• The Korean Journal of Physiology and Pharmacology
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• v.14 no.5
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• pp.265-272
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• 2010

Follicular cystic ovary (FCO) is one of the most frequently diagnosed ovarian diseases and is a major cause of reproductive failure in mammalian species. However, the mechanism by which FCO is induced remains unclear. Genetic alterations which affect the functioning of many kinds of cells and/or tissues could be present in cystic ovaries. In this study, we performed a comparison analysis of gene expression in order to identify new molecules useful in discrimination of bovine FCO with follicular cystic follicles (FCFs). Normal follicles and FCFs were classified based on their sizes (5 to 10 mm and $\geq25mm$). These follicles had granulosa cell layer and theca interna and the hormone $17{\beta}$-estradiol ($E_2$)/ progesterone ($P_4$) ratio in follicles was greater than one. Perifollicular regions including follicles were used for the preparation of RNA or protein. Differentially expressed genes (DEG) that showed greater than a 2-fold change in expression were screened by the annealing control primer (ACP)-based PCR method using $GeneFishing^{TM}$ DEG kits in bovine normal follicles and FCFs. We identified two DEGs in the FCFs: ribosomal protein L15 (RPL15) and microtubule-associated protein 1B (MAP1B) based on BLAST searches of the NCBI GenBank. Consistent with the ACP analysis, semi-quantitative PCR data and Western blot analyses revealed an up-regulation of RPL15 and a down-regulation of MAP1B in FCFs. These results suggest that RPL15 and MAP1B may be involved in the regulation of pathological processes in bovine FCOs and may help to establish a bovine gene data-base for the discrimination of FCOs from normal ovaries.

• Molecules and Cells
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• v.41 no.6
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• pp.532-544
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• 2018

Gastrointestinal stromal tumours (GIST) are the most common mesenchymal tumors of the gastrointestinal (GI) tract. In order to investigate a new treatment fot GIST, we hypothesized the effect of miR-374b targeting PTEN gene-mediated PI3K/Akt signal transduction pathway on proliferation and apoptosis of human gastrointestinal stromal tumor (GIST) cells. We obtained GIST tissues and adjacent normal tissues from 143 patients with GIST to measure the levels of miR-374b, PTEN, PI3K, Akt, caspase9, Bax, MMP2, MMP9, ki67, PCNA, P53 and cyclinD1. Finally, cell viability, cell cycle and apoptosis were detected. According to the KFGG analysis of DEGs, PTEN was involved in a variety of signaling pathways and miRs were associated with cancer development. The results showed that MiR-374b was highly expressed, while PTEN was downregulated in the GIST tissues. The levels of miR-374b, PI3K, AKT and PTEN were related to tumor diameter and pathological stage. Additionally, miR-374b increased the mRNA and protein levels of PI3K, Akt, MMP2, MMP9, P53 and cyclinD1, suggesting that miR-374b activates PI3K/Akt signaling pathway in GIST-T1 cells. Moreover, MiR374b promoted cell viability, migration, invasion, and cell cycle entry, and inhibited apoptosis in GIST cells. Taken together, the results indicated that miR-374b promotes viability and inhibits apoptosis of human GIST cells by targeting PTEN gene through the PI3K/Akt signaling pathway. Thus, this study provides a new potential target for GIST treatment.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.359-366
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• 2016

Tradescantia is a perennial plant in the family of Commelinaceae. It is known to be sensitive to radiation. In this study, Tradescantia BNL 4430 was irradiated with gamma radiation at doses of 50 to 1,000 mGy in a phytotron equipped with a $^{60}Co$ radiation source at Korea Atomic Energy Research Institute, Korea. At 13 days after irradiation, we extracted RNA from irradiated floral tissues for RNA-seq. Transcriptome assembly produced a total of 77, 326 unique transcripts. In plantlets exposed to 50, 250, 500, and 1000 mGy, the numbers of up-regulated genes with more than 2-fold of expression compared that in the control were 116, 222, 246, and 308, respectively. Most of the up-regulated genes induced by 50 mGy were heat shock proteins (HSPs) such as HSP 70, indicating that protein misfolding, aggregation, and translocation might have occurred during radiation stress. Similarly, highly up-regulated transcripts of the IQ-domain 6 were induced by 250 mGy, KAR-UP oxidoreductase 1 was induced by 500 mGy, and zinc transporter 1 precursor was induced by 1000 mGy. Reverse transcriptase (RT) PCR and quantitative real time PCR (qRT-PCR) further validated the increased mRNA expression levels of selected genes, consistent with DEG analysis results. However, 2.3 to 97- fold higher expression activities were induced by different doses of radiation based on qRT-PCR results. Results on the transcriptome of Tradescantia in response to radiation might provide unique identifiers to develop in situ monitoring kit for measuring radiation exposure around radiation facilities.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.347-358
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• 2016

