• Journal of Veterinary Science
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• 제22권6호
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• pp.66.1-66.9
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• 2021

Background: Maedi/Visna virus (MVV) is a contagious viral pathogen that causes considerable economic losses to the sheep industry worldwide. Objectives: In China, MVV has been detected in several regions, but its molecular characteristics and genetic variations were not thoroughly investigated. Methods: Therefore, in this study, we conducted next-generation sequencing on an MVV strain obtained from northwest China to reveal its genetic evolution via phylogenetic analysis. Results: A MVV strain obtained from Inner Mongolia (NM) of China was identified. Sequence analysis indicated that its whole-genome length is 9193 bp. Homology comparison of nucleotides between the NM strain and reference strains showed that the sequence homology of gag and env were 77.1%-86.8% and 67.7%-75.5%, respectively. Phylogenetic analysis revealed that the NM strain was closely related to the reference strains isolated from America, which belong to the A2 type. Notably, there were 5 amino acid insertions in variable region 4 and a highly variable motif at the C-terminal of the surface glycoprotein (SU5). Conclusions: The present study is the first to show the whole-genome sequence of an MVV obtained from China. The detailed analyses provide essential information for understanding the genetic characteristics of MVV, and the results enrich the MVV library.

• 한국균학회지
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• 제25권1호통권80호
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• pp.46-67
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• 1997

1985년부터 1993년까지 장원도 일대에서 채집한 20균주와 외부에서 분양 받은 6균주를 대상으로 교배실험, PCR-RFLP 분석, 그리고 RAPD분석을 통해 상호 유연 관계를 알고자 하였다. 교배실험에서는 A. gallica 6균주, A. ostoyae 5균주, A. tabescens 2균주만이 친화성을 나타내었다. A8(KNU-250)균주는 A. gallica와 A. ostoyae에 모두 친화성을 나타내어 배양적 특징과 유사한 결과가 나타났다. rDNA의 IGS영역의 PCR-RFLP분석에서 A. mellea와 A. ostoyae 각 균주들 간의 유사도는 1.000으로 100%의 상동성을 보여주었다. A. tabescens는 $0.919{\sim}0.974$로 높은 유사성을 나타냈다. A. gallica는 $0.619{\sim}1.000$의 유사도로 나타났다. A19와 A22균주는 고립된 한 집단으로 나타났으며 유사도는 1.000으로 100% 상동성을 보였고, 다른 집단과의 유사도가 $0.051{\sim}0.108$로 10% 미만의 상동성을 나타내고 있다. RAPD분석을 통한 A. mellea의 유사도는 $0.983{\sim}1.000$으로 상동성이 높게 나타났으며, A. ostoyae도 $0.994{\sim}1.000$으로 높은 상동성을 보여 주었다. A. tabescens의 균주간의 유사도는 $0.594{\sim}0.953$으로 나타났으며, A. gallica는 $0.280{\sim}0.733$의 유사도를 나타내 균주간의 변이가 나타난 것으로 생각된다. 특히, A19, A22균주가 다른 집단과 거리가 먼 한 집단으로 나타났는데 그들 간의 유사도는 0.921로 92%의 상동성을 보였고, 다른 4개 집단과의 유사도가 $0.012{\sim}0.069$로 7% 미만의 상동성을 나타내고 있다. 본 실험에서 분류된 Armillaria속균은 5종으로 4종은 각각 이미 알려진 종으로 A. mellea, A. ostoyae, A. tabescens, A. gallica로 동정되었고 남은 1종은 미기록종이라고 생각된다.

• 대한기계학회논문집A
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• 제31권10호
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• pp.999-1008
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• 2007

The spacer grid set is a component in the nuclear fuel assembly. The set supports the fuel rods safely. Therefore, the spacer grid set should have sufficient strength for the external impact forces such as earthquake. The fretting wear occurs between the spring of the fuel rod and the spacer grid due to flow-induced vibration. Conceptual design of the spacer grid set is performed based on the Independence Axiom of axiomatic design. Two functional requirements are defined for the impact load and the fretting wear, and corresponding design parameters are selected. The overall flow of design is defined according to the application of axiomatic design. Design for the impact load is carried out by using nonlinear dynamic analysis to determine the length of the dimple. Topology optimization is carried out to determine a new configuration of the spring. The fretting wear is reduced by shape optimization using the homology theory. The deformation of a structure is called homologous if a given geometrical relationship holds before, during, and after the deformation. In the design to reduce the fretting wear, the deformed shape of the spring should be the same as that of the fuel rod. This condition is transformed to a function and considered as a constraint in the shape optimization process. The fretting wear is expected to be reduced due to the homology constraint. The objective function is minimizing the maximum stress to allow a slight plastic deformation. Shape optimization results are confirmed through nonlinear static analysis.

