• Archives of Pharmacal Research
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• v.25 no.3
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• pp.375-380
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• 2002

Cytochrome P4501A2 (CYP1A2) is a member of the cytochrome P450 family of isozymes involved in the phase I drug metabolism of vertebrates. CYP1A2 is responsible for the activation of a number of aromatic amines to mutagenic and carcinogenic forms. Thus, the level of CYP1A2, which varies among different populations, may determine an individual's susceptibility to these chemicals. We have previously reported on the importance of a cis element named PRB (protected region B) in the regulation of human Cytochrome P4501A2 (CYP1A2) gene, which appeared to act as a positive regulatory element. Closer examination of the PRB sequence (-2218 to -2187 bp) revealed a putative AP-1 binding site, TGACTAA, at -2212 bp (Chung and Bresnick, 1997). To elucidate the role of AP-1 in CYP1A2 regulation, we transiently overexpressed c-Jun and c-Fos transcription factors in human hepatoma HepG2 cells, and examined their influence on the CYP1A2 promoter activity by reporter gene assays. Cotransfection of the c-Jun and the c-Fos expression vectors increased the induced transactivation by five to six fold from the CYP1A2 promoter constructs. However, deletion of the PRB element did not affect the degree of activation by the c-Jun and the c-Fos. Therefore, it is unlikely that the c-Jun and the c-Fos activate the CYP1A2 promoter through this AP-1 consensus-like sequence in the PRB region.

• The Plant Pathology Journal
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• v.24 no.3
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• pp.289-295
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• 2008

RNA-RNA interactions and the dynamic RNA conformations are important regulators in virus replication in several RNA virus systems and may also involved in the regulation of many important virus life cycle phases, including translation, replication, assembly, and switches in these important stages. The 5' non-translated region of Potato virus X(PVX) contains multiple cis-acting elements that facilitate various viral processes. It has previously been proposed that RNA-RNA interactions between various RNA elements present in PVX RNA genome are required for PVX RNA accumulation(Hu et al., 2007; Kim and Hemenway, 1999). This model was based on the potential base-pairing between conserved sequence elements at the upstream of subgenomic RNAs(sgRNAs) and at the 5' and 3' end of RNA genome. We now provide more evidence that RNA-RNA base-pairing between elements present at the 5' end and upstream of each sgRNA is required for efficient replication of genomic and subgenomic plus-strand RNA accumulation. Site-directed mutations introduced at the 5' end of plus-strand RNA replication defective mutant(${\Delta}12$) increasing base-pairing possibility with conserved sequence elements located upstream of each sgRNAs restored genomic and subgenomic plus-strand RNA accumulation and caused symptom development in inoculated Nicotiana benthamiana plants. Serial passage of a deletion mutant(${\Delta}8$) caused more severe symptoms and restored wild type sequences and thus retained possible RNA-RNA base-pairing. Altogether, these results indicate that the RNA element located at the 5' end of PVX genome involved in RNA-RNA interactions and play a key role in high-level accumulation of plus-strand RNA in vivo.

• Animal Systematics, Evolution and Diversity
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• no.nspc3
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• pp.139-146
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• 1992

The primary sequence of the 18S rRNA gene of a crustacean Pugettia quadridens (Decapoda: Pleocyemata: Brachyura) was determined by the PCR cloning and Taq sequencing. The 18S rRNA gene of this species in 1837 bases long, and 46 bases shorter than that of another crustacean decapod Oedignathus inermis. The similarity between two species is 90.8% when the insertion and/or deletion sites were excluded. Within the molecule, the most conservative (identical) region locates at the position of 1137-1206 and it is 70 bases long. The most long consecutive nucleotide differences occur at the position between 46-55 and the second most between 399-407. The sequence variation in the primary structure of 18S rRNA gene are not evenly distributed throughout the molecule.

• Plant Biotechnology Reports
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• v.3 no.4
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• pp.309-315
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• 2009

