• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.247-247
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• 2022

• Proceedings of the Korean Society of Crop Science Conference
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• 2023.04a
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• pp.128-128
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• 2023

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.04a
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• pp.98-98
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• 2022

• IMMUNE NETWORK
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• v.23 no.5
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• pp.36.1-36.16
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• 2023

Thymic epithelial cells (TECs) play a critical role in thymic development and thymopoiesis. As individuals age, TECs undergo various changes that impact their functions, leading to a reduction in cell numbers and impaired thymic selection. These age-related alterations have been observed in both mice and humans. However, the precise mechanisms underlying age-related TEC dysfunction remain unclear. Furthermore, there is a lack of a comprehensive study that connects mouse and human biological processes in this area. To address this gap, we conducted an extensive transcriptome analysis of young and old TECs in mice, complemented by further analysis of publicly available human TEC single-cell RNA sequencing data. Our analysis revealed alterations in both known and unknown pathways that potentially contribute to age-related TEC dysfunction. Specifically, we observed downregulation of pathways related to cell proliferation, T cell development, metabolism, and cytokine signaling in old age TECs. Conversely, TGF-β, BMP, and Wnt signaling pathways were upregulated, which have been known to be associated with age-related TEC dysfunctions or newly discovered in this study. Importantly, we found that these age-related changes in mouse TECs were consistently present in human TECs as well. This cross-species validation further strengthens the significance of our findings. In conclusion, our comprehensive analysis provides valuable insight into the biological and immunological characteristics of aged TECs in both mice and humans. These findings contribute to a better understanding of thymic involution and age-induced immune dysfunction.

• Genes and Genomics
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• v.40 no.12
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• pp.1287-1300
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• 2018

Hydrogen sulfide ($H_2S$), a small bioactive gas, has been proved functioning in plant growth and development as well as alleviation of abiotic stresses, which including promoting seed germination, accelerating embryonic root growth, regulating flower senescence, inducing stomatal closure, and defending drought, heat, heavy metals and osmotic stresses etc. However, the molecular functioning mechanism of $H_2S$ was still unclear. The primary objective of this research was to analyze the transcriptional differences and functional genes involved in the $H_2S$ responses. In details, 4-week-old plantlets in tissue culture of grapevine (Vitis vinifera L.) cultivar 'Zuoyouhong' were sprayed with 0.1 mM NaHS for 12 h, and then transcriptome sequencing and qRT-PCR analysis were used to study the transcriptional differences and functional genes involved in the $H_2S$ responses. Our results indicated that 650 genes were differentially expressed after $H_2S$ treatment, in which 224 genes were up-regulated and 426 genes were down-regulated. The GO enrichment analysis and KEGG enrichment analysis results indicated that the up-regulated genes after $H_2S$ treatment focused on carbon metabolism, biosynthesis of amino acids, and glycolysis/gluconeogenesis, and the down-regulated genes were mainly in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. Analyzing the transcription factor coding genes in details, it was indicated that 10 AP2/EREBPs, 5 NACs, 3 WRKYs, 3 MYBs, and 2 bHLHs etc. transcription factor coding genes were up-regulated, while 4 MYBs, 3 OFPs, 3 bHLHs, 2 AP2/EREBPs, 2 HBs etc. transcription factor coding genes were down-regulated. Taken together, $H_2S$ increased the productions in secondary metabolites and a variety of defensive compounds to improve plant development and abiotic resistance, and extend fruits postharvest shelf life by regulating the expression of AP2/EREBPs, WRKYs, MYBs, CABs, GRIP22, FERRITINs, TPSs, UGTs, and GHs etc.

• Animal Bioscience
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• v.35 no.2
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• pp.196-203
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• 2022

Objective: This study compared differentially expressed genes (DEGs) between groups with high and low numbers of fine marbling particles (NFMP) in the longissimus thoracis muscle (LT) of Korean cattle to understand the molecular events associated with fine marbling particle formation. Methods: The size and distribution of marbling particles in the LT were assessed with a computer image analysis method. Based on the NFMP, 10 LT samples were selected and assigned to either high- (n = 5) or low- (n = 5) NFMP groups. Using RNA sequencing, LT transcriptomic profiles were compared between the high- and low-NFMP groups. DEGs were selected at p<0.05 and |fold change| >2 and subjected to functional annotation. Results: In total, 328 DEGs were identified, with 207 up-regulated and 121 down-regulated genes in the high-NFMP group. Pathway analysis of these DEGs revealed five significant (p<0.05) Kyoto encyclopedia of genes and genomes pathways; the significant terms included endocytosis (p = 0.023), protein processing in endoplasmic reticulum (p = 0.019), and adipocytokine signaling pathway (p = 0.024), which are thought to regulate adipocyte hypertrophy and hyperplasia. The expression of sirtuin4 (p<0.001) and insulin receptor substrate 2 (p = 0.043), which are associated with glucose uptake and adipocyte differentiation, was higher in the high-NFMP group than in the low-NFMP group. Conclusion: Transcriptome differences between the high- and low-NFMP groups suggest that pathways regulating adipocyte hyperplasia and hypertrophy are involved in the marbling fineness of the LT.

• Mycobiology
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• v.51 no.5
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• pp.360-371
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• 2023

Hispidin is an important styrylpyrone produced by Sanghuangporus sanghuang. To analyze hispidin biosynthesis in S. sanghuang, the transcriptomes of hispidin-producing and non-producing S. sanghuang were determined by Illumina sequencing. Five PKSs were identified using genome annotation. Comparative analysis with the reference transcriptome showed that two PKSs (ShPKS3 and ShPKS4) had low expression levels in four types of media. The gene expression pattern of only ShPKS1 was consistent with the yield variation of hispidin. The combined analyses of gene expression with qPCR and hispidin detection by liquid chromatography-mass spectrometry coupled with ion-trap and time-of-flight technologies (LCMS-IT-TOF) showed that ShPKS1 was involved in hispidin biosynthesis in S. sanghuang. ShPKS1 is a partially reducing PKS gene with extra AMP and ACP domains before the KS domain. The domain architecture of ShPKS1 was AMP-ACP-KS-AT-DH-KR-ACP-ACP. Phylogenetic analysis shows that ShPKS1 and other PKS genes from Hymenochaetaceae form a unique monophyletic clade closely related to the clade containing Agaricales hispidin synthase. Taken together, our data indicate that ShPKS1 is a novel PKS of S. sanghuang involved in hispidin biosynthesis.

• Genomics & Informatics
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• v.16 no.4
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• The Plant Pathology Journal
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• v.33 no.5
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• pp.458-466
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• 2017

Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight, is a major threat to rice productivity. Here, we performed RNA-Seq based transcriptomic analysis of Xoo transcripts isolated under in planta growth (on both susceptible and resistant hosts) and in vitro culture conditions. Our in planta extraction method resulted in successful enrichment of Xoo cells and provided RNA samples of high quality. A total of 4,619 differentially expressed genes were identified between in planta and in vitro growth conditions. The majority of the differentially expressed genes identified under in planta growth conditions were related to the nutrient transport, protease activity, stress tolerance, and pathogenicity. Among them, over 1,300 differentially expressed genes were determined to be secretory, including 184 putative type III effectors that may be involved in Xoo pathogenicity. Expression pattern of some of these identified genes were further validated by semi-quantitative RT-PCR. Taken together, these results provide a transcriptome overview of Xoo under in planta and in vitro growth conditions with a focus on its pathogenic processes, deepening our understanding of the behavior and pathogenicity of Xoo.

• Molecules and Cells
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• v.39 no.2
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• pp.141-148
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• 2016

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.