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基于组学数据表达谱的下呼吸道铜绿假单胞菌毒力基因exoS和exoU的共表达网络分析 被引量:1
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作者 焦二莉 陈博 《国际检验医学杂志》 CAS 2019年第20期2529-2533,共5页
目的以铜绿假单胞菌的基因芯片为研究样本,并对其进行组学数据层面的挖掘,旨在从分子生物学的层面阐明下呼吸道铜绿假单胞菌毒力基因exoS和exoU的共表达网络特征,并发现其关键的调控基因。方法于2016年3月至2018年5月采用定群抽样的方... 目的以铜绿假单胞菌的基因芯片为研究样本,并对其进行组学数据层面的挖掘,旨在从分子生物学的层面阐明下呼吸道铜绿假单胞菌毒力基因exoS和exoU的共表达网络特征,并发现其关键的调控基因。方法于2016年3月至2018年5月采用定群抽样的方法选取内蒙古包钢医院呼吸内科接诊并在该院接受后续治疗的312例下呼吸道铜绿假单胞菌感染者为受试对象,生物标本为患者的肺泡灌洗液及痰液。使用寡聚核苷酸探针对铜绿假单胞菌的基因进行检测,对芯片数据进行预处理。选择头孢他啶、庆大霉素、哌拉西林、阿米卡星、环丙沙星、左旋氧氟沙星、多尼培南、替卡西林共8种呼吸内科针对革兰阴性菌常用的抗菌药物对生物标本进行耐药性测定,利用MCODE算法构建以exoS/exoU为核心的耐药基因共表达网络模型。结果耐药组exoS/exoU表达量均显著高于非耐药组,差异有统计学意义(P<0.05);耐药组肺泡灌洗液标本前5位差异表达基因差异表达量从高到低排序依次为RAC1、ITGB1、ITGB5、CRK及IGF1R。痰标本顺序为RAC1、CRK、IGF1R、ITGB1及ITGB5。肺泡灌洗液标本中仅RAC1与exoS、exoU表达呈正相关性(P<0.05);痰标本中RAC1、ITGB1、ITGB5、CRK及IGF1R与exoS、exoU表达呈正相关性(P<0.05)。共表达网络中纳入的基因包括exoS、exoU、RAC1、ITGB1、ITGB5、CRK、CAMK2D、RHOA、FLNA、IGF1R、TGFBR2、FOS。其中RAC1基因调控能力评分最高(72.00),调控基因数最多(6个);其后依次为ITGB1、ITGB5及CRK基因。结论痰标本出现exoS和exoU高表达提示铜绿假单胞菌有更高概率产生耐药性;RAC1、ITGB1、ITGB5及CRK基因可能是调控exoS和exoU表达的关键基因。 展开更多
关键词 组学数据表达谱 下呼吸道 铜绿假单胞菌 exoS exoU 共表网络
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玉米油脂代谢相关基因的全基因组挖掘、表达谱及与籽粒油份QTL共定位分析 被引量:2
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作者 李林 李慧 +4 位作者 李骥英 徐淑兔 杨小红 李建生 严建兵 《中国科学(C辑)》 CSCD 北大核心 2009年第12期1162-1174,共13页
油脂是植物中广泛存在且参与众多生物学过程的一类物质,具有重要的生物学功能.本研究从拟南芥和水稻油脂代谢基因出发,基于序列相似和功能域相同原则,克隆并注释了1003个玉米油脂代谢相关基因,其中,774个从GenBank中直接注释,229个为新... 油脂是植物中广泛存在且参与众多生物学过程的一类物质,具有重要的生物学功能.本研究从拟南芥和水稻油脂代谢基因出发,基于序列相似和功能域相同原则,克隆并注释了1003个玉米油脂代谢相关基因,其中,774个从GenBank中直接注释,229个为新克隆基因.电子表达谱分析发现97个基因在玉米籽粒、根、叶或分生组织中特异高表达.整合已发表籽粒油分相关QTL,在玉米基因组中发现70个控制籽粒油份的QTL富集区(分布于34%的基因组区域),其中59个QTL富集区内存在油脂代谢候选基因147个.在玉米籽粒中特异高表达的13个脂肪酸合成代谢基因都落在QTL富集区.本研究挖掘的油脂代谢相关基因信息,电子表达谱数据及整合的油份QTL结果,为玉米油份QTL的进一步精细定位和克隆、玉米籽粒油份形成的分子生物学基础研究提供了有益信息. 展开更多
关键词 油脂代谢 电子克隆 电子表达谱 数量性状位点 玉米
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美谱达紫外可见分光光度计UV-6100S应用
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作者 高娜娜 孙宏娜 +1 位作者 杨颖 唐亚娟 《中国食品工业》 2013年第3期41-41,共1页
检测仪器的灵敏度,验证仪器是否满足检测要求,是否试运于实验室使用。
关键词 龙尼柯分光光度计 紫外可见分光光度计 灵敏度
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肝细胞癌中差异表达EST的生物信息学分析和功能预测 被引量:4
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作者 陈香宇 段芳龄 +6 位作者 李建生 朱武凌 韩泽广 李玉龙 曾艳丽 孙艳 孙嫣 《胃肠病学和肝病学杂志》 CAS 2004年第1期43-48,共6页
目的 采用生物信息学方法分析、预测在原发性肝细胞癌中差异表达表达序列标签 (expressionsequencetag ,EST)的全长、ORF、电子表达谱、染色体定位和编码蛋白质的功能 ,指导实验研究。方法 应用多种生物学软件进行分析。结果 获得两... 目的 采用生物信息学方法分析、预测在原发性肝细胞癌中差异表达表达序列标签 (expressionsequencetag ,EST)的全长、ORF、电子表达谱、染色体定位和编码蛋白质的功能 ,指导实验研究。方法 应用多种生物学软件进行分析。结果 获得两条新基因的全长序列 ,和RACE方法、测序获得的结果一致 ;两条EST分别定位于 2p13~ 15、3p14 ;高表达EST主要表达于肿瘤组织 ,低表达EST主要表达于正常组织 ;高表达基因所编码蛋白质参与细胞信号转导、前mRNA加工和细胞骨架组装 ,低表达编码蛋白质和机体T淋巴细胞介导的免疫反应有关。结论 采用生物信息学技术有助于高效、快速地克隆、鉴定新基因。 展开更多
关键词 肝细胞癌 EST 生物信息学 免疫反应 电子基因定位 电子表达谱
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多类簇功率谱对MIMO信道与性能影响
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作者 陈姜高路 周杰 吴鹏 《计算机工程与设计》 北大核心 2018年第9期2719-2724,共6页
为分析在各种功率谱下接收信号相关性参数及其近似计算,建立功率谱在典型均匀角分布、高斯分布及拉普拉斯等分布下的闭合函数表达式,提出近似方法和MIMO系统的接收信道模型。推导在复杂反射物环境下形成多类簇的多边波达信号分布,并得... 为分析在各种功率谱下接收信号相关性参数及其近似计算,建立功率谱在典型均匀角分布、高斯分布及拉普拉斯等分布下的闭合函数表达式,提出近似方法和MIMO系统的接收信道模型。推导在复杂反射物环境下形成多类簇的多边波达信号分布,并得出各种组合分布情况下的无线信道衰落相关性特征。实例计算和仿真实验结果表明,表达式和部分近似法可更有效分析波达信号多种组合功率谱下MIMO系统接收信道衰落参数及性能。 展开更多
关键词 多输入多输出 多边分布 多类簇 信号功率方位 空间衰落相关性
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Generation of Antibodies Against DMRT1 and DMRT4 of Oreochromis aurea and Analysis of Their Expression Profile in Oreochromis aurea Tissues 被引量:6
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作者 曹谨玲 曹哲民 吴婷婷 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第6期497-509,共13页
