• Journal of Ginseng Research
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• v.47 no.4
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• pp.561-571
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• 2023

Background: Escalating evidence shows that ginseng possesses an antiaging potential with cognitive enhancing activity. As mountain cultivated ginseng (MCG) is cultivated without agricultural chemicals, MCG has emerged as a popular herb medicine. However, little is known about the MCG-mediated pharmacological mechanism on brain aging. Methods: As we demonstrated that glutathione peroxidase (GPx) is important for enhancing memory function in the animal model of aging, we investigated the role of MCG as a GPx inducer using GPx-1 (a major type of GPx) knockout (KO) mice. We assessed whether MCG modulates redox and cholinergic parameters, and memory function in aged GPx-1 knockout KOmice. Results: Redox burden of aged GPx-1 KO mice was more evident than that of aged wild-type (WT) mice. Alteration of Nrf2 DNA binding activity appeared to be more evident than that of NFκB DNA binding activity in aged GPx-1 KO mice. Alteration in choline acetyltransferase (ChAT) activity was more evident than that in acetylcholine esterase activity. MCG significantly attenuated reductions in Nrf2 system and ChAT level. MCG significantly enhanced the co-localization of Nrf2-immunoreactivity and ChAT-immunoreactivity in the same cell population. Nrf2 inhibitor brusatol significantly counteracted MCG-mediated up-regulation in ChAT level and ChAT inhibition (by k252a) significantly reduced ERK phosphorylation by MCG, suggesting that MCG might require signal cascade of Nrf2/ChAT/ERK to enhance cognition. Conclusion: GPx-1 depletion might be a prerequisite for cognitive impairment in aged animals. MCG-mediated cognition enhancement might be associated with the activations of Nrf2, ChAT, and ERK signaling cascade.

• Journal of Life Science
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• v.33 no.7
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• pp.574-585
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• 2023

Sarcopenia is a leading cause of increased medical and nursing care costs among the elderly. In Korea, preventive measures for sarcopenia are mostly targeted toward the general elderly population without specific diseases. However, it is also necessary to implement measures for elderly individuals living in nursing homes and hospitals, where the prevalence of sarcopenia is high. Currently, computed tomography and/or magnetic resonance imaging are considered standard diagnostic tools. However, their complexity and time-consuming nature make them unsuitable for clinical use. The exact pathophysiological mechanisms of sarcopenia are unclear, as they involve various molecular biological pathways, including decreased exercise, protein and nutrient intake, changes in testosterone and growth hormone, and inflammation. Sarcopenia symptoms can lead to several diseases, such as osteoporosis, fractures, dementia, diabetes, and cardiovascular disease. Vitamin B deficiency is a significant factor in sarcopenia induction, with B vitamins being directly involved in energy and protein metabolism and nerve function. Vitamin B deficiency can lead to neuromuscular and neurogenic disorders, which often overlap with sarcopenia. Suboptimal intake of B vitamins, malabsorption, and anorexia are common among the elderly. This study aims to provide information on the role of water-soluble B vitamins in preventing and controlling muscle mass loss and deterioration among the elderly with sarcopenia. In addition, we discuss the potential of myokines from the B vitamin family in modulating sarcopenia.

• BMB Reports
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• v.56 no.10
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• pp.569-574
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• 2023

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments.

• IMMUNE NETWORK
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• v.23 no.4
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• pp.35.1-35.16
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• 2023

Defining the molecular dynamics associated with T cell differentiation enhances our understanding of T cell biology and opens up new possibilities for clinical implications. In this study, we investigated the dynamics of CD5 expression in CD8⁺ T cell differentiation and explored its potential clinical uses. Using PBMCs from 29 healthy donors, we observed a stepwise decrease in CD5 expression as CD8⁺ T cells progressed through the differentiation stages. Interestingly, we found that CD5 expression was initially upregulated in response to T cell receptor stimulation, but diminished as the cells underwent proliferation, potentially explaining the differentiation-associated CD5 downregulation. Based on the proliferation-dependent downregulation of CD5, we hypothesized that relative CD5 expression could serve as a marker to distinguish the heterogeneous CD8⁺ T cell population based on their proliferation history. In support of this, we demonstrated that effector memory CD8⁺ T cells with higher CD5 expression exhibited phenotypic and functional characteristics resembling less differentiated cells compared to those with lower CD5 expression. Furthermore, in the retrospective analysis of PBMCs from 30 non-small cell lung cancer patients, we found that patients with higher CD5 expression in effector memory T cells displayed CD8⁺ T cells with a phenotype closer to the less differentiated cells, leading to favorable clinical outcomes in response to immune checkpoint inhibitor (ICI) therapy. These findings highlight the dynamics of CD5 expression as an indicator of CD8⁺ T cell differentiation status, and have implications for the development of predictive biomarker for ICI therapy.

