• Journal of Animal Science and Technology
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• v.44 no.1
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• pp.13-22
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• 2002

To identify the differentially expressed genes at growth stage of Hanwoo, we constructed the subtractive cDNA library from loin mRNA of 12- and 24-month old Hanwoo by PCR-based subtraction. The fourteen genes were confirmed by sequencing and reverse northern blot analysis, and they were selected as candidate of putative genes differentially expressed at the growth stage of Hanwoo. Three subtracted cDNA fragments that expressed specific signal to cDNA probe for 6-month-old loin of Hanwoo were highly homologous to those of the genes encoding EPV 20, Ca2＋ATPase, and TCTP, respectively. The nine cDNA clones showed intense signal to cDNA probe from 12-month-old loin of Hanwoo, and highly homologus to those of genes encoding VCP, HSP 70, aldolase A, MSSK1, GM-2 activator protein, ryanodine receptor, acidic ribosomal phosphoprotein p1, ADP/ATP translocase, and UCP 2, respectively. Two subtracted cDNA clones that expressed specific signal to cDNA probes for 12- and 24-month-old loin of Hanwoo were detected. One of them was highly homologus to the gene encoding ferrochelatase and the other was highly homologus to the gene encoding ADRP.

• Journal of Life Science
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• v.21 no.9
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• pp.1329-1335
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• 2011

Korean native goats, which are characterized by black coat color, have existed on the Korean peninsula for a long time. Until now, there has been no comprehensive investigation concerning their genetic diversity, phylogenetic analysis or origin. In this study, we investigated the genetic diversity and verified phylogenetic status of the Korean native goat using the 453-bp fragment of the hypervariable fragment I (HVI) of mitochondrial DNA (mtDNA) D-loop region from 60 individuals among 5 populations. The Korean native goat showed less haplotype diversity when compared with goats from other countries. In addition, 6 haplotypes that had not been previously reported were verified in this study. In phylogenetic analyses with other country's goats, 10 haplotypes from Korean native goats were classified into mtDNA lineage A. Moreover, in a phylogenetic tree for goats which contained mtDNA lineage A, 8 of 10 haplotypes could be included in a subgroup with goats from Vietnam and an area of China. However, none of the remaining haplotypes belonged to a major group of Korean native goats and were located on different independent positions. These results suggest that almost Korean native goats aligned more closely to China and Vietnam breeds in mtDNA lineage A and there was no gene flow from other mtDNA lineages. Our results will contribute to conservation strategies and genetic breeding of Korean native goats.

• Journal of Life Science
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• v.31 no.4
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• pp.410-417
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• 2021

Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, premapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.

• The Journal of the Korea Contents Association
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• v.13 no.8
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• pp.466-473
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• 2013

Gene expression is regulated by a wide range of mechanisms at the DNA sequence level. In addition, gene expression is also regulated by epigenetic mechanisms through DNA methylation, histone modification, and ncRNA. To understand the regulation of gene expression at the epigenetic level, we constructed aging related gene database and analyzed epigenetic properties that are focused on DNA methylation. The DNA methylation of promoter or upstream region of the genes induces to repress the gene expression. We compared and analyzed distribution between whole human genes and aging related genes in the epigenetic properties such as CGI distribution, methylation motif pattern, and TFBS (transcription factor binding site) distribution. In contrast to methylation motif pattern, CGI and TFBS distributions are positively correlated with epigenetic regulation of aging related gene expression. In this study, the epigenetic data about DNA methylation of the aging genes will provide us to understand phenomena of the aging and epigenetic mechanism for regulation of aging related genes.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.27 no.5
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• pp.613-619
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• 1994

To investigate the population differences of small yellow croaker (Pseudosciaena polyactis BLEEKER) in the Yellow Sea, five catching sites (three from China; Zoushan, Shanghai and Qingdao, two from Korea; Inchon and Mokpo) were selected for sampling. The populations of small yellow croaker from all five catching sites were investigated to analyze their mtDNA's restriction fragment length polymorphism (RFLP) using 18 kinds of restriction enzymes. The average molecular size of the entire mtDNA was estimated at $16.9{\pm}0.6\;kb$. According to the results of RFLP analysis, a total of 40 restriction sites were identified in every population surveyed and the overall cleavage patterns of mtDNA, based on the RFLP, showed similar tendencies. However, the five restriction enzymes such as ApaI, EcoRI, PstI, SmaI and SstII showed slightly different cleavage patterns which could have resulted from individual variations between the populations of Korea and China.

• Animal Systematics, Evolution and Diversity
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• v.13 no.1
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• pp.29-36
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• 1997

한국산 기름종개속 어류중 Cobitis taenia complex의 집단간 유전적 차이에 따른 종 분화 여부를 밝히고자 6개 집단을 대상으로 mitochondrial DNA(mtDNA)의 RFLP분석을 실 시하였다. C. taenia complex mtDNA를 10개의 6-base cutting 제한효소로 처리한 다음 그 절편 양상을 비교, 분석한 결과 6개 집단 공히 mtDNA 의 전체 genome 크기는 약 17.0$\pm$ 0.5Kbp였으며 공동절편수(F)에서 C. t. taenia 2개집단과 C. t. stria와 C. t. lutheri 4개 집단 간의 F값은 평균 0.263으로 차이가 있었으나, C. t. striata 와 C. t. lutheri 사이는 F=0.569로 가깝게 나타났다. 염기치환율 (p)에 있어 C. t. taenia는 C. t. striata 및 C. t. lutheri와 평균 p=0.082로 뚜렷한 종간차이를 보였으나, C. t. striata와 C. t. lutheri 집단들은 p=0.033으로 매우 가까운 유사성을 나타내었다. MtDNA 분석결과 C. taenia complex 중 C. t. taenia는 완전히 종분화가 이루어진 별종으로, C. t. striata와 C. t. lutherisms 아직 종수준의 분화가 이루어지지 않은 아종으로 분류함이 타당하다고 사료된다.

