• Journal of Plant Biotechnology
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• v.45 no.3
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• pp.183-189
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• 2018

The plant hormone auxin regulates the overall metabolic processes essential for plant growth and development. Auxin signaling is mediated by early auxin response genes, which are classified into three major families: AUXIN/INDOLE ACETIC ACID (AUX/IAA), GRETCHEN HAGEN3 (GH3) and SMALL AUIN UP RNA (SAUR). The SAUR gene family is the largest family among early auxin response genes and encodes the small and highly unstable gene products. The functional roles of SAUR genes have remained unclear for many years. The traditional genetic and molecular studies on the SAUR functions have been hampered by their likely genetic redundancy and tandem arrays of highly related genes in the plant genome, together with the molecular characteristics of SAUR. However, recent studies have suggested possible roles of SAUR in a variety of tissues and developmental stages in accordance with the novel approaches such as gain-of-function and RNA silencing techniques. In this review, the recent research progress on the functional roles and regulatory mechanisms of SAUR and a set of possible future works are discussed.

• BMB Reports
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• v.41 no.6
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• pp.461-465
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• 2008

IL-18 production may enhance immune system defense against KG-1 cells ; NB4 cells, which are associated with good prognosis, do not produce IL-18. In this study, we treated KG-1 cells with IL-18 and used microarray technology to assess subsequent effects on gene expression. In UniGene-array of 7488 human genes, expression of 57 genes, including stress related genes, increased at least 2-fold, whereas expression of 48 genes decreased at least 2-fold. Following exogenous exposure of KG-1 cells to IL-18, expression of CRYGC, $NF{\kappa}BIA$ and NACA gene were monitored. The latter is a transcriptional coactivator potentiating c-Jun-mediated transcription.$NF{\kappa}BIA$ is an inhibitor of $NF{\kappa}B$, and affects growth regulation, apoptosis and hypoxic stress. Studies, such as this one, are beginning to clarify the differences between cells associated with good and bad cancer prognoses, which may ultimately assist in medical treatment for acute myeloid leukemia.

• Animal Bioscience
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• v.35 no.10
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• pp.1512-1523
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• 2022

Objective: The growth of pigs involves multiple regulatory mechanisms, and modern molecular breeding techniques can be used to understand the skeletal muscle growth and development to promote the selection process of pigs. This study aims to explore candidate lncRNAs and mRNAs related to skeletal muscle growth and development among Duroc pigs with different average daily gain (ADG). Methods: A total of 8 pigs were selected and divided into two groups: H group (high-ADG) and L group (low-ADG). And followed by whole transcriptome sequencing to identify differentially expressed (DE) lncRNAs and mRNAs. Results: In RNA-seq, 703 DE mRNAs (263 up-regulated and 440 down-regulated) and 74 DE lncRNAs (45 up-regulated and 29 down-regulated) were identified. In addition, 1,418 Transcription factors (TFs) were found. Compared with mRNAs, lncRNAs had fewer exons, shorter transcript length and open reading frame length. DE mRNAs and DE lncRNAs can form 417 lncRNA-mRNA pairs (antisense, cis and trans). DE mRNAs and target genes of lncRNAs were enriched in cellular processes, biological regulation, and regulation of biological processes. In addition, quantitative trait locus (QTL) analysis was used to detect the functions of DE mRNAs and lncRNAs, the most of DE mRNAs and target genes of lncRNAs were enriched in QTLs related to growth traits and skeletal muscle development. In single-nucleotide polymorphism/insertion-deletion (SNP/INDEL) analysis, 1,081,182 SNP and 131,721 INDEL were found, and transition was more than transversion. Over 60% of percentage were skipped exon events among alternative splicing events. Conclusion: The results showed that different ADG among Duroc pigs with the same diet maybe due to the DE mRNAs and DE lncRNAs related to skeletal muscle growth and development.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.233-239
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• 2010

