• The Plant Pathology Journal
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• 제33권5호
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• pp.508-513
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• 2017

The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semiquantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology. Possible differences in the intra-isolate variability and polymorphism between viral populations propagating in these tomato genotypes were evaluated by analysis of the capsid protein (CP) encoding region. Irrespective of genotype infected, the intra-isolate haplotype structure showed the presence of the same highly dominant CP sequence and the low level of population diversity (0.08-0.19%). Our results suggest that ToMV CP encoding sequence is relatively stable in the viral population during its replication in vivo and provides further demonstration that RNA viruses may show high sequence stability, probably as a result of purifying selection.

• Animal Systematics, Evolution and Diversity
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• 제28권3호
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• pp.215-219
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• 2012

To examine genetic divergences of two endemic Sorex caecutiens subspecies from Korea (S. c. hallamontanus in Korean Jeju Island and S. c. annexus in the mainland Korean Peninsula), we obtained partial cytochrome oxidase I (COI) sequences (429 bp) and complete cytochrome b sequences (1,140 bp) from the two Korean subspecies, and we compared these sequences to the corresponding sequences of S. caecutiens, obtained from GenBank. We found that Jeju S. c. hallamontanus is one of three clades within S. caecutiens, with an average Jukes-Cantor distance of 1.57% in the COI sequences and the distance of 2.07% and 11 fixed site differences in the cytochrome b sequences, indicating that Jeju S. c. hallamontanus is one endemic subspecies with concordant genetic distinctness, although further analyses with nuclear DNA sequences are necessary to confirm these findings. However, S. c. annexus from the mainland Korean Peninsula was not divergent from S. c. macropygmaeus from northeastern China and adjacent Russia, indicating that S. c. annexus from the mainland Korean Peninsula is another endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of S. c. annexus.

• International Journal of Industrial Entomology and Biomaterials
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• 제7권2호
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• pp.181-189
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• 2003

We describe here the complete nucleotide sequence and the exon-intron structure of the luciferase gene of the firefly, Pyrocoelia rufa. The luciferase gene of the P. rufa firefly consisted of six introns and seven exons coding for 548 amino acid residues. From the translational start site to the end of last exon, however, the genomic DNA length of the P. rufa luciferase gene from the Korean and Chinese samples spans 1,968 bp and 1983 bp, respectively, and 3 amino acid residues were different to each other. Additionally, we also analyzed mitochondrial cytochrome oxidase I(COI) gene of the Chinese P. rufa fireflies. Analysis of DNA sequences from the mitochondrial COI protein-coding gene revealed 4 mitochondrial DNA sequence-based haplotypes with a maximum divergence of 0.7％. With the 20 P. rufa haplotypes found in Korea, phylogenetic analyses using PAUP and PHYLIP subdivided the P. rufa into three clades, termed clades A and B for the Korean sample, and clade C for the Chinese sample.

• The Plant Pathology Journal
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• 제30권2호
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• pp.183-187
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• 2014

Lettuce mosaic virus (LMV) causes disease of plants in the family Asteraceae, especially lettuce crops. LMV isolates have previously been clustered in three main groups, LMV-Yar, LMV-Greek and LMV-RoW. The first two groups, LMV-Yar and LMV-Greek, have similar characteristics such as no seed-borne transmission and non-resistance-breaking. The latter one, LMV-RoW, comprising a large percentage of the LMV isolates contains two large subgroups, LMV-Common and LMV-Most. To date, however, no Korean LMV isolate has been classified and characterized. In this study, LMV-Muju, the Korean LMV isolate, was isolated from lettuce showing pale green and mottle symptoms, and its complete genome sequence was determined. Classification method of LMV isolates based on nucleotide sequence divergence of the NIb-CP junction showed that LMV-Muju was categorized as LMV-Common. LMV-Muju was more similar to LMV-O (LMV-Common subgroup) than to LMV-E (LMV-RoW group but not LMV-Common subgroup) even in the amino acid domains of HC-Pro associated with pathogenicity, and in the CI and VPg regions related to ability to overcome resistance. Taken together, LMV-Muju belongs to the LMV-Common subgroup, and is expected to be a seed-borne, non-resistance-breaking isolate. According to our analysis, all other LMV isolates not previously assigned to a subgroup were also included in the LMV-RoW group.

