorphisms of MMP-1 promoter genes were determined by polymerase chain reaction and restriction fragment length product (PCR-RFLP) method. The distribution of genotype and allele frequency was compared between 2 groups by ${\chi}^2$ test. Results: There was a significant difference in the distribution of genotypes and frequency of alleles between the GAP and reference groups at the position - 519 of MMP-1 gene promoter (P<0.05). Allele G carrier rate was significantly lower in GAP group than that of the reference group (P< 0.001). At the position -1607 of MMP-1 gene promoter, genotype distribution and allele frequency showed no statistically significant difference between the groups. However, in the female group, a significant difference was observed between the groups for the genotype distribution, allele frequency and allele 1G carrier rate (P< 0.05). Conclusions: The DNA polymorphism at the MMP-1 gene promoter might be associated with GAP in Korean.

• Tuberculosis and Respiratory Diseases
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• v.69 no.5
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• pp.331-336
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• 2010

Background: Recently, the rate of infections with non-tuberculous mycobacteria (NTM) has been increasing in Korea. Precise identification of NTM is critical to determination of the pathogen and to target treatment of NTM patients. Methods: Sixty-eight unclassified mycobacteria isolates by rpoB PCR-RFLP assay (PRA) collected in 2008 were analyzed by National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) search after sequencing of 16S rRNA, hsp65, rpoB genes. Results: Nineteen strains of 68 isolates were specified as species after sequencing analysis of 3 gene types. We found 3 M. lentifulavum, 5 M. arupense, 4 M. triviale, 4 M. parascrofulaceum, and one M. obuense. One M. tuberculosis and another M. peregrinum were mutated at the Msp I recognition site needed for rpoB PRA. The remaining 49 isolates did not coincide with identical species at the 3 kinds genes. Conclusion: Sequencing analysis of 16S rRNA, hsp65, rpoB was useful for identification of NTM unclassified by rpoB PRA.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.5
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• pp.393-399
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• 2004

Useful genes can be Screened from various environments by construction of metagenomic DNA libraries. In this study, water samples were collected from several lakes in mid Korea, and analyzed by T-RFLP to examine diversities of the microbial communities. The crude DNAs r were extracted by the SDS-based freezing-thawing method, and then further purified using an $UltraClean^{TM}$ kit (MoBio, USA). The metagenomic libraries were constructed with the DNAs partially digested with EcoR I, BamH I, and Sac II in Escherichia coli DH 10B using the pBACe3.6 vector. About 44.0 Mb of metagenomic libraries were obtained with average inserts 13-15 kb in size. The bphC genes responsible for degradation of aromatic hydrocarbons via mets-cleavage were identified from the metagenomic libraries by colony hybridization using the bphC specific sequence as a probe. The 2,3-dihydroxybiphenyl (2, 3-DHBP) dioxygenase gene (bphC ), capable of degradation of 2,3-DHBP, was cloned and its nucleotide Sequences analyzed. The genes consisted of 966 and 897 base pairs with an ATG initiation codon and a TGA termination codon. The activity of the 2,3-DHBP dioxygenase was highly expressed to 2,3-DHBP and Showed a broad substrate range to 2,3-DHBP, catechol, 3-methylcatechol and 4-methylcatechol. These results in-dicated that the bphC gene identified from the metagenomes derived from lake water might be useful in the development of a potent strain for degradation of aromatic pollutants.

• IMMUNE NETWORK
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• v.2 no.4
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• pp.248-255
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• 2002

Background: TAP1 and TAP2 are two ABC transporter genes located within the class II region of the human MHC. Their protein products form a heterodimer whose function is to transport peptides from the cytoplasm into the endoplasmic reticulum. This study was performed to examine the polymorphism of TAP genes and the distribution of HLA-TAP haplotypes in the Korean population through family analysis. Methods: The subjects used in this study were 50 healthy Korean families consisting of 233 individuals. TAP1 (codons 333 and 637) and TAP2 (codons 379, 565, 577, 651, 665, and 687) typings were carried out by the PCR-restriction fragment length polymorphism (RFLP) method. HLA-DRB1 and DQB1 genotyping results from a previous study were used for HLA-TAP haplotype analysis. Results: The number (gene frequency) of TAP1 and TAP2 alleles detected were 3 for TAP1 (A 81.5%, B 17.0%, and C 1.5%) and 8 for TAP2 (A1 32.0%, A2 12.5%, B 34.0%, Bky2 6.5%, C 7.0%, D 3.0%, E 4.5%, and G 0.5%). Eleven TAP1-TAP2 haplotypes were observed with $frequency{\geq}1%$, among which 4 haplotypes (A-B, B-A1, A-Bky2, and C-E) showed weak but significant positive linkage disequilibrium (P<0.05). When DRB1-DQB1 haplotypes were extended to TAP1 and TAP2 loci, much diversification of haplotypes was observed: 19 different DRB1-DQB1 haplotypes formed 58 different haplotypes extended to TAP1 and TAP2 loci. These results add more evidence to the view that recombination hotspot is present within and around TAP gene region. Conclusion: The allele frequencies of TAP1 and TAP2 genes and the distribution of TAP1-TAP2 and HLA-TAP haplotypes were studied in Koreans based on a family study.

