• Molecules and Cells
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• v.42 no.10
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• pp.693-701
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• 2019

Plants monitor changes in day length to coordinate their flowering time with appropriate seasons. In Arabidopsis, the diel and seasonal regulation of CONSTANS (CO) protein stability is crucial for the induction of FLOWERING LOCUS T (FT) gene in long days. FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) and ZEITLUPE (ZTL) proteins control the shape of CO expression profile antagonistically, although regulation mechanisms remain unknown. In this study, we show that GIGANTEA (GI) protein modulates the stability and nuclear function of FKF1, which is closely related to the stabilization of CO in the afternoon of long days. The abundance of FKF1 protein is decreased by the gi mutation, but increased by GI overexpression throughout the day. Unlike the previous report, the translocation of FKF1 to the nucleus was not prevented by ZTL overexpression. In addition, the FKF1-ZTL complex formation is higher in the nucleus than in the cytosol. GI interacts with ZTL in the nucleus, implicating the attenuation of ZTL activity by the GI binding and, in turn, the sequestration of FKF1 from ZTL in the nucleus. We also found that the CO-ZTL complex presents in the nucleus, and CO protein abundance is largely reduced in the afternoon by ZTL overexpression, indicating that ZTL promotes CO degradation by capturing FKF1 in the nucleus under these conditions. Collectively, our findings suggest that GI plays a pivotal role in CO stability for the precise control of flowering by coordinating balanced functional properties of FKF1 and ZTL.

• Journal of Animal Reproduction and Biotechnology
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• v.36 no.1
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• pp.35-44
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• 2021

A pregnancy diagnosis is an important standard for control of livestock's reproduction in paricular dairy cattle. High reproductive performance in dairy animals is a essential condition to realize of high life-time production. Pregnancy diagnosis is crucial to shortening the calving interval by enabling the farmer to identify open animals so as to treat or re-breed them at the earliest opportunity. MicroRNAs are short RNA molecules which are critically involved in regulating gene expression during both health and disease. This study is sought to establish the feasible of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from 12 non-pregnant cows ("open" cows: samples were collected before insemination (non-pregnant state) and after pregnancy check at the indicated time points) on weeks 0, 4, 8, 12 and 16. Using small RNA sequencing we identified a total of 115 miRNAs that were differentially expressed weeks 16 relative to non-pregnancy ("open" cows). Weeks 8, 12 and 16 of pregnancy commonly showed a distinct increase in circulating levels of miR-221 and miR-320a. Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with pregnancy in cattle. Their application in the field of reproductive biology has opened up opportunities for research communities to look for pregnancy biomarker molecules in dairy cattle.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.157-157
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• 2022

Plants being sessile are prone to various abiotic challenges, including salinity. Plants generally cope with salt stress by regulating their endogenous NO levels. NO exogenously applied in various forms also successfully impedes the salt stress, but its small size, short half life, and high volatility rate hamper its application in agriculture. NO application via CS as a nanocarrier is an alternate option to ensure the optimal kinetic release of NO for a long period compared to the free NO form. Herein, we synthesized and characterized GSNO-CS NP by ionic gelation of TPP with CS and then reacting with GSH, followed by reaction with NaNO₂ suspension. The synthesized NPs were characterized using non-destructive analytical techniques such as DLS, FTIR, and SEM to ensure their synthesis and surface morphology. NO-release profile confirmed optimal kinetic NO release for 24 h from NO-CS NP as compared to free NO form. The efficiency of NO-CS NP was checked on Arabidopsis plants under salinity stress by gauging the morphological, physiological, and enzymatic antioxidant system and SOS pathway gene expression levels. Overall, the results revealed that NO-CS NP successfully mitigates salinity stress compared to free GSNO. Concluding, the findings provide sufficient experimental evidence for the application of nanotechnology to enhance NO delivery, thus inducing more benefits for the plants under stress conditions by mitigating the deleterious impacts of salt stress on the morphological and physiological status of the plants, and regulating the ions exchange by overexpression of SOS pathway candidate genes.

