生物信息学在基因芯片中的应用

生物信息学和基因芯片是生命科学研究领域中的两种新方法和新技术,生物信息学与基因芯片密切相关,生物信息学促进了基因芯片的研究与应用,而基因芯片则丰富了生物信息学的研究内容。本论文探讨生物信息学在基因芯片中的应用,将生物信息学方法运用到高密度基因芯片设计和芯片实验数据管理及分析。从信息学的角度提出基因芯片设计准则,提出寡核苷酸探针的优化设计方法,将该方法运用于再测序型芯片和基因表达型芯片的设计,在此基础上研制出高密度基因芯片设计软件系统和实验结果分析系统。     

Evolutionary significance of gene expression divergence

Recent large-scale studies of evolutionary changes in gene expression among mammalian species have led to the proposal that gene expression divergence may be neutral with respect to organismic fitness. Here, we employ a comparative analysis of mammalian gene sequence divergence and gene expression divergence to test the hypothesis that the evolution of gene expression is predominantly neutral. Two models of neutral gene expression evolution are considered: 1-purely neutral evolution (i.e., no selective constraint) of gene expression levels and patterns and 2-neutral evolution accompanied by selective constraint. With respect to purely neutral evolution, levels of change in gene expression between human-mouse orthologs are correlated with levels of gene sequence divergence that are determined largely by purifying selection. In contrast, evolutionary changes of tissue-specific gene expression profiles do not show such a correlation with sequence divergence. However, divergence of both gene expression levels and profiles are significantly lower for orthologous human-mouse gene pairs than for pairs of randomly chosen human and mouse genes. These data clearly point to the action of selective constraint on gene expression divergence and are inconsistent with the purely neutral model; however, there is likely to be a neutral component in evolution of gene expression, particularly, in tissues where the expression of a given gene is low and functionally irrelevant. The model of neutral evolution with selective constraint predicts a regular, clock-like accumulation of gene expression divergence. However, relative rate tests of the divergence among human-mouse-rat orthologous gene sets reveal clock-like evolution for gene sequence divergence, and to a lesser extent for gene expression level divergence, but not for the divergence of tissue-specific gene expression profiles. Taken together, these results indicate that gene expression divergence is subject to the effects of purifying selective constraint and suggest that it might also be substantially influenced by positive Darwinian selection.     

Use of gene networks for identifying and validating drug targets

We propose a new method for identifying and validating drug targets by using gene networks, which are estimated from cDNA microarray gene expression profile data. We created novel gene disruption and drug response microarray gene expression profile data libraries for the purpose of drug target elucidation. We use two types of microarray gene expression profile data for estimating gene networks and then identifying drug targets. The estimated gene networks play an essential role in understanding drug response data and this information is unattainable from clustering methods, which are the standard for gene expression analysis. In the construction of gene networks, we use the Bayesian network model. We use an actual example from analysis of the Saccharomyces cerevisiae gene expression profile data to express a concrete strategy for the application of gene network information to drug discovery.     

Taking the good out of the bad: lentiviral-based gene therapy of the hemoglobinopathies

Sickle cell disease and beta-thalassemia are excellent candidates for gene therapy since transfer of a single gene into hematopoietic stem cells should theoretically elicit a therapeutic response. Initial attempts at gene therapy of these hemoglobinopathies have proved unsuccessful due to limitations of available gene transfer vectors. With the extensive research on human immunodeficiency virus-1 due to the acquired immune deficiency syndrome pandemic, researchers have realized that this lentivirus, engineered to be devoid of any pathogenic elements, can be an effective gene transfer vector. This review discusses the gene therapy strategy for the hemoglobinopathies and outlines why lentiviral-derived vectors are particularly suited for this type of application, keeping past failures at gene therapy of these hemoglobinopathies in mind. Development, improvement, and methods for preparation of lentiviral-derived vectors are examined. Recently published results of successful gene therapy treatment of beta-thalassemic and sickle cell diseased mice using lentiviral-derived vectors are described. Finally, criticisms and future directions of lentiviral-based biotechnology are considered.     

