• 대한한의학회지
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• 제25권3호
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• pp.105-110
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• 2004

Objectives : Sasang Constitutional Medicine is based on the diversity of human beings and medically developing a variation of responses to diseases and medicines. This diversity is categorized into four concerning morphology, physiology, pathology, and pharmacology. It is supposed that sasang constitutional medicine is related the genetic diversity of individuals. Single nucleotide polymorphism is the basic tool to research genetic polymorphism as a landmark of genomes. Each constitution has different processes of pathophysiology and metabolisms to herb medications. In clinical research, the stroke incidence is significantly different by constitution. Methods : We researched whether the polymorphic expression of CCK (rs=2241997) depends on sasang constitution. The [c/t] polymorphism site of promotor region of CCK gene on 3p22-p21.3 was investigated. Results : The allele frequency of [c/t] polymorphism of CCK promotor region was different in constitution groups compared to the average allele frequency of SNP DB. The allele frequencies of Soeumin and Soyangin groups were (c:0.70/t:0.30). and (c:0.71/t:0.29), that of Taeumin group was (c:0.57/t:0.43) and of Taeyangin group was (c:1.00/t:0.00) Conclusions : It was regarded the [c/t] polymorphism of CCK promotor region is available to classify the constitution. However, it is necessary to research about CCK gene polymorphism and more constitution population groups. It is also necessary to research the more functional gene's polymorphism and sasang constitution.

• 생명과학회지
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• 제25권11호
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• pp.1304-1310
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• 2015

주기성 시계 유전자 3(period circadian clock gene 3, PER3)는 포유류에서 생물학적 주기 타이밍 시스템의 역할을 수행 한다. 이 유전자는 규칙적인 운동 체계에 의해 근육에서 전사 개시 되는 것으로 알려져 있다. 인간과 마우스에서는 본 유전자에 대해 잘 알려져 있지만, 주기 및 연주기 동안 낮의 길이에 영향을 많이 받는 말에서 운동 연관 연구는 존재하지 않는다. 운동 시 근육의 기능에 중요한 역할을 하는 PER3 유전자에 대해 대표적인 경주마인 국내산 더러브렛 품종의 운동 전과 운동 후 유전자 발현을 분석하기 위해 본 연구를 수행하였다. 그 결과, 골격근에서 PER3 유전자의 발현은 운동 전에 비해 운동 후에 유의적으로 증가하는 것으로 나타났다. 또한, 인실리코상에서 4개의 비동의성 단일 염기 변이(non-synonymous single nucleotide polymorphism, nsSNP) 분석과 이러한 nsSNP의 단백질 구조 및 기능 분석 결과, 전체 자유 에너지와 RMSD 값은 돌연변이의 원인이 될 수 있음으로 나타났다. 이 중, nsSNP–s395916798 (G72R)은 구조적 기능적 측면에서 중요한 잔기의 안정화 효과와 연관된 것을 알 수 있었다. 본 연구는 운동에 따라 더러브렛 골격근 내 PER3 발현 차이는 운동이라는 표현형에 대표될 수 있음을 확인하였다. 또한, SNP의 조합을 활용하여 운동 후 경주마의 조기 회복의 평가 지표로써 유용한 바이오마커가 될 수 있음을 시사한다.

• Journal of Plant Biotechnology
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• 제5권4호
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• pp.193-195
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• 2003

A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.

• 동의생리병리학회지
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• 제19권2호
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• pp.515-519
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• 2005

We hypothesized that the IL10 gene is important candidate in the development of Bell's palsy and specific genotypic and allelic variations should be associated with Bell's palsy in the Korean population. In this study, we assessed the SNP (single-nucleotide polymorphism) of IL10 in patients with Bell's palsy. 62 patients with Bell's palsy were selected from the subjects who visited for the Bell's palsy service of the department of acupuncture & moxibustion, college of Oriental Medicine, Daegu Haany University from May 2002 to May 2003. Pyrosequencing was performed for genetic analyses. There was no statistically significant genotypic distribution difference between control and Bell's palsy group And there was not statistically significant allelic frequency difference between control and Bell's palsy group. In this study the IL10 genotypemight not be the risk factor of Bell's palsy patients in Korean. studies will be necessary for the exact genetic markers. Establishment of more systemic approach and high quality of prospective cohorts will be necessary for the good prediction of genetic markers.

