中华大蟾蜍斯钙素基因的组织表达及其在肾脏中的细胞定位

斯钙素(Stanniocalcin, STC)是一类首先在鱼类特有的内分泌腺--斯坦尼氏小体(Corpuscles of Stannius, CS)、随后又在人和哺乳动物中发现的同型二聚体糖蛋白激素,具有广泛的组织表达模式和多种生物学效应.为阐明两栖类动物是否存在STC1基因的表达及其表达模式,本研究基于部分已知鱼类和哺乳动物的STC1基因序列,从中华大蟾蜍(Bufo bufo gargarizans)卵巢获得了STC1基因的部分序列(GenBank注册号为EF586886).同源性分析显示,所获得的中华大蟾蜍STC1基因部分序列与鱼类STC1基因相应序列的同源性在40%-48%,而与小鼠和人STC1基因相应序列的同源性分别为41.89%和37.95%.RT-PCR分析显示STC1基因可在肾脏、性腺等多种组织中表达;原位杂交(in situ hybridization, ISH)技术表明中华大蟾蜍肾脏的近端小管、远端小管和集合管细胞内表达STC1 mRNA.这些结果首次证实两栖类动物中华大蟾蜍组织中存在STC1基因的表达     

Evaluation and optimization of clustering in gene expression data analysis

MOTIVATION: A measurement of cluster quality is needed to choose potential clusters of genes that contain biologically relevant patterns of gene expression. This is strongly desirable when a large number of gene expression profiles have to be analyzed and proper clusters of genes need to be identified for further analysis, such as the search for meaningful patterns, identification of gene functions or gene response analysis. RESULTS: We propose a new cluster quality method, called stability, by which unsupervised learning of gene expression data can be performed efficiently. The method takes into account a cluster's stability on partition. We evaluate this method and demonstrate its performance using four independent, real gene expression and three simulated datasets. We demonstrate that our method outperforms other techniques listed in the literature. The method has applications in evaluating clustering validity as well as identifying stable clusters. AVAILABILITY: Please contact the first author.     

鸡akirin同源基因的克隆与组织表达分析

Akirin是最近被发现的,在果蝇和小鼠的免疫炎症反应和调控肌肉 发生再生中起着重要作用的新基因．本实验采用电子克隆技术成功克隆获 得了海兰褐鸡Akirin基因的全长编码序列.利用生物信息学方法对Akirin 基因进行序列分析和预测,并利用半定量RT-PCR技术对雏鸡和成鸡的 Akirin基因进行组织表达谱分析．结果表明,鸡Akirin同源基因可读框长 576 bp,进化保守高,编码蛋白的氨基酸序列存在PFAM、RGS、TOP1Bc、 UTG、HMG和low complexity sequence几种结构域,和蛋白激酶C磷酸化位 点、酪氨酸激酶磷酸化位点和 N端豆蔻酰化位点3个功能位点,同时在鸡 Akirin的3′ 非翻译区预测到1个microRNA靶位点．Akirin在鸡的心、脾、 脑等多种组织中广泛表达,推测鸡Akirin基因是一个可能具有多种功能作 用的新基因．本研究将为深入研究鸡Akirin基因功能作用奠定基础．     

Precise quantitation of 5alpha-reductase type 1 mRNA by RT-PCR in rat liver and its positive regulation by testosterone and dihydrotestosterone

The liver is a multifunctional organ responsible for steroid hormones catabolism. Thus, the enzymes responsible for steroid catabolism are located in the liver, including the steroid 5alpha-Reductase (5alpha-R) (EC 1.3.99.5) which catalyzes the conversion of compounds with Delta(4,5) double bonds such as testosterone (T) into their respective reduced derivatives such as dihydrotestosterone (DHT), which are more hydrosoluble, therefore facilitating their excretion. We present precise measurements of mRNA levels of steroid 5alpha-Reductase type 1 isozyme (5alpha-R1) in the liver of male rats with different androgen status, using a quantitative RT-PCR coupled to laser-induced fluorescence capillary electrophoresis (LIF-CE). By means of this technique, we demonstrate a high level of expression of the gene that encodes 5alpha-R1 isozyme in male rat liver, and both T and DHT exert a positive control on the genetic expression of liver 5alpha-R1 isozyme. Since DHT does not contain a Delta(4,5) double bond, our results raise the possibility that hepatic 5alpha-R type 1 not only participates in the catabolism of steroids with Delta(4,5) double bonds, but also in other physiological functions, perhaps in the masculinization of the external genitalia in males with 5alpha-R type 2 gene deficiency.     

