• Annals of Laboratory Medicine
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• 제38권6호
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• pp.591-598
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• 2018

Background: Forkhead box P3 (FOXP3) is an important marker of regulatory T cells. FOXP3 polymorphisms are associated with autoimmune diseases, cancers, and allograft outcomes. We examined whether single nucleotide polymorphisms (SNPs) at the FOXP3 locus are associated with clinical outcomes after allogenic hematopoietic stem cell transplantation (HSCT). Methods: Five FOXP3 SNPs (rs5902434, rs3761549, rs3761548, rs2232365, and rs2280883) were analyzed by PCR-sequencing of 172 DNA samples from allogenic HSCT patients. We examined the relationship between each SNP and the occurrence of graft-versus-host disease (GVHD), post-HSCT infection, relapse, and patient survival. Results: Patients with acute GVHD (grades II-IV) showed higher frequencies of the rs3761549 T/T genotype, rs5902434 ATT/ATT genotype, and rs2232365 G/G genotype than did patients without acute GVHD (P =0.017, odds ratio [OR]=5.3; P =0.031, OR=2.4; and P =0.023, OR=2.6, respectively). Multivariate analysis showed that the TT genotype of rs3761549 was an independent risk factor for occurrence of acute GVHD (P =0.032, hazard ratio=5.6). In contrast, the genotype frequencies of rs3761549 T/T, rs5902434 ATT/ATT, and rs2232365 G/G were lower in patients with post-HSCT infection than in patients without infection (P =0.026, P =0.046, and P =0.031, respectively). Conclusions: rs3761549, rs5902434, and rs2232365 are associated with an increased risk of acute GVHD and decreased risk of post-HSCT infection.

• The Plant Pathology Journal
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• 제34권6호
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• pp.506-513
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• 2018

Clubroot is one of the most economically important diseases of the Brassicaceae family. Clubroot disease is caused by the obligate parasite Plasmodiophora brassicae, which is difficult to study because it is nonculturable in the laboratory and its races are genetically variable worldwide. In Korea, there are at least five races that belongs to four pathotype groups. A recent study conducted in Korea attempted to develop molecular markers based on ribosomal DNA polymorphism to detect P. brassicae isolates, but none of those markers was either race-specific or pathotype-specific. Our current study aimed to develop race- and isolate-specific markers by exploiting genomic sequence variations. A total of 119 markers were developed based on unique variation exists in genomic sequences of each of the races. Only 12 markers were able to detect P. brassicae strains of each isolate or race. Ycheon14 markers was specific to isolates of race 2, Yeoncheon and Hoengseong. Ycheon9 and Ycheon10 markers were specific to Yeoncheon isolate (race 2, pathotype 3), ZJ1-3, ZJ1-4 and ZJ1-5 markers were specific to Haenam2 (race 4) isolate, ZJ1-35, ZJ1-40, ZJ1-41 and ZJ1-49 markers were specific to Hoengseong isolate and ZJ1-56 and ZJ1-64 markers were specific to Pyeongchang isolate (race 4, pathotype 3). The PCR-based sequence characterized amplified region (SCAR) markers developed in this study are able to detect five Korean isolates of P. brassicae. These markers can be utilized in identifying four Korean P. brassicae isolates from different regions. Additional effort is required to develop race- and isolate-specific markers for the remaining Korean isolates.

• International journal of thyroidology
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• 제11권2호
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• pp.123-129
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• 2018

