SCGPred： A Score-based Method for Gene Structure Prediction by Combining Multiple Sources of Evidence

Predicting protein-coding genes still remains a significant challenge. Although a variety of computational programs that use commonly machine learning methods have emerged, the accuracy of predictions remains a low level when implementing in large genomic sequences. Moreover, computational gene finding in newly se- quenced genomes is especially a difficult task due to the absence of a training set of abundant validated genes. Here we present a new gene-finding program, SCGPred, to improve the accuracy of prediction by combining multiple sources of evidence. SCGPred can perform both supervised method in previously well-studied genomes and unsupervised one in novel genomes. By testing with datasets composed of large DNA sequences from human and a novel genome of Ustilago maydi, SCGPred gains a significant improvement in comparison to the popular ab initio gene predictors. We also demonstrate that SCGPred can significantly improve prediction in novel genomes by combining several foreign gene finders with similarity alignments, which is superior to other unsupervised methods. Therefore, SCGPred can serve as an alternative gene-finding tool for newly sequenced eukaryotic genomes. The program is freely available at http：//bio.scu.edu.cn/SCGPred/.     

基因克隆技术的研究进展

为能快速而准确地克隆目的基因,综述了一些基因克隆常用技术,包括差异表达基因分离技术、转座子标签技术、图位克隆技术、同源序列技术、表达序列标签技术的原理、应用及应用潜力,并对其作了简要的评价.这些技术有利有弊,应根据不同的实验目的和水平来选择相应的技术.     

以neo作选择标记富集和筛选阳性重组杆状病毒

将苜蓿银纹夜蛾(AcNPV)极早期基因IEI启动子控制的neo基因表达盒插入p10型转载体pAcEP106中得到pAcPIneo,将它和野生型AcNPV DNA共转染Sf细胞得到neo^+重组病毒.因为neo基因的表达使得neo^+基因的重组病毒可以在G418的存在下复制,而野生型则不能.将共转染得到的上清液以很低的感染复数连续传代,通过G418的选择作用,使重组病毒得到富集,三代以后重组病毒比例可达90%以上,如此之高的重组比例使得重组病毒的筛选不须经空斑纯化只须有限稀释即可得到.利用杆状病毒早期基因启动子表达neo基因为用早期基因表达外源毒素基因作重组病毒杀虫剂打下了基础,同时也建立了一种简便有效的筛选、富集阳性重组病毒的方法.     

电化学发光在基因检测中的应用

电化学发光基因检测是把电化学发光的高灵敏性和传统分子生物学方法的稳定性结合于一体的一种新型的基因检测技术。与传统的基因检测方法相比,它具有无放射性危害、高灵敏度、操作简便等优点。近年被广泛地应用于核酸序列分析,基因突变分析,遗传病、转基因物种、病毒、微生物等的检测。本文概述了电化学发光的基本原理以及传统的基因检测技术,详细地介绍了电化学发光在当前基因检测中的应用现状,并对其前景作了展望。     

BMPR-IB和BMP15基因作为小尾寒羊多胎性能候选基因的研究

以控制BooroolaMerino羊多胎性能的BMPR IB基因 ,以及影响Invedale和Hanna羊排卵数的BMP15基因作为候选基因 ,从分子水平上对小尾寒羊的多胎机制进行研究 ,分析突变位点的特性 ,并通过大规模的群体检测统计推断其遗传效应。实验结果表明 :多胎品种小尾寒羊在BMPR IB基因的相应位置上发生了与BooroolaMerino羊相同的突变 (A74 6G) ,该基因的BB基因型在小尾寒羊群体内为优势基因型 ,且小尾寒羊初产和经产母羊的BB基因型比 ++基因型分别多产 0 97羔 (P <0 0 5 )和 1 5羔 (P <0 0 1) ,推测BMPR IB基因与控制小尾寒羊多胎性能的主效基因存在紧密的遗传连锁。而BMP15基因在小尾寒羊中不存在V31D或Q2 3Ter突变 ,说明小尾寒羊的多胎遗传机制与Romney羊不同 ,因此排除了BMP15突变影响小尾寒羊排卵数的可能性。     

基于纳米颗粒的基因突变检测方法研究进展

基因突变是指在分子结构上发生碱基对的组成或排列顺序的改变.它与人类疾病的发生息息相关,一直以来备受关注,开发准确可靠的检测方法,进一步探索核酸功能调控以及相关疾病的早期发现和治疗是研究人员不断努力的方向.近年来,纳米颗粒因其优异的光学、电学和生物相容性,在生物医学领域得到广泛应用.首次系统地论述基于纳米颗粒在基因突变检...     