可用于实时荧光定量PCR标准化的白桦内参基因

为了快速、准确的对白桦多个样品进行基因表达分析,本研究应用荧光定量PCR技术,对白桦持家基因微管蛋白基因（Tu）和泛素基因（UbQ）在不同处理的细胞及不同树龄或不同生长季节白桦植株各部位表达的稳定性进行检测。结果表明,对于茉莉酸甲酯（MeJA）、水杨酸（SA）处理的白桦细胞和不同生长季节白桦植株的基因定量表达分析,可同时使用Tu和UbQ平衡化qRT-PCR数据;而针对不同树龄白桦茎皮中基因表达研究时,单独使用UbQ基因作为内参对照即可获得精确的表达数据。     

甘薯谷胱甘肽-S-转移酶基因在胁迫条件下的表达分析

成功地构建了甘薯谷胱甘肽-S-转移酶基因IBGSTU1 的原核表达质粒pET-IbGST, 并在大肠杆菌 BL21(DE3)中进行IPTG 诱导表达。重组蛋白部分以包涵体形式存在, 部分以可溶性蛋白形式存在。酶活性测定表明可溶的重组蛋白具有GST的活性。纯化的重组蛋白质用于多克隆抗体的制备。半定量RT-PCR 和 Western blotting 分析结果显示, 在正常的生长条件下, 甘薯组织不启动IBGSTU1 基因的转录和翻译, 但是在冷胁迫或重金属离子等的作用下, 可以检测到该基因的mRNA和编码的蛋白质, 表明该基因在甘薯的胁迫耐受中行使重要功能, 并发现该基因的表达具有组织特异性。     

EARLY FLOWERING 4 functions in phytochrome B-regulated seedling de-etiolation

To define the functions of genes previously identified by expression profiling as being rapidly light induced under phytochrome (phy) control, we are investigating the seedling de-etiolation phenotypes of mutants carrying T-DNA insertional disruptions at these loci. Mutants at one such locus displayed reduced responsiveness to continuous red, but not continuous far-red light, suggesting a role in phyB signaling but not phyA signaling. Consistent with such a role, expression of this gene is induced by continuous red light in wild-type seedlings, but the level of induction is strongly reduced in phyB-null mutants. The locus encodes a novel protein that we show localizes to the nucleus, thus suggesting a function in light-regulated gene expression. Recently, this locus was identified as EARLY FLOWERING 4, a gene implicated in floral induction and regulating the expression of the gene CIRCADIAN CLOCK-ASSOCIATED 1. Together with these previous data, our findings suggest that EARLY FLOWERING 4 functions as a signaling intermediate in phy-regulated gene expression involved in promotion of seedling de-etiolation, circadian clock function, and photoperiod perception.     

Quantification of PCR products by phosphate measurement

Various techniques for quantification of PCR are available. Most frequently, the densitometric intensities of ethidium bromide-stained PCR products separated in gels are compared after normalizing to the levels of housekeeping gene products such as β-actin. More precise, but extremely time consuming, is the technique of competitive PCR. Newer methods, such as tracking amplification in real-time, have high start-up and maintenance costs (e.g., TaqMan, Applied Biosystems; LightCycler, Roche; I-Cycler, Bio-Rad). Here, I describe an alternative, simple technique to quantify PCR products by determining the entire phosphate released during PCR. The method can be performed using common laboratory equipment, and the reagents needed are extremely cheap. The method is validated by measuring the induction of inducible nitric oxide synthase gene expression in cell culture and comparing the results with data obtained by LightCycler experiments and RNase protection assays.     

