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Analysis of genome-wide gene expression in root of wheat hybrid and its parents using Barleyl genechip

Progress in Natural Science:Materials International 2006年第7期16卷 712-720页

作者： ZHANG Yinhong, NI Zhongfu, YAO Yingyin, ZHAO Jun and SUN Qixin (Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Genomics and Genetic Improvement, Ministry of Agriculture / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China) China Agr Univ Dept Genet & Plant Breeding Beijing 100094 Peoples R China China Agr Univ Minist AgrBeijing Key Lab Crop Genet Improvement State Key Lab Agrobiotechnol Key Lab Crop Genom & Genet Improvement Beijing 100094 Peoples R China

Previous studies indicated that differential gene expression between hybrids and their parents is responsible for the hct-crosis. In this paper, we report genome-wide gene expression analysis in roots of a highly heterotic inter-specific hybrid 3338/2463 and its parental inbreds using Barley genechip. A total of 1187 genes displayed difference in gene expressions between hybrid 3338/2463 and its parents, and they can be clustered into eight differential expression patterns. Further analysis revealed that among these 1187 genes, 975 genes showed high sequence similarity to the GenBank entries, and represented diverse functional categories, such as metabolism, cell growth and maintenance, signal transduction, response to stress, transcription regulation and others. Fourteen genes were selected for RT-PCR analysis and expression patterns of 9 (64. 29% ) genes were confirmed. Remarkably, 380 differentially expressed genes could be mapped on the Chinese Spring deletion bins, and with the number of genes in seven homoeologous groups being 158, 148, 121, 140, 132, 94 and 127 respectively. It is concluded that a combination of systematic identification of differentially expressed genes with comparative mapping would provide further insight into understanding of molecular basis of heterosis.

关键词： genechip gene expression heterosis hybrid wheat.

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基因芯片检测5种动物冠状病毒的初步研究

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畜牧与兽医 2010年第12期42卷 16-21页

作者：李健谢爱织陈沁王巧全熊炜张建武王权胡永强上海出入境检验检疫局上海200135 上海大学生命科学学院上海200444 中国农业科学院上海兽医研究所上海200032

采用蔗糖密度梯度离心,纯化浓缩犬冠状病毒(CCV)、猫冠状病毒(FCV)、猫传染性腹膜炎病毒(FIPV)、猪传染性胃肠炎病毒(TGEV)、猪呼吸道冠状病毒(PRCV)的细胞培养物,分别设计7,17,11,10和4对引物,构建了49个基因片段的克隆。煮沸裂解法制... 详细信息

采用蔗糖密度梯度离心,纯化浓缩犬冠状病毒(CCV)、猫冠状病毒(FCV)、猫传染性腹膜炎病毒(FIPV)、猪传染性胃肠炎病毒(TGEV)、猪呼吸道冠状病毒(PRCV)的细胞培养物,分别设计7,17,11,10和4对引物,构建了49个基因片段的克隆。煮沸裂解法制备质粒DNA,回收PCR扩增产物,点制冠状病毒基因芯片。抽提病毒总RNA,利用Cy3-dCTP随机渗入反转录PCR标记,与芯片进行杂交检测,淘汰交叉的克隆片段。结果表明:克隆CCV1,CCV2,CCV5和CCV7可特异诊断CCV,克隆FCV6,FCV7,FCV8和FCV9可特异诊断FCV,克隆FIPV2,FIPV7,FIPV8和FIPV9可特异诊断FIPV,克隆PRCV1,PRCV2和PRCV3可特异诊断PRCV,克隆TGEV3,TGEV4,TGEV5和TGEV6可特异诊断TGEV。将这些特异克隆扩增片段重新点制基因芯片,与病毒PCR产物杂交,未发现交叉现象。基因芯片检测比传统PCR敏感1000倍,可有效应用于这5种动物冠状病毒的检测与区分。

关键词：基因芯片检测动物冠状病毒初步研究 genechip 特异诊断克隆猪传染性胃肠炎病毒猪呼吸道冠状病毒蔗糖密度梯度离心猫传染性腹膜炎扩增片段 PCR扩增产物细胞培养物犬冠状病毒杂交检测交叉现象基因片段纯化浓缩 TGEV PCR产物

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Transcriptome research on spermatogenic molecular drive in mammals

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Asian Journal of Andrology 2015年第6期17卷 961-971,I0009页

作者： Zi-Jue Zhu Shi Yang Zheng Li Department of Urology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China Department of Andrology Urologic Medical CenterShanghai General Hospital Shanghai Jiao Tong University Shanghai 200080 China Shanghai Key Laboratory of Reproductive Medicine Shanghai 200025 China.

