• The Korean Journal of Zoology
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• v.24 no.3
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• pp.133-144
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• 1981

The ultrastructures of the pigment cells in the Asiatic land salamander (Hynobius leechi) dorsal skin were obtained by means of electron microscope. The results were as follows; 1. The pigment cells of the epidermis consisted of the melanocytes in the germinal layer and of the melanophores distributing to the keratinocyte layer. The traits of these cells in the epidermis were as follows: A. The nuclei of the melanocytes were round or oval in shape and appeared as partly small or large infoldings of the nuclear envelope. B. Rough-surfaced endoplasmic reticulums and Golgi complexes were well developed in infranuclear cytoplasm. Many ribosomes were mainly distributed around the perinuclear portion. C. The melanosomes of the melanocytes were observed as a found or an oval shape and strong electron-dense or less electron-dense melanosomes were observed. D. The infoldings of the nuclear envelope in the melanophore were partly found deeper than those of the melanocyte. The cytoplasm of the melanophore filled with melanosomes caused organelles not to be observed in that. 2. The pigment cells in the dermis were composed of the xanthophores just beneath basement membrane and the melanophores in the connective tissue. The traits of these cells in the dermis were as follows: A. The xanthophores contained round or oval vesicles, and these vesicles were divided into 6 types (type I pterinosome, type II pterinosome, type III pterinosomes, type iv pterinosome, type V pterinosome, type VI pterinosome). B. Most of the nuclei of the melanophores in the dermis were elongate in shape, and a portion of the nuclear envelope was deep infolded. C. Becuase the cytoplasm was filled with the melanosomes of the same electron-density, organelles were not observed in the cytoplasm. D. Two processes of the melanophore in the dermis extended in parallel with a xanthophore and the cytoplasm in those processes were filled with the melanosomes.

• Journal of Life Science
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• v.27 no.9
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• pp.1040-1046
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• 2017

We describe the isolation and characterization of six different intestinal microorganisms from the digestive tract of the cricket Gryllus bimaculatus. Based on 16S rRNA gene sequences, we obtained six isolates belonging to four different genera: Staphylococcus, Bacillus, Citrobacter, and Proteus. All the isolates were resistant to ampicillin. Ampicillin is an irreversible inhibitor of the enzymeetranspeptidase, which is needed to make bacterial cell walls. None of the isolates were resistant to kanamycin, which binds to the 30S subunit of the bacterial ribosome and then inhibits total protein synthesis. Gram staining was conducted, in addition to morphological classification under a microscope. Four grampositive isolates and two gram-negative isolates were detected. The gram-positive isolates were GL1 (round shaped, 2 am in diameter), GL2 (rod shaped, $2.5{\mu}m$ in length), GL3 (rod shaped, $2{\mu}m$ in length), and GL4 (round shaped, $1.5{\mu}m$ in diameter). The gram-negative isolates were GL5 (rod shaped, $2{\mu}m$ in length) and GL6 (rod-shaped, $2.5{\mu}m$ in length). Notably, two of the isolates, GL2 and GL4, secreted specific extracellular proteins. These were determined by MALDI-TOF-MS spectral analysis to be a 87 kDa collagenase, 56 kDa hypothetical protein, and 200 kDa hypothetical protein. The six isolates in this study could be used for various biotechnological applications and pest management, both in the field and in greenhouse systems. In addition, it would be interesting to determine the relationship between these isolates and their host.

• KSBB Journal
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• v.21 no.2
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• pp.144-150
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• 2006

The exploitation of metagenome, the access to the natural extant of enormous potential resources, is the way for elucidating the functions of organism in environmental communities, for genomic analyses of uncultured microorganism, and also for the recovery of entirely novel natural products from microbial communities. The major breakthrough in metagenomics is opened by the construction of libraries with total DNAs directly isolated from environmental samples and screening of these libraries by activity and sequence-based approaches. Screening with activity-based approach is presumed as a plausible route for finding new catabolic genes under designed conditions without any prior sequence information. The main limitation of these approaches, however, is the very low positive hits in a single round of screening because transcription, translation and appropriate folding are not always possible in E. coli, a typical surrogate host. Thus, to obtain information about these obstacles, we studied the genetic organization of individual URF's(unidentified open reading frame from metagenome sequenced and deposited in GenBank), especially on the expression factors such as codon usage, promoter region and ribosome binding site(rbs), based on DNA sequence analyses using bioinformatics tools. And then we also investigated the above-mentioned properties for 4100 ORFs(Open Reading Frames) of E. coli K-12 generally used as a host cell for the screening of noble genes from metagenome. Finally, we analyzed the differences between the properties of URFs of metagenome and ORFs of E. coli. Information derived from these comparative metagenomic analyses can provide some specific features or environmental blueprint available to screen a novel biocatalyst efficiently.

