• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.52-61
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• 2005

Transcript profiling is a particularly valuable tool in the field of steroid receptor biology, as these receptors are ligand-activated transcription factors and therefore exert their initial effects through altering gene expression in responsive cells. Also, an awareness of endocrine disrupting chemicals (EDCs) and their potential screening methods to identify endocrine activity have been increased. Here we developed an in-house cDNA microarray, named KISTCHIP-400 ver. 1.0, with 416 clones, based on public database and research papers. These clones contained estrogen, androgen, thyroid hormone & receptors, sex hormone signal transduction & regulation, c-fos, c-myc, ps2 gene, metabolism related genes etc. Also, to validate the KISTCHIP-400 ver. 1.0, we investigated gene expression profiles with reference hormones, $10^{8}\;M\;17{\beta}-estradiol,\;10^{-7}\;M\;testosterone\;and\;10^{-7}\;M$ progesterone in MCF-7 cell line. As the results, gene expression profiles of three reference hormones were distinguished from each other with significant and identified 33 $17{\beta}-estradiol$ responsive genes. This study is in first step of validation for KISTCHIP-400 ver. 1.0, as following step transcriptional profile analysis on not only low concentrations of EDCs but suspected EDCs using KISTCHIP-400 ver. 1.0 is processing. Our results indicate that the developed microarray may be a useful laboratory tool for screening EDCs and elucidating endocrine disrupting mechanism.

• The Plant Pathology Journal
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• 제40권1호
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• pp.83-97
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• 2024

Fusarium graminearum, the causal agent of Fusarium head blight (FHB) in cereal crops, employs the production of sexual fruiting bodies (perithecia) on plant debris as a strategy for overwintering and dissemination. In an artificial condition (e.g., carrot agar medium), the F. graminearum Z3643 strain was capable of producing perithecia predominantly in the central region of the fungal culture where aerial hyphae naturally collapsed. To unravel the intricate relationship between natural aerial hyphae collapse and sexual development in this fungus, we focused on 699 genes differentially expressed during aerial hyphae collapse, with 26 selected for further analysis. Targeted gene deletion and quantitative real-time PCR analyses elucidated the functions of specific genes during natural aerial hyphae collapse and perithecium formation. Furthermore, comparative gene expression analyses between natural collapse and artificial removal conditions reveal distinct temporal profiles, with the latter inducing a more rapid and pronounced response, particularly in MAT gene expression. Notably, FGSG_09210 and FGSG_09896 play crucial roles in sexual development and aerial hyphae growth, respectively. Taken together, it is plausible that if aerial hyphae collapse occurs on plant debris, it may serve as a physical cue for inducing perithecium formation in crop fields, representing a survival strategy for F. graminearum during winter. Insights into the molecular mechanisms underlying aerial hyphae collapse provides offer potential strategies for disease control against FHB caused by F. graminearum.

• Nutrition Research and Practice
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• 제10권1호
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• pp.67-73
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• 2016

BACKGROUND/OBJECTIVES: This study was aimed at examining the association between dietary flavanones intake and lipid profiles according to the presence of metabolic syndrome (MetS) in Korean women with type 2 diabetes mellitus (T2DM). SUBJECTS/METHODS: A cross-sectional analysis was performed among 502 female T2DM patients (non-MetS group; n = 129, MetS group; n = 373) who were recruited from the Huh's Diabetes Clinic in Seoul, Korea between 2005 and 2011. The dietary intake was assessed by a validated semi-quantitative food frequency questionnaire (FFQ) and the data was analyzed using the Computer Aided Nutritional Analysis program (CAN-Pro) version 4.0 software. The intake of flavanones was estimated on the basis of the flavonoid database. RESULTS: In the multiple linear regression analysis after adjustment for confounding factors, daily flavanones intake was negatively associated with CVD risk factors such as total cholesterol, LDL-cholesterol, and apoB and apoB/apoA1 ratio only in the MetS group but not in the non-MetS group. Multiple logistic regression analysis revealed that the odds ratio for a higher apoB/apoA1 ratio above the median (${\geq}0.74$) was significantly low in the $4^{th}$ quartile compared to that in the $1^{st}$ quartile of dietary flavanones intake [OR: 0.477, 95% CI: 0.255-0.894, P for trend = 0.0377] in the MetS group. CONCLUSIONS: Dietary flavanones intake was inversely associated with the apoB/apoA1 ratio, suggesting a potential protective effect of flavanones against CVD in T2DM women with MetS.

