• Journal of Life Science
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• v.29 no.9
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• pp.986-995
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• 2019

Intestinal microbiota play a key role in maintaining the host's health, and variety and richness of this microbiota is directly influenced and modulated by the host's diet. Kimchi is a fermented food rich in dietary fibers and lactic acid bacteria (LAB). To investigate the effect of fermented kimchi on the host's response and the composition of intestinal microbiota, 45 male Sprague-Dawley rats six weeks old were divided into three experimental groups that received either a basal diet (CON) or a basal diet supplemented with fermented kimchi (FK) or chitosan-added fermented kimchi (CFK) for four weeks. Body weights and feed intakes were measured weekly, and the intestinal contents were collected aseptically and were used for 16S rRNA gene profiling via pyrosequencing. As compared to the control, FK and CFK groups showed less body weight gain, feed efficiency, and blood triglyceride concentration. The diversity of intestinal microbiota was increased in both FK and CFK as compared to the control. At the phylum level, obesity-associated Firmicutes decreased, while leanness-associated Bacteroidetes increased. At the genus-level, the genera that consist of LAB, leanness-associated bacteria, and butyric acid-producing bacteria increased in FK and CFK as compared to the control. The overall results suggest that the consumption of fermented kimchi can reduce obesity and promote the host's health through mechanisms involving the modulation of intestinal microbiota.

• Journal of Ginseng Research
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• v.47 no.1
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• pp.44-53
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• 2023

Background: The genus Panax in the Araliaceae family has been used as traditional medicinal plants worldwide and is known to biosynthesize ginsenosides and phytosterols. However, genetic variation between Panax species has influenced their biosynthetic pathways is not fully understood. Methods: Simultaneous analysis of transcriptomes and metabolomes obtained from adventitious roots of two tetraploid species (Panax ginseng and P. quinquefolius) and two diploid species (P. notoginseng and P. vietnamensis) revealed the diversity of their metabolites and related gene expression profiles. Results: The transcriptome analysis showed that 2,3-OXIDOSQUALENE CYCLASEs (OSCs) involved in phytosterol biosynthesis are upregulated in the diploid species, while the expression of OSCs contributing to ginsenoside biosynthesis is higher in the tetraploid species. In agreement with these results, the contents of dammarenediol-type ginsenosides were higher in the tetraploid species relative to the diploid species. Conclusion: These results suggest that a whole-genome duplication event has influenced the triterpene biosynthesis pathway in tetraploid Panax species during their evolution or ecological adaptation. This study provides a basis for further efforts to explore the genetic variation of the Panax genus.

• Journal of Life Science
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• v.33 no.6
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• pp.481-489
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• 2023

The taste and quality of soy sauce, a fermented liquid condiment, is greatly influenced by microbial metabolism during fermentation. To investigate the microbiological characteristics of ganjang during the initial fermentation process, we prepared meju (fermented soybean) blocks fermented with starter cultures and solar salts and analyzed the microbial community quantitively using 16S rRNA gene profiling from ganjang that had been fermented over a five-week period. The ganjang samples were collected and analyzed after soaking for week one (1W), three (3W), and five (5W) weeks. We found that Halomonadaceae was significantly higher in the 1W group (89.83%) than the 3W and 5W groups (14.46%, and 13.78%, respectively). At a species level, Chromohalobacter beijerinckii and Chromohalobacter canadensis were the dominant species in the 1W group but several taxa such as Bacillus subtilis, Pediococcus acidilactici, and Enterococcus faecalis were more abundant in the 3W and 5W groups. Pearson correlation analysis of the relative abundance of the bacteria showed a negative correlation between Chromohalobacter and two bacterial genera Bacillus and Enterococcus. Beta-diversity showed a statistical distinction between the 1W and the 3W and 5W groups, while no significance was evident between the 3W and 5W groups. Linear discriminant effect size analysis was used to identify biomarkers and significant differences in the relative abundance of several halophilic bacteria, Bacillus sp. and lactic acid bacteria at 1W, 3W, and 5W, recpectively, which indicates the important role of the bacterial community at these time points.