Sex determination is composed of somatic and germ-line sex differentiation hierarchies whose interaction is poorly understood. A single gene known to control somatic sex determination, the DM-domain containing (Doubl... Sex determination is composed of somatic and germ-line sex differentiation hierarchies whose interaction is poorly understood. A single gene known to control somatic sex determination, the DM-domain containing (Doublesex/Mab-3 DNA-binding motif) gene, is highly conserved across species. Vertebrate DMRT1 (DM-related transcription factor 1) expression occurs predominantly in the testis. Here, however, isolated two distinct DM-domain cDNA from Oreochromis aurea ovary and testis have been named DMRT4 (DM-related transcription factor 4) and DMRT1 by BLAST, respectively. Despite high homology in the DM-domain there is little similarity outside the DM-domain.To better understand the structure, function, and possible roles of DMRT4 and DMRT1 as potential candidates for sex differentiation and sex determination, the intact regions encoding DMRT4 and DMRT1 obtained by PCR were sub-cloned into the vector pMAL-c2x and introduced into the Escherichia coli TB1 cell for efficient fusion expression. After purification and cleavage, DMRT4 and DMRT1 proteins were used to immunize adult rabbits following standard protocols. Consequently, it was found by using Western blot analysis that polyclonal antibodies against DMRT4 and DMRT1 had high specificity. The relative expression levels of DMRT4 and DMRT1 mRNA were determined by fluorescent Real-time RT-PCR in female and male Oreochromis aurea with 13-actin as the internal standard. DMRT1 was expressed only in testis, whereas DMRT4 was over expressed in the ovary, but in both female and male, a slight expression in the brain was also detected. Statistical analysis showed that in the brain, mean DMRT4 mRNA levels in female were significantly higher than in male. Meanwhile, the expression of DMRT4 and DMRT1 protein was also analyzed using the purified antibodies through Western blot and immunohistochemistry. It was found that DMRT4 was exclusively expressed in the ovary and DMRT1 in the testis. Study on DMRT4 and DMRT1 expression facilitated the elucidation of their roles and the understanding of sex differentiation of fish. 展开更多
关键词 DMRT 1 DMRT4 prokaryotic expression polyclonal antibody expression profile
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Screening of the Metastasis-Associated Genes by Gene Chip in High Metastatic Human Ovarian Cancer Cell Lines 被引量:1
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作者 许沈华 牟瀚舟 +3 位作者 顾琳慧 苏丹 朱赤红 刘祥麟 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第7期581-590,共10页
Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high (H) metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues (C). Bioinformatics w... Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high (H) metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues (C). Bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated [Signal Log Ratio (SLR) ≥3], and 640 genes were downregulated (SLR≤-3). Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes (115 genes, 9.3%), followed by chromosome 2 (94 genes, 7.6%), chromosome 12 (88 genes, 7.1%), chromosome 11 (76 genes, 6.1%), chromosomes X (71 genes, 5.7%), and chromosomes l7 (69 genes, 5.6%). These genes were localized on short-arm of chromosome (q), which had 805 (65.1%) genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes (306 genes, 24.7%) belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes (144 genes, 11.6%). The rest of the top two groups were signal transduction genes (137 genes, 11.1%) and proteins binding genes (116 genes, 9.4%). These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown (16.7 %). Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied. 展开更多
