• Molecules and Cells
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• 제42권2호
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• pp.123-134
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• 2019

Lysophosphatidic acid (LPA) is an endogenous lysophospholipid with signaling properties outside of the cell and it signals through specific G protein-coupled receptors, known as $LPA_{1-6}$. For one of its receptors, $LPA_1$ (gene name Lpar1), details on the cis-acting elements for transcriptional control have not been defined. Using 5'RACE analysis, we report the identification of an alternative transcription start site of mouse Lpar1 and characterize approximately 3,500 bp of non-coding flanking sequence 5' of mouse Lpar1 gene for promoter activity. Transient transfection of cells derived from mouse neocortical neuroblasts with constructs from the 5' regions of mouse Lpar1 gene revealed the region between -248 to +225 serving as the basal promoter for Lpar1. This region also lacks a TATA box. For the region between -761 to -248, a negative regulatory element affected the basal expression of Lpar1. This region has three E-box sequences and mutagenesis of these E-boxes, followed by transient expression, demonstrated that two of the E-boxes act as negative modulators of Lpar1. One of these E-box sequences bound the HeLa E-box binding protein (HEB), and modulation of HEB levels in the transfected cells regulated the transcription of the reporter gene. Based on our data, we propose that HEB may be required for a proper regulation of Lpar1 expression in the embryonic neocortical neuroblast cells and to affect its function in both normal brain development and disease settings.

• 한국유기농업학회지
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• 제26권4호
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• pp.745-757
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• 2018

We analyzed the nuclear ribosomal internal transcribed spacer (ITS) sequence of common buckwheat, Fagopyrum esculentum and tartary buckwheat, F. tataricum. The diversity of the nucleotides and haplotypes, Tajima's D, and Fu's Fs was analyzed and compared among the varieties of common buckwheat and tartary buckwheat. The diversity of nucleotides and haplotypes indicated that the buckwheat populations had undergone rapid population expansion but D and Fs did not support their expansion statistically. The phylogenetic analysis of ITS sequences did not clearly establish the phylogenetic relationships between the varieties of common buckwheat. The In/Del sequence of ITS-1 region could, therefore, be used as a DNA marker to distinguish raw or manufactured products derived from common buckwheat and tartary buckwheat.

• 한국균학회지
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• 제48권3호
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• pp.313-323
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• 2020

Hypsizygus marmoreus의 형태적 특성과 유전적 유연관계를 조사하기 위해 한국 및 다른 국가에서 111개의 균주를 수집하였다. RAPD (Random amplified polymorphic DNA) 및 ITS rDNA 염기서열 분석을 이용하여 H. marmoreus 균주간의 유전적관계를 확인하였다. URP-PCR을 이용한 RAPD 분석결과, H. marmoreus의 모든 균주는 크게 3개의 그룹으로 분류되었으나, 90% 이상의 높은 유사성을 보였다. 또한 형태적 및 지리적으로 분류가 가능하였으나 갈색 균주 및 흰색 균주는 구별되지 않았다. 따라서 형태적, 지리적 차이가 있는 16개의 균주를 선별하여, 640 bp 길이의 ITS 염기서열을 정렬하고 비교하였다. ITS 염기서열의 유사성은 공시균주와 GenBank의 H. marmoreus 균주 사이에서 94.8-99.1 %였다. 수집지역과 형태에 차이가 있었지만, 실험에 사용된 공시균주는 모두 H. marmoreus에 가까운 유연관계를 형성하였다.

• 한국통신학회논문지
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• 제24권9B호
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• pp.1755-1766
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• 1999

A region-based video codec based on the H.263+ standard is examined and its associated novel rate control scheme is proposed in this work. The region-based coding scheme is a hybrid method that consists of the traditional block DCT coding and the object-based coding. Basically, we adopt H.263+ as the platform, and develop a fast macroblock-based segmentation method to implement the region-based video codec. The proposed rate control solution includes rate control in three levels: encoding frame selection, frame-layer rate control and macroblock-layer rate control. The goal is to enhance the visual quality of decoded frames at low bit rates. The efficiency of proposed rate control scheme applied to the region-based video codes is demonstrated via several typical test sequences.

• Fisheries and Aquatic Sciences
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• 제12권2호
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• pp.90-97
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• 2009

The cytoskeletal $\beta$-actin gene and its 5'-upstream region were isolated and characterized in the rockbream (Oplegnathus fasciatus). Complementary DNA of the rockbream $\beta$-actin represented a 1,125 bp of an open reading frame encoding 375 amino acids, and the rockbream $\beta$-actin cDNA and deduced amino acid sequences were highly homologous to those of other vertebrate orthologs. At the genomic level, the $\beta$-actin gene also exhibited an organization typical of vertebrate cytoskeletal actin genes (2,159 bp composed of five translated exons interrupted by four introns) with a conserved GT/AG exon-intron splicing rule. The putative non-translated exon predicted in the rockbream $\beta$-actin gene was much more homologous with those of teleostean $\beta$-actin genes than those of mammals. The 5'-upstream regulatory region isolated by genome walking displayed conserved and essential elements such as TATA, CArG and CAAT boxes in its proximal part, while several other immune- or stress-related motifs such as those for NF-kappa B, USF, HNF, AP-1 and C/EBP were in the distal part. Semi-quantitative RT-PCR assay results demonstrated that the rockbream $\beta$-actin transcripts were ubiquitously but different-tially expressed across the tissues of juveniles.

