• International Journal of Stem Cells
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• 제16권2호
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• pp.202-214
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• 2023

Background and Objectives: To investigate the role of exosomes from periodontal ligament cells (PDLCs) in bone marrow mesenchymal stem cell (BMSC) migration. Methods and Results: Human PDLCs were applied cyclic tension stretching. Exosomes were extracted from cultured PDLCs by ultracentrifugation, then characterized for their size, morphology and protein markers by NTA, TEM and western blotting. The process that PKH26-labeled exosomes taken up by BMSCs was assessed by confocal microscope. BMSC migration was examined by Transwell assay. Exosomes derived from PDLCs were identified. Cyclic tension stretch application on PDLCs can enhance the migration ability of BMSCs through exosomes. The exosomal miRNA expression profiles of unstretched and stretched PDLCs were tested by miRNA microarray. Four miRNAs (miR-4633-5p, miR-30c-5p, miR-371a-3p and let-7b-3p) were upregulated and six (miR-4689, miR-8485, miR-4655-3p, miR-4672, miR-3180-5p and miR-4476) were downregulated in the exosomes after stretching. Sixteen hub proteins were found in the miRNA-mRNA network. Gene Ontology and KEGG pathway analyses demonstrated that the target genes of differentially expressed exosomal miRNAs closely related to the PI3K pathway and vesicle transmission. Conclusions: The exosomes derived from cyclic tension-stretched PDLCs can promote the migration of BMSCs. Alternation of microRNA profiles provides a basis for further research on the regulatory function of the exosomal miRNAs of PDLCs during orthodontic tooth movement.

• Korean Journal of Acupuncture
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• 제41권1호
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• pp.7-15
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• 2024

Objectives : This study aimed to predict the effectiveness and potential of Schizonepeta tenuifolia as an anticancer treatment for non-small cell lung cancer through network-based pharmacology and cellular experiment. Methods : To identify the major bioactive compounds in Schizonepeta tenuifolia, we used the Traditional Chinese Medicine Systems. The target genes for the cancer treatment were selected using the UniProt database and the networked using Cytoscape. We performed functional enrichment analysis based on the Gene Ontology Biological Process and Kyoto Encyclopedia of Genes and Genomes Pathways to predict the mechanisms. To investigate the effect of Schizonepeta tenuifolia on lung cancer cell growth, we treated A549 cells, a lung cancer cell line, with different concentrations of the drug and used the MTT assay for cell viability. Results : Research has shown that the most effective mechanism of active compounds from Schizonepeta tenuifolia is through the pathway of cancer. The results of the network pharmacology analysis indicate that Schizonepeta tenuifolia has potential medicinal value as an adjuvant in anticancer treatment. The concentration-dependent inhibition of cell viability was observed on A549 cells. Furthermore, synergistic anticancer activity with Doxorubicin was also observed. Conclusions : Through a network pharmacological approach, Schizonepeta tenuifolia was predicted to have potential as an anticancer agent, and its efficacy was experimentally demonstrated using A549 cells. These findings suggest that Schizonepeta tenuifolia is a promising candidate for future research.

• Journal of Ginseng Research
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• 제47권5호
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• pp.645-653
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• 2023

Background: Changes to work-life balance has increased the incidence of cervical cancer among younger people. A minor ginseng saponin known as ginsenoside Rk1 can inhibit the growth and survival of human cancer cells; however, whether ginsenoside Rk1 inhibits HeLa cell proliferation is unknown. Methods and results: Ginsenoside Rk1 blocked HeLa cells in the G0/G1 phase in a dose-dependent manner and inhibited cell division and proliferation. Ginsenoside Rk1 markedly also activated the apoptotic signaling pathway via caspase 3, PARP, and caspase 6. In addition, ginsenoside Rk1 increased LC3B protein expression, indicating the promotion of the autophagy signaling pathway. Protein processing in the endoplasmic reticulum signaling pathway was downregulated in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, consistent with teal-time quantitative PCR and western blotting that showed YOD1, HSPA4L, DNAJC3, and HSP90AA1 expression levels were dramatically decreased in HeLa cells treated with ginsenoside Rk1, with YOD1 was the most significantly inhibited by ginsenoside Rk1 treatment. Conclusion: These findings indicate that the toxicity of ginsenoside Rk1 in HeLa cells can be explained by the inhibition of protein synthesis in the endoplasmic reticulum and enhanced apoptosis, with YOD1 acting as a potential target for cervical cancer treatment.

