• Journal of Plant Biotechnology
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• 제49권4호
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• pp.271-291
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• 2022

Pectin methylesterase (PME) plays an important role in vegetative and reproductive development and biotic/abiotic stress responses by regulating the degree of methyl-esterification of pectic polysaccharides in the plant cell wall. PMEs are encoded by a large multigene family in higher land plant genomes. In general, the expression of plant PME genes shows tissue- or cell-specific patterns and is induced by endogenous and exogenous stimuli. In this study, we identified PME multigene family members (CsPMEs) from the sweet orange genome and report detailed molecular characterization and expression profiling in different citrus tissues and two fruit developmental stages. We also discussed the possible functional roles of some CsPME genes by comparing them with the known functions of PMEs from other plant species. We identified 48 CsPME genes from the citrus genome. A phylogenetic tree analysis revealed that the identified CsPMEs were divided into two groups/types. Some CsPMEs showed very close phylogenetic relationships with the PMEs whose functions were formerly addressed in Arabidopsis, tomato, and maize. Expression profiling showed that some CsPME genes are highly or specifically expressed in the leaf, root, flower, or fruit. Based on the phylogenetic relationships and gene expression profiling results, we suggest that some CsPMEs could play functional roles in pollen development, pollen tube growth, cross incompatibility, root development, embryo/seed development, stomata movement, and biotic/abiotic stress responses. Our results shed light on the biological roles of individual CsPME isoforms and contribute to the search for genetic variations in citrus genetic resources.

• Molecular & Cellular Toxicology
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• 제5권4호
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• pp.283-290
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• 2009

Differential gene expression profiling was performed in the hepatic tissue of marine medaka fish (Oryzias javanicus) after exposure to benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon (PAH), by heterologous hybridization using a medaka cDNA microarray. Thirty-eight differentially expressed candidate genes, of which 23 were induced and 15 repressed (P<0.01), were identified and found to be associated with cell cycle, development, endocrine/reproduction, immune, metabolism, nucleic acid/protein binding, signal transduction, or non-categorized. The presumptive physiological changes induced by BaP exposure were identified after considering the biological function of each gene candidate. The results obtained in this study will allow future studies to assess the molecular mechanisms of BaP toxicity and the development of a systems biology approach to the stress biology of organic chemicals.

• Asian Pacific Journal of Cancer Prevention
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• 제17권sup3호
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• pp.155-160
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• 2016

Breast cancer (BC) is the second most common cancer in the world and by far the most frequent cancer among women, with an estimated 1.67 million new cancer cases diagnosed in 2012 (25% of all cancers). Polygene expression analysis is used to predict the prognosis and determine the most appropriate treatment regimen. The objective of this study was to examine the gene expression profiles of SIRT3, HRAS, LSP1, SCUBE2 and AP2A2 in Iranian women with BC.A total of 136 patients including healthy controls were categorized into three groups based on the relapse of the disease. Expression of desired genes in formalin-fixed, paraffin embedded tissues collected from all groups of participants was analyzed via the RT PCR method. RNA extraction and cDNA synthesis were performed then real-time quantitative PCR was carried out. Gene expression analysis revealed that the expression of SIRT3 was equal among patient and control groups. LSP1 was down regulated in all patient groups relative to controls but reduced expression in the metastatic group relative to the non-metastatic one was not significant. HRAS was significantly overexpressed in total and metastatic tumor samples versus normal but not in non-metastatic cases. SCUBE2 expression showed significant over-expression in both overall tumor samples and the non-metastatic group as compared to normal tissues. Gene expression level of AP2A2 in all groups was not detectable. Our data are compatible with a tumor suppressor role of LSP1 related to potential prognostic factor for tumor recurrence and outcome. This study for the first time assayed the prognostic value and changes in the expression of SIRT3, LSP1, HRAS, SCUBE2 and AP2A2 genes in women with breast cancer in the Iranian population and findings confirmed potential biomarker and prognostic capability of these genes. Such expression profiling data can critically improve prognosis and treatment decisions in cancer patients.