p-SAGE: 基因集合的参数统计分析方法

肿瘤的发生与发展通常是由重要的细胞通路表达水平的反常导致的．尽管目前已经有很多工作利用基因表达谱数据以及一些其他的先验知识来寻找那些与肿瘤相关的基因集合,但还是没有一个恰当的基因集合的统计学方法．大多数研究都是直接将单基因的检验方法直接应用到基因集合上来．提出了基因集合的参数统计分析方法( p-SAGE ),这个方法应用到大脑肿瘤的实验中,识别了许多显著的基因集合．一些新发现的基因集合是与信号转导和免疫相关的．这个简便有效的方法可以得出有生物学意义的结果．     

蜡样芽孢杆菌检测方法的研究进展

蜡样芽胞杆菌(Bacillus cereus)是革兰氏阳性芽孢杆菌,广泛存在于自然环境中,对不良环境有较强的抵抗力,是一种人畜共患的食源性条件致病菌.蜡样芽孢杆菌能够产生多种毒素,这些毒素决定了其致病性.因此,建立快速、准确的蜡样芽孢杆菌检测方法对疾病的诊断和发病后的及时治疗至关重要.本文对近年来检测蜡样芽孢杆菌的菌体...     

毒素蛋白基因mazF在基因修饰系统中的应用进展

毒素-抗毒素系统(Toxin-antitoxin system,TA系统)存在于大部分细菌中。mazEF是大肠杆菌中一种毒素-抗毒素系统。毒素基因mazF编码的MazF毒素蛋白可以特异性地剪切自由mRNA的ACA序列,从而抑制蛋白合成、引起细胞生长停滞;近些年,许多学者利用mazF基因作为反向筛选标记对不同种微生物建立了无标记或无痕的基因修饰系统,并实现了不同菌株的基因组修饰。主要综述了大肠杆菌mazF基因作为反向筛选基因的应用原理及其在不同种类微生物的基因修饰系统中的应用进展,然后对mazF基因及其他毒素基因在基因修饰系统中的应用进行了展望。     

Rapid isolation of any known genes from whole cells of yeast by PCR

A short protocol was developed that allows the rapid isolation of any knownSaccharomyces cerevisiae gene. Two known genes,APN1 andIMP2, were isolated directly from whole cells of yeast using polymerase chain reaction, without the need for purified template genomic DNA.     

昆虫杆状病毒表达系统中阳性重组病毒的筛选

近年来,随着杆状病毒表达系统的普遍应用,阳性重组病毒筛选方法也有了很大的改进,从过去的经验性的ocu⁺／ocu^-空斑表型筛选发展到根据颜色差异,药物抗性,抗生素抗性等等筛选重组病毒.同源重组过程也可在大肠杆菌或酵母甚至体外进行,大大提高了重组率,由于重组率是如此之高,有些方法可以免去繁琐的空斑选择,很快得到重组病毒的纯培养.文章对各种筛选方法进行了比较,并指出各自的优缺点.     

拟南芥基因转移新方法一真空渗入法的研究

以拟南芥（Ａｒａｂｉｄｏｐｓｉｓｔｈａｌｉａｎａ）生态型Ｌａｎｄｓｂｅｎｇｅｒｅｃｔａ为试材,在含有所构建的ＣａＭＶＢａｒｉ－１株系基因ＶＩ的质粒（ｐＪＯ５３０Ｂａｒｉ－１ＧＶＩ）的根癌农杆菌（Ａｇｒｏｂａｃｔｅｒｉｕｍｔｕｍｅｆａｃｉｅｎｓ）菌种ＧＶ３１０１的介导下,研究了基因转移的新方法一真空渗入法。这种方法简便、快速、可靠且无需经过组织培养阶段即可获得大量转化植株。适宜的转化条件是将生长健壮,除去主苔后４－８ｄ的成株连同营养钵倒置浸入被渗入培养基稀释的农杆菌孢子悬浮液,其光密度为０．８,在吸力为１．７ｍ２／ｈ的真空泵下断续处理２ｍｉｎ／３０ｓ,置于２４ｈ连续光照下的气候室培养,待种子收获后在含有潮霉素的选择培养基选择转化植株．ＰＣＲ分析及ＥＬＩＳＡ检测,该方法的转化效果高达０．７１％。     

纳米载体介导的植物遗传转化研究现状和前景

高效遗传转化技术是植物重要性状功能基因鉴定的前提和转基因育种的基础.随着纳米生物技术的发展,以纳米载体介导的植物转基因技术已显示出巨大的应用潜力.综述了国内外应用于植物纳米载体的类型、与外源基因的结合方式以及传输细胞的原理,重点阐述了影响纳米基因载体性能与转化效率的重要因素,以及纳米载体介导外源基因转化植物细胞的方法,...     