• Journal of Microbiology and Biotechnology
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• 제34권4호
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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.

• BMB Reports
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• 제40권5호
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• pp.757-764
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• 2007

Marbling of cattle meat is dependent on the coordinated expression of multiple genes. Cattle dramatically increase their intramuscular fat content in the longissimus dorsi muscle between 12 and 27 months of age. We used the annealing control primer (ACP)-differential display RT-PCR method to identify differentially expressed genes (DEGs) that may participate in the development of intramuscular fat between early (12 months old) and late fattening stages (27 months old). Using 20 arbitrary ACP primers, we identified and sequenced 14 DEGs. BLAST searches revealed that expression of the MDH, PI4-K, ferritin, ICER, NID-2, WDNMI, telethonin, filamin, and desmin (DES) genes increased while that of GAPD, COP VII, ACTA1, CamK II, and nebulin decreased during the late fattening stage. The results of functional categorization using the Gene Ontology database for 14 known genes indicated that MDH, GAPD, and COP VII are involved in metabolic pathways such as glycolysis and the TCA cycle, whereas telethonin, filamin, nebulin, desmin, and ACTA1 contribute to the muscle contractile apparatus, and PI4-K, CamK II, and ICER have roles in signal transduction pathways regulated by growth factor or hormones. The final three genes, NID-2, WDNMI, and ferritin, are involved in iron transport and extracellular protein inhibition. The expression patterns were confirmed for seven genes (MDH, PI4-K, ferritin, ICER, nebulin, WDNMI, and telethonin) using real-time PCR. We found that the novel transcription repressor ICER gene was highly expressed in the late fattening stage and during bovine preadipocyte differentiation. This information may be helpful in selecting candidate genes that participate in intramuscular fat development in cattle.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.140-140
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• 2017

Nutritious and functional foods from crop have received great attention in recent years. Colored-grain wheat contains high phenolic compound and a large number of flavonoid. The anthocyanin and polyphenolic synthesis and accumulation is generally stimulated in response to biotic or abiotic stresses. Here, we analyzed genome wide transcripts in seedling of colored-grain wheat response to ABA and PEG treatment. About 900 and 1500 transcripts (p-value < 0.05) from ABA and PEG treatment were aligned to IWGSC1+popseq DB which is composed of over 110,000 transcripts including 100,934 coding genes. NR protein sequences of Poaceae from NCBI and protein sequence of transcription factors originated from 83 species in plant transcription factor database v3.0 were used for annotation of putative transcripts. Gene ontology analysis were conducted and KEGG mapping was performed to show expression pattern of biosynthesis genes related in flavonoid, isoflavonoid, flavons and anthocyanin biopathway. DroughtDB (http://pgsb.helmholtz-muenchen.de/droughtdb/) was used for detection of DEGs to explain that physiological and molecular drought avoidance by drought tolerance mechanisms. Drought response pathway, such as ABA signaling, water and ion channels, detoxification signaling, enzymes of osmolyte biosynthesis, phospholipid metabolism, signal transduction, and transcription factors related DEGs were selected to explain response mechanism under water deficit condition. Anthocyanin, phenol compound, and DPPH radical scavenging activity were measured and antioxidant activity enzyme assays were conducted to show biochemical adaptation under water deficit condition. Several MYB and bHLH transcription factors were up-regulated in both ABA and PEG treated condition, which means highly expressed MYB and bHLH transcription factors enhanced the expression of genes related in the biosynthesis pathways of flavonoids, such as anthocyanin and dihydroflavonols in colored wheat seedlings. Subsequently, the accumulation of total anthocyanin and phenol contents were observed in colored wheat seedlings, and antioxidant capacity was promoted by upregulation of genes involved in maintaining redox state and activation of antioxidant scavengers, such as CAT, APX, POD, and SOD in colored wheat seedlings under water deficit condition. This work may provide valuable and basic information for further investigation of the molecular responses of colored-grain wheat to water deficit stress and for further gene-based studies.

