• 한국육종학회지
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• 제43권5호
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• pp.375-382
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• 2011

A chemical, MNU-induced hulless barley mutant line designated as 'Mutant 98 (M98)' was developed from a Korean hulless waxy barley cultivar, 'Chalssalbori'. The objective of the study was to determine the genetic basis of 'M98' and the possibility of using 'M98' as breeding parent to improve lysine level. Compared to 'Chalssalbori', 'M98' had large embryo and higher lysine content in both the embryo and endosperm. Significantly different lysine content in 'M98' and the other high-lysine barley mutant stocks was observed for two years. However, the genotype by year interaction was not significant. 'M98' was higher than the other high-lysine barley mutant stocks in the percentage of lysine of total amino acid composition (0.75%). The trait of shrunken endosperm of 'M98', which was typical in the high-lysine mutants, was inherited by a single recessive gene. Based on seed morphology and lysine content of $F_1$ seeds, 'M98' had a genetically different gene from the other high-lysine mutants for shrunken endosperm. Segregation of $F_2$ for plump/shrunken endosperm did not fit the expected ratio of Mendelian inheritance except for only one cross combination (GSHO1784 (lys1)/M98). The amino acid analysis of $F_5$ and $F_6$ progenies from the cross between 'M98' and 'Chalssalbori' revealed that the attempt to increase the range of lysine content of plump lines did not go beyond the limit of the average high-lysine barley germplasm.

• Genes and Genomics
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• 제40권12호
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• pp.1279-1285
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• 2018

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.

• 대한의용생체공학회:의공학회지
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• 제42권3호
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• pp.125-142
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• 2021

The POCT (point-of-care test) sensing that has been a fast-developing field is expected to be a next generation technology in health care. The POCT sensors for the detection of proteins, small molecules and especially nucleic acids have lately attracted considerable attention. According to the World Health Organization (WHO), the POCT methods are required to follow the ASSURED guidelines (Affordable, Sensitive, Specific, User- friendly, Robust and rapid, Equipment-free, Deliverable to all people who need the test). Recently, several CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) based diagnostic techniques using the sensitive gene recognition function of CRISPR have been reported. CRISPR/Cas (Cas, CRISPR associated protein) systems based detection technology is the most innovative gene analysis technology that is following the ASSURED guidelines. It is being re-emerged as a powerful diagnostic tool that can detect nucleic acids due to its characteristics that enable rapid, sensitive and specific analyses of nucleic acid. The first CRISPR-based diagnosis begins with the discovery of the additional function of Cas13a. The enzymatic cleavage occurs when the conjugate of Cas protein and CRISPR RNA (crRNA) detect a specific complementary sequence of the target sequence. Enzymatic cleavage occurs on not only the target sequence, but also all surrounding non-target single-stranded RNAs. This discovery was immediately utilized as a biosensor, and numerous sensor studies using CRISPR have been reported since then. In this review, the concept of CRISPR, the characteristics of the Cas protein required for CRISPR diagnosis, the current research trends of CRISPR diagnostic technology, and some aspects to be improved in the future are covered.

• Animal Bioscience
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• 제35권8호
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• pp.1129-1140
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• 2022

Objective: With improvements in living standards and increase in global population, the demand for meat products has been increasing; improved meat production from livestock could effectively meet this demand. In this study, we examined the differences in the muscle traits of different male crossbred sheep and attempted to identify key genes that regulate these traits. Methods: Dubo sheep×small-tailed Han sheep (DP×STH) and Suffolk×small-tailed Han sheep (SFK×STH) were selected to determine meat quality and production performance by Masson staining. Transcriptome sequencing and bioinformatic analysis were performed to identify differentially expressed genes (DEGs) related to meat quality. The presence of DEGs was confirmed by real-time polymerase chain reaction. Results: The production performance of SFK×STH sheep was better than that of DP×STH sheep, but the meat quality of DP×STH sheep was better than that of SFK×STH sheep. The muscle fiber diameter of DP×STH sheep was smaller than that of SFK×STH sheep. Twenty-two DEGs were identified. Among them, four gene ontology terms were related to muscle traits, and three DEGs were related to muscle or muscle fibers. There were no significant differences in the number of single nucleotide mutations and mutation sites in the different male parent cross combinations. Conclusion: This study provides genetic resources for future sheep muscle development and cross-breeding research.

