Serial Analysis of Gene Expression (SAGE) of<Emphasis Type="Italic"> Magnaporthe grisea</Emphasis>: genes involved in appressorium formation

Treatment with cyclic AMP (cAMP) induces appressorium formation in the phytopathogenic fungus Magnaporthe grisea, the causative agent of rice blast disease. In a search for the M. grisea genes responsible for appressorium formation and host invasion, SAGE (Serial Analysis of Gene Expression) was carried out using mRNA isolated from fungal conidia germinating in the presence and absence of cAMP. From cAMP-treated conidia 5087 tags including 2889 unique tags were isolated, whereas untreated conidia yielded 2342 unique tags out of total of 3938. cAMP treatment resulted in up- and down-regulation of genes corresponding to 57 and 53 unique tags, respectively. Upon consultation of EST/cDNA databases, 22 tags with higher representation in cAMP-treated conidia were annotated with putative gene names. Furthermore, 28 tags corresponding to cAMP-induced genes could be annotated with the help of the recently published genome sequence of M. grisea. cAMP-induced genes identified by SAGE included many genes that have not been described so far, as well as a number of genes known to be involved in pathogenicity, e.g. MPG1, MAS1 and MAC1. RT-PCR of 13 randomly selected genes confirmed the SAGE results, verifying the fidelity of the SAGE data.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by E. Cerdá-Olmedo     

基因表达系列分析法(SAGE)的改进及其在植物功能基因组研究中的应用

基因表达系列分析方法(SAGE)是一种新的基因表达分析方法,与基因芯片技术一样具有高通量的特点,可测定特定组织的基因表达水平,在全基因组水平上同时定量检测数万个基因表达模式;可在未知目的基因的前提下,分析来自一个细胞的全部转录本信息;对已知或未知基因表达进行定性和定量分析.目前,虽然在疾病、发育、细胞凋亡、药物筛选等多个领域已有利用SAGE方法进行的研究,但该方法在植物功能基因组研究中的应用相对较少.本文主要综述了该方法在RNA用量、PCR循环次数、SAGE效能和可靠性、标签长度和未知标签分析等方面的改进及其在植物中构建SAGE文库、筛选新基因、基因表达图谱分析等方面的应用,从而为其在植物功能基因组研究中的进一步应用提供理论参考.     

Gene expression profiling of human diseases by serial analysis of gene expression

Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases.     

缺磷对黑麦草-内生真菌共生体生长和根中酚含量的影响

培养液中缺磷或内生真菌感染对黑麦草地上部生长的影响不显著,但二者的交互作用却有着显著影响。随着磷浓度的下降,感染内生真菌的黑麦草显示出较强的生长优势,其根长和根中酚类物质的含量显著增加。     

基因表达分析方法及其研究进展

近几年来,随着功能基因组学研究的兴起,基因表达研究的分析方法也在不断发展,主要有：差减杂交、差异显示、表达序列标签、基因表达的序列分析、微阵列杂交等。简要评述这五种方法的原理、优缺点等。     

Characterization of genes with tissue-specific differential expression patterns in Populus

Like many plants, Populus has an evolutionary history in which several, both recent and more ancient, genome duplication events have occurred and, therefore, constitutes an excellent model system for studying the functional evolution of genes. In the present study, we have focused on the properties of genes with tissue-specific differential expression patterns in poplar. We identified the genes by analyzing digital expression profiles derived by mapping 90,000+ expressed sequence tags (ESTs) from 18 sources to the predicted genes of Populus. Our sequence analysis suggests that tissue-specific differentially expressed genes have less diverged paralogs than average, indicating that gene duplication events is an important event in the pathway leading to this type of expression pattern. The functional analysis showed that genes coding for proteins involved in processes of functional importance for the specific tissue(s) in which they are expressed and genes coding for regulatory or responsive proteins are most common among the differentially expressed genes, demonstrating that the expression differentiation process is under strong selective pressure. Thus, our data supports a model where gene duplication followed by gene specialization or expansion of the regulatory and responsive networks leads to tissue-specific differential expression patterns. We have also searched for clustering of genes with similar expression pattern into gene-expression neighborhoods within the Populus genome. However, we could not detect any major clustering among the analyzed genes with highly specific expression patterns. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Using ANOVA for gene selection from microarray studies of the nervous system

Methods are presented for detecting differential expression using statistical hypothesis testing methods including analysis of variance (ANOVA). Practicalities of experimental design, power, and sample size are discussed. Methods for multiple testing correction and their application are described. Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/.     

