• Mycobiology
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• v.47 no.4
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• pp.355-367
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• 2019

Arthonia dokdoensis sp. nov., a lichenicolous fungus from the subcosmopolitan Arthonia molendoi complex growing on crustose thalli of species of the genus Orientophila (subfamily Xanthorioideae, Teloschistaceae), as well as the lichen species Rufoplaca toktoana sp. nov. (subfamily Caloplacoideae, Teloschistaceae) similar to Rufoplaca kaernefeltiana, both from Dokdo Islands, Republic of Korea, are described, illustrated, and compared with closely related taxa. In the phylogenetic tree of the Arthoniaceae based on 12S mtSSU and RPB2 gene sequences, the phylogenetic position of the A. dokdoensis and the relationship with the A. molendoi group are illustrated, while the position of the newly described R. toktoana is confirmed by phylogenetic tree based on ITS nrDNA data.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.275-275
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• 2002

Pseudomonas sp. S-47 is capable of catabolizing 4-chlorobenzoate (4CBA) as carbon and energy sources under aerobic conditions via the mesa-cleavage pathway. 4CBA-dioxygenase and 4CBA-dihydrodiol dehydrogenase (4CBA-DD) catalyzed the degradation af 4CBA to produce 4-chlorocatechol in the pathway. In this study, the xylL gene encoding 4CBA-DD was cloned from the chromosomal DNA of Pseudomonas sp. S-47 and its nucleotide sequence was analyzed. The xylL gene was found to be composed of 777 nucleotide pairs and to encode a polypeptide of 28 kDa with 258 amino acid residues. The deduced amino acid sequence of the dehydrogenase (XylL) from strain S-47 exhibited 98% and 60% homologies with these of the corresponding enzymes, Pseudomonas putida mt-2 (XyIL) and Acinetobacter calcoaceticus (BenD), respectively. However, the amino arid sequences show 30% or less homology with those of Pseudomonas putida (BnzE), Pseudomonas putida Fl (TodD), Pseudomonas pseudoalcaligenes KF707 (BphB), and Pseudomonas sp. C18 (NahB). Therefore, the 4CBA-dihydrodiol dehdrogenase of strain S-47 belongs to the group I dehydrogenase involved in the degradation of mono-aryls with a carboxyl group.

• Development and Reproduction
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• v.23 no.4
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• pp.385-390
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• 2019

Upon gene inactivation in animal models, the zebrafish (Danio rerio) has become a useful model organism for many reasons, including the fact that it is amenable to various forms of genetic manipulation. Genome editing is a type of genetic engineering in which DNA is inserted, deleted, modified, or replaced in the genome of a living organism. Mainly, CRISPR (clustered regularly interspaced short palindromic repeats) Cas9 (CRISPR-associated protein 9) is a technology that enables geneticists to edit parts of the genome. In this study, we utilized this technology to generate an mmp15b mutant by using zebrafish as an animal model. MMP15 is the membrane-type MMP (MT-MMP) which is a recently identified matrix metalloproteinase (MMP) capable of degrading all kinds of extracellular matrix proteins as well as numerous bioactive molecules. Although the newly-established mmp15b zebrafish mutant didn't exhibit morphological phenotypes in the developing embryos, it might be further utilized to understand the role of MMP15 in liver-related diseases, such as liver fibrosis, and associated pathogeneses in humans.

• Animal cells and systems
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• v.13 no.4
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• pp.453-460
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• 2009

Morphological and molecular classifications were attempted in an effort to establish species-specific classifications of three species of the genus Pholis in Korea; these species were subjected to morphological and molecular methodologies using body measurements, RFLP, RAPD, and phylogenetic trees using the nucleotide sequences of mitochondrial 16S and 12S ribosomal DNAs, cytochrome c oxidase I, and cytochrome b. The data demonstrated that the three species of genus Pholis are distinct from each other, both morphologically and genetically.

• Journal of Aquaculture
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• v.10 no.4
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• pp.403-407
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• 1997

Intraspecific sequence variation was detected by polymerase chain reaction (PCR) and direct sequencing of a 350-nucleotide region of the mitochondrial 12S rRNA gene of two natural populations (Han River and Nakdong River) and one hatchery stock (Jinhae Inland Fisheries Institute) of local strain common carp, one Israeli strain of common carp stock from Pukyong National University (PKU), and one hybrid between Israeli strain of common carp female and local strain common carp male from PKU stock. There is little variation in 350 bases of the mitochondrial 12S rRNA gene sequences among 2 natural and 1 hatchery local strain common carp populatins, representing abut 7 to 20 nucleotide differences (less than 6%). The sequence of specimens from Han River was more similar to that from Nakdong River (identity=98.0%) than to that from Jinhae Inland Fisheries Institute (identity=96.3%). Sequence variation between Israeli strain and wild local strain common carp was higher than the variation within natural stocks. The level of variation was ranged from 15.7 to 17.7%. The hybrid showed very similar nucleotide4 sequence of 12S rRNA gene to the sequence of Israeli strain with the identity of 98.9%.