• Asian Pacific Journal of Cancer Prevention
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• 제16권12호
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• pp.5069-5073
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• 2015

The single nucleotide polymorphism (SNP) rs1053004 in Signal transducer and activator of transcription 3 (STAT3) was recently reported to be associated with chronic hepatitis B (CHB)-related hepatocellular carcinoma (HCC) in a Chinese cohort. This study was aimed at investigating whether the SNP might also contribute to HCC susceptibility in the Thai population. Study subjects were enrolled and divided into 3 groups including CHB-related HCC (n=211), CHB without HCC (n=233) and healthy controls (n=206). The SNP was genotyped using allelic discrimination assays based on TaqMan real-time PCR. Data analysis revealed that the distribution of different genotypes was in Hardy-Weinberg equilibrium (P>0.05). The frequencies of allele T (major allele) in HCC patients, CHB patients and healthy controls were 51.4%, 58.6% and 61.4%, respectively, whereas the frequencies of C allele (minor allele) were 48.6%, 41.4% and 38.6%. The C allele frequency was higher in HCC when compared with CHB patients (odds ratio (OR)=1.34, 95% confidence interval (CI)=1.02-1.74, P=0.032). The genotype of SNP rs1053004 (CC versus TT+TC) was significantly associated with an increased risk when compared with CHB patients (OR=1.83, 95% CI=1.13-2.99, P=0.015). In addition, we observed a similar trend of association when comparing HCC patients with healthy controls (OR=1.77, 95% CI=1.07-2.93, P=0.025) and all controls (OR=1.81, 95% CI=1.19-2.74, P=0.005). These findings suggest that the SNP rs1053004 in STAT3 might contribute to HCC susceptibility and could be used as a genetic marker for HCC in the Thai population.

• Communications for Statistical Applications and Methods
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• 제26권1호
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• pp.1-9
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• 2019

Various probabilistic methods have been proposed for using interpopulation allele frequency differences to infer the ethnic group of a DNA specimen. The selection of the statistical method is critical because the accuracy of the statistical classification results vary. For the ancestry classification, we proposed a new ancestry evaluation method that estimate the combined ethnicity index as well as compared its performance with various classical classification methods using two real data sets. We selected 13 SNPs that are useful for the inference of ethnic origin. These single nucleotide polymorphisms (SNPs) were analyzed by restriction fragment mass polymorphism assay and followed by classification among ethnic groups. We genotyped 400 individuals from four ethnic groups (100 African-American, 100 Caucasian, 100 Korean, and 100 Mexican-American) for 13 SNPs and allele frequencies that differed among the four ethnic groups. Additionally, we applied our new method to HapMap SNP genotypes for 1,011 samples from 4 populations (African, European, East Asian, and Central-South Asian). Our proposed method yielded the highest accuracy among statistical classification methods. Our ethnic group classification system based on the analysis of ancestry informative SNP markers can provide a useful statistical tool to identify ethnic groups.