Four genes (yqfR, yfmL, ydbR, deaD) were identified as putative DEAD-box RNA helicase genes in the genomic sequence of Bacillus subtilis by homology search. To understand the function of these genes, each of the genes was deleted and the constructed strains were tested for their growth charateristics at different temperatures. The growth rate of ydbR deletion mutant ($T_d$=53 min) was a little bit reduced at $37^{\circ}C$ as compared to that of wild type strain (CU1065). But the growth rate of other three (yqfR, yfmL, deaD) deletion mutants ($T_d$=30-40 min) is nearly equal to the growth rate of wild type ($T_d$=32 min). On the other hands, the growth rate of deletion mutants were reduced at $22^{\circ}C$ in order of yqfR ($T_d$=151 min), yfmL ($T_d$=214 min), ydbR ($T_d$=343 min), which showed cold-sensitive phenotype. The deletion mutant of deaD ($T_d$=109 min) grew equally as compared to the growth rate ($T_d$=102 min) of the wild type at $22^{\circ}C$ and did not show cold-sensitive growth. Double, triple and quadruple deletion mutants of these genes were constructed, and growth rate of these mutants were measured at various temperature conditions ($22^{\circ}C$, $37^{\circ}C$, $42^{\circ}C$) using LB broth. Multiple deletion mutations showed more severe cold-sensitive growth than single deletion mutations, and double deletion of ydbR and yfmL ($T_d$=984 min) showed most cold-sensitive growth than any other double mutants. Such a cold-sensitive growth of these mutations is quite similar to the result of csdA or srmB deletion in E. coli and suggested that physiological role of ydbR and yfmL is related with ribosome assembly.

• Molecules and Cells
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• v.41 no.5
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• pp.390-400
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• 2018

Studies have revealed that miR-103a-3p contributes to tumor growth in several human cancers, and high miR-103a-3p expression is associated with poor prognosis in advanced gastric cancer (GC) patients. Moreover, bioinformatics analysis has shown that miR-103a-3p is upregulated in The Cancer Genome Atlas (TCGA) stomach cancer cohort. These results suggest that miR-103a-3p may function as an oncogene in GC. The present study aimed to investigate the role of miR-103a-3p in human GC. miR-103a-3p expression levels were increased in 33 clinical GC specimens compared with adjacent nontumor stomach tissues. Gain- and loss-of-function studies were performed to identify the correlation between miR-103a-3p and tumorigenesis in human GC. Inhibiting miR-103a-3p suppressed GC cell proliferation and blocked the S-G2/M transition in MKN-45/SGC-7901 cells, whereas miR-103a-3p overexpression improved GC cell proliferation and promoted the S-G2/M transition in vitro. Bioinformatics and dual-luciferase reporter assays confirmed that ATF7 is a direct target of miR-103a-3p. Analysis of the TCGA stomach cancer cohort further revealed that miR-103a-3p expression was inversely correlated with ATF7 expression. Notably, silencing ATF7 showed similar cellular and molecular effects as miR-103a-3p overexpression, namely, increased GC cell proliferation, improved CDK2 expression and decreased P27 expression. ATF7 overexpression eliminated the effects of miR-103a-3p expression. These findings indicate that miR-103a-3p promotes the proliferation of GC cell by targeting and suppressing ATF7 in vitro.

• Journal of Veterinary Science
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• v.23 no.6
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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.

• Korean Journal of Environmental Biology
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• v.36 no.2
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• pp.131-139
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• 2018

The warming of water as a result of climate change affects fish habitat. Variations in water temperature affect fish physiology almost totally. The rise in water temperature due to climate change leads to hypoxia following decreased oxygen solubility and decreased binding capacity of oxygen-carrying hemoglobin. This study was conducted to evaluate the health status of Atlantic salmon (Salmo salar) fry at elevated water temperatures($20^{\circ}C$) compared with optimum water temperature ($15^{\circ}C$). The method facilitated the detection of biomarker genes using NGS RNAseq analysis and evaluation of their expression pattern using RT-qPCR analysis. The biomarker genes included interferon alpha-inducible protein 27-like protein 2A transcript variant X3, protein L-Myc-1b-like, placenta growth factor-like transcript variant X1, fibroblast growth factor receptor-like 1 transcript variant X1, transferrin, intelectin, thioredoxin-like, c-type lectin lectoxin-Thr1-like, ladderlectin-like and calponin-1. The selected biomarker genes were sensitive to changes in water temperature based on NGS RNAseq analysis. The expression patterns of these genes based on RT-qPCR were similar to those of NGS RNAseq analysis.