关键词 ovarian cancer cell line metastatic associated gene chromosomal localization molecular function
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Expression Profile Changes of Genes Involved in Lipid Metabolism Pathway During Liver Regeneration in Mice 被引量:1
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作者 袁运生 张夕原 +3 位作者 严德珺 杨婷旭 郜尽 俞雁 《Agricultural Science & Technology》 CAS 2009年第2期41-45,共5页
[ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regene... [ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regeneration was established and the total RNA was isolated from liver tissue of mouse. Then the changes of genes involved in lipid metabolism pathway during different stages of liver regeneration were detected through micro-array chip gene technique and their specific functions were also analyzed. [ Result] Dudng the process of liver regeneration, the expression level of 98 genes involved in lipid metabolism pathway changed, which were divided into eight groups according to change trend. In the mass, the expression of genes was inhibited in the early stage and up-regulated in the late phase. And the gene expression associated with fatty acid synthesis pathway was mainly up-regulated while the catabolic pathway did not change significantly. Most of genes involved in bile acid synthesis pathway were suppressed before 4.5 d and up-regulated after 4.5 d or 7 d. [ Conclusion] During the process of liver regeneration, the genes associated with lipid metabolism are expressed in different trends, and this data should provide a specific range of genes for further studying the regulation effect of lipid metabolism related pathway on liver regeneration. 展开更多
关键词 Upid metabolism Gene expression profiles Liver regeneration Micro-array chip
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Hyperspectral image classification based on spatial and spectral features and sparse representation 被引量:4
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作者 杨京辉 王立国 钱晋希 《Applied Geophysics》 SCIE CSCD 2014年第4期489-499,511,共12页
To minimize the low classification accuracy and low utilization of spatial information in traditional hyperspectral image classification methods, we propose a new hyperspectral image classification method, which is ba... To minimize the low classification accuracy and low utilization of spatial information in traditional hyperspectral image classification methods, we propose a new hyperspectral image classification method, which is based on the Gabor spatial texture features and nonparametric weighted spectral features, and the sparse representation classification method(Gabor–NWSF and SRC), abbreviated GNWSF–SRC. The proposed(GNWSF–SRC) method first combines the Gabor spatial features and nonparametric weighted spectral features to describe the hyperspectral image, and then applies the sparse representation method. Finally, the classification is obtained by analyzing the reconstruction error. We use the proposed method to process two typical hyperspectral data sets with different percentages of training samples. Theoretical analysis and simulation demonstrate that the proposed method improves the classification accuracy and Kappa coefficient compared with traditional classification methods and achieves better classification performance. 展开更多
关键词 HYPERSPECTRAL CLASSIFICATION sparse representation spatial features spectral features
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Genes Expression Profile Difference in Peripheral Blood Between Esophageal Carcinoma Patients and Normal Subjects 被引量:1
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作者 钱丽娟 许沈华 +3 位作者 牟瀚舟 冯建国 朱赤红 刘祥麟 《The Chinese-German Journal of Clinical Oncology》 CAS 2005年第5期279-283,324,共6页
