• Title/Summary/Keyword: motif analysis

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Development of Structural Analysis and Construction Management System for Composite Cable Stayed Bridges (합성형 사장교의 시공단계해석 및 시공관리 시스템 개발)

  • 서주원;박정일;김남식;심옥진
    • Proceedings of the Computational Structural Engineering Institute Conference
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    • 1994.10a
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    • pp.95-102
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    • 1994
  • This paper presents a Cable Stayed Bridge Construction Management System, which consists of Structural System Identification Method (SSIM), Error Sensitivity Analysis and Optimum Error Adjustment & Prediction System. The 1st System Identification Method builds an error influence matrix using the linear superposition of each error modes. The 2nd SSIM also considers the second error mode term, which shows good error factor estimation. The optimal cable adjustment can be accomplished within the allowable range of both cable tension and camber. The Post processor, constituted with Motif and GL library on SGI platform, is useful for monitoring construction stage management by displaying construction data, adjustment and prediction results at each construction step.

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Characterization of ORF39 from Helicoverpa armigera Single-nucleocapsid Nucleopolyhedrovirus, the Gene Containing RNA Recognition Motif

  • Xu, Hai-Jun;Liu, Yan-He;Yang, Zhang-Nv;Zhang, Chuan-Xi
    • BMB Reports
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    • v.39 no.3
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    • pp.263-269
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    • 2006
  • In the genome of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus, open reading frame 39 (Ha39) is the only gene predicted to encode an RNA recognition protein. Computer analysis revealed that Ha39 homologues were found in 15 NPVs, but not in GVs. Its transcripts were detected from 3 through 72 hours post infection (h p.i.) using RT-PCR and Northern blot analysis. The protein was detected in infected-cell lysates from 6 h p.i. Western blot assay of ODV and BV preparations revealed that Ha39 encodes a structural protein associated with BVs. Additionally, immunofluorescence microscopy demonstrated that the protein was present within cytoplasm in virus-infected cells, but not in the nuclear region.

Isolation and characterization of the rice NPR1 promoter

  • Hwang, Seon-Hee;Hwang, Duk-Ju
    • Plant Biotechnology Reports
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    • v.4 no.1
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    • pp.29-35
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    • 2010
  • NPR1 is a positive regulator of systemic acquired resistance in Arabidopsis and rice. Expression of the rice gene OsNPR1 is induced by salicylic acid (SA). To identify the region of the OsNPR1 promoter involved in response to SA, we carried out deletion mutagenesis of the region 1005 bp upstream of the OsNPR1 start codon. Ciselement analysis revealed that the OsNPR1 promoter contains W-boxes and ASF1 motifs, both of which are known to be functional cis-elements of the WRKY and bZIP proteins, respectively. The deletion constructs 1005:LUC and 752:LUC, were induced by up to 4.3- and 3.8-fold, respectively, following SA treatment, suggesting that W-boxes and ASF1 motifs may play an important role in the strong induction of these constructs by SA. Using mutation analysis, we also showed that both the W-box and ASF1 motif are necessary for SA-induced expression of OsNPR1.

Functional Analysis of RAD4 Gene Required for Nucleotide Excision Repair of UV-induced DNA Damage in Saccharomyces cerevisiae

  • Park, Sang Dai;Park, In Soon
    • Animal cells and systems
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    • v.6 no.4
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    • pp.311-315
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    • 2002
  • The RAD4 gene is essential for nucleotide excision repair in Saccharomyces cerevisiae. It has been known that the deduced amino acid sequence of Rad4 protein contains three DNA-dependent ATPase/helicase motifs. To determine the biochemical activities and functional role of RAD4 the Rad4 protein was expressed and purified. Immunoblot analysis showed a specific band of 21 kDa, which was well-matched with the size of open reading frame of the RAD4 gene. The purified Rad4 protein had no detectable helicase activity. However, the protein could interact with double stranded oligonucleotides, as judged by mobility shift assay. This result suggests that the Rad4 protein is a DNA binding protein.

