• The Korea Journal of Herbology
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• v.28 no.3
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• pp.75-84
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• 2013

Objectives : The origin of Breeae Herba (So-gye) and Cirsii Herba (Dae-gye) is differently prescribed in Korean and Chinese modern pharmacopoeia. Since the similar morphological characteristics and chaotic plant names, moreover, the aerial part of Carduus crispus have been used as the Cirsii Herba. To develop a reliable method for correct identification of these herbal medicines and to evaluate the genetic relationship of these closely related plant species, we analyzed sequences of DNA barcode regions. Methods : Thirty-one samples of 6 medicinal plants (B. segeta, B. setosa, C. japonicum var. maackii, C. setidens, C. chanroenicum, and C. crispus) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL) were analyzed after amplification using appropriate primers reported in previous studies. The nucleotides of species-specific authentic marker and phylogenetic relations were estimated based on the entire sequences of DNA barcodes by the analysis of ClastalW and UPGMA, respectively. Results : In comparative analysis of DNA barcode sequences, we obtained specific nucleotides to discriminate the medicinal plant of Breeae/Cirsii Herba in species level and evaluated the phylogenetic relationship of these species. Futhermore, we identified distinct marker nucleotides enough to authenticate respective species. These sequence differences at corresponding positions were avaliable genetic markers to determine the botanical origins of Breeae Herbal as well as Cirsii Herba. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by providing of definitive information that can identify each plant species and distinguish from unauthentic adulterants and substitutes.

• The Plant Pathology Journal
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• v.23 no.2
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• pp.37-44
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• 2007

Colletotrichum contains many important pathogens which cause economically significant diseases of crops like pepper, strawberry, tomato and apple. Forty four isolates were collected to characterize the diversity of Colletotrichum causing apple anthracnose in various regions of Korea. They were analyzed by random amplified polymorphic DNA (RAPD), internal transcribed spacer (ITS) of rDNA and partial $\beta$-tubulin gene DNA sequence, and culture characteristics on PDA and PDA-Benomyl. From the results of molecular analyses, 31 strains belonged to Colletotrichum gloeosporioides, ribosomal DNA group (RG) 4 of Moriwaki et al. (2002), 8 strains belonged to C. acutatum, A2 group of Talhinhas et al. (2005) and 5 strains to C. acutatum, A3 group of Talhinhas et al. (2005). Most isolates of C. gloeosporioides RG4 grew faster on PDA than strains of C. acutatum, A2 and A3 groups and most RG4 strains were sensitive to Benomyl. However, a few strains of RG4 grew slower and were resistant to Benomyl. On the basis of molecular characteristics, apple isolates of C. acutatum were clearly differentiated from red pepper isolates of the species, but apple isolates of C. gloeosporioides were not.

• BMB Reports
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• v.34 no.2
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• pp.156-165
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• 2001

Leptin is a circulating non-glycosylated protein that is mainly produced in adipocytes. Leptin acts in the brain to regulate food intake and energy expenditure. Previously we reported our success in the isolation of a partial cDNA of the long form of the leptin receptor, OB-Rb, from rat spleen, and showed that leptin might also play a role in peripheral immune organs. In the present study, for the first time, the complete coding region of OB-Rb cDNA was cloned from rat splenocytes, and its nucleotide sequence was determined. The cDNA was then further expressed in E. coli and mammalian cells, thereby confirming the functional integrity of this receptor. Prokaryotically overexpressed OB-R protein was then used as an immunizing antigen in BALE/c mice to produce leptin receptor-specific antibodies. By using them, we confirmed the cell surface expression of OB-Rb in transfected CHO cells. It is our belief that the reagents, as produced in this study, will be of great use in further studies of the biological role of rat leptin.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.529-533
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• 2001

