• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.274-283
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• 2020

Seed dormancy is an adaptive trait in which seeds do not germinate under unfavorable environmental conditions. Low dormancy seeds are easily germinated under optimal environmental conditions, and these characteristics greatly reduce the yield and quality of crops. In the present study, we compared the pre-harvest sprouting (PHS) rate of two cultivars, Joun and Jopyeong, using the Winkler scale after heading day and temperature of the test. The PHS rate increased as the Winkler scale after heading day increased from 700℃ to 1100℃ and the temperature of the test increased. In all conditions, the PHS rate of Jopyeong was higher than that of Joun. RNA-sequencing was used to analyze the cause of the high PHS rate. We analyzed the biological metabolic processes related to the abscisic acid (ABA) metabolite pathway using the KEGG mapper with selected differentially expressed genes in PHS seeds. We found that the expression of ABA biosynthesis genes (OsNCEDs) was down-regulated and that ABA catabolic genes (OsCYP707As) was up-regulated in PHS seeds. However, the quantitative real-time PCR results showed that Joun had a higher expression of OsNCEDs than that of Jopyeong, but OsCYP707As did not yield a significant result. Joun displayed higher ABA content than that of Jopyeong not only during ripeness time but also during PHS treatment. Taken together, we provided evidence that the ABA content remaining in the seed is important to the PHS rate, which is determined by the expression level of the ABA biosynthesis gene OsNCEDs.

• BMB Reports
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• v.53 no.8
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• pp.393-399
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• 2020

Recent advancements in the resolution and throughput of single-cell analyses, including single-cell RNA sequencing (scRNA-seq), have achieved significant progress in biomedical research in the last decade. These techniques have been used to understand cellular heterogeneity by identifying many rare and novel cell types and characterizing subpopulations of cells that make up organs and tissues. Analysis across various datasets can elucidate temporal patterning in gene expression and developmental cues and is also employed to examine the response of cells to acute injury, damage, or disruption. Specifically, scRNA-seq and spatially resolved transcriptomics have been used to describe the identity of novel or rare cell subpopulations and transcriptional variations that are related to normal and pathological conditions in mammalian models and human tissues. These applications have critically contributed to advance basic cardiovascular research in the past decade by identifying novel cell types implicated in development and disease. In this review, we describe current scRNA-seq technologies and how current scRNA-seq and spatial transcriptomic (ST) techniques have advanced our understanding of cardiovascular development and disease.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.415-418
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• 2013

Since the development of the next generation sequencing (NGS) technology, 16S rRNA gene sequencing has become a major tool for microbial community analysis. Recently, human microbiome project (HMP) has been completed to identify microbes associated with human health and diseases. HMP achieved characterization of several diseases caused by bacteria, especially the ones in human gut. While human intestinal bacteria have been well characterized, little have been studied about other animal intestinal bacteria. In this study, we surveyed diversity of livestock animal fecal microbiota and discuss importance of studying fecal microbiota. Here, we report the initiation of the fecal microbiome project in South Korea.

• Journal of Sericultural and Entomological Science
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• v.42 no.1
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• pp.14-23
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• 2000

