• Molecules and Cells
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• v.37 no.1
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• pp.74-80
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• 2014

The peroxisome is an intracellular organelle that responds dynamically to environmental changes. Various model organisms have been used to study the roles of peroxisomal proteins in maintaining cellular homeostasis. By taking advantage of the zebrafish model whose early stage of embryogenesis is dependent on yolk components, we examined the developmental roles of the D-bifunctional protein (Dbp), an essential enzyme in the peroxisomal ${\beta}$-oxidation. The knockdown of dbp in zebrafish phenocopied clinical manifestations of its deficiency in human, including defective craniofacial morphogenesis, growth retardation, and abnormal neuronal development. Overexpression of murine Dbp rescued the morphological phenotypes induced by dbp knockdown, indicative of conserved roles of Dbp during zebrafish and mammalian development. Knockdown of dbp impaired normal development of blood, blood vessels, and most strikingly, endoderm-derived organs including the liver and pancreas - a phenotype not reported elsewhere in connection with peroxisome dysfunction. Taken together, our results demonstrate for the first time that zebrafish might be a useful model animal to study the role of peroxisomes during vertebrate development.

• Korean Journal of Ecology and Environment
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• v.53 no.4
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• pp.344-354
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• 2020

Identification of the target species of 2-MIB (2-methyllisoborneol) production is crucial in the management of off-flavor problem in the freshwater system. This study was conducted to identify 2-MIB-producing Pseudanabaena strains occurring in the North Han River system using molecular genetic method. Eleven phenotypes of Pseudanabaena were isolated from several mainstream sites of the North Han River, including Sambong-ri, Joam-myun, and Lake Uiam areas. Despite of morphological similarity of the strains, the phylogenetic analysis using 16S rDNA classified them into different species with low genetic similarity (40~55%). Isolated Pseudanabaena strains were converged to four species; Pseudanabaena cinerea, P. yagii, P. mucicola, and P. redekei. Among them, the 2-MIB synthesizing gene (mibC) was detected in P. cinerea, P. yagii, and P. redekei. However, actual 2-MIB production was detected only in P. cinerea and P. redekei based on gas chromatography analysis. This study is the first report of the molecular identification of Pseudanabaena strains and their 2-MIB production potential in Korea. The results of this study provides an evidence of species diversity of Pseudanabaena occurring in the North Han River.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.53-53
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• 2015

Agrobacterium tumefaciens-mediated transformation(ATMT) of Flammulina velutipes was used to produce a diverse number of transformants to discover the functions of gene that is vital for its variation color, spore pattern and cellulolytic activity. Futhermore, the transformant pool will be used as a good genetic resource for studying gene functions. Agrobacterium-mediated transformation was conducted in order to generate intentional mutants of F. velutipes strain KACC42777. Then Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into F. velutipes. This method is use to determine the functional gene of F. velutipes. Inverse PCR was used to insert T-DNA into the tagged chromosomal DNA segments and conducting sequence analysis of the F. velutipes. But this experiment had trouble in diverse morphological mutants because of dikaryotic nature of mushroom. It needed to make monokaryotic fruiting varients which introduced genes of compatible mating types. In this study, next generation sequencing data was generated from 28 strains of Flammulina velutipes with different phenotypes using Illumina Hiseq platform. Filtered short reads were initially aligned to the reference genome (KACC42780) to construct a SNP matrix. And then we built a phylogenetic tree based on the validated SNPs. The inferred tree represented that white- and brown- fruitbody forming strains were generally separated although three brown strains, 4103, 4028, and 4195, were grouped with white ones. This topological relationship was consistently reappeared even when we used randomly selected SNPs. Group I containing 4062, 4148, and 4195 strains and group II containing 4188, 4190, and 4194 strains formed early-divergent lineages with robust nodal supports, suggesting that they are independent groups from the members in main clades. To elucidate the distinction between white-fruitbody forming strains isolated from Korea and Japan, phylogenetic analysis was performed using their SNP data with group I members as outgroup. However, no significant genetic variation was noticed in this study. A total of 28 strains of Flammulina velutipes were analyzed to identify the genomic regions responsible for producing white-fruiting body. NGS data was yielded by using Illumina Hiseq platform. Short reads were filtered by quality score and read length were mapped on the reference genome (KACC42780). Between the white- and brown fruitbody forming strains. There is a high possibility that SNPs can be detected among the white strains as homozygous because white phenotype is recessive in F. velutipes. Thus, we constructed SNP matrix within 8 white strains. SNPs discovered between mono3 and mono19, the parental monokaryotic strains of 4210 strain (white), were excluded from the candidate. If the genotypes of SNPs detected between white and brown strains were identical with those in mono3 and mono19 strains, they were included in candidate as a priority. As a result, if more than 5 candidates SNPs were localized in single gene, we regarded as they are possibly related to the white color. In F. velutipes genome, chr01, chr04, chr07,chr11 regions were identified to be associated with white fruitbody forming. White and Brown Fruitbody strains can be used as an identification marker for F. veluipes. We can develop some molecular markers to identify colored strains and discriminate national white varieties against Japanese ones.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.4
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• pp.375-383
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• 2009