• Genomics & Informatics
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• 제17권1호
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• International Journal of Naval Architecture and Ocean Engineering
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• 제4권3호
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• pp.281-290
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• 2012

Hydrodynamic analysis of a surface-piercing body with an open chamber was performed with incident regular waves and forced-heaving body motions. The floating body was simulated in the time domain using a 2D fully nonlinear numerical wave tank (NWT) technique based on potential theory. This paper focuses on the hydrodynamic behavior of the free surfaces inside the chamber for various input conditions, including a two-input system: both incident wave profiles and forced body velocities were implemented in order to calculate the maximum surface elevations for the respective inputs and evaluate their interactions. An appropriate equivalent linear or quadratic viscous damping coefficient, which was selected from experimental data, was employed on the free surface boundary inside the chamber to account for the viscous energy loss on the system. Then a comprehensive parametric study was performed to investigate the nonlinear behavior of the wave-body interaction.

• Structural Engineering and Mechanics
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• 제31권3호
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• pp.277-296
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• 2009

The paper investigates the dynamic behaviour of stiffened panels. The coupled differential equations for eccentric stiffening configuration are first derived. Then a semi-analytical procedure for dynamic analysis of stiffened panels is presented. Unlike finite element or finite strip methods, where the plate is discretized into a set of elements or strips, the plate in this procedure is treated as a single element. The potential energy of the structure is first expressed in terms generalized functions that describe the longitudinal and transverse displacement profiles. The resulting non-linear strain energy functions are then transformed into unconstrained optimization problem in which mathematical programming techniques are employed to determine the magnitude of the lowest natural frequency and the associated mode shape for pre-selected plate/stiffener geometric parameters. The described procedure is verified with other numerical methods for several stiffened panels. Results are then presented showing the variation of the natural frequency with plate/stiffener geometric parameters for various stiffening configurations.

• Journal of Microbiology and Biotechnology
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• 제30권2호
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• pp.248-258
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• 2020

The vaginal microbiota may be important for pregnancy prognosis because vaginal dysbiosis during pregnancy appears to be related to preterm birth (PTB) or pregnancy loss. Previous reports have indicated that a Lactobacillus-poor microbial flora in the vagina and intrauterine infection by diverse anaerobes ascending from the vagina are associated with undesirable delivery outcomes. However, no research has involved the use of pyrosequencing analysis to examine vaginal microbiota profiles or their potential associations with high-risk pregnancy in Korean women. Vaginal swabs were collected from 500 Korean women for the identification of community state types (CSTs). Of these, 137 samples were further analyzed using a Roche/454 GS Junior pyrosequencer. Three distinct CSTs were identified based on the dominant vaginal microbes: CST I (Lactobacillus crispatus dominated), CST III (Lactobacillus iners dominated), and CST IV (with diverse species of anaerobes). Twelve of the 67 pregnant women had undesirable pregnancy outcomes (four miscarriages and eight PTBs). The dominant microbe in the vaginal microbiota of women who gave birth at full-term was L. crispatus. In contrast, L. iners was the dominant vaginal microbe in women who miscarried. Most (n = 6/8) vaginal microbiota profiles of women who experienced PTB could be classified as CST IV, with diverse bacteria, including anaerobic vaginal species. The present study provides valuable information regarding the characteristics of the vaginal microbiota of Korean women related to high-risk pregnancy. Investigation of the vaginal microbiotic structure in pregnant Korean women is necessary to enable better prediction of adverse pregnancy outcomes.

• 농업과학연구
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• 제45권3호
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• pp.447-454
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• 2018

