• Genes and Genomics
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• 제40권11호
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• pp.1199-1211
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• 2018

Soil acidification is one of major problems limiting crop growth and especially becoming increasingly serious in China owing to excessive use of nitrogen fertilizer. Only the STOP1 of Arabidopsis was identified clearly sensitive to proton rhizotoxicity and the molecular mechanism for proton toxicity tolerance of plants is still poorly understood. The main objective of this study was to investigate the transcriptomic change in plants under the low pH stress. The low pH as a single factor was employed to induce the response of the wheat seedling roots. Wheat cDNA microarray was used to identify differentially expressed genes (DEGs). A total of 1057 DEGs were identified, of which 761 genes were up-regulated and 296 were down-regulated. The greater percentage of up-regulated genes involved in developmental processes, immune system processes, multi-organism processes, positive regulation of biological processes and metabolic processes of the biological processes. The more proportion of down-regulation genes belong to the molecular function category including transporter activity, antioxidant activity and molecular transducer activity and to the extracellular region of the cellular components category. Moreover, most genes among 41 genes involved in ion binding, 17 WAKY transcription factor genes and 17 genes related to transport activity were up-regulated. KEGG analysis showed that the jasmonate signal transduction and flavonoid biosynthesis might play important roles in response to the low pH stress in wheat seedling roots. Based on the data, it is can be deduced that WRKY transcription factors might play a critical role in the transcriptional regulation, and the alkalifying of the rhizosphere might be the earliest response process to low pH stress in wheat seedling roots. These results provide a basis to reveal the molecular mechanism of proton toxicity tolerance in plants.

• 한국어병학회지
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• 제37권1호
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• pp.123-132
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• 2024

Viral diseases cause enormous economic losses to the olive flounder (Paralichthys olivaceus) aquaculture industry in Korea. This study aimed to identify immune-related genes expressed in the kidney of olive flounder injected with Polyinosinic-polycytidylic acid (Poly (I:C)). Thirty fish were divided into two groups by intraperitoneal injection of 100µl of diethylpyrocarbonate-treated water or poly I:C per fish. Kidney tissues at day 3 and 30 after the injection were used for RNA-seq analysis to identify differentially expressed genes (DEGs). Poly I:C group upregulated il8, cfh, tnfaip2b, c3b.2, ly6d and cd38 genes at 3 days post-injection. Additionally, cd22, ccl34a.3, c9, cxcl19, ccl27a, ccl7, and cfh genes were upregulated at 30 days post-injection. Differential expression gene analysis showed that poly I:C has both short and long-term immune effects in olive flounder. This study provides a theoretical basis for understanding the molecular mechanism of the short and long-term immune effects of poly I:C.

• Interdisciplinary Bio Central
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• 제2권2호
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• pp.4.1-4.6
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• 2010

The most common type of microarray experiment has a simple design using microarray data obtained from two different groups or conditions. A typical method to identify differentially expressed genes (DEGs) between two conditions is the conventional Student's t-test. The t-test is based on the simple estimation of the population variance for a gene using the sample variance of its expression levels. Although empirical Bayes approach improves on the t-statistic by not giving a high rank to genes only because they have a small sample variance, the basic assumption for this is same as the ordinary t-test which is the equality of variances across experimental groups. The t-test and empirical Bayes approach suffer from low statistical power because of the assumption of normal and unimodal distributions for the microarray data analysis. We propose a method to address these problems that is robust to outliers or skewed data, while maintaining the advantages of the classical t-test or modified t-statistics. The resulting data transformation to fit the normality assumption increases the statistical power for identifying DEGs using these statistics.

• 한국임상수의학회지
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• 제40권2호
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• pp.164-174
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• 2023

Canine splenic tumors (STs) are commonly diagnosed during imaging examinations, such as in X-ray and ultrasonography examinations, suggesting their higher prevalence, especially in older dogs. Despite this high prevalence, there are no effective treatment options for STs because of the difficulties in determining therapeutic targets. However, recently, the importance of microRNAs (miRNAs) has evolved owing to their ambivalent characteristics. Biomarkers and novel therapies using miRNAs have been well-studied in human cancer research compared to canine research, except for mammary gland tumors. Therefore, this study aimed to comparatively analyze miRNA expression profiles according to malignancy and biopsy sites to identify novel therapeutic and diagnostic targets. Tissue samples were collected directly from splenic tumor masses and immersed in RNAlater solution for further analysis. To investigate differentially expressed genes (DEGs) between tumor and normal tissues, we used RNA-seq and miRNA microarray analysis. Then, functional analysis based on DEGs was conducted to sort tumor-related DEGs. We found that cfa-miR-150 was upregulated in benign tumors, whereas cfa-miR-134 was upregulated in malignant tumors. Despite limited information on canine miRNAs, we identified two potential biomarkers for the differential diagnosis of STs.

