• Proceedings of the Korean Society of Crop Science Conference
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• 2019.09a
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• pp.148-148
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• 2019

Wheat is a very important crop as a food source worldwide, but gluten in wheat causes a variety of allergic reactions. Previous studies have developed ${\omega}-5$ gliadin deleted O-free, known as the central antigen of WDEIA (wheat-dependent exercise-induced anaphylaxis). In this study, we performed RNA sequencing on the grains and leaves of the allergic-reduced species O-free and their cultivars, Keumkang and Olgeuru, to analyze differentially expressed genes (DEG) based on different cultivars and tissues. Tissues of all species were biologically repeated three times. We used bowtie2 version 2.3.5.1 to get sequence data from RNAseq and used cufflinks and Tophat programs to find DEG. When comparing leaf and grain tissues, a total of 1,244 DEGs were found in the leaf tissues while only 563 DEGs were found in the grain tissues. As a result of gene ontology analysis of differentially expressed genes, the leaf tissues were mostly included in the "catalytic activity" part of molecular function, "metabolic process" part of biological process, and "membrane" part of cell component. The grain tissues were mostly included in the "metabolic process" part of biological process, "binding" and "catalytic activity" part of molecular function, and "membrane, cell, cell part" parts of cell component. Based on these results, we present information on the differentially expressed genes of the three cultivars of leaves and grains. This study could be an important basis for studying the characteriztion of O-free.

• Journal of Animal Science and Technology
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• v.54 no.6
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• pp.383-394
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• 2012

Microarray analyses provide information that can be used to enhance the efficiency of livestock production. For example, microarray profiling can potentially identify the biological processes responsible for the phenotypic characteristics of porcine liver. We performed transcriptome profiling to identify differentially expressed genes (DEGs) in liver of pigs from two breeds, the Korean native pigs (KNP) and Yorkshire pigs. We correctly identified expected DEGs using factor analysis for robust microarray summarization (FARMS) and robust multi-array average (RMA) strategies. We identified 366 DEGs in liver (p<0.05, fold-change>2). We also performed functional analyses, including gene ontology and molecular network analyses. In addition, we identified the regulatory relationship between DEGs and their transcription factors using in silico and qRT-PCR analysis. Our findings suggest that DEGs and their transcription factors may have a potential role in adipogenesis and/or lipid deposition in liver tissues of two pig breeds.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7501-7508
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• 2013

Background: Chronic myeloid leukemia (CML) is a myeloproliferative disorder of hematopoietic stem cell scarrying the Philadelphia (Ph) chromosome and an oncogenic BCR-ABL1 fusion gene. The tyrosine kinase inhibitor (TKI) of BCR-ABL1 kinase is a treatment of choice for control of CML. Objective: Recent studies have demonstrated that miRNAs within exosomes from cancer cells play crucial roles in initiation and progression. This study was performed to assess miRNAs within exosomes of K562 cells. Methods: miRNA microarray analysis of K562 cells and K562 cell-derived exosomes was conducted with the 6th generation miRCURYTM LNA Array (v.16.0). Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were also carried out. GO terms and signaling pathways were categorized into 66 classes (including homophilic cell adhesion, negative regulation of apoptotic process, cell adhesion) and 26 signaling pathways (such as Wnt). Results: In exosomes, 49 miRNAs were up regulated as compared to K562 cells, and two of them were further confirmed by quantitative real-time PCR. There are differentially expressed miRNAs between K562 cell derived-exosomes and K562 cells. Conclusion: Selectively expressed miRNAs in exosomes may promote the development of CML via effects on interactions (e.g. adhesion) of CML cells with their microenvironment.

• Environmental Analysis Health and Toxicology
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• v.26
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• pp.10.1-10.7
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• 2011

Objects: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. Method: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C.ripairus using pyrosequencing method. Results: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value${\leq}1^{-5}$) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. Conclusions: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

• Parasites, Hosts and Diseases
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• v.49 no.3
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• pp.221-228
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• 2011

Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.

