• Animal Bioscience
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• v.37 no.6
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• pp.1021-1030
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• 2024

Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. Methods: In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. Results: We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. Conclusion: These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.

• Journal of Ginseng Research
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• v.48 no.4
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• pp.395-404
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• 2024

Background: Ginsenoside Rg₁ (Rg₁) is one of the main active components in Chinese medicines, Panax ginseng and Panax notoginseng. Research has shown that Rg₁ has a protective effect on the cardiovascular system, including anti-myocardial ischemia-reperfusion injury, anti-apoptosis, and promotion of myocardial angiogenesis, suggesting it a potential cardiovascular agent. However, the protective mechanism involved is still not fully understood. Methods: Based on network pharmacology, ligand-based protein docking, proteomics, Western blot, protein recombination and spectroscopic analysis (UV-Vis and fluorescence spectra) techniques, potential targets and pathways for Rg₁ against myocardial ischemia (MI) were screened and explored. Results: An important target set containing 19 proteins was constructed. Two target proteins with more favorable binding activity for Rg₁ against MI were further identified by molecular docking, including mitogen-activated protein kinase 1 (MAPK1) and adenosine kinase (ADK). Meanwhile, Rg₁ intervention on H9c2 cells injured by H₂O₂ showed an inhibitory oxidative phosphorylation (OXPHOS) pathway. The inhibition of Rg₁ on MAPK1 and OXPHOS pathway was confirmed by Western blot assay. By protein recombination and spectroscopic analysis, the binding reaction between ADK and Rg₁ was also evaluated. Conclusion: Rg₁ can effectively alleviate cardiomyocytes oxidative stress injury via targeting MAPK1 and ADK, and inhibiting oxidative phosphorylation (OXPHOS) pathway. The present study provides scientific basis for the clinical application of the natural active ingredient, Rg₁, and also gives rise to a methodological reference to the searching of action targets and pathways of other natural active ingredients.

• Korean Journal of Poultry Science
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• v.37 no.3
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• pp.275-282
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• 2010

Chicken is an important livestock as a valuable biomedical model as well as food for human, and there is a strong rationale for improving our understanding on metabolism and physiology of this organism. The first draft of chicken genome assembly was released in 2004, which enables elaboration on the linkage between genetic and metabolic traits of chicken. The objectives of this study were thus to reconstruct metabolic pathway of the chicken genome and to construct a chicken specific pathway genome database (PGDB). We developed a comprehensive genome database for chicken by integrating all the known annotations for chicken genes and proteins using a pipeline written in Perl. Based on the comprehensive genome annotations, metabolic pathways of the chicken genome were reconstructed using the PathoLogic algorithm in Pathway Tools software. We identified a total of 212 metabolic pathways, 2,709 enzymes, 71 transporters, 1,698 enzymatic reactions, 8 transport reactions, and 1,360 compounds in the current chicken genome build, Gallus_gallus-2.1. Comparative metabolic analysis with the human, mouse and cattle genomes revealed that core metabolic pathways are highly conserved in the chicken genome. It was indicated the quality of assembly and annotations of the chicken genome need to be improved and more researches are required for improving our understanding on function of genes and metabolic pathways of avian species. We conclude that the chicken PGDB is useful for studies on avian and chicken metabolism and provides a platform for comparative genomic and metabolic analysis of animal biology and biomedicine.

• 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.

• Journal of Food Hygiene and Safety
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• v.25 no.3
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• pp.269-277
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• 2010

Selenium is an essential micronutrient for normal body function and functions as an essential constituent of selenoproteins. This study was carried out to investigate effect of selenium on the formation of colonic aberrant crypt foci (ACF) and tumor formation in a mouse model. Five-week old ICR mice were acclimated for one week and fed different selenium diet (0.02, 0.1, and 0.5 ppm) for 12 weeks. Animals received three intraperitoneal injections of azoxymethane (10 mg/kg B.W. in saline for 3 weeks), followed by 2% dextran sodium sulfate in the drinking water for a week. There were four experimental groups, including a normal control group and three different selenium levels groups. After sacrifice, the total numbers of aberrant crypt (AC) and ACF were measured in the colonic mucosa after methylene blue staining. The number of tumors was noted for tumor incidence. Liver selenium concentration was measured using ICP-AES method. Gutathione peroxidase (GPx) activity was determined using a GPx assay kit in the liver and colon. TUNEL assay and proliferating cell nuclear antigen (PCNA) staining were performed to examine the cell apoptosis and cell proliferation, respectively. Immunohistochemistry of $\beta$-catenin was also performed on the mucous membrane tissue of colon. The activity of GPx in the liver and colon was decreased in the selenium-deficient diet group while it was increased in the selenium-overloaded diet group. Apoptotic positive cells were increased in the selenium-overloaded diet group but decreased in the selenium-deficient diet group. PCNA staining area was decreased in the selenium-overloaded diet group. In addition, the $\beta$-catenin protein level in the selenium-deficient diet group was increased but decreased in the selenium-overloaded diet group. These results indicate that dietary selenium might exert a modulating effect on colon cancer by inhibiting the development of ACF and colon tumor formation in this mouse model.

