真菌侵染引发的茶树内源糖苷酶基因差异表达

通过探讨顺-3-己烯醇、芳樟醇氧化物、芳樟醇、水杨酸甲酯、香叶醇、苯甲醇和苯乙醇7种茶叶游离态香气组分和糖苷类香气前体对茶炭疽病菌、茶云纹叶枯病菌、茶轮斑病菌和茶赤叶斑病菌4种致病菌的抑制作用,以及真菌侵染引发的茶树（Camellia sinensis）内源β-樱草糖苷酶、β-木糖苷酶、β-葡萄糖苷酶I、β-葡萄糖苷酶II、β-葡萄糖基转移酶基因的表达差异,结果表明：7种游离态香气组分和糖苷类香气前体对4种致病菌均有明显的抑制作用,其中香叶醇的抑制作用最强,在浓度为0.1mg.mL-1时即对茶炭疽病菌的抑制率达到100%。实时定量PCR结果显示：真菌侵染可不同程度诱导茶树内源糖苷酶和β-葡萄糖基转移酶基因的表达上调,且上调多发生于染病初期。     

开放的差异基因表达技术研究进展

自 90年代早期发展以来 ,差异基因表达 (DGE)技术在许多领域得到了应用 .“开放”结构系统的DGE技术不需原始的生物学或序列信息 ,而且可应用于任何种群 .主要介绍 6项开放的DGE技术 :cDNA代表性差示分析 (cDNA RDA)、基因表达系统分析 (SAGE)、表达序列标签串联排列连接(TALEST) ,和早期的DGE技术差异显示 (DD)、随机引物聚合酶链反应 (AP PCR) ,以及一项受专利保护的技术———GeneCalling .通过几项重要的参数对这些技术进行了比较 ,认为DD虽然有其致命的弱点 ,但在目前仍然应用得非常广泛 .cDNA RDA能有效富增特异片段 ,扣除共有序列 ,如能和SAGE结合 ,将能进一步促进其发展 .TALEST和GeneCalling操作较简便 ,一次试验能获得大量的数据 ,但是分析这些数据比较麻烦 ,须借助另外的分析软件 .最后介绍了应用DGE技术取得的最新成果 .     

ABI 1700芯片分析系统在基因差异表达研究中的应用

应用化学发光法标记技术分别对正常和临床慢性髓细胞性白血病（chronic myelogenous leukemia,CML）病人骨髓单个核细胞的RNA进行标记,然后与ABI的人全基因组表达谱芯片杂交,对于杂交后所得到的荧光信号数据,应用1700芯片分析系统对其进行生物信息学分析.实验结果表明,ABI1700芯片分析系统可以对基因芯片杂交后得到的差异表达基因进行疾病学分类和生物功能分类分析,同时还发现与CML相关的差异表达基因75个,因此ABI1700芯片分析系统在芯片研究领域中具有重要的应用价值.     

利用mRNA差别显示技术分析枸杞体细胞胚发生早期基因的差别表达

本研究选用枸杞体细胞胚发生体系中的继代愈伤组织(对照)、胚性愈伤组织和早期胚体为实验材料,提取细胞总RNA,在12种锚定真核生物mRNA3'末端的OligodT12VN中,随机选用OligodT12GA为引物合成了以上三种材料的cDNA第一链,以此cDNA为模板,用随机引物进行PCR扩增,选择差别表达的片段。我们选用了OPA、OPH、OPK和OPB四组的60个随机引物对所得的c DNA进行了PCR扩增,得到了三个在体细胞胚发生早期组织中基因特异表达的片段。结果表明,在体细胞胚发生早期有胚胎发生特异性基因的表达,而且这种特异表达的基因在继代愈伤组织中没有表达,说明植物的体细胞胚发生过程就是细胞内基因差别表达的结果。 Abstract:Embryogenic calli and early embryo can be obtained from both auxin and auxin-free medium.The analysis of differential gene expression in early somatic embryogenesis has been hindered by above-mentioned material.The modifications of the recently described mRNA differential display method were reported and differential gene expression in early slmatic embryogenesis was analyzed.We have obtained three differential bands of cDNA in early somatic embryogenesis.The results indicate that gene expression has temperal and spalil order in early somatic embryogenesis of Lycium barbarum L.Plant somatic embryogenesis is the results of differential gene expression in cell.     

