• Fibers and Polymers
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• 제6권1호
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• pp.72-78
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• 2005

The impact of fiber friction, yarn twist, and splicing air pressure on mechanical and structural properties of spliced portion have been reported in the present paper. The mechanical properties include the tensile and bending related properties and, in the structural properties, the diameter and packing density of the splices are studied. A three variable three level facto­rial design approach proposed by Box and Behnken has been used to design the experiment. The results indicate that there is a strong correlation between retained spliced strength (RSS) and retained splice elongation (RSE) with all the experimental variables. It has been observed that RSS increases with the increase in splice air pressure and after certain level it drops, whereas it consistently increases with the increase in yarn twist. The RSE increases with the increase in both fiber friction and yarn twist. It has also been observed that the yarn twist and splicing air pressure have significant influence on splice diameter, percent increase in diameter and retained packing coefficient, but the fiber friction has negligible influence on these parame­ters. Yarn twist and splicing air pressure has a strong correlation with splice flexural rigidity, where as poor correlation with retained flexural rigidity.

• Bulletin of the Korean Chemical Society
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• 제30권2호
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• pp.323-326
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• 2009

SR proteins are essential splicing regulators and also modulate alternative splicing events, which function both as redundant and substrate-specific manner. The Drosophila B52/SRp55, a member of the SR protein family, is essential for the fly development in vivo, as deletion of B52 gene results in lethality of animals at the second instar larval stage. Identification of the splicing target genes of B52 thus should be crucial for the understanding of the specific developmental role of B52 in vivo. In this study, we performed whole-genome DNA microarray experiments with a B52- knock-out animal. Analysis of the microarray data not only provided the B52-dependent gene expression signature, but also revealed a larval-stage specific, alternative splicing target gene of B52. Our result thus provides a starting point to understand the essential function of B52 at the organismal level.

• 한국광학회지
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• 제19권3호
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• pp.169-174
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• 2008

열처리에 의한 광섬유 코어의 모드 확산과 모드 진화 현상을 이용하여 일반 통신용 단일모드 광섬유와 하이텔타(high ${\Delta}$) 광섬유 사이의 접속 손실을 줄일 수 있는 기법들을 제시하였다. 실험결과는 하이텔타 광섬유의 적절한 열처리를 통해 기계적 접속 손실이 2.3 dB에서 0.1 dB까지 감소함을 나타내었다. 반면 융착접속 후 접속 부위에 전기 방전이나 산소 불꽃으로 열을 인가하는 방법으로 $0.2{\sim}0.4dB$ 정도의 접속 손실을 달성하였다.

• BMB Reports
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• 제49권11호
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• pp.612-616
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• 2016

CD44 pre-mRNA includes 20 exons, of which exons 1-5 ($C_1-C_5$) and exons 16-20 ($C_6-C_{10}$) are constant exons, whereas exons 6-15 ($V_1-V_{10}$) are variant exons. $V_6$-exon-containing isoforms have been known to be implicated in tumor cell invasion and metastasis. In the present study, we performed a SR protein screen for CD44 $V_6$ splicing using overexpression and lentivirus-mediated shRNA treatment. Using a CD44 $V_6$ minigene, we demonstrate that increased SRSF3 and SRSF4 expression do not affect $V_6$ splicing, but increased expression of SRSF1, SRSF6 and SRSF9 significantly inhibit $V_6$ splicing. In addition, using a constitutive exon-specific primer set, we could not detect alterations of CD44 splicing after SR protein-targeting shRNA treatment. However, using a $V_6$ specific primer, we identified that reduced SRSF2 expression significantly reduced the $V_6$ isoform, but increased $V_{6-10}$ and $V_{6,8-10}$ isoforms. Our results indicate that SR proteins are important regulatory proteins for CD44 $V_6$ splicing.

• Journal of Microbiology
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• 제41권4호
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• pp.340-344
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• 2003

The group I intron from Tetrahymena thermophila has been demonstrated to employ splicing reactions with its substrate RNA in the trans configuration. Moreover, we have recently shown that the transsplicing group I ribozyme can replace HCV-specific transcripts with a new RNA that exerts anti-viral activity. In this study, we explored the potential use of RNA replacement for cancer treatment by developing trans-splicing group I ribozymes, which could replace tumor-associated RNAs with the RNA sequence attached to the 3' end of the ribozymes. Thymidine phosphorylase (TP) RNA was chosen as a target RNA because it is known as a valid cancer prognostic factor. By performing an RNA mapping strategy that is based on a trans-splicing ribozyme library, we first determined which regions of the TP RNA are accessible to ribozymes, and found that the leader sequences upstream of the AUG start codon appeared to be particularly accessible. Next, we assessed the ribozyme activities by comparing trans-splicing activities of several ribozymes that targeted different regions of the TP RNA. This assessment was performed to verify if the target site predicted to be accessible is truly the most accessible. The ribozyme that could target the most accessible site, identified by mapping studies, was the most active with high fidelity in vitro. Moreover, the specific trans-splicing ribozyme reacted with and altered the TP transcripts by transferring an intended 3' exon tag sequence onto the targeted TP RNA in mammalian cells with high fidelity. These results suggest that the Tetrahymena ribozyme can be utilized to replace TP RNAs in tumors with a new RNA harboring anti-cancer activity, which would revert the malignant phenotype.