高羊茅和多年生黑麦草内生真菌的分子检测

根据GenBank上报道的内生真菌Neotyphodium coenophialum和N.lolii的Nc25基因序列,设计了2对特异性引物FM1/R1和F3/R652,建立了一套适合于从高羊茅和多年生黑麦草种子中检测内生真菌N.coenophialum和N.lolii的常规PCR和巢式PCR方法。     

适合于miRNA的荧光定量PCR优化体系的建立及其标准

实时荧光定量PCR是目前基因表达量差异分析的首选方法之一。虽然其操作简单,但如何保证其定量结果的可信度一直是个难题,特别是针对只有20多个碱基的miRNA的定量分析。本研究以水稻miR408在不同组织中的表达差异为实例,系统地优化和阐述了有关荧光定量的新标准及要求。结果表明,引物的浓度对于荧光定量PCR体系的优化至关重要。     

cDNA微阵列分析人apoE4转基因鼠肾脏基因表达谱的变化

目的研究人apoE4转基因鼠肾脏的基因表达谱变化.方法分别提取人apoE4转基因鼠和正常C57BL/6J小鼠的肾脏总RNA,经逆转录合成cDNA探针后分别与鼠cDNA表达点阵杂交,再用ESTblot软件进行分析,并用Northern印迹证明基因表达的改变.结果人apoE4转基因鼠肾脏中有38个基因的mRNA表达升高,22个基因的mRNA表达降低.其中血浆谷胱甘肽过氧化物酶前体、视黄酸γ受体和白介素5受体等基因的表达明显增加.B-raf原癌基因、促红细胞生成素受体、整联蛋白α4的基因表达显著降低.Northern杂交证明转基因鼠肾脏的c-Jun基因表达升高.结论人apoE4转基因鼠肾脏的c-Jun、血浆谷胱甘肽过氧化物酶前体、白介素5受体等基因的表达增加;促红细胞生成素受体、整联蛋白α4等基因的表达减少.     

含翻译增强子的表达载体pSC34的构建及初步应用

１９８８年Ｏｌｉｎｓ［１］发现Ｔ７噬菌体基因１０的先导序列（Ｔ７ｇ１０Ｌ）具有明显的促进基因翻译的作用．本文构建了含Ｔ７ｇ１０Ｌ的表达载体ｐＳＣ３４,并尝试表达了几个不同类型的基因．１材料与方法１．１菌株大肠杆菌菌株ＴＡＰ１０６为本室储存．ＴＡＰ１０...     

UBC and YWHAZ as suitable reference genes for accurate normalisation of gene expression using MCF7, HCT116 and HepG2 cell lines

Relative quantification of in vitro gene expression using real-time PCR requires stably expressed reference gene for normalisation. In this study, total RNA from MCF7, HCT116 and HepG2 cells were extracted and converted to cDNA using commercially available kit, and real-time PCR was then performed to analyse the expression levels of twelve reference genes to select the most ideal reference gene for accurate normalisation in gene expression study. geNorm and NormFinder software were used to analyse the stabilities of the reference genes, which showed a wide range of C_t values. The geNorm analysis showed the following ranking for stability of genes: UBC, YWHAZ > RPLP > TBP > ACTB > HPRT1 > PPIA > GAPDH > GUSB > B2M > TUBB > RRN18S. A similar ranking of reference genes was obtained by NormFinder, and the four most stable reference genes were identical using both approaches. UBC and YWHAZ were proposed to be the two most suitable reference genes based on the above analyses. To further assess the stabilities of the UBC and YWHAZ in a formal experiment, MCF7, HCT116 and HepG2 cell lines were subjected to treatments with 5-aza-dC and TSA. Both UBC and YWHAZ exhibited stable expression levels across control and treatment groups. Therefore, we propose that UBC and YWHAZ are the two most suitable reference genes for our gene expression studies using MCF7, HCT116 and HepG2 cell lines.     

EBV阳性胃癌细胞系与阴性胃癌细胞系全基因组表达谱差异比较

目的：探讨EB病毒阳性胃癌细胞系与EB 病毒阴性胃癌细胞系全基因组表达谱的差异。方法：利用Agilent 人类全基因组表达谱芯片技术在3 种EB病毒阳性胃癌细胞系和3 种EB 病毒阴性胃癌细胞系中筛选EB病毒相关胃癌肿瘤相关基因。选取6条差异表达基因,应用实时荧光定量PCR验证芯片结果的可靠性。结果：聚类热图及矩阵图分析显示,EB病毒阳性胃癌细胞系与阴性胃癌细胞系之间表达谱存在明显差异。差异表达基因涉及多种生物学过程。选取的6 条差异基因进行验证,其表达趋势与芯片结果一致。结论：感染EB病毒可能会改变肿瘤相关基因的表达,进而在EB病毒相关胃癌的发生、发展及预后中发挥作用。筛选出的肿瘤相关基因涉及多种生物学过程,提示多基因及相关基因的变异参与了EB病毒相关胃癌的形成。     

甘蔗天冬氨酰半醛脱氢酶基因的电子克隆与分析

应用电子克隆技术,以水稻EF576477序列为探针,获得了甘蔗天冬氨酰半醛脱氢酶基因（aspartate．semialdehydedehy—drogenase,ASADH）的一条cDNA全长序列,命名为ScASADH。采用生物信息学方法,对该基因编码蛋白从氨基酸组成、理化性质、亚细胞定位、跨膜结构域、疏水性／亲水性、高级结构及功能域等方面进行预测和分析。结果表明：该基因全长1711bp,包含一个1128bp的开放阅读框,编码375个氨基酸,该基因编码蛋白定位于细胞核,为可溶性蛋白,存在信号肽,二级结构原件多为无规卷曲,含有多个保守功能域,主要功能为翻译。电子表达分析结果显示,该基因在甘蔗根尖、幼苗、花序、叶片和茎中组成型表达,其中在茎中的表达量比其他组织类型中表达量高。该基因的表达受葡萄糖杆菌和赤腐病菌的调控。