• Interdisciplinary Bio Central
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• 제4권4호
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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.

• 한국자기공명학회논문지
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• 제7권2호
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• pp.89-97
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• 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.

• 한국인터넷방송통신학회논문지
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• 제20권6호
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• pp.41-50
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• 2020

본 논문에서는 기존의 점자 학습 제품의 단점들을 보완한 점자 교육 시스템을 다룬다. 시각장애인 전용 어플리케이션은 사용자 편의성을 위해 터치 제스처 및 음성 안내를 통하여 전체 기능을 수행할 수 있도록 구성한다. 점자키트는 아두이노와 3D 프린팅을 통해 교육 목적에 맞게 제작한다. 시스템은 다음과 같은 기능들을 지원한다. 첫 째, 초성·종성·모음·약어 등 기초적인 점자의 학습. 둘 째, 단계별 퀴즈를 풀어 학습한 점자를 확인하는 기능. 셋 째, 모르는 점자가 있을 때 번역하는 기능이다. 실험을 통한 터치 제스처의 인식률과 점자 표현의 정확도를 확인하였고 번역의 경우 의도한대로 번역이 되는 것을 확인하였다. 이 시스템을 통해 시각장애인이 효율적으로 점자를 학습할 수 있다.

• Journal of Advanced Marine Engineering and Technology
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• 제38권5호
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• pp.557-565
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• 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.

• 한국수정란이식학회:학술대회논문집
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• 한국수정란이식학회 2002년도 국제심포지엄
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• pp.117-117
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• 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.

• 대한전자공학회:학술대회논문집
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• 대한전자공학회 2002년도 하계종합학술대회 논문집(2)
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• pp.353-356
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• 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.

• 한국컴퓨터정보학회논문지
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• 제8권4호
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• pp.21-27
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• 2003

본 논문에서는 정확한 분석 모델을 제시하기 위해서 객체 모델을 정의하고, 이 모델을 정형화와 표준화에 필요한 형식명세로 변환하는 방법을 제안한다. VDM 형식으로 변환된 모델은 정확성, 일관성, 완전성을 제공할 수 있다. 증명의 대상인 VDM 명세에서 오류가 발생한다면 초기 객체 모델 단계에 적용하여 객체 모델의 검증이 가능하다. 검증된 객체 모델을 설계 단계의 기반 명세로 사용하므로 추후 개발 단계의 비용과 노력을 최소화하고 객체 모델 선택의 정확성을 높일 수 있다.

• 정보처리학회논문지A
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• 제10A권3호
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• pp.207-214
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• 2003

계층적 자료구조인 사진트리는 이진 영상을 표현하는데 매우 중요한 자료구조이다. 사진트리를 메모리에 저장하는 방법 중 선형사진트리 표현 방법은 다른 표현 방법과 비교할 때 저장 공간을 매우 효율적으로 절약할 수 있는 이점이 있기 때문에 사진트리와 관련된 연산의 수행을 위해 선형 사진트리를 사용하는 효율적인 알고리즘 개발에 많은 연구가 진행되어 왔다. 선형이동은 영상을 주어진 거리만큼 이동시키는 연산으로, 영상 처리의 응용에서 중요하게 사용되는 연산에 속한다. 본 논문에서는 RMESH (Reconfigurable MESH) 구조에서 3-차원 n${\times}$n${\times}$n 프로세서를 사용하여 선형 사진트리로 표현된 이진 영상의 선형 이동을 수행하는 효율적인 알고리즘을 제안한다. 이 알고리즘은 n${\times}$n${\times}$n RMESH의 계층구조에서 선형 사진트리의 위치코드들을 효율적으로 전송할 수 있는 기본적인 연산들을 이용함으로써 상수 시간의 시간 복잡도를 갖는다.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2001년도 Proceedings of 2001 International Symposium
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• pp.83-89
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• 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
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• 제11권6호
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• pp.915-921
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• 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.