Molecular markers developed from the flanking sequences of two cytoplasmic male sterility (CMS)-associated genes, orf456 and ${\Psi}atp6-2$, have been used for marker-assisted selection of CMS in pepper. However, in practice, the presence of orf456 and ${\Psi}atp6-2$ at substoichiometric levels even in maintainer lines hampers reliable selection of plants containing the CMS gene. In this study, we developed a novel CMS-specific molecular marker, accD-U, for reliable determination of CMS lines in pepper, and used the newly and previously developed markers to determine the cytoplasm types of pepper breeding lines and germplasms. This marker was developed from a deletion in a chloroplast-derived sequence in the mitochondrial genome of a CMS pepper line. CMS pepper lines could be unambiguously determined by presence or absence of the accD-U marker band. Application of orf456, ${\Psi}atp6-2$and accD-U to various pepper breeding lines and germplasms revealed that accD-U is the most reliable CMS selection marker. A wide distribution of orf456, but not ${\Psi}atp6-2$, in germplasms suggests that the pepper cytoplasm containing both orf456 and ${\Psi}atp6-2$ has been selected as CMS cytoplasm from cytoplasm containing only orf456. Furthermore, factors other than orf456 may be required for the regulation of male sterility in pepper.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.292-300
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• 2003

Pseudomonas fluorescens B16 is a plant glowth-prornoting rhizobacterium, which produces an antibacterial compound that is effective against plant root pathogens, such as Agrobacrerium tumefaciens and Raistonia solanacearum. We mutagenized the strain B16 with Omegon-Km and isolated six antibacterial-activity-deficient mutants. Two cosmid clones that hybridized with the mutant clones also were isolated from a genomic library of tile parent strain. Using deletion and complementation analyses, it was found that the biosynthesis genes resided in a 4.3-kb SalI-NarI fragment. When a plasmid clone carrying the fragment was introduced into P. fluorescens strain 1855.344, which does not exhibit any antibacterial activity, the transconjugants exhibited antibacterial activity, indicating that the plasmid clone carried all the genes essential for production of the antibacterial compound. DNA sequence analysis of the fragment identified four putative open reading frames (ORFs): orf1 through orf4 The deduced amino acid sequences of ORF1, ORF2, and ORF4 were similar to cystathionine gamma lyase, pyruvate formate-lyase activating enzyme, and transcriptional regulator, respectively, yet the amino acid sequence of ORF3 showed no similarities to any known proteins. It was also demonstrated that the antibacterial activity was responsible for biological control of the bacterial wilt caused by R. solanacearum.

• Journal of Microbiology and Biotechnology
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• v.31 no.7
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• pp.912-920
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• 2021

SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.

• The Korea Journal of Herbology
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• v.34 no.6
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• pp.91-97
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• 2019

Objective : To establish a reliable tool between for the distinction of original plants of Sanguisorbae Radix, we analyzed the complete chloroplast genome sequence of Sanguisorbae Radix and identified single nucleotide polymorphisms (SNPs). Materials and methods : The chloroplast genome sequence of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link obtained using next-generation sequencing technology were described and compared with those of other species to develop specific markers. Candidate genetic markers were identified to distinguish species from the chloroplast sequences of each species using Modified Phred Phrap Consed and CLC Genomics Workbench programs. Results : The structure of the chloroplast genome of each sample that had been assembled and verified was circular, and the length was about 155 kbp. Through comparative analysis of the chloroplast sequences, we found 220 nucleotides, 158 SNPs, and 62 Indel (insertion and/or deletion), to distinguish Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link. Finally, 15 specific SNP genetic markers were selected for the verification at positions. Avaliable primers for the dried herb, which is used as medicine, were used to develop the PCR amplification product of Sanguisorbae Radix to assess the applicability of PCR analysis. Conclusion : In this study, we found that Fendel-qPCR analysis based on the chloroplast DNA sequences can be an efficient tool for discrimination of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link.

• Microbiology and Biotechnology Letters
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• v.48 no.2
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• pp.158-166
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• 2020

A gene coding for the xylanase was cloned from Paenibacillus woosongensis, followed by determination of its complete nucleotide sequence. This xylanase gene, designated as xyn10A, consists of 1,446 nucleotides encoding a polypeptide of 481 amino acid residues. Based on the deduced amino acid sequence, Xyn10A was identified to be a modular enzyme composed of a catalytic domain highly homologous to the glycosyl hydrolase family 10 xylanase and a putative carbohydrate-binding module (CBM) in the C-terminus. By using DEAE-sepharose and phenyl-sepharose column chromatography, Xyn10A was purified from the cellfree extract of recombinant Escherichia coli carrying a P. woosongensis xyn10A gene. The N-terminal amino acid sequence of the purified Xyn10A was identified to exactly match the sequence immediately following the signal peptide predicted by the Signal5.0 server. The purified Xyn10A was a truncated protein of 33 kDa, suggesting the deletion of CBM in the C-terminus by intracellular hydrolysis. The purified enzyme had an optimum pH and temperature of 6.0 and 55-60℃, respectively, with the kinetic parameters V_max and K_m of 298.8 U/mg and 2.47 mg/ml, respectively, for oat spelt xylan. The enzyme was more active on arabinoxylan than on oat spelt xylan and birchood xylan with low activity for p-nitrophenyl-β-xylopyranoside. Xylanase activity was significantly inhibited by 5 mM Cu²⁺, Mn²⁺, and SDS, and was noticeably enhanced by K⁺, Ni²⁺, and Ca²⁺. The enzyme could hydrolyze xylooligosaccharides larger than xylobiose. The predominant products resulting from xylooligosaccharide hydrolysis were xylobiose and xylose.

