• BMB Reports
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• v.54 no.3
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• pp.176-181
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• 2021

Bcl-x, a member of the Bcl-2 family, plays a key role in apoptosis. Alternative splicing of Bcl-x pre-mRNA through alternative 5' splice-site selection produces an anti-apoptotic mRNA isoform that includes exon 2b and a pro-apoptotic Bcl-x mRNA isoform that excludes exon 2b. Here we used Bcl-x minigene and identified SRSF2 and SRSF6 as two regulatory factors of 5' splice-site selection of Bcl-x pre-mRNA. We selected binding clusters closer to 5' splice-sites from multiple potential binding sites of SRSF2 and SRSF6 to perform loss of functions analysis through site-directed mutagenesis. Our results demonstrated that these mutations did not abolish regulatory functions of SRSF2 or SRSF6, indicating that a single binding motif or a cluster was not a functional target of these proteins in Bcl-x pre-mRNA splicing. Random deletion mutagenesis did not disrupt the role of SRSF2 and SRSF6. Importantly, mutagenesis of 5' splice-site to a conserved or a weaker score demonstrated that the weaker strength of the target 5' splice-site or higher strength of the other 5' splice-site strength limited the role of SRSF2 and SRSF6 in 5' splice-site activation.

• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.167-172
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• 2005

This paper introduces a method which improves the performance of the identification of splice sites in the genomic DNA sequence of eukaryotes. This method combines a low order Markov model in series with a neural network for the predictions of splice sites. The lower order Markov model incorporates the biological knowledge surrounding the splice sites as probabilistic parameters. The Neural network takes the Markov encoded parameters as the inputs and produces the prediction. Two types of neural networks are used for the comparison. This method reduces the computational complexity and shows encouraging accuracy in the predictions of splice sites when applied to several standard splice site dataset.

• Korean Journal of Microbiology
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• v.27 no.1
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• pp.1-9
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• 1989

The locations of 5' ends as well as the splicing pattern of viral poly A(-) 19S RNA from monkey cells infected with SV40 were determined by a modification of primer extension method. The 5' end of this RNA mapped at the major cap site at nucleotide residue 325, used most frequently by SV40 late RNAs. The intron from nt.373 to nt.558 was removed as the ordinary cytoplasmic poly A(+) 19S RNA. The 3'end of this RNA was very heterogeneous and distributed over 1 kb upstream of polyadenylation site, as determined by S1 nuclease mapping. The reason for this normally initiated and spliced RNA to accumulate in the nucleus was investigated. In order to test whether the presence of unused 3' splice region on this RNA caused such subcellular distribution, cells were transfected with SV40 mutant KNA containing deletion around 3' splice site. The RNA deleted of 3' splice region accumulated mainly in the cytoplasm. This accumulation did not result from the increased stability of the RNA due to the deletion, since the wild type and mutant RNAs exhibited similar half lives after chase with actinomycin D. Therefore it is likely that the 19S spliced RNA is hindered from being transported into the cytoplasm due to some pre-splicing complexes formed at the unused 3' splice site.

• Journal of the Society of Disaster Information
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• v.11 no.4
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• pp.520-526
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• 2015

Reinforcing bar splices are inevitable in reinforced concrete structure. In these days, there are three main types of splices used in reinforced concrete construction site - lapped splice, mechanical splice and welded splice. Low cost, practicality in construction site, less time consuming and high performance make gas pressure welding become a favorable splice method. However, reinforcing bar splice experiences thermal loading history during the welding procedure. This may lead to the presence of residual stress in the vicinity of the splice which affects the fatigue life of the reinforcing bar. Therefore, residual stress analysis and tensile test of the gas pressure welded splice are carried out in order to verify the load bearing capacity of the gas pressure welded splice. The reinforcing bar used in this work is SD400, which is manufactured in accordance with KS D 3504. The results show that the residual stresses in welded splice is relatively small, thus not affecting the performance of the reinforcing bar. Moreover, the strength of the gas pressure welded splice is high enough for the development of yielding in the bar. As such, the reinforcing bar with gas pressure welded splice has enough capacity to behave as continuous bar.