• BMB Reports
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• v.54 no.9
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• pp.464-469
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• 2021

Cardiomyocyte differentiation occurs through complex and finely regulated processes including cardiac lineage commitment and maturation from pluripotent stem cells (PSCs). To gain some insight into the genome-wide characteristics of cardiac lineage commitment, we performed transcriptome analysis on both mouse embryonic stem cells (mESCs) and human induced PSCs (hiPSCs) at specific stages of cardiomyocyte differentiation. Specifically, the gene expression profiles and the protein-protein interaction networks of the mESC-derived platelet-derived growth factor receptor-alpha (PDGFRα)⁺ cardiac lineage-committed cells (CLCs) and hiPSC-derived kinase insert domain receptor (KDR)⁺ and PDGFRα⁺ cardiac progenitor cells (CPCs) at cardiac lineage commitment were compared with those of mesodermal cells and differentiated cardiomyocytes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the genes significantly upregulated at cardiac lineage commitment were associated with responses to organic substances and external stimuli, extracellular and myocardial contractile components, receptor binding, gated channel activity, PI3K-AKT signaling, and cardiac hypertrophy and dilation pathways. Protein-protein interaction network analysis revealed that the expression levels of genes that regulate cardiac maturation, heart contraction, and calcium handling showed a consistent increase during cardiac differentiation; however, the expression levels of genes that regulate cell differentiation and multicellular organism development decreased at the cardiac maturation stage following lineage commitment. Additionally, we identified for the first time the protein-protein interaction network connecting cardiac development, the immune system, and metabolism during cardiac lineage commitment in both mESC-derived PDGFRα⁺ CLCs and hiPSC-derived KDR⁺PDGFRα⁺ CPCs. These findings shed light on the regulation of cardiac lineage commitment and the pathogenesis of cardiometabolic diseases.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2023.04a
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• pp.63-63
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• 2023

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops and provides up to 30% of the world's sugar production. In this study, we mainly performed RNA-sequencing to obtain identify putative genes involved in biosynthesis pathway of sucrose in sugar beet and comparative transcriptomic analyses in the four developmental stages (50, 90, 160 and 330 days after seedling). As a result of the sugar content analysis, it was increased significantly from 50 to 160 days after seedling (DAS), and then decreased at 330 DAS. On the other hand, the taproot weight, length, and width were increased during all the growth periods. Out of 21,451 genes with expressed value, 21,402 (99.77%) genes had functional descriptions. Among the three comparisons, S1 (50 DAS) vs. S2 (90 DAS), S1 vs. S3 (160 DAS), and S1 vs. S4 (330 DAS), expression profiling of the transcripts was identified 4,991 with differentially expressed genes (DEGs). By comparing the top 20 enriched gene ontology (GO) terms as three comparisons, the top GO terms were commonly confirmed with external encapsulating structure, cell wall, and extracellular regions. In addition, the 38 enriched candidate genes related to sucrose biosynthetic pathway were screened from the entire DEG pool, and the candidate genes might be providing a basic data for further sugar metabolism studies in development of sugar beet taproot.

• Journal of Microbiology and Biotechnology
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• v.34 no.2
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• pp.270-279
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• 2024