It is known that spermatogenic disorders are associated with genetic deficiency, although the primary mechanism is still unclear. It is difficult to demonstrate the molecular events occurring in testis, which contains germ cells at different developmental stages. However, transcriptomic methods can help us reveal the molecular drive of male gamete generation. Many transcriptomic studies have been performed on rodents by utilizing the timing of the first wave of spermatogenesis, which is not a suitable strategy for research in fertile men. With the development of separation methods for male germ cells, transcriptome research on the molecular drive of spermatogenesis in fertile men has seen great progress, and the results could be ultimately applied to improve the diagnosis and treatment for male infertility.

关键词： genechip germ cell RNA-Seq sorting spermatogenesis transcriptome

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Overexpression of microRNA-124 promotes the neuronal differentiation of bone marrow-derived mesenchymal stem cells

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Neural Regeneration Research 2014年第12期9卷 1241-1248页

作者： Defeng Zou Yi Chen Yaxin Han Chen Lv Guanjun Tu Department of Orthopedics First Affiliated Hospital of China Medical University Department of Orthopedics Jinhua Central Hospital of Zhejiang University

microRNAs （miRNAs） play an important regulatory role in the self-renewal and differentiation of stem cells. In this study, we examined the effects of miRNA-124 （miR-124） overexpression in bone marrow-derived mesenchymal stem cells. In particular, we focused on the effect of overexpression on the differentiation of bone marrow-derived mesenchymal stem cells into neurons. First, we used genechip technology to analyze the expression of miRNAs in bone marrow-derived mesen- chymal stem cells, neural stem cells and neurons, miR-124 expression was substantially reduced in bone marrow-derived mesenchymal stem cells compared with the other cell types. We con- structed a lentiviral vector overexpressing miR-124 and transfected it into bone marrow-derived mesenchymal stem cells. Intracellular expression levels of the neuronal early markers [3-III tu- bulin and microtubule-associated protein-2 were significantly increased, and apoptosis induced by oxygen and glucose deprivation was reduced in transfected cells. After miR-124-transfected bone marrow-derived mesenchymal stem cells were transplanted into the injured rat spinal cord, a large number of cells positive for the neuronal marker neurofilament-200 were observed in the transplanted region. The Basso-Beattie-Bresnahan locomotion scores showed that the motor function of the hind limb of rats with spinal cord injury was substantially improved. These re- sults suggest that miR-124 plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells into neurons. Our findings should facilitate the development of novel strategies for enhancing the therapeutic efficacy of bone marrow-derived mesenchymal stem cell transplantation for spinal cord injury.

关键词： nerve regeneration microRNA-124 lentivirus overexpression bone marrow-de-rived mesenchymal stem cells neural stern cells spinal cord injury neurogenesis genechip motor function NSFC grant neural regeneration

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Brain stem global gene expression profiles in human spina bifida embryos

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Neural Regeneration Research 2011年第5期6卷 366-372页

作者： Hong Zhao Xiang Li Wan-I Li Quanren He Ting Zhang Xiaoying Zheng Ran Zhou JunXie Department of Biochemistry and Molecular Biology Ministry of Education Key Laboratory of Cellular Physiology Shanxi Medical University Taiyuan 030001 Shanxi Province China Department of Physiology and Pharmacology University of Georgia Georgia 361004 USA Capital Institute of Pediatrics Beijing 100020 China Institute of Population Research Peking University Beijing 100732 China Shanxi Traditional Medical College Taiyuan 030024 Shanxi Province China

