• Animal Systematics, Evolution and Diversity
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• v.11 no.4
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• pp.469-477
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• 1995

Drosophila lacertosa and D. sordidula are members of the robusta species group in virilis section of Drosophila. The mtDNA of both species was analyzed, using 10 restriction endonucleases. The mtDNA genome size of D. lacertosa and D. sordidula was 15.7 kbp, altogether, and the numbers of mtDNA fragment were 26 and 32, respectively. Restriction cleavage map of mtDNA in these species was constructed. The patterns of cleavage map were very different between two species and it means that speciation was taken for a long time ago.

• Analytical Science and Technology
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• v.8 no.4
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• pp.887-894
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• 1995

Toward the development of universal, sensitive, and convenient method of DNA (or RNA) detection, two kinds of electrochemically active DNA ligands. acridine - viologen and oligonucleotide - ferrocene conjugate, were prepared. Thermodynamic and electrochemical study revealed that these probes bound strongly to DNA, and showed a typical cyclic voltammograms, indicating a potential for use as a reversible electrochemical labelling agent for DNA. Especially, using the electrochemically active oligonucleotide, we have been able to demonstrate the detection of DNA at femtomole levels by HPLC equipped with ordinary electrochemical detector (ECD). These results lead to the conclusion that the redox-active probes are very useful for the microanalysis of nucleic acid due to the stabilily of the complexes, high detection sensitivity, and wide applicability to the target structures (single- and double strands) and sequences.

• Journal of Korea Society of Industrial Information Systems
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• v.15 no.1
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• pp.37-46
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• 2010

A Suffix Tree is an efficient data structure that exposes the internal structure of a string and allows efficient solutions to a wide range of complex string problems, in particular, in the area of computational biology. However, as the biological information explodes, it is impossible to construct the suffix trees in main memory. We should find an efficient technique to construct the trees in a secondary storage. In this paper, we present a method for constructing a suffix tree in a disk for large set of DNA strings using new index scheme. We also show a typical application example with a suffix tree in the disk.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.66-66
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• 2022

속성수로 활용되는 버드나무속 식물들은 생식기관과 영양기관의 성장 시기가 달라 형태적 특성 평가를 위해 수년간의 조사 기간이 요구된다. 따라서 바이오매스 우수 버드나무속 교잡종 육성의 성공 여부를 조기 판별하기 위한 식별 기술이 필요하다. DNA 마커는 식물의 생장단계와 관련 없이 탐색할 수 있으며 환경에 영향을 받지 않는 장점이 있다. 식물의 계통 분류 시 주로 사용되는 엽록체 DNA는 유전자 염기서열의 변이가 비교적 크지 않은 장점이 있으나 대부분의 활엽수에서 모계를 통해 유전되는 특징이 있다. 하지만 종간 교잡종의 식별은 각각의 부모종과 구분할 수 있어야 하므로 본 연구는 엽록체 DNA가 아닌 핵 DNA를 대상으로 분석하였다. 본 연구의 목적은 호랑버들을 암나무로 갯버들을 수나무로 인공교배하여 육성된 종간 교잡종을 식별하는 핵 DNA 마커를 탐색하는 것이다. 이를 위해 버드나무속에서 개발된 총 35개의 nSSR (nuclear Simple Sequence Repeat) 마커를 대상으로 호랑버들과 갯버들, 종간 교잡종의 식별 가능성을 평가하였다. 분석 결과 호랑버들과 갯버들, 종간 교잡종 간 차이를 나타내는 2개의 핵 DNA 마커를 선발하였다. 따라서 선발된 핵 DNA 마커를 활용하여 호랑버들과 갯버들, 종간 교잡종의 조기 식별에 활용이 가능할 것으로 사료된다.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.1
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• pp.88-94
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• 1997

The mitochondrial DNA (mtDNA) restriction fragment length polymorphi는 (RFLPs) of five populations were analyzed to delineate the stocks of Penaeus chinensis (Osbeck) in the Yellow Sea. Comparison of P. chinensis with P. japonicus to clarify the nucleotide divergence between two species was also carried out. Based on the fragment patterns, three composite haplotypes were analyzed in P. chinensis mtDNA as four naplotypes were in P. japonicus. Most individuals of each P. chinensis population are shared by one dominant haplotype. Another two haplotypes haying variations at the C/a I and hull sites were also distributed evenly in the Korean and Chinese populations. It is suggested that the gene exchange occurring between populations in the Yellow Sea is frequent. Average length of the mtDNA molecule was estimated to be about 16.44 kb in P. chinensis and 16.31 kb in P. japonicus, Sequence divergence (p) of mtDNA between two species estimated by using Upholt's (1977) fomula was $13.7\%$.

• Journal of Life Science
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• v.19 no.4
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• pp.467-471
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• 2009

The entire D-loop region of the porcine mitochondrial DNA (mtDNA) was amplified from six pig breeds (Landrace, Duroc, Large White, Korean native pig, Berkshire, and Hampshire) using a primer set designed on the basis of reported porcine mtDNA sequences. From analyses through cloning, DNA sequencing and multiple sequence alignment, an 11-bp (TAAAACACTTA) duplication was observed after known tandem repetition in the D-loop region, which promoted hetroplasmy in mtDNA. Although the existence of the 11-bp duplication has been previously reported in Duroc and Japanese native pigs, there have not been any attempts to know the characteristics of this duplication in other breeds so far. A 150 bp fragment containing the 11-duplication was amplified and typed by polyacrylamide gel electrophoresis (PAGE). All Large Whites had two duplication units and Duroc showed heteromorphic patterns, 11.2% (9/80) of the animals had the 11-bp duplication in total. On the other hand, Landrace, Berkshire, Hampshire and Korean native pigs were non-duplicated. This result showed that the 11-bp duplication could be used as a breed-specific DNA marker for distinguishing pure Landrace and Large White breeds.