The ${\beta}$-Amylase cDNA fragment from the oomcete Saprolegnia parasitica was cloned by reverse transcription-polymerase chain reaction (RT-PCR) using degenerate oligonucleotide primers derived from conserved ${\beta}$-amylase sequences. The 5'and 3'regions of the $\beta$-amylase gene were amplified using the rapid amplification of cDNA ends (rACE) system. It consisted of an open reading frame of 1,350 bp for a protein of 450 amino acids. Comparison between the genomic and cDNA sequences revealed that the intron was not present in the coding region. The deduced amino acid sequence of the ${\beta}$-amylase gene had a 97% similarity to the ${\beta}$-amylase of Saprolegnia ferax, followed by 41% similarity to those of Arabidopsis thaliana, Hordeum vulgare, and Zea mays. The ${\beta}$-amylase gene was also expressed in Saccharomyces cerevisiae by placing it under the control of the alcohol dehydrogenase gene (ADC1) promoter.

• Fisheries and Aquatic Sciences
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• v.21 no.3
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• pp.8.1-8.6
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• 2018

Desmarestia japonica (Phaeophyceae, Desmarestiales) was recently established from the Japanese ligulate Desmarestia and is morphologically similar to D. ligulata. This species has been reported only from Japan. However, the taxonomic reports based on additional regional distributions are needed to clarify this taxonomic entity and its species boundaries. Because Desmarestia species have restricted distributions in Korea, we reexamined herbarium specimens of D. ligulata deposited at the National Institute of Biological Resources (South Korea). To improve the amplification efficiency of the polymerase chain reaction and avoid contamination by the DNA of other organisms, we developed taxon-specific molecular markers suitable for DNA barcoding of Desmarestia species. Nuclear ribosomal small subunit RNA (18S rDNA) and mitochondrial cytochrome c oxidase 1 (cox1) regions were selected as target DNA. As a result, both were successfully isolated from herbarium specimens of D. japonica acquired over 10 years. These molecular markers provide useful genetic information for herbarium specimens for which conventional molecular analysis is challenging.

• Molecules and Cells
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• v.23 no.3
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• pp.379-390
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• 2007

We sequenced and characterized the complete mitochondrial genome of the Japanese fish tapeworm D. nihonkaiense. The genome is a circular-DNA molecule of 13607 bp (one nucleotide shorter than that of D. latum mtDNA) containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and two rRNA genes. Gene order and genome content are identical to those of the other cestodes reported thus far, including its congener D. latum. The only exception is Hymenolepis diminuta in which the positions of trnS2 and trnL1 are switched. We tested a PCR-based molecular assay designed to rapidly and accurately differentiate between D. nihonkaiense and D. latum using species-specific primers based on a comparison of their mtDNA sequences. We found the PCR-based system to be very reliable and specific, and suggest that PCR-based identification methods using mtDNA sequences could contribute to the study of the epidemiology and larval ecology of Diphyllobothrium species.

• Journal of KIISE:Databases
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• v.32 no.3
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• pp.263-275
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• 2005

In a large DNA database, indexing techniques are widely used for rapid approximate sequence searching. However, most indexing techniques require a space larger than original databases, and also suffer from difficulties in seamless integration with DBMS. In this paper, we suggest a space-efficient and disk-based indexing and query processing algorithm for approximate DNA sequence searching, specially exact match queries, wildcard match queries, and k-mismatch queries. Our indexing method places a sliding window at every possible location of a DNA sequence and extracts its signature by considering the occurrence frequency of each nucleotide. It then stores a set of signatures using a multi-dimensional index, such as R*-tree. Especially, by assigning a weight to each position of a window, it prevents signatures from being concentrated around a few spots in index space. Our query processing algorithm converts a query sequence into a multi-dimensional rectangle and searches the index for the signatures overlapped with the rectangle. The experiments with real biological data sets revealed that the proposed method is at least three times, twice, and several orders of magnitude faster than the suffix-tree-based method in exact match, wildcard match, and k- mismatch, respectively.