• Applied Microscopy
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• v.29 no.1
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• pp.105-124
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• 1999

Histological and ultrastructural differentiations of the neuroepithelial cells in the mouse embryo during neurulation were observed. The neural plates and grooves consisted of pseudostratified columnar epithelium in the embryonic day (ED) 8 embryo were developed. In the ED 9 embryo, the neural tube was developed in all body length of embryo except both the cephalic and caudal ends. Secondary neurulation was shown at the tail bud of the ED 10 embryo. In the ED 8 embryo, the primitive streak was shown in the posterior end of the embryonic disc. The neuroepithelium, notochord and mesenchyme were well differentiated in the cephalic and cervical portions. In the ED 9 and 10 embryos, the roof plates of neural tubes were constituted of the closing of the surface ectodermal cells in the hindbrain and the neuroepithelial cells in the spinal cord. The floor plate of neural tube were consisted of the low pseudostratified columnar epithelium. The spinal motor nerve fibers were initially differentiated in the ED 10 embryo. According to the electron density of the cell and the differentiation of tell organelles, the neuroepithelial cells in the ED 9 and 10 embryos were classified into three types: dark, intermediate and light types. All types in the ED 9 embryo were observed but the dark cell in the ED 10 embryo was not done. The free ribosomes and polysomes in all neuroepithelial cells were developed. The RER and lipid droplets in the dark cell and the Golgi complex in the intermediate and light cells were observed. Many microfilaments in the cytoplasmic processes of intermediate cell and the microfilaments and microtubules in the light cell processes were observed to be well differentiated.

• Journal of Life Science
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• v.22 no.3
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• pp.417-427
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• 2012

We compared the transcriptome in response to propanol stress in wild-type and propanol-resistant mutant Escherichia coli using the DNA microarray technique. The correlation value of RNA expression between the propanol-treated wild type and the untreated-one was about 0.949, and 50 genes were differentially expressed by more than twofold in both samples. The correlation value of RNA expression between the propanol-treated mutant and the untreated one was about 0.951, and 71 genes in two samples showed differential expression patterns. However, the values between the wild type and mutant, regardless of propanol addition, were 0.974-0.992 and only 1-2 genes were differentially expressed in the two strains. The representative characteristics among differentially expressed genes in W3110 or P19 treated with propanol compared to untreated samples were up-regulation of hest shock response genes and down-regulation of genes relating to ribosome biosynthesis. In addition, many genes were regulated by transcription regulation factors such as ArcA, CRP, FNR, H-NS, GatR, or PurR and overexpressed by sigma factor RpoH. We confirmed that RpoH mediated an important host defense function in propanol stress in E. coli W3110 and P19 by comparison of cell growth rate among the wild type, rpoH disruptant mutant, and rpoH-complemented strain.

• Journal of Biomedical and Translational Research
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• v.19 no.4
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• pp.116-124
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• 2018

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP ${\times}$ Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (${\left|log2FC\right|}$ > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

• Animal Bioscience
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• v.34 no.9
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• pp.1466-1478
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• 2021