• Molecules and Cells
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• v.37 no.2
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• pp.109-117
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• 2014

Microbiota in the niches of the rhizosphere zones can affect plant growth and responses to environmental stress conditions via mutualistic interactions with host plants. Specifically, some beneficial bacteria, collectively referred to as Plant Growth Promoting Rhizobacteria (PGPRs), increase plant biomass and innate immunity potential. Here, we report that Enterobacter sp. EJ01, a bacterium isolated from sea china pink (Dianthus japonicus thunb) in reclaimed land of Gyehwa-do in Korea, improved the vegetative growth and alleviated salt stress in tomato and Arabidopsis. EJ01 was capable of producing 1-aminocy-clopropane-1-carboxylate (ACC) deaminase and also exhibited indole-3-acetic acid (IAA) production. The isolate EJ01 conferred increases in fresh weight, dry weight, and plant height of tomato and Arabidopsis under both normal and high salinity conditions. At the molecular level, short-term treatment with EJ01 increased the expression of salt stress responsive genes such as DREB2b, RD29A, RD29B, and RAB18 in Arabidopsis. The expression of proline biosynthetic genes (i.e. P5CS1 and P5CS2) and of genes related to priming processes (i.e. MPK3 and MPK6) were also up-regulated. In addition, reactive oxygen species scavenging activities were enhanced in tomatoes treated with EJ01 in stressed conditions. GFP-tagged EJ01 displayed colonization in the rhizosphere and endosphere in the roots of Arabidopsis. In conclusion, the newly isolated Enterobacter sp. EJ01 is a likely PGPR and alleviates salt stress in host plants through multiple mechanisms, including the rapid up-regulation of conserved plant salt stress responsive signaling pathways.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.284-284
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• 2022

The overall effects of gibberellic acid (GA3) with NaCl on different rice genotypes are inadequately understood. The present study determines the effect of different GA3 concentrations on the morphophysiological, molecular and biochemical effects of 120 mM NaCl salt stress in rice seedlings. Salt stress reduced germination percentages and seedling growth and decreased bioactive GA content. It also downregulated the relative expression of a-amylase-related genes - OsAmy1A, OsAmy1C, and OsAmy3C in the salt-sensitive IR28 cultivar. Salt stress differentially regulated the expression of GA biosynthetic genes. Salt stress increased antioxidant activity in all rice genotypes tested, except in IR28. GA3 (50 and 100 µM) mitigates the effect of salt stress, rescuing seed germination and growth attributes. GA3 significantly increased bioactive GA content in Nagdong and pokkali (50 µM) and Cheongcheong and IR28 (100 µM) cultivars. The a-amylase genes were also significantly upregulated by GA3. Similarly, GA3 upregulated OsGA2oxl and OsGA2ox9 expression in the Cheongcheong and salt-sensitive IR28 cultivars. The present study demonstrated that salt stress inactivates bioactive GA - inhibiting germination and seedlings growth - and decreases bioactive GA content and GSH activity in IR28 and Pokkali cultivars. Further, GA3 significantly reversed the effects of 120 mM NaCl salt stress in different rice genotypes. The current study also suggests if we know the coastal area water NaCl concentration we can apply the exogenous GA3 accordingly. Thus, we would be able to grow rice cultivars near the coastal area and reduce the rice damage by salinity.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.24
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• pp.10825-10830
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• 2015

The present study was conducted to investigate effects and mechanisms of action of phenolic alkaloids of Menispermum dauricum (PAMD) on gastric cancer in vivo. In vitro, cell apoptosis of human gastric cancer cell line SGC-7901 was observed using fluorescence staining. In vivo, a mice model was constructed to observe tumor growth with different doses. Cell apoptosis was examined using flow cytometry and K-RAS protein expression using Western blotting. The mRNA expression of P53, BCL-2, BAX, CASPASE-3, K-RAS was examined by real-time PCR. PAMD significantly suppressed tumor growth in the xenograft model of gastric cancer in a dose-dependent manner (p<0.01). Functionally, PAMD promoted cell apoptosis of the SGC-7901 cells and significantly increased the rate of cell apoptosis of gastric tumor cells (p<0.05). Mechanically, PAMD inhibited the expression of oncogenic K-RAS both at the mRNA and protein levels. In addition, PAMD affected the mRNA expression of the cell apoptosis-related genes (P53, BCL-2, BAX, CASPASE-3). PAMD could suppress gastric tumor growth in vivo, possibly through inhibiting oncogenic K-RAS, and induce cell apoptosis possibly by targeting the cell apoptosis-related genes of P53, BCL-2, BAX, CASPASE-3.