• 한국육종학회지
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• 제41권3호
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• pp.194-204
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• 2009

Cytoplasmic male sterility (CMS) and fertility restoration have been utilized as valuable tools for $F_1$-hybrid seed production in many crops despite laborious breeding processes. Molecular markers for the selection of CMS-related genes help reduce the expenses and breeding times. A previously reported genomic region containing the Ppr-B gene, which is responsible for restoration of fertility and corresponds to the Rfo locus, was used to develop gene-based or so-called "functional" markers for allelic selection of the restorer-of-fertility gene (Rfo) in $F_1$-hybrid breeding of radish (Raphanus sativus L.) Polymorphic sequences among Rfo alleles of diverse breeding lines of radish were examined by sequencing the Ppr-B alleles. However, presence of Ppr-B homolog, designated as Ppr-D, interferes on specific PCR amplification of Ppr-B in certain breeding lines. The organization of Ppr-D, resolved by genome walking, revealed extended homology with Ppr-B even in the promoter region. Interestingly, PCR amplification of Ppr-D was repeatedly unsuccessful in certain breeding lines implying the lack of Ppr-D in these radishes. Ppr-B could only be successfully amplified for analysis through designing primers based on the sequences unique to Ppr-B that exclude interference from Ppr-D gene. Four variants of Rfo alleles were identified from 20 breeding lines. A combination of three molecular markers was developed in order to genotype the Rfo locus based on polymorphisms among four different variants. These markers will be useful in facilitating $F_1$-hybrid cultivar development in radish.

• 한국전통의학지
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• 제15권1호
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• pp.83-89
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• 2006

Many naturally occurring plant extracts are studied for their beneficial effects for health and particularly on cancer. Apoptosis, or programmed cell death, occurs in both normal and pathological conditions, including cancer. Dysregulation of apoptosis allows transformed cells to continually and uninhibitedly enter the cell cycle, thus perpetuating the sequence of mutation, genomic instability and, finally, oncogenesis. To investigate the apoptosis-Inducing effect of the extract of Fructus Trichosanthis (EFT) on leukemic HL-60 cells and its mechanism, HL-60 cells in vitro in culture medium were given different doses of the extract. The inhibitory rate of cells were measured by microculture tetrazolium assay, cell apoptotic rate was detected by flow cytometry, morphology of cell apoptosis was observed by DAPI fluorescence staining, and the activations of caspases and PARP were detected using Western blotting analysis. The extract could activate the caspase-3 and caspase-8, induce PARP cleavage, inhibit growth of HL-60 cells, and cause apoptosis significantly. The suppression was in dose-dependent manner. Marked morphological changes of cell apoptosis including condensation of chromatin and nuclear fragmentation were observed clearly by DAPI fluorescence staining especially. These results will provide strong laboratory evidence of EFT for clinical treatment of acute leukemia.

• 한국자원식물학회지
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• 제14권3호
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• pp.235-240
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• 2001

Polyphenol 화합물이 다량 함유된 식물종의 유연관계 분석이나 형질전환 유전자 확인 등을 위해 PCR을 이용할 경우 다량의 재료로부터 신속 간편하게 분리한 DNA를 이용할 수 있는 조건을 설정 하였다. 폴리페놀 함량이 높은 포도, 사과, 복분자와 같은 과수류에서 간편법에 의해 추출된 DNA를 이용한 PCR 반응액에 2%의 BLOTTO를 첨가함으로서 DNA의 재현적 증폭이 가능하였다. 간편 추출 DNA를 이용한 PCR에서 의 BLOTTO효과는 primer, 품종, 식물종에 관계없이 일반적으로 발현되었다. 상추의 형질전환 유전자 검색을 위한 PCR에서 도 BLOTTO 효과가 확인되었다. 따라서 PCR 반응액에 2% BLOTTO를 첨가하면 간편 법 에 의해 추출된 polyphenol 화합물 고함유 식물종의 DNA를 이용하여서도 PCR에 의한 유전배경 및 특정 유전자의 대량 신속 분석이 가능할 것이다.

• 한국자원식물학회지
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• 제13권2호
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• pp.104-110
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• 2000

가시오갈피 및 오갈피의 수집종 간의 유연관계를 구명하기 위하여 RAPD 분석을 한 결과 10개의 primer를 선발하였으며 G+C의 수가 모두 60%이상이었다. 10개의 primer를 사용하여 얻을 수 있는 총 밴드 수는 106개 였으며 이중 monomorphic한 밴드는 17.9%에 해당하는 19개였으며 나머지 87개는 polymorphic한 것으로 나타났다. 10개의 primer를 사용하여 얻은 106개의 밴드를 각각 하나의 형질(character)로 보아 이를 유연관계를 분석한 결과 영월 수집종과 일본종 및 지리산 오갈피와 서울오갈피를 포함하는 군(Group I )과 국내종과 러시아종, 중국종을 포함하는 군(Group II)으로 나뉘어졌으며 genetic distance값의 평균은 0.61이었다. Group I으로 분류된 북해도 가시오갈피는 국내의 각 수집지역의 가시오갈피나 러시아 가시오갈피와 원연의 관계인 것으로 나타났으며 2군에 포함된 수집 지역종 간의 원연 관계 중 춘천 수집종은 국내의 다른 지역인 잠곡이나 태기산 오대산 등과 비교하여 러시아 산이나 중국산에 대하여 더 근연의 관계를 나타내었다.

