• Journal of Acupuncture Research
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• 제23권1호
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• pp.39-51
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• 2006

목적 : 본 연구는 뇌경색에서 일반적으로 많이 사용하는 한방치료가 뇌경색 환자의 단일유전자 염기 다형성에 미치는 영향에 대하여 분석하였다. 2003년 3월부터 2003년 12월까지 경희대학교 한의과대학 부속한방병원 침구과에 입원한 뇌경색 환자 146명과 경희의료원 종합검진센터에 건강검진을 위해 내원한 건강인 192명을 대상으로 하였다. 방법 : 한국인 뇌경색 환자와 건강인에서 혈액을 채취하여 개인마다 DNA를 분리 정제하고 Taq polymerase로 증폭한 후 Pyrosequencing을 통하여 IL4R(interleukin 4 receptor)의 유전형을 관찰하였다. 결과 : 본 연구 결과 IL4R 유전자의 경우 한국인 뇌경색 환자군과 대조군 사이에 유의성 있는 차이가 나타나지 않았다. 결론 : 이상의 결과를 통하여 IL4R 유전자 다형성은 한국인에서 뇌경색의 발병에 관련이 적은 것으로 사려되며 더 많은 환자를 대상으로 다른 환경요인 또는 유전자와의 연관성에 대한 심도 깊은 연구가 필요할 것으로 사려된다.

• Molecules and Cells
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• 제21권3호
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• pp.411-417
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• 2006

We have developed a polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) marker that can distinguish male-fertile (N) and male-sterile (S) cytoplasm in onions. The PCR-RFLP marker was located in a chloroplast psbA gene amplicon. Digesting the amplicons from different cytoplasm-containing varieties with the restriction enzyme MspI revealed that N-cytoplasm plants have a functional MspI site (CCGG), whereas the S-cytoplasm plants has a substitution in that site (CTGG), and thus no MspI target. The results obtained using this PCR-RFLP marker to distinguish between cytoplasmic male sterile factors in 35 onion varieties corresponded with those using a CMS-specific sequence-characterized amplified region (SCAR) marker. Moreover, the PCR-RFLP marker can identify N- ot S-cytoplasms in DNA sample mixtures in which they are in up to a 10-fold minority, indicating that use of the marker has high diagnostic precision. We also demonstrated the usefulness of the SNP detected in the psbA gene for high-throughput discrimination of CMS factors using Real-time PCR and a TaqMan probe assay.

• 농업과학연구
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• 제49권4호
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• pp.795-807
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• 2022

The development and commercialization of industrial genetically modified (GM) organisms is actively progressing worldwide, highlighting an increased need for improved safety management protocols. We sought to establish an environmental monitoring method, using real-time polymerase chain reaction (PCR) and propidium monoazide (PMA) treatment to develop a quantitative detection protocol for living GM microorganisms. We developed a duplex TaqMan quantitative PCR (qPCR) assay to simultaneously detect the selectable antibiotic gene, ampicillin (AmpR), and the single-copy Escherichia coli taxon-specific gene, D-1-deoxyxylulose 5-phosphate synthase (dxs), using a direct cell suspension culture. We identified viable engineered E. coli cells by performing qPCR on PMA-treated cells. The theoretical cell density (true copy numbers) calculated from mean quantification cycle (Cq) values of PMA-qPCR showed a bias of 7.71% from the colony-forming unit (CFU), which was within ±25% of the acceptance criteria of the European Network of GMO Laboratories (ENGL). PMA-qPCR to detect AmpR and dxs was highly sensitive and was able to detect target genes from a 10,000-fold (10^-4) diluted cell suspension, with a limit of detection at 95% confidence (LOD_95%) of 134 viable E. coli cells. Compared to DNA-based qPCR methods, the cell suspension direct PMA-qPCR analysis provides reliable results and is a quick and accurate method to monitor living GM E. coli cells that can potentially be released into the environment.

• Asian Pacific Journal of Cancer Prevention
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• 제17권8호
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• pp.4107-4111
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• 2016

Background: Oral cancers account for approximately 2% of all cancers diagnosed each year; however, the vast majority (80%) of the affected individuals are smokers whose risk of developing a lesion is five to nine times greater than that of non-smokers. Tobacco smoke contains numerous carcinogens that cause DNA damage, including oxidative lesions that are removed effectively by the base-excision repair (BER) pathway, in which poly (ADP-ribose) polymerase 1 (PARP-1), plays key roles. Genetic variations in the genes encoding DNA repair enzymes may alter their functions. Several studies reported mixed effects on the association between PARP-1 variants and the risk of cancer development. Till now no reported studies have investigated the association between PARP-1 variants and oral squamous cell carcinoma (OSCC) risk in an Indian population. Materials and Methods: In the present case control study 100 OSCC patients and 100 matched controls were genotyped using PARP1 single nucleotide peptides (SNP's) rs1136410 and rs3219090 using TaqMan assays. Results: The results indicated significantly higher risk with PARP1 rs1136410 minor allele "C" (OR=1.909; p=0.02942; CI, 1.060-3.439). SNP rs1136410 also showed significantly increased risk in patients with smoking habit at C/C genotype and at minor allele C. Conclusions: The PAPR-1 Ala762Val polymorphism may play a role in progression of OSCC. Larger studies with a greater number of samples are needed to verify these findings.