• Animal cells and systems
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• 제16권2호
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• pp.145-153
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• 2012

The pear psylla, $Cacopsylla$ $pyricola$ (Hemiptera: Psyllidae), is a serious insect pest of commercial pear crops. The species, which resides on pear trees throughout its life cycle, is rapidly spreading in some regions of the world. The population genetic structure of the species collected from several pear orchards in Korea was studied to understand the nature of dispersal and field ecology of the species. The 658-bp region of mitochondrial COI gene and the 716-bp long complete internal transcribed spacer 2 (ITS2) of the nuclear ribosomal DNA were sequenced. Unlike other previously studied insect pests, the COI-based genetic diversity of the pear psylla was extremely low (maximum sequence divergence of 0.15%). This finding allowed us to conclude that the species may have been introduced in Korea relatively recently. ITS2 sequence-based analyses of phylogeny, population differentiation, gene flow, and hierarchical population structure all concordantly suggested that the pear psylla populations in Korea are neither genetically isolated nor hampered for gene flow. These genetic data are concordant with the dispersal of an overwintering winterform morph outside the non-pear habitat in the fall.

• 한국항해항만학회:학술대회논문집
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• 한국항해항만학회 2006년도 International Symposium on GPS/GNSS Vol.1
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• pp.9-14
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• 2006

This paper develops a complete methodology for the mitigation of ionosphere spatial anomalies by GBAS systems fielded in the Conterminous U.S. (CONUS). It defines an ionosphere anomaly threat model based on validated observations of unusual ionosphere events in CONUS impacting GBAS sites in the form of a linear ‘wave front’ of constant slope and velocity. It then develops a simulation-based methodology for selecting the worst-case ionosphere wave front impact impacting two satellites simultaneously for a given GBAS site and satellite geometry, taking into account the mitigating effects of code-carrier divergence monitoring within the GBAS ground station. The resulting maximum ionosphere error in vertical position (MIEV) is calculated and compared to a unique vertical alert limit, or $VAL_{H2,I}$, that applies to the special situation of worst-case ionosphere gradients. If MIEV exceeds $VAL_{H2,I}$ for one or more otherwise-usable subset geometries (i.e., geometries for which the 'normal' vertical protection level, or $VPL_{H0}$, is less than the 'normal' VAL), the broadcast ${\sigma}_{pr_{-}gnd}$ and/or ${\sigma}_{vig}$ must be increased such that all such potentially-threatening geometries have VPL$_{H0}$ > VAL and thus become unavailable. In addition to surveying all aspects of the methods used to generate the required ${\sigma}_{pr_{-}gnd}$ and ${\sigma}_{vig}$ inflation factors for CONUS GBAS sites, related methods for deriving similar results for GBAS sites outside CONUS are suggested.

• 식물병연구
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• 제28권2호
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• pp.98-107
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• 2022

The incidence of Tomato brown rugose fruit virus (ToBRFV) and biological and molecular characterization of the Palestinian isolates of ToBRFV are described in this study. Symptomatic leaf samples obtained from Solanum lycopersicum L. (tomatoes) and Nicotiana tabacum L. (cultivated tobacco) plants were tested for tobamoviruses infection by reverse transcription polymerase chain reaction. Tomato leaf samples collected from Tulkarm and Qalqilia are infected with ToBRFV-PAL with an infection rate of 76% and 72.5%, respectively. Leaf samples collected from Jenin and Nablus were found to be mixed infected with ToBRFV-PAL and Tobacco mosaic virus (TMV) (100%). Sequence analysis of the ToBRFV-PAL genome showed that the net average nucleotide divergence between ToBRFV/F48-PAL strain and the Israeli and Turkish strains was 0.0026398±0.0006638 (±standard error of mean), while it was 0.0033066±0.0007433 between ToBRFV/F42-PAL and these two isolates. In the phylogenetic tree constructed with the complete genomic sequence, all the ToBRFV isolates were clustered together and formed a sister branch with the TMV. The sequenced Palestinian isolates of ToBRFV-PAL shared the highest nucleotide identity with the Israeli ToBRFV isolate suggesting that the virus was introduced to Palestine from Israel. The findings of this study enhance our understanding of the biological and molecular characteristics of ToBRFV which would help in the management of the disease.