Background and Objectives: Hypermethylation of the tumor suppressor gene RASSF1A and activating mutation of BRAF gene have been recently reported in thyroid cancers. To investigate the role of these two epigenetic and genetic alterations in thyroid tumor progression, methylation of RASSF1A and BRAF mutation were examined in thyroid tumors. Materials and Methods: During 2007 to 2017, 69 papillary carcinomas, 18 nodular hyperplasia, 3 follicular carcinomas, and 13 follicular adenomas were selected. The methylation-specific polymerase chain reaction (MSP) technique was used in detecting RASSF1A methylation and polymerase chain reaction (PCR)-single-stranded conformation polymorphism and sequencing were used for BRAF gene mutation study. Results: The hypermethylation of the RASSF1A gene was found in 84.6%, 100% and 57.9% of follicular adenomas, follicular carcinomas, and papillary carcinomas, respectively. Nodular hyperplasia showed a hypermethylation in 33.3%. The BRAF mutation at V600E was found in 60.7% of papillary carcinoma and 27.0% of nodular hyperplasia, but none of follicular neoplasms. The BRAF mutation was correlated with the lymph node metastasis and MACIS clinical stage. There is an inverse correlation between RASSF1A methylation and BRAF mutation in thyroid lesions. Conclusion: Epigenetic inactivation of RASSF1A through aberrant methylation is considered to be an early step in thyroid tumorigenesis, and the BRAF mutation plays an important role in the carcinogenesis of papillary carcinoma, providing a genetic marker.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.413-425
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• 2018

A previous work developed and identified a new omega-5 gliadin deficient wheat line named O-free by crossing Keumkang and Olgeuru, which is nutritionally quite meaningful in that omega-5 gliadin is one of the known wheat allergens. To verify the characteristics of the O-free, we performed RNA sequencing (RNAseq) analysis of the O-free and the two parent lines (Keumkang and Olgeuru). The results of the similarity analysis with the ESTs for gliadins and glutenins showed that the O-free ESTs had no similarity with the omega-5 gliadin sequences but had similarity to other gliadins and glutenins. Furthermore, mapping results between the raw RNAseq data from the O-free and the omega-5 gliadin sequence showed a clear deletion of the N-terminal sequences which are an important signature of omega-5 gliadin. We also designed specific PCR primers that could identify omega-5 gliadin in the genomic DNA. The results showed that no omega-5 gliadin fragments were detected in the O-free. According to these results, we confirmed that the deficiency of omega-5 gliadin in the O-free is not caused by post-transcriptional or post-translational regulations such as epigenetic phenomena but by a simple deletion in the chromosome. Furthermore, we showed that the low-molecular weight glutenin subunit (LMW-GS) gene in the O-free had a single nucleotide polymorphism (SNP) causing a premature stop codon, resulting in a truncated polypeptide. We expect that the O-free line may serve as an excellent source of wheat that could prevail in the hypo-allergen wheat market, which has recently gained interest world-wide.

• 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.

• The Plant Pathology Journal
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• 제37권2호
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• pp.194-199
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• 2021

Blackleg is a serious disease in Brassica plants, causing moderate to severe yield losses in rapeseed worldwide. Although China has not suffered from this disease yet (more aggressive Leptosphaeria maculans is not present yet), it is crucial to take provisions in breeding for disease resistance to have excellent blackleg-resistant cultivars already in the fields or in the breeding pipeline. The most efficient strategy for controlling this disease is breeding plants with identified resistance genes. We selected 135 rapeseed accessions in Sichuan, including 30 parental materials and 105 hybrids, and we determined their glucosinolate and erucic acid content and confirmed 17 double-low materials. A recently developed single-nucleotide polymorphism (SNP) marker, SNP_208, was used to genotype allelic Rlm1/rlm1 on chromosome A07, and 87 AvrLm1-resistant materials. Combined with the above-mentioned seed quality data, we identified 11 AvrLm1-resistant double-low rapeseed accessions, including nine parental materials and two hybrids. This study lays the foundation of specific R gene-oriented breeding, in the case that the aggressive Leptosphaeria maculans invades and establishes in China in the future and a robust and less labor consuming method to identify resistance in canola germplasm.