• Korean journal of applied entomology
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• v.39 no.4
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• pp.211-226
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• 2000

Genetic divergence and phylogenetic relationships among the major Korean fireflies (Hotaria papariensis, Luciola lateralis, and Pyrocoelia rufa) were studied. A portion of mitochondrial COI (403 bp) and 165 rRNA (490~504 bp) genes were sequenced, and the GenBank-registered, homologous 165 rRNA sequences of Japanese fireflies were compared (27 species of Lampyridae, one of Lycidae, and one of Rhgophthalmidae). Greatest DNA and/or amino acid sequence divergence was found when P rufa, belonging to Lampyrinae was compared with H. papariensis and L. lateralis, both belong-ing to Luciolinae, confirming the current taxonomic status of the species. In the PAUP and PHYLIP analyses with 165 rRNA data, grouping of the two geographic samples of H. papariensis with H. tsushimana validate the use of generic name, Hotaria. Nevertheless, lack of sister-group relationship of the two geographic samples of H. papariensis renders further investigation on this group . Although the Korean and Japanese L. lateralis formed a strong monophyletic group, a substantial genetic differentiation was detected between them (2.9% of 165 rRNA gene sequence divergence). Finally, the geographic samples of Korean p. rufa strongly formed a group with Japanese p. rufa, warranting the use of generic name, Pyrocoelia, but the genetic distance observed between the Cheju-Island individual and all others requires further investigation on this subject. Summarized, this study supports the current taxonomic status of the Korean fireflies in that each respectively formed a strong monophyletic group with its own species or genus.

• The Korean Journal of Mycology
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• v.41 no.1
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• pp.47-51
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• 2013

Yeasts isolated from wild flowers of Gyejoksan in Daejeon city, Oseosan in Chungchungnamdo, and Baekamsan in Jeollabukdo, Korea were identified by comparison of nucleotide sequences for PCR-amplified D1/D2 region of 26S rDNA or internal transcribed spacer (ITS) 1 and 2 including 5.8S rDNA using BLAST. Twelve yeast strains of ten species and seventeen yeast strains of ten species were isolated from wild flowers of Gyejoksan and Oseosan, respectively. And thirty seven yeast strains of twenty four species were isolated from wild flowers of Baekamsan. Total thirty four yeast species were isolated from three different sample collection areas, but only nine species were overlapped from the at least two different sampling areas: Cryptococcus sp., Cryptococcus aureus, Cryptococcus flavescens, Cryptococcus flavus, Metschnikowia sp., Pseudozyma aphidis, Rhodotorula glutinis, Sporobolomyces carnicolor, and Sporobolomyces ruberrimus. Among them only Cryptococcus aureus was occurred from all three different collection sites. Other twenty five species were restricted to specific collection site suggesting that each area has distinctive yeast flora.

• Korean Journal of Ichthyology
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• v.22 no.3
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• pp.201-205
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• 2010

One specimen of a natural hybrid of an Oplegnathus (Oplegnathus fasciatus $\times$ Oplegnathus punctatus) was found in Tongyeong, Korea in August 2008. We, herein, describe its morphological and genetic characteristics and compare them with those of O. fasciatus and O. punctatus. In morphology, the hybrid showed many distinctive black rounded blotches on body sides and four faint vertical bars, being in those features similar to O. punctatus. Although the counts and measurements of the hybrid mostly overlapped between O. fasciatus and O. punctatus, the Oplegnathus hybrid resembled O. punctatus in the ratio of pelvic-fin length in standard length: Oplegnathus hybrid (26.7%) was closer to O. punctatus (26.4%) than to O. fasciatus (17.2~23.6%). In genetics, as a result of analysis of 510 base pair sequences of mitochondrial DNA 16S rRNA, the hybrid was closer to O. fasciatus (d=0.000~0.010) than to O. punctatus (d=0.020). Our results suggest that the natural hybridization represented by the subject specimen occurred between an O. fasciatus female and an O. punctatus male.