基因沉默：获得性免疫的新途径

基因沉默 (ｇｅｎｅｓｉｌｅｎｃｉｎｇ)首先发现于转基因植物。发生沉默的基因可以是外源性转移基因 ,也可以是入侵的病毒或宿主内源性基因。双链ＲＮＡ(ｄｓＲＮＡ)作为启动因素或中间体为不同生物基因沉默所共有。通常 ,基因沉默发生在两种水平上 ,一是由于ＤＮＡ甲基化、异染色质化及位置效应等引起的转录水平上的基因沉默 (ｔｒａｎｓｃｒｉｐｔｉｏｎａｌｇｅｎｅｓｉ ｌｅｎｃｉｎｇ ,ＴＧＳ) ,另一种是在基因转录后水平上通过对目标ＲＮＡ特异性降解而使基因失活的转录后基因沉默 (ｐｏｓｔ ｔｒａｎｓｃｒｉｐｔｉｏｎａｌｇｅｎｅ…     

amiRNAi-实现高效稳定的特异基因沉默新方法

RNA干扰技术(RNA interference,RNAi)是实现基因沉默的有效工具。近年来,随着分子生物学与生物技术的快速发展,在RNAi基础上又发展出另一种特异性更高的基因沉默技术—amiRNAi (artificial microRNA interference)。amiRNAs是一类由内源miRNA前体生成的长21个核苷酸的人工小RNA分子,它能在不影响其他基因表达的情况下特异地介导单个或多个靶基因高效稳定沉默。与普通的RNAi相比,amiRNAi具有特异性高、稳定性强和沉默效应可预见等优点。因而amiRNAi可能成为基因功能分析的最有效工具之一,同时amiRNAi对于基因负调控研究和应用而言前景广阔。着重介绍了amiRNAi技术的原理、优势及其潜在的应用价值。     

Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data

Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.     

Agrobacterium-Mediated Transient Gene Expression and Silencing: A Rapid Tool for Functional Gene Assay in Potato

Potato is the third most important food crop worldwide. However, genetic and genomic research of potato has lagged behind other major crops due to the autopolyploidy and highly heterozygous nature associated with the potato genome. Reliable and technically undemanding techniques are not available for functional gene assays in potato. Here we report the development of a transient gene expression and silencing system in potato. Gene expression or RNAi-based gene silencing constructs were delivered into potato leaf cells using Agrobacterium-mediated infiltration. Agroinfiltration of various gene constructs consistently resulted in potato cell transformation and spread of the transgenic cells around infiltration zones. The efficiency of agroinfiltration was affected by potato genotypes, concentration of Agrobacterium, and plant growth conditions. We demonstrated that the agroinfiltration-based transient gene expression can be used to detect potato proteins in sub-cellular compartments in living cells. We established a double agroinfiltration procedure that allows to test whether a specific gene is associated with potato late blight resistance pathway mediated by the resistance gene RB. This procedure provides a powerful approach for high throughput functional assay for a large number of candidate genes in potato late blight resistance.     

ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data

Comparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: 1) Analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and 2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole-genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.     

沉默Bmi-1基因表达稳定细胞株的建立及其生物学特性的研究

B细胞特异性莫洛尼鼠白血病病毒插入位点1(B-cell-specific moloney murine leukemia virus insertionsite 1,Bmi-1)基因是多梳基因家族成员,参与细胞增殖调控.研究发现Bmi-1基因可能参与肿瘤的形成,可能成为肿瘤潜在的治疗靶点.用RNA干扰(RNA interference,RNAi)沉默Bmi-1基因表达观察其对乳腺癌细胞株MCF-7侵袭和转移等生物学特性的影响,以探讨Bmi-1在乳腺癌发生发展中的作用.PT67细胞包装质粒后产生的逆转录病毒感染MCF-7细胞,嘌呤霉素筛选建立稳定细胞株,稳定抑制Bmi-1的细胞株命名为MCF-7/Bmi-1si.通过RT-PCR和Western blot分别从mRNA和蛋白水平检测Bmi-1的表达量;平板克隆形成实验检测细胞克隆形成能力;Transwell侵袭小室模型检测细胞体外侵袭和转移能力.MCF-7/Bmi-1si组与MCF-7和MCF-7/GFPsi组相比,Bmi-1 mRNA和蛋白表达量明显减少,克隆形成数及形成率也明显减少(P<0.05).侵袭和转移实验表明:与MCF-7和MCF-7/GFPsi组相比,MCF-7/Bmi-1si组细胞在Transwell侵袭小室中24 h穿膜细胞数明显减少(P<0.05).结果表明沉默Bmi-1基因表达稳定细胞株构建成功,Bmi-1基因表达的沉默能显著降低MCF-7细胞的体外增殖及侵袭转移能力.     