• Asian Pacific Journal of Cancer Prevention
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• 제14권11호
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• pp.6403-6409
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• 2013

Purpose: Biallelic germline variants of the 8-hydroxyguanine (8-OG) repair gene MYH have been associated with colorectal neoplasms that display somatic $G:C{\rightarrow}T:A$ transversions. However, the effect of single germline variants has not been widely studied, prompting the present investigation of monoallelic MYH variants and susceptibility to sporadic colorectal cancer (CRC) in a Chinese population. Patients and Methods: Between January 2006 and December 2012, 400 cases of sporadic CRC and 600 age- and sex-matched normal blood donors were screened randomly for 7 potentially pathogenic germline MYH exons using genetic testing technology. Variants of heterozygosity at the MYH locus were assessed in both sporadic cancer patients and healthy controls. Univariate and multivariate analyses were performed to determine risk factors for cancer onset. Results: Five monoallelic single nucleotide polymorphisms (SNPs) were identified in the 7 exon regions of MYH, which were detected in 75 (18.75%) of 400 CRC patients as well as 42 (7%) of 600 normal controls. The region of exon 1 proved to be a linked polymorphic region for the first time, a triple linked variant including exon 1-316 $G{\rightarrow}A$, exon 1-292 $G{\rightarrow}A$ and intron 1+11 $C{\rightarrow}T$, being identified in 13 CRC patients and 2 normal blood donors. A variant of base replacement, intron 10-2 $A{\rightarrow}G$, was identified in the exon 10 region in 21 cases and 7 controls, while a similar type of variant in the exon 13 region, intron 13+12 $C{\rightarrow}T$, was identified in 8 cases and 6 controls. Not the only but a newly missense variant in the present study, p. V463E (Exon 14+74 $T{\rightarrow}A$), was identified in exon 14 in 6 patients and 1 normal control. In exon 16, nt. 1678-80 del GTT with loss of heterozygosity (LOH) was identified in 27 CRC cases and 26 controls. There was no Y165C in exon 7 or G382D in exon 14, the hot-spot variants which have been reported most frequently in Caucasian studies. After univariate analysis and multivariate analysis, the linked variant in exon 1 region (p=0.002), intron 10-2 $A{\rightarrow}G$ (p=0.004) and p. V463E (p=0.036) in the MYH gene were selected as 3 independent risk factors for CRC. Conclusions: According to these results, the linked variant in Exon 1 region, Intron 10-2 $A{\rightarrow}G$ of base replacement and p. V463E of missense variant, the 3 heterozygosity variants of MYH gene in a Chinese population, may relate to the susceptibility to sporadic CRC. Lack of the hot-spot variants of Caucasians in the present study may due to the ethnic difference in MYH gene.

• Journal of Genetic Medicine
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• 제5권1호
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• pp.34-40
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• 2008

