绵羊腺病毒287作为基因传递载体的应用前景

绵羊腺病毒287(OAdV287) 具有独特的基因组结构,全长29 576bp。基因组最大的特点是有很高的A/T含量(66.4%)和缺少典型的E1区,以及含有一段较长的冗余片段。已识别出其基因组中有3个外源基因插入区,理论上最多可容纳6.3kb的外源DNA。OAdV287的纤维和五邻体结构结构独特,衣壳蛋白上缺少可识别的整合蛋白结合域。OAdV287能感染一系列人和动物的细胞系,但是不能在非绵羊源细胞内成功复制。OAdV287载体可以避免人腺病毒的免疫干扰,具有很高的转染效率。目前,OAdV287已成为研究最热的动物源腺病毒载体之一。     

Multiattribute evaluation of regional cotton variety trials

Summary The Australian Cotton Cultivar Trials (ACCT) are designed to investigate various cotton [Gossypium hirsutum (L.)] lines in several locations in New South Wales and Queensland each year. If these lines are to be assessed by the simultaneous use of yield and lint quality data, then a multivariate technique applicable to three-way data is desirable. Two such techniques, the mixture maximum likelihood method of clustering and three-mode principal component analysis, are described and used to analyze these data. Applied together, the methods enhance each other's usefulness in interpreting the information on the line response patterns across the locations. The methods provide a good integration of the responses across environments of the entries for the different attributes in the trials. For instance, using yield as the sole criterion, the excellence of the namcala and coker group for quality is overlooked. The analyses point to a decision in favor of either high yields of moderate to good quality lint or moderate yield but superior lint quality. The decisions indicated by the methods confirmed the selections made by the plant breeders. The procedures provide a less subjective, relatively easy to apply and interpret analytical method of describing the patterns of performance and associations in complex multiattribute and multilocation trials. This should lead to more efficient selection among lines in such trials.     

以Ca-Ca距离为基础的构象空间的可视化研究

蛋白质结构构象呈现明显的规律,研究其在特定构象空间的分布对蛋白质结构预测和模拟具有重要意义。本文以449个非冗余的高分辨串蛋白质结构为材料,以Ga-Ga距离向量代表蛋白质片段。然后利用主成分分析方法,建立蛋白质片段构象空间的可视化构图,并且单个蛋白质分子可以映射到该空间形成一个顺序连接的路径。从而,可以很直观的分析各长度片段（4-9个残基的片段）的分布情况及其内在的连接关系。图形显示了明显的聚集性,以及各种类型片段与二级结构明显的对应关系。     

Systematic tuning of parameters in support vector clustering

Clustering algorithms divide a set of observations into groups so that members of the same group share common features. In most of the algorithms, tunable parameters are set arbitrarily or by trial and error, resulting in less than optimal clustering. This paper presents a global optimization strategy for the systematic and optimal selection of parameter values associated with a clustering method. In the process, a performance criterion for the optimization model is proposed and benchmarked against popular performance criteria from the literature (namely, the Silhouette coefficient, Dunn's index, and Davies-Bouldin index). The tuning strategy is illustrated using the support vector clustering (SVC) algorithm and simulated annealing. In order to reduce the computational burden, the paper also proposes an alternative to the adjacency matrix method (used for the assignment of cluster labels), namely the contour plotting approach. Datasets tested include the iris and the thyroid datasets from the UCI repository, as well as lymphoma and breast cancer data. The optimal tuning parameters are determined efficiently, while the contour plotting approach leads to significant reductions in computational effort (CPU time) especially for large datasets. The performance criteria comparisons indicate mixed results. Specifically, the Silhouette coefficient and the Davies-Bouldin index perform better, while the Dunn's index is worse on average than the proposed performance index.     

Discrimination of higher plant calluses based on embryogenic capacity and taxonomic classification by pyrolysis mass spectrometry

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum, and has been widely applied to the discrimination of closely related microbial strains. Minimally prepared samples of embryogenic and non-embryogenic calluses derived from various higher plants (sweet potato, morning glory, Korean ginseng, Siberian ginseng, and balloon flower) were subjected to PyMS for spectral fingerprinting. A dendrogram based on the unweighted pair group method, with arithmetic mean of pyrolysis mass spectra, divided the calluses into Siberian ginseng embryogenic callus and the others, which were subsequently divided into embryogenic and non-embryogenic callus groups, regardless of plant species from which the calluses were derived. In the non-embryogenic callus group, the dendrogram was in agreement with the known taxonomy of the plants. These results indicate that PyMS analysis could be applied for discriminating plant calluses based on embryogenic capacity and taxonomic classification.     

