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.     

hepaCAM和VEGF基因表达与肾透明细胞癌侵袭转移关系的探讨

研究肾癌细胞株786-0,RC-2及肾透明细胞癌组织中肝细胞黏附分子(hepatocyte cell adhesion molecule,hepaC-AM)和血管内皮生长因子(VEGF)mRNA表达及其与肾透明细胞癌侵袭转移的关系。应用逆转录聚合酶链反应(RT-PCR)检测786-0、RC-2、正常肾组织hepaCAM和VEGFmRNA表达,73例肾透明细胞癌组织及相应癌旁组织中hepaCAMmRNA表达,43例肾透明细胞癌组织及相应癌旁组织VEGFmRNA表达,并比较它们之间的差异性和相关性。与正常肾组织比较786-0,RC-2的hepaCAMmRNA显著降低(P0.05);VEGFmRNA显著升高(P0.05)。肾透明细胞癌组织hepaCAMmRNA显著低于癌旁组织(P0.05);VEGFmRNA显著高于癌旁组织(P0.05)。在肾透明细胞癌组织中临床Ⅰ+Ⅱ期和Ⅲ+Ⅳ期两组VEGFmRNA表达差异具有统计学意义(P0.05),hepaCAM与VEGFmRNA呈负相关(r=-0.329,P0.05)。提示hepaC-AM基因缺失可能参与肾透明细胞癌侵袭转移,其机制可能与调节VFGF表达改变有关,hepaCAM有望成为一种新的肾癌基因治疗的靶分子。     

基因表达数据小波降噪与肿瘤识别

建立了基于小波降噪和支持向量机的结肠癌基因表达数据肿瘤识别模型.对试验数据进行小波分解,并利用交叉验证的方法计算试验样本的平均分类准确率,确定小波函数与小波分解层数;引入能量阈值方法对小波分解系数进行阈值处理,达到降噪的目的;提出了基因分类贡献率与主成分分析结合的方法,提取结肠癌样本数据特征;利用支持向量机强大的非线性映射能力,实现对结肠癌样本数据的非线性分类.为了减弱样本集的划分对分类准确率的影响,本文采取Jackknife检验方法对支持向量分类器的分类器检验,其分类准确率为96.77%.试验结果证明了该方法的有效性,该方法对结肠癌的识别具有一定的参考价值.     

Generation of new TRAIL mutants DR5-A and DR5-B with improved selectivity to death receptor 5

TRAIL (tumor necrosis factor (TNF) related apoptosis-inducing ligand) has been introduced as an extrinsic pathway inducer of apoptosis that does not have the toxicities of Fas and TNF. However, the therapeutic potential of TRAIL is limited because of many primary tumor cells are resistant to TRAIL. Despite intensive investigations, little is known in regards to the mechanisms underlying TRAIL selectivity and efficiency. A major reason likely lies in the complexity of the interaction of TRAIL with its five receptors, of which only two DR4 and DR5 are death receptors. Binding of TRAIL with decoy receptors DcR1 and DcR2 or soluble receptor osteoprotegerin (OPG) fail to induce apoptosis. Here we describe design and expression in Escherichia coli of DR5-selective TRAIL variants DR5-A and DR5-B. The measurements of dissociation constants of these mutants with all five receptors show that they practically do not interact with DR4 and DcR1 and have highly reduced affinity to DcR2 and OPG receptors. These mutants are more effective than wild type TRAIL in induction of apoptosis in different cancer cell lines. In combination with the drugs targeted to cytoskeleton (taxol, cytochalasin D) the mutants of TRAIL induced apoptosis in resistant Hela cells overexpressing Bcl-2. The novel highly selective and effective DR5-A and DR5-B TRAIL variants will be useful in studies on the role of different receptors in TRAIL-induced apoptosis in sensitive and resistant cell lines. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

RU5区对BFV3026基因表达的调控

以牛泡沫病毒(Bovine foamy virus,BFV)中国株BFV3026原病毒DNA为材料,构建R区系列缺失质粒,通过对其转染细胞中RT水平及对缺失质粒与luc报告质粒共转染细胞中萤火虫荧光素酶活性的测定,确立U5区对于BFV3026两类启动子LTR和IP均具有负调控作用;同时将带有不同R区的BFV3026结构基因片段克隆于异源启动子CMV之下,通过对其转染细胞293T中RT酶活性的测定,确立R区对于病毒结构基因pol的表达具有一定的调节作用,并将其功能区域初步界定在R区5′端100bp内。     

RU5区对BFV3026基因表达的调控

以牛泡沫病毒(Bovine foamy virus, BFV)中国株BFV3026原病毒DNA为材料,构建R区系列缺失质粒, 通过对其转染细胞中RT水平及对缺失质粒与luc报告质粒共转染细胞中萤火虫荧光素酶活性的测定,确立U5区对于BFV3026两类启动子LTR和IP均具有负调控作用;同时将带有不同R区的BFV3026结构基因片段克隆于异源启动子CMV之下,通过对其转染细胞293T中RT酶活性的测定,确立R区对于病毒结构基因pol的表达具有一定的调节作用,并将其功能区域初步界定在R区5′端100bp内.     