Differential Gene Expression Analysis by DNA Microarray Technology and Its Application in Molecular Oncology

Accumulation of genetic and epigenetic aberrations leads to malignant transformation of normal cells. Functional studies of cancer using genomic and proteomic tools aim to reveal the true complexity of the processes leading to cancer development in humans. Until recently, diagnosis and prognosis of cancer was based on conventional pathologic criteria and epidemiological evidence. Certain tumors were divided only into relatively broad histological and morphological subcategories. Rapidly developing methods of differential gene expression analysis promote the search for clinically relevant genes changing their expression levels during malignant transformation. DNA microarrays offer a unique possibility to rapidly assess the global expression picture of thousands genes in any given time point and compare the results of detailed combinatory analysis of global expression profiles for normal and malignant cells at various functional stages or separate experimental conditions. Acquisition of such genetic portraits allows searching for regularity and difference in expression patterns of certain genes, understanding their function and pathological importance, and ultimately developing the molecular nosology of cancer. This review describes the basis of DNA microarray technology and methodology, and focuses on their application in molecular classification of tumors, drug sensitivity and resistance studies, and identification of biological markers of cancer.     

Differential Gene Expression in a Marine Sponge in Relation to Its Symbiotic State

The molecular mechanisms involved in the establishment and maintenance of sponge photosymbiosis, and in particular the association with cyanobacteria, are unknown. In the present study we analyzed gene expression in a common Mediterranean sponge (Petrosia ficiformis) in relation to its symbiotic (with cyanobacteria) or aposymbiotic status. A screening approach was applied to identify genes expressed differentially in symbiotic specimens growing in the light and aposymbiotic specimens growing in a dark cave at a short distance from the illuminated specimens. Out of the various differentially expressed sequences, we isolated two novel genes (here named PfSym1 and PfSym2) that were up-regulated when cyanobacterial symbionts were harbored inside the sponge cells. The sequence of one of these genes (PfSym2) was found to contain a conserved domain: the scavenger receptor cysteine rich (SRCR) domain. This is the first report on the expression of sponge genes in relation to symbiosis and, according to the presence of an SRCR domain, we suggest possible functions for one of the genes found in the sponge-cyanobacteria symbiosis.     

激活蛋白处理水稻引发基因差异表达的研究

利用抑制性消减杂交技术(Suppression Subtractive Hybridization,SSH)成功构建了植物激活蛋白处理水稻与非处理组水稻中差异表达的消减cDNA文库。从文库中一共筛选到1756个克隆,通过反向Northern杂交,从中得到264个有效克隆并测序,利用BLAST在GenBank数据库进行序列相似性比对分析,获得28个上升表达差异基因。通过分析这些基因与植物的光合作用、营养物质的运输代谢等多种植物的生理生化功能相关。本研究为揭示激活蛋白的作用机理奠定基础。     

鲈鱼酰基辅酶A结合蛋白Acbp基因cDNA的克隆和诱导表达

酰基辅酶A结合蛋白(acyl-CoA-binding protein,ACBP)对长链脂酰基辅酶A(long-chainfatty acyl-CoA esters,LCACoA)有很高的亲和力,因而对LCACoA在细胞内的运输和利用过程起重要的作用。本文采用RACE技术从鲈鱼肝脏中克隆了Acbp基因的全长cDNA序列,该基因全长cDNA 679 bp,5'端和3'端的非翻译区分别为83 bp和326 bp,开放阅读框为270 bp。推测编码89个氨基酸,理论等电点为5.44,分子量为10.14 kDa。鲈鱼Acbp与青鳉鱼、银鳕鱼、大西洋鲑和人的同源性分别为87%、84%、78%和68%。用RT-PCR和实时定量PCR检测鲈鱼肌肉、心脏、眼、大脑、消化道、肾脏、脂肪组织、脾脏、鳃和肝脏等10种组织的Acbp基因的表达情况,结果表明,在肾脏和肝脏的表达量高,肌肉、眼睛和大脑中表达低。定量PCR检测表明鲈鱼肝脏Acbp的表达在饥饿时明显下降,胰岛素上调其表达,葡萄糖对其表达则没有影响。     

HSV-1感染细胞中HTRP基因的克隆及表达纯化

在对单纯疱疹病毒1型（HSV－1）感染KMB－17细胞后的早期基因反应的研究中,从HSV－1感染后细胞特异性cDNA文库中筛选出一个1381bp基因一HTRP,基因测序分析表明为与HSV－1感染相关基因（GenBank登录号：AF450482）,含有完整的ORF框架,cds全长924bp,编码308个氨基酸。构建了pGEX-HTRP表达质粒,在大肠杆菌B21加获得了较高的表达,采用Glutathione Sepharose4B进行亲和纯化后获得较高纯度的HTRP蛋白。用该蛋白免疫小鼠后制备的特异抗血清,在蛋白印迹实验中表现出抗体的特异性。     