Using principal component analysis to find correlations between loop-related and thermodynamic variables for G-quadruplex-forming sequences

The application of Principal Component Analysis (PCA) is proposed here as a simple means of revealing correlations between thermodynamic variables corresponding to folding equilibria of intramolecular G-quadruplexes and Watson–Crick duplexes, and the length of loops in the corresponding guanine-rich DNA sequences. To this end, two previously studied data sets were analyzed (Arora and Maiti, J. Phys. Chem. B. 2009 and Kumar and Maiti, Nucleic Acids. Res. 2008). All of the sequences considered shared the common structure 5’- GGG - loop1 - GGG - loop2 - GGG - loop3 - GGG -3’. PCA of these data sets supported a series of correlations between the variables studied. First, the association of loop length with thermodynamic stability and quadruplex structure was corroborated. Secondly, it is proposed that the addition of ethylene glycol produces a stronger stabilization on those sequences showing long loop1 and/or loop3. Thirdly, it is proposed that a low content of adenine in loop1 and/or loop3 will produce an increase in the stability of G-quadruplex and its related Watson–Crick duplex.     

Analysis of the genetic diversity of garlic (Allium sativum L.) germplasm by SRAP

Cluster analysis and principal component analysis were used to investigate the genetic diversity of 40 garlic germplasms analyzed with 23 sequence-related amplified polymorphism (SRAP) primer combinations. A total of 130 polymorphic loci were detected among these germplasms, with an average of 5.65 polymorphic loci per SRAP primer combination. The percentage of polymorphic loci was 69.1%, whereas the mean effective number of alleles, the mean Nei's gene diversity, and the mean Shannon's information index were 1.4446, 0.2788, and 0.4365, respectively. Cluster analysis revealed that the 40 germplasms could be divided into 3 groups. The results of principal component analysis were consistent with those of unweighted pair-group method with arithmetic averages (UPGMA) clustering analysis. The Shannon-Weaver information index ranged from 0.2419 to 0.4202, indicating that the garlic germplasms had high genetic diversity.     

西藏鲁朗森林立地分类的初步研究

采用主成分分析法对西藏鲁朗森林立地66个标准地调查实测材料分析,选取海拔高度、坡度、坡向、土层厚度、土壤质地、石砾含量、土壤有机质含量7个因子,共划分出8个森林立地类型.结果表明,在西藏高山峡谷林区以此方法划分森林立地类型较适宜.     

粤西海域浮游植物群落结构特征的多元分析与评价

根据1998-1999年对粤西海域浮游植物的周年调查资料,本文采用主成分分析和聚类分析等多元统计分析方法研究该海域浮游植物的主要种类组成和群落结构的基本特征。研究结果表明,中肋骨条藻（Skeletonema costatum）、伏氏海毛藻（Thalassiothrix fauenfeldii）、小舟形藻（Navicula subminuscula）、颤藻（Oscillatoria sp．）、菱形海线藻（Thalassionema nitzschioides）、细弱海链藻（Thalassiosira subtilis）、齿角毛藻（Chaetoceros denticulatus）、北方劳德藻（Lauderia borealis）、中华盒形藻（Biddulphia sinensis）、纺锤角藻（Ceratium fusus）、翼根管藻（Rhizosolenia alata）、斯氏根管藻（Rhizosolenia stolterforthii）、短角弯角藻（Eucampia zoodiacu）、笔尖形根管藻（Rhizosolenia styliformis）、拟弯角毛藻（Chaetoceros pseudocurvisetus）等种类构成了粤西海域浮游植物的主体。春季、夏季和秋季该海域浮游植物可明显划分为近岸类群和近外海类群2个群落,冬季群落结构分化不显著,不形成明显的类群。各主要种类的季节演替现象十分明显。     

内蒙古78份葱属野生种表型遗传多样性分析

为了揭示内蒙古葱属野生种表型遗传多样性,采用方差分析、主成分分析、聚类分析等方法,对收集的78份野生种的种质资源14个表型性状进行了遗传多样性评价。结果表明:内蒙古葱属野生资源存在丰富的遗传多样性。(1)14个表型性状平均变异系数为43.0%,叶片宽的变异系数最大,为94.7%;种子厚的变异系数最小,为14.6%。14个表型性状在居群间的差异除叶片宽达到显著(P0.05)水平外,其余性状均表现差异不显著;(2)14个表型性状可归成为6个主成分因子,累计贡献率达到80.77%,最大程度上反映了所有78份葱属种质资源的表型特征,在前6个主成分包括的14个农艺性状中的株丛直径、叶片长、叶片宽、单株叶片数、花序长度、花序宽度和种子宽等性状是造成葱属种质资源表型差异的主要因素;(3)14个表型性状间存在显著或极显著的相关性;(4)采用欧氏距离系统聚类法将供试材料分为7大类,78份葱属种质资源基本上按种区分开,并和地理条件有一定的关系,种间和材料间表型差异很明显。本研究为内蒙古葱属资源的利用提供了科学依据。     

