• Korean Journal of Ichthyology
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• v.25 no.3
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• pp.149-156
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• 2013

Phylogenetic relationships and DNA polymorphism among local populations of two Korean gobiidae species: Boleophthalmus pectinirostris and Scartelaos gigas were investigated based on 12S and 16S mitochondrial DNA and mitochondrial cytochrome b DNA sequences. DNA polymorphisms of B. pectinirostris between Suncheon and Gunsan populations were 100% identity from 434 bp segment of 12S rRNA gene and from 444 bp segment of mitochondrial cytochrome b genes, and 99.6% (2 bp different) identity from 484 bp segments of 16S rRNA genes. These results indicated the long period of geographic isolation between two populations of B. pectinirostris in Korea caused such high degrees of DNA polymorphisms. Based on the phylogenetic tree constructed from the two gobiid species in Korea, two genetically distinct groups of B. pectinirostris and S. gigas groups were recognized.

• Journal of KIISE:Software and Applications
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• v.30 no.3_4
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• pp.379-387
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• 2003

A lot of microbial genome projects have been completed to pour the enormous amount of genomic sequence data. In this context. the problem of identifying promoters in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. In this paper, we propose a new model of prokaryotic core promoter region including the -10 region and transcription initiation site, that is Dependency-Reflecting Decomposition Model (DRDM), which captures the most significant biological dependencies between positions (allowing for non-adjacent as well as adjacent dependencies). DRDM showed a good result of performance test and it will be employed effectively in predicting promoters in long microbial genomic Contigs.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.82-90
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• 2016

Most Araliaceae plant species distributed in Korea are economically important because of their high medicinal values. This study was conducted to develop barcode markers from sequence analysis of chloroplast DNA in 14 taxa of Araliaceae species grown in South Korea. Sequencing of seven chloroplast DNA regions was performed to establish the DNA barcode markers, as suggested by the Consortium for the Barcode of Life (CBOL). From the sequence analysis of chloroplast DNA, we identified specific sequences and nucleotides that allowed us to discriminate among each other 14 Korean Araliaceae species. The sequence in the region of psbA-trnH revealed the most frequent DNA indels and substitutions of all 7 regions studied. This psbA-trnH marker alone can discriminate among all 14 species. There are no differences between Korean and Chinese Panax ginseng in all seven sequenced chloroplast DNA regions. A phylogenetic tree constructed using the seven chloroplast DNA regions revealed that Tetrapanax papyriferus should be classified as an independent clade. The Aralia and Panax genera showed a close phylogenetic relationship. Five species in the Eleutherococcus genus were more closely related to Kalopanax septemlobus than to any Panax species.

• Journal of Food Hygiene and Safety
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• v.35 no.6
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• pp.574-580
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• 2020

In this study we sought to determine the food fraud by discriminating species of commercial seafood product such as Larimichthys polyactis, Larimichthys crocea, Pennahia argentatus, and Miichthys miiuy, which are difficult to morphologically discriminate. After amplifying the mitochondrial cytochrome c oxidase subunit I gene of the reference fish, the DNA sequences of the amplified PCR products were analyzed. As a result, a 655 bp sequence for species identification was selected for use as DNA barcodes. To confirm the DNA data and primer set, the DNA barcode sequence of each fish was compared to that in that in the NCBI. All of the DNA barcode data were matched with the gene sequence of each fish in the NCBI. A total of 32 processed seafood products (8 L. polyactis, 12 L. crocea, 3 Pennahia argentatus, and 9 Miichthys miiuy) were investigated. Homology of 97% or more in DNA sequences was judged as the same species. As a result of the monitoring, there were no discovered cases of forgery or alteration. However, the use of a raw material name having no matching standard name in the Korea Food Code may cause consumer confusion. Therefore, it is suggested that the standard name or scientific name be co-labeled with the raw material name on seafood products to prevent consumer confusion.

• Microbiology and Biotechnology Letters
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• v.26 no.1
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• pp.23-33
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• 1998

The entire sequence of a 4,214,810 bp genome of the Bacillus subtilis 168 has been determined by an international project, and the completion has been announced on July 19, 1997. For the sequencing project an international consortium was established and 25 European, 7 Japanese laboratories, 2 biotechnology companies, and our laboratory participated in the project. Within this framework we determined the complete nucleotide sequence of a 53,289 bp fragment upstream of the odhA gene (181 $^{\circ}$) of the B. subtilis 168 chromosome. On the basis of the published DNA sequences of the B. subtilis sspC and odhA genes, we obtained genomic fragments by plasmid rescue and long-range PCR. The sequenced fragment contains 56 putative open reading frames (designated yojA-yolI and 9 known genes (sspC, cge cluster, orfE5, orfRMl and odhA), in which we found many interesting features. In addition, the entire nucleotide sequence of a 53,289 bp region enabled us to revise the current genetic map of this region.

