DNA Building Blocks at the Foundation of Better Survival

No abstract available.     

The performances of the chi-square test and complexity measures for signal recognition in biological sequences

With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the Pearson's chi-square test method to determine which parts of the Open Reading Frame (ORF) have significant effect on discriminating genes form pseudogenes. Moreover, different complexity measures and Pearson's chi-square test applied on the genes with high value of Pearson's chi-square statistic. We also compute the measures on homologous of these genes. The results illustrate that there is a region near the start codon with high value of chi-square statistic and low complexity that is conserve between homologous genes.     

细胞图象分析仪的研制及其对细胞DNA含量测定的初探

本文介绍在微机上开发的细胞图象处理分析系统,该系统图象处理功能强,细胞测量参数多,操作简便,实用性强。可用于生物医学图象的处理和分析。     

基于图像处理的树叶面积测量系统

以数字图像处理技术为基础,对数码相机拍摄的含有参照硬板和树叶的照片进行图像分析处理,提出了获取树叶的实际面积测量系统的一种独特实现方案。采用此方案开发出相应的应用软件,应用于树叶面积的测量计算,获得十分满意的结果。     

Synthesis of Fmoc-Gly-Ile Phosphinic Pseudodipeptide: Residue Specific Conditions for Construction of Matrix Metalloproteinase Inhibitor Building Blocks

The efficient synthesis of an Fmoc-Gly-Ile phosphinic pseudodipeptide was desired as an eventual building block for construction of matrix metalloproteinase inhibitors. A Michael-type addition reaction of bis(trimethylsilyl) phosphonite with the appropriate acrylate generated the pseudodipeptide bond. Additional of adamantyl (Ad) protection by our prior route (reaction of in situ generated phosphinic acid chloride with the sodium salt of adamantanol) was surprisingly inefficient. Adamantyl protection was achieved in high yield by refluxing the phosphinic acid, Ag₂O, and 1-AdBr in chloroform. Subsequently a concise one-pot three-step reaction comprising a double deprotection of the N- and C-termini under catalytic hydrogenation conditions followed by selective protection of the N-terminus with an Fmoc group yielded Fmoc-NHCH₂PO(OAd)CH₂CH(2-butyl)CO₂H in 41?% overall yield. These results indicate that, as the diversity of phosphinic pseudodipeptides is increased to create selective matrix metalloproteinase inhibitors, different synthetic pathways may be required for efficient building block preparation.     

三维肺部图像中疑似肺结节结构的自动提取

本文提出了一种肺部CT图像三维数据中自动提取疑似结节区域的方法。首先结合阈值分割、种子填充等方法,在三维体数据上分割出肺实质。进而利用改进的模糊C均值聚类,提取出结节及具有结节特征的血管、支气管等感兴趣区域。该工作对感兴趣区域的特征提取有重要意义,是早期肺癌计算机辅助诊断重要的一步。     

微机在核医学图像处理系统中的应用研究

本文以一种较具代表性的核医学图像设备为例,在简要介绍单光子发射型计算机断层摄影基本工作原理的基础上,对该设备的核心部分－计算机系统的结构进行剖析。并进一步介绍了对这种大型核医学成像系统进行诊断功能扩展方法的基本原理。     

LZ complexity distance of DNA sequences and its application in phylogenetic tree reconstruction

DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.     

一种新型的基于图像的DNA序列可视化模型

传统的DNA序列可视化模型局限于短DNA序列的可视化,并且缺乏对可视化图形的通用分析方法。因此,文章提出了一种基于图像的DNA序列可视化模型,这种模型通过将一维的DNA序列转换为二维的256色的灰度图像,可以实现长DNA序列的可视化,具有很高的空间紧密性。借助成熟的图像处理方法来分析DNA可视化图像,可以获取原始DNA序列的规模、4种不同碱基的分布、无序程度等重要信息。通过比较不同DNA序列的可视化图像,可以获取这些序列的相似性信息。     