• Journal of Environmental Science International
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• v.14 no.5
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• pp.499-511
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• 2005

This study was performed to determine the effects of genetic polymorphisms, such as glutathione S-transferase ${\mu}1(GSTM1)$, glutathione S-transferase ${\Theta}1\;(GSTM1)$, glutathione S-transferase ${\pi}l (GSTP1)$, aryl hydrocarbon N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1), cytochrome P450 1A1 (CYP1A1) on the concentrations of urinary 1-hydroxypyrene (1-OHP) and 2-naphthol in general population with no occupational exposure to polycyclic aromatic hydrocarbons (PAHs). Study subjects were 257 men who visited a health promotion center in Susan. A questionnaire was used to obtain detailed data about age, smoking, drinking, body fat mass, intake of fat etc. Urinary l-OHP and 2-naphthol concentration were analyzed by HPLC system with a fluorescence detector. A multiplex PCR method was used to identify the genotypes for GSTM1 and GSTT1. The polymorphisms of GSTP1, NAT2, CYP1A1 and CYP2E1 were determined by the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method. Urinary 1-OHP concentration was higher in deleted genotype of GSTM1, increased as smoking and alcohol drinking increased. Urinary 2-naphthol concentration was also rely on the age and smoking. Neither genetic polymorphism nor drinking-related factors were significantly related to urinary 2-naphthol concentration. No significant relation was found between physical characteristics and concentrations of urinary PAHs metabolites in the subjects, but the geometric mean of urinary 1-OHP and 2-naphthol was higher in the group with higher value compared to median value. These data suggest that in general population occupationally not exposed to PAHs, urinary concentration of PAHs metabolites is influenced by smoking, alcohol drinking and deleted genotype of GSTM1 in 1-OHP and smoking in 2-naphthol.

• Parasites, Hosts and Diseases
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• v.54 no.4
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• pp.423-429
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• 2016

Cryptosporidium is an important pathogen causing gastrointestinal disease in snakes and is distributed worldwide. The main objectives of this study were to detect and identify Cryptosporidium species in captive snakes from exotic pet shops and snake farms in Thailand. In total, 165 fecal samples were examined from 8 snake species, boa constrictor (Boa constrictor constrictor), corn snake (Elaphe guttata), ball python (Python regius), milk snake (Lampropeltis triangulum), king snake (Lampropeltis getula), rock python (Python sebae), rainbow boa (Epicrates cenchria), and carpet python (Morelia spilota). Cryptosporidium oocysts were examined using the dimethyl sulfoxide (DMSO)-modified acid-fast staining and a molecular method based on nested-PCR, PCR-RFLP analysis, and sequencing amplification of the SSU rRNA gene. DMSO-modified acid-fast staining revealed the presence of Cryptosporidium oocysts in 12 out of 165 (7.3%) samples, whereas PCR produced positive results in 40 (24.2%) samples. Molecular characterization indicated the presence of Cryptosporidium parvum (mouse genotype) as the most common species in 24 samples (60%) from 5 species of snake followed by Cryptosporidium serpentis in 9 samples (22.5%) from 2 species of snake and Cryptosporidium muris in 3 samples (7.5%) from P. regius.

• Journal of Genetic Medicine
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• v.1 no.1
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• pp.39-43
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• 1997

The mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is inherited maternally, in which the MTTL1*MELAS 3243 mutation has been most commonly found as a heteroplasmy of A to G point mutation in the $tRNA^{Leu(UUR)}$ gene. The MTTL1*MELAS 3271 mutation is known to be the second common mutation, though clinical features of both mutations are not remarkably different. Recently, a variety of minor mutations have been reported in patients with MELAS. In this study, major efforts have been made to investigate the allele frequency of major three mutations including MTTL1*MELAS 3243, 3252, 3271 in 10 Korean families with MELAS probands. The PCR and subsequent direct sequencing of the PCR product in the regions spanning these three mutation sites were employed to identify the mutation in each proband. All family members have been screened for the presence of these three mutations by PCR-RFLP assay using Apa I, Acc I and Bfr I restriction enzymes. The MTTL1*MELAS 3243 mutation was most commonly found (7 out of 10 families tested) followed by the MTTL1*MELAS 3271 which was identified in 1 out of 10 families. In the remaining 2 families none of three mutations were found, indicating the presence of either nuclear mutation or yet unidentified mitochondrial DNA mutation in these families.

