• Korean Journal of Ichthyology
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• v.33 no.2
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• pp.107-116
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• 2021

Two stone loaches (Nemacheilidae, Cypriniformes), Barbatula toni (Dybowski, 1869) and B. nuda (Bleeker, 1864), have been recognized in the Korean waters to date. Recently, due to indiscriminate artificial introduction as well as the change of their habitats induced by natural disasters, it seems to be concerned about the damage of species-specific geographic boundaries. We examined the genetic difference of two Korean Barbatula species by the haplotype network based on the Cytochrome b sequences of mitochondrial DNA and the phylogenetic relationships among them including Barbatula fishes occurring around the Korean peninsula. As a result, three and 29 haplotypes were obtained from B. toni and B. nuda, respectively, and totally three clades comprising "toni group", "nuda hangang group", and "nuda donghae group" were identified. The sequence variable sites among them was 10~24%, showing a difference of interspecific level. Phylogenetic relationships of the latter group, especially, forms an independent cluster discriminating with other two groups as well as the Chinese, Japanese, Russian, and European Barbatula species, suggesting the possibility of the specific level divergence.

• Biotechnology and Bioprocess Engineering:BBE
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• v.7 no.5
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• pp.323-326
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• 2002

To detect whole ammonia-oxidizing bacteria in the activated sludge, group-specific primers targeting the 16S-rRNA gene of ammonia-oxidizing bacteria were used. The electrophoresis pattern of the PCR products seemed to produce a single band of approximately 1.0 k bp for the bacteria in activated sludge and Nitrosomonas europaea. No band was observed for nitrite-oxidizer Nitrobacter winogradskyi and heterotrophs such as Pseudomonas putida. Then direct measurement of the PCR product was made by fluorometry using the reagent Hoechist 33258, so that the fluorescent intensity was in proportional to the cell number of the sample up to 240. Total time required for the test was about 4 h including DNA extraction. The DNA fragments produced were cloned and their sequences showed high similarity to those of Nitrosomonas spp. This study showed the feasibility to detect ammonia-oxidizing bacteria and to esti-mate their population rapidly for the control of the nitrogen elimination process.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.651-658
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• 2010

Garcinia is commonly found in Malaysia, but limited information is available regarding endophytic fungi associated with this plant. In this study, 24 endophytic fungi were successfully recovered from different parts of two Garcinia species. Characterization of endophytic fungi was performed based on the conserved internal transcribed spacer (ITS) region sequence analysis and the antimicrobial properties. Results revealed that fruits of the plant appeared to be the highest inhabitation site (38%) as compared with others. Glomerella sp., Guignardia sp., and Phomopsis sp. appeared to be the predominant endophytic fungi group in Garcinia mangostana and Garcinia parvifolia. Phylogenetic relationships of the isolated endophytic fungi were estimated from the sequences of the ITS region. On the other hand, antibacterial screening showed 11 of the isolates possessed positive response towards pathogenic and nonpathogenic bacteria. However, there was no direct association between certain antibacterial properties with the specific genus observed.

• The Plant Pathology Journal
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• v.23 no.3
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• pp.151-154
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• 2007

Phytoplasma was identified from leaf lettuce (Lactuca sativa) cultivated in commercial green-house in Korea. Diseased leaf lettuce revealed proliferation of shoots, and yellowing and shrinking of leaves (lettuce proliferation-K). Polymerase chain reaction (PCR) with universal primer pair P1/P6, and aster yellows (AY) specific primer pair R16F1/R1 amplified 1.5kb and 1.1kb length of DNA fragments, respectively. Nucleotide sequences of 16S rRNA gene were determined (Gen Bank accession no EF489024). Phylogenetic analysis of 16S rDNA showed the closest relationship with AY phytoplasma (GenBank accession no. AY389822 and AY389826), indicating that lettuce proliferation-K is a member of AY. Phytoplasma bodies were detected in phloem sieve tubes of diseased lettuce by transmission electron microscopy. The structures had round or pleomorphic shapes with a diameter of 130-300nm. Phylogenetic analysis of 16S rRNA gene, microscopic observation of phytoplasma bodies and symptomatology indicated that lettuce proliferation-K is caused by phytoplasma in the AY group. This is the first report of phytoplasma disease in lettuce in Korea.

• The Plant Pathology Journal
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• v.18 no.3
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• pp.109-114
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• 2002

To evaluate the phylogenetic and taxonomic status of the phytoplasmas associated with water dropwort (Oenanthe javanica DC) disease in Korea and Japan, their 16S rDNA was analyzed. DNAs extracted from water dropworts collected in Korea (Kyongnam province) and Japan (Chiba prefecture) affected by witches' broom and yellows were subjected to PCR using phytoplasma-specific primers, which amplified a 1.4-kbp fragment that included the 16S rDNA. Phytoplasmas were characterized by RFLP analysis using AluI, HaeIII, HhaI, KpnI, MseI, and RsaI restriction enzymes and by sequence analysis of the PCR products. The mater dropwort witches'broom (WDWB) and water dropwort yellows (WDY) 16S rDNA sequences were identical and closely related to onion yellows (OY, 99.9% identity), which belong to the aster yellows (AY) 16S-subgroup. However, the KpnI RFLP analyses clearly distinguished the WDY and WDWB phytoplasmas from the OY phytoplasma. The phylogenetic analysis based on 16S rDNA showed that WDWE and WDY phytoplasmas are members of a relatively homogeneous group that evolved from a common ancestor.