• Journal of Acupuncture Research
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• 제19권4호
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• pp.183-189
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• 2002

목적 : 본 연구는 catalase 유전자 다형성이 중풍의 발병과 관련이 있는지 알아보기 위해 수행되었다. 대상 : 경산대학교부속구미 한방병원에 입원한 중풍환자 86 명과 종합건진센터에 내원한 중풍기왕력이 없는 건강인 165 명을 대상으로 하였다. 방법 : 각 그룹에서 개개인마다 DNA를 분리 정제한 후 Taq polymerase로 증폭하여 한천 겔에서 전기영동을 하여 잘려진 DNA fragment의 양상을 관찰하였다. 결과 : T/T, T/A, A/A의 세가지 유전자형이 검출되었으며 중풍군과 건강인 사이에 통계적인 유의성이 나타나지 않았다. 결론 : 이상의 결과를 통하여 catalase 유전자 다형성은 중풍의 발병과는 관련성이 없는 것으로 사려되며 더 많은 환자를 대상으로 다른 환경요인 또는 유전자와의 연관성에 대한 심도있는 연구가 필요하다고 하겠다.

• Journal of Acupuncture Research
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• 제19권1호
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• pp.111-117
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• 2002

목적 : 본 연구는 serotonin transporter (5-HTT) 유전자다형성이 중풍의 발병과 관련이 있는지 알아보기 위해 수행하였다. 대상 : 경희의료원 한방병원에 입원한 중풍환자 139명과 각 병원 중풍 기왕력이 없는 건강인 138명을 대상으로 하였다. 방법 : 각 그룹에서 개개인마다 DNA를 분리 정제한 후 Taq polymerase로 증폭하여 한천 겔에서 전기영동을 하여 잘려진 DNA fragment의 양상을 관찰하였다. 결과 : L/L, L/S, S/S의 세가지 유전자형이 검출되었으며 중풍군과 대조군 사이에 유의성 있는 차이는 발견되지 않았다. 개별 allele 빈도에 있어 중풍군과 건강인 사이에는 통계적인 유의성이 나타나지 않았다. 결론 : 이상의 결과를 통하여 5-HTT 유전자다형성은 중풍의 발병과는 직접적인 관련이 없는 것으로 사려되며 더 많은 환자를 대상으로 다른 환경요인 또는 유전자와 연관성에 대한 심도깊은 연구가 필요하다고 하겠다.

• Tuberculosis and Respiratory Diseases
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• 제62권5호
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• pp.406-416
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• 2007

연구배경: 단일염기다형성(Single nucleotide polymorphism, SNP)은 인간의 유전자 서열 1000염기에 1개 빈도로 발견되어 인간은 대략 300만개의 유전자 다형성을 가지고 있다. 이 유전자 다형성의 조합결과로 인간의 개체 간 특성들이 결정되는 것으로 이해되고 있다. 이러한 다형성들의 조합양상에 따라 특이 질환에 대한 유전자 감수성 또한 달라지게 되므로 최근에는 많은 질환들과 유전자 다형성들과의 상관관계를 보는 연구들도 활발하게 진행되고 있다. 이러한 SNP분석은 큰 집단을 대상으로 진행되어 지므로 적은 비용으로 정확하게 그리고 대용량으로 분석할 수 있는 방법이 필요하다. 방 법: 대상 환자 89명의 genomic DNA를 가지고서 promotor상에 위치한 -37과 -524 염기부위에서 유전자 다형성을 보이는 것으로 보고되어져 있는 RRM1(ribonucleotide reductase M1) 유전자를 대상으로 PCR-RFLP(polymerase chain reaction-restriction fragment length polymorphism)와 real-time PCR(RTPCR, TaqMan probe assay)을 동시에 시행한 후 각각의 결과를 비교 분석하였다. 결 과: 대상 DNA 89예 중 -37에서는 2예(2.17%), -524에서는 15예(16.26%)가 서로 다른 양상을 보였다. 결과 차이를 보인 샘플 17예를 대상으로 직접 염기서열 분석을 시행하여 본 결과, 17예 모두 RT-PCR에서 확인되었던 결과와 일치함을 확인할 수 있었다. 추가 샘플 138예를 대상으로 RT-PCR을 2회 연속 실행하여 genotyping을 해 본 결과 98%이상의 높은 일치율을 보였으며, 그중 10예를 무작위로 골라 직접 염기서열 분석을 시행하여 본 결과, 역시 100%일치, 높은 정확도를 보였고 이는 in-tube assay 방식으로 샘플의 오염을 최소화 할 수 있었으며 72 well based system(Corbett Research)을 이용함으로 1회 유전자 증폭반응을 통해 많은 검체를 한 번에 확인할 수 있어 매우 빠른 검사방법 이었다. 결 론: 큰 집단을 대상으로 다량의 SNP를 분석하기 위한 실험 방법으로는 RT-PCR이 신속하면서도 정확한 결과를 얻을 수 있는 방법으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제19권9호
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• pp.1257-1261
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• 2006

