• Korean journal of applied entomology
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• v.62 no.4
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• pp.347-354
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• 2023

Mythimna loreyi (Duponchel, 1827) (Lepidoptera: Noctuidae) is a pest that damages agricultural plants, such as rice, wheat, and maize. We sequenced the entire 15,314-bp mitochondrial genome of this species. It has a typical set of genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) as well as one major non-coding A+T-rich region. Using concatenated sequences of 13 protein-coding genes and two rRNAs (13,376 bp, including gaps), phylogenetic analysis demonstrated that the sister relationship between M. loreyi and M. separata had the highest nodal support. The monophyly of each family (Noctuidae, Euteliidae, Nolidae, Erebidae, and Notodontidae) of the superfamily Noctuoidea was supported by the highest nodal support.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.226-239
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• 2021

Sebastes minor, Sebastes trivittatus, Sebastes owstoni, and Sebastes steindachneri are indigenous fish species inhabiting the central part of the East Sea, Korea. In order to understand the molecular evolution of these four rockfishes, we sequenced the complete mitochondrial genomes (mitogenomes) of S. minor and S. trivittatus. To further analyze the phylogeny of Sebastes species, the mitogenomes of 16 rockfishes were comparatively investigated. The complete mitochondrial DNA (mtDNA) nucleotide sequences of S. minor and S. trivittatus were 16,408 bp and 16,409 bp in length, respectively. A total of 37 genes were found in mtDNA of S. minor and S. trivittatus, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which exhibited similar characters with other Sebastes species in the East Sea, Korea. In addition, we detected a conserved motif "ATGTA" in the control region of the four Sebastes species, but no tandem repeat units. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that control regions were more variable than the concatenated protein-coding genes. As a result of analysing phylogenetic relationships of four Sebastes species by using concatenated nucleotide sequences of 13 protein-coding genes, S. minor, S. trivittatus, S. owstoni and S. steindachneri were clustered into three clades. The phylogenetic tree exhibited that S. minor and S. steindachneri shared a closer relationship, whereas S. trivittatus and S. vulpes formed another distinct clade. Our results contribute to a better understanding of evolutionary patterns of Sebastes species inhabiting the middle East Sea, Korea.

• Journal of Life Science
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• v.22 no.4
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• pp.437-446
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• 2012

A metagenomic library of cow rumen in the pCC1FOS phage vector was screened in $E.$ $coli$ EPI300 for cellulase activity on carboxymethyl cellulose agar plates. One clone was partially digested with $Sau$3AI, ligated into the $Bam$HI site of the pBluescript II SK+ vector, and transformed into $E.$ $coli$ $DH5{\alpha}$. We obtained a 1.5 kb insert DNA, designated $cel$5C, which hydrolyzes carboxymethyl cellulose. The cel5C gene has an open reading frame (ORF) of 1,125 bp encoding 374 amino acids. It belongs to the glycosyl hydrolase family 5 with the conserved domain LIMEGFNEIN. The molecular mass of the Cel5C protein induced from $E.$ $coli$ $DH5{\alpha}$, as analyzed by CMC SDS-PAGE, appeared to be approximately 42 kDa. The enzyme showed optimum cellulase activity at pH 4.0, and $50^{\circ}C$. We examined whether the $cel$5C gene comes from the 49 identified cow rumen bacteria using PCR. No PCR bands were identified, suggesting that the $cel$5C gene came from the unidentified cow rumen bacteria.

• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.322-328
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• 2003

The Transformation-Associated Recombination (TAR) cloning technique allows selective isolation of chromosomal regions and genes from complex genomes. The procedure requires knowledge of relatively small genomic sequences that reside adjacent to the chromosomal region of interest. This technique involves homologous recombination during yeast spheroplast transformation between genomic DNA and a TAR vector that has 5'and 3' gene targeting sequences. In this study, we examined the minimum size of specific hooks required for a single-copy gene isolation and compared the utility of different TAR vectors, radial and unique vectors, by cloning the same single-copy gene. The efficiency of TAR cloning of the hHPRT gene was same using hooks varying from 750 to 63 bp. The number of transformants decreased approximately 20-fold when the TAR vector contained two unique hooks versus using a radial vector, but the percentage of positive recombinants increased over 2-fold when a unique TAR vector was used. Therefore, we suggest that the two-unique TAR vector is suitable for general TAR cloning given its high selectivity, and the radial TAR vector is more suitable when genomic DNA is in limited quantity, for example, DNA isolated from pathological specimens. Moreover, we confirm the minimal length of a unique sequence in a TAR vector is approximately 60 bp for a single-copy gene isolation.

• KIISE Transactions on Computing Practices
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• v.20 no.9
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• pp.513-518
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• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

• Journal of Korean Society of Forest Science
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• v.87 no.3
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• pp.422-428
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• 1998

Polymerase chain reaction(PCR)-based inter-simple sequence repeats(I-SSR) markers were analyzed in 48 megagametophytes of a single tree of Abies koreana $W_{ILS}$. Nineteen of the 35 primers, screened with 6 megagametophyte DNA and produced the clearest amplification products in the preliminary experiment, were used for PCR with 48 megagametophyte DNAs sampled from a single tree. On the basis of the chi-square test, a total of 51 amplicons, amplified by the 19 primers, were revealed to be segregated according to the Mendelian ratio(i.e., 1 : 1 segregation ratio) in the 48 megagametophytes at 5% significance level. Based on the linkage analysis, the observed 51 Mendelian loci turned out to be unlinked each other, which suggested that they are evenly distributed in the genome. However, majority of RAPD markers are known to belong to the independent linkage blocks, which frequently results in the amplification of RAPD markers from the restricted regions of the genome. Owing to the nature of even distribution of the 51 loci observed in this study, the I-SSR markers could give better resolution of estimating genetic diversity from the whole genome than RAPD markers. And I-SSR markers are also more suitable than RAPD markers for reconstructing phylogenetic relationship by a cladistic method which requires to fulfil the assumption of independent evolution of the different characters.

• Digital Contents
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• no.5 s.120
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• pp.158-164
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• 2003

컴퓨터 게임속의 새롭고 독특한 주인공을 만들어 내는 게임 제작을 위해 캐릭터의 '유전자 설계'를 해야 한다. 이렇게 탄생하는 캐릭터들은 性을 비롯해, 모양, 크기, 색깔 등 모든 특성을 포함하는 게놈(Genome)을 갖고 있는 것이다. 게임 캐릭터의 유전자 설계를 통해 불가능한 것은 없다. 돌연변이, 수명의 결정, 후천적인 캐릭터 계승, 그리고 학습된 행동까지 지정할 수 있는 것이다. 컴퓨터 게임에서는 좋아하는 어떤 것이다 디자인 할 수 있다.

• Bioindustry News
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• v.9 no.1
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• pp.8-13
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• 1996

• The Science & Technology
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• no.2 s.441
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• pp.29-33
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• 2006

사이언스는 지난해 12월 23일자에서 2005년 세계의 획기적인 과학 연구 성과 10가지를 발표하고 잇따라 공개된 침팬지 게놈과 새로운 종의 등장 등 진화의 증거들을 최고 연구 성과로 선정했다. 또 이 중에는 경상대 김민철 교수가 참여하여 식물이 계절에 맞춰 꽃을 피우는 매커니즘을 규명한 '개화호르몬 발견'이 3위에 올랐다.