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microarray analysis of the phytoremediation and phytosensing of occupational toxicant naphthalene

JOURNAL OF HAZARDOUS MATERIALS 2011年第1-2期189卷 19-26页

作者： Peng, Ri-He Xu, Ran-Ran Fu, Xiao-Yan Xiong, Ai-Sheng Zhao, Wei Tian, Yong-Sheng Zhu, Bo Jin, Xiao-Fen Chen, Chen Han, Hong-Juan Yao, Quan-Hong Shanghai Acad Agr Sci Shanghai Key Lab Agr Genet & Breeding Agrobiotechnol Res Inst Shanghai 201106 Peoples R China

Naphthalene is of global environmental concern because it is assumed to contribute considerably to human cancer risk. Plants are important in removing naphthalene from the atmosphere and soil. However, there remains insufficient knowledge on plant response to this compound. To determine the mechanism of naphthalene uptake and transduction in plants, as well as plant response to this compound, a microarray system was used to analyze gene expression patterns in Arabidopsis thaliana after irrigation with 2.0 mm naphthalene. A total of 247 differentially expressed genes were identified as upregulated by naphthalene. These genes might specifically contribute to naphthalene uptake, transformation, conjugation, and compartmentalization in the plant. The potential role of upregulated genes in plant defense to naphthalene and the use of phytosensing for naphthalene detection were also discussed. (C) 2011 Elsevier B.V. All rights reserved.

关键词： microarray analysis Naphthalene Arabidopsis thaliana Phytoremediation Phytosensing

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microarray analysis of apoptosis gene expression in liver injury induced by chronic exposure to arsenic and high-fat diet in male mice

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ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH 2019年第25期26卷 26351-26366页

作者： Kalantari, Heibatullah Khodayar, Mohammad Javad Saki, Najmaldin Khorsandi, Layasadat Teymoori, Ali Alidadi, Hadis Samimi, Azin Ahvaz Jundishpur Univ Med Sci Sch Pharm Dept Pharmacol & Toxicol Ahvaz Iran Ahvaz Jundishapur Univ Med Sci Hlth Res Inst Res Ctr Thalassemia & Hemoglobinopathy Ahvaz Iran Ahvaz Jundishapur Univ Med Sci Cellular & Mol Res Ctr Ahvaz Iran Ahvaz Jundishapur Univ Med Sci Sch Med Dept Virol Ahvaz Iran

Rapid growth in the incidence of liver disease is largely attributable to lifestyle and environmental contaminants, which are often overlooked as the leading causes of this problem. Thus, the possible contribution of arsenic (As) to high-fat diet (HFD)-induced liver damage was examined via microarray analysis. To perform this experiment, a total number of 40 healthy adult male NMRI mice (22-30 g) were used. To this end, these animals were randomly assigned to four groups of 10. Oxidative stress and histopathological parameters were also evaluated in the liver of the mice exposed to a minimally cytotoxic concentration of As (50 ppm) in drinking water while being fed with a HFD for 20 weeks. Subsequently, apoptosis gene expression profiling was utilized via real-time (RT) PCR array analysis. The results showed that As had increased the amount of HFD-induced liver damage and consequently amplified changes in oxidative stress factors, histopathological parameters, as well as apoptosis pathway genes. Investigating the expression profile of apoptosis pathway genes similarly revealed that caspase-8, as a main upstream contributor to the apoptosis pathway, might play an important role in the induction of apoptosis generated by As and HFD. Ultimately, this study highlighted that As in drinking water could increase sensitivity in mice to HFD-induced liver disease through strengthening apoptosis pathway.

