• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.1
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• pp.537-545
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• 2018

In this study, transcriptome analysis was conducted to collect various information from Fagopyrum esculentum and Fagopyrum tataricum during the early germination stage. Total RNA was extracted from the seeds and at 12, 24, and 36 hrs after germination of Jeju native Fagopyrum esculentum and Fagopyrum tataricum and sequenced using the Illumina Hiseq 2000 platform. Raw data analysis was conducted using the Dynamic Trim and Lengths ORT programs in the SolexaQA package, and assembly and annotation were performed. Based on RNA-seq raw data, we obtained 16.5 Gb and 16.2 Gb of transcriptome data corresponding to about 84.2% and 81.5% of raw data, respectively. De novo assembly and annotation revealed 43,494 representative transcripts corresponding to 47.5Mb. Among them, 23,165 sequences were shown to have similar sequences with annotation DB. Moreover, Gene Ontology (GO) analysis of buckwheat representative transcripts confirmed that the gene is involved in metabolic processes (49.49%) of biological processes, as well as cell function (46.12%) in metabolic process, and catalytic activity (80.43%) in molecular function In the case of gibberellin receptor GID1C, which is related to germination of seeds, the expression levels increased with time after germination in both F. esculentum and F. tataricum. The expression levels of gibberellin 20-oxidase 1 were increased within 12 hrs of gemination in F. esculentum but continuously until 36 hrs in F. tataricum. This buckwheat transcriptome profile analysis of the early germination stage will help to identify the mechanism causing functional and morphological differences between species.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.26 no.3
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• pp.248-262
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• 2021

Marine planktonic ciliates include two major groups, loricated tintinnids and naked oligotrichs. The study of marine ciliate plankton in Korea began with taxonomic efforts on tintinnids based on the morphology of lorica, a vase-shaped shell. Despite polymorphism in the lorica, it is utilized as a key characteristic in identification of tintinnid species. However, oligotrichs have been studied only recently in Korea due to challenges associated with the observation of ciliary arrangements and the technical development for cell staining. Species diversity and phylogenetic classification of the ciliates have been informed by recent advances in morphological and molecular analyses. Illustrations of the planktonic ciliate in Korea have been published on the basis of taxonomic data of tintinnids and oligotrichs. Planktonic ciliates acting as the major consumers of pico- and nanoplankton as well as the prey of mesozooplankton, has been monitored by spatial and temporal investigations in Korean coastal waters. A practical approach addressing the limitations and potential of marine ciliate studies in Korea is proposed here to improve the data quality of planktonic ciliates, providing an enhanced basis for quality control of ciliate monitoring.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.53-53
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• 2015