Environmental and genetic factors influence the occurrence of neural tube defects, such as spina bifida. Specific disease expression patterns will help to elucidate the pathogenesis of disease. However, results obtained from animal models, which often exhibit organism specificity, do not fully explain the mechanisms of human spina bifida onset. In the present study, three embryos with a gestational age of approximately 17 weeks and a confirmed diagnosis of spina bifida, as well as 3 age-matched normal embryos, were obtained from abortions. Fetal brain stem tissues were dissected for RNA isolation, and microarray analyses were conducted to examine profiles of gene expression in brain stems of spina bifida and normal embryos using Affymetrix HG-U133A 2.0 genechip arrays. Of the 14 500 gene transcripts examined, a total of 182 genes exhibited at least 2.5-fold change in expression, including 140 upregulated and 42 downregulated genes. These genes were placed into 19 main functional categories according to the Gene Ontology Consortium database for biological functions. Of the 182 altered genes, approximately 50% were involved in cellular apoptosis, growth, adhesion, cell cycle, stress, DNA replication and repair, signal transduction, nervous system development, oxidoreduction, immune responses, and regulation of gene transcription. Gene expression in multiple biological pathways was altered in the brain stem of human spina bifida embryos.

关键词： apoptosis genechip gene expression neural tube defect spina bifida

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Gene-Ontology Analysis on the Differentially Expressed Genes in Maize （Zea mays L.） Ear Rot

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Journal of Life Sciences 2013年第3期7卷 219-226页

作者： Guang-Sheng Yuan Jian Gao Zhi-Ming Zhang Juan Du Gui-Qing Mu Guang-Tang Pan Maize Research Institute Sichuan Agricultural University Ya 'An 625014 China

To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This gene annotation system was widely used to investigate large numbers of genes involving in real active role or regulator in cell response. First of all, differentially expressed genes were isolated by using genechip platform at 96 h post-inoculation with FM in maize inbred Bt-1. In total, 482 differentially expressed unique genes were screened out in inbred Bt-1 when compared to mock-inoculated bract tissues. Then, each gene was annotated to define functional class by GO method. Finally, these large FM-responsive genes with significant differentially change were sorted into cellular component, molecular function and biological process with complicated network by molecular annotation system. The demonstrated information in the GO analysis could provide another view for understanding the molecular mechanism and indicate a deeply complicated network with gene function underlying disease development in the host tissue. The findings in this study provide important bases to probe the molecular processes, the alteration of metabolism and the immune mechanism upon the FM infection in maize.

关键词： Ear rot genechip Fusarium moniliforme gene ontology Zea mays.

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Ligustrazine protect kidney through down regulation of fibronogen gene under ischemic condition

Ligustrazine protect kidney through down regulation of fibro...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Zhong Wang Xinwei Li The First Hospital of Guangdong Pharmaceutical University

Objectives:To study the effect of ligustrazine to the gene of fibrinogen with genechip and RT PCR through the rat model of renal ischemia and reperfusion. Methods:SD rat to random divide into two groups:The experimental group with ligustrazine treatment and the control group without ligustrazine *** experimental rat group are treated with ligustrazine for 1 week,before remove the right renal,after *** occlusion of the right renal artery 60 minute to make the induce renal failure, and then check the right ranal genchip and RT PCR. Results:*** content of the fibrinogen concentration is 3.48±0.64g/L in the control group and the Ligustrazine group is 3.90±0.68g/L of the renal ischemia,that in the control whereas the concentration is 6.40±0.87g/L in control group and the Ligustrazine is 5.28±0.76g/ L in Ligustrazine treatment group of the renal after renal reperfusion of the *** genechip result of gene of fibrinogen is cy5:377,cy3:3049,Ratio gene is 0.113 indicating down regulation of the *** PCR amplification spectrum of the experimental group is dimmer than that of the blank group. Conclusion:Ligustrazine could protect the kidney under ischemic and reperfusion condition by down-regulation to fibrinogen gene and then to lighten to poison it.

关键词： Gene of Fibrinogen Ligustrazine Ischemia and Reperfusion genechip

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基因微矩阵技术在骨肉瘤发病相关基因研究中的应用

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中华实验外科杂志 2005年第9期22卷 1094-1097页

作者：李国东蔡郑东陈正军卢雪峰雷会宁郑龙坡第二军医大学附属长海医院骨科上海200433 中科院上海生化细胞研究所

目的探索骨肉瘤发病相关基因,研究基因表达水平对于骨肉瘤发病的重要意义。方法采用3个公认的骨肉瘤细胞株及1个成骨细胞株,提取总RNA,合成生物素标记的cRNA与AffymetrixgenechipU133A芯片杂交。随机挑选10个差异表达基因,分别设计合成... 详细信息

