• Journal of Crop Science and Biotechnology
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• v.11 no.4
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• pp.237-242
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• 2008

A liguleless mutant, which showed complete loss of lamina joint region at the junction between leaf blade and leaf sheath, was isolated from a Ds insertional mutants derived from the source cultivar, Dongjin. This mutant could not affect other developmental patterns like phyllotaxis. Southern blot analysis, using GUS as a probe, revealed that the liguleless mutant contained three Ds copies transposed in the rice genome. Among the four genomic sequences flanking the Ds, one was mapped in the intergenic region (31661640 - 31661759), and the other two predicted a protein kinase domain (12098980 - 12098667) as an original insertion site within a starter line used for massive production of Ds insertional mutant lines. Another predicted and inserted in first exon of liguleless 1 protein (OsLG1) that was mapped in coding region (LOC_Os04g56170) of chromosome 4. RT-PCR revealed that the OsLG1 gene was not expressed liguleless mutants. Structure analysis of OsLG1 protein revealed that it predicted transcription factor with a highly conserved SBP domain consisting of 79 amino acids that overlapped a nuclear localization signal (NLS). RT-PCR revealed that OsLG1 is mainly expressed in vegetative organs.

• Korean Journal of Veterinary Service
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• v.34 no.2
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• pp.103-109
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• 2011

Asia1/Shamir that has been recommended by World Reference Laboratory for foot-and-mouth disease (FMD) is used as a vaccine strain, and is being prepared in many countries including Korea. Although it is assumed that vaccine strain Asia1/Shamir has a wide antigenicity, sufficient molecular biological analysis has not been accomplished yet. Complete genome sequence analysis showed that the region with the most severe variations was 1D region of structural protein-coding sequence; particularly amino acid 141~157 residues in 1D region RGD sites for binding to susceptible cells. In addition, five amino acids in 1D region were identified as characteristic sites that are different from other known Asia1 viruses. Asia1/Shamir strain was shown to be genetically similar to group VI that had occurred in the Middle East, but showed low level of genetic similarity to the group V viruses that had occurred in the Southeast Asia and China. It is considered that, if these viruses, group I and II including group V are introduced into Korea, care would be paid in case of inoculating the vaccine strain Shamir available in Korea.

• Food Science of Animal Resources
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• v.35 no.5
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• pp.692-702
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• 2015

Lactobacillus mucosae is a natural resident of the gastrointestinal tract of humans and animals and a potential probiotic bacterium. To understand the global protein expression profile and metabolic features of L. mucosae LM1 in the early stationary phase, the QExactive^TM Hybrid Quadrupole-Orbitrap Mass Spectrometer was used. Characterization of the intracellular proteome identified 842 proteins, accounting for approximately 35% of the 2,404 protein-coding sequences in the complete genome of L. mucosae LM1. Proteome quantification using QExactive^TM Orbitrap MS detected 19 highly abundant proteins (> 1.0% of the intracellular proteome), including CysK (cysteine synthase, 5.41%) and EF-Tu (elongation factor Tu, 4.91%), which are involved in cell survival against environmental stresses. Metabolic pathway annotation of LM1 proteome using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed that half of the proteins expressed are important for basic metabolic and biosynthetic processes, and the other half might be structurally important or involved in basic cellular processes. In addition, glycogen biosynthesis was activated in the early stationary phase, which is important for energy storage and maintenance. The proteogenomic data presented in this study provide a suitable reference to understand the protein expression pattern of lactobacilli in standard conditions

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1570-1576
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• 2006

An encephalomyocarditis virus (EMCV-CBNU) was isolated from an aborted swine fetus in October 2005. To investigate the genetic origin and virulence of the EMCV-CBNU strain, we determined the complete sequence of the virus and tested its virulence in mice. Genetic characterization revealed that the RNA genome was composed of 7,713 nucleotides with a single open reading frame (2,292 amino acids), coding 12 proteins. The EMCV-CBNU had the shortest poly(C) tract, consisting of 10 C's ($C_{10}$), compared with all the other EMCV strains reported in GenBank. Amino acid and phylogenetic analyses showed that EMCV-CBNU had the highest genetic identity with strain 2887A (99.7%), which was originally isolated from a fetus in a pig breeding farm that had a history of reproductive failure. Because rodents are the natural host of EMCV, we investigated the virulence of EMCV-CBNU in mice. Surprisingly, all mice inoculated with more than $1{\times}10^2\;TCID_{50}/0.1ml$ of EMCV-CBNU showed symptoms of hind limb paralysis and eventually died during 3 and 8 days postinoculation (DPI). Furthermore, when we inoculated the virus into pregnant mice, all dams and their fetuses died in 6 DPI. This is the first report on a full genomic analysis of swine EMCV in Korea, which exhibits high virulence in mice.

