• Tuberculosis and Respiratory Diseases
• /
• v.79 no.2
• /
• pp.85-90
• /
• 2016

Background: Lung cancer is the most common cause of cancer related death. Alterations in gene sequence, structure, and expression have an important role in the pathogenesis of lung cancer. Fusion genes and alternative splicing of cancer-related genes have the potential to be oncogenic. In the current study, we performed RNA-sequencing (RNA-seq) to investigate potential fusion genes and alternative splicing in non-small cell lung cancer. Methods: RNA was isolated from lung tissues obtained from 86 subjects with lung cancer. The RNA samples from lung cancer and normal tissues were processed with RNA-seq using the HiSeq 2000 system. Fusion genes were evaluated using Defuse and ChimeraScan. Candidate fusion transcripts were validated by Sanger sequencing. Alternative splicing was analyzed using multivariate analysis of transcript sequencing and validated using quantitative real time polymerase chain reaction. Results: RNA-seq data identified oncogenic fusion genes EML4-ALK and SLC34A2-ROS1 in three of 86 normal-cancer paired samples. Nine distinct fusion transcripts were selected using DeFuse and ChimeraScan; of which, four fusion transcripts were validated by Sanger sequencing. In 33 squamous cell carcinoma, 29 tumor specific skipped exon events and six mutually exclusive exon events were identified. ITGB4 and PYCR1 were top genes that showed significant tumor specific splice variants. Conclusion: In conclusion, RNA-seq data identified novel potential fusion transcripts and splice variants. Further evaluation of their functional significance in the pathogenesis of lung cancer is required.

• BMB Reports
• /
• v.38 no.3
• /
• pp.320-327
• /
• 2005

Five ripening-related ACC synthase cDNA isoforms were cloned from 80% ripe papaya cv. 'Sinta' by reverse transcription-PCR using gene-specific primers. Clone 2 had the longest transcript and contained all common exons and three alternative exons. Clones 3 and 4 contained common exons and one alternative exon each, while clone 1, the most common transcript, contained only the common exons. Clone 5 could be due to cloning artifacts and might not be a unique cDNA fragment. Thus, there are only four isoforms of ACC synthase mRNA. Southern blot analysis indicates that all five clones came from only one gene existing as a single copy in the 'Sinta' papaya genome. Multiple sequence alignment indicates that the four isoforms arise from a single gene, possibly through alternative splicing mechanisms. All the putative alternative exons were present at the 5'-end of the gene comprising the N-terminal region of the protein. 'Sinta' ACC synthase cDNAs were of the capacs 1 type and are most closely related to a 1.4 kb capacs 1-type DNA(AJ277160) from Eksotika papaya. No capacs 2-type cDNAs were cloned from 'Sinta' by RT-PCR. This is the first report of possible alternative splicing mechanism in ripening-related ACC synthase genes in hybrid papaya, possibly to modulate or fine-tune gene expression relevant to fruit ripening.

• Journal of the Korean Statistical Society
• /
• v.30 no.4
• /
• pp.679-691
• /
• 2001

Two truncated sequential tests are developed for the two-sample scale problem based on the usual Wilcoxon rank-sum statistic for two different dispersion indices - absolute median deviations, when the medians of the two populations X and Y are equal or known and sums of squared mean deviations, when the medians are either unknown or unequal. The first test is briefly called SWAMD test and the second SWSMD test. For the SWAMD test, the percentile points for both the one-sided and two-sided alternatives, (equation omitted) have been found by Wiener approximation and their values computed for a range of values of a and N; analytical expression for the power function has been derived through Wiener process and its performance studied for various sequential designs for exponential distribution. This test has been illustrated by a numerical example. All the results of the SWAMD test, being directly applicable to the SWSMD test, are not dealt with separately Both the tests are compared and their suitable applications indicated.

• The Bulletin of The Korean Astronomical Society
• /
• v.37 no.2
• /
• pp.160.1-160.1
• /
• 2012

We present an alternative approach for satellite formation reconfiguration by an optimal impulsive-thrust strategy to minimize the total characteristic velocity in a near-circular-orbit. Linear transformation decouples the Hill-Clohessy-Wiltshire(HCW) dynamics into a new block-diagonal system matrix consisting of 1-dimensional harmonic oscillator and 2-dimensional subsystem. In contrast to a solution based on the conventional primer vector theory, the optimal solution and the necessary conditions are represented as times and directions of impulses. New analytical expression of the total characteristic velocity is found for each sub systems under general boundary conditions including transfer time constraint. To minimize the total characteristic velocity, necessary conditions for times and directions of impulses are analytically solved. While the solution to the 1-dimensional harmonic oscillator has been found, the solution to the 2-dimensional subsystem is currently under construction. Our approach is expected to be applicable to more challenging problems.

• Molecules and Cells
• /
• v.37 no.2
• /
• pp.118-125
• /
• 2014

Osteosarcoma is the most common primary malignant bone tumor with a very poor prognosis. Treating osteosarcoma remains a challenge due to its high transitivity. Tenascin-C, with large molecular weight variants including different combinations of its alternative spliced FNIII repeats, is specifically over expressed in tumor tissues. This study examined the expression of Tenascin-C FNIIIA1 in osteosarcoma tissues, and estimated the effect of mechanical stimulation on A1 expression in MG-63 cells. Through immunohistochemical analysis, we found that the A1 protein was expressed at a higher level in osteosarcoma tissues than in adjacent normal tissues. By cell migration assay, we observed that there was a significant correlation between A1 expression and MG-63 cell migration. The relation is that Tenascin-C FNIIIA1 can promote MG-63 cell migration. According to our further study into the effect of mechanical stimulation on A1 expression in MG-63 cells, the mRNA and protein levels of A1 were significantly up-regulated under mechanical stress with the mTOR molecule proving indispensable. Meanwhile, 4E-BP1 and S6K1 (downstream molecule of mTOR) are necessary for A1 normal expression in MG-63 cells whether or not mechanical stress has been encountered. We found that Tenascin-C FNIIIA1 is over-expressed in osteosar-coma tissues and can promote MG-63 cell migration. Furthermore, mechanical stress can facilitate MG-63 cell migration though facilitating A1 overexpression with the necessary molecules (mTOR, 4E-BP1 and S6K1). In con-clusion, high expression of A1 may promote the meta-stasis of osteosarcoma by facilitating MG-63 cell migration. Tenascin-C FNIIIA1 could be used as an indicator in metastatic osteosarcoma patients.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.163-163
• /
• 2017