The mitochondrial genome of domesticated silkworm (Bombyx mori) was mapped with five restriction endonucleases (BamHI, EcoRI, HindIII, PstI and XbaI), the entire genome was cloned with HindIII and EcoRI. From the end sequencing results of 5$^1$and 3$^1$region for full genome set of eleven mitochondrial clones, the seven mitochondrial genes (NADH dehydrogenase 6, ATPase 6, ATPase 8, tRN $A^{Lys}$, tRN $A^{Asp}$, tRN $A^{Thr}$ and tRN $A^{Phe}$ of mori were identified on the basis of their nucleotide sequence homology. The nucleotide composition of NADH dehydrogenase 6 was heavily biased towards adenine and thymine, which accounted for 87.76%. On basis of the sequence similarity with published tRNA genes from six insect species, the tRN $A^{Lys}$, tRN $A^{Asp}$ and tRN $A^{Thr}$ were showed stable canonical clover-leaf tRNA structures with acceptible anticodons. However, both the DHU and T$\psi$C arms of tRN $A^{Phe}$ could not form any stable stem-loop structure. The two overlapping gene pairs (tRN $A^{Lys}$ -tRN $A^{ASP}$ and ATPase8-ATPase6) were found from our sequencing results. The genes are encoded on the same strad. ATPase8 and ATPase6 overlaps (ATGATAA) which are a single example of overlapping events between abutted protein-coding genes are common, and there is evidence that the two proteins are transcribed from a single bicistronic message by initiation at 5$^1$terminal start site for ATPase8 and at an internal start site for ATPase6. Ultimately, this result will provide assistance in designing oligo-nucleotides for PCR amplification, and sequencing the specific mitochondrial genes for phylogenetics of geographic races, genetically improved silkworm strains and wild silkworm (mandarina) which is estimated as ancestal of domesticated silkworm.sticated silkworm.

• Journal of Microbiology and Biotechnology
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• v.18 no.10
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• pp.1678-1682
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• 2008

To investigate lactic acid bacterial population in Korean traditional rice wines, biotyping was performed using cell morphology and whole-cell protein pattern analysis by SDS-PAGE, and then the isolates were identified by 16S rRNA sequencing analysis. Based on the morphological characteristics, 103 LAB isolates were detected in wine samples, characterized by whole-cell protein pattern analysis, and they were then divided into 18 patterns. By 16S rRNA gene sequencing, the isolates were identified as Lactobacillus paracasei, Lb. arizonensis, Lb. plantarum, Lb. harbinensis, Lb. parabuchneri, Lb. brevis, and Lb. hilgardii when listed by their frequency of occurrence. It was found that the difference in bacterial diversity between rice and grape wines depends on the raw materials, especially the com position of starch and glucose.

• Korean Journal of Veterinary Service
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• v.39 no.1
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• pp.1-6
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• 2016

In this study, Bacillus licheniformis which has been used as probiotics was isolated from Korean traditional fermented soybean. A total of 69 strains were presumptively identified as B. licheniformis by phenotypic methods. Based on PCR amplification and 16S rRNA gene sequencing, the multilocus sequence typing of gyrA and rpoB, followed by phylogenetic analysis was performed. The isolates were distinctly differentiated and found to be closely related to B. amyloliquefaciens, B. subtilis, and B. aerius. The partial 16S rRNA gene sequences of those strains matched those of B. sonorensis (97%) and B. aerius (98%) in the phylogenetic tree. In contrast, multilocus phylogenetic analysis (MLPA) showed that only 61 (86.9%) out of 69 strains were B. licheniformis. The rest of those strains were found to be B. subtilis (5.8%), B. amyloliquefaciens (2.9%), and B. sonorensis (2.9%), respectively. Therefore, our results suggested that since the 16S rRNA gene sequencing alone was not sufficient to compare and discriminate closely related lineages of Bacillus spp., it was required to analyze the MLPA simultaneously to avoid any misleading phenotype-based grouping of these closely related species.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.643-650
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• 2020

Korean ginseng (Panax ginseng) is a dicotyledonous, medicinal, perennial plant belonging to the genus Panax of the family Araliaceae. We investigated the occurrence and incidence of plant viruses in Panax ginseng in Korea. A total of 656 leaf samples were combined into one and total RNA was extracted from the polled sample, using RNA sequencing (RNA-Seq), a metatranscriptome analysis of the plant virome was conducted. The virus present in Panax ginseng was confirmed by reverse transcription polymerase chain reaction (RT-PCR) assay using virus-specific primers. In RNA-Seq data analysis, the multiplication protein of four viral contigs including Aristotelia chilensis virus 1 (AcV1), Turnip mosaic virus (TuMV), Watermelon mosaic virus (WMV), and Tobamovirus multiplication protein were discovered. From our metatranscriptome analysis and RT-PCR assay, TuMV and WMV were detected, whereas the three viruses reported in China such as tomato yellow leaf curl China virus; panax notoginseng virus A; and panax virus Y were not found in this study. The distribution of domestic ginseng viruses seems different from that recorded in China. Overall, this is the first plant virome analysis of Panax ginseng in Korea.