Macrophages are versatile immune cells that play crucial roles in tissue repair, immune defense, and the regulation of immune responses. In the context of skeletal muscle, they are vital for maintaining muscle homeostasis but macrophage-induced chronic inflammation can lead to muscle dysfunction, resulting in skeletal muscle atrophy characterized by reduced muscle mass and impaired insulin regulation and glucose uptake. Although the involvement of macrophage-secreted factors in inflammation-induced muscle atrophy is well-established, the precise intracellular signaling pathways and secretion factors affecting skeletal muscle homeostasis require further investigation. This study aimed to explore the regulation of macrophage-secreted factors and their impact on muscle atrophy and glucose metabolism. By employing RNA sequencing (RNA-seq) and proteome array, we uncovered that factors secreted by lipopolysaccharide (LPS)-stimulated macrophages upregulated markers of muscle atrophy and pro-inflammatory cytokines, while concurrently reducing glucose uptake in muscle cells. The RNA-seq analysis identified alterations in gene expression patterns associated with immune system pathways and nutrient metabolism. The utilization of gene ontology (GO) analysis and proteome array with macrophage-conditioned media revealed the involvement of macrophage-secreted cytokines and chemokines associated with muscle atrophy. These findings offer valuable insights into the regulatory mechanisms of macrophage-secreted factors and their contributions to muscle-related diseases.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.4
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• pp.595-606
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• 2018

Objective: The Fusarium mycotoxins of deoxynivalenol (DON) and zerolenone (ZEN) cause health hazards for both humans and farm animals. Therefore, the main intention of this study was to reveal DON and ZEN effects on the mRNA expression of pro-inflammatory cytokines and other immune related genes in the liver of piglets. Methods: In the present study, 15 six-week-old piglets were randomly assigned to the following three different dietary treatments for 4 weeks: control diet, diet containing 8 mg DON/kg feed, and diet containing 0.8 mg ZEN/kg feed. After 4 weeks, liver samples were collected and sequenced using RNA-Seq to investigate the effects of the mycotoxins on genes and gene networks associated with the immune systems of the piglets. Results: Our analysis identified a total of 249 differentially expressed genes (DEGs), which included 99 upregulated and 150 downregulated genes in both the DON and ZEN dietary treatment groups. After biological pathway analysis, the DEGs were determined to be significantly enriched in gene ontology terms associated with many biological pathways, including immune response and cellular and metabolic processes. Consistent with inflammatory stimulation due to the mycotoxin-contaminated diet, the following Kyoto encyclopedia of genes and genomes pathways, which were related to disease and immune responses, were found to be enriched in the DEGs: allograft rejection pathway, cell adhesion molecules, graft-versus-host disease, autoimmune thyroid disease (AITD), type I diabetes mellitus, human T-cell leukemia lymphoma virus infection, and viral carcinogenesis. Genome-wide expression analysis revealed that DON and ZEN treatments downregulated the expression of the majority of the DEGs that were associated with inflammatory cytokines (interleukin 10 receptor, beta, chemokine [C-X-C motif] ligand 9), proliferation (insulin-like growth factor 1, major facilitator superfamily domain containing 2A, insulin-like growth factor binding protein 2, lipase G, and salt inducible kinase 1), and other immune response networks (paired immunoglobulin-like type 2 receptor beta, Src-like-adaptor-1 [SLA1], SLA3, SLA5, SLA7, claudin 4, nicotinamide N-methyltransferase, thyrotropin-releasing hormone degrading enzyme, ubiquitin D, histone $H_2B$ type 1, and serum amyloid A). Conclusion: In summary, our results demonstrated that high concentrations DON and ZEN disrupt immune-related processes in the liver.

• Horticultural Science & Technology
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• v.29 no.2
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• pp.116-122
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• 2011

In this study, we report the generation and analysis of 1,392 expressed sequence tags (ESTs) from Korean Stewartia (Stewartia koreana Nakai). A cDNA library was generated from the young leaf tissue and a total of 1,392 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. Finally, 1,301 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 100 nucleotides. A total of 893 unigene, consisting of 150 contigs and 743 singletons, was identified after assembling. Also, we identified 95 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 65% of ESTs were homologous with known function and 11.6% of ESTs were matched with putative or unknown function. The remaining 23.2% of ESTs showed no significant similarity to any protein sequences found in the public database. Annotation based searches against multiple databases including wine grape and populus sequences helped to identify putative functions of ESTs and unigenes. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Stewartia and provided for the useful tools as a genetic resource.