基于二阶C0复杂度的癫痫发作预测

癫痫发作的预测是近年来在临床医学和神经系统科学研究领域中备受关注的问题。如果癫痫发作能够被可靠地预测,则可以提前采取有效的临床预防措施,从而能较大程度地改善癫痫患者的生活质量。文章提出了一种基于二阶C0复杂度的预测算法用于预测癫痫发作。该算法通过分析癫痫患者颅内脑电信号的二阶C0复杂度,利用发作前期复杂度曲线的变化特征预测癫痫发作。作者运用该算法对21组癫痫病人87次发作的临床颅内脑电数据和4组大鼠4次发作的颅内脑电数据进行分析计算,预测准确率分别为94.3%和100%。实验结果表明该算法可以有效地预测癫痫发作,具有潜在的重要临床应用价值。     

Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction

A new DNA computing algorithm based on a ligase chain reaction is demonstrated to solve an SAT problem. The proposed DNA algorithm can solve an n-variable m-clause SAT problem in m steps and the computation time required is O (3m+n). Instead of generating the full-solution DNA library, we start with an empty test tube and then generate solutions that partially satisfy the SAT formula. These partial solutions are then extended step by step by the ligation of new variables using Taq DNA ligase. Correct strands are amplified and false strands are pruned by a ligase chain reaction (LCR) as soon as they fail to satisfy the conditions. If we score and sort the clauses, we can use this algorithm to markedly reduce the number of DNA strands required throughout the computing process. In a computer simulation, the maximum number of DNA strands required was 2(0.48n) when n=50, and the exponent ratio varied inversely with the number of variables n and the clause/variable ratio m/n. This algorithm is highly space-efficient and error-tolerant compared to conventional brute-force searching, and thus can be scaled-up to solve large and hard SAT problems.     

基于EST-SSR标记的甘薯种质资源DNA指纹图谱构建

采用EST-SSR标记构建了国家种质广州甘薯圃中52份甘薯种质资源的DNA指纹图谱。利用52份供试资源,从早期筛选出的342对候选多态性引物中筛选出16对核心引物,16对引物在52份资源中共扩增出159个等位位点,每对引物的等位位点数为5~19个不等,平均为9.94个,多态性信息含量变化范围为0.6235~0.9593,平均为0.7991。选择带型清晰、重复性好、易于统计且能将52份资源完全区分开的2对引物组合构建供试资源的DNA指纹图谱。NTSYS软件聚类分析表明,EST-SSR标记能正确反映出不同资源间的亲缘关系,为构建甘薯大型DNA指纹图谱数据库奠定了基础。     

Removal of background signal from in situ data on the expression of segmentation genes in <Emphasis Type="Italic">Drosophila</Emphasis>

Here we present a method for the removal of nonspecific background signal from fluorescently localized expression patterns of Drosophila segmentation genes. Our algorithm for removal of background signal brings the data to a common standard form with zero background and removes systematic error in gene expression levels caused by the presence of background. The method is based on the discovery, reported here, that background is well fit by a very broad two-dimensional paraboloid. The paraboloid is determined from the area of the embryo in which a given gene is not expressed and the whole pattern is then normalized by this paraboloid to remove background from the entire embryo. The software implementing this algorithm is available from the authors.Edited by C. Desplan     

利用植物DNA条形码构建亚热带森林群落系统发育关系——以鼎湖山样地为例

在群落水平上重建植物系统发育关系是当前植物系统学研究的一项重要内容;DNA条形码技术的出现为这一工作的开展提供了便利。本文选取国际通用的植物DNA条形码（rbcL,matK和psbA trnH）,对鼎湖山大样地的183个物种（隶属于24目51科110属）进行测序;分别利用两位点和三位点DNA条形码组合构建该样地植物群落的系统发育关系,并比较不同位点组合构建出的群落系统发育关系的拓扑结构和节点支持率;最后选出一个具有最好拓扑结构和最高节点支持率的鼎湖山大样地群落系统发育关系。在目、科和属这三个水平上,三位点条形码片段组合构建的群落系统发育关系与APG系统获得较好匹配;有些进化分支在相应的APG系统位置解决得不好,却在条形码序列构建的系统发育关系中得到了较好解决。表明综合使用不同进化速率的DNA条形码片段并采取三位点超级矩阵的组合策略,在未采用APG系统大框架的情况下,也能快速而又相对准确地构建出鼎湖山南亚热带森林植物群落的系统发育关系。     

