• 대한의생명과학회지
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• 제29권4호
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• pp.302-313
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• 2023

Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex^® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10^-2) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10^-3). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

• International Journal of Stem Cells
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• 제16권4호
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• pp.438-447
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• 2023

Recently, ex-vivo gene therapy has emerged as a promising approach to enhance the therapeutic potential of mesenchymal stem cells (MSCs) by introducing functional genes in vitro. Here, we explored the need of using selection markers to increase the gene delivery efficiency and evaluated the potential risks associated with their use in the manufacturing process. We used MSCs/CD that carry the cytosine deaminase gene (CD) as a therapeutic gene and a puromycin resistance gene (PuroR) as a selection marker. We evaluated the correlation between the therapeutic efficacy and the purity of therapeutic MSCs/CD by examining their anti-cancer effect on co-cultured U87/GFP cells. To simulate in vivo horizontal transfer of the PuroR gene in vivo, we generated a puromycin-resistant E. coli (E. coli/PuroR) by introducing the PuroR gene and assessed its responsiveness to various antibiotics. We found that the anti-cancer effect of MSCs/CD was directly proportional to their purity, suggesting the crucial role of the PuroR gene in eliminating impure unmodified MSCs and enhancing the purity of MSCs/CD during the manufacturing process. Additionally, we found that clinically available antibiotics were effective in inhibiting the growth of hypothetical microorganism, E. coli/PuroR. In summary, our study highlights the potential benefits of using the PuroR gene as a selection marker to enhance the purity and efficacy of therapeutic cells in MSC-based gene therapy. Furthermore, our study suggests that the potential risk of horizontal transfer of antibiotics resistance genes in vivo can be effectively managed by clinically available antibiotics.

• 한국육종학회지
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• 제50권4호
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• pp.387-395
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• 2018

다산 등 15개의 통일형 벼 품종을 이용하여 mesotrione을 처리한 후 5일부터 다산 등 13개 품종들은 신엽에서 백화현상이 발생하였으나, 밀양154호와 수원382호는 백화현상이 발생하지 않아 저항성 품종으로 선발되었다. Mesotrione 처리 후 다산 등 13개 품종들의 초장 및 건물중 억제율은 밀양154호와 수원382호보다 더 높았으며 약량에 따른 억제율이 증가하였다. 한아름2호/밀양154호의 $F_2$ 집단을 이용한 유전분석 결과 저항성이 149개체, 감수성이 41개체로 이론적 분리비 3:1($X^2=1.19$, P=0.31)에 적합하여, mesotrione 저항성 관련 유전자는 1개의 우성유전자에 지배되는 것으로 나타났다. BSA방법을 이용하여 mesotrione 저항성 관련 유전자를 탐색한 결과, 2번 염색체의 10.2 Mb에 위치한 SSR marker RM1358과 RM3501을 선발하였다. Fine mapping을 위해 선발된 5개의 저항성 개체 중에서 $F_2-137$은 RM12921부터 RM3501까지 재조환이 일어났고, $F_2-76$은 RM324부터 RM5101까지 재조환이 일어났다. 따라서, mesotrione 저항성 관련 유전자는 RM3501과 RM324 사이인 10.2 Mb~11.4 Mb에 존재하며, RM3501과 RM324의 조환률이 각각 0.53%과 2.65%이므로, RM3501을 mesotrione저항성 유전자 DNA 연관 marker로 선발하였다. 다산 등 20개 통일형 품종 및 mesotrione에 저항성을 나타내는 자포니카 품종인 운광과 감수성인 통일형 한아름의 $BC_2F_2$ 집단을 이용하여 RM3501의 MAS 이용 가능성을 검토한 결과, mesotrione 저항성 선발 marker로 활용은 가능하나, 정확한 선발 maker로 활용하기 위해서는 추가적인 실험이 필요할 것으로 판단된다.

• 미생물학회지
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• 제30권2호
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• pp.83-87
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• 1992

선택적 표식인자가 전위인자일때, 표식인자의 선택 순서에 따라 동시형질도가 달라진다. 본 연구에서는 이 현상을 설명하기 위하여 아래와 같은 수학적 접근을 시도하였다. 먼저, transducing particle 들의 형성과정을 다섯종류로 유별하였다. 그런다음, 하나의 표지가 고정될 가능성을 의미하는 확률함수들을 확률밀도 개념에 근거하여 수학적으로 정식화였다. 그리고 실제 값들과 유용한 가정들을 이식들에 결합하여 그로부터 얻어진 이론적인 빈도를 실측 값들과 비교하였다. 이려한 분석에 의하여 그 빈도의 상이성이 일반 재조합에 필요한 상용성을 전위인자가 제공하지 봇하고, 그 주변에 재조합 빈도를 거리에 의존하는 형태로 감소시키기 때문이라는 결론을 얻었다.

• 한국정보통신학회논문지
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• 제14권10호
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• pp.2365-2370
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• 2010

마이크로어레이를 기반으로 하는 암 분류 방법은 암 종류에 따라 다르게 발현되는 유전자 양상을 통계적으로 발견함으로써 정확한 암 분류에 기여할 수 있다. 따라서 현재의 마이크로어레이 기술을 이용해서 효과적으로 암을 분류하기 위해서는 특정 암과 밀접하게 관련이 있는 정보력 있는 유전자를 선택하는 과정이 필수적이다. 본 논문에서는 난소 암 마이크로어레이 데이터를 이용하여 암에 영향을 미치는 가장 다르게 발현할 가능성이 있는 표지 유전자를 추출할 수 있는 시스템을 고안하고, 다층퍼셉트론 분류기를 이용하여 기존의 마이크로어레이 시스템과 분류 성능을 비교분석하였다. 그 결과 ANOVA를 이용하여 선택된 표지 유전자를 포함하는 마이크로어레이 데이터 셋에서 98.61%의 향상된 분류 성능을 보였다.