• 한국가금학회지
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• 제41권4호
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• pp.305-311
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• 2014

복제수변이(Copy number variation, CNV)는 DNA 다양한 구조적 변화의 한 형태이다. 복제수변이는 인간의 질병 및 농업의 생산성에 영향을 미치는 것으로 알려져 있다. 이전 우리나라의 닭의 품종은 유럽에서 유입되어진 품종을 기반으로 구축되어져 있었다. 따라서 농촌진흥청 국립축산과학원에서는 20년 동안 재래품종을 복원하려고 노력하였고, 5품종 12계통으로 복원하였다. 최근 염기서열분석 기술의 발달로, 해상도가 좋은 게놈 전체의 복제수변이를 발굴할 수 있게 되었다. 그러나 한국 재래닭 품종에 대해서는 체계적인 연구가 이루어지지 않고 있다. 본 연구에서는 한국 재래 닭(계통 L)에 대해서 게놈 전체의 염기서열을 분석하고 닭의 참고서열과 비교하여 재래닭에서 확인된 복제수 변이를 보고하였다. 닭의 28개 염색체에서 총 501개의 복제수 변이를 확인하였고, 이를 Gain과 Loss로 나누어서 표시하였다. 또한 우리는 501개의 복제수 변이를 포함하고 있는 유전자의 기능을 분류하였다. 그 결과, 전사 및 유전자 조절에 관련된 유전자들이 많이 분류되었다. 본 연구의 결과는 복제수 변이와 한국 재래닭의 경제형질 간의 연관성을 설명할 수 있는 기초자료로 활용될 것으로 사료된다.

• 한국가금학회지
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• 제47권1호
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• pp.9-19
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• 2020

본 연구는 고병원성 조류 인플루엔자 바이러스(high pathogenic avian influenza virus; HPAIV)와 저병원성 조류인플루엔자 바이러스(low pathogenic avian virus; LPAIV)가 감염된 오리의 폐세포에서 보고된 기존 전사체 데이터를 재분석하여 조류 인플루엔자 감염에 대응하는 숙주의 공통 전사체를 발굴하고, 생물정보 분석을 실시하여 바이오 마커로서 가능성을 제시하기 위하여 수행하였다. 이전 연구에서 생산된 microarray 데이터 세트를 재분석하여, HPAIV와 LPAIV가 각각 감염된 오리의 폐세포에서 각각 총 731 및 439개의 차등발현 유전자를 발굴하였다. 이들 차등발현 유전자 중에서, 227개의 유전자가 HPAIV와 LPAIV가 감염된 세포에서 공통적으로 조절되어, 193개의 유전자는 발현이 증가한 반면, 34개의 유전자는 발현이 감소하였다. 생물정보 분석을 통하여 차등발현 유전자들의 기능에 대한 주석달기를 실시하여, 리보솜과 단백질 대사 및 유전자 발현 관련 GO가 풍부해짐을 확인하였다. REACTOME 분석을 통하여 단백질 및 RNA 대사 경로 및 콜라겐 생합성과 변형을 포함한 조직 복구 경로가 조절됨을 확인하였다. 보다 구체적으로, 번역 및 RNA 품질 관리 경로에 관여하는 단백질을 코딩하는 유전자는 HPAIV 및 LPAIV 감염에 반응하여 발현의 증가 또는 감소하는 방향으로 조절되어 AIV가 숙주 번역 기계를 억제함으로써 숙주 방어 시스템을 회피할 수 있거나 번역을 위해 세포질로 내보내기 전에 AIV가 억제될 수 있음을 시사한다. AIV 감염은 바이러스 감염으로 인한 조직의 병변 형성을 조절하는 경로를 활성화시킬 수 있음을 시사한다.