• BMB Reports
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• v.56 no.10
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• pp.563-568
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• 2023

DNA methylation regulates gene expression and contributes to tumorigenesis in the early stages of cancer. In colorectal cancer (CRC), CpG island methylator phenotype (CIMP) is recognized as a distinct subset that is associated with specific molecular and clinical features. In this study, we investigated the genome-wide DNA methylation patterns among patients with CRC. The methylation data of 1 unmatched normal, 142 adjacent normal, and 294 tumor samples were analyzed. We identified 40,003 differentially methylated positions with 6,933 (79.8%) hypermethylated and 16,145 (51.6%) hypomethylated probes in the genic region. Hypermethylated probes were predominantly found in promoter-like regions, CpG islands, and N shore sites; hypomethylated probes were enriched in open-sea regions. CRC tumors were categorized into three CIMP subgroups, with 90 (30.6%) in the CIMP-high (CIMP-H), 115 (39.1%) in the CIMP-low (CIMP-L), and 89 (30.3%) in the non-CIMP group. The CIMP-H group was associated with microsatellite instability-high tumors, hypermethylation of MLH1, older age, and right-sided tumors. Our results showed that genome-wide methylation analyses classified patients with CRC into three subgroups according to CIMP levels, with clinical and molecular features consistent with previous data.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.08a
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• pp.33-33
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• 2020

Watermelon (Citrullus lanatus) is a non-seasonal, economically important, cucurbit cultivated throughout the world with Asia as a continent contributing the most. As part of the effort in diversifying watermelon genetic resources in the already cultivated group, this study was devoted to providing baseline data on morphological quality traits and health-beneficial phytonutrients of watermelon germplasm collections, thereby promoting watermelon research and cultivation programs. To this end, we reported morphological traits, citrulline, and arginine levels of watermelon genetic resources obtained from the gene bank of Agrobiodiversity Center, Republic of Korea, and discussed the relationship between each other. Diverse characteristics were observed among many of the traits. But, most of the genetic resources (>90%) were either red or pink-fleshed. Korean origin fruits contained intermediate levels of soluble solid content (SSC) while The USA, Russian, Tajikistan, Turkmenistan, Taiwan, and Uruguay originated had generally the highest levels of soluble solids. The citrulline and arginine contents using HPLC method were ranged from 6.9 to 52.1 mg/g (average, 27.3 mg/g) and 1.8 to 21.3 mg/g (average, 9.8 mg/g), respectively. The citrulline content determined using Citrulline Assay Kit was ranged from 6.5 to 42.8 mg/g (average, 27.0 mg/g). Resources with high citrulline and arginine levels contained low SSC. Whereas, red- and pink-colored flesh samples had less citrulline compared to yellow and orange. In addition to the profiling of morphological characters and phytonutrients, molecular marker characterization and identification of sources of resistance to diseases and pests are recommended for a more complete diversity analysis of watermelon genetic resources.

• Journal of Life Science
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• v.27 no.2
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• pp.149-154
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• 2017

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-hodgkin lymphoma. Advances in the chemotherapeutic treatment of this disease have improved the outcomes of DLBCL; nonetheless, many patients still die of DLBCL, and therefore, a better understanding of this disease and identification of novel therapeutic targets are urgently required. In a recent gene expression profiling study, PDE (phosphodiesterase) 4B was found to be overexpressed in chemotherapy-resistant tumors. The major function of PDE4B is to inactivate the second messenger cyclic 3',5' monophosphate (cAMP) by catalyzing the hydrolysis of cAMP to 5'AMP. It is known that cAMP induces cell cycle arrest and/or apoptosis in B cells, and PDE4B abolishes cAMP's effect on B cells. However, the mechanism by which PDE4B is overexpressed remains unclear. Here, we show that the aberrant expression of miRNA may be associated with the overexpression of this gene. The PDE4B 3' untranslated region (UTR) has three functional binding sites of miR-23b, as confirmed by luciferase reporter assays. Interestingly, miR-23b-binding sites were evolutionarily conserved from humans to lizards, implying the critical role of PDE4B-miR-23b interaction in cellular physiology. The ectopic expression of miR-2 3b repressed PDE4B mRNA levels and enhanced intracellular cAMP concentrations. Additionally, miR-23b expression inhibited cell proliferation and survival of DLBCL cells only in the presence of forskolin, an activator of adenylyl cyclase, suggesting that miR-23b's effect is via the downregulation of PDE4B. These results together suggest that miR-23b could be a therapeutic target for overcoming drug resistance by repressing PDE4B in DLBCL.

