• Molecules and Cells
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• v.44 no.8
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• pp.602-612
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• 2021

DNA methylation is an important epigenetic mechanism affecting genome structure, gene regulation, and the silencing of transposable elements. Cell- and tissue-specific methylation patterns are critical for differentiation and development in eukaryotes. Dynamic spatiotemporal methylation data in these cells or tissues is, therefore, of great interest. However, the construction of bisulfite sequencing libraries can be challenging if the starting material is limited or the genome size is small, such as in Arabidopsis. Here, we describe detailed methods for the purification of Arabidopsis embryos at all stages, and the construction of comprehensive bisulfite libraries from small quantities of input. We constructed bisulfite libraries by releasing embryos from intact seeds, using a different approach for each developmental stage, and manually picking single-embryo with microcapillaries. From these libraries, reliable Arabidopsis methylome data were collected allowing, on average, 11-fold coverage of the genome using as few as five globular, heart, and torpedo embryos as raw input material without the need for DNA purification step. On the other hand, purified DNA from as few as eight bending torpedo embryos or a single mature embryo is sufficient for library construction when RNase A is treated before DNA extraction. This method can be broadly applied to cells from different tissues or cells from other model organisms. Methylome construction can be achieved using a minimal amount of input material using our method; thereby, it has the potential to increase our understanding of dynamic spatiotemporal methylation patterns in model organisms.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.24 no.2
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• pp.268-275
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• 2020

A lightweight hardware design of self-timed ring based true random number generator (TRNG) suitable for information security applications is described. To reduce hardware complexity of TRNG, an entropy extractor with feedback structure was proposed, which minimizes the number of ring stages. The number of ring stages of the FSTR-TRNG was determined to be a multiple of eleven, taking into account operating clock frequency and entropy extraction circuit, and the ratio of tokens to bubbles was determined to operate in evenly-spaced mode. The hardware operation of FSTR-TRNG was verified by FPGA implementation. A set of statistical randomness tests defined by NIST 800-22 were performed by extracting 20 million bits of binary sequences generated by FSTR-TRNG, and all of the fifteen test items were found to meet the criteria. The FSTR-TRNG occupied 46 slices of Spartan-6 FPGA device, and it was implemented with about 2,500 gate equivalents (GEs) when synthesized in 180 nm CMOS standard cell library.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.2
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• pp.162-169
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• 2021

Global warming has affected the distribution of organisms for decades and has displayed rapid ascent recently. Research into the effects on tropical organisms are vital. Padina boryana is a resourceful marine microalgae in the Maldives Sea in the Laccadive region. A 70% ethanol extraction (PBE) of this seaweed was used to investigate its antioxidant potential. Both in vitro and in vivo models were implemented. PBE exhibited protective potential against H₂O₂ induced apoptosis. ROS levels were suppressed due to PBE. PBE expressed a cytoprotective nature. In vivo experiments involving the zebra fish model conformed its validity. The antioxidant efficacy of PBE was dose dependent. Study outcomes suggest PBE has potential as a novel and valuable marine resource to aid the functional food and cosmeceutical industries.

• Journal of Microbiology and Biotechnology
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• v.32 no.3
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• pp.365-377
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• 2022

Mammalian target of rapamycin (mTOR) is a serine-threonine kinase member of the cellular phosphatidylinositol 3-kinase (PI3K) pathway, which is involved in multiple biological functions by transcriptional and translational control. mTOR is a downstream mediator in the PI3K/Akt signaling pathway and plays a critical role in cell survival. In cancer, this pathway can be activated by membrane receptors, including the HER (or ErbB) family of growth factor receptors, the insulin-like growth factor receptor, and the estrogen receptor. In the present work, we congregated an electronic network of mTORC1 built on an assembly of data using natural language processing, consisting of 470 edges (activations/interactions and/or inhibitions) and 206 nodes representing genes/proteins, using the Cytoscape 3.6.0 editor and its plugins for analysis. The experimental design included the extraction of gene expression data related to five distinct types of cancers, namely, pancreatic ductal adenocarcinoma, hepatic cirrhosis, cervical cancer, glioblastoma, and anaplastic thyroid cancer from Gene Expression Omnibus (NCBI GEO) followed by pre-processing and normalization of the data using R & Bioconductor. ExprEssence plugin was used for network condensation to identify differentially expressed genes across the gene expression samples. Gene Ontology (GO) analysis was performed to find out the over-represented GO terms in the network. In addition, pathway enrichment and functional module analysis of the protein-protein interaction (PPI) network were also conducted. Our results indicated NOTCH1, NOTCH3, FLCN, SOD1, SOD2, NF1, and TLR4 as upregulated proteins in different cancer types highlighting their role in cancer progression. The MCODE analysis identified gene clusters for each cancer type with MYC, PCNA, PARP1, IDH1, FGF10, PTEN, and CCND1 as hub genes with high connectivity. MYC for cervical cancer, IDH1 for hepatic cirrhosis, MGMT for glioblastoma and CCND1 for anaplastic thyroid cancer were identified as genes with prognostic importance using survival analysis.