• BMB Reports
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• 제39권4호
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• pp.457-463
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• 2006

Insulin resistance is commonly observed in patients prior to the development of type 2 diabetes and may predict the onset of the disease. We tested the hypothesis that impairment in insulin stimulated glucose-disposal in insulin resistant patients would be reflected in the gene expression profile of skeletal muscle. We performed gene expression profiling on skeletal muscle of insulin resistant and insulin sensitive subjects using microarrays. Microarray analysis of 19,000 genes in skeletal muscle did not display a significant difference between insulin resistant and insulin sensitive muscle. This was confirmed with real-time PCR. Our results suggest that insulin resistance is not reflected by changes in the gene expression profile in skeletal muscle.

• Journal of Ginseng Research
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• 제45권3호
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• pp.450-455
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• 2021

Korean Red Ginseng (KRG) is an herbal oriental medicine known to alleviate cardiovascular dysfunction. To analysis the expression of diabetic cardiac complication-associated genes in db/db mice, we studied the cardiac gene expression following KRG treatment. In result, a total of 585 genes were found to be changed in db/db mice. Among the changed expression, 245 genes were found to 2-fold upregulated, and 340 genes were 2-fold downregulated. In addition, the changed gene expressions were ameliorated by KRG. In conclusion, KRG may be possible to normalize cardiac gene expressions in db/db mice.

• Asian Pacific Journal of Cancer Prevention
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• 제15권7호
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• pp.3145-3149
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• 2014

Gene expression profiling facilitates the understanding of biological characteristics of gliomas. Previous studies mainly used regression/variance analysis without considering various background biological and environmental factors. The aim of this study was to investigate gene expression differences between grade III and IV gliomas through partial least squares (PLS) based analysis. The expression data set was from the Gene Expression Omnibus database. PLS based analysis was performed with the R statistical software. A total of 1,378 differentially expressed genes were identified. Survival analysis identified four pathways, including Prion diseases, colorectal cancer, CAMs, and PI3K-Akt signaling, which may be related with the prognosis of the patients. Network analysis identified two hub genes, ELAVL1 and FN1, which have been reported to be related with glioma previously. Our results provide new understanding of glioma pathogenesis and prognosis with the hope to offer theoretical support for future therapeutic studies.

• Reproductive and Developmental Biology
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• 제34권2호
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• pp.103-109
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• 2010

Functional regulation of a specific tissue or organ is controlled by a number of ways, including local cell-cell interaction. Of several forms of cell-cell junctional complexes, gap junctions are caught a great attention due to a formation of direct linkage between neighboring cells. Gap junctions are consisted of connexin (Cx) isoforms. In the present study, we evaluated expressional profiling of Cx isoforms in the rat initial segment (IS) of the male reproductive tract at different postnatal ages. The presence and expression of 13 Cx isoform mRNAs were determined by semi-quantitative real-time PCR analyses. A total of 8 Cx isoform mRNAs were detected in the IS of the male rats during postnatal development. The highest level of Cx30.3 mRNA was found at 5 months of age, while abundance of Cx31 mRNA was the highest at 1 year of age. Expression of Cx31.1 gene was relatively consistent during the postnatal development. Fluctuation of Cx32 and 37 gene expression was observed during the postnatal period. Significant elevation of Cx40 mRNA abundance was detected at 25 days of age and older ages. Expression patterns of Cx43 and 45 genes were similar with the highest level at 2 weeks of age, followed by gradual decreases at older ages. These results indicate differential regulation on expression of Cx isoforms in the rat IS during postnatal development. A complicated regulation of gene expression of Cx isoforms in the IS at different postnatal ages is suggested.