A comparison among different techniques for human ERG signals processing and classification

Feature detection in biomedical signals is crucial for deepening our knowledge about the involved physiological processes. To achieve this aim, many analytic approaches can be applied but only few are able to deal with signals whose time dependent features provide useful clinical information. Among the biomedical signals, the electroretinogram (ERG), that records the retinal response to a light flash, can improve our comprehension of the complex photoreceptoral activities.The present study is focused on the analysis of the early response of the photoreceptoral human system, known as a-wave ERG-component. This wave reflects the functional integrity of the photoreceptors, rods and cones, whose activation dynamics are not yet completely understood. Moreover, since in incipient photoreceptoral pathologies eventual anomalies in a-wave are not always detectable with a “naked eye” analysis of the traces, the possibility to discriminate pathologic from healthy traces, by means of appropriate analytical techniques, could help in clinical diagnosis.In the present paper, we discuss and compare the efficiency of various techniques of signal processing, such as Fourier analysis (FA), Principal Component Analysis (PCA), Wavelet Analysis (WA) in recognising pathological traces from the healthy ones. The investigated retinal pathologies are Achromatopsia, a cone disease and Congenital Stationary Night Blindness, affecting the photoreceptoral signal transmission. Our findings prove that both PCA and FA of conventional ERGs, don't add clinical information useful for the diagnosis of ocular pathologies, whereas the use of a more sophisticated analysis, based on the wavelet transform, provides a powerful tool for routine clinical examinations of patients.     

Biomechanics in posture space: Properties and relevance of principal accelerations for characterizing movement control

Human movements, recorded through kinematic data, can be described by means of principal component analysis (PCA) through a small set of variables representing correlated segment movements. The PC-eigenvectors then form a basis in the associated vector space of postural changes. Similar to 3D movements, the kinematics in this posture space can be quantified through ‘principal’ positions (PPs), velocities (PVs) and accelerations (PAs). The PAs represent a novel set of variables characterizing neuro-muscular control. The aim of the current technical note was to (i) compare the variance explained by PAs with the variance explained by PPs; (ii) clarify the relationship between PAs and segment accelerations; and (iii) compare variability of the first principal acceleration (PA₁) with the local dynamic stability (largest Lyapunov exponent, LyE) of the first principal position (PP₁). A PCA was applied on 3D upper-body positions collected by an Xsens inertial sensor system as nineteen volunteers performed a bimanual repetitive tapping task. The main finding revealed that the PP-explained variance considerably differed from the PA-explained variance, indicating that the latter should be considered when reducing the dimensionality in postural movement analysis through a PCA. Further, the current study formally established that the acceleration curves obtained from differentiating segment positions and from linear combinations of PAs are identical. Finally, a strong correlation, r(17) = 0.92, p < 0.001, was observed between the cycle-to-cycle variability in PA₁ and the LyE calculated for PP₁, supporting the notion that PA variability and LyE share some of the information they provide about movement control.     

Spherical classification of wavelet transformed EMG intensity patterns

Electromyograms of different muscles can be submitted to a wavelet-transform and arranged in a Multi-Muscle Pattern (MMP). The MMP represents the intensity of the EMG signals of a number of muscles simultaneously in time/frequency space. As previously shown, the MMPs can be represented by points in an Euclidian vector space that was called pattern space. The variability of the MMPs is represented by the distribution of the scattered points in pattern space. The purpose of this study was to investigate the distribution of the points and use the properties of the distribution to classify MMPs. The first task was to test whether the points representing a group of MMPs were located between the inner and outer boundary of a sphere-like domain in whitened pattern space as theoretically predicted. The mean of these points and thus of the MMPs is represented by a point at the center of the sphere. The hypothesis was that the spheres representing points of the MMPs of barefoot and shod runners were sufficiently separated and distinguishable in pattern space to allow classification of the runners according to their shod condition. The results confirmed the hypothesis and revealed that the recognition rate was over 80%. One can conclude and generalize that the points representing MMPs recorded for a certain condition reside between the inner and outer boundary of the sphere. The classification based on the spherical feature represents a much better discrimination than one based on the distance from the mean.     