• 대한본초학회지
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• 제24권3호
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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.

• Mycobiology
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• 제38권3호
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• pp.166-170
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• 2010

Gummy stem blight is a major foliar disease of muskmelon (Cucumis melo L.). In this study, morphological characteristics and rDNA internal transcribed spacer (ITS) sequences were analyzed to identify the causal organism of this disease. Morphological examination of the Jeonbuk isolate revealed that the percentage of monoseptal conidia ranged from 0% to 10%, and the average length $\times$ width of the conidia was 70 ($\pm$ 0.96) $\times$ 32.0 ($\pm$ 0.15) ${\mu}m$ on potato dextrose agar. The BLAST analysis showed nucleotide gaps of 1/494, 2/492, and 1/478 with identities of 485/492 (98%), 492/494 (99%), 491/494 (99%), and 476/478 (99%). The similarity in sequence identity between the rDNA ITS region of the Jeonbuk isolate and other Didymella bryoniae from BLAST searches of GenBank was 100% and was 95.0% within the group. Nucleotide sequences of the rDNA ITS region from pure culture ranged from 98.2% to 99.8%. Phylogenetic analysis with related species of D. bryoniae revealed that D. bryoniae is a monophyletic group distinguishable from other Didymella spp., including Ascochyta pinodes, Mycosphaerella pinodes, M. zeae-maydis, D. pinodes, D. applanata, D. exigua, D. rabiei, D. lentis, D. fabae, and D. vitalbina. Phylogenetic analysis, based on rDNA ITS sequence, clearly distinguished D. bryoniae and Didymella spp. from the 10 other species studied. This study identified the Jeonbuk isolate to be D. bryoniae.

• Journal of Microbiology
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• 제44권6호
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• pp.607-616
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• 2006

Molecular characterization of ten marine cyanobacterial isolates belonging to the order Oscillatoriales was carried out using the phycocyanin locus (cpcBA-IGS) and the 16S-23S internally transcribed spacer region. DNA sequences from the phycocyanin operon discriminated ten genotypes, which corresponded to seven morphotypes identified by traditional microscopic analysis. The cpcB coding region revealed 17% nucleotide variation, while cpcA exhibited 29% variation across the studied species. Phylogenetic analyses support the conclusion that the Phormidium and Leptolyngbya genera are not monophyletic. The nucleotide variations were heterogeneously distributed with no or minimal informative nucleotides. Our results suggest that the discriminatory power of the phycocyanin region varies across the cyanobacterial species and strains. The DNA sequence analysis of the 16S-23S internally transcribed spacer region also supports the polyphyletic nature of the studied oscillatorian cyanobacteria. This study demonstrated that morphologically very similar strains might differ genotypically. Thus, molecular approaches comprising different gene regions in combination with morphological criteria may provide better taxonomical resolution of the order Oscillatoriales.

• Journal of Microbiology and Biotechnology
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• 제14권4호
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• pp.816-821
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• 2004

A reliable molecular phylogenetic method to identify Hericium erinaceum, the most industrially valuable species in the Hericium genus, was established. Sequencing and phylogenetic analyses of the PCR-amplified ITS and 5.8S rDNA from Hericium fungi, including 6 species and 23 isolates, showed that variation in nucleotide sequences and size exists in both ITS1 and ITS2 regions, but not in the 5.8S region. These two ITS regions provided different levels of information on the relationship of H. erinaceum to other Hericium species. Based on the ITS1 sequence, both the parsimony and neighbor joining trees clearly distinguished Asian H. erinaceum isolates from other Hericium species and isolates. The intraspecific divergence of the ITS2 region was suitable to dissect the Asian H. erinaceum isolates into a few groups.

• 한국버섯학회지
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• 제10권3호
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• pp.143-149
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• 2012

수집한 83개의 뽕나무버섯속 균주의 rDNA의 ITS 영역을 증폭하여 염기서열을 분석한 결과 수집한 균주목록과 종이 다르게 동정된 균주가 52%였으며. 같은 종으로 분류한 균주들 간에도 균사 및 균사체의 배양 특성에 많은 차이를 보였다. 수집 균주간의 유전적인 유연관계 분석 결과 A. tabescens, A. mellea, A. novae-zelandia, A. gallica, A. ostoyae 등으로 분류되었고, A. gallica, A, cepistipes, A, gemina는 매우 가까운 유연관계를 보여 ITS 유전자 수준에서 종을 동정하기는 어려웠다. ASI10104 등 12균주는 A. gallica, A, cepistipes, A, gemina와 매우 가까운 유연관계를 보였으며, ASI10017과 ASI10114는 A. sinapina, ASI10045는 A. borealis, ASI10002와 ASI10025는 A. ostoyae와 같은 그룹으로 분류되었다. 따라서 뽕나무버섯속 균주에 대한 보다 정확한 동정을 위해서는 보다 많은 종류의 유전적인 분석이 필요할 것으로 판단된다.