• Molecules and Cells
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• 제26권6호
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• pp.566-575
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• 2008

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia - northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia - northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.

• Journal of Animal Science and Technology
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• 제46권6호
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• pp.937-946
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• 2004

Duroc 품종은 돼지 사육에 있어 산육성과 육질 향상을 위해 이용되고 있다. 본 연구는 육종에 많이 이용되는 Duroc 품종의 모계 특이적인 서열의 검색과 계통유전학적 유연관계의 정립을 위하여 미토콘드리아 유전체의 전체 염기서열을 결정하고 집단 내 다형성을 조사하였다. mtDNA 전체 서열의 길이는 16,584-bp 이고, D-loop과 tRNA, rRNA 유전자 영역에서는 삽입/결실이 확인되었다. 4개의 coding gene (COⅡ, COⅢ, ND3, ND4)에서 불완전한 종결코돈을, ND4L과 ND2 유전자는 선택적 개시코돈 양상을 보였다. Duroc 집단에 대한 분석 결과 조절영역에서의 특이적인 11-bp 중복 단위가 일부 개체(15.2%)에서 발견되었고, ND2의 개시코돈과 CYTB 유전자에서도 다형현상을 보였다. 각각의 유전자 영역에서의 다형성은 서로 연관되어 있었고, 그 결과 Duroc 집단은 크게 두 가지 haplotype으로 구분되었다. 계통수에서 Duroc mtDNA 서열은 유럽계열 cluster에 위치하였으나, haplotype 분석과 기존에 연구결과들을 종합해 보면 Duroc 품종은 여러 모계선조 집단에서 기원한 것으로 보이며, 유럽과 아시아 계열 모두가 품종 형성에 이용된 것으로 사료된다된 것으로 사료된다.

• 대한구강악안면병리학회지
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• 제41권3호
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• pp.121-129
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• 2017

Coffee (Coffea spp.) is one of the most important agricultural commodities, being widely consumed in the world. Various beneficial health effects of coffee have been extensively investigated, but data on habitual coffee consumption and its bio-physiological effect have not been clearly explained as well as it is not proved the cause and effect between drinking coffee and its bio-physiological reactions. We made the dialyzed coffee extract (DCE), which is absorbable through gastrointestinal tract, in order to elucidate the cellular effect of whole small coffee molecules. RAW 264.7 cells, a murine macrophage lineage, were directly treated with DCE, i.e., DCE-2.5 (equivalent to 2.5 cups of coffee a day), DCE-5, and DCE-10, for 12 hours, and their protein extracts were examined by immunoprecipitation high performance liquid chromatography (IP-HPLC). RAW 264.7 cells differently expressed the inflammation-related proteins depending on the doses of DCE. RAW 264.7 cells treated with DCE showed marked increase of cathepsin C, cathepsin G, CD20, CD28, CD31, CD68, indicating the activation of innate immunity. Particularly, the macrophage biomarkers, cathepsin G, cathepsin C, CD31, and CD68 were markedly increased after DCE-5 and DCE-10 treatments, and the lymphocyte biomarkers, CD20 and CD28 were consistently increased and became marked after DCE-10 treatment. On the other hand, RAW 264.7 cells treated with DCE showed consistent increase of IL-10, an anti-inflammatory factor, but gradual decreases of different pro-inflammatory proteins including $TNF{\alpha}$, COX-2, lysozyme, MMP-2, and MMP-3. In particular, the cellular signaling of inflammation was gradually mitigated by the reduction of $TNF{\alpha}$, COX-2, IL-12, and M-CSF, and also the matrix inflammatory reaction was reduced by marked deceases of MMP-2, MMP-3, and lysozyme. These anti-inflammatory expressions were consistently found until DCE-10 treatment. Therefore, it is presumed that DCE may have dynamic effects of innate immunity activation and pro-inflammation suppression on RAW264.7 cells simultaneously. These effects were consistently found in the highest dose of coffee, DCE-10 (equivalent to 10 cups of coffee a day in man), that might imply the small coffee molecules were accumulated in RAW 264.7 cells after DCE-10 treatment and produce synergistic cytokine effects for innate immunity activation and anti-inflammatory reaction concurrently.

• Journal of Veterinary Science
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• 제24권4호
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• pp.51.1-51.17
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• 2023

Background: To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants. Objective: This study aims to investigate the putative major amino acid substitutions for the variants in GI-19. Methods: The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3). Results: Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1. Conclusions: Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2003년도 가을 학술발표논문집 Vol.30 No.2 (3)
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• pp.49-51
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• 2003

Developers of network games have used several prediction techniques for hiding transmission delay to support the real­time requirement of network games. Nowadays many researches that are related with network game are in progress to solve delay problems more radically, such as to propose new routers architecture and transport protocols suitable to characteristics of network game traffic. So for these advanced researches the tasks to grasp the traffic characteristics of a network game are needed. In this paper we aimed to capture the traffic of MMORPG and present the statistical analysis of measured data. The measurement and the analysis were accomplished with the server of 'Lineage' that regarded as the most successful MMORPG. Next, we have implemented a traffic generator that reflects the characteristics of MMORPG and shown that the trace generated by MMORPG traffic generator had identical characteristics with actual traffic using statistical testing method. We expect that this traffic generator can be used in many researches related with a network game.