This study was carried out to develop transgenic rice cultivars with the CAX1 (accession no. U57411) gene. We successfully selected the transgenic rice plants over-expressing the Arabidopsis H+/$Ca^{2+}$ antiporter CAX1 (accession no. U57411) gene in T6 generation. The brown rice of the CAX1 expressing rice contained 13.4~68.0 % more calcium $(Ca^{2+})$ than that of the wild type and 5 lines were selected based on the phenotypes compared to the control cultivar at the GMO field. The CAX1 expressing transgenic rice plants were similar in phenotype to the wild type during the whole growth period. Also these selected 4 lines appeared to be resistant to blast, cold and water solution compared with the wild type. Difference in 1,000 grain weight of brown rice was observed among each line but grain shape did not show any morphological alternations. These results suggest the enhanced Ca-substrate specificity of CAX1 exchanger in donor plant. Therefore, intact CAX1 exchanger can be functionally useful for $Ca^{2+}$ nutrient enrichment of rice with reduced accumulation of undesirable cation.

• Korean Journal of Plant Resources
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• v.33 no.5
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• pp.446-459
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• 2020

This study analyzed the phenotypes and chemotypes of 74 tartary buckwheat (Fagopyrum tataricum) germplasms using principal component analysis and cluster analysis. The average seed size of tartary buckwheat germplasm was 5.2 × 3.4 mm, which is smaller than the seed size of common buckwheat. The dark browned colored ovate or elliptic shape was mostly observed in collected germplasm. The average content of rutin was 1,393 mg per 100 g dry weight (DW) in tartary buckwheat seed. Similarly, the flavonoid and polyphenol contents ranged from 253 to 2,669 and 209 to 1,823 mg, respectively, per 100 g DW in the collected germplasm. The three components (PC1, 2, and 3) of principal component analysis revealed 68.55% of the total variance of the collected accessions. Cluster analysis using descriptors showed that 74 accessions were clustered into five groups. The study showed that the most interesting resources for functional breeding programs are: Five resources (HLB1004, HLB1005, HLB1007, HLB1009, and HLB1013) due to the rich rutin, polyphenol, and flavonoid.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.233-240
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• 2011

Food security has been a main global issue due to climate changes and growing world population expected to 9 billion by 2050. While biodiversity is becoming more highlight, breeders are confronting shortage of various genetic materials needed for new variety to tackle food shortage challenge. Though biotechnology is still under debate on potential risk to human and environment, it is considered as one of alternative tools to address food supply issue for its potential to create a number of variations in genetic resource. The new technology, phenomics, is developing to improve efficiency of crop improvement. Phenomics is concerned with the measurement of phenomes which are the physical, morphological, physiological and/or biochemical traits of organisms as they change in response to genetic mutation and environmental influences. It can be served to provide better understanding of phenotypes at whole plant. For last decades, high-throughput screening (HTS) systems have been developed to measure phenomes, rapidly and quantitatively. Imaging technology such as thermal and chlorophyll fluorescence imaging systems is an area of HTS which has been used in agriculture. In this article, we review the current statues of high-throughput screening system in phenomics and its application for crop improvement.