Objective: To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early concera... Objective: To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early conceration associated genes. Methods: The total RNA was extracted and purified in the peripheral blood obtained from the patients with esophageal carcinoma and normal subjects. The first strand of cDNA was synthesized through retro-transcription and labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with a piece of 4096 double dot human whole gene chip. The acquired image was analyzed by microarrav suite software using a digital computer, and the intensity of ttuorescence signal and its ratio were calculated. Results: A total of 92 genes were screened out and its expression difference was more than 2 times in the peripheral blood between the patients with esophageal carcinoma and normal subjects. Among these, the expression difference of 36 genes was more than 3 times. Two human urokinase plasminogen activator surface receptor (UPAR) genes, 80K-L protein gene, human protein tyrosine-phosphatase gent arid proto-oncogene protein mRNA were significantly up-regulated, while the collagen V type (α-2 gene was markedly down-regulated. Conclusion: 80K-L protein gene, tyrosinephophatase gene, proto-oncogene protein arid the collagen V type α-2 gene might be associated with the ontogenesis, development and its metastasis in the esophageal carcinoma. The UPAR gene may play important roles in the diagnosing the micrometastasis in the peripheral blood of esophageal carcinoma. 展开更多
关键词 human esophageal carcinoma: peripheral blood gene expression profile
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Molecular Detection of Healthiness of Bombyx mori
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作者 刘彬斌 罗峰 +3 位作者 杜周和 吴建梅 陈义安 刘俊凤 《Agricultural Science & Technology》 CAS 2012年第11期2273-2277,2322,共6页
[Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screene... [Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screened by bioinfor- matic analysis method, and carried out real-time PCR expression analysis. [Result] The target gene Bmhsp24.3 expressed in different B. mori materials, but the expres- sion level in different materials significantly varied. The relative expression level of the gene had different degrees of changes under different rearing conditions. With the increase of rearing temperature, the gene expression was upregulated. The ma- terials with better healthiness had remarkable increase in expression of target gene, while the materials with poorer healthiness had less increase in expression of target gene. The expression difference of target gene Bmhsp24.3 was exactly consistent with the healthiness of breeds. [Conclusion] The healthiness of materials had rela- tionship with expression of target gene Bmhsp24.3. the higher the expression of tar- get gene Bmhsp24.3 was, the better the healthiness of materials was; conversely, the lower the expression of target gene Bmhsp24.3 was, the poorer the healthiness of materials was. 展开更多
关键词 Bombyx mori Bmhsp24.3 Healthiness Real-time PCR
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波达信号功率谱分布对信号接收衰落相关性的影响
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作者 周杰 刘鹏 菊池久和 《通信技术》 2014年第10期1114-1120,共7页
本文推导波达信号功率谱对MIMO(Multiple Input Multiple Output)多天线信号接收衰落相关性通用式,并分析了在各种功率谱分布下的接收信号相关性。结果证明分析可以很好地应用于波达信号功率谱为高斯分布、拉普拉斯分布和均匀角分布时... 本文推导波达信号功率谱对MIMO(Multiple Input Multiple Output)多天线信号接收衰落相关性通用式,并分析了在各种功率谱分布下的接收信号相关性。结果证明分析可以很好地应用于波达信号功率谱为高斯分布、拉普拉斯分布和均匀角分布时的信道情况。在功率谱分布是双边分布时,导出了其接收信号衰落相关性特征。分析结果发现功率谱分布的标准偏差或角度扩展大小是确定接收信号衰落相关性的主导因素。数值结果表明在一定范围内增大天线阵列单元间的距离以及功率谱分布标准差可以减小天线阵列接收信号衰落相关性,改善系统性能。在阵列天线单元间在中长距离内,功率谱高斯分布更符合实际和有利于分析和提高无线信道多天线MIMO系统性能。 展开更多
关键词 信号功率 信号衰落相关性 电磁传播 双边分布
