• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2003년도 춘계 학술발표대회
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• pp.65-66
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• 2003

Korean ginseng (Panax ginseng C. A. Meyer) is an representative medicinal herb. It is classified as an adaptogen, helping the body to adapt to stress, improving stamina and concentration, and providing a normalizing and restorative effect. However, cultivation and breeding of the plant is very difficult because it requires at least 4-year cultivation from seed germination to root harvest.(중략)

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2018년도 춘계 종합학술대회 논문집
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• pp.545-546
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• 2018

In this study identify potentially new alkaloids predicted from transcription information will provide insight into the pathways and molecular regulation of alkaloid biosynthesis.

• Molecules and Cells
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• 제46권1호
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• pp.65-67
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• 2023

SMILES (simplified molecular-input line-entry system) information of small molecules parsed by one-hot array is passed to a convolutional neural network called black box. Outputs data representing a gene signature is then matched to the genetic signature of a disease to predict the appropriate small molecule. Efficacy of the predicted small molecules is examined by in vivo animal models. GSEA, gene set enrichment analysis.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2020년도 춘계학술대회
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• pp.133-133
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• 2020

• 한국어류학회지
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• 제32권3호
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• pp.117-129
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• 2020

생물의 종 구분에 이용하는 지표 중 체색은 특징이 뚜렷한 형태 지표로서, 어류의 종 동정에 유용한 형태형질이다. 개볼락은 한국 중부와 남부, 일본 홋카이도 남쪽 등지에 분포하는 상업적으로 중요한 어종으로, 피부에 반점의 유무 및 마킹이 있는 위치에 따라 4개의 아종으로 구분하는 복잡한 체색 특성을 갖는다. 그러나 개볼락의 다양한 체색 패턴과 관련된 유전자 탐색 및 유전자 변이 발굴 등 체색 형성에 관여하는 유전자 규명에 관한 연구는 없다. 이에 따라 본 연구에서는 개볼락의 체색 패턴 관련 유전자 발굴 및 유전자 발현 특성을 규명하기 위한 기초 연구로 체색 타입별 피부 전사체를 프로파일링하였다. 개볼락을 Wild type (반점과 marking 없음)과 Color type (반점과 마킹 모두 있음)으로 구분하였고, 피부 전사체를 RNA-seq 방법을 이용하여 분석하였다. 개볼락 피부 전사체의 발현량을 비교하여 체색 타입별 차등발현유전자 164개를 확보하였다. 이들 차등발현유전자의 기능을 Gene ontology(GO) 분석으로 확인한 결과, 2개는 molecular function, 46개는 biological process, 6개는 cellular component 기능그룹에 속하였다. 차등발현유전자 중 CTL (Galactose-specific lectin nattectin), CUL1 (Cullin-1), CMAS (N-acylneuraminate cytidylyltransferase), NMRK2 (Nicotinamide riboside kinase 2), ALOXE3 (Hydroperoxide isomerase ALOXE3), SLC4A7 (Sodium bicarbonate cotransporter 3) 등은 특정 체색 타입 특이적인 발현양상을 나타냈다. 이번 연구는 개볼락의 체색 패턴 형성에 관여하는 전사체를 탐색한 첫 번째 연구로, 체색 형성 관련 기능유전자 발굴을 위한 후보유전자로 개볼락의 체색 타입별 차등발현유전자를 확보한 것에 의의가 있다. 향후에는 이들 후보유전자의 발현양상 및 기능을 분석하여 개볼락의 복잡한 체색 패턴과 관련된 기능유전자의 특성을 밝히고자 한다.

• Molecules and Cells
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• 제46권2호
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• pp.120-129
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• 2023

Recent technical advances have enabled unbiased transcriptomic and epigenetic analysis of each cell, known as "single-cell analysis". Single-cell analysis has a variety of technical approaches to investigate the state of each cell, including mRNA levels (transcriptome), the immune repertoire (immune repertoire analysis), cell surface proteins (surface proteome analysis), chromatin accessibility (epigenome), and accordance with genome variants (eQTLs; expression quantitative trait loci). As an effective tool for investigating robust immune responses in coronavirus disease 2019 (COVID-19), many researchers performed single-cell analysis to capture the diverse, unbiased immune cell activation and differentiation. Despite challenges elucidating the complicated immune microenvironments of chronic inflammatory diseases using existing experimental methods, it is now possible to capture the simultaneous immune features of different cell types across inflamed tissues using various single-cell tools. In this review, we introduce patient-based and experimental mouse model research utilizing single-cell analyses in the field of chronic inflammatory diseases, as well as multi-organ atlas targeting immune cells.