• Clinical and Experimental Reproductive Medicine
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• v.49 no.1
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• pp.62-69
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• 2022

Objective: This study aimed to describe a distinct subpopulation of azoospermic patients with isolated elevation of follicle-stimulating hormone (iFSH) and poor outcomes of microdissection testicular sperm extraction (microTESE). Methods: A retrospective analysis of microTESE outcomes was conducted among 565 patients with non-obstructive azoospermia (NOA). Testicular pathology was assessed by the dominant histological pattern and Bergmann-Kliesch score (BKS). Descriptive statistics were presented for the iFSH subgroup. Inhibin B levels, the sperm retrieval rate (SRR), and BKS were compared in iFSH patients and other NOA patients. Results: The overall SRR was 33.3% per microTESE attempt. The median BKS was 0.6 (interquartile range, 0-2). Of all NOA patients, 132 had iFSH, and microTESE was successful only in 11 of those cases, with an SRR of 8.3%, while the total SRR in other NOA patients was 38.1% (p<0.001). iFSH had a sensitivity of 32.1% (95% confidence interval [CI], 27.4%-36.8%) and specificity of 94.1% (95% CI, 90.8-97.5%) as a predictor of negative microTESE outcomes. Conclusion: Patients with iFSH may harbor a distinct testicular phenotype with total loss of the germ cell population and poor outcomes of surgical sperm retrieval.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.6
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• pp.927-937
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• 2021

This study was performed to screen the antimicrobial activities of the extract from the Pacific oyster Crassostrea gigas against skin pathogens and to purify the relevant antibacterial peptide. The acidified extract showed potent antibacterial activities against gram-positive and gram-negative bacteria but showed no activity against Candida albicans and no significant cell toxicity. Among acne-causing pathogens, the acidified extract showed potent antibacterial activity only against Staphylococcus aureus, and its antibacterial activity was completely abolished by treatment with trypsin or chymotrypsin, and was inhibited by salt treatment. The acidified extract showed strong DNA-binding ability but did not show bacterial membrane permeabilizing ability. Based on antimicrobial activity screening and cytotoxic effects, a novel antibacterial peptide was purified from the acidified gill extract using solid-phase extraction, cation-exchange, and reversed-phase HPLC. The resulting peptide had a molecular weight of 4800.8 Da and showed partial sequence homology with the carbonic anhydrase 4 (CA4) protein in the hard-shelled mussel. Overall, we purified a novel antibacterial peptide, named cgCAFLP, which is related to carbonic anhydrase 4 (CA4) protein, against skin pathogens. Our results suggest that the Pacific oyster extract could be used as an additive to control some acne-related skin pathogens (S. aureus).

• The Korea Journal of Herbology
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• v.32 no.6
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• pp.55-62
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• 2017

Objectives : This study aims to evaluate the effects of natural herb mixutre (NHM) on atopic dermatitis and skin regeneration using in vivo test. Methods : NHM was prepared with DW. 25% of NHM was applied to skin lesion, where atopic dermatitis was induced by DNCB in NC/Nga mice. The levels of cytokines (IL-4, IL-5, IL-6, IL-13, TNF-a, and $IFN-{\gamma}$), and IgE in serum were measured by Luminex. Immune cells (WBC, eosinophil, lymphocyte, and monocyte) in blood were counted by coulter counter. The gross investigation of atopic dermatitis index score test were performed during the NHM treatment period. Also, the histopathological change of dorsal skin was observed by H&E and M&T staining. Results : NHM showed the levels of IL-4, IL-5, IL-6, IL-13, IgE, WBC, eosinophil, lymphocyte, and monocyte in serum or blood were significantly decreased. On the contrary, the productions of FGF, and VEGF were increased in the serum. Also, atopic dermatitis index score in NHM-treated mice were observed in the similar levels to those of normal group. Histological examination demonstrated that NHM suppressed immune cell infiltration and thickening of epidermis, meanwhile the extraction induced collagen production in the dorsal skin. Conclusion : This study demonstrated that NHM is appeared to be effective on atopic dermatitis and skin regeneration efficacy based on the observations with hematologic, gross, and histologic examinations. Therefore, we suggest that NHM could be effectively used as an external therapeutics against atopic dermatitis and a consequence skin damage.