• Journal of Animal Science and Technology
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• 제65권3호
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• pp.511-518
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• 2023

This study examined the association between functional sequence variants (FSVs) of myosin heavy chain 3 (MYH3) genotypes and collagen content in a Landrace and Jeju native pig (JNP) crossbred population. Four muscles (Musculus longissimus dorsi, Musculus semimembranosus, Musculus triceps brachii, and Musculus biceps femoris) were used for the analysis of meat collagen content, and the same animals were genotyped for the FSVs of the MYH3 gene by using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism). Three FSVs of MYH3 genotypes were identified and had genotype frequencies of 0.358, 0.551, and 0.091 for QQ, Qq, and qq, respectively. QQ animals for the FSVs of the MYH3 genotypes showed higher collagen content in their M. longissimus dorsi (p < 0.001), M. semimembranosus (p < 0.001), M. triceps brachii (p < 0.001), and M. biceps femoris (p < 0.001) than qq homozygous animals. After the validation of this result in other independent populations, the FSVs of MYH3 genotypes can be a valuable genetic marker for improving collagen content in porcine muscles and can also be applied to increase the amount of collagen for biomedical purposes.

• 생명과학회지
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• 제30권1호
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• pp.58-63
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• 2020

본 연구에서는 제주재래돼지와 듀록 품종 사이에서 생산된 F₂ 참조축군에서 melanocortin-4-receptor (MC4R) 유전자형과 지방산 조성간의 관련성을 연구하였다. 전체 290 여두의 F₂ 자손을 이용하여 14개의 지방산 조성을 측정하였다. Taq I PCR-RFLP 방법을 이용하여 MC4R c.1426A>G (p.Asp298Asn)의 단일염기다형성(single nucleotide polymorphism, SNP)을 확인하였다. MC4R 세 가지 유전자형(AA, AB, BB)이 모두 발견되었고, 그 빈도는 각각 0.299, 0.542, 0.159로 확인되었다. AA 유전자형을 가진 개체에서 palmitic acid (C16:0, p<0.05), stearic acid (C18:0, p<0.01), eicosenoic acid (C20:1n9, p<0.05), saturated fatty acid (SFA, p<0.01) 함량이 GG 유전자형을 가진 개체보다 더 높은 것으로 확인되었다. 반면에 GG 유전자형을 가진 개체는 linoleic acid (C18:2n6, p<0.001), linolenic acid (C18:3n3, p<0.001), linolenic acid (C18:3n6, p<0.001), arachidonic acid (C20:4n6, p<0.001)과 같은 불포화지방산(unsaturated fatty acid) 함량이 AA 유전자형을 가진 개체보다 더 높은 것을 확인하였다. 제주재래돼지와 듀록 품종 사이에서 생산된 F₂ 참조축군에서 MC4R GG 유전자형이 포화지방산은 낮추고, 불포화지방산은 높이는 것으로 확인되었다. 본 연구 결과 MC4R의 유전적 다형성이 듀록과 제주재래돼지 교배 프로그램에서 육질 향상과, 고기내의 지방산 함량을 조절할 수 있는 유전적 표지 인자로 활용될 수 있을 것이라 사료된다.

• Journal of Animal Science and Technology
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• 제44권2호
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• pp.181-190
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• 2002

본 연구는 한우 mt DNA 염기서열 가운데 $tRNA^{Pro}$와 $tRNA^{Pre}$ 유전자 사이에 위치하고 있는 D-loop 영역의 염기서열을 결정하고 한우의 염기변이 다형성을 분석하기 위하여 mt DNA의 D-loop 영역내 404번부터 15061까지 1142bp 크기의 염기서열 부위를 특이적인 primer를 이용하여 PCR로 증폭하였다. 한우의 mt DNA내 D-loop 영역에서 단일염기의 치환 및 삽입에 의해 총 24개의 polymorphic site가 확인되었다. 한우 mt DNA D-loop 영역 가운데 16042～16122번째에 위치하고 있는 영역의 염기치환율이 다른 염기서열 영역에 비하여 약 50%를 점유하고 있었으며 이들 polymorphic site에서 16055, 16230 및 16260 번의 염기치환은 한우에서만 검출된 새로운 염기변이로 확인되었다. 따라서, 한우 D-loop 영역내 특이적인 염기변이는 모계 및 세포질 DNA marker로서 한우품종을 특정하는데 활용할 수 있는 가능성을 시사하였다. Polymorphic site의 출현빈도는 169번째 염기가 81.3%로 가장 출현율이 높았고 다음으로 16302번과 16093번째는 56.3% 그리고 16042번와 16119번째 염기가 각각 50.0%와 43.8%의 치환율을 보였으며 나머지 14개 염기는 6.3%에서 25.0% 수준의 출현율을 나타냈다. 한우와 타 품종간의 유전적 근연관계를 추정한 결과 Bos taurus 계통의 유럽종과 유전적 유사도가 높은 것으로 추정되었고, Africa와 India의 Bos indicus 계통의 품종과는 상대적으로 근연관계가 먼 것으로 나타났다. 본 연구에서 검출한 mt DNA내 D-loop 영역의 염기서열 다형성은 한우집단의 유전적 변이성 추정과 모계유전 분석 및 나아가 경제적으로 중요한 형질들과의 연관성 분석에 유용하게 활용할 수 있을 것으로 기대된다.