关键词： Arsenic High-fat diet Oxidative stress Apoptosis microarray analysis

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microarray analysis of gene expression differences in microglia after exposure to graphene quantum dots

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SCIENCE OF THE TOTAL ENVIRONMENT 2020年 749卷 141385-141385页

作者： Liang, Xue Wu, Tianshu Tang, Meng Southeast Univ Key Lab Environm Med & Engn Minist Educ Sch Publ Hlth Nanjing 210009 Peoples R China

Graphene quantum dub (GQDs) have been broadly applied in biomedicine in recent years. So far, researches have reported that GQDs might contribute to he injury of the central nervous system (CNS), yet the latent toxicological mechanism is not clear. This study aims to investigate the underlying biological mechanism responsible for the neurotoxicity of nitrogen-doped GQDs (N-GQDs) and amino-functionalized GQDs (A-GQDs) by use of genome-wide transcription microarray. The findings showed that 174 and 1341 genes were altered significantly in the BV2 cells treated by 25 mu g/mL N-GQDs and 100 mu g/mL N-GQDs compared with the control, respectively. As for he BV2 cells exposed to 100 mu g/mL A-GQDs, 1396 diversely expressed genes were detected. By comparing he 100 mu g/mL N-GQDs exposed group with 100 mu g/mL A-GQDs exposed group, the expression of 256 genes was extensively altered, including 58 upregulated genes and 198 downregulated genes. From Gene Ontology (GO) analysis, the altered genes were mainly enriched in functions of ion channel activation and cellular processes. Based on the KEGG pathway and signal-net analysis, the toxicity of GQDs in BV2 cells was closely related to calcium signaling pathway, cell cycle and endocytosis. And the pathways that the shared mRNAs involved all served as the crucial roles in the neurotoxicity of GQDs despite the chemical functionalization (N-GQDs Of A-GQDs). In addition, the consequences from qRT-PCR, Western blot, intracellular calcium level measurements and comet assay further confirmed that calcium dyshomeostasis DNA damage and cell cycle arrest were the key factors responsible for the GQDs-incluced neurotoxicity through affecting several classical signaling pathways. In conclusion, our research will supply essential data for further studies on mechanisms of GQDs-inclucecl neurotoxicity by use of genome-wide screening. (C) 2020 Elsevier B.V. All rights reserved.

关键词： Graphene quantum dot microarray analysis mRNA Signal-net BV2 cells Neurotoxicity

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microarray analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders

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Neuroscience Bulletin 2018年第5期34卷 779-788页

作者： Huanhuan Li Jiujiang Zeng Liang Huang Dandan Wu Lifen Liu Yutong Liu Qionglan Yuan Department of Neurology Shanghai Tongji Hospital Tongji University School of Medicine Department of Radiology University of Nebraska Medical Center

Neuroplastin 65 （Np65） is an immunoglobulin superfamily cell adhesion molecule involved in synaptic formation and plasticity. Our recent study showed that Np65-knockout （KO） mice exhibit abnormal cognition and emotional disorders. However, the underlying mechanisms remain unclear. In this study, we found 588 differentially- expressed genes in Np65-KO mice by microarray analysis. RT-PCR analysis also revealed the altered expression of genes associated with development and synaptic structure, such as Cdhl, Htr3a, and Kcnj9. In addition, the expression of Wnt-3, a Wnt protein involved in development, was decreased in Np65-KO mice as evidenced by western blotting. Surprisingly, MRI and DAPI staining showed a significant reduction in the lateral ventricular volume of Np65-KO mice. Together, these findings suggest that ablation of Np65 influences gene expression, which may contribute to abnormal brain development. These results provide clues to the mechanisms underlying the altered brain functions of Np65-deficient mice.

关键词： Neuroplastin 65 microarray analysis Gene expression profile Htr3a Wnt

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microarray analysis of developing Arabidopsis seeds

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PLANT PHYSIOLOGY 2000年第4期124卷 1570-1581页

作者： Girke, T Todd, J Ruuska, S White, J Benning, C Ohlrogge, J Michigan State Univ Dept Bot & Plant Pathol E Lansing MI 48824 USA Michigan State Univ Dept Biochem E Lansing MI 48824 USA

