• Korean Journal of Ecology and Environment
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• v.53 no.1
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• pp.63-72
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• 2020

In this study, to discuss on the applicability of eDNA as a new method to investigate fish diversity at streams, we applied eDNA at 4 streams (Geum River, Ji Stream, Hwangji Stream, Seomjin River), where endangered species are inhabits, with conventional survey (cast net and kick net). The average (±standard deviation) number of species investigated by eDNA were 19 species (±4.4), and it was relatively higher than average of conventional survey, 10 species (±4.8). Most of case, in this study, eDNA was more efficient than conventional survey. However, there were errors on species identification of Korean endemic species and aliied species from eDNA, and it seems the universal primer (MiFish primer set) is not suitable for them. Furthermore, some of endangered species, caught by conventional method, was not detected by eDNA. As the present universal primer is not suitable for identify the every freshwater fish species in Korea, the complementing or development of universal primer is needed, and the eDNA application after species specific marker development for detecting specific species like endangered species should be considered. In conclusion, if the manual for field survey method by eDNA is developed, we expect applicability enlargement for water ecosystem survey.

• Korean Journal of Plant Taxonomy
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• v.38 no.2
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• pp.121-149
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• 2008

Taxonomic treatment and the identification key for 6 species and 4 varieties from the genus Asarum (Aristolochiaceae) in Korea were presented on the basis of the morphological analyses. Recently the taxonomy of the genus Asarum in Korea is controversial in the definition of species and the establishment of variation range. Our morphological studies supported that the species A. patens, A. misandrum and A. versicolor should be recognized as independent species by the unique morphological characters such as calyx lobes, stylar protuberance and leaf variegation. Second, A. sieboldii var. cornutum, A. koreanum, A. maculatum and A. sonunsanense, regarded as species or variety by different scholars, showed a close relationship with A. sieboldii by the similar calyx characters. Thus, new combinations, such as A. sieboldii for. cornutum, A. sieboldii for. koreanum, A. sieboldii for. maculatum and A. sieboldii for. sonunsanense, are proposed. And A. heterotropoides var. seoulense and A. heterotropoides var. mandshuricum also had a close relationship, thus, new combinations, A. mandshuricum for. seoulense, A. mandshuricum for. mandshuricum, are proposed. Furthermore, it is appropriate that A. heterotropoides var. heterotropoides, only distributed in Japan, is revised into A. heterotropoides as independent species by the unique character from the 2 varieties above. Consequently, the genus Asarum in Korea is classified into 3 species and 7 forma.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.97.1-97
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• 2003

An antagonistic bacterium, KJ1R5,, to Phytophthora capsici was obtained from root interior of a healthy pepper plant. To identify the bacterial antagonist, 16S rDNA sequence analysis, Biolog system, fatty acid methyl-esters (FAMEs), and physiological and biochemical characterization were conducted. The determined 165 rDNA sequence of KJ1R5, showed higher similarities to those of a group consisting of several Chryseobacterium strains with 95.2, 95.2, and 95,1％ similarity to C. defluvii, Chryseobacterium sp. FR2, and C. scophthalmum, respectively, In addition, Halounella gailinarum, Bergeyella zoohelcum, and Riemerella anatipestifer are another group for KJ1R5, with 94.1, 89.7, and 87.2％ similarities, respectively When identification of the antagonistic bacterium, KJ1R5, was conducted using BIOLOG system, the strain KJ1R5, was identified as Flavobacterium tirrenicum (similarity； 0.75％). Fatty acid profiles of the strain KJ1R5, were composed mainly of iso-17：0 w9c and iso-15：0 and identified as Chryseobacterium balustinum (similarity 0.524％). KJ1R5, was Gram-negative, regular short rods ranging from 0.8 $\mu\textrm{m}$ to 1.0 $\mu\textrm{m}$ and had no flagella. Phenotypic characterization of the antagonistic bacterium indicated that KJ1R5, were included in the genus Chreseobacterium, which belongs to the family Flavobacteriaceae. The strain was distinguished from these six existing species. These results indicated that strain might be placed as a new species in the genus Chryseobacterium.

• The Korean Journal of Mycology
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• v.49 no.4
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• pp.455-467
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• 2021

Macrofungi are valuable resources as novel drug candidates, new biomaterials, and edible materials. Recently, genetic approaches pertaining to macrofungi have been continuously growing for their identification, molecular breeding, and genetic engineering. However, purification and amplification of fungal DNA is challenging because of the rigid cell wall and presence of PCR inhibitory metabolites. Here, we established a direct PCR method to provide a rapid and efficient method for PCR-grade macrofungal DNA preparation applicable to both conventional PCR and real-time PCR. We first optimized the procedure of lysis and PCR using the mycelia of Lentinula edodes, one of the most widely consumed macrofungal species. Lysates prepared by neutralizing with (NH₄)₂SO₄ after heating the mycelia in a mixture of TE buffer and KOH at 65℃ for 10 min showed successful amplification in both conventional and real-time PCR. Moreover, the addition of bovine serum albumin to the PCR mixture enhanced the amplification in conventional PCR. Using this method, we successfully amplified not only internal transcribed spacer fragments but also low-copy genes ranging in length from 500 to 3,000 bp. Next, we applied this method to 62 different species (54 genera) of macrofungi, including edible mushrooms, such as Pleurotus ostreatus, and medicinal mushrooms such as Cordyceps militaris. It was found that our method is widely applicable to both ascomycetes and basidiomycetes. We expect that our method will contribute to accelerating PCR-based approaches, such as molecular identification, DNA marker typing, gene cloning, and transformant screening, in macrofungal studies.