• Radiation Oncology Journal
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• 제24권1호
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• pp.30-36
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• 2006

목적: 방사선치료와 항암제치료의 급성부작용은 환자 개인에 따라 차이가 많다는 것은 임상경험을 통하여 널리 알려져 있다. 그러나 아직 이를 미리 예측할 수 있는 인자로 알려진 것은 없다. XRCC1 유전자는 DNA base-excision repair에 관여하는 유전자로 알려져 있다 저자들은 대장 직장암 환자를 대상으로 방사선치료와 항암제치료로 인한 급성부작용과 XRCC1 유전자의 다형성이 관련이 있는지를 알아보고자 본 연구를 수행하게 되었다. 대상 및 방법: 1997년 7월부터 2003년 6월까지 인하대학교병원에서 치료를 받은 대장 직장암 환자 85명을 대상으로 하였다. 대장암이 2명, 5자결장암이 13명, 직장암이 71명이었다 병기는 B기가 22명, C기가 50명, D기가 8명이었고 절제 불가능한 경우가 6명이었다 방사선치료 범위는 골반강만 조사된 경우가 81명, extended field로 조사된 경우가 5명이었고 방사선량은 일일 1.8 Gy로 주 5회 조사하여 총 $30.6 Gy{\sim}59.4 Gy$ (중앙값: 54 Gy)를 조사하였다. 항암제치료는 전 환자에서 5FU를 근간으로 한 약제를 투여받았고 방사선 치료기간 중에 시행된 횟수는 1회가 24명, 2회가 45명이었고 17명은 동시에 투여 받지는 않았다. 치료의 급성부작용은 상부위장관과 하부위장관으로 나누어 기록하였고 증상이 전혀 없는 경우를 0, 증상이 있으나 투약이 필요하지 않은 경우를 1, 투약이 필요한 경우를 2, 투약에도 불구하고 증상이 심하여 치료의 휴식 또는 입원을 한 경우를 3으로 분류하였고 전 치료기간 중 최초, 최저 수치와 방사선치료기간 중 최초, 최저 백혈구, 혈소판 수치를 조사하였다. 환자의 동의 하에 혈액을 채취하여 림프구를 분리한 후 DNA를 추출하여 PCR-RFLP 방법으로 XRCC1 유전자의 코돈 194, 280, 399번 위치의 다형성을 분석하였다. 통계는 Chi-square, t-test, logistic regression, ANOVA를 사용하였다. 결과: 다변량 분석결과 상부위장관 부작용에 영향을 미치는 인자는 재발유무였고, 하부위장관의 부작용에 영향을 미치는 인자는 XRCC1 339 다형성, 방사선량, 방사선 중 항암제횟수 순이었다. 방사선 치료 중 백혈구 감소에 영향을 미치는 인자는 XRCC1 399 다형성, 194 다형성이었고, 혈소판 감소에 영향을 미치는 인자는 진단명, XRCC1 399 다형성이었다. 결론: 대장 직장암 환자에서 방사선치료와 항암제의 치료에 따른 정상조직의 급성부작용을 예측하는데 XRCC1 유전자의 코돈 399번의 다형성이 사용될 가능성이 있을 것으로 생각된다.