• BMB Reports
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• 제52권11호
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• pp.641-646
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• 2019

The Ron proto-oncogene is a human receptor for macrophage-stimulating protein (MSP). The exclusion of exon 11 in alternative splicing generates ${\Delta}RON$ protein that is constitutively activated. Heterogenous ribonucleaoprotein (hnRNP) $C_1/C_2$ is one of the most abundant proteins in cells. In this manuscript, we showed that both hnRNP $C_1$ and $C_2$ promoted exon 11 inclusion of Ron pre-mRNA and that hnRNP $C_1$ and hnRNP $C_2$ functioned independently but not cooperatively. Moreover, hnRNP $C_1$ stimulated exon 11 splicing through intron 10 activation but not through intron 11 splicing. Furthermore, we showed that, whereas the RRM domain was required for hnRNP $C_1$ function, the Asp/Glu domain was not. In conclusion, hnRNP $C_1/C_2$ promoted exon 11 splicing independently by stimulating intron 10 splicing through RRM but not through the Asp/Glu domain.

• Journal of Microbiology
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• 제42권4호
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• pp.361-364
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• 2004

Internal ribosome entry site (IRES) of the hepatitis C virus (HCV) is known to be essential for HCV replication and most conserved among HCV variants. Hence, IRES RNA is a good therapeutic target for RNA-based inhibitors, such as ribozymes. We previously proposed a new anti-HCV modulation strategy based on trans-splicing ribozymes, which can selectively replace HCV transcripts with a new RNA that exerts anti-HCV activity. To explore this procedure, sites which are accessible to ribozymes in HCV IRES were previously determined by employing an RNA mapping method in vitro. In this study, we evaluate the intracellular accessibility of the ribozymes by comparing the trans-splicing activ­ities in cells of several ribozymes targeting different sites of the HCV IRES RNA. We assessed the intra­cellular activities of the ribozymes by monitoring their target-specific induction degree of both reporter gene activity and cytotoxin expression. The ribozyme capable of targeting the most accessible site iden­tified by the mapping studies then harbored the most active trans-splicing activity in cells. These results suggest that the target sites predicted to be accessible are truly the most accessible in the cells, and thus, could be applied to the development of various RNA-based anti-HCV therapies.

• Genomics & Informatics
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• 제4권1호
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• pp.33-39
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• 2006

Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.

• BMB Reports
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• 제45권3호
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• pp.133-140
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• 2012

Cancers claim millions of lives each year. Early detection that can enable a higher chance of cure is of paramount importance to cancer patients. However, diagnostic tools for many forms of tumors have been lacking. Over the last few years, studies of chimeric RNAs as biomarkers have emerged. Numerous reports using bioinformatics and screening methodologies have described more than 30,000 expressed sequence tags (EST) or cDNA sequences as putative chimeric RNAs. While cancer cells have been well known to contain fusion genes derived from chromosomal translocations, rearrangements or deletions, recent studies suggest that trans-splicing in cells may be another source of chimeric RNA production. Unlike cis-splicing, trans-splicing takes place between two pre-mRNA molecules, which are in most cases derived from two different genes, generating a chimeric non-co-linear RNA. It is possible that trans-splicing occurs in normal cells at high frequencies but the resulting chimeric RNAs exist only at low levels. However the levels of certain RNA chimeras may be elevated in cancers, leading to the formation of fusion genes. In light of the fact that chimeric RNAs have been shown to be overrepresented in various tumors, studies of the mechanisms that produce chimeric RNAs and identification of signature RNA chimeras as biomarkers present an opportunity for the development of diagnoses for early tumor detection.

• 전자공학회논문지
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• 제51권9호
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• pp.111-118
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• 2014

본 논문에서는 영상접합 조작 검출을 위한 효율적인 마코프 특징을 추출하는 방법을 제안한다. 제안 방법에서 사용하는 마코프 상태는 이산 코사인 변환 영역에서 인접한 블록간 계수의 차이로 구성되며, 블록간 대칭성을 이용하여 다양한 1차 마코프 천이확률을 접합 검출을 위한 특징으로 추출한다. 아울러 마코프 확률의 분포를 분석하여 특징의 수를 줄이는 방법을 제안한다. 추출된 특징 벡터를 SVM(support vector machine) 분류기를 이용하여 학습한 후 영상의 접합 여부를 판별한다. 실험 결과를 통하여 본 논문의 방법이 기존의 방법보다 적은 수의 특징으로 높은 영상접합 조작 결과를 보임을 확인하였다.