• Steel and Composite Structures
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• v.35 no.3
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• pp.353-370
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• 2020

This paper describes a new type of replaceable fuse for moment resisting frames. Column-tree connections with beam splice connections are frequently preferred in the moment resisting frames since they eliminate field welding and provide good quality. In the column-tree connections, a part of the beam is welded to the column in the shop and the rest of the beam is bolted with the splice connection in the field. In this study, a replaceable reduced beam section (R-RBS) connection is proposed in order to eliminate welding process and facilitate assembly at the site. In the proposed R-RBS connection, one end is connected by a beam splice connection to the beam and the other end is connected by a bolted end-plate connection to the column. More importantly is that the proposed R-RBS connection allows the replacement of the damaged R-RBS easily right after an earthquake. Pursuant to this goal, experimental and numerical studies have been undertaken to investigate the performance of the R-RBS connection. An experimental study on the RBS connection was used to substantiate the numerical model using ABAQUS, a commercially available finite element software. Additionally, five different finite element models were developed to conduct a parametric study. The results of the analysis were compared in terms of the moment and energy absorption capacities, PEEQ, rupture and tri-axiality indexes. The design process as well as the optimum dimensions of the R-RBS connections are presented. It was also demonstrated that the proposed R-RBS connection satisfies AISC criteria based on the nonlinear finite element analysis results.

• Journal of the Korean Society for Railway
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• v.20 no.2
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• pp.257-264
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• 2017

The PC (Precast Concrete) construction method is a technique where concrete members that have been produced in a plant are constructed on site. Thus, continuity and secure integration of a structure that can be obtained by connecting rebars at splicing joint for PC members are the main areas of concern for this method. To evaluate the splicing and bonding performance according to application of a splice sleeve for connecting rebar in this research study, the diameter of rebar, development length, grouting strength etc. were set as variables. The performance and stiffness of splicing according to the development length of grout strength were measured and evaluated. In addition, by conducting comparative analysis on each of the variables, the factors that affected the splice sleeve for connecting rebar were discussed. The results confirmed that the strength and stiffness of the splice sleeve for connecting rebar were significantly affected by the development length while the increase in performance according to grout strength was not as significant.

• Journal of the Korea Institute of Building Construction
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• v.22 no.6
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• pp.531-542
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• 2022

As buildings become taller, the strength of structural materials must increase and the amount of rebar reinforcement also increases while the application of an appropriate rebar splice method in the construction process become one of the essential factors. In this research, the current status of quality check for rebar coupler is identified by an expert questionnaire and an appropriate quality check method is proposed through a quality test on specimens similar to actual on-site construction. In the test results, it was revealed that, among the quality check methods for rebar coupler joints, the coupler tightening method and face to face degree of between upper and lower rebar did not affect the strength the specimen. Therefore, it is considered to be an appropriate way to check the coupler quality check to check whether the threads are completely assembled during on-site construction through manufacture the number of threads of rebar and coupler with a margin beyond the calculated thread number.

• BMB Reports
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• v.35 no.5
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• pp.513-517
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• 2002

We describe a new method for identifying the sequences that signal the start of translation, and the boundaries between exons and introns (donor and acceptor sites) in human mRNA. According to the mandatory keyword, ORGANISM, and feature key, CDS, a large set of standard data for each signal site was extracted from the ASCII flat file, gbpri.seq, in the GenBank release 108.0. This was used to generate the scoring matrices, which summarize the sequence information for each signal site. The scoring matrices take into account the independent nucleotide frequencies between adjacent bases in each position within the signal site regions, and the relative weight on each nucleotide in proportion to their probabilities in the known signal sites. Using a scoring scheme that is based on the nucleotide scoring matrices, the method has great sensitivity and specificity when used to locate signals in uncharacterized human genomic DNA. These matrices are especially effective at distinguishing true and false sites.

• Genomics & Informatics
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• v.4 no.1
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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.