• BMB Reports
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• v.57 no.2
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• pp.110-115
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• 2024

Alterations in DNA methylation play an important pathophysiological role in the development and progression of colorectal cancer. We comprehensively profiled DNA methylation alterations in 165 Korean patients with colorectal cancer (CRC), and conducted an in-depth investigation of cancer-specific methylation patterns. Our analysis of the tumor samples revealed a significant presence of hypomethylated probes, primarily within the gene body regions; few hypermethylated sites were observed, which were mostly enriched in promoter-like and CpG island regions. The CpG Island Methylator Phenotype-High (CIMP-H) exhibited notable enrichment of microsatellite instability-high (MSI-H). Additionally, our findings indicated a significant correlation between methylation of the MLH1 gene and MSI-H status. Furthermore, we found that the CIMP-H had a higher tendency to affect the right-side of the colon tissues and was slightly more prevalent among older patients. Through our methylome profile analysis, we successfully verified the methylation patterns and clinical characteristics of Korean patients with CRC. This valuable dataset lays a strong foundation for exploring novel molecular insights and potential therapeutic targets for the treatment of CRC.

• Research in Plant Disease
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• v.27 no.4
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• pp.172-179
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• 2021

This study aimed to assess the disease incidence and distribution of toxigenic in Korean triticale. The pathogen of triticale that cause Fusarium head blight were isolated from five different triticale cultivars that cultivated in Suwon Korea at 2021 year. The 72 candidate were classified as a Fusarium asiaticum by morphology analysis and by ITS1, TEF-1α gene sequence analysis. And the results of pathogenicity with 72 isolates on seedling triticale, 71 isolates were showed disease symptom. Also, seven out of 71 Fusarium isolates were inoculated on the wheat, to test the pathogenicity on the different host. The results showed more low pathogenicity on the wheat than triticale. The results of analysis of toxin type with 72 isolates, 64.6% isolates were produced nivalenol type toxin and other 4.6% and 30.8% isolates were produce 3-acetyldeoxynivalenol and 15-acetyldeoxynivalenol, respectively. To select fungicide for control, the 72 Fusarium isolates were cultivated on the media that containing four kinds fungicide. The captan, hexaconazole, and difenoconazole·propiconazole treated Fusarium isolates were not showed resistance response against each fungicide. However, six isolates out of 72 isolates, showed resistance response to fludioxonil. This study is first report that F. asiaticum causes Fusarium head blight disease of triticale in Korea.

• Journal of Science Education
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• v.47 no.2
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• pp.192-210
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• 2023

This study was intended to develop the plant molecular biology experimental program using Rapid-cycling Brassica rapa (RcBr) based on the teaching steps and teaching methods of the cognitive apprenticeship model and to determine its application effects. In order to improve a subject's cognitive function and expertise on molecular biology experiments, two themes composed of a total 8 class sessions were selected: 'Identification of DFR gene in purple RcBr and non-purple RcBr' and 'Identification of RcBr's genetic polymorphism site using the DNA profiling method'. Research subjects were 18 pre-service teaching majors in biology education of H University in Chungbuk, Korea. The effectiveness of the developed program was verified by analyzing the enhancement of 'cognitive function' related to the use of molecular biology knowledge and technology, and the enhancement of 'domain-general metacognitive abilities.' The effect of the developed program was also determined by analyzing the task flow diagram provided. The developed program was effective in improving the cognitive functions of the pre-service teachers on the use of knowledge and technology of molecular biology experiments. It was especially effective to improve the higher cognitive function of pre-service teachers who did not have the previous experience. The developed program also showed a significant improvement in the task of metacognitive knowledge and in the planning, checking, and evaluation of metacognitive regulation, which are sub-elements of domain-general metacognitive abilities. It was found that the developed program's self-test activity could help the pre-service teachers to improve their metacognitive regulation. Therefore, this developed program turned out to be helpful for pre-service teachers to develop core competencies needed for molecular biology experimental classes. If the teaching and learning materials of the developed program could be reconstructed and applied to in-service teachers or high school students, it would be expected to improve their metacognitive abilities.