To provide a broad analysis of gene expression in developing Arabidopsis seeds, microarrays have been produced that display approximately 2,600 seed-expressed genes. DNA for genes spotted on the arrays were selected from >10,000 clones partially sequenced from a cDNA library of developing seeds. Based on a series of controls, sensitivity of the arrays was estimated at one to two copies of mRNA per cell and cross hybridization was estimated to occur if closely related genes have >70% to 80% sequence identity. These arrays have been hybridized in a series of experiments with probes derived from seeds, leaves, and roots of Arabidopsis. analysis of expression ratios between the different tissues has allowed the tissue-specific expression patterns of many hundreds of genes to be described for the first time. Approximately 25% of the 2,600 genes were expressed at ratios greater than or equal to 2-fold higher in seeds than leaves or roots and 10% at ratios greater than or equal to 10. Included in this list are a large number of proteins of unknown function, and potential regulatory factors such as protein kinases, phosphatases, and transcription factors. The Arabidopsis arrays were also found to be useful for transcriptional profiling of mRNA isolated from developing oilseed rape (Brassica napus) seeds and expression patterns correlated well between the two species.

关键词： Ribonucleic-acid populations Gene-expression Developmental biochemistry Cottonseed embryogenesis Genome analysis Germination. Thaliana Profiles Plants Arrays biochemistry Genes genome analysis symmetric self-electro-optic effect devices Greater than or equal to Arabidopsis Germination serial analysis of gene expression microarray analysis arrays

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microarray analysis of long noncoding RNA expression patterns in diabetic nephropathy

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JOURNAL OF DIABETES AND ITS COMPLICATIONS 2017年第3期31卷 569-576页

作者： Chen, Sheng Dong, Chenglong Qian, Xiaoxiao Huang, Shanshan Feng, Yamin Ye, Xiaolong Miao, Heng You, Qiang Lu, Yibing Ding, Dafa Nanjing Med Univ Affiliated Hosp 2 Dept Endocrinol Nanjing 210000 Jiangsu Peoples R China Nanjing Med Univ Nanjing 210029 Jiangsu Peoples R China Yancheng First Peoples Hosp Dept Endocrinol Yancheng 224006 Peoples R China Nanjing Mil Command Nanjing Gen Hosp Dept Endocrinol Nanjing 210002 Jiangsu Peoples R China

Aims: Long noncoding RNAs (IncRNAs) are implicated in various biological processes and human diseases. Diabetic nephropathy (DN) is the leading cause of end-stage renal disease (ESRD). We explored the potential functions of IncRNAs in DN. Methods: We established a mouse model of DN and compared IncRNA expression patterns between DN model and db/m control mouse kidney tissues using microarray analysis. IncRNA function was predicted by gene ontology enrichment and KEGG pathway analyses of IncRNAs-coexpressed mRNAs. Quantitative reverse-transcription PCR was used for validation. Cis- and trans-regulation analyses were conducted to reveal potential relationships between IncRNAs and their target genes. Results: In DN, 311 IncRNAs were dysregulated. LncRNA-coexpressed mRNAs were mainly targeted to golgi apparatus (ontology: cellular component), catalytic activity (ontology: molecular function), and mitotic nuclear division (ontology: biological process), and were mostly enriched in glutathione metabolism signaling. One hundred forty-seven IncRNAs were regarded as cis-regulatory. Several groups of IncRNAs may participate in biological pathways related to DN via trans-regulation of protein-coding genes. Conclusion: Hundreds of IncRNAs are dysregulated in DN. These IncRNAs might be involved in the pathogenesis of DN by modulating multiple molecular pathways. Our findings provide potential candidate biomarkers for predicting or diagnosing DN. (C) 2016 Elsevier Inc. All rights reserved.

关键词： Diabetic nephropathy Long noncoding RNA microarray analysis MAPK Biomarkers

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microarray analysis of cultured human brain aggregates following cortisol exposure: Implications for cellular functions relevant to mood disorders

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NEUROBIOLOGY OF DISEASE 2006年第3期23卷 630-636页

作者： Salaria, S. Chana, G. Caldara, F. Feltrin, E. Altieri, M. Faggioni, F. Domenici, E. Merlo-Pich, E. Everall, I. P. Univ Calif San Diego Dept Psychiat La Jolla CA 92093 USA GlaxoSmithKline Inc Ctr Excellence Drug Discovery Psychiat I-37135 Verona Italy