• Korean Journal of Heritage: History & Science
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• v.40
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• pp.387-411
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• 2007

The analysis of ancient DNA (aDNA) has become increasingly considerable anthropological, archaeological, biological and public interest. Although this approach is complicated by the natural damage and exogenous contamination of a DNA, archaeologists and biologists have attempted to understand issues such as human evolutionary history, migration and social organization, funeral custom and disease, and even evolutionary phylogeny of extinct animals. Polymerase chain reaction(PCR) is powerful technique that analyzes DNA sequences from a little extract of an ancient specimen. However, deamination and fragmentation are common molecular damages of aDNA and cause enzymatic inhibition in PCR for DNA amplification. Besides, the deamination of a cytosine residue yielded an uracil residue in the ancient template, and results in the misincorporation of an adenine residue in PCR. This promotes a consistent substitution (cytosine thymine, guanine adenine) to original nucleotide sequences. Contamination with exogenous DNA is a major problem in aDNA analysis, and causes oversight as erroneous conclusion. This report represents serious problems that DNA modification and contamination are the main issues in result validation of aDNA analysis. Now, we introduce several criterions suggested to authenticate reliance of aDNA analysis by many researchers in this field.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.28 no.5
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• pp.649-658
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• 1995

In order to estimate the level of genetic differences among the pleuronectid species, mitochondrial DNAs were isolated from four species: brown sole, Limanda herensteini; marbled sole, Limanda Yokohamae; stone flounder, Kareius bicoloratus; starry flounder, Platichthys stellatus, and the number of nucleotide substitutions was calculated by the restriction fragment length polymorphisms (RFIPs) generated by f4 sin base recognition restriction endonucleases. Total lengths of the mitochondrial DNA were measured as about 17.6 kbp in all species. Ten different composite genotypes were observed in brown sole, four different genotypes in marbled sole, and two different genotypes in starry flounder. However, only one genotype was observed in stone flounder. The calculated haplotypic diversity value of brown sole was higher than that of marbled sole. The average number of nucleotide substitutions per sites in four species was estimated to be 0.0045 in the intraspecies, 0.0344 in the interspecies, and 0.0457 in the genera, respectively. From these results, we could estimate that the genetic differences among interspecies were not influenced by nucleotide substitutions but genetical discontinuous.

• Journal of Animal Science and Technology
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• v.50 no.1
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• pp.9-18
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• 2008

Species-specific polymorphisms in chicken, pheasant, turkey, and quail were identified by cloning and sequencing of the immunoglobulin constant domain (IgLC). A set of species-specific primers were then designed on the basis of polymorphisms in the IgLC between species, as well as two additional sets of primers for the cytochrome b and tapasin genes, for the purpose of species identification. Together, the primers successfully distinguished specific species from chicken by species-specific PCR. This simple but unambiguous method may be used to screen avian inter-species germline chimeras, which are valuable models for the conservation of endangered species.

• Korean Journal of Microbiology
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• v.35 no.3
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• pp.180-184
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• 1999

Molecular spslemaucs of Agaricus species was investigated on the base of the sequences of the internal transcribed spaceriITS) regions in ribosomal DNA (rDNA). The sequences of the ITS region in 5 species and two group of Agaricus genus were resolved. In the phylogenetic trees. the species generally divided inlo two subclusters, refered to here as the group I and group 11. The group I consisted of Agaricus blazei ATCC 76739, Agarictrs blazei species cultivated in Korean hmings. Ago/-icus anmensis IMSNU 32049 and Agaricus can~pestris VPI-OKM 25665. Between Agaricus blazei NCC 76739 and the Agaricus blazei species cultivated in Korean farmings had the variation in lhe 5 nucleotide on the ITS regions. These varieties were presumed the variation by the geographic and cultivated conditions. In addition the subgroup of group I was formed by Agaricus arvensis LMSNU 32049 and Agaricus carnpests VPI-OKM 25665. The group IT included Agnrictrs bispoms CH 3004 and Agaricus pocillotor DUKE-J 173.

• Horticultural Science & Technology
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• v.33 no.2
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• pp.242-250
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• 2015

Insertional mutagenesis induced by T-DNA or transposon tagging offers possibilities for analysis of gene function. However, its potential remains limited unless good methods for detecting the target locus are developed. We describe a PCR technique for efficient identification of DNA sequences adjacent to the inserted T-DNA in a higher plant, Chinese cabbage (Brassica rapa ssp. pekinensis). This strategy, which we named variable argument thermal asymmetric interlaced PCR (VA-TAIL PCR), was designed by modifying a single-step annealing-extension PCR by including a touch-up PCR protocol and using long gene-specific primers. Amplification efficiency of this PCR program was significantly increased by employing an autosegment extension method and linked sequence strategy in nested long gene-specific primers. For this technique, arbitrary degenerate (AD) primers specific to B. rapa were designed by analyzing the Integr8 proteome database. These primers showed higher accuracy and utility in the identification of flanking DNA sequences from individual transgenic Chinese cabbages in a large T-DNA inserted population. The VA-TAIL PCR method described in this study allows the identification of DNA regions flanking known DNA fragments. This method has potential biotechnological applications, being highly suitable for identification of target genomic loci in insertional mutagenesis screens.