Retroposons of Alu family from <Emphasis Type="Italic">cis</Emphasis>-regulatory modules of <Emphasis Type="Italic">DNAse II</Emphasis> and <Emphasis Type="Italic">CAML</Emphasis> genes affect gene expression in A549 and HEK 293 cells

Promoter fragments of deoxyribonuclease II (DNAse II) and calcium-modulating cyclophilin ligand (CAML) associated with Alu family repeats have been inserted into luciferase reporter vectors. The constructs were introduced into A549 and HEK293 cell lines by transient transfection. Transfected cells were lysed to analyze luciferase activities. It has been shown that Alu repeats inserted into constructs influence the luciferase expression. Therefore, Alu copies associated with cis-regulatory modules in protein-coding genes have biological activity.     

DNase I hypersensitivity and expression of the Shrunken-1 gene of maize

The local chromatin structure of the Shrunken-1 (Sh) gene of maize was probed by analyzing DNase I hypersensitivity. Sh encodes the gene for sucrose synthetase, a major starch biosynthetic enzyme, which is maximally expressed in the endosperm during seed maturation. In addition to general DNase I sensitivity, specific DNase I hypersensitive sites were identified in endosperm chromatin that mapped near the 5 end of the Sh gene. The pattern of hypersensitive sites and their relative sensitivity were altered in other non-dormant tissues that produce little or no enzyme. However, some changes in chromatin structure appear to be independent of Sh gene expression and may reflect general alterations associated with plant development. The chromatin structure of several sh mutations, induced by Ds controlling element insertions, was also analyzed. Although the insertions perturbed expression of the gene, there were no notable effects on local chromatin structure.     

Large-scale analysis of gene expression profiles

The accumulation of DNA microarray data has now made it possible to use gene expression profiles to analyse expression data. A gene expression profile contains the expression data for a given gene over various samples, and can be contrasted with an expression signature, which contains the expression data for a single sample. Gene expression profiles are most revealing when samples are grouped appropriately, either by standard clinical or pathological categories or by categories discovered through cluster analysis techniques. Expression profiles can exist at various levels of abstraction, yielding information across various tissues or across diseases within a particular tissue. Hypothesis tests may be applied to expression profiles on a large scale to identify candidate genes of interest.     

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.     

基因表达系列分析技术在动物科学中的研究进展

基因表达系列分析（serialanalysisofgeneexpression,SAGE）是一种快速分析特定组织或细胞内基因表达信息的技术,不但可以比较不同组织细胞在不同时间、空间条件下基因表达的差异,还能发现新基因。近几年来,SAGE技术在动物基因表达研究中的应用取得了飞速发展。就SAGE技术的原理、实验路线、优缺点和改进以及SAGE在动物科学研究中的研究现状及应用前景作一简要介绍。     

Mass mortality in Pacific oysters is associated with a specific gene expression signature

Mass mortality events occur in natural and cultured communities of bivalve molluscs. The Pacific oyster, Crassostrea gigas, is a dominant species in many intertidal locations as well as an important aquacultured bivalve species, and for the last 50 years, adult oysters have suffered frequent and extreme mass mortality events during summer months. To investigate the molecular changes that precede these mortality events, we employed a novel nonlethal sampling approach to collect haemolymph samples from individual oysters during the period that preceded a mortality event. Microarray-based gene expression screening of the collected haemolymph was used to identify a mortality gene expression signature that distinguished oysters that survived the mortality event from those individuals that died during the event. The signature was cross-validated by comparing two separate episodes of mortality. Here, we report that near-mortality oysters can be distinguished from longer-lived oysters by the elevated expression of genes associated with cell death, lysosomal proteolysis, and cellular assembly and organization. These results show the potential utility of nonlethal sampling approaches for investigating the environmental causes of mortality in natural populations in the field, and for predicting when such events could occur and which individuals will be affected.     

A note on joint versus gene-specific mixed model analysis of microarray gene expression data

Currently, linear mixed model analyses of expression microarray experiments are performed either in a gene-specific or global mode. The joint analysis provides more flexibility in terms of how parameters are fitted and estimated and tends to be more powerful than the gene-specific analysis. Here we show how to implement the gene-specific linear mixed model analysis as an exact algorithm for the joint linear mixed model analysis. The gene-specific algorithm is exact, when the mixed model equations can be partitioned into unrelated components: One for all global fixed and random effects and the others for the gene-specific fixed and random effects for each gene separately. This unrelatedness holds under three conditions: (1) any gene must have the same number of replicates or probes on all arrays, but these numbers can differ among genes; (2) the residual variance of the (transformed) expression data must be homogeneous or constant across genes (other variance components need not be homogeneous) and (3) the number of genes in the experiment is large. When these conditions are violated, the gene-specific algorithm is expected to be nearly exact.     