Pleiomorphic adenoma gene-like1 (PLAGL1) encodes a zinc-finger (ZF) protein with seven ZFs of the C2H2-type which is a regulator of apoptosis and cell cycle arrest, and also regulates the secretion of insulin. In both human and mouse, PLAGL1 is a candidate gene for tumor suppressor and transient neonatal diabetes mellitus (TNDM). In this study, a 2,238 bp fragment covering the complete coding region was obtained and deposited to GenBank (accession number: DQ288899). The reverse transcriptase-polymerase chain reaction (RT-PCR) indicated that PLAGL1 was expressed almost equally in heart, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, fat, uterus and ovary. Comparing the sequences of Large White and Meishan pigs, a C-T transition in exon 6 was found. The polymorphism could be detected by TaqI and was genotyped in five purebreds (Large White, Landrace, Meishan, Tongcheng and Bamei). Association analysis was performed between the polymorphism and carcass traits in 276 pigs of a "Large White${\times}$Meishan" F2 resource population. As a consequence, significant associations of the genotypes with shoulder backfat thickness (SFT) and internal fat rate (IFR) were observed. Pigs with TT genotype had low SFT and high IFR compared with TC or CC genotypes.

• 한국작물학회지
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• 제50권5호
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• pp.361-367
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• 2005

Single nucleotide polymorphisms (SNPs) are valuable DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed. In this report, one of effective and high throughput SNP genotyping assays, which was named the template-directed dye-terminator incorporation with fluorescence polarization detection (FP-TDI) was described. Although the most of this assay succeed, the objective of this work was to deter­mine the reasons for the failures, find ways to improve the assay and reduce the running cost. Ninety $F_2$-derived soybean, Glycine max (L.) Merr., RILs from a cross between 'Pureunkong' and 'Jinpumkong 2' were genotyped at four SNPs. FP measurement was done on $Victot^3$ microplate reader (perkinelmer Inc., Boston, MA, USA). Increasing the number of thermal cycles in the single-base extension step increased the separation of the FP values between the products corresponding to different genotypes. But in some assays, excess of heterozygous genotypes was observed with increase of PCR cycles. We discovered that the excess heterozygous was due to misincorporation of one of the dye­terminators during the primer extension reaction. After pyrophosphatase incubation and thermal cycle control, misincoporation can be effectively prevented. Using long amplicons instead of short amplicons for SNP genotyping and decreasing the amount of dye terminator and Acyclopol Taq polymerase to 1/2 or 1/3 decreased the cost of the assay. With these minor adjustments, the FP-TDI assay can be used more accurately and cost-effectively.

• Asian Pacific Journal of Cancer Prevention
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• 제14권1호
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• pp.179-182
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• 2013

Human cytochrome P4502E1 (CYP2E1) is a well-conserved xenobiotic-metabolizing enzyme expressed in liver, kidney, nasal mucosa, brain, lung, and other tissues. CYP2E1 is inducible by ethanol, acetone, and other low-molecular weight substrates and may mediate development of chemically-mediated cancers. CYP2E1 polymorphisms alter the transcriptional activity of the gene. This study was conducted in order to investigate the allele frequency variation in different populations of Andhra Pradesh. Two hundred and twelve subjects belonging to six populations were studied. Genotype and allele frequency were assessed through TaqMan allelic discrimination (rs6413419) and polymerase chain reaction-sequencing (-1295G>C and -1055C>T) after DNA isolation from peripheral leukocytes. The data were compared with other available world populations. The SNP rs6413419 is monomorphic in the present study, -1295G>C and -1055C>T are less polymorphic and followed Hardy-Weinberg equilibrium in all the populations studied. The -1295G>C and -1055C>T frequencies were similar and acted as surrogates in all the populations. Analysis of HapMap populations data revealed no significant LD between these markers in all the populations. Low frequency of $CYP2E1^*c2$ could be useful in the understanding of south Indian population gene composition, alcohol metabolism, and alcoholic liver disease development. However, screening of additional populations and further association studies are necessary. The heterogeneity of Indian population as evidenced by the different distribution of $CYP2E1^*c2$ may help in understanding the population genetic and evolutionary aspects of this gene.