• Journal of Microbiology and Biotechnology
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• 제32권6호
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• pp.718-729
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• 2022

Esophageal squamous cell carcinoma (ESCC) is the most common primary esophageal malignancy with poor prognosis. Here, due to the necessity for exploring potential therapies against ESCC, we obtained the gene expression data on ESCC from the TCGA and GEO databases. Venn diagram analysis was applied to identify common targets. The protein-protein interaction network was constructed by Cytoscape software, and the hub targets were extracted from the network via cytoHubba. The potential hub nodes as drug targets were found by pharmacophore-based virtual screening and molecular modeling, and the antitumor activity was evaluated through in vitro studies. A total of 364 differentially expressed genes (DEGs) in ESCC were identified. Pathway enrichment analyses suggested that most DEGs were mainly involved in the cell cycle. Three hub targets were retrieved, including CENPF, CCNA2 (cyclin A), and CCNB1 (cyclin B1), which were highly expressed in esophageal cancer and associated with prognosis. Moreover, amentoflavone, a promising drug candidate found by pharmacophore-based virtual screening, showed antiproliferative and proapoptotic effects and induced G1 in esophageal squamous carcinoma cells. Taken together, our findings suggested that amentoflavone could be a potential cell cycle inhibitor targeting cyclin B1, and is therefore expected to serve as a great therapeutic agent for treating esophageal squamous cell carcinoma.

• Asian Pacific Journal of Cancer Prevention
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• 제13권3호
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• pp.767-773
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• 2012

The esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with a poor prognosis. Understanding molecular changes in ESCC should improve identification of risk factors with different molecular subtypes and provide potential targets for early detection and therapy. Our study aimed to obtain a molecular signature of ESCC through the regulation network based on differentially expressed genes (DEGs). We used the GSE23400 series to identify potential genes related to ESCC. Based on bioinformatics we constructed a regulation network. From the results, we could establish that many transcription factors and pathways closely related with ESCC were linked by our method. STAT1 also arose as a hub node in our transcriptome network, along with some transcription factors like CCNB1, TAP1, RARG and IFITM1 proven to be related with ESCC by previous studies. In conclusion, our regulation network provided information on important genes which might be useful in investigating the complex interacting mechanisms underlying the disease.

• Journal of Animal Science and Technology
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• 제60권7호
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• pp.18.1-18.12
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• 2018

Background: Xanthosine treatment has been previously reported to increase mammary stem cell population and milk production in cattle and goats. However, the underlying molecular mechanisms associated with the increase in stem cell population and milk production remain unclear. Methods: Primiparous Beetal goats were assigned to the study. Five days post-partum, one mammary gland of each goat was infused with xanthosine (TRT) twice daily ($2{\times}$) for 3 days consecutively, and the other gland served as a control (CON). Milk samples from the TRT and CON glands were collected on the 10th day after the last xanthosine infusion and the total RNA was isolated from milk fat globules (MEGs). Total RNA in MFGs was mainly derived from the milk epithelial cells (MECs) as evidenced by expression of milk synthesis genes. Significant differentially expressed genes (DEGs) were subjected to Gene Ontology (GO) terms using PANTHER and gene networks were generated using STRING db. Results: Preliminary analysis indicated that each individual goat responded to xanthosine treatment differently, with this trend being correlated with specific DEGs within the same animal's mammary gland. Several pathways are impacted by these DEGs, including cell communication, cell proliferation and anti-microbials. Conclusions: This study provides valuable insights into transcriptomic changes in milk producing epithelial cells in response to xanthosine treatment. Further characterization of DEGs identified in this study is likely to delineate the molecular mechanisms of increased milk production and stem or progenitor cell population by the xanthosine treatment.

• Animal Bioscience
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• 제37권5호
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• pp.929-943
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• 2024

Objective: The present study was executed to explore the molecular mechanism of fibroblast growth factor 10 (FGF10) gene in bovine adipogenesis. Methods: The bovine FGF10 gene was overexpressed through Ad-FGF10 or inhibited through siFGF10 and their negative control (NC) in bovine adipocytes, and the multiplicity of infection, transfection efficiency, interference efficiency were evaluated through quantitative real-time polymerase chain reaction, western blotting and fluorescence microscopy. The lipid droplets, triglycerides (TG) content and the expression levels of adipogenic marker genes were measured during preadipocytes differentiation. The differentially expressed genes were explored through deep RNA sequencing. Results: The highest mRNA level was found in omasum, subcutaneous fat, and intramuscular fat. Moreover, the highest mRNA level was found in adipocytes at day 4 of differentiation. The results of red-oil o staining showed that overexpression (Ad-FGF10) of the FGF10 gene significantly (p<0.05) reduced the lipid droplets and TG content, and their down-regulation (siFGF10) increased the measurement of lipid droplets and TG in differentiated bovine adipocytes. Furthermore, the overexpression of the FGF10 gene down regulated the mRNA levels of adipogenic marker genes such as CCAAT enhancer binding protein alpha (C/EBPα), fatty acid binding protein (FABP4), peroxisome proliferator-activated receptor-γ (PPARγ), lipoprotein lipase (LPL), and Fas cell surface death receptor (FAS), similarly, down-regulation of the FGF10 gene enriched the mRNA levels of C/EBPα, PPARγ, FABP4, and LPL genes (p<0.01). Additionally, the protein levels of PPARγ and FABP4 were reduced (p<0.05) in adipocytes infected with Ad-FGF10 gene and enriched in adipocytes transfected with siFGF10. Moreover, a total of 1,774 differentially expressed genes (DEGs) including 157 up regulated and 1,617 down regulated genes were explored in adipocytes infected with Ad-FGF10 or Ad-NC through deep RNA-sequencing. The top Kyoto encyclopedia of genes and genomes pathways regulated through DEGs were the PPAR signaling pathway, cell cycle, base excision repair, DNA replication, apoptosis, and regulation of lipolysis in adipocytes. Conclusion: Therefore, we can conclude that the FGF10 gene is a negative regulator of bovine adipogenesis and could be used as a candidate gene in marker-assisted selection.