목 적 : 자간전증은 임신부와 신생아의 사망 및 이환의 주된 원인으로 유전적 소질과 환경적 요인에 의해 발생하는 다요인성 질환이다. ET-1은 강력한 혈관수축 펩티드로 ET-1 시스템 내의 변경이 자간전증에서의 혈관수축을 자극하는 것으로 생각되고 있다. 본 연구에서는 정상 임신부와 자간전증 임신부에서 ET-1 유전자의 4가지 단일염기다형성들(c.1370T>G, c.137_139delinsA, c.3539+2T>C, and c.5665G >T)의 양상을 조사하여 비교함으로써 이러한 유전자 다형성들과 한국인 자간전증의 연관성에 대하여 알아보고자 하였다. 방 법 : 자간전증 임신부 206명과 임신기간 동안 자간전증이 발생하지 않은 정상 임신부 216명의 혈액으로부터 DNA를 추출하고 ET-1 유전자 다형성들의 양상을 SNapShot kit와 ABI Prism 3100 Genetic analyzer를 사용하여 분석하였다. 결 과 : 자간전증 환자군에서 ET-1 유전자의 4가지 단일 염기다형성 각각의 유전자형 및 대립유전자의 빈도는 대조군과 유의한 차이가 없었다. 또한 자간전증 환자군에서 3가지 일배체형(TDTG, GDCT, and TICT)의 빈도도 대조군과 유의한 차이가 없었다: 61%(TDTG), 13%(GDCT), 13%(TICT) vs. 62%, 14%, 12%. 나이, 미산부률, 분만주수, 신체질량지수 등의 자간전증 발생요인을 공변량으로 하여 유전자형과 자간전증 발생의 위험도 사이의 연관성을 확인하기 위해 다중회귀분석을 시행한 결과 열성모델과 우성모델에서 모두 ET-1 유전자의 단일염기다형성들에 대한 자간전증 발생의 위험도가 증가하지 않았다. 결 론 : 한국인 임신부에서 ET-1 유전자의 4가지 단일염기 다형성들은 자간전증 발생과 연관이 없는 것으로 사료된다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권9호
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• pp.4327-4330
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• 2012

The mouse double minute 2 (MDM2) gene plays a key role in the p53 pathway, and the SNP 309T/G single-nucleotide polymorphism in the promoter region of MDM2 has been shown to be associated with increased risk of cancer. However, no consistent results were found concerning the relationships between the polymorphism and prostate cancer risk. This meta-analysis, covering 4 independent case-control studies, was conducted to better understand the association between MDM2-SNP T309G and prostate cancer risk focusing on overall and subgroup aspects. The analysis revealed, no matter what kind of genetic model was used, no significant association between MDM2-SNP T309G and prostate cancer risk in overall analysis (GT/TT: OR = 0.84, 95%CI = 0.60-1.19; GG/TT: OR = 0.69, 95%CI = 0.43-1.11; dominant model: OR = 0.81, 95%CI= 0.58-1.13; recessive model: OR = 1.23, 95%CI = 0.95-1.59). In subgroup analysis, the polymorphism seemed more likely to be a protective factor in Europeans (GG/TT: OR = 0.52, 95%CI = 0.31-0.87; recessive model: OR = 0.58, 95%CI = 0.36-0.95) than in Asian populations, and a protective effect of the polymorphism was also seen in hospital-based studies in all models (GT/TT: OR = 0.74, 95%CI = 0.57-0.97; GG/TT: OR = 0.55, 95%CI = 0.38-0.79; dominant model: OR = 0.69, 95%CI = 0.54-0.89; recessive model: OR = 0.70, 95%CI = 0.51-0.97). However, more primary studies with a larger number of samples are required to confirm our findings.

• Journal of Crop Science and Biotechnology
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• 제11권2호
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• pp.91-100
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• 2008

Melting curve analysis of fluorescently labeled DNA fragments is used extensively for genotyping single nucleotide polymorphism(SNP). Here, we evaluated a SNP genotyping method by melting curve analysis with the two probe chemistries in a 384-well plate format on a Roche LightCycler 480. The HybProbe chemistry is based on the fluorescence resonance energy transfer(FRET) and the SimpleProbe chemistry uses a terminal self-quenching fluorophore. We evaluated FRET HybProbes and SimpleProbes for two SNP sites closely linked to two quantitative trait loci(QTL) for southern root-knot nematode resistance. These probes were used to genotype the two parents and 94 $F_2$ plants from the cross of PI 96354$\times$Bossier. The SNP genotypes of all samples determined by the LightCycler software agreed with previously determined SSR genotypes and the SNP genotypes determined on a Luminex 100 flow cytometry instrument. Multiplexed HybProbes for the two SNPs showed a 98.4% success rate and 100% concordance between repeats two of the same 96 DNA samples. Also, we developed a HybProbe assay for the Rcs3 gene conditioning broad resistance to the frogeye leaf spot(FLS) disease. The LightCycler 480 provides rapid PCR on 384-well plate and allows simultaneous amplification and analysis in approximately 2 hours without any additional steps after amplification. This allowed for a reduction of the potential contamination of PCR products, simplicity, and enablement of a streamlined workflow. The melting curve analysis on the LightCycler 480 provided high-throughput and rapid SNP genotyping and appears highly effective for marker-assisted selection in soybean.