• Animal Bioscience
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• 제35권1호
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• pp.115-125
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• 2022

Objective: Intramuscular fat (IMF) is a critical economic indicator of pork quality. Studies on IMF among different pig breeds have been performed via high-throughput sequencing, but comparisons within the same pig breed remain unreported. Methods: This study was performed to explore the gene profile and identify candidate long noncoding RNA (lncRNAs) and mRNAs associated with IMF deposition among Laiwu pigs with different IMF contents. Based on the longissimus dorsi muscle IMF content, eight pigs from the same breed and management were selected and divided into two groups: a high IMF (>12%, H) and low IMF group (<5%, L). Whole-transcriptome sequencing was performed to explore the differentially expressed (DE) genes between these two groups. Results: The IMF content varied greatly among Laiwu pig individuals (2.17% to 13.93%). Seventeen DE lncRNAs (11 upregulated and 6 downregulated) and 180 mRNAs (112 upregulated and 68 downregulated) were found. Gene Ontology analysis indicated that the following biological processes played an important role in IMF deposition: fatty acid and lipid biosynthetic processes; the extracellular signal-regulated kinase cascade; and white fat cell differentiation. In addition, the peroxisome proliferator-activated receptor, phosphatidylinositol-3-kinase-protein kinase B, and mammalian target of rapamycin pathways were enriched in the pathway analysis. Intersection analysis of the target genes of DE lncRNAs and mRNAs revealed seven candidate genes associated with IMF accumulation. Five DE lncRNAs and 20 DE mRNAs based on the pig quantitative trait locus database were identified and shown to be related to fat deposition. The expression of five DE lncRNAs and mRNAs was verified by quantitative real time polymerase chain reaction (qRT-PCR). The results of qRT-PCR and RNA-sequencing were consistent. Conclusion: These results demonstrated that the different IMF contents among pig individuals may be due to the DE lncRNAs and mRNAs associated with lipid droplets and fat deposition.

• Journal of Veterinary Science
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• 제23권6호
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• pp.90.01-90.13
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• 2022

Background: Insulin regulates glucose homeostasis and has important effects on metabolism, cell growth, and differentiation. Depending on the cell type and physiological context, insulin signal has specific pathways and biological outcomes in different tissues and cells. For studying the signal pathway of insulin on glycolipid metabolism in porcine embryonic fibroblast (PEF), we used high-throughput sequencing to monitor gene expression patterns regulated by insulin. Objectives: The goal of our research was to see how insulin affected glucose and lipid metabolism in PEFs. Methods: We cultured the PEFs with the addition of insulin and sampled them at 0, 48, and 72 h for RNA-Seq analysis in triplicate for each time point. Results: At 48 and 72 h, 801 and 1,176 genes were differentially expressed, respectively. Of these, 272 up-regulated genes and 264 down-regulated genes were common to both time points. Gene Ontology analysis was used to annotate the functions of the differentially expressed genes (DEGs), the biological processes related to lipid metabolism and cell cycle were dominant. And the DEGs were significantly enriched in interleukin-17 signaling pathway, phosphatidylinositol-3-kinase-protein kinase B signaling pathway, pyruvate metabolism, and others pathways related to lipid metabolism by Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Conclusions: These results elucidate the transcriptomic response to insulin in PEF. The genes and pathways involved in the transcriptome mechanisms provide useful information for further research into the complicated molecular processes of insulin in PEF.