• Food Science and Biotechnology
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• 제14권6호
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• pp.854-859
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• 2005

Although action modes of equol and genistein have been extensively studied, their precise roles in tumor cells remain elusive. To address possible effects of these compounds on protein expression in mammary tumor cells, proteins modulated in MCF-7 mammary tumor cells when incubated in absence and presence of 10 uM equol or genistein were identified through 2-dimensional gel electrophoresis, MALDI-TOF MS/MS, and NCBInr database search using Mascot software. Most proteins differentially expressed in MCF-7 cells after treatment with 10 uM genistein or equol were identified as being the same. Exposure to both compounds caused decreased cellular expression of RNA-binding protein regulatory subunit and oncogene DJ1 tubulin beta-1 chain, and increased expression of heterogeneous ribonucleoproteins F and L, KH-type splicing regulatory protein, and translation elongation factor EF-Tu precursor. Genistein and equol at dose used in this study showed common action mechanism.

• Nuclear Engineering and Technology
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• 제47권3호
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• pp.362-379
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• 2015

In this study, Nuclear Power Plant (NPP) construction schedule delay risk assessment methodology is developed and the construction delay risk is assessed for turnkey international NPP projects. Three levels of delay factors were selected through literature review and discussions with nuclear industry experts. A questionnaire survey was conducted on the basis of an analytic hierarchy process (AHP) and Relative Importance Index (RII) methods and the schedule delay risk is assessed qualitatively and quantitatively by severity and frequency of occurrence of delay factors. This study assigns four main delay factors to the first level: main contractor, utility, regulatory authority, and financial and country factor. The second and the third levels are designed with 12 sub-factors and 32 sub-sub-factors, respectively. This study finds the top five most important sub-sub-factors, which are as follows: policy changes, political instability and public intervention; uncompromising regulatory criteria and licensing documents conflicting with existing regulations; robust design document review procedures; redesign due to errors in design and design changes; and worldwide shortage of qualified and experienced nuclear specific equipment manufacturers. The proposed combined AHP-RII methodology is capable of assessing delay risk effectively and efficiently. Decision makers can apply risk informed decision making to avoid unexpected construction delays of NPPs.

• Bulletin of the Korean Chemical Society
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• 제31권11호
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• pp.3241-3246
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• 2010

NHERF ($Na^+/H^+$ exchanger regulatory factor) and E3KARP (NHE3 kinase A regulatory protein) play important roles in membrane targeting, trafficking and sorting of ion channels, transmembrane receptors and signaling proteins in many tissues. Each of these proteins contains two PDZ (PSD-95/Dlg-1/ZO-1) domains, which mediate the assembly of transmembrane and cytosolic proteins into functional signal transduction complexes. The interaction between NHERF and E3KARP was investigated by surface plasmon resonance spectroscopy (BIAcore), fluorescence measurement, His-tagged pull-down experiment, and size-exclusion column (SEC) chromatography. BIAcore experiments revealed that NHERF bound to E3KARP with an apparent $K_D$ of 7 nM. Fluorescence emission spectra of the NHERF-E3KARP complex suggested that the tight interaction between these proteins was accompanied by significant conformational changes in one or both. The CD spectra of NHERF and E3KARP show that the conformational changes of these proteins were dependent on pH and temperature. These results implicate that the NHERF-E3KARP complex allows intracellular signaling complexes to form through PDZ-PDZ interactions.

• International Journal of Oral Biology
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• 제43권1호
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• pp.29-35
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• 2018

It is noted that chalcone derivatives have characteristic diverse pharmacological properties, and that precise evidence has been growing that they could regulate a tumor necrosis $factor-{\alpha}$ ($TNF-{\alpha}$) induced insulin resistance. The purpose of the present investigation is to elucidate the effects of the identified chalcone derivatives on adipogenesis, and to find the underlying mechanism of action in that case. Consequently, we first investigated whether the chalcone derivatives could affect the identified $PPAR{\gamma}$-induced transcriptional activity on the proliferator-activated receptor response elements (PPRE) at target promoters, and find that trans-chalcone most significantly increased the $PPAR{\gamma}$-induced transcriptional activity. Additionally, we confirmed that there were up-regulatory effects of trans-chalcone during the adipogenesis and lipid accumulation, and on the mRNA of adipogenic factors in 3T3-L1 cells. Next, we examined the effect of trans-chalcone on the inhibition induced by $TNF-{\alpha}$ on adipogenesis. To that end, we noted that the treatment with trans-chalcone attenuated the effect of $TNF-{\alpha}$ mediated secretion of various adipokines that are involved in insulin sensitivity. For this reason, we noted that this study clearly demonstrates that trans-chalcone enhanced adipogenesis, in part, by its potent effect on $PPAR{\gamma}$ activation and by its reverse effect on $TNF-{\alpha}$.