• Proceedings of the KIEE Conference
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• 2001.07c
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• pp.1869-1871
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• 2001

DNA 센서의 중요한 역할 중의 하나는 염기서열을 분석함으로써 유전적인 질병이나 돌연변이를 찾아낸다는 점이다. 염기서열 분석법으로 질량, 광학, 전기 화학적 측정법 등이 있는데, 그 중 전기 화학적 측정방법이 타 방법에 비해 간편하고 비용도 저렴해서 전망이 매우 밝다. 전기 화학적 측정을 위해서는 전극의 표면 처리 공정과 전극 표면에서의 DNA immobilization, hybridization 공정 및 전기적 신호를 발생시키는 intercalator, 그리고 전기적 신호 검출을 위한 측정 장비가 필요하다. 본 논문에서는 전극의 표면 처리 물질로서 2-mercaptoethanol을 사용했고 double strand DNA의 intercalator로써 methylene blue를 사용했으며, methylene blue의 환원 전류값을 측정하여 double strand DNA를 bare Au 또는 single strand DNA와 구분할 수 있었다. 이러한 연구 결과를 토대로 하여 전기 화학적 신호 검출을 이용한 DNA 센서의 가능성과 개발 방향을 제시하고자 한다.

• Proceedings of the KSAR Conference
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• 2001.03a
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• pp.37-37
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• 2001

포유동물의 정자형성과정 (spermatogenesis) 은 유사분열과 감수분열이 동시에 일어나는 매우 복잡하지만, 효율적으로 생식세포를 증식, 분화시키는 시스템이다 정상적인 spermatogenesis가 일어나는 testis에서는 haploid (IN), diploid (2N), 그리고 tetraploid(4N)과 같은 핵형을 갖는 세포들이 일정한 비율로 존재한다. DNA flow cytometry(DNA FCM) 는 세포의 핵형(ploidy)을 신속·정확하게 측정하여, 1N, 2N 그리고 4N에 대한 비율을 예측할 수 있어서, 생식세포를 포함한 다양한 유형의 세포주기를 분석하는데 적용되어져 왔다. 세포주기 분석법 중 이와 같은 FCM이외에, flow cytometer와 static image cytometer를 결합시켜 새롭게 고안된 laser scanning cytometer (LSC)가 있다. 그리고, 이제까지 LSC를 사용한 spermatogenesis에 관한 연구에 대해서는 보고된 바가 없다. 본 실험은 설치류에 있어 각기 다른 발달단계에 있는 정상적인 정소세포를 분리하여 PI (propidium iodide) 로 DNA를 염색한 후, DNA함량을 LSC로 분석하였다. 이것을 FCM에 의한 정소세포의 DNA분석과 비교·검토하였으며, 이 방법을 정상적인 spermatogenesis 가 일어나지 않는 동물시스템에 적용시켰다. 생식세포를 소멸시키기 위해 항암제인 busulfan과 비타민 A를 결핍시켜 이것이 세포주기의 어떤 시점에서 어떻게 작용하여, 생식세포를 소멸시키는지 알아보았다. 위의 실험·분석결과로부터 LSC를 사용한 DNA함량과 핵형의 결정은 FCM과 동일한 수준의 정확성을 제시하였다. busulfan 또는 비타민 A의 결손은 살아있는 세포의 80% 이상이 2N의 핵형에 해당하는 G0/G1 기에 있는 것으로 나타났다. 그리고 1N:2N 및 4N:2N의 핵형비율의 변화를 가져왔다. 이러한 자극은 생식세포주기제어에 관여하며, 생식세포가 증폭하고 분화로 들어가는 단계를 차단, G0/G1 기에서 정체(arrest)되는 것으로 시사된다.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.93-103
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• 2023

eDNA, an abbreviation for environmental DNA, means DNA derived from organisms inhabiting in a specific environment. The utilization of eDNA extracted from environmental samples allows for efficient and accurate monitoring of organisms inhabiting the respective environment. Specifically, eDNA obtained from seawater samples can be used to analyze marine biodiversity. After collecting seawater samples and extracting eDNA, metagenome analysis enables the taxonomic and diversity analysis among marine organisms inhabiting the sampled area. This review proposed an overall process of marine biodiversity analysis by utilizing eDNA from seawater. Currently, the application of eDNA for analyzing marine biodiversity in domestic setting is not yet widespread. This review can contribute to establishment of marine eDNA research methods in Korea, providing valuable assistance in standardizing the use of eDNA in marine biodiversity studies.

• Journal of Sasang Constitutional Medicine
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• v.8 no.2
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• pp.151-163
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• 1996

VNTR and STR DNA typing are typical genetic analysis methods which are widely used in DNA-fingerprinting for forensic science and other genetic research purposes. In this study, genomic DNA of different constitutions(Taeun, Soyang and Soum) were analyzed by VNTR and STR DNA typing to provide scientific and objective references for Sasang Medicine. It was found out in this study that VNTR-MCT118 and YNZ22 loci showed too many different variation of allele distribution and numbers for each constitution. Therefore, it is thought that VNTR typing can not used for genetic classification study for Sasang Constitution which classifies human body into 4 groups. However, vWA locus, one of the STR loci investigated in this study, showed slight difference in allele distribution for each different constitution.