纯种与杂种鸡之间肝脏组织基因差异表达及其与肉用性状杂种优势的关系

以白洛克肉鸡 (EE)、中国丝羽乌骨鸡 (CC)、农大褐 (DD)和白来航 (AA) 4个纯种鸡为材料 ,进行 4× 4完全双列杂交 ,共得到 16种杂交组合。应用mRNA差异显示技术 (DDRT PCR)检测了 8周龄纯种和杂种鸡之间肝脏组织基因的差异表达。结果表明 ,在纯种和杂种间共有 8种 15类基因差异表达模式 ,杂种和纯种之间基因表达存在明显的差异。对各种基因差异表达模式与 10个肉用性状的杂种优势率进行相关分析发现 ,表达一致型P8(t1111)与肉用性状的杂种优势率相关不显著 (P >0 0 5) ,这说明杂种优势的形成与某些基因的差异表达有关 ;正交或反交特异表达型P4(t0 10 0、t0 0 10 )与 8周龄个体重、腿肌重、半净膛重、全净膛重相关显著 (P <0 0 5) ,与胸肌重相关极显著 (P <0 0 1) ;单亲特异表达型P1(t10 0 0、t0 0 0 1)与腹脂重相关显著 (P <0 0 5) ,与体斜长相关极显著 (P <0 0 1) ;双亲特异表达型P7(t10 0 1)与腿肌重、翅重、半净膛重、肌间脂宽的杂种优势率相关显著 (P <0 0 5) ;正交或反交单亲表达一致型P2 (t110 0、t0 0 11、t10 10、t0 10 1)与肌间脂宽的杂种优势率相关显著 (P <0 0 5) ;单亲表达一致型P5(t1110、t0 111)胫骨长的杂种优势率相关显著 (P <0 0 5)。     

The Methodology Used to Measure Differential Gene Expression Affects the Outcome

Confirmation of gene expression by a second methodology is critical in order to detect false-positive findings associated with microarrays. However, the impact of methodology upon the measurement of gene expression has not been rigorously evaluated. In the current study, we compared differential gene expression between PC3 and PC3-M human prostate cancer cell lines using three separate methods: microarray, quantitative RT/PCR (qRT/PCR), and Northern blotting. The PC3 to PC3-M ratio of gene expression was determined for each of 24 different genes evaluated, by each of the three methods. Comparison of gene expression ratios between Northern and microarray, Northern and qRT/PCR, and microarray and qRT/PCR, gave correlation coefficients (r) of 0.72, 0.39, and 0.63, respectively. In each instance, one to two outlier genes were apparent. Their exclusion from analysis gave r values of 0.79, 0.72, and 0.83, respectively. These findings demonstrate that the assessment of differential gene expression is dependent upon the methodology used in each situation where outcome between different methodologies was compared, the presence of a relatively limited number of outlier genes precludes high overall correlation between the methods. Validation of gene expression by different methods should be performed whenever possible.     

应用GeneSifter软件分析范可尼贫血基因表达谱的报告

目的:探讨范可尼贫血(Fanconi anemia,FA)发病的分子机制。方法:用GeneSifter软件对FA转录子协会公布的FA基因芯片表达数据进行统计学分析,结合Gene Ontologe和KEGG通路分析。结果:从FA细胞中筛选出690个差异表达基因,涉及DNA损伤与修复等多种生物过程及多条通路,发现了TOP2A、MCM2、PCNA等多个与FA发病相关基因。结论:FA发病的分子机制主要与DNA损伤和修复过程中的解螺旋相关,RAD-6通路可能是其损伤后的重要修复通路,其次亦与钙离子信号通路等密切联系。     

热休克后表达受抑基因的分子克隆及其表达特性

以人成骨肉瘤细胞株ＨＯＳ－８６０３为热休克模型,在利用ＤＤｍＲＮＡ方法筛选和克隆了一个热休克后表达受抑基因的ｃＤＮＡ片段的基础上,以该片段为探针,筛选ＨＯＳ－８６０３细胞的ｃＤＮＡ文库,获得该基因的全长ｃＤＮＡ克隆（ＨＳＳＧ－１）;ＤＮＡ序列测定表明该ｃＤＮＡ全长１４５６ｂｐ,编码２７６个氨基酸,经计算机辅助分析,该ｃＤＮＡ序列尚未被报道。经ＲＮＡ斑点杂交证实,该基因的表达于多种组织细胞之中,并且     

Preservation of Gene Expression Ratios Among Multiple Complex cDNAs After PCR Amplification: Application to Differential Gene Expression Studies