• Molecules and Cells
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• 제44권9호
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• pp.680-687
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• 2021

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing.

• BMB Reports
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• 제54권7호
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• pp.386-391
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• 2021

Owing to rapid advancements in NGS (next generation sequencing), genomic alteration is now considered an essential predictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was considered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly compared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture region, which might lead to different values of TMB; the evaluation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evaluated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R² = 0.887). This was also reflected in clinical samples (n = 100), which showed R² of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.

• Journal of Breast Cancer
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• 제21권4호
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• pp.391-398
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• 2018

Purpose: The aim of this study was to investigate the association of telomere length with breast cancer risk. We simultaneously explored the association between telomerase reverse transcriptase gene polymorphisms and telomere length. Methods: We used real-time quantitative polymerase chain reaction to measure relative telomere length (RTL) in genomic DNA extracted from peripheral blood from 183 breast cancer cases and 191 healthy controls. Genotyping was performed using the Sequenom MassARRAY platform. Results: Our results show that breast cancer patients had significantly shorter RTLs than control subjects (p<0.05). When the RTLs were categorized into tertiles, we found that the lowest RTL was significantly associated with increased breast cancer risk compared with the highest RTL (odds ratio [OR], 2.33; 95% confidence interval [CI], 1.40-3.90; p=0.001). Subgroup analyses indicated that risk of breast cancer was also significantly increased in the lowest RTL compared with the highest RTL in age >40 years (OR, 2.41; 95% CI, 1.31-4.43;p=0.005), body mass index ${\leq}24kg/m^2$ (OR, 2.81; 95% CI, 1.55-5.10; p=0.001), and postmenopausal women (OR, 3.94; 95% CI, 1.63-9.51; p=0.002), respectively. In addition, individuals with the AA genotype of rs2853677 have longer telomeres than those of breast cancer patients with the AG genotype (p=0.011). Conclusion: Our results suggest that shorter RTL was associated with an increased risk of breast cancer. An association was found between the AA genotype of rs2853677 and longer RTLs in the case group. Functional studies are warranted to validate this association and further investigate our findings.

• Plant Breeding and Biotechnology
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• 제5권3호
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• pp.237-242
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• 2017

AT-hook proteins of plant have shown to be involved in growth and development through the modification of chromatin architecture to co-regulate transcription of genes. Recently, many genes encoding AT-hook protein have been identified and their involvement in senescence delay is investigated. In this study, soybean transgenic plants overexpressing chromatin architecture-controlling ATPG7 gene was produced by Agrobacterium-mediated transformation and investigated for the positive effect on the important agronomic traits mainly focusing on yield-related components. A total of 27 transgenic soybean plants were produced from about 400 explants. $T_1$ seeds were harvested from all transgenic plants. In the analysis of genomic DNAs from soybean transformants, ATPG7 and Bar fragments were amplified as expected, 975 bp and 408 bp in size, respectively. And also exact gene expression was confirmed by reverse transcriptase-PCR (RT-PCR) from transgenic line #6, #7 and #8. In a field evaluation of yield components of ATPG7 transgenic plants ($T_3$), higher plant height, more of pod number and greater average total seed weight were observed with statistical significance. The results of this study indicate that the introduction of ATPG7 gene in soybean may have the positive effect on yield components.

• 한국육종학회지
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• 제42권5호
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• pp.481-487
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• 2010

The ripening behavior of three apple cultivars, 'Tsugaru', 'Hongro' and 'Fuji' was distinctive and the involvement of POLYGALACTURONASE(PG) in the fruit softening process was confirmed to be ethylene dependent. Fruit softening is genetically coordinated by the action of several cell wall enzymes, including PG which depolymerizes cell wall pectin. Also, loss of firmness is associated with increasing of the ripening hormone, ethylene. In this work, climacteric ripening of three apple cultivars, Tsugaru, Hongro and Fuji, producing different ethylene levels and ripening responses, was examined. Correspondingly in Fuji, a linear and basal ethylene level was observed over the entire period of measurements, and Tsugaru and Hongro displayed a typical climacteric rise in ethylene production. Transcript accumulation of genes involved in ethylene biosynthesis (MdACS3 and MdACO1) and MdPG1 was studied in Tsugaru, Hongro and Fuji cultivars. Expression of MdACO1 transcripts was shown in all three ripened apple fruits. However, the MdACS3 and MdPG1 were transcribed differently in these cultivars. Comparing the MdPG1 of 'Tsugaru', 'Hongro' and 'Fuji', structural difference was discovered by genomic Southern analysis. Overall results pointed out that MdACS3 and MdPG1 play an important role in regulation of fruit ripening in apple cultivar.

• 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.