• Journal of Life Science
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• v.33 no.1
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• pp.34-42
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• 2023

In a signal transduction network, from the perception of stress signals to stress-responsive gene ex- pression, binding of various transcription factors to cis-acting elements in stress-responsive promoters coordinate the adaptation of plants to abiotic stresses. Among the AP2/ERF transcription factor family genes, group VII ERF genes, such as RAP2.12, RAP2.2, RAP2.3, AtERF73/HRE1, and AtERF71/ HRE2, are known to be involved in the response to hypoxia stress in Arabidopsis. In this study, we dissected the HRE1 promoter to identify hypoxia-responsive region(s). The 1,000 bp upstream promoter region of HRE1 showed increased promoter activity in Arabidopsis protoplasts and transgenic plants under hypoxia conditions. Analysis of the promoter deletion series of HRE1, including 1,000 bp, 800 bp, 600 bp, 400 bp, 200 bp, 100 bp, and 50 bp upstream promoter regions, using firefly luciferase and GUS as reporter genes indicated that the -200 to -100 region of the HRE1 promoter is responsible for the transcriptional activation of HRE1 in response to hypoxia. In addition, we identified two putative hypoxia-responsive cis-acting elements, the ERF-binding site and DOF-binding site, in the -200 to -100 region of the HRE1 promoter, suggesting that the expression of HRE1 might be regulated via the ERF transcription factor(s) and/or DOF transcription factor(s). Collectively, our results suggest that HRE1 contains hypoxia-responsive cis-acting elements in the -200 to -100 region of its promoter.

• Genomics & Informatics
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• v.5 no.1
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Journal of Ginseng Research
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• v.39 no.1
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• pp.61-68
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• 2015

Background: Korean Red Ginseng (KRG) is a representative traditional herbal medicine with many different pharmacological properties including anticancer, anti-atherosclerosis, anti-diabetes, and anti-inflammatory activities. Only a few studies have explored the molecular mechanism of KRG-mediated anti-inflammatory activity. Methods: We investigated the anti-inflammatory mechanisms of the protopanaxadiol saponin fraction (PPD-SF) of KRG using in vitro and in vivo inflammatory models. Results: PPD-SF dose-dependently diminished the release of inflammatory mediators [nitric oxide (NO), tumor necrosis factor-${\alpha}$, and prostaglandin $E_2$], and downregulated the mRNA expression of their corresponding genes (inducible NO synthase, tumor necrosis factor-${\alpha}$, and cyclooxygenase-2), without altering cell viability. The PPD-SF-mediated suppression of these events appeared to be regulated by a blockade of p38, c-Jun N-terminal kinase (JNK), and TANK (TRAF family member-associated NF-kappa-B activator)-binding kinase 1 (TBK1), which are linked to the activation of activating transcription factor 2 (ATF2) and interferon regulatory transcription factor 3 (IRF3). Moreover, this fraction also ameliorated HCl/ethanol/-induced gastritis via suppression of phospho-JNK2 levels. Conclusion: These results strongly suggest that the anti-inflammatory action of PPD-SF could be mediated by a reduction in the activation of p38-, JNK2-, and TANK-binding-kinase-1-linked pathways and their corresponding transcription factors (ATF2 and IRF3).

• Journal of Life Science
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• v.29 no.2
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• pp.209-214
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• 2019