A Major Gene for Resting Metabolic Rate Unassociated with Body Composition: Results from the Québec Family Study

A major gene hypothesis for resting metabolic rate (RMR) was investigated using segregation analysis (POINTER) of data on families participating in Phase 2 of the Québec Family Study. Complete analyses were conducted on RMR adjusted for age, and also on RMR adjusted for age and other covariates, primarily fat mass (FM) and fat-free mass (FFM). Prior to adjustment for covariates, support for a major gene hypothesis was equivocal — i.e., there was evidence for either a major gene or a multifactorial component (i.e., polygenic and/or familial environment). The multifactorial model was preferred over the major gene model, although the latter did segregate according to Mendelian expectations. However, after the effects of FM and FFM were accounted for, a major gene effect was unambiguous and compelling. The putative locus accounted for 57% of the variance, affected 7% of the sample, and led to high values of RMR. The lack of a significant multifactorial effect suggested that the familial etiology of RMR adjusted for FM and FFM was likely to be entirely a function of the major locus. Comparing the RMR results from pre- and post-adjustment for FM and FFM suggests a plausible hypothesis. We know from earlier studies in this sample that there is a putative major gene for FM and a major non-Mendelian effect for FFM. The current study leads us to speculate that: (1) the gene(s) affecting body size and body composition also may have an effect on RMR, and further (2) removal of the effect of the major gene(s) for body size and composition allowed for detection of an additional major gene affecting only the RMR. Thus, RMR appears to be an oligogenic trait.     

RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding

RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.     

酿酒酵母中双链RNA介导基因沉默技术研究GRE3基因表达抑制

RNA沉默技术作为探索基因功能的实验手段应用于多种生物.以编码酿酒酵母NADPH依赖型醛糖还原酶的GRE3基因为对象,检测酿酒酵母双链RNA介导的基因沉默效应.以pESC-LEU为骨架,构建重组质粒psiLENT-GRE3并用于转化酿酒酵母YPH499.用RT-PCR检测到诱导1 kb RNA双螺旋和136 bp loop结构引起的GRE3基因表达下调.结果表明,双链RNA介导的基因沉默技术,能够用作降低酿酒酵母某一特定基因表达水平的工具.并有助于理解芽殖酵母的RNA干扰现象.     

Estimation of the Stationary Gene Migration Rate: A Cartographic Approach

A method of geographic mapping of the stationary (limiting) gene migration rate has been developed. The method is based on approximation of the empirical distribution of gene frequencies by a theoretical steady-state distribution. The maximum likelihood method and the ² minimization method are used to obtain consistent estimations of the gene migration rate as a parameter of the steady-state distribution. The new method makes it possible to determine the geographical distribution of the ratio between the properties of the population migration structure described by the stepping-stone and island models and to construct a geographical map of ² values. This map approximately reflects the distribution of natural selection pressure on the gene pool if genetic processes are quasisteady.     

在肝癌细胞SK-Hep1中沉默STAT3基因增强sorafenib疗效的初步研究

目的:研究STAT3在肝癌细胞SK-Hep1对sorafenib抗性中的作用,并探讨STAT3基因沉默在增强sorafenib肝癌疗效中的作用。方法:应用基于shRNA的基因沉默技术在肝癌细胞SKHep1中敲减STAT3;用CCK8法检测细胞的生长情况与对sorafenib的敏感性;蛋白印迹法(Western blot)检测STAT3、p-STAT3(Y705)、p-STAT3(S727)以及其下游蛋白的表达变化。结果:成功构建了STAT3敲减的细胞株SK-Hep1-sh STAT3。该细胞中STAT3蛋白表达降低,细胞增殖明显受到抑制。Sorafenib的处理下调了STAT3的磷酸化水平及其下游蛋白Mcl-1和Cyclin D1的表达。STAT3基因敲减的SK-Hep1细胞,对sorafenib的敏感性增强。结论:基于shRNA的STAT3基因沉默能明显抑制SK-Hep1细胞增殖,提高细胞对sorafenib的敏感性,有望成为提高sorafenib抗肝癌疗效的一种新手段。     

5'-Triphosphate-Short Interfering RNA: Potent Inhibition of Influenza A Virus Infection by Gene Silencing and RIG-I Activation

Limited protection of current vaccines and antiviral drugs against influenza A virus infection underscores the urgent need for development of novel anti-influenza virus interventions. While short interfering RNA (siRNA) has been shown to be able to inhibit influenza virus infection in a gene-specific manner, activation of the retinoic acid-inducible gene I protein (RIG-I) pathway has an antiviral effect in a non-gene-specific mode. In this study, we designed and tested the anti-influenza virus effect of a short double-stranded RNA, designated 3p-mNP1496-siRNA, that possesses dual functions: an siRNA-targeting influenza NP gene and an agonist for RIG-I activation. This double-stranded siRNA possesses a triphosphate group at the 5' end of the sense strand and is blunt ended. Our study showed that 3p-mNP1496-siRNA could potently inhibit influenza A virus infection both in cell culture and in mice. The strong inhibition effect was attributed to its siRNA function as well as its ability to activate the RIG-I pathway. To the best of our knowledge, this is the first report that the combination of siRNA and RIG-I pathway activation can synergistically inhibit influenza A virus infection. The development of such dual functional RNA molecules will greatly contribute to the arsenal of tools to combat not only influenza viruses but also other important viral pathogens.     