• Journal of Life Science
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• v.27 no.12
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• pp.1494-1499
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• 2017

Oral infection due to Candida albicans is a widely recognized and frequent cause of superficial infections of the oral mucosa (oral candidiasis). Although oral candidiasis is not a life-threatening fungemia, it can cause severe problems in individuals under certain conditions. MicroRNAs (miRNAs) are noncoding, small RNA molecules, which regulate the expression of other genes by inhibiting the translation of target mRNAs. The present study was designed to identify miRNAs in C. albicans and determine their possible roles in this organism. miRNA-sized small RNAs (msRNAs) were cloned in C. albicans by deep sequencing, and their secondary structures were analyzed. All the cloned msRNAs satisfied conditions required to qualify them as miRNAs. Bioinformatics analysis revealed that two of the most highly expressed C. albicans msRNAs, Ca-363 and Ca-2019, were located in the 3' untranslated region of the corticosteroid-binding protein 1 (CBP1) gene in a reverse orientation. miRNA mimics were transformed into C. albicans to investigate their RNA-inhibitory functions. RNA oligonucleotide-transformed C. albicans was then observed by fluorescent microscopy. Quantitative PCR analysis showed that these msRNAs did not inhibit CBP1 gene expression 4 hr and 8 hr after ectopic miRNA transformation. These results suggest that msRNAs in C. albicans possess an miRNA-triggered RNA interference gene-silencing function, which is distinct from that exhibited by other eukaryotic systems.

• Korean Journal of Medicinal Crop Science
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• v.17 no.1
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• pp.26-32
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• 2009

The region containing 18S rRNA gene, ITS 1 and part of the 5.8S rRNA gene of the Atractylodes japonica Koidz was amplified by PCR and the product cloned in a pBluescript SK II plasmid. DNA sequence of the cloned DNA was determined and submitted to the GenBank (accession number EU678363). Phylogenetic analysis of the ITS 1 DNA showed close similarity with the other plant species of the family Compositae. The extract of the plant materials of five different members of the family Compositae was analyzed by HPLC to detect atractylon. Extract of the A. japonica Koidz showed presence of significant amount of atractylon. However, noticeable amount of atractylon was not detected by the same analyses from the extracts of the other plants belonging to the family Compositae including Artemisia capillaris, Chrysantemum zawadskii, Eclipta prostrata or Taraxacum platycarpum.

• Korean Journal of Poultry Science
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• v.44 no.3
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• pp.199-209
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• 2017

Mitogen-activated protein kinase (MAPK) signaling pathways play a key role in innate immunity, inflammation, cell proliferation, cell differentiation, and cell death. The main objective of this study was to investigate the expression level of candidate MAPK pathway genes in the intestinal mucosal layer of two genetically disparate chicken lines (Marek's disease-resistant line 6.3 and Marek's disease-susceptible line 7.2) induced with necrotic enteritis (NE). Using high-throughput RNA sequencing, we investigated 178 MAPK signaling pathway related genes that were significantly and differentially expressed between the intestinal mucosal layers of the NE-afflicted and control chickens. In total, 15 MAPK pathway genes were further measured by quantitative real-time PCR(qRT-PCR) and the results were consistent with the RNA-sequencing data. All 178 identified genes were annotated through Gene Ontology and mapped onto the KEGG chicken MAPK signaling pathway. Several key genes of the MAPK pathway, ERK1/2, JNK1-3, p38 MAPK, MAP2K1-4, $NF-{\kappa}B1/2$, c-Fos, AP-1, Jun-D, and Jun, were differentially expressed in the two chicken lines. Therefore, we believe that RNA sequencing and qRT-PCR analysis provide resourceful information for future studies on MAPK signaling of genetically disparate chicken lines in response to pathogens.