Comparative gene expression studies are often limited by low availability of tissue and poor quality of extractable mRNA. Collective PCR amplification of minute quantities of mRNA has great potential for overcoming these limitations. However, there remains significant concern about the effects of amplification on the absolute and relative abundance of individual mRNAs that could complicate subsequent gene expression studies. To address this problem, we systematically compared the relative abundance of many specific mRNAs from complex cDNA preparations (from tissue and cultured cells) both before and after amplification by PCR. Our results demonstrated that, as expected, the absolute abundance of different mRNAs in a cDNA library is altered in an unpredictable manner by PCR amplification. However, we found that the concentration ratios of specific mRNAs among different cDNA preparations were routinely well conserved after PCR amplification. Thus, for the purpose of comparative expression studies for specific mRNAs in two (or more) complex cDNAs, PCR-amplified cDNA is equally useful as unamplified cDNA. These results provide a rigorous experimental validation and offer a theoretical treatment to support the utility of PCR amplified cDNA for differential gene expression studies. We conclude that the inherent difficulties in performing differential screening studies such as gene chip and array analyses on limited amounts of biological materials can be overcome by a PCR amplification step without compromising data quality. This revised version was published online in July 2006 with corrections to the Cover Date.     

一种基于基因表达模型识别酵母细胞周期条件特异调控子网的方法

由高通量微阵列技术产生的数据集可以用于解释生物系统基因调控的未知机制.生物过程是动态的,所以很有必要关注某些条件下特异的基因调控子网络.细胞周期是一个基本的细胞过程,识别酵母的细胞周期特异调控子网是理解细胞周期过程的基础,并且有助于揭示其他细胞条件的基因调控机理.使用一个基因表达微分方程模型(GEDEM),从静态网络中识别了动态的细胞周期相关调控关系.与已经报道的细胞周期相关调控相互作用相比,该方法识别了更多的真实存在的条件特异调控关系,取得了比当前的方法更好的性能.在大数据集上,GEDEM 识别了具有高敏感性和特异性的调控子网.组合调控的深入分析显示,条件特异调控子网的转录因子之间的相关性呈现出比静态网络中转录因子相关性更强,这说明条件特异网络比静态网络更加接近真实情况.另外,GEDEM 方法还识别更多潜在的共调控转录因子.     

绝经对血液单核细胞基因表达谱的影响:基因芯片初步研究

绝经是女性一生中很重要的生理现象之一,它能增加一系列复杂免疫、神经退化、新陈代谢和心血管方面的疾病。血液单核细胞能分化成各种各样的细胞,这些细胞在组织形态发生和免疫应答方面起着很重要的作用。本研究中采用了包含大约14,500个基因探针的Affymetrix Human U133A基因芯片来研究健康的绝经前和绝经后女性外周血液单核细胞中的基因表达谱。样本之间的对比分析表明有20个基因上调,20个基因下调。其中的28个基因根据它们的生物过程如细胞繁殖、免疫应答、细胞代谢等等被分成了6个主要的GO类别;剩下的12个基因其生物学功能还没有被鉴定。研究结果支持了我们的假设:血液单核细胞的功能状态确实受到绝经的影响,而且由此带来的改变可能是由全基因组范围的基因表达谱而决定的。本研究中鉴定的一些差异表达基因有可能作为以后研究与绝经相关的系统免疫、神经退化和心血管疾病的候选基因研究。此工作是这个研究方向的第一次尝试,为将来的进一步研究奠定了基础。     

光和底物对乙醇酸氧化酶的基因表达的诱导

从菠菜中提纯了乙醇酸氧化酶并制备其抗体,经免疫双扩散、Ｗｅｓｔｅｒｎｂｌｏｔ和Ｎｏｒｔｈｅｒｎｂｌｏｔ证实水稻和豌豆黄化苗中不存在乙醇酸氧化酶。在黑暗中,底物可促进该酶基因的表达,而在黄化苗光照初期,推测光可能是不经过底物促进该酶基因的表达。     

利用表达谱基因芯片筛选溃疡性结肠炎差异表达基因

目的:利用人类全基因组表达谱芯片技术,分析溃疡性结肠炎患者和健康者基因表达谱差异,筛选出溃疡性结肠炎相关基因。方法:采用Trizol法提取8例溃疡性结肠炎患者和8例健康对照者结肠粘膜组织总RNA并纯化,逆转录合成c DNA,利用荧光染料Cy3标记aa UTP,转录合成标记的c RNA,并与Agilent人类全基因组表达谱芯片杂交,扫描荧光信号图像,对芯片原始数据进行归一化处理,利用倍数差异和t检验计算筛选出相关差异表达基因,采用DAVID在线分析系统进行基因的功能注释和关联分析,明确差异基因的生物学功能,并对部分差异表达基因进行实时荧光定量PCR验证。结果:筛查出溃疡性结肠炎结肠粘膜组织差异表达基因4132个,其中上调基因2004个,下调基因2128个。选取6条差异表达基因进行PCR验证,结果有3条基因表达上调,3条基因表达下调,表达趋势与芯片结果一致。结论:溃疡性结肠炎患者与健康对照者基因表达存在明显差异,分析这些差异表达基因有助于我们探索溃疡性结肠炎的发病机制,为疾病的治疗提供理论依据。