• Journal of Microbiology
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• v.42 no.1
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• pp.56-59
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• 2004

Together with the previous reports, my computer survey revealed that several bacteria contain six copies of the type group II intron IntA. The sequence analysis of IntAs showed the high level of homology in the nucleotide sequence (91.9-99.8%). The consensus sequence, 2,270 base pair long, was derived from the nucleotide sequences of all IntA members. The size of the open reading frame intA was 502 amino acids long, that is homologous to reverse transcriptase-like proteins encoded within the group II introns. It was reported that EPEC.IntA and Sf.IntA were inserted into IS911 and IS629, respectively. The sequence of the flanking region IntA was analyzed here. The data show the insertion of EC.IntA into IS629, the insertion of EHEC.IntA into IS3, the insertion of Yp.IntA into IS904-like sequence, and the insertion of EK12.IntA into IS911. Interestingly, these IS elements nested by IntAs were the members of IS3 family elements. The sequences of the IS3 members correspond to the OrfB with the DDE motif conserved in retroviral integrases. Alignment of the flanking sequences of IntAs revealed that the flanking regions -25 to + 10 of insertion sites, that are generally believed to be required for the retrohoming, were not strongly conserved. The data presented here suggests that the retrohoming pathway of IntA seems to differ from those of other group II introns.

• Journal of Microbiology
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• v.45 no.3
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• pp.219-226
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• 2007

Insertion sequence IS1112 is a repetitive element with a relatively high number of copies in Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice (Oryza sativa L.). Three new loci of IS1112 were identified in seven Chinese strains of Xoo using a single oligonucleotide primer J3; 5'-GCTCA GGTCAGGTGGCCTGG-3' by insertion-sequence-based polymerase chain reaction (IS-PCR). Among the three new loci of IS1112, two were located in the open-reading frame region of genes fhuA and cirA, which encode TonB-dependent receptors, and the third in ISXo2, another type of insertion sequence in Xoo genome. Three variants of IS1112 were identified in those three loci based on their sequence similarities: two were identical to IS1112a and IS1112b, reported in strain PXO86 from the Philippines, while the third was a new member of IS1112, defined as IS1112d. Inserting IS1112 in gene fhuA caused three bases, GGT, to be duplicated at the target site, but inserting it in gene cirA did not cause any duplication in the target site. The diversity of IS1112 sequence and insertion loci in Xoo genome and their potential effects are discussed.

• The Plant Pathology Journal
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• v.16 no.2
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• pp.105-109
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• 2000

The Pi-b is the rice gene conferring race specific resistance to the blast fungus Magnaporthe grisea race having a corresponding avirulence gene, AVR-Pi-b. All resistant cultivars have two copies of the Pi-b gene, but susceptible cultivars have a single copy of the gene. About 1 Kbp insertion sequence was detected in the open reading frame of the Pi-b gene from the susceptible cv. Nipponbare. The nature of insertion sequence was identified as a solo long terminal repeat (LTR) of new rice Tyl-copia-like retrotransposon. LTR was widely distributed in the rice genome. Various types of different patterns of restriction fragment length polymorphism of LTR were detected in indica cultivars, whereas a single type was detected from japonica cultivars. The insertion of LTR sequence in the Pi-b gene in the susceptible cultivar suggested that retrotransposon-mediated insertional mutation might played an important role in the resistance breakdown as well as evolution of resistance genes in rice.

• The Journal of Korean Institute of Electromagnetic Engineering and Science
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• v.14 no.12
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• pp.1239-1247
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• 2003

OFDM(orthogonal frequency division multiplexing) communications system is very attractive for the high data rate transmission in the frequency selective lading channel. Since OFDM has high PAPR(peak-to-average power ratio), OFDM signal may be distorted by the nonlinear HPA(high power amplifier). In this paper, we propose the DSI(dummy sequence insertion) method for OFDM communication system. Some sub-carriers are inserted for PAPR reduction. They carry the specified dummy data sequence which are used for only PAPR reduction and do not work as side information like the conventional PTS(partial transmit sequence) or SLM(selected mapping) method. We use the complementary sequence and the combination of the correlation sequence as the dummy sequence. Flipping technique is used for the DSI method to get the effective PAPR reduction. It is important that BER of the proposed method is independent of the damage of the dummy data sequence. And DSI method has better spectral efficiency than the conventional block coding. On the other hand, threshold PAPR method is applied to cut down the processing time. However, this DSI method is not better than the conventional PTS method in the respect of the PAPR reduction performance. The DSI method includes the threshold PAPR lower than the PAPR of the OFDM signal, reduces the processing time and improves the BER performance.