• Fisheries and Aquatic Sciences
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• 제15권4호
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• pp.317-324
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• 2012

We characterized the cytoskeletal beta-actin (${\beta}$-ACT) gene (actb) and its 5'-upstream regulatory region in the Javanese ricefish Oryzias javanicus. The gene and protein structures were deduced from amino acid sequences of the actb gene and conserved in the teleost lineage. The O. javanicus actb gene has common transcription factor binding motifs in its regulatory region found in teleostean orthologues. Following quantitative reverse transcription-PCR, actb gene transcripts were detected in all tissues examined; however, the basal expression levels were different. During early development, O. javanicus actb mRNA levels showed a gradual increase and peaked between late somitogenesis and the heartbeat stage. Microinjection of O. javanicus embryos with the actb gene promoter-driven red fluorescent protein (RFP) gene reporter vector showed a ubiquitous distribution of RFP signals, although most exhibited a mosaic pattern of transgene expression. A small number of microinjected embryos displayed a wide distribution of RFP signals over their entire body, which resembled the expression pattern of endogenous actb. Data from this study provide a basis to develop a transgenic system with ubiquitous expression of foreign genes in O. javanicus.

• Fisheries and Aquatic Sciences
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• 제15권4호
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• pp.325-335
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• 2012

The present study characterized the fast skeletal myosin light chain-2 gene (mlc2f) in the euryhaline Javanese ricefish (Oryzias javanicus: Beloniformes). Coding nucleotide and deduced amino acid sequences of Javanese ricefish mlc2f were well conserved in the vertebrate lineage. Javanese ricefish mlc2f showed a typical seven-exon structure, and its promoter exhibited transcription factor binding motifs common to most muscle-specific genes. However, Javanese ricefish mlc2f also displayed tandem duplications of intronic sequences in both intron 1 and intron 3. Based on quantitative reverse transcription-polymerase chain reaction, the mlc2f transcripts were highly predominant in skeletal muscles of adults and were differentially modulated during embryonic development. Microinjection of the mlc2f promoter-driven red fluorescent protein (RFP) reporter construct successfully exhibited heterologous expression of the fluorescent reporter, primarily in muscular areas of hatchlings, although the distribution pattern of RFP signals was not uniform due to the mosaic nature of the introduced transgene. Data from this study indicate that the Javanese ricefish mlc2f gene has undergone "intra-intronic" duplication events in a species-specific manner and that the mlc2f regulator may also be useful in heterologous expression assays of the skeletal muscles of this species.

• Molecules and Cells
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• 제37권9호
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• pp.685-690
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• 2014

Osteoclasts are large polykaryons that have the unique capacity to degrade bone and are generated by the differentiation of myeloid lineage progenitors. To identify the genes involved in osteoclast development, we performed microarray analysis, and we found that carboxypeptidase E (CPE), a prohormone processing enzyme, was highly upregulated in osteoclasts compared with their precursors, bone marrow-derived macrophages (BMMs). Here, we demonstrate a novel role for CPE in receptor activator of NF-${\kappa}B$ ligand (RANKL)-induced osteoclast differentiation. The overexpression of CPE in BMMs increases the formation of tartrate-resistant acid phosphatase (TRAP)-positive multinuclear osteoclasts and the expression of c-Fos and nuclear factor of activated T cells c1 (NFATc1), which are key regulators in osteoclastogenesis. Furthermore, employing CPE knockout mice, we show that CPE deficiency attenuates osteoclast formation. Together, our data suggest that CPE might be an important modulator of RANKL-induced osteoclast differentiation.

• Weed & Turfgrass Science
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• 제3권3호
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• pp.183-189
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• 2014

The genus Echinochloa (L.) P. Beauv. comprised of approximately 30-40 species in the tropical and warm temperate regions of the world, including numerous interspecific and intraspecific types which make the genus difficult to identify. As an attempt to identify the species within the genus easier, the taxonomy of the genus Echinochloa, Poaceae in Korea was reviewed on the basis of sequencing data derived from nuclear ribosomal DNA internal transcribed spacer (ITS) and external transcribe spacer and chloroplast DNA trnL intron, trnL-F intergenic spacer and matK regions using a total of 46 accessions representing all the species in Korea. The results of maximum parsimony found separate lineage comprised of E. colona and E. frumentaceae which are not Korean species, but no resolution within Korean Echinochloa species, supporting the suggestion of Yamaguchi group that E. crus-galli, E. oryzoides, and E. esculenta should be considered to belong to the same species. However, the relationship between these three species and the other species, i.e. E. oryzicola should be better understood with more detail studies.

• ETRI Journal
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• 제41권3호
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• pp.358-370
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• 2019

The main aim of this study is to select the optimal set of genes from microarray cancer datasets that contribute to the prediction of specific cancer types. This study proposes the enhancement of the feature selection filter algorithm based on Joe's normalized mutual information and its use for gene selection. The proposed algorithm is implemented and evaluated on seven benchmark microarray cancer datasets, namely, central nervous system, leukemia (binary), leukemia (3 class), leukemia (4 class), lymphoma, mixed lineage leukemia, and small round blue cell tumor, using five well-known classifiers, including the naive Bayes, radial basis function network, instance-based classifier, decision-based table, and decision tree. An average increase in the prediction accuracy of 5.1% is observed on all seven datasets averaged over all five classifiers. The average reduction in training time is 2.86 seconds. The performance of the proposed method is also compared with those of three other popular mutual information-based feature selection filters, namely, information gain, gain ratio, and symmetric uncertainty. The results are impressive when all five classifiers are used on all the datasets.