• Journal of Microbiology
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• v.34 no.2
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• pp.124-130
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• 1996

A survey was conducted to determine the prevalance of infectious pancreatic necrosis virus (IPNV) on fish farms in Korea and the epidemiology of IPNV infection in the farmed rainbow trout. In total, 43 pools of rainbow trout with apparent signs of viral infection from five provinces were obtained and analyzed. Evident cytopathic effects, including karyopycnosis and cell destruction, were observed in CHSE (chinook samlmon embyro)-214 cells infected with the virus isolates. Of these, ten viral isolates were assumed to be IPNV based on biophysical properties. RNA analysis revealed that the isolates contained two-segmented RNA genomes, further indicating that the viral isolates are IPNV. Antigenic comparison of the IPNV isolates identified three distinct serological groups separable by the cross-neutralization test. Of the ten IPNV isolates, six could be classified as strain DRT, two as strain Ab, and two as strain VR299. We were not able to isolate new strain of IPNV or any isolate serologically similar to the standard strain Sp.poraceae and families of the Agaricales, they are genetically more related to the Polyporaceae. These results are consistent with morphological characters observed in those mushrooms. However, it is premature to conclude taxonomic status Ganoderma species in the present study employing small sample size.

• Journal of Dairy Science and Biotechnology
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• v.18 no.1
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• pp.47-60
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• 2000

Over decades of work, the probiotic research has grown rapidly with a number of new cultures, which is claimed a variety of benefit. However, many of the specific effects attributed to the ingestion of probiotics remain convoluted and scientifically unsubstantiated. Accordingly, the scientific community faces a greater challenge and must objectively seek cause and effect relationships for many potential and currently investigated probiotic species. Rational selection and design of probiotics remains an important challenge and will require a solid information about the physiology and genetics of candidate strains relevant to their intestinal roles, functional activities, and interaction of with other resident micro flora. As far as beneficial culture of lactic acid bacteria (LAB) is concerned, simple, cost-effective, and exact identification of candidate strains is of foremost importance among others. Until recently, the relatedness of bacterial isolates has been determined sorely by testing for one or several phenotyphic markers, using methods such as serotyping, phage-typing, biotyping, and so forth. However, there are problems in the use of many of these phenotype-based methods. In contrast, some of newer molecular typing methods involving the analysis of DNA offer many advantages over traditional techniques. These DNA-based methods have the greater discriminatory power than that of phenotypic procedures. This review focuses on the importance and the basis of molecular typing methods along with some considerations on de-sign and selection of probiotic culture for human consumption.

• Korean Journal of Plant Resources
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• v.28 no.6
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• pp.743-751
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• 2015

Reynoutria japonica and R. sachalinensis have been used as medicinal resources in Korea. However, it is difficult to identify and determine these medicinal herbs correctly because they are usually customized and purchased as the fragmented rhizomes types. To develop molecular markers for distinguishing two species, we analyzed and compared the chloroplast DNA sequences of seven loci (atpB, matK, ccD-psaI, atpF-H, trnL-trnF, psbK-I and rpl32-trnL). Among them, we found two effective SNPs in psbK-I region for R. japonica and atpF-H region for R. sachalinensis. Based on these SNP sites, we designed the new R. japonica- specific primer which is able to amplify 300 bp fragment in psbK-I region. A similar strategy was applied for the atpF-H region of R. sachalinensis. These molecular markers would be successfully applied to recognize R. japonica and R. sachalinensis.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.57 no.2
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• pp.169-176
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• 2024

On November 9, 2022, a goatfish (Mullidae) that had not been previously reported in Korea was collected during offshore fisheries resources research near Jeju Island. Based on the morphological identification, this goatfish was identified as the genus Upeneus owing to the presence of palatine teeth and vomerine teeth, as well as the proximal part of anterior part of second dorsal fin. Additionally, through molecular identification, the previously unreported goatfish was identified as U. subvittatus with a 99.8% match in the mtDNA COI region. Goatfish U. subvittatus has no patterns on its body and dark bands on both the lower and upper caudal fins, making it well distinguishable from the four species of genus Upeneus reported in Korea. U. vittatus, reported in Japan, showed morphological differences from U. subvittatus in that the dark band on the lower lobe of the caudal fin was wider, and longitudinal stripes were present on the body. Based on the morphological characteristics of U. subvittatus, we suggest a new Korean name, "Jul-mu-nui-kko-li-chog-su".

• Korean journal of applied entomology
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• v.54 no.2
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• pp.111-114
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• 2015

We report three lepidopteran insect pests of non-astringent persimmon leaf for the first time from Korea; Hypocala deflorata (Noctuidae), Teliphasa elegans (Pyralidae), and Cuphodes diospyrosella (Gracillariidae). Larvae of these species were collected from an organic farming or abandoned persimmon orchard in Changwon and Jinju cities, Gyeongnam province, and reared for the identification in the laboratory. Some information, such as collection records, hosts, simple morphological characteristics, and ecology were introduced for each species.

• Mycobiology
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• v.42 no.3
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• pp.241-248
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• 2014

NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferric-chelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bioinformatic approaches used to identify Nox-encoding genes. Further, most studies on fungal Nox genes have focused mainly on functionality, rather than sequence properties, and consequently clear differentiation among the various Nox isoforms has not been achieved. We conducted an extensive sequence analysis to identify putative Nox genes among 34 eukaryotes, including 28 fungal genomes and one Oomycota genome. Analyses were performed with respect to phylogeny, transmembrane helices, di-histidine distance and glycosylation. Our analyses indicate that the sequence properties of fungal Nox genes are different from those of human and plant Nox genes, thus providing novel insight that will enable more accurate identification and characterization of fungal Nox genes.