• The Korea Journal of Herbology
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• v.39 no.3
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• pp.85-95
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• 2024

Objectives : We proposed the hypothesis that administering Trigonella foenum-graecum seed extract (TSE) could alleviate menopausal symptoms and osteoporosis resulting from estrogen deficiency. Methods : Ovariectomized (OVX) rats were administered TSE at doses of 300 or 600 mg/kg body weight for 8 weeks, followed by measurement of serum lipid profile and serum bone markers using ELISA kits. Additionally, analysis of related genes in the femur and uterus was performed using Western blot and real-time PCR. Additionally, micro-CT analysis was performed to investigate the protective effect of TSE against bone loss due to oophorectomy. Results : The administration of TSE led to significant reductions in triglyceride (TG), total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, and glucose levels in the serum of OVX rats. Furthermore, TSE increased estradiol levels in the serum and notably improved the levels of biochemical markers associated with bone metabolism. Additionally, TSE exerted significant regulatory effects on the mRNA levels of alkaline phosphatase (ALP) and receptor activator of nuclear factor kappa-B ligand (RANKL)-genes closely associated with bone metabolism in the femur. TSE also demonstrated pronounced effects on uterine tissue, with improvements observed in gene expression related to estrogen receptors. Conclusion : Our findings confirm the efficacy of TSE in ameliorating menopause symptoms by modulating elements associated with both bone and lipid metabolism in the serum, uterine tissue, and femur of OVX rats. The present findings suggest that TSE may offer potential therapeutic effects for symptoms related to menopause and osteoporosis in females.

• Journal of Microbiology and Biotechnology
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• v.34 no.4
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• pp.958-968
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• 2024

In recent years, there has been a growing recognition of the important role that long non-coding RNAs (lncRNAs) play in the immunological process of hepatocellular carcinoma (LIHC). An increasing number of studies have shown that certain lncRNAs hold great potential as viable options for diagnosis and treatment in clinical practice. The primary objective of our investigation was to devise an immune lncRNA profile to explore the significance of immune-associated lncRNAs in the accurate diagnosis and prognosis of LIHC. Gene expression profiles of LIHC samples obtained from TCGA database were screened for immune-related genes. The optimal immune-related lncRNA signature was built via correlational analysis, univariate and multivariate Cox analysis. Then, the Kaplan-Meier plot, ROC curve, clinical analysis, gene set enrichment analysis, and principal component analysis were performed to evaluate the capability of the immune lncRNA signature as a prognostic indicator. Six long non-coding RNAs were identified via correlation analysis and Cox regression analysis considering their interactions with immune genes. Subsequently, tumor samples were categorized into two distinct risk groups based on different clinical outcomes. Stratification analysis indicated that the prognostic ability of this signature acted as an independent factor. The Kaplan-Meier method was employed to conduct survival analysis, results showed a significant difference between the two risk groups. The predictive performance of this signature was validated by principal component analysis (PCA). Additionally, data obtained from gene set enrichment analysis (GSEA) revealed several potential biological processes in which these biomarkers may be involved. To summarize, this study demonstrated that this six-lncRNA signature could be identified as a potential factor that can independently predict the prognosis of LIHC patients.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.1
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• pp.537-545
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• 2018