• Asian-Australasian Journal of Animal Sciences
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• 제22권9호
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• pp.1241-1247
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• 2009

A large number of branded chicken products exist in Japan, and in some cases, the breed of chicken is an important factor used to attract consumer interest in the retail product. In order to establish a simple method for verifying such breed claims we applied the amplified fragment length polymorphism (AFLP) technique to nine chicken breeds (White Cornish, Red Cornish, White Plymouth Rock, New Hampshire, Rhode Island Red, Barred Plymouth Rock, Hinaidori, Tosajidori, Tsushimajidori) to search for molecular markers able to discriminate chicken breeds. Three breed-specific single nucleotide polymorphisms (SNP) were identified, one for each of Hinaidori, Tosajidori, or New Hampshire. A total of 219 individuals from the nine breeds were analyzed using a specific PCR test for each of these SNP. The PCR tests made it possible to discriminate between the breeds of chickens to identify products from these three breeds. This PCR method provides an efficient method for the routine analysis and verification of certified chicken products.

• Journal of Gastric Cancer
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• 제8권3호
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• pp.113-119
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• 2008

목적: TFF1 유전자의 -2bp에 위치하고 있는 단일염기다형성의 유전자형 및 대립형질 빈도와 H. pylori 감염 및 위암발생 민감성과의 연관성을 조사하고자 하였다. 대상 및 방법: 2000년 1월부터 2003년 12월까지 위 샘암종으로 근치적 수술을 시행 받은 167명과 정상 건강인 299명의 DNA를 이용하였다. TFF1 유전자의 단일염기다형성의 유전자형은 중합효소연쇄반응 후 제한효소를 이용한 제한 분절길이다형성과 single strand conformation polymorphism의 방법으로 분석하였다. 또한, H. pylori 감염은 Giemsa 염색으로 조사하였다. 결과: 정상 건강인의 TFF1 단일염기다형성에 대한 유전자형 및 대립형질의 빈도를 위암 환자군과 비교한 결과 통계적으로 의의가 없었다(P=0.715 & P=0.595). 위암 환자군을 성별로 나누어 정상 건강인과 비교한 경우에도 통계적 의의를 발견할 수 없었다. 또한, 위암 조직의 조직학적 소견 및 환자 연령과 TFF1 단일염기다형성의 유전자형 및 대립형질 빈도를 조사한 결과, 위암 조직의 조직학적 소견 및 연령은 TFF1 유전자 단일염기다형성과 무관하였다(P=0.088 & P=0.551). 한편, H. pylori 감염은 모두 39예에서 관찰되었는데 TFF1 유전자형과는 통계적으로 연관성이 없었다(P=0.7200). 결론: TFF1 유전자의 -2bp에 존재하는 단일염기다형성은 TFF1 단백의 합성에 큰 영향이 없으며 H. pylori 감염과 위암의 발생과는 무관하다는 것을 의미한다.

• 한국양봉학회지
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• 제32권4호
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• pp.281-293
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• 2017

Sacbrood virus (SBV) is one of the main pathogenic RNA viruses of honeybee. SBV is found worldwide and many local strains have been reported, such as kSBV, cSBV, and wSBV. In this study, SBV-specific DNA fragments were cloned and sequenced by reverse-transcription PCR from 4 populations of A. mellifera, 4 sequences from 1 population belonged to the 2134D51 genotype (349 nucleotides, nt) and 12 sequences from 3 populations belonged to the 2100D0 genotype (400 nt) among the 16 determined sequences. A total of 87 points of mismatches were found by comparison with the most similar sequences in GenBank. Seventeen single-nucleotide polymorphisms (SNP) were detected, and 6 SNP-patterns in the 2100D0 genotype and 2 SNP-patterns in the 2134D51 genotype were identified based on SNP positions. In SNP-pattern 2, 10 SNPs were detected, but only 2 SNPs were found in SNP-pattern7. Meanwhile, one SNP-pattern was found from one RNA-sample, multi SNP-patterns were detected from other RNA-samples. Large numbers of SNP variants indicate that vast numbers of point-mutations on SBV have occurred since SBV invaded Korea and that SNP smay have been introduced individually over time. Thorough analysis of SNP variants will not only define the local infection-route, but also the relationships between SNP-pattern and SBV-pathogenic abilities.

• Journal of Ginseng Research
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• 제43권3호
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.