Analysis of the solution structure of the human antibiotic peptide dermcidin and its interaction with phospholipid vesicles

  • Jung, Hyun-Ho;Yang, Sung-Tae;Sim, Ji-Yeong;Lee, Seung-Kyu;Lee, Ju-Yeon;Kim, Ha-Hyung;Shin, Song-Yub;Kim, Jae-Il
    • BMB Reports
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    • v.43 no.5
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    • pp.362-368
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    • 2010
  • Dermcidin is a human antibiotic peptide that is secreted by the sweat glands and has no homology to other known antimicrobial peptides. As an initial step toward understanding dermcidin's mode of action at bacterial membranes, we used homonuclear and heteronuclear NMR to determine the conformation of the peptide in 50% trifluoroethanol solution. We found that dermcidin adopts a flexible amphipathic $\alpha$-helical structure with a helix-hinge-helix motif, which is a common molecular fold among antimicrobial peptides. Spin-down assays of dermcidin and several related peptides revealed that the affinity with which dermcidin binds to bacterial-mimetic membranes is primarily dependent on its amphipathic $\alpha$-helical structure and its length (>30 residues); its negative net charge and acidic pI have little effect on binding. These findings suggest that the mode of action of dermcidin is similar to that of other membrane-targeting antimicrobial peptides, though the details of its antimicrobial action remain to be determined.

The Cultural Identity Found in Tote Bags as a Cultural Product and the a Development of a Design -Focused on Hanbok Motifs- (문화상품으로서 토트 가방에 나타난 문화정체성과 디자인 개발 -한복의 모티브를 중심으로-)

  • Jung, Dawool;Kim, Tae-Eun;Bang, Haeun;Cho, Sunhyung;Kim, Minja
    • Journal of the Korean Society of Clothing and Textiles
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    • v.38 no.4
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    • pp.506-517
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    • 2014
  • A bag is a daily article carried in one's hand or on one's shoulder for things as well as a fashion item. The functions of a bag were derived to include portability, decorativeness, brand identity, message communicability and cultural identity. Souvenir bags sold at a gallery or a museum are goods to maximize the cultural identity of a bag based on national emblems, exhibitions and characters as design motifs. Based on the typological analysis of souvenir bags showing cultural identity, this study developed a design with a motif of Hanbok from Korean traditional cultural content to develop a tote bag design that reveals Korean cultural identity. Under a traditional Hanbok motif colors, sizes and patterns were reinterpreted in a modern perspective. For such a research purpose, 8 kinds of tote bags were developed. A tote bag design that reflects Korean cultural identity will contribute to raising the potential to develop cultural goods that are modern, popular and differentiated in the global market.

Computational Analysis of the 3-D structure of Human GPR87 Protein: Implications for Structure-Based Drug Design

  • Rani, Mukta;Nischal, Anuradha;Sahoo, Ganesh Chandra;Khattri, Sanjay
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.12
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    • pp.7473-7482
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    • 2013
  • The G-protein coupled receptor 87 (GPR87) is a recently discovered orphan GPCR which means that the search of their endogenous ligands has been a novel challenge. GPR87 has been shown to be overexpressed in squamous cell carcinomas (SCCs) or adenocarcinomas in lungs and bladder. The 3D structure of GPR87 was here modeled using two templates (2VT4 and 2ZIY) by a threading method. Functional assignment of GPR87 by SVM revealed that along with transporter activity, various novel functions were predicted. The 3D structure was further validated by comparison with structural features of the templates through Verify-3D, ProSA and ERRAT for determining correct stereochemical parameters. The resulting model was evaluated by Ramachandran plot and good 3D structure compatibility was evidenced by DOPE score. Molecular dynamics simulation and solvation of protein were studied through explicit spherical boundaries with a harmonic restraint membrane water system. A DRY-motif (Asp-Arg-Tyr sequence) was found at the end of transmembrane helix3, where GPCR binds and thus activation of signals is transduced. In a search for better inhibitors of GPR87, in silico modification of some substrate ligands was carried out to form polar interactions with Arg115 and Lys296. Thus, this study provides early insights into the structure of a major drug target for SCCs.

