• Journal of Life Science
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• v.32 no.3
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• pp.249-255
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• 2022

Metabolism is essential for survival and reproduction, and there is a metabolic pathways entry in the clusters of orthologous groups of proteins (COGs) database, updated in 2020. In this study, the metabolic pathways of 1309 prokaryotes were analyzed using COGs. There were 822 COGs associated with 63 metabolic pathways, and the mean for each taxon was between 200.50 (mollicutes) and 527.07 (cyanobacteria) COGs. The metabolic pathway composition ratio (MPCR) was defined as the number of COGs present in one genome in relation to the total number of COGs constituting each metabolic pathway, and the number of pathways with 100% MPCR ranged from 0 to 26 in each prokaryote. Among 1309 species, the 100% MPCR pathways included murein biosynthesis associated with cell wall synthesis (922 species); glycine cleavage (918); and ribosomal 30S subunit synthesis (903). The metabolic pathways with 0% MPCR were those involving photosystem I (1263 species); archaea/vacuolar-type ATP synthase (1028); and Na⁺-translocation NADH dehydrogenase (976). Depending on the prokaryote, three to 49 metabolic pathways could not be performed at all. The sequence of most highly conserved metabolic pathways was ribosome 30S subunit synthesis (96.1% of 1309 species); murein biosynthesis (86.8%); arginine biosynthesis (80.4%); serine biosynthesis (80.3%); and aminoacyl-tRNA synthesis (82.2%). Protein and cell wall synthesis have been shown to be important metabolic pathways in prokaryotes, and the results of this study of COGs related to such pathways can be utilized in, for example, the development of antibiotics and artificial cells.

• Journal of Preventive Medicine and Public Health
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• v.54 no.6
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• pp.412-421
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• 2021

Objectives: Non-alcoholic fatty liver disease (NAFLD) is an increasingly prevalent metabolic disease. Muscle is known to influence NAFLD development. Therefore, this study aimed to determine the relationships among low muscle mass, NAFLD, and hepatic fibrosis using various definitions of low muscle mass and NAFLD diagnostic methods, including magnetic resonance imaging-based proton density fat fraction (MRI-PDFF). Methods: This cross-sectional study included 320 participants (107 males, 213 females) from the Korean Genome and Epidemiology Study on Atherosclerosis Risk of Rural Areas in the Korean General Population cohort. Muscle mass was assessed using whole-body dual-energy X-ray absorptiometry and adjusted for the height squared, body weight, and body mass index (BMI). NAFLD was diagnosed using ultrasonography (US), MRI-PDFF, and the comprehensive NAFLD score (CNS). Hepatic fibrosis was assessed using magnetic resonance elastography. Multivariable logistic and linear regression analyses were performed to determine the aforementioned associations. Results: According to US, 183 participants (57.2%) had NAFLD. Muscle mass adjusted for body weight was associated with NAFLD diagnosed using US (odds ratio [OR], 3.00; 95% confidence interval [CI], 1.70 to 5.31), MRI-PDFF (OR, 2.00; 95% CI, 1.13 to 3.53), and CNS (OR, 3.39; 95% CI, 1.73 to 6.65) and hepatic fibrosis (males: β=-0.070, p<0.01; females: β=-0.037, p<0.04). Muscle mass adjusted for BMI was associated with NAFLD diagnosed by US (OR, 1.71; 95% CI, 1.02 to 2.86) and CNS (OR, 1.95; 95% CI, 1.04 to 3.65), whereas muscle mass adjusted for height was not associated with NAFLD. Conclusions: Low muscle mass was associated with NAFLD and liver fibrosis; therefore, maintaining sufficient muscle mass is important to prevent NAFLD. A prospective study and additional consideration of muscle quality are needed to strengthen the findings regarding this association.

• Korean Journal of Plant Resources
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• v.35 no.2
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• pp.346-361
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• 2022

Food poisoning accidents caused by poisonous plants occur every year. As certain poisonous plants are mistaken for edible plants causing food poisoning, accurate species identification of poisonous plants is required. DNA barcodes suitable for species identification of poisonous plants and database that can be used for accurate species identification are necessary for their use in forensic cases. In this study, species identification of 19 poisonous plants native to Jeju Island using seven DNA barcodes (trnH-psbA, trnL-trnF, trnL intron, rbcL, matK, ITS1-ITS4, 18S rRNA) was performed to construct a database containing sequence information and DNA barcode universality. trnL-trnF barcode and ITS1-ITS4 barcode were the easiest markers for PCR amplification and sequence retrieval, and the combination of the two barcodes enabled single species identification in 18 out of 19 plants. Therefore, when an investigation of unknown poisonous plants is requested, combination of trnL-trnF and ITS1-ITS4 barcodes is considered as a primary marker for species identification. The database of recommended DNA barcodes for each poisonous plant presented in this study will be helpful in plants poisoning cases.