Agrobacterium tumefaciens-mediated transformation(ATMT) of Flammulina velutipes was used to produce a diverse number of transformants to discover the functions of gene that is vital for its variation color, spore pattern and cellulolytic activity. Futhermore, the transformant pool will be used as a good genetic resource for studying gene functions. Agrobacterium-mediated transformation was conducted in order to generate intentional mutants of F. velutipes strain KACC42777. Then Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into F. velutipes. This method is use to determine the functional gene of F. velutipes. Inverse PCR was used to insert T-DNA into the tagged chromosomal DNA segments and conducting sequence analysis of the F. velutipes. But this experiment had trouble in diverse morphological mutants because of dikaryotic nature of mushroom. It needed to make monokaryotic fruiting varients which introduced genes of compatible mating types. In this study, next generation sequencing data was generated from 28 strains of Flammulina velutipes with different phenotypes using Illumina Hiseq platform. Filtered short reads were initially aligned to the reference genome (KACC42780) to construct a SNP matrix. And then we built a phylogenetic tree based on the validated SNPs. The inferred tree represented that white- and brown- fruitbody forming strains were generally separated although three brown strains, 4103, 4028, and 4195, were grouped with white ones. This topological relationship was consistently reappeared even when we used randomly selected SNPs. Group I containing 4062, 4148, and 4195 strains and group II containing 4188, 4190, and 4194 strains formed early-divergent lineages with robust nodal supports, suggesting that they are independent groups from the members in main clades. To elucidate the distinction between white-fruitbody forming strains isolated from Korea and Japan, phylogenetic analysis was performed using their SNP data with group I members as outgroup. However, no significant genetic variation was noticed in this study. A total of 28 strains of Flammulina velutipes were analyzed to identify the genomic regions responsible for producing white-fruiting body. NGS data was yielded by using Illumina Hiseq platform. Short reads were filtered by quality score and read length were mapped on the reference genome (KACC42780). Between the white- and brown fruitbody forming strains. There is a high possibility that SNPs can be detected among the white strains as homozygous because white phenotype is recessive in F. velutipes. Thus, we constructed SNP matrix within 8 white strains. SNPs discovered between mono3 and mono19, the parental monokaryotic strains of 4210 strain (white), were excluded from the candidate. If the genotypes of SNPs detected between white and brown strains were identical with those in mono3 and mono19 strains, they were included in candidate as a priority. As a result, if more than 5 candidates SNPs were localized in single gene, we regarded as they are possibly related to the white color. In F. velutipes genome, chr01, chr04, chr07,chr11 regions were identified to be associated with white fruitbody forming. White and Brown Fruitbody strains can be used as an identification marker for F. veluipes. We can develop some molecular markers to identify colored strains and discriminate national white varieties against Japanese ones.

• Korean Journal of Microbiology
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• v.41 no.3
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• pp.208-215
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• 2005

This study was accomplished in order to collect fundamental data on microbial roles in recycling process of reed rhizosphere. Sunchon bay, which is considered as one of the marsh and mud environments severely affected by human activities such agriculture and fisheries, was selected as a model place. In our initial efforts, two bacterial consortia were obtained by enrichment culture using PAH mixtures containing anthracene, naphthalene, phenanthrene and pyrene as the sources of carbon and energy, and four pure bacteria capable of rapid degradation of PAH were isolated from them. Four strains designated as SCB1, SCB2, SCB6, and SCB7 revealed by morphological, physiological and molecular analyses were identified as Burkholderia anthina, Alcaligenes sp., Achromobacter xylosoxidans., and Pseudomonas putida, respectively with over $99{\%}$ confidence. Notably, Burkholderia anthina SCB1 and Alcaligenes sp. SCB2 were found to utilize anthracene and pyrene more quickly than naphthalene and phenanthrene, whereas Achromobacter xylosoxidans SCB6 and Pseudomonas putida SCB7 exhibited similar growth and degradation patterns except for pyrene. These facts suggest that the rhizosphere microorganisms capable of PAH degradation might be used to clean up the contamination sites with polycyclic aromatic hydrocarbons.

• The Journal of Advanced Prosthodontics
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• v.7 no.2
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• pp.138-145
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• 2015

PURPOSE. The objective of this study was to conduct an in vitro comparative evaluation of polished and laser-dimpled titanium (Ti) surfaces to determine whether either surface has an advantage in promoting the attachment of epithelial-like cells and fibroblast to Ti. MATERIALS AND METHODS. Forty-eight coin-shaped samples of commercially pure, grade 4 Ti plates were used in this study. These discs were cleaned to a surface roughness (Ra: roughness centerline average) of 180 nm by polishing and were divided into three groups: SM (n=16) had no dimples and served as the control, SM15 (n=16) had $5-{\mu}m$ dimples at $10-{\mu}m$ intervals, and SM30 (n=16) had $5-{\mu}m$ dimples at $25-{\mu}m$ intervals in a $2{\times}4mm^2$ area at the center of the disc. Human gingival squamous cell carcinoma cells (YD-38) and human lung fibroblasts (MRC-5) were cultured and used in cell proliferation assays, adhesion assays, immunofluorescent staining of adhesion proteins, and morphological analysis by SEM. The data were analyzed statistically to determine the significance of differences. RESULTS. The adhesion strength of epithelial cells was higher on Ti surfaces with $5-{\mu}m$ laser dimples than on polished Ti surfaces, while the adhesion of fibroblasts was not significantly changed by laser treatment of implant surfaces. However, epithelial cells and fibroblasts around the laser dimples appeared larger and showed increased expression of adhesion proteins. CONCLUSION. These findings demonstrate that laser dimpling may contribute to improving the peri-implant soft tissue barrier. This study provided helpful information for developing the transmucosal surface of the abutment.