• Mycobiology
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• v.45 no.3
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• pp.139-149
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• 2017

The genus Hyaloperonospora (Peronosporaceae; Oomycota) is an obligate biotrophic group that causes downy mildew disease on the Brassicaceae and allied families of Brassicales, including many economically relevant crops, such as broccoli, cabbage, radish, rape, and wasabi. To investigate the diversity of Hyaloperonospora species in northeast Asia, we performed a morphological analysis for the dried herbarium specimens collected in Korea, along with molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mtDNA sequences. It was confirmed that 14 species of Hyaloperonospora exist in Korea. Of these, three species, previously classified under the genus Peronospora, were combined to Hyaloperonospora: H. arabidis-glabrae comb. nov. (ex Arabis glabra), H. nasturtii-montani comb. nov. (ex Rorippa indica), and H. nasturtii-palustris comb. nov. (ex Rorippa palustris). In addition, finding two potentially new species specific to northeast Asian plants is noteworthy in support of the view that the species abundance of Hyaloperonospora has been underestimated hitherto.

• Proceedings of the Botanical Society of Korea Conference
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• 1998.07a
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• pp.61-70
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• 1998

Genome and chromosome analyses in plants using fluorescence in situ hybridization (FISH) and immuno-staining (IMS) methods are reviewed by presenting the recent results obtained by the Chromosome Link, a group of chromosome and genome researchers. FISH is now effective to detect unique nucleotide sequences with 153 bp on the extended DNA fibers. Genomic in situ hybridization (GISH) also allows painting plant chromosomes of different genomes. GISH is quite effective to detect the genomic differentiation in the individual chromosomes within a nucleus. Three dimensional (3D) analyses are now available by confocal microscopy and a deconvolution system. These techniques are invaluable to visualize both the structural and functional dynamics within a nucleus. 3D-FISH revealed the spatial differentiation of different genomees within a nucleus. 3D-FISH also proved structural partition of centromeric and telomeric domains within a barely nucleus. The dynamic acetylation of histone H4 at the specific regions of a genome during a cell cycle is also analyzed using 3D-IMS. It is anticipated that these methods will provide us powerful tools to understand the structural and functional significance of plant chromosomes and genomes.

• Biotechnology and Bioprocess Engineering:BBE
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• v.8 no.3
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• pp.199-204
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• 2003

Among 59 Korean isolated, 20 were confirmed as members of the genus Bifidobaferium species based on gram staining, microscopic examination of cell morphology and the TLC method, The oxygen tolerance and antioxidative activities of these 20 Bifidobacterium strains and 5 standard Bifidobaferium strains were tested. All the strains demonstrated antioxidative activities as regards inhibiting linoleic acid peroxidation. The antioxidative activities of isolated and standard strains were found to range from 10.7-46.4% and from 10.7-22.2%, respectively. In addition, all tested strains exhibited a Scavenging ability on DPPH free radicals, range from 15-41% for the isolated strains and 8.3-22% for the standard strain. Accordingly. the isolated Bifidobarterium strains demonstrated higher antioxidative artivities than the 5 standa rd Bifidobarterium strains. On the base of grades for each test, HJL 7511 was identified 35 the best strain, followed by HJL 7501. 2 strains were identified with Polymerase Chain Reaction (PCR) assay using group-specific primers designed from the nucleotide Sequences of the 16S rRNA and internal transcribed spacer (ITS) regions of the Bifidobacteria. Based on the Sequencing results, HJL 7511 and HJL 7501 were identified as Bifidobacterium infantis.

• Mycobiology
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• v.45 no.4
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• pp.263-269
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• 2017

The genus Peronospora, an obligate biotrophic group belonging to Oomycota, causes serious damage to a variety of wild and ornamental plants, as well as cultivated crops, such as beet, rose, spinach, and tobacco. To investigate the diversity of Peronospora species parasitic to Stellaria and Pseudostellaria (Caryophyllaceae) plants in Korea, we performed a morphological analysis on dried herbarium specimens and molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mitochondrial DNA sequences. As a result, it was confirmed that there are four species of Peronospora parasitic to specific species of Stellaria and Pseudostellaria, all of which were hitherto unrecorded in Korea: P. alsinearum (ex Stellaria media), P. stellariae-aquaticae (ex Stellaria aquatica), P. stellariae-uliginosae (ex Stellaria alsine), and P. pseudostellariae (ex Pseudostellaria palibiniana). In addition, Peronospora specimens parasitic to Pseudostellaria davidii differed morphologically from P. pseudostellariae owing to the large and ellipsoidal conidia; this morphological discrepancy was also validated by the high genetic divergence between the two species. Peronospora casparyi sp. nov. is described and illustrated here.

• Journal of Life Science
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• v.10 no.2
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• pp.45-49
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• 2000

Long terminal repeat (LTR) of human endogenous retrovirus K family (HERV-K) has been found to be coexpressed with sequences of closely located genes. We examined the transcribed HERV-K LTR elements in human liver and kidney tissues. Using the cDNA synthesized from mRNA of human liver and kidney, we performed PCR amplification and identified six HERV-K LTR elements. Those LTR elements showed a high degree of sequence similarity (93.3∼96.6%) with human-specific LTR. A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-K LTR elements (Liv-1, 2, 3 and Kid-1, 2, 3) were belonged to group I. Our data suggests that HERV-K LTR elements are active on human liver and kidney tissues and may represent a source of genetic variation connected to human disease.