基因相关研究与诺贝尔奖

基因是能够表达和产生基因产物（蛋白质或RNA）的DNA序列。到2003年为止,因为研究基因而获得诺贝尔奖的共有51人,其中获生理学或医学奖44人（占生理学或医学总获奖人数178的24.72%）、化学奖7人（占化学总获奖人数123的5.69 %）。文章从6个方面对此作了评述：果蝇是基因研究的良好材料;DNA双螺旋模型的提出为基因研究提供了坚实基础;基因调控研究阐明了基因的许多功能;遗传学中心法则造就了11位获奖者;基因工程技术使人们有可能改造和利用基因;基因特性的深入研究使人们更加容易理解许多生命现象。Abstract: Gene is a DNA sequence which can be expressed and produces gene products (protein or RNA). By 2003, there are 51 Nobel Prize owners related to gene studies. Among them, 44 persons are in physiology or medicine (account for 24.72% of total 178), 7 persons are in chemistry (account for 5.69% of total 123). The paper reviews them in following 6 aspects: Drosophlie melanogaster is a good material for gene study; the double helix model of DNA structure provides a hard foundation in gene study; the studies on gene regulation illuminate many functions of gene; genetic central dogma researches created 11 Noble Prize laureates; gene engineering technologies make possible to modify and use genes; and the thorough studies of gene characteristic made us easier to understand many life phenomena.     

植物——病原互作系统中基因对基因识别研究

从自然植物种群对Ｒ基因的选择和淘汰、对属和种的专化性、抗病基因的复杂性、抗病基因的分子专化性、信号传导中基因的相互作用,以及Ｒ基因的开发利用与持久抗性战略等方面总结评述了当前在植物－病原互作系统中基因对基因识别研究领域的新进展,并且提出了需进一步研究的问题。     

Coliphage P1 morphogenesis: analysis of mutants by electron microscopy.

We used electron microscopy and serum blocking power tests to determine the phenotypes of 47 phage P1 amber mutants that have defects in particle morphogenesis. Eleven mutants showed head defects, 30 showed tail defects, and 6 had a defect in particle maturation (which could be either in the head or in the tail). Consideration of previous complementation test results, genetic and physical positions of the mutations, and phenotypes of the mutants allowed assignment of most of the 47 mutations to genes. Thus, a minimum of 12 tail genes, 4 head genes, and 1 particle maturation gene are now known for P1. Of the 12 tail genes, 1 (gene 19, located within the invertible C loop) codes for tail fibers, 6 (genes 3, 5, 16, 20, 21, and 26) code for baseplate components (although one of these genes could code for the tail tube), 1 (gene 22) codes for the sheath, 1 (gene 6) affects tail length, 2 (genes 7 and 25) are involved in tail stability, and 1 (gene 24) either codes for a baseplate component or is involved in tail stability. Of the four head genes, gene 9 codes for a protein required for DNA packaging. The function of head gene 4 is unclear. Head gene 8 probably codes for a minor head protein, whereas head gene 23 could code for either a minor head protein or the major head protein. Excluding the particle maturation gene (gene 1), the 12 tail genes are clustered in three regions of the P1 physical genome. The four head genes are at four separate locations. However, some P1 head genes have not yet been detected and could be located in two regions (for which there are no known genes) adjacent to genes 4 and 8. The P1 morphogenetic gene clusters are interrupted by many genes that are expressed in the prophage.     

基因强化在难降解污染物生物处理和修复中的应用

基因强化通过强化降解基因在土著菌群中的水平迁移和传播, 促进土著降解菌群的进化, 改善基因工程菌生物强化作用的稳定性, 提高难降解污染物的生物去除效果。介绍了基因强化的原理-微生物群落内水平基因迁移, 讨论了基因载体、细胞接触条件和环境条件等影响基因强化的因素, 综述了目前基因强化在土壤生物修复和废水生物处理中的应用现状, 并提出了基因强化中存在的问题。     

Polymer based cardiovascular gene therapy

Therapeutic angiogenesis is a new potential treatment in cardiovascular disease. It is performed by the delivery of the angiogenic agents (protein, gene). Most important consideration for gene therapy is the construction of an effective therapeutic gene. Currently, VEGF is the most effective therapeutic gene for the neovascularization. We constructed the hypoxia-regulated VEGF plasmid using the Epo enhancer and RTP801 promoter. The efficiency of the pEpo-SV-VEGF and pRTP801-VEGF were evaluated by various methodsin vitro andin vivo. The results suggested that the hypoxia-inducible VEGF gene therapy system is effective and safe, which may be useful for the gene therapy of ischemic heart disease. Development of a safe and efficient gene carrier is another main requirement for successful gene therapy. Although viralbased gene delivery is currently the most effective way to transfer genes to cells, nonviral vectors are increasingly being considered forin vivo gene delivery. The advantages of nonviral gene therapy are lack of specific immunogenecity, simplicity of use, and ease of large-scale production. In addition, the simple conjugation of a targeting moiety to nonviral gene carrier can facilitate tissue-targeting gene delivery. We have developed two new gene carrier systems, TerplexDNA and WSLP (water soluble lipopolymer). These two are efficient carrier to ischemic myocardium and has low toxicity and high transfection efficiency. So it may allow for application ofin vivo gene therapy in the treatment of heart disease.     