• The Korean Journal of Mycology
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• v.27 no.5 s.92
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• pp.337-340
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• 1999

The context and upper surface of Phellinus basidiocarp become blackened, rimose and woody. The basidiocarp is sessile, dimidiate and elongate. The basidiospores are pigmented and ovoid to globose. Hymenial setae are $17{\sim}35{\times}6{\sim}8{\mu}m$. Nineteen isolates of Phellinus species, including Phellinus linteus, were used for sequencing of the internal transcribed spacer (ITS) region of the nuclear rDNA. Based on these sequence data, specific primers were designed for identification of Phellinus linteus isolates in Korea. The specific primers were within the ITS1 and ITS2 regions and were nested within the universal primers flanking the spacer regions. A total of four primers (the universal primers ITS-1F and ITS-4, and the specific primers PL-F and PL-R) were used for detection of Phellinus linteus collected in Korea. The length of the four amplification products of Phellinus linteus DNA were 800 bp (ITS-1F/ITS-4), two bands of about 720 bp (ITS-1F/PL-R and PL-F/ITS-4), and 610 bp (PL-F/PL-R). Among 23 isolates of Phellinus species collected in Korea, Thirteen isolates were identified as Phellinus linteus based on the presence of the four bands. The other species produced only the single ITS-1F/ITS-4 product.

• Microbiology and Biotechnology Letters
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• v.32 no.4
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• pp.334-340
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• 2004

This study was initially performed to obtain fundamental data on lichen distribution depending on environmental condiLichens distributed on coastal rocks atleast 20 m far away from the coast were also investigated. Analyof morphological characteristics and rDNA ITS clones revealed that lichens containing 9 families and 15 genera were distributed in coastal rocks of V-do, while lichens containing 10 families and 14 genera were in field rocks, demonstrating little difference of diversity between both sites. Foliose lichens such as PhaeophysPhyscia, Pyxine belonging to the family Physciaceae were representatives distributed in coastal rocks of V-do, along with Xanthoparmelia belonging to Parmeliaceae, fruticose lichens such as Ramalina to Ramaliand crustose lichen Lecanora to Lecanoraceae. In contrast, foliose lichen Cladonia belonging to the family Cladoniaceae, fruitcose lichen Stereocaulon to Streocaulaceae, and crustose lichen Porpidia to Porpidwere found only on the surface of field rocks. Crustose lichens containing genera Caloplaca, CanDirinaria, Graphis, Rhizocarpon, and Pertusaria were rarely distributed in coastal rocks, and most of them were also found in field rocks.

• Journal of Life Science
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• v.28 no.11
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• pp.1321-1331
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• 2018