• Food Science of Animal Resources
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• v.31 no.4
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• pp.537-542
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• 2011

Biological or physiological genes that regulate metabolism and energy partitioning have the potential to influence economically important traits such as carcass and meat quality traits in beef cattle. The neuropeptide Y (NPY) functions as a central appetite stimulator and plays a major role in feed intake and energy-balance control. Therefore, the NPY gene is an excellent biological and physiological candidate gene for body weight, feeding, fatness or growth related traits in beef cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the NPY gene and to evaluate the association of NPY SNP markers with carcass and meat quality traits in Korean cattle. The genomic region (711 bp) including intron 2 of NPY gene was amplified and sequenced, and five SNPs, g.4389 Del(C), g.4371Del(C), g.4271T>C, g.1899A>G and g.1517A>C, were identified. The PCR-RFLP method was then developed to genotype the individuals examined. The g.4271T>C SNP was significantly associated with M. Longissimus dori area (LDA) value (p<0.027). Animals with the TT ($78.144{\pm}0.950\;cm^2$) genotype had higher LDA than those with the CC ($72.266{\pm}2.039\;cm^2$), and animals with TC genotype showed intermediate value. This SNP genotype also showed a highly significant additive genetic effect for the LDA (p<0.01). No significant associations, however, was detected between any of the SNP genotype and other carcass traits measured in this study. In conclusion, SNP genotype of the NPY gene may be used as DNA markers to select animals that have a higher meat yield.

• Clinical and Experimental Reproductive Medicine
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• v.27 no.1
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• pp.107-110
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• 2000

연구목적: 본 연구는 자궁내막증과 무월경 불임환자들을 대상으로 $LH{\beta}$ exon 2 유전자의 돌연변이를 탐색하고자 시도하였다. 연구재료 및 방법: 그 대상으로 22명의 자궁내막증 환자와 12명의 무월경 환자 그리고, 54명의 건강한 비임신 여성을 대조군으로 사용하였다. 이들을 대상으로 한 돌연변이 탐색은 PCR-RFLP(polymerase chain reaction-restriction fragment polymorphism) 방법으로 수행되었다. 결과: 그 결과 자궁내막증과 무월경증 환자에서 그 변이의 비율이 각각 18.2%, 16.7% 그리고, 대조군에서 역시 16.7%의 빈도를 나타냈다. 결론: 따라서, 자궁내막증과 무월경증 환자는 $LH{\beta}$ exon 2 돌연변이와는 서로 관련이 없거나 매우 적음을 알 수 있었다.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.3
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• pp.1009-1014
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• 2016

It is not clear how gene polymorphisms affecting drugs can contributes totheir efficacy in multiple myeloma (MM). We here aimed to explore associations among gene polymorphisms of tumor necrosis factor alpha (TNFalpha), nitric oxide synthesis 3 (NOS3) and multi-drug resistance 1 (MDR1), clinical parameters, prognosis and survival in MM patients treated with VAD (vincristine-adriamycine-dexamethasone), MP (mephalane-prednisolone), autolougus stem cell transplantation (ASCT), BODEC (bortezomib-dexamethasone-cyclophosphamide) and TD (thalidomide-dexamethasone). We analyzed TNFalpha, NOS 3 and MDR1 in 77 patients with MM and 77 healthy controls. The genotyping was performed with PCR and/or PCR-RFLP. There was no clinically significant difference between MM and control groups when TNFalpha (-238) and (-857) and MDR1 gene polymorphisms were studied. However, the TNFalpha gene polymorphism (-308) GG genotype (p=0.012) and NOS3 (+894) TT genotype (p=0.008) were more common in the MM group compared to healthy controls. NOS3 (VNTR) AA (p=0.007) and NOS3 (+894) GG genotypes (p=0.004) were decreased in the MM group in contrast. In conclusion, the NOS3 (+894) TT and TNFalpha (-308) GG genotypes may have roles in myeloma pathogenesis.