Normalization and quantification of differential expression in gene expression microarrays

Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a number of technical and statistical problems. Possible remedies on the level of computational analysis lie in appropriate preprocessing steps, proper normalization of the data and application of statistical testing procedures in the derivation of differentially expressed genes. This review summarizes methods that are available for these purposes and provides a brief overview of the available software tools.     

Changes in reproductive roles are associated with changes in gene expression in fire ant queens

In species with social hierarchies, the death of dominant individuals typically upheaves the social hierarchy and provides an opportunity for subordinate individuals to become reproductives. Such a phenomenon occurs in the monogyne form of the fire ant, Solenopsis invicta, where colonies typically contain a single wingless reproductive queen, thousands of workers and hundreds of winged nonreproductive virgin queens. Upon the death of the mother queen, many virgin queens shed their wings and initiate reproductive development instead of departing on a mating flight. Workers progressively execute almost all of them over the following weeks. To identify the molecular changes that occur in virgin queens as they perceive the loss of their mother queen and begin to compete for reproductive dominance, we collected virgin queens before the loss of their mother queen, 6 h after orphaning and 24 h after orphaning. Their RNA was extracted and hybridized against microarrays to examine the expression levels of approximately 10 000 genes. We identified 297 genes that were consistently differentially expressed after orphaning. These include genes that are putatively involved in the signalling and onset of reproductive development, as well as genes underlying major physiological changes in the young queens.     

An improved biclustering algorithm and its application to gene expression spectrum analysis

Cheng and Church algorithm is an important approach in biclustering algorithms. In this paper, the process of the extended space in the second stage of Cheng and Church algorithm is improved and the selections of two important parameters are discussed. The results of the improved algorithm used in the gene expression spectrum analysis show that, compared with Cheng and Church algorithm, the quality of clustering results is enhanced obviously, the mining expression models are better, and the data possess a strong consistency with fluctuation on the condition while the computational time does not increase significantly.     

来源嗜碱性芽孢杆菌N-227β-环糊精葡基转移酶基因分析及在大肠杆菌中的诱导表达

很多细菌可以产生环糊精葡基转移酶,对来源于嗜碱性芽孢杆菌N-227菌株染色体上一段编码β-环糊精葡基转移酶基因、包含有自己的启动子且能够直接在大肠杆菌中表达的DNA序列进行测序分析,该片断DNA包含有4114bp,从745位点到2883位点包含2139个碱基,为一个推定的编码713个氨基酸的蛋白质阅读框,和来源于Bacillus circulansA11的β-环糊精葡基转移酶氨基酸完全一致;具有环糊精葡基转移酶典型的五个结构域A-E,在A-B结构域中包含有七个属于α-淀粉酶家族的保守区域(I-VII)。对该酶基因进行PCR并克隆到表达载体pET28b上,利用乳糖进行诱导表达,获得了高效表达,环化活性为11.75mg/min/mL。这对于β-环糊精葡基转移酶的应用和降低成本具有重要的价值。     

基于信息论k—modes聚类法的基因表达数据分析

k-均值聚类算法是一种广泛应用于基因表达数据聚类分析中的迭代变换算法,它通常用距离法来表示基因间的关系,但不能有效的反应基因间的相互依赖的关系。为此,提出基于信息论的k-modes聚类算法,克服了以上缺点。另外,还引入了伪F统计量,一方面,可以对空间中有部分重叠的点进行有效的分类;另一方面,可以给出最佳聚类数目,从而弥补了k-modes聚类法的不足。使其成为一种非常有效的算法,从而达到较优的聚类效果。     

用表达性差异显示分析技术分离人胎肝组织选择性表达基因

目的：建立4月龄人胎肝组织选择性表达基因EST库,为研究胚胎肝组织特异表达基因提供有力的工具。方法：采用表达性差异显示分析（representational difference analysis,RDA) 技术建立4月龄人胎肝组织选择性表达基因EST库,并测定部分克隆核苷酸序列,以竞争PCR检测代表性基因的差异表达。结果与结论：以珠蛋白家族基因为标志,所建差减cDNA文库中α－珠蛋白家族基因的表达频率较未差减cDNA文库增高7倍,同时该文库也含有多种与肝生长密切相关的基因,表明RDA技术确是研究差异表达基因的有效手段,所建EST库富集胎肝特异表达基因。部分克隆序列分析获得2种未报道序列,其中一株含有丝／苏氨酸激酶结构域,表明可望从此库中分离具有重要未知功能的新基因。