The aim of this study was to separate the photosensitizer that induces apoptosis of U937 and SK-HEP-1 cells from Nostoc commune. Dried N. commune was extracted with $CH_2Cl_2/MeOH$ (1:1) to separate the photosensitizer using various chromatographic techniques. The isolated compound was identified as pheophytin a ($C_{55}H_{74}N_4O_5$) with a molecular weight of 870. Its photodynamic activities were assessed under different irradiation conditions (light and non-light) at the same concentration range of $1.15-23.0{\mu}M$. The apoptosis inducing activity in U937 or SK-HEP-1 cells appeared only in the light. The mechanisms underlying the pheophytin a-mediated photodynamic inhibition of cancer cells were further investigated by examining cell morphology changes, cytotoxicity, caspase-3/7 activity, fluorescence staining, flow cytometry analysis, and DNA fragmentation in these two cell lines. The positive control and the light irradiation group showed typical apoptotic responses, including morphological changes, cytotoxicity, caspase activity, nucleus shrinkage owing to chromatin condensation, DNA laddering, and the presence of apoptotic bodies. Cytotoxicity markedly increased in a dose-dependent manner after a 12 hr exposure. Caspase-3/7 activity was higher in U937 cells than in SK-HEP-1 cells. Apoptosis induction therefore appeared to be both concentration- and light-dependent. In conclusion, pheophytin a, isolated from the blue green alga N. commune, had a photodynamic apoptosis-inducing effect on U937 and SK-HEP-1 cells. The findings reported here can be used as basic data for the development of next-generation photosensitizers from N. commune.

• Journal of fish pathology
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• v.22 no.1
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• pp.53-65
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• 2009

Tenacibaculum maritimum (formerly Flexibacter maritimus) is the aetiological agent of an ulcerative and necrotic disease commonly called tenacibaculosis in marine fish. Tenacibaculosis is an economically important disease in a great variety species in Jeju Island cultured fish and leading to this pathogen initially affected by skin, mouth, fins, tail causing severe necrotic and ulcerative lesions on the body surface. In the present study, A-7 strain was isolated from Paralichthys olivaceus showing symptoms of tenacibaculosis and identified as T. maritimum by morphological, biochemical and molecular biological analysis. T. maritimum A-7 is experimentally infected through immersion route in Paralichthys olivaceus which the disease outbreaks in land-based fish tanks of Jeju Island. Up to data a number of treatments proposed for the tenacibaculosis outbreaks are based on the immersion administration of drugs in tank. Oxytetracycline is the most widely used disinfectants in fish farms. However, most of fish farms manager and consumers have expressed concern as bioaccumulation in tissue and its environmental. In addition, this antimicrobial compounds is expensive in fish farmers. The overcome of this problem is desired the application of natural plant derived products. To obtain as 70% EtOH extract antimicrobial compounds against tenacibaculosis from 35 species of Jeju Island native plants were screened for antimicrobial activity against T. maritimum. In the present study were identified most of the plant extracts were better antimicrobial activity against T. maritimum.

• Korean Journal of Plant Taxonomy
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• v.40 no.4
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• pp.226-233
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• 2010

An intensive study of the embryology of Gymnospermium microrrhynchum was conducted to provide information regarding a discussion of the phylogenetic relationships of the genus, which is yet unstudied. Our results indicated that Gymnospermium is similar to other genera of Berberidaceae in terms of its embryological features. Nevertheless, newly reported and unique features are the well-developed endothelium and the undifferentiated seed coat type. Until the study of Gymnospermium, it may have been considered to be closer to Caulophyllum and Leontice in the tribe Leonticeae. These three genera share many morphological features as well as molecular similarities, by which they are kept in the same tribe, Leonticeae. However, very little detailed embryological data regarding these genera have been published thus far. Gymnospermium was characterized according to the basic type of anther wall formation as well as its glandular tapetum, successive cytokinesis in the microspore mother cell, two-celled mature pollen grains, anatropous and crassinucellate ovules with a nucellar cap, well-developed endothelium, its Polygonum type of embryo sac formation, its nuclear type of endosperm formation, and its undifferentiated seed coat type. In comparison with Nandina, there are many differences, such as the dehiscence of the anther, the cytokinesis in the microspore mother cells, the shape of the megaspore dyad, and the seed characteristics. Although we had no available detailed embryological information regarding Caulophyllum and Leontice, which are genera that are more closely related to Gymnospermium, we could deduce from the phylogenetic relationship that Gymnospermium, Caulophyllum, and Leontice are more closely related to each other than other genera of Berberidaceae on the basis of the seed characteristics.