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

• Journal of the Korean Magnetic Resonance Society
• /
• v.7 no.2
• /
• pp.89-97
• /
• 2003

Foot-and-mouth disease virus (FMDV) belongs to the aphthovirus genus within the picornavirus which has a single copy of a positive sense RNA. The translation initiation process of FMDV occurs by a cap-independent mechanism directed by a highly structured element (∼435 nt) termed an internal ribosome entry site (IRES). We have designed and prepared FMDV 4-2 RNA (28nt) by in vitro transcription. The 2D NMR data revealed that FMDV 4-2 IRES domain RNA has a flexible loop and bulge conformation. In further study, we need to make an isotope labeled RNA sample and conduct 3D NMR experiments to completely determine the 3D structure. This study may establish a new drug design strategy to treat foot-and mouth disease.

• The Journal of the Institute of Internet, Broadcasting and Communication
• /
• v.20 no.6
• /
• pp.41-50
• /
• 2020

This paper deals with the Braille Education System which complements the shortcomings of the existing Braille Learning Products. An application dedicated to the blind is configured to perform full functions through touch gestures and voice guidance for user convenience. Braille kit is produced for educational purposes through Arduino and 3D printing. The system supports the following functions. First, the learning of the most basic braille, such as initial consonants, final consonant, vowels, abbreviations, etc. Second, the ability to check learned braille by solving step quizzes. Third, translation of braille. Through the experiment, the recognition rate of touch gestures and the accuracy of braille expression were confirmed, and in case of translation, the translation was done as intended. The system allows blind people to learn braille efficiently.

• Journal of Advanced Marine Engineering and Technology
• /
• v.38 no.5
• /
• pp.557-565
• /
• 2014

This paper describes the extended pivot-based approach for bilingual lexicon extraction. The basic features of the approach can be described as follows: First, the approach builds context vectors between a source (or target) language and a pivot language like English, respectively. This is the same as the standard pivot-based approach which is useful for extracting bilingual lexicons between low-resource languages such as Korean-French. Second, unlike the standard pivot-based approach, the approach looks for similar context vectors in a source language. This is helpful to extract translation candidates for polysemous words as well as lets the translations be more confident. Third, the approach extracts translation candidates from target context vectors through the similarity between source and target context vectors. Based on these features, this paper describes the extended pivot-based approach and does various experiments in a language pair, Korean-French (KR-FR). We have observed that the approach is useful for extracting the most proper translation candidate as well as for a low-resource language pair.

• Proceedings of the Korean Society of Embryo Transfer Conference
• /
• 2002.11a
• /
• pp.117-117
• /
• 2002

The oocytes from most of animal species accumulate genetic information and other necessary materials during oogenesis for the later use in the early development. Over the years oocyte maturation has been studied extensively both in vitro and in vivo. Particularly, maturation of follicular oocyte in vitro becomes one of the important tools for the studies of basic cell biology, the in vitro technology of animal production, and in particular, the somatic cell cloning by nuclear transfer. We examined meiotic maturation and cumulus expansion in the presence of translation or transcription inhibitors for varying periods of in viかo maturation (IVM) of pig oocyte. In Experiment 1, the results revealed that translation and transcription inhibitors inhibited cumulus expansion and meiotic maturation during 35h of IVM. However, 50 to 60% of the oocytes underwent nuclear maturation without cumulus expansion during 75h of IVM. The rest of the oocytes were arrested at metaphase I (40-50%) in the presence of the inhibitors. In Experiment II, the OCCs were exposed to the drugs only for 15h to examine translation and transcription inhibitors on cumulus expansion and meiotic maturation. Transcription inhibitors for 15h did not arrest meiotic maturation when the oocytes were cultured for subsequent, necessary period of IVM, whereas cumulus expansion was completely inhibited, suggesting that initial 15h is critical transcription activity far cumulus expansion. Translation inhibitors for 15h exposure did not alter cumulus expansion and meiotic maturation during subsequent culture in the absence of the drugs. In Experiment III, the OCCs were exposed to the drugs only for later 30h to examine the influence of transcription and translation inhibitors on oocyte maturation. Interestingly, all meiotic maturation underwent normally with full expansion of cumulus. Similar results were obtained from Experiment IV where 5h of exposure from 15 to 20h of IVM culture to the drugs was performed and subsequently cultured for same period in fresh medium. Taken there results together, both transcription and translation are necessary for nuclear maturation and cumulus expansion, and first 15h IVM for cumulus expansion is critical. The arrested oocytes by the drugs were still capable of undergoing nuclear maturation, although cumulus expansion was affected.

• Proceedings of the IEEK Conference
• /
• 2002.06b
• /
• pp.353-356
• /
• 2002

Due to the increased complexity and size of digital system and the need of the H/W-S/W co-design, C/C++ based system design methodology gains more Interests than ever in EDA field. This paper suggests the methodology in which handshake module corresponding to each basic statement of C is provided of the form of STG(Signal Transition Graph) and then, C statements is synthesized into asynchronous circuit through syntax-oriented translation. The 4-phase handshaking protocol is used for the communications between modules, and the modules are synthesized by the Petrify which is asynchronous logic synthesis CAD tool.