Brassinosteroid (BR), a plant steroid hormone, plays key roles in numerous growth and developmental processes as well as tolerance to both abiotic and biotic stress. To understand the biological networks involved in BR-mediated signaling pathways and stress tolerance, we performed comparative genome-wide transcriptome analysis of a constitutively activated BR bes1-D mutant with an Agilent Arabidopsis $4{\times}44K$ oligo chip. As a result, we newly identified 1,091 (562 up-regulated and 529 down-regulated) significant differentially expressed genes (DEGs). The combination of GO enrichment and protein network analysis revealed that stress-related processes, such as metabolism, development, abiotic/biotic stress, immunity, and defense, were critically linked to BR signaling pathways. Among the identified gene sets, we confirmed more than a 6-fold up-regulation of NB-ARC and FLS2 in bes1-D plants. However, some genes, including TIR1, TSA1 and OCP3, were down-regulated. Consistently, BR-activated plants showed higher tolerance to drought stress and pathogen infection compared to wild-type controls. In this study, we newly developed a useful, comprehensive method for large-scale identification of critical network and gene sets with global transcriptome analysis using a microarray. This study also showed that gain of function in the bes1-D gene can regulate the adaptive response of plants to various stressful conditions.

• Korean Journal of Poultry Science
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• v.44 no.3
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• pp.211-223
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• 2017

Transforming growth factor beta ($TGF-{\beta}$) signaling pathways are involved in the regulation of proliferation, differentiation, immunity, survival, and apoptosis of many cells. The aim of this study was to investigate the differential expression of $TGF-{\beta}$-related genes, and their interactions and regulators in the spleen 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) by Eimeria maxima and Clostridium perfringens infection. By using high-throughput RNA-sequencing, we investigated 76 $TGF-{\beta}$-related genes that were significantly and differentially expressed in the spleens of the chickens. Approximately 20 $TGF-{\beta}$ pathway genes were further verified by qRT-PCR, and the results were consistent with our RNA sequencing data. All 76 identified genes were analyzed through Gene Ontology and mapped onto the KEGG chicken $TGF-{\beta}$ pathway. Our results demonstrated that several key genes, including $TGF-{\beta}$1-3, bone morphogenetic proteins (BMP)1-7, inhibitor of differentiation (ID) proteins ID1-3, SMAD1-9, and Jun, showed a markedly differential expression between the two chicken lines, relative to their respective controls. We then further predicted 24 known miRNAs that targeted BMP7 mRNA from 139 known miRNAs in the two chicken lines. Among these, six miRNAs were measured by qRT-PCR. In conclusion, this study is the first to analyze most of the genes, interactions, and regulators of the $TGF-{\beta}$ pathway in the innate immune responses of NE afflicted chickens.

• Journal of The Korean Society of Grassland and Forage Science
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• v.37 no.3
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• pp.231-236
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• 2017

Salt stress is one of the most limiting factors that reduce plant growth, development and yield. However, identification of salt-inducible genes is an initial step for understanding the adaptive response of plants to salt stress. In this study, we used an annealing control primer (ACP) based GeneFishing technique to identify differentially expressed genes (DEGs) in Italian ryegrass seedlings under salt stress. Ten-day-old seedlings were exposed to 100 mM NaCl for 6 h. Using 60 ACPs, a total 8 up-regulated genes were identified and sequenced. We identified several promising genes encoding alpha-glactosidase b, light harvesting chlorophyll a/b binding protein, metallothionein-like protein 3B-like, translation factor SUI, translation initiation factor eIF1, glyceraldehyde-3-phosphate dehydrogenase 2 and elongation factor 1-alpha. These genes were mostly involved in plant development, signaling, ROS detoxification and salt acclimation. However, this study provides new molecular information of several genes to understand the salt stress response. These genes would be useful for the enhancement of salt stress tolerance in plants.