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Comparative Analysis of Five Different Homologous Feeder Cell Lines in the Ability to Support Rhesus Embryonic Stem Cells
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作者 陈栋梁 李荣荣 +5 位作者 张敬 卢斌 魏强 王淑芬 谢云华 季维智 《Zoological Research》 CAS CSCD 北大核心 2009年第4期345-353,共9页
In our previous study, five homologous feeder cell lines, Monkey ear skin fibroblasts (MESFs), clonally derived fibroblasts from the MESFs (CMESFs), monkey oviductal fibroblasts (MOFs), monkey follicular granulo... In our previous study, five homologous feeder cell lines, Monkey ear skin fibroblasts (MESFs), clonally derived fibroblasts from the MESFs (CMESFs), monkey oviductal fibroblasts (MOFs), monkey follicular granulosa fibroblast-like (MFGs) cells, monkey follicular granulosa epithelium-like (MFGEs) cells, were developed for the maintenance of rhesus embryonic stem cells (rESCs). We found that MESFs, CMESFs, MOFs and MFGs, but not MFGEs, support the growth of rhesus embryonic stem cells. Moreover, we detected some genes that are upregulated in supportive feeder cell lines by semi-quantitative PCR. In the present study, we applied the GeneChip Rhesus Macaque Genome Array of Affymetrix Corporation to study the expression profiles of these five feeder cell lines, in purpose to find out which cytokines and signaling pathways were important in maintaining the rESCs, mRNAs of eight genes, including GREM2, bFGF, KITLG, DKK3, GREM1, AREG, SERPINF1 and LTBP1, were found to be upregulated in supportive feeder cell lines, but not in MFGE. The results indicate that many signaling pathways may play redundant roles in supporting the undifferentiated growth and maintenance of pluripotency in rESCs. 展开更多
关键词 Embryonic stem cells Rhesus monkey feeders SELF-RENEWAL PLURIPOTENCY Expression profile Signaling pathway
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Aquaporin-8 expression is reduced in ileum and induced in colon of patients with ulcerative colitis 被引量:13
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作者 Alexandra Zahn Christoph Moehle +4 位作者 Thomas Langmann Robert Ehehalt Frank Autschbach Wolfgang Stremmel Gerd Schmitz 《World Journal of Gastroenterology》 SCIE CAS CSCD 2007年第11期1687-1695,共9页
AIM: To study susceptibility genes which may play a potential role in the pathogenesis and etiology of inflammatory bowel disease (IBD). METHODS: To identify potential susceptibility genes we performed global gene... AIM: To study susceptibility genes which may play a potential role in the pathogenesis and etiology of inflammatory bowel disease (IBD). METHODS: To identify potential susceptibility genes we performed global gene expression profiling in patients with IBD and control specimens. For determination of an intrinsic gene expression profile in ulcerative colitis (UC) and Crohn's disease (CD) compared to normal subjects, mucosal biopsies of non-inflamed regions of the colon and the terminal ileum were subjected to DNA microarray analysis. Real-time RT-PCR and immunohistochemistry were used for verification of selected regulated candidate genes and a genetic analysis was performed. RESULTS: We could show that aquaporin-8 (AQP8) mRNA and protein levels were significantly increased in the colon of UC patients compared to controls. Genetic analysis of the six exons and the promoter region of AQPS, however, revealed no mutations or polymorphisms in IBD patients. CONCLUSION: Our results suggest that upregulation of AQP8 in the colon of UC patients represents a secondary phenomenon which may, due to altered water exchange of the distal intestinal mucosa, disturb the physiologic colonic mucus barrier and thus lead to chronic inflao mmation and ulceration. 展开更多