利用植物DNA条形码构建亚热带森林群落系统发育关系——以鼎湖山样地为例

在群落水平上重建植物系统发育关系是当前植物系统学研究的一项重要内容;DNA条形码技术的出现为这一工作的开展提供了便利。本文选取国际通用的植物DNA条形码（rbcL,matK和psbA trnH）,对鼎湖山大样地的183个物种（隶属于24目51科110属）进行测序;分别利用两位点和三位点DNA条形码组合构建该样地植物群落的系统发育关系,并比较不同位点组合构建出的群落系统发育关系的拓扑结构和节点支持率;最后选出一个具有最好拓扑结构和最高节点支持率的鼎湖山大样地群落系统发育关系。在目、科和属这三个水平上,三位点条形码片段组合构建的群落系统发育关系与APG系统获得较好匹配;有些进化分支在相应的APG系统位置解决得不好,却在条形码序列构建的系统发育关系中得到了较好解决。表明综合使用不同进化速率的DNA条形码片段并采取三位点超级矩阵的组合策略,在未采用APG系统大框架的情况下,也能快速而又相对准确地构建出鼎湖山南亚热带森林植物群落的系统发育关系。     

Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition

The main work of this paper is to propose a new theory and method, which is based on the idea of the pseudo-amino acid composition, for phylogenetic analysis of DNA primary sequences. In our method, we revise the part of the occurrence frequency of 20 amino acids in the method of the pseudo-amino acid composition by replacing the frequency of 16 dinucleotides. And we select eight LZ complexity factors of eight (0,1) sequences of a DNA primary sequence as PseAA components. Finally, we characterize a DNA sequence with a 24-dimensional vector. We reconstruct the phylogenetic trees of two datasets. The results show that our method is efficient and significant.     

昆虫翅脉特征自动获取技术的初步研究

昆虫翅的形态特征是某些类群昆虫分类中的重要依据,怎样快速科学提取这些数据是昆虫数字鉴定技术中必须解决的重要问题之一。本文介绍了目前国内外这方面的进展,并介绍了DrawWing软件的详细功能。该软件能比较准确方便地提取昆虫翅轮廓和翅脉特征值,因此详细描述了其算法原理。利用该软件的DOS和Windows两种不同版本对意大利蜜蜂和昼鸣蝉的翅进行了其特征提取的实验研究,结果证明该软件可以成功提取蜜蜂翅脉特征值,但对昼鸣蝉翅处理尚存在问题。在此基础上,本文对昆虫翅脉特征自动获取技术乃至昆虫种类的计算机识别方法的进一步发展提出了讨论。     

Classification of leaf epidermis microphotographs using texture features

We present the results of a Gray Level Co-occurrence Matrix (GLCM) analysis for two sets of leaf epidermis images for the adaxial (20×_H) and abaxial sides (20×_E). The leaves were collected from a dry forest in Mona Island which is located between the Dominican Republic and Puerto Rico. For each set of images (GLCM) texture features were calculated namely the energy, correlation, contrast, absolute value, inverse difference, homogeneity, and entropy. From the calculated statistics a features matrix was obtained for each image and randomly divided into training set and test set using the hold-out method. In this method 70% of the images were considered as a training set and 30% as the test set. For each training and test set a linear discrimination analysis (LDA) was performed resulting in a average correct classification percent of 90% for the abaxial side in comparison with 80% for the adaxial side.     

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.