• 한국초지조사료학회지
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• 제34권2호
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• pp.114-119
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• 2014

염 또는 건조 스트레스 처리에 의한 톨 페스큐 종자의 발아율 변화와 유식물체 수준에서의 유전자 발현을 조사하기 위하여 in vitro 조건에서 NaCl과 PEG를 처리하여 분석하였다. NaCl 처리시 톨 페스큐 품종별 발아율은 50 mM 농도에서 발아율이 서서히 감소하기 시작하였으며 350 mM의 농도에서는 모든 품종에서 발아가 되지 않는 경향을 보였다. NaCl 처리 농도에 따른 발아율 감소율은 Fawn 품종이 가장 큰 변화를 보였으며 Kentucky-31(E-) 품종이 가장 강한 내성을 보였다. 또한, PEG 처리시 톨 페스큐 품종별 발아율의 변화도 NaCl 처리시와 유사한 경향을 보였으며 고농도인 30% PEG 처리구에서는 모든 품종에서 발아가 되지 않는 경향을 보였으며 Kentucky-31(E-) 품종이 가장 강한 내성을 보였다. 톨 페스큐 유식물체 수준에서 염해와 건조 스트레스에 의한 유전자 발현양상을 조사하기 위하여 DEGs (differentially expressed genes) 탐색을 위한 ACP-based GeneFishing$^{TM}$ PCR 분석을 통해 NaCl 또는 PEG 처리에 따른 발현량의 차이를 보이는 총 4개의 DEG를 선발하여 클로닝하고 염기서열을 분석하였다. 무처리구에 비해 NaCl 처리시 4개의 DEG가 증가하였고 감소하는 DEG는 확인 되지 않았으나, PEG 처리에서는 3개의 DEG (DEG 1, 3, 및 4)가 증가하였고 1개의 DEG가 감소하는 경향을 나타내었다. 발굴된 DEG들을 blastx 검색에 의하여 rubisco large subunit (DEG1), microsomal glutathion S-transferase (GST) 3-like isoform 1 (DEG2) 유전자로 동정되었다.

• Journal of Animal Science and Technology
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• 제63권4호
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• pp.934-953
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• 2021

Ciglitazone is a member of the thiazolidinedione family, and specifically binds to peroxisome proliferator-activated receptor-γ (PPARγ), thereby promoting adipocyte differentiation. We hypothesized that ciglitazone as a PPARγ ligand in the absence of an adipocyte differentiation cocktail would increase adiponectin and adipogenic gene expression in bovine satellite cells (BSC). Muscle-derived BSCs were isolated from six, 18-month-old Yanbian Yellow Cattle. The BSC were cultured for 96 h in differentiation medium containing 5 µM ciglitazone (CL), 10 µM ciglitazone (CM), or 20 µM ciglitazone (CH). Control (CON) BSC were cultured only in a differentiation medium (containing 2% horse serum). The presence of myogenin, desmin, and paired box 7 (Pax7) proteins was confirmed in the BSC by immunofluorescence staining. The CL, CM, and CH treatments produced higher concentrations of triacylglycerol and lipid droplet accumulation in myotubes than those of the CON treatment. Ciglitazone treatments significantly increased the relative expression of PPARγ, CCAAT/enhancer-binding protein alpha (C/EBPα), C/EBPβ, fatty acid synthase, stearoyl-CoA desaturase, and perilipin 2. Ciglitazone treatments increased gene expression of Pax3 and Pax7 and decreased expression of myogenic differentiation-1, myogenin, myogenic regulatory factor-5, and myogenin-4 (p < 0.01). Adiponectin concentration caused by ciglitazone treatments was significantly greater than CON (p < 0.01). RNA sequencing showed that 281 differentially expressed genes (DEGs) were found in the treatments of ciglitazone. DEGs gene ontology (GO) analysis showed that the top 10 GO enrichment significantly changed the biological processes such as protein trimerization, negative regulation of cell proliferation, adipocytes differentiation, and cellular response to external stimulus. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that DEGs were involved in the p53 signaling pathway, PPAR signaling pathway, biosynthesis of amino acids, tumor necrosis factor signaling pathway, non-alcoholic fatty liver disease, PI3K-Akt signaling pathway, and Wnt signaling pathway. These results indicate that ciglitazone acts as PPARγ agonist, effectively increases the adiponectin concentration and adipogenic gene expression, and stimulates the conversion of BSC to adipocyte-like cells in the absence of adipocyte differentiation cocktail.