• Asian-Australasian Journal of Animal Sciences
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• 제28권10호
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• pp.1496-1511
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• 2015

The study aimed to compare the necrotic enteritis (NE)-induced transcriptome differences between the spleens of Marek's disease resistant chicken line 6.3 and susceptible line 7.2 co-infected with Eimeria maxima/Clostridium perfringens using RNA-Seq. Total RNA from the spleens of two chicken lines were used to make libraries, generating 42,736,296 and 42,617,720 usable reads, which were assembled into groups of 29,897 and 29,833 mRNA genes, respectively. The transcriptome changes were investigated using the differentially expressed genes (DEGs) package, which indicated 3,255, 2,468 and 2,234 DEGs of line 6.3, line 7.2, and comparison between two lines, respectively (fold change ${\geq}2$, p<0.01). The transcription levels of 14 genes identified were further examined using qRT-PCR. The results of qRT-PCR were consistent with the RNA-seq data. All of the DEGs were analysed using gene ontology terms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the DEGs in each term were found to be more highly expressed in line 6.3 than in line 7.2. RNA-seq analysis indicated 139 immune related genes, 44 CD molecular genes and 150 cytokines genes which were differentially expressed among chicken lines 6.3 and 7.2 (fold change ${\geq}2$, p<0.01). Novel mRNA analysis indicated 15,518 novel genes, for which the expression was shown to be higher in line 6.3 than in line 7.2 including some immune-related targets. These findings will help to understand host-pathogen interaction in the spleen and elucidate the mechanism of host genetic control of NE, and provide basis for future studies that can lead to the development of marker-based selection of highly disease-resistant chickens.

• Journal of Microbiology and Biotechnology
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• 제30권3호
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• pp.417-426
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• 2020

Bacillus amyloliquefaciens is an important plant disease-preventing and growth-promoting microorganism. B. amyloliquefaciens WS-8 can stimulate plant growth and has strong antifungal properties. In this study, we sequenced the complete genome of B. amyloliquefaciens WS-8 by Pacific Biosciences RSII (PacBio) Single Molecule Real-Time (SMRT) sequencing. The genome consists of one chromosome (3,929,787 bp) and no additional plasmids. The main bacteriostatic substances were determined by genome, transcriptome, and mass spectrometry data. We thereby laid a theoretical foundation for the utilization of the strain. By genomic analysis, we identified 19 putative biosynthetic gene clusters for secondary metabolites, most of which are potentially involved in the biosynthesis of numerous bioactive metabolites, including difficidin, fengycin, and surfactin. Furthermore, a potential class II lanthipeptide biosynthetic gene cluster and genes that are involved in auxin biosynthesis were found. Through the analysis of transcriptome data, we found that the key bacteriostatic genes, as predicted in the genome, exhibited different levels of mRNA expression. Through metabolite isolation, purification, and exposure experiments, we found that a variety of metabolites of WS-8 exert an inhibitory effect on the necrotrophic fungus Botrytis cinerea, which causes gray mold; by mass spectrometry, we found that the main substances are mainly iturins and fengycins. Therefore, this strain has the potential to be utilized as an antifungal agent in agriculture.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.111-111
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• 2017

The development and productivity of maize (Zea mays L.) is frequently impacted by water scarcity, and consequently to increased drought tolerance in a priority target in maize breeding programs. To elucidate the molecular mechanisms of resistance to drought stress in maize, RNA-seq of the public database was used for transcriptome profiling of the seedling stage exposed to drought stress of three levels, such as moderate, severe drought stress and re-watering. In silico analysis of differentially expressed genes (DEGs), 176 up-regulated and 166 down-regulated DEGs was detected at moderated stress in tolerance type. These DEGs was increasing degradation of amino acid metabolism in biological pathways. Six modules based on a total of 4,771 DEGs responses to drought stress by the analysis of co-expression network between tolerance and susceptible type was constructed and showed to similar module types. These modules were discriminated yellow, greenyellow, turquoise, royalblue, brown4 and plum1 with 318, 2433, 375, 183, 1405 and 56 DEGs, respectively. This study was selected 30 DEGs to predicted drought stress response gene and was evaluated expression levels using drought stress treated sample and re-watering sample by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). 23 genes was shown increasing with drought stress and decreasing with re-watering. This study contribute to a better understanding of the molecular mechanisms of maize seedling stage responses to drought stress and could be useful for developing maize cultivar resistant to drought stress.

• Asian-Australasian Journal of Animal Sciences
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• 제32권1호
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• pp.38-48
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• 2019

Objective: In this study, the transcriptome profile of cow experiencing miscarriage during peri-implantation was investigated. Methods: Total transcriptomes were checked by RNA sequencing, and the analyzed by bioinformatics methods, the differentially expressed genes (DEGs) were analysed with hierarchical clustering and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Results: The results suggested that serum progesterone levels were significantly decreased in cows that miscarried as compared to the pregnant cows at 18, 21, 33, 39, and 51 days after artificial insemination. The RNA sequencing results suggested that 32, 176, 5, 10, and 2 DEGs were identified in the pregnant cows and miscarried cows at 18, 21, 33, 39, and 51 d after artificial insemination. And 15, 101, 1, 2, and 2 DEGs were upregulated, and 17, 74, 4, and 8 DEGs were downregulated in the cows in the pregnant and miscarriage groups, respectively at 18, 21, 33, and 39, but no gene was downregulated at 51 d after artificial insemination. These DEGs were distributed to 13, 20, 3, 6, and 20 pathways, and some pathway essential for pregnancy, such as cell adhesion molecules, tumor necrosis factor signaling pathway and PI3K-Akt signaling pathway. Conclusion: This analysis has identified several genes and related pathways crucial for pregnancy and miscarriage in cows, as well as these genes supply molecular markers to predict the miscarriage in cows.