• Journal of the Korea Society of Computer and Information
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• v.27 no.7
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• pp.1-7
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• 2022

Recently, as the use of applications such as big data programs and machine learning programs that are driven while generating large amounts of data in the program itself becomes common, the existing main memory alone lacks memory, making it difficult to execute the program quickly. In particular, the need to derive results more quickly has emerged in a situation where it is necessary to analyze whether the entire sequence is genetically altered due to the outbreak of the coronavirus. As a result of measuring performance by applying large-capacity data to a computing system equipped with a self-developed memory pool MOCA host adapter instead of processing large-capacity data from an existing SSD, performance improved by 16% compared to the existing SSD system. In addition, in various other benchmark tests, IO performance was 92.8%, 80.6%, and 32.8% faster than SSD in computing systems equipped with memory pool MOCA host adapters such as SortSampleBam, ApplyBQSR, and GatherBamFiles by task of workflow. When analyzing large amounts of data, such as electrical dielectric pipeline analysis, it is judged that the measurement delay occurring at runtime can be reduced in the computing system equipped with the memory pool MOCA host adapter developed in this research.

• Journal of Life Science
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• v.32 no.2
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• pp.161-166
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• 2022

Mitosis is a process in which a replicated genome is distributed to two daughter cells, and it is necessary for cell survival and organismal development. During mitosis, the spindle assembly checkpoint (SAC) ensures faithful chromosome segregation by monitoring the kinetochore attachment to the mitotic spindle. Although the SAC mechanism has been extensively studied over the last 30 years, the mechanism by which a single unattached kinetochore activates the SAC remains unclear. The key components of the SAC are Mad1, Mad2, Mad3 (BubR1 in higher eukaryotes), Bub1, Bub3, and Cdc20, which are all required for SAC activation. An essential step for SAC activation is the formation of the Mad2 - Cdc20 complex in the unattached kinetochore, which is kinetically disfavored. Although the mechanism by which Mad2 and Cdc20 are recruited to unattached kinetochores is well-known, it is not clear how they form a complex. Recently, a key mechanism for the formation of the Mad2 - Cdc20 complex has been identified, which is catalyzed by an unattached kinetochore. This supports the evidence that a single unattached kinetochore can activate the SAC signaling. Herein, we discuss the known key mechanism for SAC activation, review the recent studies on SAC, and conclude how their discoveries improved the understanding of mitosis.

• Genomics & Informatics
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• v.20 no.3
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• pp.29.1-29.12
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• 2022

Several studies have shown associations between irinotecan toxicity and UGT1A genetic variations in colorectal and lung cancer, but only limited data are available for gastric cancer patients. We evaluated the frequencies of UGT1A polymorphisms and their relationship with clinicopathologic parameters in 382 Korean gastric cancer patients. Polymorphisms of UGT1A1*6, UGT1A1*27, UGT1A1*28, UGT1A1*60, UGT1A7*2, UGT1A7*3, and UGT1A9*22 were genotyped by direct sequencing. In 98 patients treated with irinotecan-containing regimens, toxicity and response were compared according to the genotype. The UGT1A1*6 and UGT1A9*22 genotypes showed a higher prevalence in Korean gastric cancer patients, while the prevalence of the UG1A1*28 polymorphism was lower than in normal Koreans, as has been found in other studies of Asian populations. The incidence of severe diarrhea after irinotecan-containing treatment was more common in patients with the UGT1A1*6, UGT1A7*3 and UGT1A9*22 polymorphisms than in controls. The presence of the UGT1A1*6 allele also showed a significant association with grade III-IV neutropenia. Upon haplotype and diplotype analyses, almost every patient bearing the UGT1A1*6 or UGT1A7*3 variant also had the UGT1A9*22 polymorphism, and all severe manifestations of UGT1A polymorphism-associated toxicity were related to the UGT1A9*22 polymorphism. By genotyping UGT1A9*22 polymorphisms, we could identify high-risk gastric cancer patients receiving irinotecan-containing chemotherapy, who would experience severe toxicity. When treating high-risk patients with the UGT1A9*22 polymorphism, clinicians should closely monitor them for signs of toxicity such as severe diarrhea or neutropenia.