Increased cortisol levels in humans are often observed in patients suffering from mood disorders. In this study human fetal brain aggregates were exposed to cortisol at 500 nM for 3 weeks, as an in-vitro model of chronic cortisol exposure. microarray analysis on extracted mRNA using the Affymetrix U133A platform was then performed. Our results demonstrated a significant effect of cortisol on 1648 transcripts;736 up-regulated and 912 down-regulated genes. The most differentially regulated biological categories were: RNA processing, protein metabolism, and cell growth. Within these categories we observed a down-regulation of fibroblast growth factor 2 (FGF2) (-1.5-fold) and aquaporin4 (AQP4) (-1.7-fold), alongside an upregulation of fibroblast growth factor 9 (FGF9) (+1.7-fold) and vesicle associated membrane protein2 (VAMP2) (+1.7-fold). FGF2, FGF9, AQP4 and VAMP2 changes were confirmed at the protein level by immunohistochemistry. Alterations in FGF transcripts are in keeping with recent literature demonstrating such effects in patients with mood disorders. (c) 2006 Elsevier Inc. All rights reserved.

关键词： human fetal brain aggregates glucocorticoids gene expression microarray analysis fibroblast growth factors mood disorders

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microarray analysis of gene expression of bone marrow stem cells cocultured with salivary acinar cells

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JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION 2013年第11期112卷 713-720页

作者： Lin, Chia-Yung Yang, Jhih-Ren Teng, Sheng-Lin Tsai, Stephanie Chen, Min-Huey Natl Taiwan Univ Hosp Dept Dent Hsinchu Branch Hsinchu Taiwan Natl Taiwan Univ Sch Dent Grad Inst Clin Dent Taipei 10764 Taiwan

Background/Purpose: Our previous work has demonstrated that rat bone marrow stem cells (BMSCs) can transdifferentiate into alpha-amylase-producing cells after coculture with rat submandibular gland acinar cells. These transdifferentiated cells may be used for regeneration of damaged salivary gland. The purpose of this study was to investigate the global gene expression of rat BMSCs cocultured with rat submandibular gland acinar cells and the factors inducing this transdifferentiation. Methods: Rat BMSCs were indirectly cocultured with rat submandibular gland acinar cells by using the double chamber system for Sand 10 days. The global gene expression of BMSCs during transdifferentiation into acinar cells was investigated by microarray analysis. Results: A total of 45,018 probes were used and 41,012 genes were detected. After coculture for 5 days, 1409 genes were upregulated more than twofold and 1417 genes were downregulated more than twofold (p < 0.005). Moreover, after coculture for 10 days, 1356 genes were upregulated more than twofold and 1231 genes were downregulated more than twofold (p < 0.005). Bone morphogenetic protein (BMP)-6 was one of the top-ranked upregulated genes. The hub genes were interleukin-6 and CCAAT/enhancer-binding protein beta (CEBPB) in the early and late response gene groups, respectively. Conclusion: This is believed to be the first study on the global gene expression of rat BMSCs cocultured with rat acinar cells. Many genes related to the function of salivary acinar cells such as those responsible for the production of alpha-amylase protein were upregulated and many genes related to the differentiation of BMSCs into adipocytes and osteoblasts were downregulated. In addition, BMP-6 gene was found to be highly upregulated. We proposed that three target genes, BMP-6, interleukin-6 and CEBPB, play important roles in the transdifferentiation of BMSCs into acinar cells, and are worthy of further investigation. Copyright (C) 2012, Elsevier Taiw

关键词： bone marrow stem cells salivary acinar cells bone morphogenetic protein-6 transdifferentiation microarray analysis

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microarray analysis on Phase II drug metabolizing enzymes expression in pregnant rats after treatment with pregnenolone-16α-carbonitrile or phenobarbital

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EXPERIMENTAL AND MOLECULAR PATHOLOGY 2005年第3期79卷 272-277页

作者： Ejiri, N Katayama, K Kiyosawa, N Baba, Y Doi, K Univ Tokyo Grad Sch Agr & Life Sci Dept Vet Pathol Bunkyo Ku Tokyo 1138657 Japan Sankyo Co Ltd Med Safety Res Labs Shizuoka Japan