• Journal of the Korea Society of Computer and Information
• /
• v.8 no.4
• /
• pp.21-27
• /
• 2003

In these paper, we define object models in order to represent a correct analysis model, propose translation method to formal specification necessary to uniform and standard. The translated model provide to correctness, consistency and completeness. If it is happen to error in the VDM specification, we can verify model to adapt initial object model step. It increase correctness to retrieval, reduce the costs and efforts of after development because of the verified model used to basic specification in design step.

• The KIPS Transactions:PartA
• /
• v.10A no.3
• /
• pp.207-214
• /
• 2003

Quadtree, which is a hierarchical data structure, is a very important data structure to represent binary images. The linear quadtree representation as a way to store a quadtree is efficient to save space compared with other representations. Therefore, it has been widely studied to develop efficient algorithms to execute operations related with quadtrees. The linear translation is one of important operations in image processing, which moves the image by a given distance. In this paper, we present an algorithm to perform the linear translation of binary images represented by quadtrees, using three-dimensional $n{\times}n{\times}n$ processors on RMESH (Reconfigurable MESH). This algorithm has constant-time complexity by using efficient basic operations to route the locational codes of quardtree on the hierarchical structure of n${\times}$n${\times}$n RMESH.

• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2001.06a
• /
• pp.83-89
• /
• 2001

Recent advances in the structural and molecular biology uncovered that a set of translation factors resembles a tRNA shape and, in one case, even mimics a tRNA function for deciphering the genetic ：ode. Nature must have evolved this 'art' of molecular mimicry between protein and ribonucleic acid using different protein architectures to fulfill the requirement of a ribosome 'machine'. Termination of protein synthesis takes place on the ribosomes as a response to a stop, rather than a sense, codon in the 'decoding' site (A site). Translation termination requires two classes of polypeptide release factors (RFs)： a class-I factor, codon-specific RFs (RFI and RF2 in prokaryotes; eRFI in eukaryotes), and a class-IT factor, non-specific RFs (RF3 in prokaryotes; eRF3 in eukaryotes) that bind guanine nucleotides and stimulate class-I RF activity. The underlying mechanism for translation termination represents a long-standing coding problem of considerable interest since it entails protein-RNA recognition instead of the well-understood codon-anticodon pairing during the mRNA-tRNA interaction. Molecular mimicry between protein and nucleic acid is a novel concept in biology, proposed in 1995 from three crystallographic discoveries, one, on protein-RNA mimicry, and the other two, on protein-DNA mimicry. Nyborg, Clark and colleagues have first described this concept when they solved the crystal structure of elongation factor EF- Tu：GTP：aminoacyl-tRNA ternary complex and found its overall structural similarity with another elongation factor EF-G including the resemblance of part of EF-G to the anticodon stem of tRNA (Nissen et al. 1995). Protein mimicry of DNA has been shown in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex (Mol et al. 1995; Savva and Pear 1995) as well as in the NMR structure of transcription factor TBP-TA $F_{II}$ 230 complex (Liu et al. 1998). Consistent with this discovery, functional mimicry of a major autoantigenic epitope of the human insulin receptor by RNA has been suggested (Doudna et al. 1995) but its nature of mimic is. still largely unknown. The milestone of functional mimicry between protein and nucleic acid has been achieved by the discovery of 'peptide anticodon' that deciphers stop codons in mRNA (Ito et al. 2000). It is surprising that it took 4 decades since the discovery of the genetic code to figure out the basic mechanisms behind the deciphering of its 64 codons.

• Journal of Microbiology and Biotechnology
• /
• v.11 no.6
• /
• pp.915-921
• /
• 2001

Phytase improves the bioavailability of phytate phosphorus in plant foods to humans and animals, and reduces the phosphorus pollution of animal waste. In order to express a high level of fungal phytase in Saccharomyces cerevisiae, various expression vectors were constructed with different combinations of promoters, translation enhancers, signal peptides, and terminator. Three different promoters fused to the phytase gene (phyA) from Aspergillus niger were tested: a galactokinase (GAL1) promoter, glyceraldehyde-3-phosphate dehydrogenase (GPD) promoter, and yeast hybrid ADH2-GPD promoter consisting of alcohol dehydrogenase II (ADH2) and a GPD promoter. The signal peptides of phytase, glucose oxidase (GO), and rice amylase 1A(RAmy1A) were included. Plus, the translation enhancers of the ${\Omega}$ sequence and UTR70 from the tobacco mosaic virus (TMV) and spinach, respectively, were also tested. Among the recombinant vectors, pGphyA06 containing the GPD promoter, the ${\Omega}$ sequence, RAmy1A, and GAL7 terminator expressed the highest phytase activity in a culture filtrate, which was estimated at 20 IU/ml. An intracellular localization of the expressed phytase activity in a culture filtrate, which was estimated at 20 IU/ml. An intracellular localization of the expressed phytase was also performed by inserting an endoplasmic reticulum (ER) retention signal, KDEL sequence, into the C-terminus of the phytase within the vector pHphyA-6. It appeared that the KDEL sequence directed most of the early expression of phytase into the intracellular compartment yet more than $60\%$ of the total phytase activity was still retained within the cell even after the prolonged (>3 days) incubation of the transformant. However, the intracellular enzyme activity of the transformant without a KDEL sequence was as high as that of the extracellular one, thereby strongly suggesting that the secretion of phytase in S. cerevisiae appeared to be the rate-limiting step for the expression of a large amount of extracellular recombinant phytase, when compared with other yeasts.