• Animal cells and systems
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• v.6 no.3
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• pp.271-275
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• 2002

Rph1 and Gisl are damage-responsive repressors involved in PHR1 expression. They have two $C_{2}$H/ sub 2/ zinc finger motifs as putative DNA binding domains and N-terminal conserved domain with unknown function. They are also found in the human retinoblastoma binding protein 2 and the mouse jumonji- encoded protein. The repressors are able to bind to A $G_{4}$ sequence within a 39-bp sequence called upstream repressing sequence of PHR1 promoter (UR $S_{PHR1}$) responsible for the damage-response of PHR1. We report here that Rph1 is predominantly localized in the nucleus as examined by fluorescence microscopic analysis with GFP-Rph1 fusion protein. On the basis of the fact that the A $G_{4}$ sequence that is recognized by Rph1 and Gisl is also recognized by Msn2 and Msn4 in a process of stress response, we a1so tried to examine the in vivo function of A $G_{4}$ and the role of Msn2 and Msn4 in PHR1 expression. Our results demonstrate that Msn2 and Msn4 are actually required for the basal transcription of PHR1 expression but not for its damage induction. When A $G_{4}$ sequence was inserted into the minimal promoter of the cyc1-LacZ reporter, the increased LacZ expression was observed indicating its involvement in transcriptional activation. The data suggest that the A $G_{4}$ is primarily required for basal transcriptional activation of PHR1 or CYC1 promoter through the possible involvement of Msn2 and Msn4. However, since the A $G_{4}$ is also involved in the repression of PHR1 via Rphl and Gisl, it is proposed that A $G_{4}$ functions as either URS or upstream activating sequence (UAS) depending on the promoter context.t.

• Molecules and Cells
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• v.27 no.3
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• pp.365-381
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• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• Applied Biological Chemistry
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• v.31 no.3
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• pp.274-283
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• 1988

Aqualysin I is an alkaline serine protease which is secretet into the culture medium by Thermus aquaticus YT-1, an extreme thermophile. Aqualysin I was purified, and its partial amino acid sequence was determined. The gene encoding aqualysin I was cloned into E. coli using synthetic oligodeoxyribonucleotides as hybridization probes. The nucleotide sequence of the cloned DNA was determined. The primary structure of aqualysin I, deduced from the nucleotide sequenc, agreed with the determid amino acid sequences, including the $NH_2-$ and COOH terminal sequence of the tryptides derived from aqualysin I. Aqualysin I comprised 281 amino acid residues and its molecular mass was determined to be 28350. On alignment of the whole amino acid sequence, aqualysin I showed high sequence homology with the subtilisin type serine protease, and 43% identity with proteinase K, 37-30% with subtilisins and 34% with thermitase. Extremely high sequence identity was observed in the regions containing the active-site residues, corresponding to Asp32, His64 and Ser221 of subtilisin BPN'. Aqualysin I contains two disulfide bonds, Cys67-Cys99 and Cys163-Cys194, and these disulfide bonds seem to contribute to the heat stability of the enzyme. The determined positions of the twe disulfide bonds of aqualysin I agreed with those predicted previously on the basis of computer graphics of the crystallographic data for subtilisin BPN'. Therefore, these findings sugests that the three-dimensional structure of aqualysin I is similar to that of subtilisin BPN' Aqualysin I is produced as a lage precursor, which contains $NH_2-$ and COOH- terminal portions besides the mature protease sequence.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• The KIPS Transactions:PartC
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• v.12C no.2 s.98
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• pp.281-288
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• 2005

It is generally accepted that self-similar (or fractal) Processes may provide better models for teletraffic in modem computer networks than Poisson processes. f this is not taken into account, it can lead to inaccurate conclusions about performance of computer networks. Thus, an important requirement for conducting simulation studies of telecommunication networks is the ability to generate long synthetic stochastic self-similar sequences. A generator of pseudo-random self similar sequences, based on the SRA (successive random addition) method, is implemented and analysed in this paper. Properties of this generator were experimentally studied in the sense of its statistical accuracy and the time required to produce sequences of a given (long) length. This generator shows acceptable level of accuracy of the output data (in the sense of relative accuracy of the Hurst parameter) and is fast. The theoretical algorithmic complexity is O(n).

• The Korean Journal of Applied Statistics
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• v.22 no.3
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• pp.617-626
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• 2009

A series of recent papers reported that the inter-gene correlations in Affymetrix microarray data sets were strong and long-ranged, and the assumption of independence or weak dependence among gene expression signals which was often employed without justification was in conflict with actual data. Qui et al. (2005) indicated that applying the nonparametric empirical Bayes method in which test statistics were pooled across genes for performing the statistical inference resulted in the large variance of the number of differentially expressed genes. Qui et al. (2005) attributed this effect to strong and long-ranged inter-gene correlations. Klebanov and Yakovlev (2007) demonstrated that the inter-gene correlations provided a rich source of information rather than being a nuisance in the statistical analysis and they developed, by transforming the original gene expression sequence, a sequence of independent random variables which they referred to as a ${\delta}$-sequence. We note in this report using two cDNA microarray data sets experimented in this country that the strong and long-ranged inter-gene correlations were still valid in cDNA microarray data and also the ${\delta}$-sequence of independence could be derived from the cDNA microarray data. This note suggests that the inter-gene correlations be considered in the future analysis of the cDNA microarray data sets.

• The Korea Genome Conference
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• 2005.09a
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• pp.74-74
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• 2005

• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.1A
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• pp.99-106
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• 2004

In this Paper, the matched filter for searching initial synchronization in DSSS (direct sequence spread spectrum) receiver is studied. The matched filter with a single data flow path is described which can be presented by HDL (Hardware Description Language). In order to improve the processing time of operations for the filter, equations are arranged to represent two data flow paths and the associated hardware model is proposed. The model has an architecture based on parallelism and pipeline for fast processing, in which two data flow paths with a series of memory, multiplier and accumulator are placed in parallel. The performance of the model is analyzed and compared with the matched filter with a single data flow path.

• Journal of Institute of Control, Robotics and Systems
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• v.13 no.3
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• pp.230-234
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• 2007

Generally, huge amounts of data traffic are generated by using broadcasting method to deliver sensing data to a sink node reliably so that it makes a severe network saturation problem resulting in unreliable data transfer. In order to handle this problem, a new congestion control protocol is required for supporting reliable data transfer, minimal use of energy and network resources at the same time in wireless sensor networks. In this paper, it proposes a Protocol to guarantee both a reliable transfer in data accuracy and minimum consumption of energy waste by using Hop-by-Hop sequence number and DSbACK(Delayed and Selective ACK Buffer Condition) scheme. In addition, it proves that reliability and energy efficiency are enhanced by the proposed method with the simulation results performed on TinyOS platform which is a component based built-in OS announced by UC Berkely with the performance comparison of other existing methods.

• Journal of the Korean Institute of Intelligent Systems
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• v.21 no.6
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• pp.724-729
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• 2011

Information retrieval is a method to search the needed data by users. Generally, when a user searches some data in the large scale data set like the internet, ranking-based search is widely used because it is not easy to find the exactly needed data at once. In this paper, we propose a novel ranking-based search method based on sequence and adjacency relationship of user query by the help of TF-IDF and n-gram. As a result, it was possible to find the needed data more accurately with 73% accuracy in more than 19,000 data set.