• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.8C
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• pp.1025-1033
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• 2004

This paper covers the detection of covert direct sequence spread spectrum signal without the PN(Pseudo Noise) code information. Due to its low probability of interception, the difficulty of spectrum surveillance increases. Detection parameters are the signal existence of given bandwidth, the length of spreading sequence used by transmitter, and the identification of spreading code for detected chip length. The triple correlation function(TCF) value which is one of the higher order statistical signal processing techniques can be used to detect spread spectrum signal without a prior knowledge, but, it has weakness that TCF results depend on the spread data sequence in actual application. This paper proposes the new scheme that not only overcomes the weakness but also presents better performance than the traditional TCF scheme. The performance comparison of conventional TCF with proposed technique shows that the triple correlation estimator(TCE) has better detection capability.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.22 no.2
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• pp.241-249
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• 1997

In this paper, a new technique is proposed for generating a minimum-length synchronizable test sequence that can be applied in the distributed test architecture where both external synchtonization and input/output operation costs are taken into consideration. the method defines a set of transformation rules that constructs a duplex digraph from a given finite state machine representation of a protocol specification rules that constructs a duplex digraph from a given finite state machine representation of a protocol specificatio such that a rural chinese postman tour of the duplex digraph can be used to generate a minimum-length synchronizable test sequence using synchronizable distinguishing sequences as the state identification sequence for each state of the given finite state machine. The method provides an elegant solution to the synchronization problem that arises during the application of a predetermined test sequence in some protocol test architectures that utilize remote testers.

• Journal of Digital Convergence
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• v.12 no.12
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• pp.265-275
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• 2014

This paper introduces a new algorithms for reconstructing the suffix tree of character string, when a substring id deleted from the string or a string is inserted into the string as a substring. The algorithem has two main functions, delete-structure and insert-structure. The main objective of this algorithm is to save the time for constructing the suffix tree of an edited string, when the suffix tree of the original string is available. We tested the performance of this algorithm with some DNA sequences. This test shows that delete-reconstructing can save time when the length of the subsequence deleted is less than 30% of the original sequence, and the insert-reconstructing takes less time with regard to the length of inserted sequence.

• Biomedical Science Letters
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• v.7 no.2
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• pp.59-64
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• 2001

Nebulin is an unusually large actin-binding protein specific to the skeletal muscle of vertebrates. The correlation of nebulin size with thin filament length have led to the suggestion that nebulin acts as a molecular ruler for the length of thin filaments. An SH3 domain occupies the C terminus of nebulin, in the sarcomeric Z-disk and is preceded by a 120-residue stretch containing multiple putative phosphorylation sites. SH3 domain mediates protein-protein interaction involved in the subcellular localization of proteins, cytoskeletal organization and signal transduction. However the binding partner and physiological role of nebulin SH3 domains remains unknown. Using the yeast two-hybrid system, we identified supervillin, an actin-binding protein, as a nebulin SH3 domain-interacting protein. The SH3 domain of nebulin binds to the sequence encoding amino acids 977 to 1335 of supervillin. But the sequence encoding amino acids 977 to 1335 displays weaker binding than the sequence encoding amino acids 977 to 1788.

• BMB Reports
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• v.30 no.6
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• pp.426-430
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• 1997

The helical periodicity of the triple-stranded $(dT)_n{\cdot}(dA)_n{\cdot}(dT)_n$ sequence was determined by measuring gel-mobilities of bent DNA fragments containing the sequence. In the bent DNA fragments, a $GA_{22}G$ $CT_{22}C$ sequence was located between two bent DNA loci composed of six $A_{6}{\cdot}T_{6}$ repeats. and the DNA length between the bent DNA loci was varied by 1 base pair over a full helical turn. The gel mobility of each bent DNA fragment reflected the overall extent of DNA bending and varied with the DNA length between the two bent loci. Mobilities of the bent DNA fragments in 5% polyacrylamide gel were measured after preincubating the DNA fragments both in the presence and absence of $CT_{22}C$ oligonucleotide. By comparing the bent DNA fragments containing an intermolecular triplex structure with those of a genuine duplex structure in the gel mobilities, the helical periodicity of the $T_n{\cdot}A_n{\cdot}T_n$ triplex DNA was determined to be $11.5({\pm}0.3)bp/turn$.