• Journal of Food Hygiene and Safety
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• v.24 no.4
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• pp.391-397
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• 2009

Carnosine is a dipeptide ($\beta$-alanyl-L-histidine) found in mammalian brain, eye, olfactory bulb and skeletal muscle at high concentrations. Its biological functions include antioxidant and anti-glycation activities. The objectives of this study were to investigate anti-diabetic effects of carnosine as determined by blood glucose levels in glucose tolerance test (GTT) and insulin tolerance test (ITT), insulin level and serum biochemical and lipid levels in male C57BL/6J db/db mice. There were five experimental groups including normal (C57BL/6J), control (vehicle), and three groups of carnosine at doses of 6, 30, and 150 mg/kg b.w. Carnosine was orally administered to the diabetic mice everyday for 8 weeks. There was no significant difference in body weight changes in carnosine-treated groups compared to the control. The treatments of carnosine significantly decreased the blood glucose level in the diabetic mice compared with the control (p < 0.05) after 5 weeks. The treatments of carnosine also significantly decreased the blood glucose levels in GTT and ITT and glycosylated hemoglobin (HbA1c), compared with the control (p < 0.05). Carnosine at the dose of 6 mg/kg significantly decreased the serum insulin level compared to the control (p < 0.05). Carnosine significantly increased total proteins but significantly decreased lactate dehydrogenase and blood urea nitrogen compared with the control (p < 0.05). Carnosine also significantly decreased glucose, LDL, and triglyceride in the serum of diabetic mice compared to the control (p < 0.05). These results suggest that carnosine has a hypoglycermic effect resulting from reduction of glucose and lipid levels and that high carnosine-containing diets or drugs may give a benefit for controlling diabetes mellitus in humans.

• Journal of the Korean Magnetics Society
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• v.15 no.2
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• pp.100-105
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• 2005

$Ni_{0.9}Zn_{0.1}Fe_2O_4$ nanoparticles have been prepared by a sol-gel method. The structural and magnetic properties have been investigated by DTA/TGA, XRD, SEM, and $M\ddot{o}ssbauer$ spectroscopy, VSM. $Ni_{0.9}Zn_{0.1}Fe_2O_4$ powder that was annealed at $300^{\circ}C$ has spinel structure and behaved superparamagnetically. The estimated size of superparammagnetic Ni-Zn ferrite nanoparticle is around 10 nm. The hyperfine fields at 13 K for the A and B patterns were found to be 533 and 507 kOe, respectively. The blocking temperature ($T_B$) of superparammagnetic $Ni_{0.9}Zn_{0.1}Fe_2O_4$ nanoparticle is about 250 K. The magnetic anisotropy constant and relaxation time constant of $Ni_{0.9}Zn_{0.1}Fe_2O_4$ nanoparticle were calculated to be $1.6\times10^6\;ergs/cm^3$ and ${\tau}_0=5.0{\times}10^{-13}$ s, respectively. Also, Temperature increased up to $43^{\circ}C$ within 10 minutes under AC magnetic field of 7 MHz. It is considered that $Ni_{0.9}Zn_{0.1}Fe_2O_4$ powder that was annealed at $300^{\circ}C$ is available for biomedicine application such as hyperthermia, drug delivery system and contrast agents in MRI.

• Applied Biological Chemistry
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• v.49 no.3
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• pp.186-191
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• 2006

In the present study, an attempt has been made to produce hybrid yeast strains of different useful and dominant characteristics. The hybrid yeast strains were produced by electrofusion and their genetic analysis were performed by RAPD-PCR (random amplified polymorphic DNA-polymerase chain reaction). The protoplast of Saccharomyces cerevisiae KCTC 7904 and Zygosaccharomyces rouxii KCTC 7966 were obtained above 92% when treated with lyticase at $30^{\circ}C$ for $60{\sim}90$ min after the pretreatment of $1{\sim}2%$ 2-mercaptoethanol at $30^{\circ}C$ for $15{\sim}20$ min. The fusant was produced from paired protoplast stage under the electric pulse at high frequency conditions (1.5 MHz/50 pV, 615 $V/256\;{\mu}sec$) within glass-platinum made electrofusion chamber. Changes in RAPD patterns in mother cells and hybrid cells proved that the fusant contains two types of yeast gene originated from its parent. Furthermore, fermentation characters exhibits by the fusant cell confirmed its genetic changes. These results suggest that genetically stable hybrid yeast strains of economic importance can be produced by electrofusion technique and these electrofused yeast cells have an enormous impact in biotechnology and biomedicine.