In this study, transcriptome analysis was conducted to collect various information from Fagopyrum esculentum and Fagopyrum tataricum during the early germination stage. Total RNA was extracted from the seeds and at 12, 24, and 36 hrs after germination of Jeju native Fagopyrum esculentum and Fagopyrum tataricum and sequenced using the Illumina Hiseq 2000 platform. Raw data analysis was conducted using the Dynamic Trim and Lengths ORT programs in the SolexaQA package, and assembly and annotation were performed. Based on RNA-seq raw data, we obtained 16.5 Gb and 16.2 Gb of transcriptome data corresponding to about 84.2% and 81.5% of raw data, respectively. De novo assembly and annotation revealed 43,494 representative transcripts corresponding to 47.5Mb. Among them, 23,165 sequences were shown to have similar sequences with annotation DB. Moreover, Gene Ontology (GO) analysis of buckwheat representative transcripts confirmed that the gene is involved in metabolic processes (49.49%) of biological processes, as well as cell function (46.12%) in metabolic process, and catalytic activity (80.43%) in molecular function In the case of gibberellin receptor GID1C, which is related to germination of seeds, the expression levels increased with time after germination in both F. esculentum and F. tataricum. The expression levels of gibberellin 20-oxidase 1 were increased within 12 hrs of gemination in F. esculentum but continuously until 36 hrs in F. tataricum. This buckwheat transcriptome profile analysis of the early germination stage will help to identify the mechanism causing functional and morphological differences between species.

• Journal of Life Science
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• v.16 no.2 s.75
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• pp.231-239
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• 2006

Human mesenchymal stem cells (hMSCs) in bone marrow (BM) can be induced to differentiate into a variety of mesenchymal tissues, including adipocytes, osteoblasts and chondroblasts, under the influence of certain growth or environmental factors. In this study, we analyzed the differentiation process and the associated gene expression profiles inherent to the process by which hMSCs differentiate into osteoblasts. We conducted a comparison of gene expression profiles of the normal human BM MSCs, using human 8K cDNA microarray, incubated in media containing either a combination of $\beta$-glycerol phosphate, L-ascorbic acid, and dexamethasone, or in medium lacking these osteogenic supplements. During the osteoblastic differentiation process, 36 genes were determined to be up-regulated, and 59 genes were shown to be down-regulated. Osteoprotegerin, LRP5, and metallothionein 2A, all of which are associated with the osteogenetic process, were up-regulated, and genes associated with the differentiation of MSCs into other lineages, including muscle, adipose tissue and vascular structure were down-regulated. The set of differentially expressed genes reported in this work should contribute to our current understanding of the processes inherent to the differentiation of MSCs into osteoblasts.

• Clinical and Experimental Pediatrics
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• v.48 no.7
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• pp.779-788
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• 2005

Purpose : Echinacea, a traditional plant medicine has been used as immune-stimulant. Recent studies have revealed that extract of Echinacea has immunostimulatory effects on human blood mononuclear cells. This study was designed for the purpose of screening the genes associated with immunologic effects of Echinacea on monocytes and dendritic cells using a cDNA microarray chip. Methods : $CD14^+$ monocyte cells were cultured for one day with Echinacea extract(final concentration : $50{\mu}g/mL$) in experiment 1, but were cultured without Echinacea in experiment 2. The gene expression of these cultured monocytes was analyzed using the cDNA microarray chip. Dendritic cells produced from $CD14^+$ monocyte were cultured for five days with GM-CSF and IL-4, and then cultured for one day with Echinacea in experiment 3, but were done without Echinacea in experiment 4. Results : In experiments 1 and 2, there were 17 significantly expressed genes with average expression ratios above 2.5, including interferon gamma-inducible protein 30(IFI 30), CDC(cell-division-cylcle)-like kinase 2(CLK 2), syndecan binding protein(syntenin), superoxide dismutase 2, etc. In experiments 3 and 4, there were 24 gene, with significantly expressed genes were 24 genes, which were insulin-like growth factor 2(somatomedin A), methyl-CpG binding domain protein 3, IFI 30, small inducible cytokine subfamily A, member 22, etc. The genes encoding CD44, IFI 30, mannose receptor C type 1(MRC 1), chemokine receptor 7(CCR 7), CLK 2, syntenin and cytochrome C oxidase subunit VIII were significantly expressed in both monocytes and dendritic cells cultured with Echinacea. Conclusion : This study employed a cDNA microarray chip to elicit the immune-associated gene profile; the expression was enhanced by Echinacea in CD14+ monocytes and dendritic cells. Thus we laid the basis for the quantitative and functional analysis of genes induced by Echinacea in monocytes and monocyte-derived dendritic cells.