关键词 Aquaporin-8 Colonic mucus barrier DNA microarrays Expression profiling Ulcerative colitis
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MiRNA profile in esophageal squamous cell carcinoma:Downregulation of miR-143 and miR-145 被引量:31
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作者 Bing-Li Wu Li-Yan Xu +5 位作者 Ze-Peng Du Lian-Di Liao Hai-Feng Zhang Qiao Huang Guo-Qiang Fang En-Min Li 《World Journal of Gastroenterology》 SCIE CAS CSCD 2011年第1期79-88,共10页
AIM:To investigate the expression profile of miRNA in esophageal squamous cell carcinoma(ESCC).METHODS:The expression profile of miRNA in ESCC tissues was analyzed by miRNA microarray.The expression levels of miR-143 ... AIM:To investigate the expression profile of miRNA in esophageal squamous cell carcinoma(ESCC).METHODS:The expression profile of miRNA in ESCC tissues was analyzed by miRNA microarray.The expression levels of miR-143 and miR-145 in 86 ESCC patients were determined by real-time polymerase chain reaction(PCR) using TaqMan assay.The mobility effect was estimated by wound-healing using esophageal carcinoma cells transfected with miRNA expression plasmids.RESULTS:A set of miRNAs was found to be deregulated in the ESCC tissues,and the expression levels of miR-143 and-145 were significantly decreased in most of the ESCC tissues examined.Both miR-143 and miR-145 expression correlated with tumor invasion depth.The transfection of human esophageal carcinoma cells with miR-143 and miR-145 expression plasmids resulted in a greater inhibition of cell mobility,however,the protein level of the previously reported target of miR-145,FSCN1,did not show any significant downregulation.CONCLUSION:These findings suggest that the deregulation of miRNAs plays an important role in the progression of ESCC.Both miR-143 and miR-145 might act as anti-oncomirs common to ESCC. 展开更多
关键词 Esophageal squamous cell carcinoma MicroRNA MIR-143 MIR-145 Tumor invasion depth
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DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments 被引量:12
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作者 Wen Hui LIN, Rui YE, Hui MA, Zhi Hong XU, Hong Wei XUE National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences and Partner Group of Max-Planck-Institute of Molecular Plant Physiology (MPI-MP) on "Plant Molecular Physiology and Signal Transduction", 300 Fenglin Road, 200032 Shanghai, China 《Cell Research》 SCIE CAS CSCD 2004年第1期34-45,共12页
The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors,and previous studies have indicated the involvement of multiple PI-related gene families during c... The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors,and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses.Through a detailed analysis of the Arabidopsis thaliana genome,82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS),PI-phosphate kinases (PIPK),phospholipases (PL),inositol polyphosphate phosphatases (IPPase),inositol polyphosphate kinases (IPK),PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK,PLC,PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly,DNA chip technology was employed to study the expression patterns of various isoforms.In total,79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf,stem and flower tissues,and leaves from plants treated with various hormones (auxin,cytokinin,gibberellin,abscisic acid and brassinosteroid) or environmental factors (temperature,calcium,sodium,drought,salicylic acid and jasmonic acid).Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions.In particular,the different isoforms of each family were specifically expressed in many cases,suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses. 展开更多
关键词 PHOSPHATIDYLINOSITOL signal transduction DNA chip expression profile.