• Journal of Electrical Engineering and Technology
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• 제13권6호
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• pp.2530-2544
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• 2018

In this paper, we propose an enhanced LiDAR-camera calibration method that extracts the marker plane from 3D point cloud information. In previous work, we estimated the straight line of each board to obtain the vertex. However, the errors in the point information in relation to the z axis were not considered. These errors are caused by the effects of user selection on the board border. Because of the nature of LiDAR, the point information is separated in the horizontal direction, causing the approximated model of the straight line to be erroneous. In the proposed work, we obtain each vertex by estimating a rectangle from a plane rather than obtaining a point from each straight line in order to obtain a vertex more precisely than the previous study. The advantage of using planes is that it is easier to select the area, and the most point information on the board is available. We demonstrated through experiments that the proposed method could be used to obtain more accurate results compared to the performance of the previous method.

• Journal of Plant Biotechnology
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• 제43권1호
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• pp.76-81
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• 2016

We performed a molecular marker-based analysis of quantitative trait loci for traits that determine the quality of appearance of grains using 120 doubled haploid lines developed by anther culture from the F1 cross between 'Cheongcheong' (Oryza sativa L. ssp. Indica) and 'Nagdong' (Oryza sativa L. ssp. Japonica). We therefore calculated the alkali digestion value (ADV), used to indirectly measure gelatinization temperature, to evaluate the quality of cooked rice in 2013 and 2014. The ADV score of frequency distribution was higher milled rice than brown rice. In total, nine different quantitative trait loci (QTLs) were found on 5 chromosomes in 2013 and 2014. Also, chromosome 5, 8 were detected over two years. We conclude that selected molecular markers from this QTL analysis could be exploited in future rice quality. In conclusion, we investigated ADV of brown and milled rice in CNDH population. This study found nine QTLs related to the ADV of brown and milled rice. The detected one marker can be used to select lines with desirable eating-quality traits because ADV is closely associated with the eating quality of cooked rice. Therefore, it will be useful to collect resources and distinguishable in many varieties for rice breeding program.

• Plant Biotechnology Reports
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• 제2권4호
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• pp.239-243
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• 2008

Simmondsia chinensis (Link) Schneider, a multipurpose and monogeneric dioecious shrub from arid zones, has emerged as a cash crop all over the globe. Its seed propagation poses severe problems due to its male-biased population: the male:female ratio is 5:1. Investigations have been carried out to generate a sex-specific Inter-simple sequence repeat (ISSR) marker for the early detection of male and female plants. Of the 42 primers analysed with a bulk sample of pooled male DNA and a bulk sample of pooled female DNA, only one primer, UBC-807, produced a unique ~1,200 base-pair fragment in the male DNA. To validate this observation, this primer was re-tested with individual male and female samples from eight cultivars. A similar unique ~1,200 bp fragment was present in the male individuals of all eight cultivars and completely absent in the female individuals tested. This is the first report of the use of ISSR markers to ascertain sex in physiologically mature S. chinensis plants.

• Molecules and Cells
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• 제20권2호
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• pp.201-209
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• 2005

We have constructed an AFLP-based linkage map of Japanese red pine (Pinus densiflora Siebold et Zucc.) using haploid DNA samples of 96 megagametophytes from a single maternal tree, selection clone Kyungbuk 4. Twenty-eight primer pairs generated a total of 5,780 AFLP fragments. Five hundreds and thirteen fragments were verified as genetic markers with two alleles by their Mendelian segregation. At the linkage criteria LOD 4.0 and maximum recombination fraction 0.25(${\theta}$), a total of 152 markers constituted 25 framework maps for 19 major linkage groups. The maps spanned a total length of 2,341 cM with an average framework marker spacing of 18.4 cM. The estimated genome size was 2,662 cM. With an assumption of equal marker density, 82.2% of the estimated genome would be within 10 cM of one of the 230 linked markers, and 68.1% would be within 10 cM of one of the 152 framework markers. We evaluated map completeness in terms of LOD value, marker density, genome length, and map coverage. The resulting map will provide crucial information for future genomic studies of the Japanese red pine, in particular for QTL mapping of economically important breeding target traits.

• Biotechnology and Bioprocess Engineering:BBE
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• 제9권3호
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• pp.217-222
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• 2004

As Agrobacterium tumefaciens, which has long been used to transform plants, is known to transfer T-DNA to budding yeast, Saccharomyces cerevisiae, a variety of fungi were subjected to the A. tumefaciens-mediated transformation to improve their transformation frequency and feasibility. The A. tumefaciens-mediated transformation of chestnut blight fungus, Cryphonectria parasitica, is performed in this study as the first example of transformation of a hardwood fungal pathogen. The transfer of the binary vector pBIN9-Hg, containing the bacterial hygromycin B phosphotransferase gene under the control of the Aspergillus nidulans trpC promoter and terminator, as a selectable marker, led to the selection of more than 1,000 stable, hygromycin B-resistant transformants per 1${\times}$10$\^$6/ conidia of C. parasitica. The putative transformants appeared to be mitotically stable. The transformation efficiency appears to depend on the bacterial strain, age of the bacteria cell culture and ratio of fungal spores to bacterial cells. PCR and Southern blot analysis indicated that the marker gene was inserted at different chromosomal sites. Moreover, three transformants out of ten showed more than two hybridizing bands, suggesting more than two copies of the inserted marker gene are not uncommon.