• The Korea Journal of Herbology
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• v.33 no.1
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• pp.1-7
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• 2018

Objectives : Puerariae Radix extracts are a rich source of isoflavones that affect the activity of hepatic antioxidant enzymes. However, the effect of these extracts on hair growth in human dermal papilla (DP) cells is unknown. The purpose of this study is to compare the effects between juice and water extracts of Puerariae Radix on the mRNA expression levels of hair growth-related genes in dermal papilla (DP) cells. Methods : The antioxidant activity of juice and water extracts of Puerariae Radix was analyzed using an ABTS assay. The cytotoxicity was analyzed using the MTS assay in DP cells. mRNA expression levels of hair growth-related genes in dermal papilla (DP) cells were analyzed using quantitative RT-PCR analysis. Results : Juice and water extracts of Puerariae Radix showed strong antioxidant activity. The cytotoxicity was confirmed to be higher in the juice extract than the water extract, using the MTS assay on DP cells. The mRNA expression levels of CTNNB1, FGF7, and BMP6 were significantly increased after treatment with water extract, whereas the juice extract did not affect the expression of hair growth-related genes. Conclusions : Our study provides evidence that water extract of Puerariae Radix is effective at inducing hair growth, by promoting the mRNA expression levels of hair growth-related genes. Also in the future, studies should be conducted to investigate the effects of Puerariae radix extracts on the various hair growth mechanisms of dermal papilla cells.

• Journal of Veterinary Clinics
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• v.40 no.1
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• pp.1-7
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• 2023

The growing market for companion animals, combined with their increasing lifespan, has generated an increased interest in companion animal immunity enhancers. Ginsenoside, a saponin component of ginseng and an essential ingredient of red ginseng marc (produced during red ginseng production), is effective in improving immunity. In this experiment, a powder mixture of red ginseng marc and steamed red ginseng extract powder (RGME) was orally administered to dogs for eight weeks. Subsequently, blood samples were collected and tested every four weeks. In addition, canine peripheral blood mononuclear cells (cPBMCs) were stimulated with or without interleukin-2 (IL-2) to evaluate their proliferation and cytokine secretion abilities. Proliferation assay suggests that the administration of RGME effectively enhanced numbers of cPBMCs under IL-2 stimulation. Furthermore, in the RGME group, a significant increase in the concentration of interferon gamma released from cPBMCs under IL-2 stimulation was observed. In conclusion, RGME might be an effective health supplement for improving immunity in dogs.

• ALGAE
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• v.38 no.1
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• pp.81-92
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• 2023

Obesity-induced inflammation is crucial in the pathogenesis of insulin resistance and type 2 diabetes. In this study, we investigated the effects of the Gracilaria chorda (GC) on lipid accumulation and obesity-induced inflammatory changes or glucose homeostasis in cell models (3T3-L1 adipocytes and RAW 264.7 macrophages). Samples of GC were extracted using solvents (water, methanol, and ethanol) and subcritical water (SW) at different temperatures (90, 150, and 210℃). The total phenolic content of GCSW extract at 210℃ (GCSW210) showed the highest content compared to others, and GCSW210 highly inhibited lipid accumulation and significantly reduced gene expressions of peroxisome proliferator-activated receptor-γ, CCAAT/enhancer-binding protein-α, sterol regulatory element-binding protein-1c, and fatty acid synthase in 3T3-L1 adipocytes. In addition, GCSW210 effectively downregulated the pro-inflammatory cytokine regulator pathways in RAW 264.7 macrophages, including mitogen-activated protein kinase, signal transducers and activators of transcription and nuclear factor-κB. In co-culture of 3T3-L1 adipocytes and RAW 264.7 macrophages, GCSW210 significantly reduced nitric oxide production and interleukin-6 levels, and improved glucose uptake with dose-dependent manner. These findings suggest that GCSW210 improves glucose metabolism by attenuating obesity-induced inflammation in adipocytes, which may be used as a possible treatment option for managing obesity and associated metabolic disorders.