• Korean Journal of Microbiology
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• v.55 no.1
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• pp.74-76
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• 2019

Gram-positive anaerobic bacilli Actinomyces spp. commonly reside on mucosal surfaces of the oropharynx, gastrointestinal tract, and urogenital tract. Here, we first report the draft genome sequence of Actinomyces georgiae KHUD_A1, isolated from dental plaque of a Korean elderly woman. The genome is 2,652,059 bp in length and has a GC content of 68.06%. The genome includes 2,242 protein-coding genes, 9 rRNAs, and 64 tRNA. We identified 157 KHUD_A1 strain-specific genes, including genes encoding CPBP family intramembrane metalloprotease, bile acid: sodium symporter family protein, Txe/YoeB family addiction module toxin and Phd/YefM family antitoxin. The sequence information of A. georgiae KHUD_A1 will help understand the general characteristics of the bacterial species and the genome diversity of the genus Actinomyces.

• Korean Journal of Ecology and Environment
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• v.52 no.3
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• pp.202-209
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• 2019

The primary productivity and production rate of photosynthetic pigment of periphyton and phytoplankton were estimated using a $^{13}C$ stable labeling technique in May 2011, in the waterfront of Lake Paldang. Primary productivity of periphyton ($28.15mgC\;m^{-2}\;d^{-1}$) was higher than phytoplankton production ($0.14mgC\;m^{-2}\;d^{-1}$). The net production rates of photosynthetic pigments(Chl a and Fucoxanthin) of periphyton were $2.53ngC\;m^{-2}\;d^{-1}$ and $0.12ngC\;m^{-2}\;d^{-1}$, respectively. On the other hand, the net production rate of pigments on phytoplankton (Chl a : $0.023ngC\;m^{-2}\;d^{-1}$, Fucoxanthin: $0.002ngC\;m^{-2}\;d^{-1}$) was lower than that of periphyton. Specific production rates of individual pigments of phytoplankton to the total primary productivity indicate the predominance of diatom (Fucoxanthin) species in phytoplankton assemblage in Lake Paldang. The net individual production rate of pigments by $^{13}C$ tracer was a useful tool to estimate the contribution of each phytoplankton class for total primary productivity, and it is possible to calculate the seasonal contribution of each phytoplankton class to the total primary productivity in the aquatic ecosystems. This study is the first report on photosynthetic pigment production rates of periphyton and phytoplankton.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.309-319
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• 2018

Previously, six Schizosaccharomyce pombe mutants that induce pheromone even in the presence of nitrogen source were isolated from a bank of temperature sensitive mutants. In this report, one of these mutants, pws6 was further characterized. The pheromone induction in pws6 mutant cells was specific to nutrient: the M-factor pheromone was induced without nitrogen starvation but not without glucose starvation. This result suggests that the pws6 mutant might have a specific defect in the pathway for nitrogen starvation. The pws6 mutant induces P-factor pheromone as well as M-factor without starvation of nitrogen in temperature sensitive mode, suggesting that the pheromone induction phenotype of pws6 mutation is not cell-type specific. From cloning of the $pws6^+$ gene by complementation of the temperature sensitive growth defect, three plasmids containing 8.1 kb, 3.3 kb, and 4.8 kb yeast DNA were recovered. These plasmids complement the growth defect of the pws6 mutant by 100%, 70%, and 10~20%, respectively. The abilities of these plasmids to complement pheromone induction phenotype of pws6 mutant cells were correlated well with the efficiencies of complementation of the growth defect. With comparison of their open reading frames to the complementation efficiencies, it is concluded that the open reading frame, SPBC19C7.06 is responsible for the complementation of temperature sensitive phenotype of the pws6 mutant. This open reading frame, named prs1, contains one long exon with no intron and encodes a putative prolyl tRNA synthetase. The putative Prs1 protein exhibits significant similarities to the prolyl tRNA synthetases of other species.