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Role of H3K27 methylation in the regulation of IncRNA expression 被引量:22
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作者 Susan C Wu 《Cell Research》 SCIE CAS CSCD 2010年第10期1109-1116,共8页
Once thought to be transcriptional noise, large non-coding RNAs (IncRNAs) have recently been demonstrated to be functional molecules. The cell-type-specific expression patterns of lncRNAs suggest that their transcri... Once thought to be transcriptional noise, large non-coding RNAs (IncRNAs) have recently been demonstrated to be functional molecules. The cell-type-specific expression patterns of lncRNAs suggest that their transcription may be regulated epigenetically. Using a custom-designed microarray, here we examine the expression profile of IncRNAs in embryonic stem (ES) cells, lineage-restricted neuronal progenitor cells, and terminally differentiated fibroblasts. In addition, we also analyze the relationship between their expression and their promoter H3K4 and H3K27 methyla- tion patterns. We find that numerous lncRNAs in these cell types undergo changes in the levels of expression and promoter H3K4me3 and H3K27me3. Interestingly, lncRNAs that are expressed at lower levels in ES cells exhibit higher levels of H3K27me3 at their promoters. Consistent with this result, knockdown of the H3K27me3 methyltransferase Ezh2 results in derepression of these IncRNAs in ES cells. Thus, our results establish a role for Ezh2-mediated H3K27 methylation in lncRNA silencing in ES cells and reveal that lncRNAs are subject to epigenetic regulation in a similar manner to that of the protein-coding genes. 展开更多
关键词 IncRNA histone methylation Polycomb repressive complex 2
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Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling 被引量:5
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作者 Yue-Zheng Zhang Lian-Hai Zhang +8 位作者 Yang Gao Chao-Hua Li Shu-Qinjia Ni Liu Feng Cheng De-Yun Niu William CS Cho Jia-Fu Ji Chang-Qing Zeng 《World Journal of Gastroenterology》 SCIE CAS CSCD 2011年第13期1710-1717,共8页
AIM: To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis. METHODS: Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we... AIM: To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis. METHODS: Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we analyzed the expression of 47 296 transcripts in two batches of gastric cancer patients who underwent surgical resection. Thirty-nine samples in the first batch were used as the training set to discover candidate markers correlated to overall survival, and thirty-three samples in the second batch were used for validation. RESULTS: A panel of ten genes were identified as prognostic marker in the first batch samples and classified patients into a lowand a high-risk group with significantly different survival times (P = 0.000047). This prognostic marker was then verified in an independent validation sample batch (P = 0.0009). By comparing with the traditional Tumor-node-metastasis (TNM) staging system, this ten-gene prognostic marker showed consistent prognosis results. It was the only independent prognostic value by multivariate Cox regression analysis (P = 0.007). Interestingly, six of these ten genes are ribosomal proteins, suggesting a possible association between the deregulation of ribosome related gene expression and the poor prognosis. CONCLUSION: A ten-gene marker correlated with overall prognosis, including 6 ribosomal proteins, was identified and verified, which may complement the predictive value of TNM staging system. 展开更多
关键词 Gastric cancer Gene expression profiling Survival markers PROGNOSIS Ribosomal proteins
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Wnt5a participates in hepatic stellate cell activation observed by gene expression profile and functional assays 被引量:18
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作者 Wu-Jun Xiong Li-Juan Hu +4 位作者 Yi-Cheng Jian Li-Jing Wang Ming Jiang Wei Li Yi He 《World Journal of Gastroenterology》 SCIE CAS CSCD 2012年第15期1745-1752,共8页