• Molecular & Cellular Toxicology
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• 제5권1호
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• pp.51-57
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• 2009

Quantum Dot (QD) nanoparticles are used in various industrial applications, such as diagnostic, drug delivery, and imaging agents of biomedicine. Although QDs are extensively used in many medical science, several studies have been demonstrated the potential toxicity of nanoparticles. The first objective of this study was to investigate the nanotoxicity of QDs in the HaCaT human keratinocyte cell line by focusing on gene expression pattern. In order to evaluate the effect of QDs on gene expression profile in HaCaT cells, we analyzed the differential genes which related to oxidative stress and antioxidant defense mechanisms by using human cDNA microarray and PCR array. A human cDNA microarray was clone set, which was sorted for a list of genes correlated with cell mechanisms. We tried to confirm results of cDNA microarray by using PCR array, which is pathway-focused gene expression profiling technology using Real-Time PCR. Although we could not find the exactly same genes in both methods, we have screened the effects of QDs on global gene expression profiles in human skin cells. In addition, our results show that QD treatment somehow regulates cellular pathways of oxidative stress and antioxidant defense mechanisms. Therefore, we suggest that this study can enlarge our knowledge of the transcriptional profile and identify new candidate biomarker genes to evaluate the toxicity of nanotoxicology.

• Molecular & Cellular Toxicology
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• 제3권2호
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• pp.137-144
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• 2007

The mechanism of cytotoxicity of doxifluridine, a prodrug fluorouracil (5-FU), has been ascribed to the misincorporation of fluoropyrimidine into RNA and DNA and to the inhibition of the nucleotide synthetic enzyme thymidylate synthase. Increased understanding of the mechanism of 5-FU has led to the development of strategies that increases its anticancer activity or predicts its sensitivity to patients. Using GeneChip?? Rhesus Macaque Genome arrays, we analyzed gene expression profiles of doxifluridine after two weeks repeated administration in cynomolgus monkey. Kegg pathway analysis suggested that cytoskeletal rearrangement and cell adhesion remodeling were commonly occurred in colon, jejunum, and liver. However, expression of genes encoding extracellular matrix was distinguished colon from others. In colon, COL6A2, COL18A1, ELN, and LAMA5 were over-expressed. In contrast, genes included in same category were down-regulated in jejunum and liver. Interestingly, MMP7 and TIMP1, the key enzymes responsible for ECM regulation, were overexpressed in colon. Several studies were reported that both gene reduced cell sensitivity to chemotherapy-induced apoptosis. Therefore, we suggest they have potential as target for modulation of 5-FU action. In addition, the expression of genes which have been previously known to involve in 5-FU pathway, were examined in three organs. Particularly, there were more remarkable changes in colon than in others. In colon, ECGF1, DYPD, TYMS, DHFR, FPGS, DUT, BCL2, BAX, and BAK1 except CAD were expressed in the direction that was good response to doxifluridine. These results may provide that colon is a prominent target of doxifluridine and transcriptional profiling is useful to find new targets affecting the response to the drug.

• Toxicological Research
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• 제25권2호
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• pp.85-92
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• 2009

4,4'-Methylenedianiline (MDA) is an aromatic amine that is widely used in the industrial synthetic process. Genotoxic MDA forms DNA adducts in the liver and is known to induce liver damage in human and rats. To elucidate the molecular mechanisms associated with MDA-induced hepatotoxicity, we have identified genes differentially expressed by microarray approach. BALB/c male mice were treated once daily with MDA (20 mg/kg) up to 7 days via intraperitoneal injection (i.p.) and hepatic damages were revealed by histopathological observation and elevation of serum marker enzymes such as AST, ALT, ALP, cholesterol, DBIL, and TBIL. Microarray analysis showed that 952 genes were differentially expressed in the liver of MDA-treated mice and their biological functions and canonical pathways were further analyzed using Ingenuity Pathways Analysis (IPA). Toxicological functional analysis showed that genes related to hepatotoxicity such hyperplasia/hyperproliferation (Timp1), necrosis/cell death (Cd14, Mt1f, Timp1, and Pmaip1), hemorrhaging (Mt1f), cholestasis (Akr1c3, Hpx, and Slc10a2), and inflammation (Cd14 and Hpx) were differentially expressed in MDA-treated group. This gene expression profiling should be useful for elucidating the genetic events associated with aromatic amine-induced hepatotoxicity and for discovering the potential biomarkers for hepatotoxicity.