• Journal of dental hygiene science
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• v.19 no.3
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• pp.181-189
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• 2019

Background: Edentulism is associated with socioeconomic status, rural residence, and chronic disease, but no studies have investigated edentulism and residence factors together. All information that drives a better understanding of the factors related to edentulism plays an important role in the planning and delivery of appropriate dental services for the elderly by national and oral health professionals. This study was designed to investigate the prevalence of edentulism in adults aged over 60 years in Korea and to examine whether there are differences in dentate status between people living in urban and rural areas after controlling for sociodemographic and other related factors. Methods: The data for this study were collected from 2013 to 2015 as part of the Korea National Health and Nutrition Examination Survey VI, those individuals aged over 60 years and who had complete datasets were included (5,071). The number of teeth and residence status were categorized into two groups: edentate and dentate (1 or more); urban and rural. Multiple multivariate logistic regression analyses were sequentially applied to assess the association between dentate status and residence status after adjusting for potential confounders. Results: Rural areas, lower household income, and lower education levels were associated with a higher edentate rate. The number of teeth was lower in rural areas than in urban areas. After adjusting for various factors, statistically significant associations were present for women, low household income, low education level, poor perceived health status, and alcohol consumption in participants. Conclusion: Elders living in rural areas had poorer oral health than elders living in urban areas. The government will need to provide effective systems for promoting oral health for elders living in rural areas.

• Genomics & Informatics
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• v.20 no.1
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• pp.12.1-12.7
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• 2022

The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.

• Journal of Veterinary Science
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• v.23 no.5
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• pp.63.1-63.14
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• 2022

Background: Chicken anemia virus (CAV) causes chicken infectious anemia, which results in immunosuppression; the virus has spread widely in chicken flocks in China. Objectives: The aim of this study was to understand recent CAV genetic evolution in chicken flocks in Guangxi Province, southern China. Methods: In total, 350 liver samples were collected from eight commercial broiler chicken farms in Guangxi Province in southern China from 2018 to 2020. CAV was detected by conventional PCR, and twenty CAV complete genomes were amplified and used for the phylogenetic analysis and recombination analysis. Results: The overall CAV-positive rate was 17.1%. The genetic analysis revealed that 84 CAVs were distributed in groups A, B, C (subgroups C1-C3) and D. In total, 30 of 47 Chinese CAV sequences from 2005-2020 belong to subgroup C3, including 15 CAVs from this study. There were some specific mutation sites among the intergenotypes in the VP1 protein. The amino acids at position 394Q in the VP1 protein of 20 CAV strains were consistent with the characteristics of a highly pathogenic strain. GX1904B was a putative recombinant. Conclusions: Subgroup C3 was the dominant genotype in Guangxi Province from 2018-2020. The 20 CAV strains in this study might be virulent according to the amino acid residue analysis. These data help improve our understanding of the epidemiological trends of CAV in southern China.

• International Journal of Industrial Entomology and Biomaterials
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• v.45 no.1
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• pp.29-34
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• 2022

Silkworms have recently attracted attention as healthy functional foods. Different varieties of silkworms have functional differences; thus, there is an emerging need for variety identification. In this study, we sequenced complete mitochondrial genomes (mitogenomes) of ten government-recommended silkworm varieties (BaekHwang, BaekOk, DaeBaek, DaeBak, DaeHwang, GoldenSilk, HanSaeng, JooHwang, KumKang, and KumOk). Comparison of these sequences allowed us to select the single nucleotide polymorphisms (SNPs) in 34 sites that are specific to six silkworm varieties: 13 in DaeBak, 8 in GoldenSilk, 9 in KumKang, 2 in BaekHwang, 1 in BaekOk, and 1 in DaeHwang. Among these each one SNP per variety was amplified by preparing variety-specific primers and then using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR). As a result, it was possible to identify these six varieties among the ten silkworm varieties, evidencing that SNPs developed from mitogenomes are useful marker for the discrimination of genetically closer silkworm varieties.

• Research in Plant Disease
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• v.28 no.2
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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.

• Research in Plant Disease
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• v.29 no.3
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• pp.286-294
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• 2023

Biological and molecular characterization of a Korean isolate of Orthotospovirus chrysanthinecrocaulis (formerly known as chrysanthemum stem necrosis virus, CSNV) isolated from Chrysanthemum morifolium was determined using host range and sequence analysis in this study. Twenty-three species of indicator plants inoculated mechanically CSNV-Kr was investigated for determination of host range. CSNV-Kr induced various local and systemic symptoms in the inoculated plant species. CSNV-Kr could not infect three plant species and induced symptomless in systemic leaves in Nicotiana tabacum cultivars, though the plant samples reacted positively with the antiserum to CSNV by double-antibody sandwich-enzyme-linked immunosorbent assay. The complete genome sequence of CSNV-Kr was determined. The L RNA of CSNV-Kr consists of 8,959 nucleotides (nt) and encodes a putative RNA-dependent RNA polymerase. The M RNA of CSNV-Kr consists of 4,835 nt and encodes the movement protein (NSm) and the glycoprotein precursor (Gn/Gc protein). The S RNA of CNSV-Kr consists of 2,836 nt and encodes NSs protein and N protein. The Gn/Gc and N sequence of CSNV-Kr were compared with those of previously published CSNV isolates originating from different countries at nucleotide and amino acid levels. The Gn/GC sequence of CSNV-Kr shared 98.8-99.5% identity with CSNV isolated from other countries and the N sequence of CSNV-Kr shared 98.8-99.6% identity. No particular region of variability could be found in either grouping of viruses. All of the CSNV isolates did not show any relationship according to geographical origins and isolation hosts, suggesting no distinct segregation of the CSNV isolates.