• Journal of the Microelectronics and Packaging Society
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• v.18 no.2
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• pp.1-9
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• 2011

Rare metals, called as vitamins of industry, are defined as the elements which are very few in the earth and are difficult to extract from ores. The requirements for total amounts of rare metals have increased as the global economics grows and the function of electronic components varies considerably. The rare metals have been maldistributed to America, CIS(Commonwealth of Independent States), China, Australia, Canada as about 80% of total natural resources, which also lead to unequal materials flow or distribution. Therefore, it was needed to investigate the feature of rare metals in terms of industry as well as technology. We could identify the industrial issues associated with the supply of critical rare elements in electronic components.

• Genomics & Informatics
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• v.19 no.1
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• pp.3.1-3.12
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• 2021

Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer-associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type-specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer-associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.

• Biomedical Science Letters
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• v.29 no.3
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• pp.103-108
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• 2023

Enhancers are cis-elements to regulate transcription of cell/tissue-specific genes in multicellular organisms. These elements locate in upstream or downstream regions of target genes and are found in a long distance up to 100 Kb in some cases. Transcription factors and coactivators bind to enhancers in a chromatin environment. Enhancers appear to facilitate the transcription of target genes by communicating with promoters and activating them. As transcription activation mechanism of enhancers, chromatin looping between enhancers and promoters, tracking of enhancer activity to promoters along the intervening regions, and movement of enhancers and promoters into transcription condensates have been suggested based on various molecular and cellular biology studies. These mechanisms are likely to act together rather than exclusive each other for gene transcription. Understanding of enhancer action mechanism may provide a way to regulate the transcription of cell/tissue-specific genes relating with aging or various diseases.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.359-365
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• 2013

The high mobility group box 1 (HMGB1) protein is a multifunctional cytokine-like molecule that plays an important role in the pathogenesis of tumors. In this study, real-time polymerase chain reactions and Western blot assays indicated that HMGB1 transcriptional activity and protein level are increased in $Tax^+$-T cells (TaxP). To clarify the mechanisms, a series of HMGB1 deletion reporter plasmids (pHLuc1 to pHLuc6) were transfected into $Tax^-$-T cells (TaxN, Jurkat) and $Tax^+$-T cells (TaxP). We found that promoter activity in $Tax^+$-T cells to be higher than that in $Tax^-$-T cells, indicating a significant increase in pHLuc6. Bay11-7082 (NF-${\kappa}B$ inhibitor) treatment did not block the enhancing effect. Chromatin immunoprecipitation assays revealed that Tax was retained on a HMGB1 promoter fragment encompassing -1163 to -975. Bioinformatics analysis showed six characteristic cis-elements for CdxA, AP-1, AML-1a, USF, v-Myb, and C/EBP in the fragment in question. Mutation of cis-elements for C/EBP reduced significant HMGB1 promoter activity induced by Tax. These findings indicate that Tax enhances the expression of HMGB1 gene at the transcriptional level, possibly by interacting with C/EBP.

• Journal of Plant Biotechnology
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• v.46 no.4
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• pp.255-273
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• 2019

Orchids are indispensable to the floriculture industry due to their unique floral organization. The flowers have two outer whorls of tepals including a lip (labellum), and two inner whorls, pollinia and gynostemiun (column). The floral organization and development is controlled at the molecular level, mainly by the MADS-box gene family, comprising homeotic genes divided into type I and type II groups. The type I group has four sub-groups, Mα, Mβ, Mγ, and Mδ, playing roles in seed, embryo, and female reproductive organ development; the type II group genes form classes A, B, C, D, and E, which are a part of the MIKC^C subgroup with specific roles in florigenesis and organization. The coordinated functioning of these classes regulates the development of various floral whorls. The availability of genome and transcriptome sequence data for Phalaenopsis equestris offers an opportunity to validate the ABCDE model of flower development. Hence, this study sought to characterize the MADS-box gene family and elucidate of the ABCDE model. A total of 48 identified MADS-box proteins, including 20 type I [Mα (12), Mγ (8)] and 28 type II [MIKC^C (27), MIKC*(1)] members, were characterized for physico-chemical features and domains and motifs organization. The exon-intron distribution and the upstream cis-regulatory elements in the promoter regions of MADS-box genes were also analysed. The discrete pace of duplication events in type I and type II genes suggested differential evolutionary constraints between groups. The correlation of spatio-temporal expression pattern with the presence of specific cis-regulatory elements and putative protein-protein interaction within the different classes of MADS-box gene family endorse the ABCDE model of floral development.