葡萄F-box基因VvF-box5基因结构与表达分析

F-box蛋白广泛存在于真核生物中,主要参与细胞周期调控、凋亡及多种激素信号转导等过程;近几年发现,F-box蛋白还介导了植物对逆境胁迫的应答响应,对维持植物正常生长发育至关重要。干旱等非生物逆境胁迫严重影响了葡萄正常生长发育和果实品质,克隆并分析干旱响应基因对改良葡萄的抗性有重要意义。本研究根据葡萄干旱转录组分析结果,发现11个F-box基因在干旱胁迫下表达量明显上调;其中,VvF-box5基因位于葡萄第19条染色体上,对干旱胁迫的响应明显高于其他F-box成员;VvF-box5基因含有5个外显子和4个内含子,内含子均含有保守的GT…AG序列;VvF-box5基因包含1824 bp的开放阅读框,编码607个氨基酸,氨基酸序列的N端含有1个保守的F-box结构域,C端包含1个FBD和2个LRR结构域。启动子元件分析表明,VvF-box5基因含有多种逆境应答元件,包括GA响应元件GARE-motif、MeJA响应元件CGTCA-motif、干旱胁迫相关元件ERE、HSE和LTR、光应答顺式作用元件ACE、Box4和Sp1以及与细胞周期调节和发育相关的原件等。实时荧光定量PCR结果显示,在干旱、高盐、ABA和MeJA处理下,VvF-box5基因的表达量明显升高;亚细胞定位结果显示,VvF-box5蛋白主要定位于圆葱表皮细胞的细胞核中;VvF-box5的过表达明显提高了转基因拟南芥在干旱处理下的成活率。另外,本研究利用原核表达系统诱导6×His-VvF-box5融合蛋白的表达,并使用蛋白标记亲和层析柱纯化获得了6×His-VvF-box5融合蛋白,为下一步深入研究VvF-box5的功能鉴定基础。     

Expression of Multiple Virus-derived Resistance Determinants in Transgenic Plants Does Not Lead to Additive Resistance Properties

Plants can be protected against infection by potyviruses by expressing different portions of potyviral genomes as transgenes. This strategy has proven effective with several potyvirus genes, including the Nla, Nlb, and coat protein coding regions. Given the effectiveness of separate potyvirus coding regions as determinants of resistance, we tested the hypothesis that combinations of potyvirus coding regions would provide additively greater protection of plants against potyviruses. For this, we compared transgenic plant lines that expressed either the coat protein (CP) or the Nla+Nlb+coat protein (NNC) coding regions from tobacco vein mottling virus (TVMV). We found that plants that carry the NNC gene combination were invariably less resistant to TVMV than were lines that contain a CP gene alone. Additionally, we found that NNC lines displayed virtually no resistance to tobacco etch virus (TEV), in contrast to the CP lines. We conclude that combining more than one virus-derived resistance determinant in a single construct is detrimental to the production of virus-resistant plants.     

人色素域解旋酶DNA结合蛋白5的基因克隆及其真核表达载体的构建

目的:克隆人色素域解旋酶DNA结合蛋白5(chromodomain helicase DNA-binding protein 5,CHD5)基因并构建真核表达载体.方法:应用PCR扩增人CHD5基因的编码区,使用基因重组方法构建真核细胞表达载体peGFPc1-CHD5,实时定量PCR技术检测重组质粒peGFPc1-CHD5转染293T工具细胞后的过表达能力.结果:经过PCR方法,有效扩增了CHD5基因编码区,构建了peGFPc1-CHD5真核细胞表达质粒,测序分析表明所克隆的CHD5基因编码区序列无误.实时定量PCR检测结果表明重组质粒peGFPc1-CHD5能有效地过表达CHD5基因.结论:成功地构建了人CHD5的真核细胞表达载体peGFPc1-CHD5.并在293T工具细胞中实现过表达,为进一步研究奠定了实验基础.     

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate

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Sequence of a Complete Chicken BG Haplotype Shows Dynamic Expansion and Contraction of Two Gene Lineages with Particular Expression Patterns

Many genes important in immunity are found as multigene families. The butyrophilin genes are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen presentation. In humans, a fixed number of butyrophilin genes are found in and around the major histocompatibility complex (MHC), and show striking association with particular autoimmune diseases. In chickens, BG genes encode homologues with somewhat different domain organisation. Only a few BG genes have been characterised, one involved in actin-myosin interaction in the intestinal brush border, and another implicated in resistance to viral diseases. We characterise all BG genes in B12 chickens, finding a multigene family organised as tandem repeats in the BG region outside the MHC, a single gene in the MHC (the BF-BL region), and another single gene on a different chromosome. There is a precise cell and tissue expression for each gene, but overall there are two kinds, those expressed by haemopoietic cells and those expressed in tissues (presumably non-haemopoietic cells), correlating with two different kinds of promoters and 5′ untranslated regions (5′UTR). However, the multigene family in the BG region contains many hybrid genes, suggesting recombination and/or deletion as major evolutionary forces. We identify BG genes in the chicken whole genome shotgun sequence, as well as by comparison to other haplotypes by fibre fluorescence in situ hybridisation, confirming dynamic expansion and contraction within the BG region. Thus, the BG genes in chickens are undergoing much more rapid evolution compared to their homologues in mammals, for reasons yet to be understood.     

叶酸白蛋白靶向纳米粒的肿瘤细胞吸收及叶酸受体相关基因表达研究

实验选用叶酸受体表达阳性FR(+)卵巢癌细胞株SKOV3与表达阴性的FR(-)肺癌细胞株A549,通过肿瘤细胞对叶酸白蛋白靶向纳米粒的吸收及叶酸受体相关基因的表达,研究分析叶酸白蛋白靶向纳米粒叶酸受体吸收特征及叶酸受体胞吞途径的参与机制。结果表明:随着叶酸白蛋白靶向纳米粒给药时间的增加,SKOV3细胞FR1基因的表达显著增强,而A549细胞未见FR1基因表达。同时SKOV3细胞FR1基因的表达程度与细胞摄取叶酸白蛋白靶向纳米粒的量成正相关。叶酸代谢通路相关的基因(RFC、FPGS、GGH)表达,研究显示叶酸白蛋白靶向纳米粒能够启动细胞膜叶酸通道相关蛋白的表达。