• Genes and Genomics
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• 제40권12호
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• pp.1331-1338
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• 2018

Although there have been plenty of dominance deviation analysis, few studies have dealt with multiple phenotypes. Because researchers focused on multiple phenotypes (final weight and backfat thickness) of Landrace pigs, the classification of the genes was possible. With genome-wide association studies (GWASs), we analyzed the additive and dominance effects of the single nucleotide polymorphisms (SNPs). The classification of the pig genes into four categories (overdominance in final weight, overdominance in backfat thickness and overdominance in final weight, underdominance in backfat thickness, etc.) can enable us not only to analyze each phenotype's dominant effects, but also to illustrate the gene ontology (GO) analysis with different aspects. We aimed to determine the additive and dominant effect in backfat thickness and final weight and performed GO analysis. Using additive model and dominance deviation analysis in GWASs, Landrace pigs' overdominant and underdominant SNP effects in final weight and backfat thickness were surveyed. Then through GO analysis, we investigated the genes that were classified in the GWASs. The major GO terms of the underdominant effects in final weight and overdominant effects in backfat thickness were ion transport with the SLC8A3, KCNJ16, P2RX7 and TRPC3 genes. Interestingly, the major GO terms in the underdominant effects in the final weight and the underdominant effects in the backfat thickness were the regulation of ion transport with the STAC, GCK, TRPC6, UBASH3B, CAMK2D, CACNG4 and SCN4B genes. These results demonstrate that ion transport and ion transport regulation genes have distinct dominant effects. Through GWASs using the mode of linear additive model and dominance deviation, overdominant effects and underdominant effects in backfat thickness was contrary to each other in GO terms (ion transport and ion transport regulation, respectively). Additionally, because ion transport and ion transport regulation genes are associative with adipose tissue accumulation, we could infer that these two groups of genes had to do with unique fat accumulation mechanisms in Landrace pigs.

• Clinical and Experimental Pediatrics
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• 제45권2호
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• pp.183-191
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• 2002

목 적 : 본 연구에서는 임상적으로 XLA로 진단받고 현재 치료 중인 한가족 3명 환아의 가계를 대상으로 말초혈액 단핵구의 Btk 단백질 발현과 Btk 유전자 변이를 분석하고자 하였다. 방 법 : 환아 말초혈액 단핵구의 Btk 발현도를 항 Btk 항체를 이용한 유세포계측을 통해 분석하고 PCR-SSCP 및 직접 염기서열 분석에 의해 Btk 유전자 변이를 분석하였다. 결 과 : 유세포 계측 및 PCR-SSCP에 의하여 가계내의 환자 3명 및 보인자 4명을 확인하였으며 환아들의 단핵구의 Btk 발현도를 조사한 결과 2.7% 미만으로 건강인에 비해 매우 유의한 감소를 나타내었다. 유전자 변이 분석 결과 Btk 유전자 exon 3에서 점돌연변이($T{\rightarrow}C$)가 발견되어 61번째 아미노산의 치환이 일어난 과오돌연변이를 확인할 수 있었다. 동일한 유전형을 지닌 3명의 환아들은 임상적으로 매우 다양한 표현형을 나타내었다. 특히 환아들의 혈청 IgG level이 낮을수록 임상 양상은 심한 소견을 보였다. 결 론 : 본 연구 결과를 종합해 볼 때 임상적으로 XLA로 진단된 환아와 가족에 대한 항 Btk 항체를 이용한 유세포계측 및 PCR-SSCP 방법은 XLA 환아 및 보인자의 진단에 매우 유용하며 신속하게 적용될 수 있는 기법으로 생각된다. 또한 분자유전학 기법을 이용하여 환아의 유전자 변이를 검색한 결과 Btk의 PH 도메인 내 한개의 과오돌연변이를 검색하여 XLA를 최종 확진할 수 있었다.