We previously reported the expression profiles of 9 cytochrome P450 isozymes (CYPs) proteins and those of 40 CYPs genes in pregnant rat's liver, placenta and fetal liver after treatment with pregnenolone-I 6 alpha-carbonitrile (PCN) or phenobarbital (PB). This study was carried out focusing on the gene expression profiles of Phase 11 drug metabolizing enzymes, Glutathione S-transferase isozymes (GSTs) and UDP-glycosyltransferase isozymes (UDPGTs). Fischer 344 (F344) pregnant rats were daily treated intraperitoneally with 50 mg/kg of PCN or 80 mg/kg of PB from 13 to 16 days of gestation (DG). They were sacrificed on 17 DG, and microarray analysis using Affymetrix Rat Expression Array 230 A was performed. Among 16 GSTs genes examined in this study, 7 genes were significantly induced in dam's liver and 3 genes in fetal liver, respectively, in the PCN-group, while 8 genes were significantly induced in dam's liver and I gene in fetal liver, respectively, in the PB-group. On the other hand, among I I UDPGTs genes examined, 5 genes were significantly induced in dam's liver and 3 genes in fetal liver, respectively, in the PCN-group, while 5 genes were significantly induced in dam's liver and I gene in fetal liver, respectively, in the PB-group. There were no significant changes in the placenta of all groups. This is the first report of the gene expression profiles of Phase 11 drug metabolizing enzymes in pregnant rat and fetal livers and placenta after treatment with typical inducers of drug metabolizing enzymes. (C) 2005 Elsevier Inc. All rights reserved.

关键词： GSTs microarray analysis pregnenolone-16 alpha-carbonitrile (PCN) phenobarbital pregnant rat UDPGTs

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microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

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PARASITES & VECTORS 2018年第1 p327-327期11卷 1-9页

作者： Yu, Aiping Wang, Ying Yin, Jianhai Zhang, Jing Cao, Shengkui Cao, Jianping Shen, Yujuan Chinese Ctr Dis Control & Prevent Natl Inst Parasit Dis Shanghai 200025 Peoples R China MOH Key Lab Parasite & Vector Biol Shanghai 200025 Peoples R China Natl Ctr Int Res Trop Dis Shanghai 200025 Peoples R China WHO Collaborating Ctr Trop Dis Shanghai 200025 Peoples R China

Background: Cystic echinococcosis is a worldwide chronic zoonotic disease caused by infection with the larval stage of Echinococcus granulosus. Previously, we found significant accumulation of myeloid-derived suppressor cells (MDSCs) in E. granulosus infection mouse models and that they play a key role in immunosuppressing T lymphocytes. Here, we compared the long non-coding RNA (lncRNA) and mRNA expression patterns between the splenic monocytic MDSCs (M-MDSCs) of E. granulosus protoscoleces-infected mice and normal mice using microarray analysis. Methods: LncRNA functions were predicted using Gene Ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Cis- and trans-regulation analyses revealed potential relationships between the lncRNAs and their target genes or related transcription factors. Results: We found that 649 lncRNAs were differentially expressed (fold change >= 2, P < 0.05): 582 lncRNAs were upregulated and 67 lncRNAs were downregulated;respectively, 28 upregulated mRNAs and 1043 downregulated mRNAs were differentially expressed. The microarray data was validated by quantitative reverse transcription-PCR. The results indicated that mRNAs co-expressed with the lncRNAs are mainly involved in regulating the actin cytoskeleton, Salmonella infection, leishmaniasis, and the vascular endothelial growth factor (VEGF) signaling pathway. The lncRNA NONMMUT021591 was predicted to cis-regulate the retinoblastoma gene (Rb1), whose expression is associated with abnormal M-MDSCs differentiation. We found that 372 lncRNAs were predicted to interact with 60 transcription factors;among these, C/EBP beta (CCAAT/enhancer binding protein beta) was previously demonstrated to be a transcription factor of MDSCs. Conclusions: Our study identified dysregulated lncRNAs in the M-MDSCs of E. granulosus infection mouse models;they might be involved in M-MDSC-derived immunosuppression in related diseases.

关键词： Echinococcus granulosus Myeloid-derived suppressor cells Long non-coding RNAs Expression profile microarray analysis

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