目的探索骨肉瘤发病相关基因,研究基因表达水平对于骨肉瘤发病的重要意义。方法采用3个公认的骨肉瘤细胞株及1个成骨细胞株,提取总RNA,合成生物素标记的cRNA与AffymetrixgenechipU133A芯片杂交。随机挑选10个差异表达基因,分别设计合成引物,用嵌合荧光法(SYBRGreenI)实时RTPCR法定量测量9例术中收集的新鲜骨肉瘤标本中各基因的表达水平,应用ABIPrism7000分析其与成骨细胞株之间的表达差异。结果以表达差异≥2.0倍为限,在AffymetrixHGU133A芯片包含的所有基因(约22000个转录本)中,3个骨肉瘤细胞株与成骨细胞株相比较,共同上调58个基因;共同下调142个基因。随机挑选10个差异表达基因的实时RTPCR结果与芯片结果完全相符。结论骨肉瘤是一种多基因病变,应用微矩列有助于发现该肿瘤的基因变化规律以及研究肿瘤内基因与基因的相互作用关系。

关键词：骨肉瘤基因骨肉瘤细胞株相关基因研究基因微矩阵 Affymetrix 发病 genechip 基因表达水平差异表达基因

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Gene Expression Profiling During Gland Morphogenesis of a Mutant and a Glandless Upland Cotton

Gene Expression Profiling During Gland Morphogenesis of a Mu...

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重庆市生物化学与分子生物学学术会议

作者： Quan Sun1,Yingfan Cai1~*,Yongfang Xie1,Jianchuan Mo1,Youlu Yuan2,Yuzhen Shi2,Shengwei Li1, Huaizhong Jiang1,Zheng Pan1,Yunling Gao1 (1 College of Bioinformation,Chongqing University of Posts and Telecommunications,Chongqing 400065,China 2 Cotton Research Institute of Chinese Academy of Agricultural Sciences,Anyang, 455000,China)

To identify genes involved in pigment gland morphogenesis in cotton,gene expression was profiled using genechip analysis(Affymetrix) during pigment gland morphogenesis in cotton variety Xiangmian- 18,which has glandless seeds but glanded plants,and a glandless line,*** results showed that 303 genes were differentially expressed by a factor greater than 2 during gland morphogenesis;59% (180) of these genes shared similarity with known genes in *** genes play roles in defense

关键词： Cotton(Gossypium) genechip gene expression profile pigment gland morphogenesis

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二乙基亚硝胺所诱导大鼠肝癌表达上调的基因

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世界华人消化杂志 2005年第20期13卷 2420-2426页

作者：阚卫兵方肇勤管冬元赵晓珍吴中华盛学仕高必峰中国上海中医药大学附属普陀医院上海市200062 中国上海中医药大学上海市201203 科罗拉多大学医学院美国科罗拉多州80220

目的:首次大范围地观察二乙基亚硝胺(DEN)诱导的大鼠肝癌组织基因表达的差异,探索DEN诱发肝癌的分子机制.方法:DEN诱导大鼠肝癌,常规抽提和纯化RNA,采用AffymetrixRat230Agenechip及技术比较肝癌组织与正常大鼠肝组织基因表达的差异.结... 详细信息

目的:首次大范围地观察二乙基亚硝胺(DEN)诱导的大鼠肝癌组织基因表达的差异,探索DEN诱发肝癌的分子机制.方法:DEN诱导大鼠肝癌,常规抽提和纯化RNA,采用AffymetrixRat230Agenechip及技术比较肝癌组织与正常大鼠肝组织基因表达的差异.结果:在芯片的15710个基因中,肝癌有84.54%的基因阳性表达,肝癌基因表达在正常肝脏5倍以上的有509个,其中325个为EST片段,已知基因184个,其中的168个基因可以检索到有关文献的报道.在这168个基因中,有100个基因被发现与肿瘤有关,其中有36个与肝癌有关;有4个基因与肝脏有关;另有64个基因与肿瘤和肝脏无关.结论:?DEN诱发大鼠肝癌的后基因组变化中168个基因值得优先关注.

关键词：肝癌基因基因芯片大鼠二乙基亚硝胺癌基因表达大鼠肝癌表达上调 Affymetrix genechip

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