• Molecules and Cells
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• v.47 no.3
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• pp.100033.1-100033.13
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• 2024

Considering the recent increase in the number of colorectal cancer (CRC) cases in South Korea, we aimed to clarify the molecular characteristics of CRC unique to the Korean population. To gain insights into the complexities of CRC and promote the exchange of critical data, RNA-sequencing analysis was performed to reveal the molecular mechanisms that drive the development and progression of CRC; this analysis is critical for developing effective treatment strategies. We performed RNA-sequencing analysis of CRC and adjacent normal tissue samples from 214 Korean participants (comprising a total of 381 including 169 normal and 212 tumor samples) to investigate differential gene expression between the groups. We identified 19,575 genes expressed in CRC and normal tissues, with 3,830 differentially expressed genes (DEGs) between the groups. Functional annotation analysis revealed that the upregulated DEGs were significantly enriched in pathways related to the cell cycle, DNA replication, and IL-17, whereas the downregulated DEGs were enriched in metabolic pathways. We also analyzed the relationship between clinical information and subtypes using the Consensus Molecular Subtype (CMS) classification. Furthermore, we compared groups clustered within our dataset to CMS groups and performed additional analysis of the methylation data between DEGs and CMS groups to provide comprehensive biological insights from various perspectives. Our study provides valuable insights into the molecular mechanisms underlying CRC in Korean patients and serves as a platform for identifying potential target genes for this disease. The raw data and processed results have been deposited in a public repository for further analysis and exploration.

• Nutrition Research and Practice
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• v.18 no.1
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• pp.19-32
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• 2024

BACKGROUND/OBJECTIVES: Atherosclerosis is associated with increased inflammation in the visceral adipose tissue (VAT). Vitamin D has been reported to modulate the inflammatory responses of stromal vascular cells (SVCs) and adipocytes in adipose tissue, but the role of vitamin D in atherosclerosis biology is unclear. This study examined the effects of in vitro 1,25-dihydroxyvitamin D₃ (1,25[OH]₂D₃) treatment on the inflammatory responses of SVCs and adipocytes from atherosclerotic mice. MATERIALS/METHODS: C57BL/6J (B6) mice were divided randomly into 2 groups and fed a 10% kcal fat control diet (control group, CON) or 41% kcal fat, 0.21% cholesterol (high fat + cholesterol, HFC) diet (obese group, OB), and B6.129S7-Ldlr^tm1Her/J (Ldlr^-/-) mice were fed a HFC diet (obese with atherosclerosis group, OBA) for 16 weeks. SVCs and adipocytes isolated from VAT were pre-incubated with 1,25(OH)₂D₃ for 24 h and stimulated with lipopolysaccarides for the next 24 h. Proinflammatory cytokine production by adipocytes and SVCs, the immune cell population in SVCs, and the expression of the genes involved in the inflammatory signaling pathway in SVCs were determined. RESULTS: The numbers of total macrophages and SVCs per mouse were higher in OB and OBA groups than the CON group. The in vitro 1,25(OH)₂D₃ treatment significantly reduced macrophages/SVCs (%) in the OBA group. Consistent with this change, the production of interleukin-6 and monocyte chemoattractant protein 1 (MCP-1) by SVCs from the OBA group was decreased by 1,25(OH)₂D₃ treatment. The 1,25(OH)₂D₃ treatment significantly reduced the toll-like receptor 4 and dual-specificity protein phosphatase 1 (also known as mitogen-activated protein kinase phosphatase 1) mRNA levels in SVCs and MCP-1 production by adipocytes from all 3 groups. CONCLUSIONS: These findings suggest that vitamin D can attribute to the inhibition of the inflammatory response in VAT from atherosclerotic mice by reducing proinflammatory cytokine production.

• Korean Journal of Clinical Laboratory Science
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• v.56 no.1
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• pp.10-20
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• 2024

RNA-sequencing (RNA-seq) is a technique used for providing global patterns of transcriptomes in samples. However, it can only provide the average gene expression across cells and does not address the heterogeneity within the samples. The advances in single-cell RNA sequencing (scRNA-seq) technology have revolutionized our understanding of heterogeneity and the dynamics of gene expression at the single-cell level. For example, scRNA-seq allows us to identify the cell types in complex tissues, which can provide information regarding the alteration of the cell population by perturbations, such as genetic modification. Since its initial introduction, scRNA-seq has rapidly become popular, leading to the development of a huge number of bioinformatic tools. However, the analysis of the big dataset generated from scRNA-seq requires a general understanding of the preprocessing of the dataset and a variety of analytical techniques. Here, we present an overview of the workflow involved in analyzing the scRNA-seq dataset. First, we describe the preprocessing of the dataset, including quality control, normalization, and dimensionality reduction. Then, we introduce the downstream analysis provided with the most commonly used computational packages. This review aims to provide a workflow guideline for new researchers interested in this field.