Objective: Ruminants are completely dependent on their microbiota for rumen fermentation, feed digestion, and consequently, their metabolism for productivity. This study aimed to evaluate the rumen bacteria of lactating yaks with different milk protein yields, using high-throughput sequencing technology, in order to understand the influence of these bacteria on milk production. Methods: Yaks with similar high milk protein yield (high milk yield and high milk protein content, HH; n = 12) and low milk protein yield (low milk yield and low milk protein content, LL; n = 12) were randomly selected from 57 mid-lactation yaks. Ruminal contents were collected using an oral stomach tube from the 24 yaks selected. High-throughput sequencing of bacterial 16S rRNA gene was used. Results: Ruminal ammonia N, total volatile fatty acids, acetate, propionate, and isobutyrate concentrations were found to be higher in HH than LL yaks. Community richness (Chao 1 index) and diversity indices (Shannon index) of rumen microbiota were higher in LL than HH yaks. Relative abundances of the Bacteroidetes and Tenericutes phyla in the rumen fluid were significantly increased in HH than LL yaks, but significantly decreased for Firmicutes. Relative abundances of the Succiniclasticum, Butyrivibrio 2, Prevotella 1, and Prevotellaceae UCG-001 genera in the rumen fluid of HH yaks was significantly increased, but significantly decreased for Christensenellaceae R-7 group and Coprococcus 1. Principal coordinates analysis on unweighted UniFrac distances revealed that the bacterial community structure of rumen differed between yaks with high and low milk protein yields. Furthermore, rumen microbiota were functionally enriched in relation to transporters, ABC transporters, ribosome, and urine metabolism, and also significantly altered in HH and LL yaks. Conclusion: We observed significant differences in the composition, diversity, fermentation product concentrations, and function of ruminal microorganisms between yaks with high and low milk protein yields, suggesting the potential influence of rumen microbiota on milk protein yield in yaks. A deeper understanding of this process may allow future modulation of the rumen microbiome for improved agricultural yield through bacterial community design.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.202-202
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• 2022

Recently days, soybean production in paddy field is increasing, from 4,422 ha in 2016 to 10,658 ha in 2021 in Korea. It is easy for Phytophthora stem and root rot (PSR) occurring in paddy field condition, when it is poorly drained soils with a high clay content, and temporary flooding and ponding. Therefore PSR resistant soybean cultivar is required. The objective of this study is to identify QTL region and candidate genes relating to PSR resistance of the race in main soybean cultivation area in Korea. 210 soybean materials including cultivars and germplasm were used for inoculation and genome-wide association study (GWAS). Inoculation was conducted using stem-scar method with 2 replications in 2-year for the race 3053 from Kimje and 3617 from Andong. 210 materials were genotyped with Soya SNP 180K chip, and structure analysis and association mapping were conducted with QTLMAX V2. The results of inoculation showed that survival ratio ranged from 0% to 96.7% and mean 9.7% for 3053 and ranged from 0% to 100% and mean 7.6% for 3617. Structure analysis showed linkage disequillibrium (LD) was decayed below r²=0.5 at 335kb of SNP distance. Significant SNPs (LOD>7.0) were identified in Chr 1, 2, 3, 4, 5, 11, 14, 15 for 3053 and Chr 1, 2, 3, 7, 10, 14 for 3617. Especially, LD blocks (AX-90455181;15,056,628bp~AX-90475572;15,298,872bp) in Chr 2 for 3053 and 3067 were duplicated. 29 genes were identified on these genetic regions including Glyma.02gl47000 relating to ribosome recycling factor and defense response to fungus in Soybase.

• Journal of Life Science
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• v.33 no.11
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• pp.944-949
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• 2023

The purpose of this study was to identify conserved metabolic pathways and conserved genes in 122 archaeal species. Using the Clusters of Orthologous Groups of Proteins (COG) database of conserved genes, we analyzed whether 122 species had 63 COG metabolic pathways, the 822 COGs that compose them, and a total of 4,877 COGs. Archaeal ribosomal proteins were the most conserved in metabolic pathways. 46 COGs in seven COG pathways among 63 COG pathways and 20 COGs in others were conserved in 122 species. Some genes involved in cell wall and extracellular matrix synthesis, replication, transcription, translation, and protein metabolism were common to all 122 species. When the distance value of the phylogenetic tree was analyzed at the phylum level or class level, the average was the lowest at the class Halobacteria of the phylum Euryarchaeota. Standard deviation was high for the class Nitosospharia of the phylum Thaumarchaeota, the unclassified members of phylum Thaumarchaeota, the class Halobacteria of the phylum Euryarchaeota, the class Thermoprotei of the phylum Crenarchaeota, and other archaea. Furthermore, the phylogenetic tree analysis revealed six commonalities. The results of this study, along with data on conserved genes, could be used for drug development and gene selection for strain improvement.

• Animal Bioscience
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• v.37 no.6
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• pp.1021-1030
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• 2024

Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. Methods: In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. Results: We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. Conclusion: These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.