• Journal of Ginseng Research
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• v.47 no.1
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• pp.159-165
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• 2023

Background: Red ginseng marc, the residue of red ginseng left after water extraction, is rich in dietary fiber. Dietary fiber derived from fruits or vegetables can promote the proliferation of probiotics, and it is a key technology in the food industry to increase the productivity of probiotics by adding growth-enhancing substances such as dietary fiber. In this study, the effect of red ginseng dietary fiber (RGDF) on the growth of probiotic bacterial strains was investigated at the phenotypic and genetic levels. Methods: We performed transcriptome profiling of Lactiplantibacillus plantarum IDCC3501 in two phases of culture (logarithmic (L)-phase and stationary (S)-phase) in two culture conditions (with or without RGDF) using RNA-seq. Differentially expressed genes (DEGs) were identified and classified according to Gene Ontology terms. Results: The growth of L.plantarum IDCC3501 was enhanced in medium supplemented with RGDF up to 2%. As a result of DEG analysis, 29 genes were upregulated and 30 were downregulated in the RGDF-treated group in the L-phase. In the S-phase, 57 genes were upregulated and 126 were downregulated in the RGDF-treated group. Among the upregulated genes, 5 were upregulated only in the L-phase, 10 were upregulated only in the S-phase, and 3 were upregulated in both the L- and S-phases. Conclusions: Transcriptome analysis could be a valuable tool for elucidating the molecular mechanisms by which RGDF promotes the proliferation of L.plantarum IDCC3501. This growth-promoting effect of RGDF is important, since RGDF could be used as a prebiotic source without additional chemical or enzymatic processing.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.197-197
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• 2022

Wheat is highly susceptible to heat stress, which significantly reduces grain yield. In this study, we used RNA-seq technology to analyze the transcript expression at three different time-points after heat treatment in three cultivars differing in their susceptibility to heat stress: Jopum, Keumkang, and Olgeuru. A total of 11,751, 8850, and 14,711; 10,959,7946, and 14,205; and 22,895,13,060, and 19,408 differentially-expressed genes (log2 fold-change > 1 and FDR (padj) < 0.05) were identified in Jopum, Keumkang, and Olgeuru in the control vs. 6-h, in the control vs. 12-h, and in the 6-h vs. 12-h heat treatment, respectively. Functional enrichment analysis showed that the biological processes for DEGs, such as the cellular response to heat and oxidative stress-and including the removal of superoxide radicals and the positive regulation of superoxide dismutase activity-were significantly enriched among the three comparisons in all three cultivars. Furthermore, we investigated the differential expression patterns of reactive oxygen species (ROS)-scavenging enzymes, heat shock proteins, and heat-stress transcription factors using qRT-PCR to confirm the differences in gene expression among the three varieties under heat stress. This study contributes to a better understanding of the wheat heat-stress response at the early growth stage and the varietal differences in heat tolerancea.

• 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.4
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• pp.880-890
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• 2024

The immunomodulatory effects of Euglena gracilis (Euglena) and its bioactive component, β-1,3-glucan (paramylon), have been clarified through various studies. However, the detailed mechanisms of the immune regulation remain to be elucidated. This study was designed not only to investigate the immunomodulatory effects but also to determine the genetic mechanisms of Euglena and β-glucan in cyclophosphamide (CCP)-induced immunosuppressed mice. The animals were orally administered saline, Euglena (800 mg/kg B.W.) or β-glucan (400 mg/kg B.W.) for 19 days, and CCP (80 mg/kg B.W.) was subsequently administered to induce immunosuppression in the mice. The mice exhibited significant decreases in body weight, organ weight, and the spleen index. However, there were significant improvements in the spleen weight and the spleen index in CCP-induced mice after the oral administration of Euglena and β-glucan. Transcriptome analysis of the splenocytes revealed immune-related differentially expressed genes (DEGs) regulated in the Euglena- and β-glucantreated groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that pathways related with interleukin (IL)-17 and cAMP play significant roles in regulating T cells, B cells, and inflammatory cytokines. Additionally, Ptgs2, a major inflammatory factor, was exclusively expressed in the Euglena-treated group, suggesting that Euglena's beneficial components, such as carotenoids, could regulate these genes by influencing immune lymphocytes and inflammatory cytokines in CCP-induced mice. This study validated the immunomodulatory effects of Euglena and highlighted its underlying mechanisms, suggesting a positive contribution to the determination of phenotypes associated with immune-related diseases and the research and development of immunotherapies.