• Applied Biological Chemistry
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• v.50 no.4
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• pp.268-275
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• 2007

Diversity of the mud flat microbial population in Suncheon Bay was investigated by studying extracellular enzyme activities and 16S rDNA sequences. Four culturable bacterial strains with CMCase, xylanase and protease activities were isolated from the wetland and the mud flat. All the strains produced more xylanase activity than CMCase or protease activity, and the properties of the isolate enzymes from the wetland were similar to those from the mud flat. About 2,000 clones were obtained with the 16S rDNA amplified from the metagenomic DNA isolated from the mud samples. Based on the restriction pattern(s), seventeen clones were selected for base sequence analysis. Of the 17 clones, only 35% (6 clones) were found to be cultured strains and 65% (11 clones) to be uncultured strains. The similarities in the base sequences of the clones ranged from 91.0% to 99.9% with an average similarity of 97.3%. The clones could be divided into 7 groups, Proteobacteria (9 clones, 52.9%), Firmicutes (3 clones, 17.6%), Bacteroidetes (1 clone), Flavobacteria (1 clone), Verrucomicrobia (1 clone), Acidobacteria (1 clone), and Chloroflexi (1 clone). Most of the Proteobacteria clones were gamma Proteobacteria associated with oxidation-reduction of sulfur.

• The Korean Journal of Pesticide Science
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• v.18 no.1
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• pp.33-40
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• 2014

To control Bemisia tabaci on tomato, we applied five different combinations of chemical treatments as below: 1) treatment of combinations of cyantraniliprole on the root area and leaf with the existing registered chemicals three times; 2) treatment of combinations of cyantraniliprole on the root area and dinotefuran + emamectin benzoate on the leaf with the existing registered chemicals three times; 3) treatment of combinations of dinotefuran on the root area and cyantraniliprole on the leaf with the existing registered chemicals three times; 4) treatment of combinations of dinotefuran on the root area and dinotefuran + emamectin benzoate on the leaf with the existing registered chemicals three times; 5) untreated control plot (Table 1). Twenty days after treatment ($17^{th}$ Aug.), the number of population of B. tabaci was zero on the 1, 2, 3, 4 treatments of combinations, and only 2 individuals were found on the 5 treatment of combination per each 20 plant. On $17^{th}$ Sep., in the last observation, the average number of population of B. tabaci was 10.3, 10.3, 10.6 on the 1, 2, 3 treatments of combinations on the 20 plants per each combination, however, the average number of 23.3 and 37.6 were examined on the 4 and 5 treatments of combinations, respectively. TYLCV was not occurring on the 1 and 2 treatments of combinations, and presented only 3% and 17% on the 3 and 4 treatments of combinations, respectively, which indicates that the treatments (1-4) should be effective on TYLCV control as considering that 33% of TYLCV occurred on the untreated control plot. However, after the third flowering period, there is no difference among the five combinations. The amount of products was 9,148g and 9,698g on the 1 and 2 treatments of combinations, respectively, which was the most among the 5 combinations. The number of fallen fruits and the average weight of fruits showed the similar tendency.

• The Korean Journal of Pesticide Science
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• v.13 no.4
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• pp.309-314
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• 2009

Incidence of rice stripe disease, caused by Rice stripe tenuivirus (RSV), was surveyed during 2002 to 2004. The incidence area and ratio of diseased fields were decreased gradually during those period. Rate of diseased plants were 45.8%, 45.0% and 43.7% in the susceptible cultivars Chucheong, Saechucheong and Ilpum, respectively. However, the rate was 4.4% in resistant cultivar Hwaseong. In addition, breakdown rate was also significantly high in the susceptible cultivars in Chucheong, Saechucheong and Ilpum showing 33.6, 33.2 and 31.9%, respectively. In Hwaseong, the breakdown rate was 0.8%. Collection efficiency was compared between two insect vector collection methods. Insect-sucking machine method was much more efficient than sweeping net method in collecting small brown plant hopper (SBPH). According to the survey of the population density of the insect vector during 2002 to 2004, the national average population density was gradually decreased year by year, 3.6, 2.3, and 1.3%, respectively. This result was significantly related with the decrease of the incidence of rice stripe disease. Control efficiency of rice stripe disease by treating several seedling box and water surface with insecticides against SBPH resulted that imidacloprid GR, Fipronil FG, Clothianidin+Probenazole GR and Thiamethoxam GR showed over 80% of control efficiency at 28 days after treatment at the early stage in nursery.