• 한국인터넷방송통신학회논문지
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• 제16권1호
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• pp.291-299
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• 2016

본 논문에서는 임의의 주기적인 현상이나 특성은 위상구조와 밀접한 관련이 있음을 추론하고 이를 실험적으로 확인한다. 실험대상으로 주기적 특성이 있는 다양한 악기음을 선택하여 이를 유클리드 공간에 임베딩하고 이로부터 호몰로지 군을 계산하여 위상특성을 분석한다. 이를 위하여, 파형신호에서 추출한 패치모음을 패치 그래프로 구성한 다음, 대표적인 다양체 학습 방식인 통근시간 임베딩 기법을 이용하여 기하구조로 변환한다. 스펙트럼이 시간에 따라 가변적인 파형신호를 통근시간 임베딩할 때, 그에 따라 생성되는 기하구조는 변화하지만 그 신호 고유의 내재된 위상구조는 거의 변하지 않는다. 본 논문에서는 임베딩 데이터의 일부를 표본화하여 단순 복합체를 구성한 다음 이로부터 호몰로지를 계산하여 임베딩 기하구조의 위상특성을 분석하고, 이의 활용방안을 논의한다.

• 한국축산식품학회지
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• 제40권5호
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• pp.758-771
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• 2020

This study was to investigate the prevalence and characteristics of antimicrobial-resistant Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) from 4,264 retail meat samples including beef, pork, and chicken in Korea between 2013 and 2018. A broth microdilution antimicrobial susceptibility testing was performed for S. aureus. Molecular typing by multilocus sequence typing (MLST), spa typing, and pulsed-field gel electrophoresis (PFGE), was performed on mecA-positive S. aureus strain. S. aureus was isolated at a rate of 18.2% (777/4,264), of which MRSA comprised 0.7% (29 strains). MLST analysis showed that 11 out of the 29 MRSA isolates were predominantly sequence type (ST) 398 (37.9%). In addition, ST72, ST692, ST188, ST9, and ST630 were identified in the MRSA isolates. The spa typing results were classified into 11 types and showed a high correlation with MLST. The antimicrobial resistance assays revealed that MRSA showed 100% resistance to cefoxitin and penicillin. In addition, resistance to tetracycline (62.1%), clindamycin (55.2%), and erythromycin (55.2%) was relatively high; 27 of the 29 MRSA isolates exhibited multidrug resistance. PFGE analysis of the 18 strains excluding the 11 ST398 strains exhibited a maximum of 100% homology and a minimum of 64.0% homology. Among these, three pairs of isolates showed 100% homology in PFGE; these results were consistent with the MLST and spa typing results. Identification of MRSA at the final consumption stage has potential risks, suggesting that continuous monitoring of retail meat products is required.

• 한국동물위생학회지
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• 제32권1호
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• pp.1-10
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• 2009

In order to obtain the genetic information of the Korean isolates of porcine circovirus 2 (PCV2), complete genomes of five isolates from Korean PCVD weaned pigs with wasting syndromes were sequenced and compared with those of other published PCV2 isolates. Of the five PCV2 isolates, four (1767 nucleotides) were classified into PCV2b, and one (1,768 nucleotides) was PCV2a. Moreover, it appeared that PCV2b is now the dominant genotype circulating in Korea herds. Total complete genomes of four PCV2b isolates shared $99.1{\sim}99.4%$ nucleotide sequence homology each other, and were only $95.4{\sim}96.2%$ similar to one PCV2a isolate. ORF2 genome of four PCV2b isolates shared over 99% nucleotide sequence and deduced amino acid sequence identity to each other. Nevertheless, those were much divergent with the PCV2a isolate of this study and ranged from $92.3{\sim}92.7%$ nucleotide homology and $91.9{\sim}92.3%$ deduced amino acid sequence homology, respectively. The amino acid sequence alignments of the putative capsid protein identified three major regions of amino acid heterogeneity at residues $59{\sim}91$, $121{\sim}136$ and $190{\sim}210$. Two of those correspond with dominant immunoreactive areas. Phylogenetic analysis based on the complete genome of PCV2 isolates showed that four PCV2b isolates of this study existed the closest relationship with European strains (Netherland, UK and France). One PCV2a isolate was closely related to Japan and North America strains.