MATLAB 7.X生物信息工具箱的应用———基因表达图谱分析（4）*

基因表达图谱原则上可了解整体细胞基因表达的信息,是基因组功能分析的重要研究手段。MATLAB 7.X生物信息工具箱为基因表达谱数据的分析和处理提供了一个综合环境,通过众多统计函数和绘图函数的结合使用,过滤不合格的基因数据和噪声数据,从而对基因表达数据进行聚类分析和主成分分析,绘制相关的基因表达图谱,完成基因芯片数据表达图谱的分析,分析结果可视化程度高,图表清晰、直观。本文主要以酿酒酵母Saccharomyces cerevisiae为例,详细描述了利用MATLAB 7.X生物信息工具箱对其基因表达图谱进行分析的过程。     

重组腺相关病毒载体临床实验研究

重组腺相关病毒载体 (rAAV)基因药物已经开展六十余项（67）临床研究,其安全、高效、稳定、表达持久等特点越来越受到业界的重视,最近的临床试验发现其在治疗先天性黑内障临床研究中呈现出显著疗效更是极大地振奋了人们的信心。临床研究案例的增加使人们对rAAV基因药物有了更为全面、深入的认识。与此同时,也对基因药物提出了更多挑战与要求,尤其是免疫原性和安全性等方面。     

DNA序列分析用于常见致病真菌鉴定和分型

随着真菌感染的增多,仅用表型方法鉴定环境中或临床上的致病真菌不足以快速准确地诊断真菌感染疾病,近年来,分子生物学方法因快速、准确而逐步得到应用,其中DNA序列分析已成为鉴定致病真菌到种水平的重要方法。现就DNA序列分析在常见致病真菌分类鉴定及基因分型的应用加以综述。     

Rational Vector Design for Efficient Non-viral Gene Delivery: Challenges Facing the Use of Plasmid DNA

Although non-viral gene delivery is a very straightforward technology, there are currently no FDA-approved gene medicinal products available. Therefore, improving potency, safety, and efficiency of current plasmid DNA vectors will be a major task for the near future. This article will provide an overview on factors influencing production yield and quality as well as safety issues that emerge from the vector design itself. Special focus will be on generating bacterial pDNA vectors by circumventing the use of antibiotic resistance genes, to generate safer gene medicinal products as well as smaller, more efficient DNA vectors.     

不同放牧强度下高寒灌丛群落特征和演替规律的数量研究

本文应用多样性指数、聚类分析等数学方法,研究了不同放牧强度下高寒灌丛群落特征的变化,用主分量分析方法,研究了不同放牧强度下高寒灌丛的演替规律。多样性分析结果表明,植物多样性指数在放牧强度为C组的草场达到最大。聚类分析结果,当相关系数R≥0.90 时,以重要值为特征的植物聚合为10类,它们分别属于植物群落不同演替阶段的建群种、优势种和伴生种。主分量分析表明,5个不同放牧强度的高寒灌丛群落聚合为3类,A和B组草场属于以灌木和杂类草为优势植物的2层结构的植物群落,C组草场属于以灌木为建群植物、杂类草和耐牧的莎草为共优势植物的2层结构的植物群落,D和E组草场属于以灌木为建群植物、禾草和莎草为共优势植物的3层结构的植物群落。     

SVM classification of human intergenic and gene sequences

Despite constant improvement in prediction accuracy, gene-finding programs are still unable to provide automatic gene discovery with the desired correctness. This paper presents an analysis of gene and intergenic sequences from the point of view of language analysis, where gene and intergenic regions are regarded as two different subjects written in the four-letter alphabet {A,C,G,T}, and high frequency simple sequences are taken as keywords. A measurement alpha(l(tau)) was introduced to describe the relative repeat ratio of simple sequences. Threshold values were found for keyword selections. After eliminating 'noise', 178 short sequences were selected as keywords. DNA sequences are mapped to 178-dimensional Euclidean space, and SVM was used for prediction of gene regions. We showed by cross-validation that the program we developed could predict 93% of gene sequences with 7% false positives. When tested on a long genomic multi-gene sequence, our method improved nucleotide level specificity by 21%, and over 60% of predicted genes corresponded to actual genes.     

ZO-1 基因的慢病毒载体构建

目的：相邻两心肌纤维的连接处称心肌闰盘,它在心肌的机电活动中扮演重要角色。目前有关闰盘相关基因Cx43 的研究已 被广泛关注,而在不同心肌病理状态下,其变化及功能都与另一闰盘相关基因ZO-1 有极为密切的联系。目前有关ZO-1 的研究比 较少,此次欲将猪ZO-1 基因克隆到慢病毒表达载体并进行鉴定,为进一步研究其功能奠定基础。方法：利用聚合酶链反应（PCR） 扩增猪ZO-1 基因,并克隆到慢病毒表达载体,通过转化、抽提质粒、双酶切和测序鉴定构建的Lenti-EF1α-EGFP-TRE-ZO-1 重组 载体。结果：猪ZO-1 基因片段重组到慢病毒载体;PCR和双酶切鉴定,电泳结果显示均能得到与理论大小相符的片段;经测序证 实成功构建Lenti-EF1α-EGFP-TRE-ZO-1 慢病毒表达载体。结论：通过一系列实验证实Lenti-EF1α-EGFP-TRE-ZO-1 慢病毒表达 载体构建成功,可利用其感染相关细胞或注入动物体内,为后续的体外及在体研究奠定基础,明确其在不同心肌病理状态下所发 挥的独特作用。