• Clinical and Experimental Reproductive Medicine
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• v.36 no.1
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• pp.35-43
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• 2009

Objectives: Seminal concentration of tumor necrosis factor-alpha (TNF-${\alpha}$) relevant to sperm nuclear DNA integrity has not been studied. The present study aimed to evaluate seminal concentration of TNF-${\alpha}$ in correlation with sperm parameters and nuclear DNA integrity in asymptomatic healthy donors. Methods: Semen samples were obtained by masturbation from forty-five healthy donors. Results: Sperm quality was assessed by computer-assisted semen analysis and nuclear DNA integrity measured by the TUNEL assay in raw semen. TNF-${\alpha}$ concentrations were measured by ELISA in frozen-thawed seminal plasmas. Sperm DNA fragmentation rates were ranged between 1.9% and 53.0% (mean${\pm}$SD, 12.4${\pm}$9.6%). Univariate analysis revealed that DNA fragmentation rate was not associated with sperm concentration or motility but had a correlation with linearity negatively (r=-0.325, p=0.03) and age positively (r=0.484, p=0.001). The mean seminal concentration of TNF-${\alpha}$ was 4.9 pg/mL with a range from 1.1 to 22.6 pg/mL. The TNF-${\alpha}$ concentration had no correlation with clinically relevant parameters of sperm quality or nuclear DNA fragmentation rate. Conclusion: Our results indicate that sperm nuclear DNA fragmentation may be not associated with seminal TNF-${\alpha}$ level or sperm quality in asymptomatic healthy donors.

• Microbiology and Biotechnology Letters
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• v.51 no.1
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• pp.99-108
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• 2023

Several challenges arise in DNA extraction and gene amplification for airborne fungal metagenome analysis from a particulate matter (PM) samples. In this study, various conditions were tested to optimize the DNA extraction method from PM samples and polymerase chain reaction (PCR) conditions with primer set and annealing temperature. As a result of comparative evaluation of DNA extraction under various conditions, chemical cell lysis using buffer and proteinase K for 20 minutes and bead beating treatment were followed by using a commercial DNA extraction kit to efficiently extract DNA from the PM filter samples. To optimize the PCR conditions, PCR was performed using 10 primer sets for amplifying the ITS2 gene region. The concentration of the PCR amplicon was relatively high when the annealing temperature was 58℃ with the ITS3tagmix3/ITS4 primer set. Even under these conditions, when the concentration of the PCR product was low, nested PCR was performed using the primary PCR amplicon as the template DNA to amplify the ITS2 gene at a satisfactory concentration. Using the methods optimized in this study, DNA extraction and PCR were performed on 15 filter samples that collected PM2.5 in Seoul, and the ITS2 gene was successfully amplified in all samples. The optimized methods can be used for research on analyzing and interpreting the fungal metagenome of atmospheric PM samples.

• The Korean Journal of Zoology
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• v.38 no.1
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• pp.87-95
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• 1995

한국산 담수어류의 잉어목, 황어아과(Leuciscinae) 어류 2속 5종의 계통적 유연관계를 구명하기 위하여 mtDNA분석을 실시하였다 6 base를 인지하는 10개의 제한효소를 처리하여 얻어진 강tDNA의 크기는 16.5-17.5 Kb였으며 Bcl I, Bgl I, Bgl II, Hin dIII, Pvu II, Xba I 등은 종간 차이가 뚜렷하였다. 각종의 집단간 mtDNA분화정도는 매우 낮았으나(p=1% 미만) M. oxyephalus의 무주집단과 제주집단은 예리적으로 큰 차이를 보였다(p=5.3%) Moroco속의 종간 분화정도를 비교한 결과 M. oxycephafus와 M. lagowsk서 사이가 평균 f=7.2%로 근면관계가 제일 가까웠고 M. keumkang과 M. semotilus는 타종들과 근연관계가 제일 멀었다. Moroco속과 Phoxinus속간의 평균 유전적 분화정도는 f=13.7%로 현저한 차이를 보였다. Brown 등(1979)의 공식을 이용하여 이들 황어아과 2속 5종의 분화시기를 추정한 결과 이들은 후기 선신세(Pliocene)와 흥적세(Pleistocene) 사이에 분화된 것으로 추정되었으며 이 결과는 동위효소 연구에서 얻어진 결파(Yang and Min, 1989)와 잘 일치한다.

• Korean Journal of Plant Taxonomy
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• v.42 no.4
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• pp.282-293
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• 2012

Phylogenetic studies were conducted to evaluate the taxonomic relationships among 28 taxa, including 2 outgroups of Korean Campanulaceae, using atpB, atpB-rbcL, atpF-H, matK, rbcL, rpl16, rpoC1 and trnL-F regions sequences in chloroplast DNA. The combined analyses of eight chloroplast DNA regions suggest that Codonopsis and Platycodon basally branches within the phylogenetic tree; Wahlenbergia distinguished an independent clade; Campanula forms a clade; Peracarpa and Asyneuma clade is a sister to the Adenophora-Hanabusaya clade; Hanabusaya is placed within the section Remotiflorae of Adenophora; Adenophora form a clade. Our present results support the generic level, although discordance remained at the infrageneric groups such as section and series based on morphological characteristics in the genus Adenophora.