• Journal of the korean academy of Pediatric Dentistry
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• v.32 no.1
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• pp.75-88
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• 2005

Ameloblastoma is the most commonly occurring odontogenic tumor in oral cavity. Although most are benign epithelial neoplasm, they are generally considered to be locally aggressive and destructive, exhibiting a high rate of recurrence. The biological behavior of this neoplasm is a slowly growing, locally invasive tumor without metastasis, therefore malignant neoplasm, changed its histological appearance to carcinoma or showed distant metastasis, is only defined clinically. In this study, we identified the differentially expressed genes(DEGs) in stages under benign or malignant ameloblastoma compared with normal patient using ordered differential display(ODD) reverse transcription(RT)-PCR and $GeneFishing^{TM}$ technology. ODD RT-PCR is rather effective when the investigation of samples containing very small amounts of total RNA must be accomplished. ODD RT-PCR used the means of amplification with anchored T-primer and adaptor specific primer. bearing definite two bases at their 3' ends and so this method could display differential 3'-expressed sequence taqs(ESTs) patterns without using full-length cDNAs. Compared with standard differential display, ODD RT-PCR is more simple and have enough sensitivity to search for molecular markers by comparing gene expression profiles, However, this method required much effort and skill to perform. $GeneFishing^{TM}$ modified from DD-PCR is an improved method for detecting differentially expressed genes in two or more related samples. This two step RT-PCR method uses a constant reverse primer(anchor ACP-T) to prime the RT reaction and arbitrary primer pairs(annealing control primers, ACPs) during PCR. Because of high annealing specificity of ACPs than ODD RT-PCR, the application of $GeneFishing^{TM}$ to DEG discovery generates reproducible, authentic, and long(100bp to 2kb) PCR products that are detectable on agarose gels. Consequently, various DEGs observed differential expression levels on agarose gels were isolated from normal, benign, and malignant tissues using these methods. The expression patterns of the some isolated DEGs through ODD RT-PCR and $GeneFishing^{TM}$ were confirmed by Northern blot analysis and RT-PCR. The results showed that these identified DEGs were implicated in ameloblastoma neoplasm processes. Therefore, the identified DEGs will be further studied in order to be applied in candidate selection for marker as an early diagnosis during ameloblastoma neoplasm processes.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3395-3402
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• 2015

Background: Preoperative 5-fluorouracil (5-FU)-based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, CRC cells often develop chemoradiation resistance (CRR). Recent studies have shown that long non-coding RNA (lncRNA) plays critical roles in a myriad of biological processes and human diseases, as well as chemotherapy resistance. Since the roles of lncRNAs in 5-FU-based CRR in human CRC cells remain unknown, they were investigated in this study. Materials and Methods: A 5-FU-based concurrent CRR cell model was established using human CRC cell line HCT116. Microarray expression profiling of lncRNAs and mRNAs was undertaken in parental HCT116 and 5-FU-based CRR cell lines. Results: In total, 2,662 differentially expressed lncRNAs and 2,398 mRNAs were identified in 5-FU-based CRR HCT116 cells when compared with those in parental HCT116. Moreover, 6 lncRNAs and 6 mRNAs found to be differentially expressed were validated by quantitative real time PCR (qRT-PCR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for the differentially expressed mRNAs indicated involvement of many, such as Jak-STAT, PI3K-Akt and NF-kappa B signaling pathways. To better understand the molecular basis of 5-FU-based CRR in CRC cells, correlated expression networks were constructed based on 8 intergenic lncRNAs and their nearby coding genes. Conclusions: Changes in lncRNA expression are involved in 5-FU-based CRR in CRC cells. These findings may provide novel insight for the prognosis and prediction of response to therapy in CRC patients.