急性粒细胞白血病珠蛋白基因表达失衡的研究

应用竞争性逆转录聚合酶链式反应（ＲＴ－ＰＣＲ）测定了１０例急性粒细胞白血病Ｍ＿２型（ＡＭＬ）患者外周血网织红细胞中α／β珠蛋白ｍＲＮＡ的相对含量,其中８例表现不同程度增高,２例正常,均值为１．５１３±０．１８２（±ｓ）,与正常对照组（１．２４±０．０８３）进行ｔ检验比较,有非常显著差异（Ｐ＜０．０１）．此外,ＰＣＲ－ＳＳＣＰ分析显示ＡＭＬ患者β珠蛋白基因启动子区序列（５＇端－１３５至＋１２２位核苷酸）无明显异常。说明ＡＭＬ患者珠蛋白基因表达失衡系由于转录异常,很可能系ＡＭＬ的发生对α／β珠蛋白基因的平衡表达产生了某种影响,从而表现为获得性β地中海贫血特征。实验结果为进一步探讨白血病的发病机理及其α／β珠蛋白基因表达失衡的机制奠定了基础。     

Expression profiling in knockout mice: lymphotoxin versus tumor necrosis factor in the maintenance of splenic microarchitecture

Expression profiling provides a powerful approach to define the underlying molecular mechanisms in disease. Several techniques referred collectively to as gene profiling may be also helpful in the analysis of the phenotype of mice with targeted mutations, especially if applied to distinct histological compartments, to specific cell types or to evaluate the effect of specific challenges, such as infection. Here we review several of the existing techniques applicable to genetic knockout studies, and share our experience from the study of mice with tumor necrosis factor (TNF) and lymphotoxin (LT) deficiencies, with specific emphasis on the distinction between TNF- and LT-mediated signalling pathways in vivo. Gene expression profiling analysis of TNF/LT-deficient mice supports the notion that TNF and LT, originally discovered as distinct biological activities, manifest both distinct and redundant functions in vivo.     

Inference of disease-related molecular logic from systems-based microarray analysis

Computational analysis of gene expression data from microarrays has been useful for medical diagnosis and prognosis. The ability to analyze such data at the level of biological modules, rather than individual genes, has been recognized as important for improving our understanding of disease-related pathways. It has proved difficult, however, to infer pathways from microarray data by deriving modules of multiple synergistically interrelated genes, rather than individual genes. Here we propose a systems-based approach called Entropy Minimization and Boolean Parsimony (EMBP) that identifies, directly from gene expression data, modules of genes that are jointly associated with disease. Furthermore, the technique provides insight into the underlying biomolecular logic by inferring a logic function connecting the joint expression levels in a gene module with the outcome of disease. Coupled with biological knowledge, this information can be useful for identifying disease-related pathways, suggesting potential therapeutic approaches for interfering with the functions of such pathways. We present an example providing such gene modules associated with prostate cancer from publicly available gene expression data, and we successfully validate the results on additional independently derived data. Our results indicate a link between prostate cancer and cellular damage from oxidative stress combined with inhibition of apoptotic mechanisms normally triggered by such damage.     

草莓钙依赖蛋白激酶基因的克隆与表达分析

以EST测序结合RACE技术,从久香草莓的茎尖中分离得到一个新基因,BLASTX分析显示这是一个钙依赖蛋白激酶编码基因,与GenBank中的FaCDPK1同源,命名为FaCDPK2,GenBank登录号为HQ829293.采用半定量RT-PCR对FaCDPK2基因在不同组织中的表达分析表明,FaCDPK2全长3 775 bp,读码框1 659bp,由12个外显子组成,编码552个氨基酸残基,在第89~349位是保守的蛋白激酶结构域,C端含4个EFhand钙结合域.该基因编码蛋白与拟南芥CPK28序列一致性为86.25%,与草莓FaCDPK1序列一致性为43.99%.表达分析显示该基因表达范围较广,在所分析的七种草莓组织材料中,以花中表达水平最高,在果实中的表达可能受成熟的诱导.     

Microarray,SAGE and their applications to cardiovascular diseases

The wealth of DNA data generated by the human genome project coupling with recently invented high-throughput gene expression profiling techniques has dramatically sped up the process for biomedical researchers on elucidating the role of genes in human diseases. One powerful method to reveal insight into gene functions is the systematic analysis of gene expression. Two popular high-throughput gene expression technologies, microarray and Serial Analysis of Gene Expression (SAGE) are capable of producing large amounts of gene expression data with the potential of providing novel insights into fundamental disease processes, especially complex syndromes such as cardiovascular disease, whose etiologies are due to multiple genetic factors and their interplay with the environment. Microarray and SAGE have already been used to examine gene expression patterns of cell-culture, animal and human tissues models of cardiovascular diseases. In this review, we will first give a brief introduction of microarray and SAGE     

Reconstructing the temporal ordering of biological samples using microarray data

MOTIVATION: Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. RESULTS: We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. AVAILABILITY: Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.