Zearalenone (ZEN), a mycotoxin produced by Fusarium in food and feed, causes serious damage to the health of humans and livestock. Therefore, we compared the metabolomic profiles in the liver, serum, and urine of piglets fed a ZEN-contaminated diet using proton nuclear magnetic resonance ($^1H-NMR$) spectroscopy. The spectra from the three different samples, treated with ZEN concentrations of 0.8 mg/kg for 4 weeks, were aligned and identified using MATLAB. The aligned data were subjected to discriminating analysis using multivariate statistical analysis and a web server for metabolite set enrichment analysis. The ZEN-exposed groups were almost separated in the three different samples. Metabolic analysis showed that 28, 29, and 20 metabolites were profiled in the liver, serum, and urine, respectively. The discriminating analysis showed that the alanine, arginine, choline, and glucose concentrations were increased in the liver. Phenylalanine and tyrosine metabolites showed high concentrations in serum, whereas valine showed a low concentration. In addition, the formate levels were increased in the ZEN-treated urine. For the integrated analysis, glucose, lactate, taurine, glycine, alanine, glutamate, glutamine, and creatine from orthogonal partial least squares discriminant analysis (OPLS-DA) were potential compounds for the discriminating analysis. In conclusion, our findings suggest that potential biomarker compounds can provide a better understanding on how ZEN contaminated feed in swine affects the liver, serum, and urine.

• Nutrition Research and Practice
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• 제14권1호
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• pp.32-44
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• 2020

BACKGROUND/OBJECTIVE: We have previously designed the anti-cancer food scoring model (ACFS) 1.0, an evidence-based quantitative tool analyzing the anti-cancer or carcinogenic potential of diets. Analysis was performed using simple quantitative indexes divided into 6 categories (S, A, B, C, D, and E). In this study, we applied this scoring model to wider recipes and evaluated its nutritional relevance. MATERIALS/METHODS: National or known regional databases were searched for recipes from 6 categories: Korean out-dining, Korean home-dining, Western, Chinese, Mediterranean, and vegetarian. These recipes were scored using the ACFS formula and the nutrition profiles were analyzed. RESULTS: Eighty-eight international recipes were analyzed. All S-graded recipes were from vegetarian or Mediterranean categories. The median code values of each category were B (Korean home-dining), C (Korean out-dining), B (Chinese), A (Mediterranean), S (vegetarian), and D (Western). The following profiles were correlated (P < 0.05) with ACFS grades in the univariate trend analysis: total calories, total fat, animal fat, animal protein, total protein, vitamin D, riboflavin, niacin, vitamin B₁₂, pantothenic acid, sodium, animal iron, zinc, selenium, and cholesterol (negative trends), and carbohydrate rate, fiber, water-soluble fiber, vitamin K, vitamin C, and plant calcium (positive trends). Multivariate analysis revealed that animal fat, animal iron, and niacin (negative trends) and animal protein, fiber, and vitamin C (positive trends) were statistically significant. Pantothenic acid and sodium showed non-significant negative trends (P < 0.1), and vitamin B₁₂ showed a non-significant positive trend. CONCLUSION: This study provided a nutritional basis and extended the utility of ACFS, which is a bridgehead for future cancer-preventive clinical trials using ACFS.

• Toxicological Research
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• 제23권1호
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• pp.55-63
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• 2007

Diethylnitrosamine (DEN) is a nitrosamine compound that can induce a variety of liver lesions including hepatic carcinoma, forming DNA-carcinogen adducts. In the present study, microarray analyses were performed with Affymetrix Murine Genome 430A Array in order to identify the gene-expression profiles for DEN and to provide valuable information for the evaluation of potential hepatotoxicity. C57BL/6NCrj mice were orally administered once with DEN at doses of 0, 3, 7 and 20 mg/kg. Liver from each animal was removed 2, 4, 8 and 24 hrs after the administration. The histopathological analysis and serum biochemical analysis showed no significant difference in DEN-treated groups compared to control group. Conversely, the principal component analysis (PCA) profiles demonstrated that a specific normal gene expression profile in control groups differed clearly from the expression profiles of DEN-treated groups. Within groups, a little variance was found between individuals. Student's t-test on the results obtained from triplicate hybridizations was performed to identify those genes with statistically significant changes in the expression. Statistical analysis revealed that 11 genes were significantly downregulated and 28 genes were upregulated in all three animals after 2 h treatment at 20 mg/kg. The upregulated group included genes encoding Gdf15, JunD1, and Mdm2, while the genes including Sox6, Shmt2, and SIc6a6 were largely down regulated. Hierarchical clustering of gene expression also allowed the identification of functionally related clusters that encode proteins related to metabolism, and MAPK signaling pathway. Taken together, this study suggests that match with a toxicant signature can assign a putative mechanism of action to the test compound if is established a database containing response patterns to various toxic compounds.