痢疾杆菌体内诱导基因筛选方法的建立

分别用氯霉素乙酰转移酶基因(cat)和天冬氨酸半醛脱氢酶基因(asd)作为报告基因,用小鼠肺感染模型和HeLa细胞侵袭模型来试验筛选痢疾杆菌体内诱导基因的可行性。结果表明,以asd为报告基因,用HeLa细胞侵袭试验作为筛选模型,可成功地用于筛选痢疾杆菌的体内诱导基因。     

SDED: a novel filter method for cancer-related gene selection

Gene selection is to detect the most significantly expressed genes under different conditions expression data. The current challenge in gene selection is the comparison of a large number of genes with limited patient samples. Thus it is trivial task in simple statistical analysis. Various statistical measurements are adopted by filter methods applied in gene selection studies. Their ability to discriminate phenotypes is crucial in classification and selection. Here we describe the standard deviation error distribution (SDED) method for gene selection. It utilizes variations within-class and among-class in gene expression data. We tested the method using 4 leukemia datasets available in the public domain. The method was compared with the GS2 and CHO methods. The Prediction accuracies by SDED are better than both GS2 and CHO for different datasets. These are 0.8-4.2% and 1.6-8.4% more that in GS2 and CHO. The related OMIM annotations and KEGG pathways analyses verified that SDED can pick out more 4.0% and 6.1% genes with biological significance than GS2 and CHO, respectively.     

Molecular cloning and characterization of cold-responsive gene <Emphasis Type="Italic">Cbrci35</Emphasis> from <Emphasis Type="Italic">Capsella bursa-pastoris</Emphasis>

A new rare cold-inducible (RCI) gene designated Cbrci35 was cloned from Capsella bursa-pastoris, an edible wild herb, using the rapid amplification of cDNA ends (RACE) method. The full-length cDNA of Cbrci35 (Database Accession No.: AY566573) was 1300 bp and contained a 978 bp ORF encoding a precursor of 326 amino acid residues with a 23 amino acids signal peptide. The predicted Cbrci35 protein contained a peroxidase active site and proximal heme-ligand signatures, an RGD cell attachment sequence motif and two leucine zipper pattern motifs. Bioinformatics analysis revealed that Cbrci35 has a high level of similarity with RCI genes from Arabidopsis thaliana and peroxidases genes from other plants. RT-PCR analysis revealed that Cbrci35 expressed only in root. A cold acclimation assay showed that Cbrci35 was expressed immediately after cold triggering, but this expression was transient, suggesting that it concerns cold acclimation. But expression was not induced exposed to dehydration, salt stress or abscisic acid, indicating that it might be subjected specifically to cold regulation. These results indicate that Cbrci35 is an analogue of RCI genes and may participate in cold-response or increasing the freezing tolerance of plants.     

苏云金杆菌抗虫基因cryI Ac 转化辣椒的研究

通过农杆菌介导法将杀虫结晶蛋白基因cryIAc导入到辣椒子叶外植体中,经卡那霉素筛选、组织化学法检测GUS活性以及PCR、southern杂交分析证实cryIAc基因已整合进辣椒核基因组中。     

Mining gene expression profiles: an integrated implementation of kernel principal component analysis and singular value decomposition

The detection of genes that show similar profiles under different experimental conditions is often an initial step in inferring the biological significance of such genes. Visualization tools are used to identify genes with similar profiles in microarray studies. Given the large number of genes recorded in microarray experiments, gene expression data are generally displayed on a low dimensional plot, based on linear methods. However, microarray data show nonlinearity, due to high-order terms of interaction between genes, so alternative approaches, such as kernel methods, may be more appropriate. We introduce a technique that combines kernel principal component analysis (KPCA) and Biplot to visualize gene expression profiles. Our approach relies on the singular value decomposition of the input matrix and incorporates an additional step that involves KPCA. The main properties of our method are the extraction of nonlinear features and the preservation of the input variables (genes) in the output display. We apply this algorithm to colon tumor, leukemia and lymphoma datasets. Our approach reveals the underlying structure of the gene expression profiles and provides a more intuitive understanding of the gene and sample association.     

微卫星荧光标记基因组扫描

微卫星荧光标记基因组扫描为 2 0世纪 90年代发展起来的一项分子生物学技术 ,在基因定位、个体识别等方面有广泛的应用 .文中对其原理、策略、分析方法及应用作了论述 ,并探讨了它的发展前景 .