• Journal of Species Research
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• v.9 no.1
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• pp.46-55
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• 2020

Chrysosplenium grayanum Maxim. (Series Nepalensia), which had been known to be restricted to Japan, was newly discovered from Mt. Cheongtae in Yeonggwang-gun, Jeollanam-do, located in the southern part of the Korean Peninsula. Species identification was confirmed using morphological characteristics and DNA sequence data, while comparing with materials obtained from Japan and herbarium specimens. Chrysosplenium grayanum is clearly distinguished from the remaining taxa of the genus Chrysosplenium by having glabrous plant body, opposite leaves, cylindrical papillae with roundish head at the tip on the smooth seed surface, and four stamens. Molecular sequence data of the nuclear ribosomal ITS regions, chloroplast rbcL and matK genes strongly supported that this previously unknown Chrysosplenium species from Korea is C. grayanum. Taking the molecular and the morphological evidence into consideration, it is clear that newly discovered Chrysosplenium population in Korea is conspecific with the widely distributed C. grayanum in Japan. In this paper, we provide a description, illustration, and photo images of Chrysosplenium grayanum from Korea and also a key to the Chrysosplenium species in Korea.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.6
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• pp.1017-1022
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• 2021

We collected a specimen of Heniochus diphreutes Jordan, 1903 belonging to the family Chaetodontidae on December 26, 2020 in Pohang-si, Gyeongsangbuk-do, using the set net. Although, H. diphreutes is morphologically very similar to Heniochus acuminatus, it can be distinguished from the latter based on the number of dorsal fin spines, mostly 12 in H. diphreutes vs 11 in H. acuminatus, and the percentage of snout length in head length, which is less than 12% in H. diphreutes vs more than 13% in H. acuminatus. Compared to H. acuminatus, H. diphreutes has a shorter snout, two-three rows of teeth, convex ventral profile of the head, more angular anal fins, and a black pattern extending to the longest soft rays on the posterior part of the anal fin. Molecular analyses showed that our specimen perfectly matched H. diphreutes based on mtDNA COI sequences data. We propose a new Korean name for H. diphreutes, "Jjal-beun-ib-du-dong-ga-li-dom".

• Genes and Genomics
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• v.40 no.11
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• pp.1137-1148
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• 2018

Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A+T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.

• Journal of Genetic Medicine
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• v.16 no.1
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• pp.31-38
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• 2019

Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome is a maternally inherited mitochondrial disorder of which m.3243A>G is the most commonly associated mutation, resulting in an inability to meet the energy requirements of various organs. MELAS poses a diagnostic challenge owing to its multiple organ involvement and great clinical variability due to its heteroplasmic nature. We report three cases from a family who were initially misdiagnosed with myasthenia gravis or undiagnosed. Although there is no optimal consensus treatment approach for patients with MELAS because of the disease's heterogeneity, our 21-year-long therapy regimen of ${\text\tiny{L}}-arginine$, ${\text\tiny{L}}-carnitine$, and coenzyme Q10 supplementation combined with dietary management appeared to provide noticeable protection from the symptoms and complications. Prompt early diagnosis is important, as optimal multidisciplinary management and early intervention may improve outcomes.

• Microbiology and Biotechnology Letters
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• v.48 no.4
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• pp.480-490
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• 2020

A novel lipase gene, Lip-1420, was isolated from a metagenomic library constructed from reed marsh from Mt. Jumbong in Korea, comprising 112,500 members of recombinant plasmids. The DNA sequence of Lip-1420-subclone (5,513 bp) was found to contain at least 11 ORFs according to the GenBank database. The ORF-3 gene was inserted into the pET21a plasmid containing the C-terminal 6-His tag and transformed into E. coli BL21(DE3) to express the recombinant lipase protein. Lip-1420 was purified using a fast protein liquid chromatography system. The gene was registered in GenBank (MH628529). The values of Km and Vmax were determined as 0.268 mM and 1.821 units, respectively, at 40℃ and pH 8.0, using p-nitrophenyl palmitate as the substrate. This lipase belongs to family IV taxonomically because it has conserved HGGG and GDSAG motifs in the constitutive amino acid sequence. According to the predicted structural model, the binding sites are represented by residues H78, G81, D150, S151, A152, V181, and D236. Finally, Lip-1420 showed triolein selectivity for methanolysis between triolein (18:1) and tristearin (18:0) substrates. Further study of the selective mechanism and structure-function relationship of this new lipase could be useful for more practical applications.