Quantitative Trait Loci Underlying Gene Product Variation: A Novel Perspective for Analyzing Regulation of Genome Expression

A methodology to dissect the genetic architecture of quantitative variation of numerous gene products simultaneously is proposed. For each individual of a segregating progeny, proteins extracted from a given organ are separated using two-dimensional electrophoresis, and their amounts are estimated with a computer-assisted system for spot quantification. Provided a complete genetic map is available, statistical procedures allow determination of the number, effects and chromosomal locations of factors controlling the amounts of individual proteins. This approach was applied to anonymous proteins of etiolated coleoptiles of maize, in an F(2) progeny between two distant lines. The genetic map included both restriction fragment length polymorphism and protein markers. Minimum estimates of one to five unlinked regulatory factors were found for 42 of the 72 proteins analyzed, with a large diversity of effects. Dominance and epistasis interactions were involved in the control of 38% and 14% of the 72 proteins, respectively. Such a methodology might help understanding the architecture of regulatory networks and the possible adaptive or phenotypic significance of the polymorphism of the genes involved.     

The Prognostic Value of Epigenetic Silencing of p16 Gene in NSCLC Patients: A Systematic Review and Meta-Analysis

Background

The prognostic significance of p16 promoter hypermethylation in patients with non-small cell lung cancer (NSCLC) is still controversial. This analysis presents pooled estimates of the association to better elucidate whether p16 methylation has a prognostic role in NSCLC.

Methods

Relevant studies were identified by searching PubMed, Embase and Web of Science databases until June 2012. The association of p16 methylation with both overall survival (OS) and disease-free survival (DFS) was preformed. Studies were pooled and summary hazard ratios (HR) were calculated. Subgroup analyses, sensitivity analysis and publication bias were also conducted.

Results

A total of 18 studies containing 2432 patients met the inclusion criteria and had sufficient survival data for quantitative aggregation. The results showed that p16 methylation was an indicator of poor prognosis in NSCLC. The HR was 1.36 (95% CI: 1.08–1.73, I² = 56.7%) and 1.68 (95% CI: 1.12–2.52, I² = 38.7%) for OS and DFS, respectively. Subgroup analyses were carried out. The HRs of fresh and paraffin tissue were 1.50 (95% CI: 1.11–2.01) and 1.10 (95% CI: 0.77–1.57). The pooled HR was 1.40 (95% CI: 1.02–1.92) for methylation-specific PCR (MSP) and 1.26 (95% CI: 0.87–1.82) for quantitative MSP (Q-MSP). The combined HR of the 16 studies reporting NSCLC as a whole indicated that patients with p16 hypermethylation had poor prognosis. No significant association was found when adenocarcinoma subtype pooled. When seven studies on DFS were aggregated, the HR was 1.68 (95% CI: 1.12–2.52) without significant heterogeneity. Moreover, no obvious publication bias was detected on both OS and DFS.

Conclusion

The meta-analysis findings support the hypothesis that p16 methylation is associated with OS and DFS in NSCLC patients. Large well-designed prospective studies are now needed to confirm the clinical utility of p16 methylation as an independent prognostic marker.     

Decision Analysis Utilizing Data from Multiple Life-Cycle Impact Assessment Methods Part I: A Theoretical Basis

Numerous methodologies for the life-cycle impact assessment (LCIA) step of life-cycle assessment (LCA) are currently in popular use. These methods, which are based on a single method or level of analysis, are limited to the environmental fates, impact categories, damage functions, and stressors included in the method or model. Because of this, it has been suggested within the LCA community that LCIA data from multiple methods and/or levels of analysis, that is, end-point and midpoint indicators, be used in LCA-based decision analysis to facilitate better or, at least more informed, decision making. In this (two-part) series of articles, we develop and present a series of LCA-based decision analysis models, based on multiattribute value theory (MAVT), which utilize data from multiple LCIA methods and/or levels of analysis. The key to accomplishing this is the recognition of what LCIA damage indicators represent with respect to decision analysis, namely, decision attributes and, in most cases, proxy attributes. The use of proxy attributes in a decision model, however, poses certain challenges, such as the assessment of decision-maker preferences for actual consequences that are only known imprecisely because of inherent limits of both LCA and scientific knowledge. In this article (part I), we provide a brief overview of MAVT and examine some of the decision-theoretic issues and implications of current LCIA methods. We illustrate the application of MAVT to develop a decision model utilizing damage indicators from a single LCIA methodology; and, we identify the decision-theoretic issues that arise when attempting to combine LCIA indicators from multiple methods and/or levels of analysis in a single decision model. Finally, we introduce the use in our methodology of constructed attributes to combine related end-point damage indicators into single decision attributes and the concept and evaluation of proxy attributes.