Gene therapy: a battle against biological barriers

One factor critical to successful human gene therapy is development of efficient gene delivery systems. Although numerous vector systems for gene transfer have been developed, a perfect vector system has not yet been constructed. Difficulties of in vivo gene transfer appear to result from resistance of living cells to invasion by foreign materials and from interference of cellular functions. We should analyze what barriers in tissues affect in vivo gene transfection and how to solve these problems for gene therapy. In this review article, the biological barriers to in vivo gene transfection are discussed and possible solutions to each barrier are discussed with respect to construction of a perfect gene therapy vector system.     

蓝藻基因转移系统的选择与建立

蓝藻是一类进行光合放氧的原核生物 ,因其结构的特殊性 ,已成为表达外源基因的理想宿主之一。然而外源基因转化系统的选择与建立一直影响着蓝藻基因工程的快速发展。总结了各类蓝藻基因转移系统的特点、影响因素、各系统间的优缺点、以及不同蓝藻株系最适基因转移系统的选择等 ,为利用蓝藻进行遗传操作提供可能 ,为蓝藻基因工程发展提供信息。     

Rdh54, a Rad54 Homologue in Saccharomyces Cerevisiae, Is Required for Mitotic Diploid-Specific Recombination and Repair and for Meiosis

Most mitotic recombination and repair genes of Saccharomyces cerevisiae show no specificity of action for the genome ploidy. We describe here a novel repair and recombination gene that is specific for recombination and repair between homologous chromosomes. The RDH54 gene is homologous to the RAD54 gene, but rdh54 mutants do not show sensitivity to methyl methanesulfonate at concentrations that sensitize a rad54 mutant. However, the rdh54 null mutation enhances the methyl methanesulfonate sensitivity of a rad54 mutant and single rdh54 mutants are sensitive to prolonged exposure at high concentrations of methyl methanesulfonate. The RDH54 gene is required for recombination, but only in a diploid. We present evidence showing that the RDH54 gene is required for interhomologue gene conversion but not intrachromosomal gene conversion. The rdh54 mutation confers diploid-specific lethalities and reduced growth in various mutant backgrounds. These phenotypes are due to attempted recombination. The RDH54 gene is also required for meiosis as homozygous mutant diploids show very poor sporulation and reduced spore viability. The role of the RDH54 gene in mitotic repair and in meiosis and the pathway in which it acts are discussed.     

Role of ribosome recycling factor (RRF) in translational coupling

RNA phage GA coat and lysis protein expression are translationally coupled through an overlapping termination and initiation codon UAAUG. Essential for this coupling are the proximity of the termination codon of the upstream coat gene to the initiation codon of the lysis gene (either a <3 nucleotide separation or physical closeness through a possible hairpin structure) but not the Shine-Dalgarno sequence. This suggests that the ribosomes completing the coat gene translation are exclusively responsible for translation of the lysis gene. Inactivation of ribosome recycling factor (RRF), which normally releases ribosomes at the termination codon, did not influence the expression of the reporter gene fused to the lysis gene. This suggests the possibility that RRF may not release ribosomes from the junction UAAUG. However, RRF is essential for correct ribosomal recognition of the AUG codon as the initiation site for the lysis gene.     

Comparing relative rates of pollen and seed gene flow in the island model using nuclear and organelle measures of population structure

We describe a method for comparing nuclear and organelle population differentiation (F(ST)) in seed plants to test the hypothesis that pollen and seed gene flow rates are equal. Wright's infinite island model is used, with arbitrary levels of self-fertilization and biparental organelle inheritance. The comparison can also be applied to gene flow in animals. Since effective population sizes are smaller for organelle genomes than for nuclear genomes and organelles are often uniparentally inherited, organelle F(ST) is expected to be higher at equilibrium than nuclear F(ST) even if pollen and seed gene flow rates are equal. To reject the null hypothesis of equal seed and pollen gene flow rates, nuclear and organelle F(ST)'s must differ significantly from their expected values under this hypothesis. Finite island model simulations indicate that infinite island model expectations are not greatly biased by finite numbers of populations (>/=100 subpopulations). The power to distinguish dissimilar rates of pollen and seed gene flow depends on confidence intervals for fixation index estimates, which shrink as more subpopulations and loci are sampled. Using data from the tropical tree Corythophora alta, we rejected the null hypothesis that seed and pollen gene flow rates are equal but cannot reject the alternative hypothesis that pollen gene flow is 200 times greater than seed gene flow.     