Sargassum horneri (Turner) C. Agardh is a marine brown algae widely distributed in the North Pacific Ocean. It is known for its anti-inflammatory and anti-atopic effects. In this study, we determined the effects of ethanol extract of Sargassum horneri (Turner) C. Agardh (EESH) on anti-obesity activities in 3T3-L1 preadipocytes. Our results indicated that treatment with EESH decreased the differentiation of 3T3-L1 preadipocytes in a dose-dependent manner, as confirmed by a decrease in lipid droplet content observed by oil red O staining. The concentrations of cellular triglycerides were also reduced in 3T3-L1 cells after treatment with EESH. Triglyceride content was inhibited by 13%, 16%, and 23% after treatment with 250, 500, and $1,000{\mu}g/ml$ of EESH in 3T3-L1 cells, respectively. Western blotting analysis showed that EESH suppressed adipogenic transcription factor expression in a dose dependent manner. Specifically, it suppressed cytidine-cytidine-adinosine-adenosine-thymidine (CCAAT) /enhancer binding proteins $(C/EBP){\alpha}$, $C/EBP{\beta}$ and peroxisome proliferator-activated receptor $(PPAR){\gamma}$. This indicated that EESH could control the expression of adipogenic transcription factors and inhibit the differentiation of adipocytes. Taken together, these findings demonstrated that EESH showed anti-obesity effects and could have potential uses in the field of nutraceuticals.

• Proceedings of the KSPS conference
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• 2000.07a
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• pp.149-164
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• 2000

It is generally said that falling intonation is used at the end of a declarative sentence. However, this is not the case with all stretches of spontaneous speech which are marked in transcription as sentences. The present paper examines intonation patterns appearing at the end of declarative sentences in oral presentations, and discusses instances where falling intonation does not appear. The texts used for analysis are eight oral presentations collected at international conferences in the field of physics. Quantitative and qualitative analyses are carried out. Three major factors related to discourse structure have been found for nonoccurrence of falling intonation at sentence boundaries.

• MALSORI
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• no.41
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• pp.83-96
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• 2001

It is generally said that falling intonation is used at the end of a declarative sentence. However, this is not the case with all stretches of spontaneous speech which are marked in transcription as sentences. The present paper examines intonation patterns appearing at the end of declarative sentences in oral presentations, and discusses instances where falling intonation does not appear. The texts used for analysis are eight oral presentations collected at international conferences in the field of physics. Quantitative and qualitative analyses are carried out. Three major factors related to discourse structure have been found for non-occurrence of falling intonation at sentence boundaries.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.166.3-167
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• 2003

Helenalin, a cell-permeable pseudoguainolide sesquiterpene lactone, is a potent anti-inflammatory agent that inhibits $NF-{\kappa}B$ DNA binding activity by selectively alkylating the p65 subunit of $NF-{\kappa}B$. Transcription factors such as $NF-{\kappa}B$ provide powerful target of drugs to use in the treatment of cancer. Human promyelocytic leukemia HL-60 cells are differentiated into monocytic or granulocytic lineage when treated with 1,25-dihydroxyvitamin $D_3{\;}[1,25-(OH)_2D_3]$ or all-trans-retinoic acid (ATRA), respectively. (omitted)

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.327.2-327.2
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• 2002

Inflammatory as well as oxidative tissue damage has been associated with pathophysiology of Alzheimer's disease (AD), and nonsteroidal anti-inflammatory drugs have been shown to retard the progress of AD. In this study, we have investigated the molecular mechanisms underlying oxidative and inflammatory cell death induced by beta-amyloid (Abeta), a neurotoxic peptide associated with senile plaques formed in the brains of patients with AD, in cultured PC12 cells. (omitted)

• Clinical and Experimental Pediatrics
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• v.49 no.8
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• pp.833-838
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• 2006

Giant platelet syndrome is a group of unique disorders characterized by the presence of abnormally large platelets, and usually accompanied by thrombocytopenia. Most cases of giant platelets are encountered in idiopathic thrombocytopenic purpura(ITP). In contrast, inherited giant platelet disorders, a group of heterogeneous diseases, are rare. Bernard-Soulier syndrome and its variants, and MYH9 related diseases have been defined at the molecular level. Abnormalities in transcription factors are implicated in a couple of macrothrombocytopenia syndromes. However, the molecular defects are unknown in gray platelet syndrome. It is important to make a proper diagnosis of congenital macrothrombocytopenia to avoid unnecessary medications and potentially dangerous treatment for presumed ITP.

• Proceedings of the PSK Conference
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• 2001.04a
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• pp.162.3-163
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• 2001