• 식물분류학회지
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• 제53권2호
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• pp.157-165
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• 2023

Paraphlomis koreana (Lamiaceae) was newly named and added to Korean flora in 2014. Paraphlomis belongs to the tribe Paraphlomideae, along with Ajugoides and Matsumurella. However, a recent study has suggested that P. koreana is morphologically similar to Matsumurella chinensis, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of P. koreana within the tribe and compare its genetic relationship with M. chinensis. We sequenced an additional complete plastid genome for an individual of P. koreana and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of P. koreana. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (rpl16 intron, rpl32-trnL, rps16 intron, and trnL-F) covering 13 Paraphlomis species and M. chinensis were conducted. Phylogenetic analyses concordantly supported that P. koreana forms a monophyletic group with M. chinensis. Moreover, our study revealed that P. koreana includes nrDNA sequences of M. chinensis as minor intra-individual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of P. koreana within Paraphlomis should be reconsidered.

• 대한치과보철학회지
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• 제47권2호
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• pp.222-231
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• 2009

연구목적: 임플란트 피개의치에서 연결고정형과 비연결고정형 보철물 지대주와 골의 변형률을 비교하고 임플란트 식립 경사에 따른 변형률을 비교 분석하고자 하였다. 연구 재료 및 방법: 2개의 아크릴릭 레진 모형의 좌측과 우측 견치 부위에 2개의 외부연결형 임플란트를 각각의 모형에 식립하였다. 한 모형에는 두 개의 임플란트를 평행하게 식립하였고, 다른 모형에는 순측과 설측으로 10도의 이개도(divergence)를 가지게 임플란트를 식립하였다. 모형에서 바를 이용한 연결고정형 지대주와 볼을 이용한 비연결고정형 지대주를 고정체에 번갈아 연결하고, 각각의 경우 대응하는 유지장치가 부착된 피개의치를 제작하여 지대주 상에 안착시켰다. 전기저항 스트레인 게이지(strain gauge)를 이용하여 피개의치에 100 N에서 200 N의 부하를 가하였을 때 지대주와 가상골 표면의 변형률(strain)을 측정하였다. 결과 및 결론: 측정된 값들을 통계분석하여 얻은 결과는 다음과 같다. 바를 이용한 연결고정형 보철물은 비연결형 보철물 보다 높은 변형률 값을 보였다. 그러나 방향은 주로 압축력이었으며 부하는 분산되었다(P<.05). 볼을 이용한 비연결고정형 보철물은 연결고정형보다 낮은 변형률 값을 보였다(P<.05). 순측경사된 임플란트에서는 비연결고정형 보철물이 연결고정형 보철물보다 더 높은 변형률 값을 보였다. 설측경사된 임플란트는 순측경사된 임플란트보다 낮은 변형률을 보였다(P<.05). 임플란트가 평행하게 식립된 경우보다 평행하지 않게 식립된 경우 지대주와 가상골의 변형률 값이 더 높았다(P<.05).

• International Journal of Industrial Entomology and Biomaterials
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• 제6권1호
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• pp.45-48
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• 2003

We have previously cloned and characterized the complete fibroin L-chain gene from one of the silkworm races Baekok-Jam (Bombyx mori) and found two variable regions (I, intron 2 ~ exon 3; II, intron 6) with the primer sets designed to cover these variable regions. We tested the utility of these regions as genetic markers among silkworm races. For the purpose of study, Japanese race (Jam 123), Chinese race (Jam 124) and their F$_1$hybrid Baekok-Jam were used. The PCR product size of region I was 787 bp in Jam 123, 770 bp in Jam 124 and 768 bp in Baekok-Jam. The size of region II was 470 bp in Jam 123, 428 bp in Jam 124 and 429 Up in Baekok-Jam. In the extended experiment, Jam 125 (Japanese race), Jam 126 (Chinese race) and their F$_1$hybrid Daeseong-Jam were also analyzed. The sizes of region I and II in Jam 125, Jam 126 and Daeseong-Jam were similar to those of Jam 123, Jam 124 and Baekok-Jam. DNA sequence divergence between the two geographic races of Jam 123 or Jam 125 and Jam 124 or Jam 126 was substantial. The result suggests that the fibroin L-chain gene of F$_1$hybrids were inherited from Chinese races. These results are concordant with cocoon shapes of tested animals, and suggested that Baekok-Jam or Daeseong-jam is more closely related to Jam 124 or Jam 126 than to Jam 123 or Jam 125. Taken these data together, the primer sets designed from two variable regions of fibroin L-chain gene would be highly useful, as the genetic markers for silkworm races, at least in Japanese and Chinese races, although an extended study including more geographic races is required.