• BMB Reports
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• v.29 no.5
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• pp.468-473
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• 1996

The P38 promoter of minute virus of mice (MVM) is a very weak promoter which is strongly transactivated by viral nonstructural proteins. To analyze the upstream sequence of the P38 promoter which is responsible for the transactivation by nonstructural proteins in MVM, chloramphenicol acetyltransferase (CAT) reporter plasm ids containing a series of 5' deletion and internal deletion mutants of the P38 promoter were constructed. The wild type and mutant CAT constructs of P38 promoter were cotransfected into murine A92L fibroblast cells with a plasmid expressing viral nonstructural proteins by DEAE-dextran method. Each promoter activity was analyzed by CAT assay. As previously reported (Ahn et al., 1992), the proximal DNA cis-elements required for transactivation of the MVM P38 promoter are GC box and TATA box. However, the analysis of 5' deletion mutants showed that H-l tar like sequence (MVM TAR) which is located between -143 and -122 relative to the transcription initiation site is also required for transactivation of the P38 promoter by nonstructural proteins. Interestingly, even if the MVM TAR was removed by internal deletion, the level of the transactivation is still 70% of wild type level of transactivation. We also found that, in addition to the MVM TAR motif, there are two other motifs which are similar to the MVM TAR sequence. When these TAR like motifs were further deleted, the levels of transactivation were decreased further. Taken together, the MVM TAR sequence and TAR like motifs located upstream of P38 promoter are playing an important role for the transactivation of P38 promoter by nonstructural proteins in minute virus of mice.

• Journal of Music and Human Behavior
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• v.15 no.2
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• pp.69-92
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• 2018

The purpose of this study was to investigate whether a songwriting intervention would improve self-expression of adolescents with cochlear implants (CI). In this study, the songwriting intervention was designed to incorporate previous research findings on music perception of individuals with CIs and to provide musical experiences in which adolescents with CIs could be successful in using music resources for their self-expression. Accordingly, stepwise songwriting procedures were constructed and music technology (i.e., GarageBand as an iPad application) was used. Two adolescents with CIs participated in the intervention once a week for 8 weeks. Changes in level of participation in songwriting tasks, verbal expression, self-reports about the songwriting process were examined. The results demonstrated that the participants showed increased attempts to express themselves via music making. It was also shown that their negative perception of their ability to verbally express themselves decreased. They were observed as becoming more competent in creating music by deciding how various musical elements should be played and making rhythm or melodic patterns by themselves. These results indicate that the songwriting intervention can facilitate self-expression of adolescents with CIs. Further implications in terms of the psychosocial needs of individuals with CIs are presented.

• Development and Reproduction
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• v.16 no.4
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• pp.379-384
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• 2012

Lhx8 (LIM homeobox 8) gene encodes a LIM homeodomain transcriptional regulator that is preferentially expressed in germ cells and critical for mammalian folliculogenesis. However, Lhx8 DNA binding sequences are not characterized yet. We aimed to identify and characterize a cis-acting sequence of germ-cell specific transcriptional factor, Lhx8. To identify Lhx8 DNA binding element, Cyclic Amplification of Sequence Target (CAST) Analysis was performed. Electrophoretic Mobility Shift Assay (EMSA) was processed for the binding specificity of Lhx8. Luciferase assay was for the transcriptional activity of Lhx8 through identified DNA binding site. We identified a putative cis-acting sequence, TGATTG as Lhx8 DNA binding element (LBE). In addition, Lhx8 binds to the LBE with high affinity and augments transcriptional activity of luciferase reporter driven by artificial promoter containing the Lhx8 binding element. These findings indicate that Lhx8 directly regulates the transcription of genes containing Lhx8 binding element in oocytes during early folliculogenesis.

• IMMUNE NETWORK
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• v.16 no.3
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• pp.176-182
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• 2016

CCR3 is a chemokine receptor that mediates the accumulation of allergic inflammatory cells, including eosinophils and Th2 cells, at inflamed sites. The regulatory sequence of the CCR3 gene, contains two Runt-related transcription factor (RUNX) 1 sites and two PU.1 sites, in addition to a functional GATA site for transactivation of the CCR3 gene. In the present study, we examined the effects of the cis-acting elements of RUNX1 and PU.1 on transcription of the gene in EoL-1 eosinophilic cells and Jurkat T cells, both of which expressed functional surface CCR3 and these two transcription factors. Introduction of RUNX1 siRNA or PU.1 siRNA resulted in a modest decrease in CCR3 reporter activity in both cell types, compared with transfection of GATA-1 siRNA. Cotransfection of the two siRNAs led to inhibition in an additive manner. EMSA analysis showed that RUNX1, in particular, bound to its binding motifs. Mutagenesis analysis revealed that all point mutants lacking RUNX1- and PU.1-binding sites exhibited reduced reporter activities. These results suggest that RUNX1 and PU.1 participate in transcriptional regulation of the CCR3 gene.

• Journal of Microbiology and Biotechnology
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• v.30 no.1
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• pp.127-135
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• 2020

Small RNAs (sRNAs) are widespread and play major roles in regulation circuits in bacteria. Previously, we have demonstrated that transcription of esrE is under the control of its own promoter. However, the regulatory elements involved in EsrE sRNA expression are still unknown. In this study, we found that different cis-regulatory elements exist in the promoter region of esrE. We then screened and analyzed seven potential corresponding trans-regulatory elements by using pull-down assays based on DNA affinity chromatography. Among these candidate regulators, we investigated the relationship between the ferric uptake regulator (Fur) and the EsrE sRNA. Electrophoresis mobility shift assays (EMSAs) and β-galactosidase activity assays demonstrated that Fur can bind to the promoter region of esrE, and positively regulate EsrE sRNA expression in the presence of Fe²⁺.