Direct Interaction Between Akt1 and Gcn5 and its Plausible Function on Hox Gene Expression in Mouse Embryonic Fibroblast Cells

  • Oh, Ji Hoon;Lee, Youra;Kong, Kyoung-Ah;Kim, Myoung Hee
    • Biomedical Science Letters
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    • v.19 no.3
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    • pp.266-269
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    • 2013
  • Hox genes encode transcription factors important for anterior-posterior body patterning at early stages of embryonic development. However, the precise mechanisms by which signal pathways are stimulated to regulate Hox gene expression are not clear. In the previous study, protein kinase B alpha (Akt1) has been identified as a putative upstream regulator of Hox genes, and Akt1 has shown to regulate Gcn5, a prototypical histone acetyltransferase (HAT), in a negative way in mouse embryonic fibroblast (MEF) cells. Since the activity of HAT such as the CBP/p300, and PCAF (a Gcn5 homolog), was down-regulated by Akt through a phosphorylation at the Akt consensus substrate motif (RXRXXS/T), the amino acid sequence of Gcn5 protein was analyzed. Mouse Gcn5 contains an Akt consensus substrate motif as RQRSQS sequence while human Gcn5 does not have it. In order to see whether Akt1 directly binds to Gcn5, immunoprecipitation with anti-Akt1 antibody was carried out in wild-type (WT) mouse embryonic fibroblast (MEF) cells, and then western blot analysis was performed with anti-Akt1 and anti-Gcn5 antibodies. Gcn5 protein was detected in the Akt1 immunoprecipitated samples of MEFs. This result demonstrates that Akt1 directly binds to Gcn5, which might have contributed the down regulation of the 5' Hoxc gene expressions in wild type MEF cells.

A Study on the Cultural Products using the Mugunghwa Motif in Museum (무궁화무늬를 활용한 박물관 패션문화상품에 대한 연구)

  • Kim, Yeo Kyung;Kim, Jeong Min;Hong, Na Young
    • Journal of the Korean Society of Costume
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    • v.63 no.7
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    • pp.49-64
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    • 2013
  • Mugunghwa, one of the most prominent national symbols of Korea, is a significant design source for producing cultural products. However, there has been a limitation to reflecting the identity of Korea using the design due to a lack of study and analysis of characteristics of Mugunghwa in history. Therefore, the researchers analyzed the design characteristics of Mugunghwa in cultural artifacts such as costumes, money, and stamps. Based on this, the study puts forward the following suggestions. First, the patterns of Mugunghwa should be categorized as a solo figure, a flower with pastels and the stem and a group of flowers as a unit. Second, there are two ways of expressing the flower: using realism and abstraction. Mugunghwa comprises of five pastels with elongated depth in the middle. The pastels spread out like the spokes of a wheel from the center; leaving a feeling of unevenness and the rims of the pastels are shaped in waves. The study puts forward the following suggestion: First, find the prototypes for different design characteristics. Second, develop motifs and patterns that reflect the given prototypes. Finally, apply the design to most popular cultural items such as T-shirts, neckties and bags. The ultimate purpose of the study lies with the hope that it will contribute to promoting the Korean beauty throughout the world.

The analysis on the possibility of applying carbon board pattern design using the woodcut technique to Interior decorating materials (목판화 기법을 활용한 carbon board용 pattern design과 interior 장식재로서의 적용 가능성 분석)

  • Kim, Eun-Ju
    • Journal of the Korean Crystal Growth and Crystal Technology
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    • v.21 no.1
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    • pp.27-33
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    • 2011
  • Carbon board, an electromagnetic shielding new material, is expected to be applied to the art wall by combining draft designs. When environment-friendly architecture materials are used as an interior wall, they are suitable as finishing materials. According to the increasing tendency of the application of carbon board, various styles could be made by decorating the whole or a part of a wall with tiles with module structure or by patterning the wall with panel-type woodcut or pictures or sculpture. And more graphic design based on diverse variation, and reconstruction and combination between other motif is being on the rise as a new expression. In this paper, make it possible to applying in MDF board and carbon board pattern design using the woodcut technique. The structural and physical properties were compared by usability of abrasion, toughness, stability. Samples are analyzed dependent on the hardness and relative density, change of detail pattern design and trimming technique. These results have shown that the possibility of applying of carbon board can be a high rank interior materials, capable of creating value of the living system, connects with MDF board, also can express humanism in a beautiful manner.