AIM:To identify differentially expressed genes in quiescent and activated hepatic stellate cells(HSCs)and explore their functions.METHODS:HSCs were isolated from the normal Sprague Dawley rats by in suit perfusion of ... AIM:To identify differentially expressed genes in quiescent and activated hepatic stellate cells(HSCs)and explore their functions.METHODS:HSCs were isolated from the normal Sprague Dawley rats by in suit perfusion of collagenase and pronase and density Nycodenz gradient centrifugation.Total RNA and mRNA of quiescent HSCs,and cultureactivated HSCs were extracted,quantified and reversely transcripted into cDNA.The global gene expression profile was analyzed by microarray with Affymetrix rat genechip.Differentially expressed genes were annotated with Gene Ontology(GO)and analyzed with Kyoto encyclopedia of genes and genomes(KEGG)pathway using the Database for Annotation,Visualization and Integrated Discovery.Microarray data were validated by quantitative real-time polymerase chain reaction(qRTPCR).The function of Wnt5a on human HSCs line LX-2 was assessed with lentivirus-mediated Wnt5a RNAi.The expression of Wnt5a in fibrotic liver of a carbon tetrachloride(CCl4)-induced fibrosis rat model was also analyzed with Western blotting.RESULTS:Of the 28 700 genes represented on this chip,2566 genes displayed at least a 2-fold increase or decrease in expression at a P<0.01 level with a false discovery rate.Of these,1396 genes were upregulated,while 1170 genes were downregulated in culture-activated HSCs.These differentially expressed transcripts were grouped into 545 GO based on biological process GO terms.The most enriched GO terms included response to wounding,wound healing,regulation of cell growth,vasculature development and actin cytoskeleton organization.KEGG pathway analysis revealed that Wnt5a signaling pathway participated in the activation of HSCs.Wnt5a was significantly increased in cultureactivated HSCs as compared with quiescent HSCs.qRTPCR validated the microarray data.Lentivirus-mediated suppression of Wnt5a expression in activated LX-2 resulted in significantly impaired proliferation,downregulated expressions of typeⅠcollagen and transforming growth factor-β1.Wnt5a was upregulated in the fibrotic liver of a CCl4-induced fibrosis rat model.CONCLUSION:Wnt5a is involved in the activation of HSCs,and it may serve as a novel therapeutic target in the treatment of liver fibrosis. 展开更多
关键词 Hepatic stellate cells WNT5A MICROARRAY Bioinformatics analyses Liver fibrosis
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Expression profiles of two small heat shock proteins and antioxidant enzyme activity in Mytilus galloprovincialis exposed to cadmium at environmentally relevant concentrations 被引量:5
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作者 由丽萍 宁璇璇 +4 位作者 陈磊磊 张林宝 赵建民 刘小莉 吴惠丰 《Chinese Journal of Oceanology and Limnology》 SCIE CAS CSCD 2014年第2期334-343,共10页
Small heat shock proteins encompass a widespread but diverse class of proteins, which play key roles in protecting organisms from various stressors. In the present study, the full-length cDNAs of two small heat shock ... Small heat shock proteins encompass a widespread but diverse class of proteins, which play key roles in protecting organisms from various stressors. In the present study, the full-length cDNAs of two small heat shock proteins (MgsHSP22 and MgsHSP24.1) were cloned from Mytilus galloprovincialis, which encoded peptides of 181 and 247 amino acids, respectively. Both MgsHSP22 and MgsHSP24.1 were detected in all tissues examined by real-time PCR, with the highest expression being observed in muscle and gonad tissues. The real-time PCR results revealed that Cd significantly inhibited MgsHSP22 expression at 24 h and MgsHSP24.1 at 24 and 48 h under 5 ug/L Cd2+ exposure. MgsHSP24.1 expression was also significantly inhibited after 50 ug/L Cd2+ exposure for 48 h. With regard to antioxidant enzymes, increased GPx and CAT activity were detected under Cd2+ stress (5 and 50 ug/L), while no significant difference in SOD activity was observed throughout the experiment. Overall, both MgsHsps and antioxidant enzymes revealed their potential as Cd stress biomarkers in M. galloprovincialis. 展开更多
关键词 Mytilus galloprovincialis small heat shock protein superoxide dismutase (SOD) catalase (CAT) glutathione peroxidase (GPx) CADMIUM
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