• International Journal of Contents
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• v.3 no.2
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• pp.18-24
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• 2007

Biological sequences such as DNA and amino acid sequences typically contain a large number of items. They have contiguous sequences that ordinarily consist of more than hundreds of frequent items. In biological sequences analysis(BSA), a frequent contiguous sequence search is one of the most important operations. Many studies have been done for mining sequential patterns efficiently. Most of the existing methods for mining sequential patterns are based on the Apriori algorithm. In particular, the prefixSpan algorithm is one of the most efficient sequential pattern mining schemes based on the Apriori algorithm. However, since the algorithm expands the sequential patterns from frequent patterns with length-1, it is not suitable for biological datasets with long frequent contiguous sequences. In recent years, the MacosVSpan algorithm was proposed based on the idea of the prefixSpan algorithm to significantly reduce its recursive process. However, the algorithm is still inefficient for mining frequent contiguous sequences from long biological data sequences. In this paper, we propose an efficient method to mine maximal frequent contiguous sequences in large biological data sequences by constructing the spanning tree with a fixed length. To verify the superiority of the proposed method, we perform experiments in various environments. The experiments show that the proposed method is much more efficient than MacosVSpan in terms of retrieval performance.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.130-135
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• 2004

The marine dinoflagellate genus Alexandrium, which produces PSP toxins, has a global distribution. As human-assisted dispersal of the species has been suggested, it is important to develop molecular tools to trace the dispersal pathway. To screen population-specific DNA sequences that differentiate Korean and Japanese A. catenella, we targeted the area downstream of the chloroplast psbA gene using PCR with population-specific DNA primers followed by RFLP (restriction fragment length polymorphism) analysis and sequencing. The RFLP patterns of the PCR products divided Korean and Japanese A. catenella regional isolates into three types: Korean, Japanese, and type CMC3, isolated from Korea. We sequenced the PCR products, but found no similar gene in a homology search. The molecular phylogeny inferred from the sequences separated the Korean and Japanese A. catenella strains, as did the RFLP patterns. However, the Japanese isolates included two slightly different sequences (types J and K), while the Korean sequence was the same as the Japanese K type. In addition, a unique sequence was found in the Korean strains CMC2 and CMC3. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers designed from the type J sequence yielded PCR products for Japanese strains only, showing that the unknown gene can be used for a population analysis of Korean and Japanese A. catenella.

• Environmental Analysis Health and Toxicology
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• v.24 no.2
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• pp.107-117
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• 2009

Metal pollution of aquatic ecosystems is a problem of economic and health importance. Information regarding molecular responses to metal exposure is sorely needed in order to identify potential biomarkers. To determine the effects of heavy metals on chironomids, the full-length cDNA of alcohol dehydrogenase (ADH3) from Chironomus riparius was determined through molecular cloning and rapid amplification of cDNA ends (RACE). The expression of ADH3 was analyzed under various cadmium and copper concentrations. A comparative and phylogenetic study among different orders of insects and vertebrates was carried out through analysis of sequence databases. The complete cDNA sequence of the ADH3 gene was 1134 bp in length. The sequence of C. riparius ADH3 shows a low degree of amino acid identity (around 70%) with homologous sequences in other insects. After exposure of C. riparius to various concentrations of copper, ADH3 gene expression significantly decreased within 1 hour. The ADH3 gene expression was also suppressed in C. riparius after cadmium exposure for 24 hour. However, the effect of cadmium on ADH3 gene expression was transient in C. riparius. The results show that the suppression of ADH3 gene by copper exposure could be used as a possible biomarker in aquatic environmental monitoring and imply differential toxicity to copper and cadmium in C. riparius larvae.

• BMB Reports
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• v.42 no.5
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• pp.271-276
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• 2009

Sweetpotato (Ipomoea batatas (L). Lam.) is relatively tolerant to unfavorable growth conditions such as drought, yet has not been exploited to provide a better understanding of the molecular basis of drought stress tolerance. We obtained 983 high-quality expressed sequence tags of 100 bp or longer (average length of 700 bp) from cDNA libraries of detached white fibrous root tissues by subjecting them to dehydration for 6 h. The 431 cDNAs were each assigned a function by alignment using the BLASTX algorithm. Among them, three genes associated with various abiotic stresses and nine genes not previously associated with drought stress were selected for expression pattern analysis through detailed reverse transcription-polymerase chain reaction. The direct and indirect relationships of the 12 genes with drought tolerance mechanisms were ascertained at different developmental stages and under various stress conditions.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.51 no.2
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• pp.163-169
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• 2018

This study examined the expression of heat shock protein 70 (Hsp70) in red seabream Pagrus major infected by the, acanthocephalan parasites Longicollum pagrosomi. We cloned the full-length Hsp70 cDNA from the liver of the red seabream. The full-length cDNA had a 1,950 bp open reading frame (ORF) that encoded a protein of 650 amino acids. The deduced amino acid sequence of Hsp70 contained all of the conserved Hsp70 family signature sequences and an adenosine triphosphate (ATP)/guanosine triphosphate (GTP) binding motif, including the EEVD (consensus sequence that terminates in Hsp70 family) consensus sequence. The expression of Hsp70 mRNA was upregulated int the fish head-kidney and liver, as determined by quantitative real-time PCR. We quantified the Hsp70 mRNA expression in normal red seabream and fish infected fish by L. pagrosomi. The expression of Hsp70 mRNA was significantly higher in the infected red seabream. These results suggest that Hsp70 play a role of protection against stress and inflammation caused by the parasite and may help maintain homeostasis.