• Korean Journal of Plant Resources
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• v.35 no.2
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• pp.169-182
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• 2022

This study was conducted to predict the distribution of rare·endemic plants (Sophora koreensis Nakai) in the border forests where wildfire damage occurred and to quantify the damage. For this purpose, we tried to derive more accurate results through forest area damage (NBR) according to the Burn severity of wildfires, damage by tree species type (Vegetation map), and MaxEnt model. For Burn severity analysis, satellite imagery (Landsat-8) was used to analyze Burn severity (ΔNBR2016-2015) and to derive the extent of damage. To prepare the Vegetation map, the land cover map prepared by the Ministry of Environment, the Vegetation map prepared by the Korea Forest Service, and the vegetation survey conducted by itself were conducted to prepare the clinical map before and after the forest fire. Lastly, for MaxEnt model analysis, the AUC value was derived by using the habitat coordinates of Sophora koreensis Nakai based on the related literature and self-report data. As a result of combining the Maxent model analysis data with the Burn severity data, it was confirmed that 45.9% of the 44,760 m² of habitat (predicted) area of Sophora koreensis Nakai in the wildfire damaged area or 20,552 m², was damaged.

• Mycobiology
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• v.50 no.1
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• pp.66-78
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• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

• Korean Journal of Ecology and Environment
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• v.55 no.4
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• pp.330-340
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• 2022

We deduced the proper estimation methodology for the amount of carbon sequestration by damaged trees for Environmental Impact Assessment (EIA). The nine development projects related to renewable energy, damaged trees occur, assessment status and used method of evaluating the carbon storage of damaged trees were summarized. And after re-calculating the carbon storage of damaged trees through allometric equations, the difference between the two groups, re-calculated the damaged trees carbon storage and the damaged trees carbon storage in the report, was validated. As a result, damaged trees carbon storage in words was more than the re-calculated damaged trees carbon storage, and it was statistically significant (p<0.005). This result means that the existing method for calculating damaged tree carbon storage is overcalculated. It was judged that it was necessary to improve the calculation method. Therefore, allometric equations suitable for each dominated-tree species should be used when calculating the damaged tree carbon storage. Furthermore, we propose to establish a carbon storage calculation system based on actual data from the ecosystem so that researchers can efficiently and accurately the damaged trees carbon storage.

• Korean Journal of Environmental Biology
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• v.39 no.4
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• pp.479-485
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• 2021

A semi-selective agar medium was developed for detecting and enumerating Colletotrichum scovillei in chili (Capsicum annum) plant material. Potato-dextrose-agar(PDA) was used as the basic medium. The composition of the semi-selective agar medium was established after several attempts to favor the development of C. scovillei and inhibit the growth of other fungi and bacteria. The semi-selective agar medium contained PDA amended with pyribencarb and pydiflumetofen at 40 ㎍ mL^-1 each and streptomycin at 100㎍ mL^-1 for preventing bacterial growth. The pH was adjusted to 4.8 with 85% lactic acid. The inhibition of the mycelial growth of C. scovillei was significantly less than that of most other fungi including Fusarium species when grown on the semi-selective medium. C. scovillei was detected from naturally infected chili plants by plating fruit and stem tissue suspensions on the semi-selective medium, which was found to be reliable and quantifiable. This was the first report of a semi-selective agar medium to detect the presence of C. scovillei in naturally infected chili tissue.