• 한국발생생물학회지:발생과생식
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• 제22권4호
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• pp.351-360
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• 2018

The adipogenesis is a maturation process of pre-adipocyte cell into mature lipid-filled adipocyte cell. The adipogenesis begins at the late prenatal stage and continues until the early postnatal age. Because the adipogenesis and formation of adipose tissue persist during postnatal period and are precisely regulated by the action of numerous gene products, the present research was attempted to determine the expressional patterns of adipose tissue-associated genes in the rat epididymal fat pad at different postnatal ages, from 7 days to 2 years of ages, using a quantitative real-time PCR analysis. The basal expression levels of CCAAT/enhancer binding protein gamma, sterol regulatory element binding transcription factor 1, fatty acid binding protein 4, adiponectin, leptin, and resistin at the early postnatal ages were significantly lower than those at the elderly ages, even though a fluctuation of expressional levels was observed at some ages. The lowest expressional level of delta like non-canonical Notch ligand 1 was detected at 44 days and 5 months of ages. The expression of peroxisome proliferator-activated receptor gamma ($PPAR{\gamma}$) was the highest at 44 days of age, followed by a diminished expression of $PPAR{\gamma}$ at the elderly ages. These results indicate the existence of a complex regulatory mechanism(s) for expression of adipose tissueassociated genes in the rat epididymal fat during postnatal period.

• Molecules and Cells
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• 제44권5호
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• pp.318-327
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• 2021

CD4+ T helper (Th) cells play a crucial role in the modulation of innate and adaptive immune responses through the differentiation of Th precursor cells into several subsets, including Th1, Th2, Th17, and regulatory T (Treg) cells. Effector Th and Treg cells are distinguished by the production of signature cytokines and are important for eliminating intracellular and extracellular pathogens and maintaining immune homeostasis. Stimulation of naive Th cells by T cell receptor and specific cytokines activates master transcription factors and induces lineage specification during the differentiation of Th cells. The master transcription factors directly activate the transcription of signature cytokine genes and also undergo post-translational modifications to fine-tune cytokine production and maintain immune balance through cross-regulation with each other. This review highlights the post-translational modifications of master transcription factors that control the differentiation of effector Th and Treg cells and provides additional insights on the immune regulation mediated by protein argininemodifying enzymes in effector Th cells.

• Genomics & Informatics
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• 제17권1호
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• pp.9.1-9.5
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• 2019

In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters.

• Molecules and Cells
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• 제45권4호
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• pp.243-256
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• 2022

Transcriptional regulation, a core component of gene regulatory networks, plays a key role in controlling individual organism's growth and development. To understand how plants modulate cellular processes for growth and development, the identification and characterization of gene regulatory networks are of importance. The SHORT-ROOT (SHR) transcription factor is known for its role in cell divisions in Arabidopsis (Arabidopsis thaliana). However, whether SHR is involved in hypocotyl cell elongation remains unknown. Here, we reveal that SHR controls hypocotyl cell elongation via the transcriptional regulation of XTH18, XTH22, and XTH24, which encode cell wall remodeling enzymes called xyloglucan endotransglucosylase/hydrolases (XTHs). Interestingly, SHR activates transcription of the XTH genes, independently of its partner SCARECROW (SCR), which is different from the known mode of action. In addition, overexpression of the XTH genes can promote cell elongation in the etiolated hypocotyl. Moreover, confinement of SHR protein in the stele still induces cell elongation, despite the aberrant organization in the hypocotyl ground tissue. Therefore, it is likely that SHR-mediated growth is uncoupled from SHR-mediated radial patterning in the etiolated hypocotyl. Our findings also suggest that intertissue communication between stele and endodermis plays a role in coordinating hypocotyl cell elongation of the Arabidopsis seedling. Taken together, our study identifies SHR as a new crucial regulator that is necessary for cell elongation in the etiolated hypocotyl.

• Molecules and Cells
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• 제45권5호
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• pp.343-352
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• 2022

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

• Genomics & Informatics
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• 제19권2호
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• pp.16.1-16.14
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• 2021

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.