• The Korea Journal of Herbology
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• v.24 no.3
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• pp.59-68
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• 2009

Objectives : Bupleuri Radix (Siho) is prescribed as the root of different Bupleurum species on the pharmarcopoeia in Korea and China. Moreover, other species and varieties of the genus Bupleurum have been also distributed on the herbal market as Bupleuri Radix. However, due to the morphological similarity and frequent occurrence of intermediate forms, the correct identification of this radix is very difficult. To develop a reliable method for correct identification and improving the quality standards of official Bupleuri Radix, we analyzed sequences of the ribosomal RNA gene and internal transcribed spacer (rDNA-ITS) region. Methods : PCR amplification of rDNA-ITS region was performed using ITS1 and ITS4 primer from 6 Bupleurum species and 1 variety, B. falcatum L. (Siho), an improved breed of B. falcatum L. (Samdo-Siho), B. chinense DC. (Buk-Siho), B. scorzonerifolium Willd. (Nam-Siho), B. longiadiatum Turcz. (Gae-Siho), B. euphorbiodes Nakai (Deungdae-Siho) and B. latissimum Nakai (Seom-Siho), and nucleotide sequence was determined after sub-cloning into the pGEM-Teasy vector. Authentic marker nucleotides were estimated by the analysis of ClastalW using entire rDNA-ITS sequence of three samples per species. Results : In comparative analysis of the rDNA-ITS sequences, we found specific nucleotides to distinguish Korean (B. falcatum L. and its variety) and Chinese official species (B. chinense DC. and B. scorzonerifolium Willd.) from others at positions 411 and 447, and positions 89, 101, 415 and 599, respectively. Futhermore, we also found nucleotide indels (insertion and/or deletion) and substitutions to identify each of different Bupleurum species, 2 positions for B. falcatum L. and its variety, 6 positions for B. chinense DC., 49 positions for B. scorzonerifolium Willd., 8 positions for B. euphorbioides Nakai, 7 positions for B. longiradiatum Nakai and 9 positions for B. latissimum Nakai. These sequence differences at corresponding positions are avaliable nucleotide markers to determine the botanical origins of Bupleuri Radix. Moreover, we confirmed the phylogenetic relationship of B. latissimum Nakai, a Korean endemic speices, among Bupleurum species based on the rDNA-ITS sequence. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by the providing of definitive information that can identify each plant species and distinguish it from unauthentic adulterant Bupleurum species.

• KIPS Transactions on Software and Data Engineering
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• v.11 no.3
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• pp.125-132
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• 2022

Sentence compression is a natural language processing task that generates concise sentences that preserves the important meaning of the original sentence. For grammatically appropriate sentence compression, early studies utilized human-defined linguistic rules. Furthermore, while the sequence-to-sequence models perform well on various natural language processing tasks, such as machine translation, there have been studies that utilize it for sentence compression. However, for the linguistic rule-based studies, all rules have to be defined by human, and for the sequence-to-sequence model based studies require a large amount of parallel data for model training. In order to address these challenges, Deleter, a sentence compression model that leverages a pre-trained language model BERT, is proposed. Because the Deleter utilizes perplexity based score computed over BERT to compress sentences, any linguistic rules and parallel dataset is not required for sentence compression. However, because Deleter compresses sentences only considering perplexity, it does not compress sentences by reflecting the linguistic information of the words in the sentences. Furthermore, since the dataset used for pre-learning BERT are far from compressed sentences, there is a problem that this can lad to incorrect sentence compression. In order to address these problems, this paper proposes a method to quantify the importance of linguistic information and reflect it in perplexity-based sentence scoring. Furthermore, by fine-tuning BERT with a corpus of news articles that often contain proper nouns and often omit the unnecessary modifiers, we allow BERT to measure the perplexity appropriate for sentence compression. The evaluations on the English and Korean dataset confirm that the sentence compression performance of sentence-scoring based models can be improved by utilizing the proposed method.