• The Plant Pathology Journal
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• v.39 no.4
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• pp.361-373
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• 2023

In plant-pathogen interactions, Magnaporthe oryzae causes blast disease on more than 50 species of 14 monocot plants, including important crops such as rice, millet, and most 15 recently wheat. M. oryzae is a model fungus for studying plant-microbe interaction, and the main source for fungal pathogenesis in the field. Here we report that MoJMJD6 is required for conidium germination and appressorium formation in M. oryzae. We obtained MoJMJD6 mutants (ΔMojmjd6) using a target gene replacement strategy. The MoJMD6 deletion mutants were delayed for conidium germination, glycogen, and lipid droplets utilization and consequently had decreased virulence. In the ΔMojmjd6 null mutants, global histone methyltransferase modifications (H3K4me3, H3K9me3, H3K27me3, and H3K36me2/3) of the genome were unaffected. Taken together, our results indicated that MoJMJD6 function as a nuclear protein which plays an important role in conidium germination and appressorium formation in the M. oryzae. Our work provides insights into MoJMJD6-mediated regulation in the early stage of pathogenesis in plant fungi.

• Animal Bioscience
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• v.37 no.2
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• pp.303-314
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• 2024

Objective: Rutin, also called vitamin P, is a flavonoids from plants. Previous studies have indicated that rutin can alleviate the injury of tissues and cells by inhibiting oxidative stress and ameliorating inflammation. There is no report on the protective effects of rutin on goat rumen epithelial cells (GRECs) at present. Hence, we investigated whether rutin can alleviate lipopolysaccharide (LPS)-induced damage in GRECs. Methods: GRECs were cultured in basal medium or basal medium containing 1 ㎍/mL LPS, or 1 ㎍/mL LPS and 20 ㎍/mL rutin. Six replicates were performed for each group. After 3-h culture, the GRECs were harvested to detect the relevant parameters. Results: Rutin significantly enhanced the cell activity (p<0.05) and transepithelial electrical resistance (TEER) (p<0.01) and significantly reduced the apoptosis rate (p<0.05) of LPS-induced GRECs. Rutin significantly increased superoxide dismutase, glutathione peroxidase, and catalase activity (p<0.01) and significantly decreased lactate dehydrogenase activity and reactive oxygen species and malondialdehyde (MDA) levels in LPS-induced GRECs (p<0.01). The mRNA and protein levels of interleukin 6 (IL-6), IL-1β, and C-X-C motif chemokine ligand 8 (CXCL8) and the mRNA level of tumor necrosis factor-α (TNF-α) and chemokine C-C motif ligand 5 (CCL5) were significantly increased in LPS-induced GRECs (p<0.05 or p<0.01), while rutin supplementation significantly decreased the mRNA and protein levels of IL-6, TNF-α, and CXCL8 in LPS-induced GRECs (p<0.05 or p<0.01). The mRNA level of toll-like receptor 2 (TLR2), and the mRNA and protein levels of TLR4 and nuclear factor κB (NF-κB) was significantly improved in LPS-induced GRECs (p<0.05 or p<0.01), whereas rutin supplementation could significantly reduce the mRNA and protein levels of TLR4 (p<0.05 or p<0.01). In addition, rutin had a tendency of decreasing the protein levels of CXCL6, NF-κB, and inhibitor of nuclear factor kappa-B alpha (0.05

• Korean Journal of Environmental Biology
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• v.42 no.1
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• pp.127-134
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• 2024

The feathery branched green alga Bryopsis plumosa (Hudson) C. Agardh bloomed at Songji Beach, Haenam, Korea, in November 2022. A terrible stench was present on the beach, and the bottom was covered in a thick green mat of green algae. The alga was identified as B. plumosa, which is an opportunistic species currently distributed worldwide. Dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) were analyzed in the bloomed area and compared with those of other vicinities. The DIN and DIP concentrations were 1.067 and 0.461 mg L^-1, respectively, which were 6 to 19 times higher than the average concentrations on southwest coasts, including Haenam. The B. plumosa bloom at Songji Beach in November 2022 appears to have depended on DIN and DIP concentrations in seawater. In this study, we report on the mass occurrence of B. plumosa, which appeared for the first time in Korea. This occurrence was found to be closely related to the concentration of nutrients in seawater. Therefore, it is necessary to manage the concentration of nutrients on land flowing into coastal waters to control green algal blooms such as Bryopsis.