• BMB Reports
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• v.55 no.9
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• pp.453-458
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• 2022

Diabetes mellitus (DM) is a serious disease in which blood sugar levels rise abnormally because of failed insulin production or decreased insulin sensitivity. Although many studies are being conducted for the treatment or early diagnosis of DM, it is not fully understood how mitochondrial genome (mtDNA) abnormalities appear in patients with DM. Here, we induced iPSCs from fibroblasts, PBMCs, or pancreatic cells of three patients with type 2 DM (T2D) and three patients with non-diabetes counterpart. The mtDNA mutations were detected randomly without any tendency among tissues or patients. In T2D patients, 62% (21/34) of iPSC clones harbored multiple mtDNA mutations, of which 37% were homoplasmy at the 100% mutation level compared to only 8% in non-diabetes. We next selected iPSC clones that were a wild type or carried mutations and differentiated into pancreatic cells. Oxygen consumption rates were significantly lower in cells carrying mutant mtDNA. Additionally, the mutant cells exhibited decreased production of insulin and reduced secretion of insulin in response to glucose. Overall, the results suggest that screening mtDNA mutations in iPSCs from patients with T2D is an essential step before pancreatic cell differentiation for disease modeling or autologous cell therapy.

• Molecules and Cells
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• v.45 no.10
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• pp.718-728
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• 2022

Splicing factor B subunit 4 (SF3B4), a component of the U2-pre-mRNA spliceosomal complex, contributes to tumorigenesis in several types of tumors. However, the oncogenic potential of SF3B4 in lung cancer has not yet been determined. The in vivo expression profiles of SF3B4 in non-small cell lung cancer (NSCLC) from publicly available data revealed a significant increase in SF3B4 expression in tumor tissues compared to that in normal tissues. The impact of SF3B4 deletion on the growth of NSCLC cells was determined using a siRNA strategy in A549 lung adenocarcinoma cells. SF3B4 silencing resulted in marked retardation of the A549 cell proliferation, accompanied by the accumulation of cells at the G0/G1 phase and increased expression of p27, p21, and p53. Double knockdown of SF3B4 and p53 resulted in the restoration of p21 expression and partial recovery of cell proliferation, indicating that the p53/p21 axis is involved, at least in part, in the SF3B4-mediated regulation of A549 cell proliferation. We also provided ubiquitination factor E4B (UBE4B) is essential for p53 accumulation after SF3B4 depletion based on followings. First, co-immunoprecipitation showed that SF3B4 interacts with UBE4B. Furthermore, UBE4B levels were decreased by SF3B4 depletion. UBE4B depletion, in turn, reproduced the outcome of SF3B4 depletion, including reduction of polyubiquitinated p53 levels, subsequent induction of p53/p21 and p27, and proliferation retardation. Collectively, our findings indicate the important role of SF3B4 in the regulation of A549 cell proliferation through the UBE4B/p53/p21 axis and p27, implicating the therapeutic strategies for NSCLC targeting SF3B4 and UBE4B.

• Animal Bioscience
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• v.36 no.1
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• pp.10-18
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• 2023

Objective: In this study, we aimed to position the Hungarian Merino among other Merinoderived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain. Methods: Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used. Results: Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise F_ST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (-log₁₀P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (-log₁₀P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain. Conclusion: The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.

• Journal of Nutrition and Health
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• v.55 no.2
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• pp.263-277
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• 2022

Purpose: The present study examined the associations of Korean Food-based Index of Dietary Inflammatory Potential (FBDI) scores with the prevalence of diabetes and hemoglobin A1c (HbA1c) level of diabetes patients in Korean adults. Methods: The Korean Genome and Epidemiology Study (KoGES) Health Examinee baseline data, collected between 2004 and 2013 and followed up between 2012 and 2016, were used in our study. A total 56,391 participants including diabetes (n = 5,733) and non-diabetes (n = 50,658) were analyzed. The subjects were classified into quartiles of FBDI scores using the semi-quantitative food-frequency questionnaire developed for KoGES. The prevalence rate of diabetes under FBDI scores was assessed by Cox proportional risk models and the severity of the diabetes was analyzed by multiple regression analysis. Results: There were 775 incident cases of diabetes after a mean follow-up of 3.97 years. There was no statistically significant association between FBDI scores and incidence of diabetes. Among diabetes patients at baseline, FBDI scores were related to the risk of progression of diabetes which was represented by greater than 9% HbA1c (Q1 vs. Q4; odds ratio, 1.562 [95% confidence intervals, 1.13-2.15]; p for trend = 0.007). The stratified analysis showed a stronger association in females, irregular exercise group, and higher body mass index group. Conclusion: These results suggest that a pro-inflammatory diet is not associated with the incidence of diabetes but is related to the HbA1c level of diabetes patients. Thus, further longitudinal studies with longer periods are required to determine a relationship between dietary inflammatory index and diabetes in Korea.