Regulation of specific genes during the cell cycle. Utilization of homologous cDNAs and cloned sequences for studying histone gene expression in human cells

Evidence for differential gene expression during the cell cycle and approaches for studying cell-cycle-stage specific gene expression are summarized. Attention is focused on regulation of histone gene expression during the cell cycle of continuously dividing cells and after stimulation of nondividing cells to proliferate. The level(s) at which control of histone gene expression occurs and the possible involvement of chromosomal proteins in the regulation of histone gene expression are discussed. The preparation of cloned human histone sequences and their use in studying the structural and functional properties of human histone genes are presented. Index Entries: Cell cycle, gene regulation during; gene regulation, during the cell cycle; regulation of specific genes, during the cell cycle; DNAs, homologous, and histone gene expression; cloned DNAs, and histone gene expression; histone gene expression; gene expression, histone; cloned human histone sequences.     

Tests for gene clustering.

Comparing chromosomal gene order in two or more related species is an important approach to studying the forces that guide genome organization and evolution. Linked clusters of similar genes found in related genomes are often used to support arguments of evolutionary relatedness or functional selection. However, as the gene order and the gene complement of sister genomes diverge progressively due to large scale rearrangements, horizontal gene transfer, gene duplication and gene loss, it becomes increasingly difficult to determine whether observed similarities in local genomic structure are indeed remnants of common ancestral gene order, or are merely coincidences. A rigorous comparative genomics requires principled methods for distinguishing chance commonalities, within or between genomes, from genuine historical or functional relationships. In this paper, we construct tests for significant groupings against null hypotheses of random gene order, taking incomplete clusters, multiple genomes, and gene families into account. We consider both the significance of individual clusters of prespecified genes and the overall degree of clustering in whole genomes.     

Non-viral gene therapy

Non-viral gene therapies are currently under development that employ drug-delivery methods for targeting genes to selected cells in the body, where they express therapeutic gene products. Various methods have been described for non-viral gene therapy, ranging from the direct intramuscular injection of purified DNA to the systemic administration of formulations comprising DNA and lipids, proteins, peptides, or polymers. Products for non-viral gene therapies are designed both for direct administration to patients by conventional routes and for expression of a therapeutic product over a finite period of time in a manner similar to conventional medicines. Initial preclinical and clinical studies indicate that non-viral gene delivery methods exhibit safety profiles similar to conventional pharmaceutical or biological products. Clinical trials have been proposed, or are currently under way, to assess the applicability of non-viral gene therapy for a variety of disorders, including cystic fibrosis, cancer, and peripheral vascular disease. Non-viral techniques may soon allow gene therapy to be applied in clinical practice alongside conventional medicines for the treatment of common diseases.     

基因强化在难降解污染物生物处理和修复中的应用

基因强化通过强化降解基因在土著菌群中的水平迁移和传播,促进土著降解菌群的进化,改善基因工程菌生物强化作用的稳定性,提高难降解污染物的生物去除效果.介绍了基因强化的原理-微生物群落内水平基因迁移,讨论了基因载体、细胞接触条件和环境条件等影响基因强化的因素,综述了目前基因强化在土壤生物修复和废水生物处理中的应用现状,并提出了基因强化中存在的问题.     

Consistency of sequence-based gene clusters

In comparative genomics, differences or similarities of gene orders are determined to predict functional relations of genes or phylogenetic relations of genomes. For this purpose, various combinatorial models can be used to specify gene clusters--groups of genes that are co-located in a set of genomes. Several approaches have been proposed to reconstruct putative ancestral gene clusters based on the gene order of contemporary species. One prevalent and natural reconstruction criterion is consistency: For a set of reconstructed gene clusters, there should exist a gene order that comprises all given clusters. For permutation-based gene cluster models, efficient methods exist to verify this condition. In this article, we discuss the consistency problem for different gene cluster models on sequences with restricted gene multiplicities. Our results range from linear-time algorithms for the simple model of adjacencies to NP-completeness proofs for more complex models like common intervals.     

植物转基因沉默与消除

植物基因工程研究是希望获得高稳定表达的转基因植株,而转基因沉默现象却限制了转基因植物的应用前景。基因沉默的机制是多方面的,包括转基因多拷贝之间的异位配对,转基因序列的甲基化,插入位点在染色体结构上的改变及转录后的衰退调控等。研究外源基因的失活原因及寻找相应的策略控制失活,对于植物基因工程的发展有着重要的意义。