• Journal of Communications and Networks
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• v.16 no.1
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• pp.92-97
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• 2014

A novel method for extracting frequency slippage signal from radar full pulse sequence is presented. For the radar full pulse sequence received by radar interception receiver, radio frequency (RF) and time of arrival (TOA) of all pulses constitute a two-dimensional information sequence. In a complex and intensive electromagnetic environment, the TOA of pulses is distributed unevenly, randomly, and in a nonstationary manner, preventing existing methods from directly analyzing such time series and effectively extracting certain signal features. This work applies Gaussian noise insertion and structure function to the TOA-RF information sequence respectively such that the equalization of time intervals and correlation processing are accomplished. The components with different frequencies in structure function series are separated using empirical mode decomposition. Additionally, a chaos detection model based on the Duffing equation is introduced to determine the useful component and extract the changing features of RF. Experimental results indicate that the proposed methodology can successfully extract the slippage signal effectively in the case that multiple radar pulse sequences overlap.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.33 no.1C
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• pp.6-11
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• 2008

From a periodic sequence, we can obtain new sequences with a longer period by r-symbol insertion to each period. In this paper we review previous results on the linear complexity of periodic sequences obtained by r-symbol insertion. We derive the distribution of the linear complexity of 1-symbol insertion sequences obtained from m-sequences over GF(p), and prove some relationship between their linear complexity and the insertion position. Then, we analyze the k-error linear complexity of the 1-symbol insertion sequences from binary m-sequences.

• Plant Breeding and Biotechnology
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• v.5 no.4
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• pp.269-281
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• 2017

With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.

• Journal of Radiation Industry
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• v.11 no.3
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• pp.145-149
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• 2017

The cel7A sequence variation was analyzed between the wild type (Lentinula edodes KACC42378) and its cellulase activity enhanced mutant LER277. LER277 was induced by using gamma ray radiation ($^{60}Co$) at the $LD_{99}$ dose (0.94 kGy). Cloning and sequencing results showed that the cel7A coding DNA sequence (CDS) of LER277 had five nucleotide substitutions ($T{\rightarrow}C$, 201, 285 and 744 nt; $A{\rightarrow}G$, 525 nt; $C{\rightarrow}T$, 540 nt) and one hexanucleotide repeat insertion (GGCACC, within 1375-1392 nt) compared to that of the wild type. The Five nucleotide substitutions did not change the deduced amino acids and the hexanucleotide insertion elongated the GT repeat in a serine/threonine/glycine-rich linker. These results suggest that the enhancement of the cellulase activity in LER277 partly stemmed from cel7A changes by which the GT repeat of the linker is elongated.

• Journal of Animal Science and Technology
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• v.63 no.4
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• pp.751-758
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• 2021

The recessive white (locus c) phenotype observed in chickens is associated with three alleles (recessive white c, albino c^a, and red-eyed white c^re) and causative mutations in the tyrosinase (TYR) gene. The recessive white mutation (c) inhibits the transcription of TYR exon 5 due to a retroviral sequence insertion in intron 4. In this study, we genotyped and sequenced the insertion in TYR intron 4 to identify the mutation causing the unusual white plumage of Yeonsan Ogye chickens, which normally have black plumage. The white chickens had a homozygous recessive white genotype that matched the sequence of the recessive white type, and the inserted sequence exhibited 98% identity with the avian leukosis virus ev-1 sequence. In comparison, brindle and normal chickens had the homozygous color genotype, and their sequences were the same as the wild-type sequence, indicating that this phenotype is derived from other mutation(s). In conclusion, white chickens have a recessive white mutation allele. Since the size of the sample used in this study was limited, further research through securing additional samples to perform validation studies is necessary. Therefore, after validation studies, a selection system for conserving the phenotypic characteristics and genetic diversity of the population could be established if additional studies to elucidate specific phenotype-related genes in Yeonsan Ogye are performed.

• The Journal of Korean Institute of Electromagnetic Engineering and Science
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• v.15 no.4
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• pp.379-386
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• 2004

OFDM(orthogonal frequency division multiplexing) communications system is very attractive for the high data rate transmissionin the frequency selective fading channel. Since OFDM has high PAPR(peak-to-average power ratio), OFDM signal may be distorted by the nonlinear HPA(high power amplifier). In this paper, we propose an improved dummy sequence scheme for reducing the PAPR in OFDM communication system. This method inserts each different dummy sequence at the predefined sub-carriers fur PAPR reduction. After IFFT, the OFDM data signal with the lowest PAPR is selected to transmit. The complementary sequence is used as dummy sequence. So, it can cut down the computation time and quantity because it dose not require the peak value optimization for finding the phase rotation factor and the transmission of the side information about the rotation factor unlike the PTS method.