• 한국양식학회:학술대회논문집
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• 한국양식학회 2003년도 추계학술발표대회 논문요약집
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• pp.43-43
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• 2003

EST analysis was performed to identify stress-responsive and immune-related genes from rock bream (Oplegnathus fasciatus). cDNA libraries were constructed with liver and randomly chosen 624 clones were subjected to automated sequence analysis. Of 624 clones sequenced in total, approximately 15% of ESTs was novel sequences (no match to GenBank) or sequences with high homology to hypothetical/unknown genes. The bioinforamtic sequence analysis including functional clustering, homology grouping, contig assembly with electronic northern and organism matches were carried out. Several potential stress-responsive biomarker and/or immune-related genes were identified in all the tissues examined. It included lectins, ferritins, CP450, proteinase, proteinase inhibitors, anti-oxidant enzymes, various heat-shock proteins, warm temperature acclimation protein, complements, methyltransferase, zinc finger proteins, lysozymes, macrophage maturation associated protein, and others. This information will offer new possibilities as fundamental baseline data for understanding and addressing their molecular mechanism involved in host defense and immune systems of this species.

• Journal of Microbiology and Biotechnology
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• 제19권2호
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• pp.121-127
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• 2009

Sequencing analysis of a 5-kb DNA fragment from Streptomyces venezuelae ATCC 15439 revealed the presence of one 3.1-kb open reading frame(ORF), designated as afsR-sv. The deduced product of afsR-sv(1,056 aa) was found to have high homology with the global regulatory protein AfsR. Homology-based analysis showed that aftR-sv represents a transcriptional activator belonging to the Streptomyces antibiotic regulatory protein(SARP) family that includes an N-terminal SARP domain containing a bacterial transcriptional activation domain(BTAD), an NB-ARC domain, and a C-terminal tetratricopeptide repeat domain. Gene expression analysis by reverse transcriptase PCR(RT-PCR) demonstrated the activation of transcription of genes belonging to pikromycin production, when aftR-sv was overexpressed in S. venezuelae. Heterologous expression of the aftR-sv in different Streptomyces strains resulted in increased production of the respective antibiotics, suggesting that afsR-sv is a positive regulator of antibiotics biosynthesis.

• International Journal of Industrial Entomology and Biomaterials
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• 제10권1호
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• pp.25-33
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• 2005

Recently a cDNA clone of apoLp-III from Hyphantria cunea was isolated and subjected to computational analysis to compare with other available sequences. Multiple sequence alignments were carried out using the amino acid sequences of apoLp-III from six insects. It was found that the H. cunea apoLp-III has relatively high sequence identities to Spodoptera litura ($69.5\%$), Manduca sexta ($66.8\%$), Galleria mellonella ($65.1\%$), Bombyx mori N4 ($54.3\%$) but less identity to Locusta migratoria ($18.3\%$). The amino acid composition was compared with other insects using EXPASY tools; it shows that alanine (Ala), glutamine (Gln), leucine (Leu) and lysine (Lys) are the major amino acid components of apoLp-III in H. cunea as well as other lepidopterans. Homology modeling performed using PSI-BLAST (PDB template M. sexta) reveals that the apoLp-III molecules consist of five, long amphipathic alpha helical bundles with short loops connecting the helices and shows homology with other insects. Phylogenetic analysis shows that the orthopteran apoLp-III represented by locust was most distantly related to the lepidopteran insects.

• 한국동물위생학회지
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• 제47권1호
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• pp.9-17
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• 2024

Porcine epidemic diarrhea (PED) is a highly contagious enteric viral disease of pigs with watery diarrhea in piglets, which ultimately results in huge economic losses in the swine industry. The spike (S) protein plays an important role in viral pathogenicity, tissue tropism, infection, dissemination and the trypsin-dependent proliferation of the PED virus (PEDV). In the present study, we determined the full-length spike (S) gene sequences of twenty PEDV field strains detected in Jeonbuk province in 2022. Phylogenetic analysis showed that the twenty PEDV field strains were classified into G2b group and shared 98.6~100% of nucleotide homology and 97.4~100% of amino acid homology with each other. Mutations of amino acid sequences on the neutralizing epitope of S protein were observed in the twenty field strains compared to the previous vaccine strain SM-98-1 (G1a group). Therefore, these amino acid mutations in the PEDV S protein may result in a new genotype of the virus and highly pathogenic virus, so continuous monitoring is required.