A deletion analysis of the Oryza sativa dihydroflavonol reductase (DFR) promoter defined a 25 bp region (-386 to -362) sufficient to confer pericarp-specific expression of ${\beta}$ -glucuronidase(GUS) reporter gene in transgenic rice. Site-specific mutagenesis of these conserved sequences and subsequent expression analysis in calli which transiently expressed the mutated promoter::GUS gene showed that both bHLH (-386 to -381) and Myb (-368 to -362) binding sites in the DEL3 (-440 to 70) promoter were necessary for complete expression of the GUS gene including the tissue-specific expression of DFR::GUS gene. The GUS gene was expressed well in the mutated Myb (-368 to -362) binding site, but not as strong as in normal condition, implying that the Myb is also necessary to express GUS gene fully. Also, we found the non-epistatic relation between Rc and DFR. There were no changes of expression patterns GUS under the Rc and rc genotypes. Thus, DFR expression might be independent of the presence of functional Rc gene and suggested that Rc and Rd (DFR) share the same pathway controlling the regulation of flavonoid synthesis but not a direct positive transcriptional regulator of DFR gene.

• Journal of Gastric Cancer
• /
• v.2 no.4
• /
• pp.213-220
• /
• 2002

Purpose: The cDNA microarray provides a powerful alternative with an unprecedented view in monitoring geneexpression levels and leads to discoveries of regulatory pathways involved in complicated biological processes. Our aim is to explore the different gene-expression patterns in gastric adenocarcinomas. Materials and Methods: By using a cDNA microarray representing 4,600 cDNA clusters, we studied the expression profiling in 10 paired gastric adenocarcinoma samples and in adjacent noncancerous gastric tissues from the same patients. Alterations in the gene-expression levels were confirmed by Vsing Northern blots and reverse-transcription PCR (RT-PCR) in all of 4 randomly selected genes. Results: Genes those were expressed differently in cancer ous and noncancerous tissues were identified. 44 (of which 26 were known) and 92 (of which 43 were known) genes or cDNA were up- and down-regulated, respectively, in more than $80\%$ of the gastric adenocarcinoma samples. In cancer ous tissues, genes related to gene/protein expression, cellcycle regulation, and metabolism were mostly up-regulated whereas genes related to the oncogene/tumor suppressor gene, cell structure/motility, and immunology were mostly down-regulated. The semi-quantitative RT-PCR results for the four genes we tested were consistent with the array findings. Conclusions: These results provide not only a new molecular basis for understanding the biological properties of gastric adenocarcinomas but also a useful resource for future development of therapeutic targets and diagnostic markers for gastric adenocarcinomas.

• Proceeding of Spring/Autumn Annual Conference of KHA
• /
• 2009.04a
• /
• pp.247-252
• /
• 2009

The purpose of this study is to analyse the facade design of the modern multistory-housing in europe and to try to find the significant factor of them. For analysing, the facade design factors are divided by three criterion, which consists of external expression, visual expression and Housing Shape. And those three criterion are schematized by subdivision. By integrating those data, this study aims at deriving the significant factor of facade designs and categorizing them. Conclusively, I suggest the alternative method to improve the facade design of multistory-housing in Korea based on results of this study.

• Fashion & Textile Research Journal
• /
• v.10 no.4
• /
• pp.436-444
• /
• 2008

Recycle fashion is suggested to the suitable alternative of the environmental problem and the exhaustion of natural resources. The purpose of this study is focused on trying to comprehend between design characteristics and aesthetic values of recycle fashion design and those from fashion brands, fashion designers, and the public. For such purpose, 1553 photos of recycle fashion design which appeared in web-site, newspaper, fashion magazines between 2002 and 2007 were analyzed. Method of analysis did content analysis. The results of the research can be summarized as follows. First, design characteristics of recycle fashion were expressed by Junk Recycle Look, Vintage Recycle Look, Contemporary Recycle Look, Artisanal Recycle Look. Second, the expression methods of recycle fashion were presented reuse, reform, and regeneration. Third, aesthetic values of recycle fashion can be explained by the promotion of environment, the variableness, and the deconstruction.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2000.11a
• /
• pp.69-70
• /
• 2000

The completion of sequencing human genome would motivate us to map millions of human cDNAs onto the unique ruler "genome sequence", in order to identify the exact address of each cDNA together with its exons, its promoter region, and its alternative splicing patterns. The expression patterns of some cDNAs could therefore be associated with these precise gene addresses, which further accelerate studies on mining correlations between motifs of promoters and expressions of genes in tissues. Towards the realization of this goal, we have developed a time-and-space efficient software named SQUALL that is able to map one cDNA sequence of length a few thousand onto a long genome sequence of length thirty million in a couple of minutes on average. Using SQUALL, we have mapped twenty thousand of our Bodymap (http://bodymap.ims.u-tokyo.ac.jp) cDNAs onto the genome sequences of Chr.21st and 22nd. In this talk, I will report the status of this ongoing project.