含CpG motifs的乙肝表面抗原载体的构建及表达(英文)

构建了编码乙肝表面抗原中蛋白的卡那霉素抗性真核表达质粒 pVAX_CpGS2 S ,其中通过PCR克隆了若干个CpGmotifs到质粒载体中 .经酶切鉴定和测序正确后将重组质粒体外转染COS7细胞 ,ELISA法检测上清液中的HBsAg呈阳性 ,说明重组质粒 pVAX_CpGS2 S在体外能够有效表达HBsAg ,为探讨CpGmotifs克隆入DNA疫苗载体后对体内免疫反应的影响打下基础 .

生物信息学Blocks和Motifs方法在病毒研究中的应用

评述了生物信息学分析方法及几种主要分析软件的基本原理 ;提出了蛋白质、核酸序列分析、搜索Blocks和 Motifs的基本方法 。

一种对预测Motifs算法的评价策略

主要研究了如何评价蛋白质家族Motifs预测算法的预测结果,目的是在对传统的算法预测问题分析优化的基础上,制定新的评价策略。主要方法是通过对MEME算法和PKG算法预测结果的比较分析,计算同一家族中Motifs的敏感性和特异性并比较它们对应的ROC曲线,确定真实的Motifs,进而获得该蛋白质家族的最佳Motifs的模型。实验结果表明这种评价策略可用于算法对蛋白质家族Motifs预测结果的评价,还可利用确定的最佳Motifs搜索数据库来预测蛋白质家族中其他的Motifs。

预测Motifs算法的改进评价策略

论文主要研究了如何评价蛋白质家族Motifs预测算法的预测结果,在对传统的算法预测问题分析优化的基础上,制定新的评价策略。工作重点是通过对MEME算法和PKGE算法预测结果的比较分析,计算同一家族中Motifs的敏感性和特异性并比较它们对应的ROC曲线,确定真实的Motifs,进而获得该蛋白质家族的最佳Motifs的模型。实验结果表明这种评价策略可用于算法对蛋白质家族Motifs预测结果的评价,还可利用确定的最佳Motifs搜索数据库来预测蛋白质家族中其他的Motifs。

基于行为motifs的多线程程序抄袭检测方法

软件动态胎记技术是实现混淆对抗的软件抄袭检测的有效手段之一.然而,多线程程序中线程交织的不确定性对其造成了不可忽视的影响;极端情况下,传统动态胎记技术甚至会判定同一个程序与其自身不存在抄袭关系.对此,提出从多线程程序在同一输入下的多条执行轨迹中进行相似部分的识别,并从中抽象出不易受线程交织影响的行为motifs来实现多线程程序的抄袭检测.该方法捕捉程序的动态执行轨迹,经过轨迹修剪、gram匹配以及扩展和抽象,从中提取motifs胎记建模多线程程序的行为;最终,通过衡量motifs胎记的相似性实现程序间潜在抄袭的判定.在一个包含234个不同版本多线程程序的公共数据集上开展的实验表明,motifs胎记是一种可靠的线程感知胎记方法,不仅可有效对抗当下主流的代码混淆技术,相比现有的2种多线程程序抄袭检测方法TreSB(thread-related system call birthmark)和TOB(thread-oblivious birthmark),也体现出更优秀的检测能力.

Cancer bioinformatics:detection of chromatin states, SNP-containing motifs, and functional enrichment modules

In this editorial preface, I briefly r eview cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP- containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.

On the Wisdoms of Human Life Embodied in Robert Frost's Poems-A Brief Analysis of Motifs of Robert Frost's Poems

Robert Frost is one of the famous poets of the 20th century American literature who won the Pulitzer Prize for four times. The reason for his popularity is partially because he employs traditional verse form and iambic pentameter pattern in poem writing, but the most important reason for the reputation of his poems lies in the thematic concern of something universal, such as death and life, love and hate, war and peace, the good and the evil, the wisdom of human life and etc. . A brief analysis will be given in the following text about the wisdoms of human life embodied in Robert Frost's poems from three aspects: 1. Relaxation and responsibility of man. 2. The decisions in life.

PFP-RFSM: Protein fold prediction by using random forests and sequence motifs

Protein tertiary structure is indispensible in revealing the biological functions of proteins. De novo perdition of protein tertiary structure is dependent on protein fold recognition. This study proposes a novel method for prediction of protein fold types which takes primary sequence as input. The proposed method, PFP-RFSM, employs a random forest classifier and a comprehensive feature representation, including both sequence and predicted structure descriptors. Particularly, we propose a method for generation of features based on sequence motifs and those features are firstly employed in protein fold prediction. PFP-RFSM and ten representative protein fold predictors are validated in a benchmark dataset consisting of 27 fold types. Experiments demonstrate that PFP-RFSM outperforms all existing protein fold predictors and improves the success rates by 2%-14%. The results suggest sequence motifs are effective in classification and analysis of protein sequences.

A Photoluminescent Bimetallic Zinc-pyridinedicarboxylate:Diverse Supramolecular Motifs from Distinct Hydrogen Bonds

A cyclic bimetallic metal-organic complex [Zn（C）（H-fmpdc）（H2O）]2·2H2O （fmpdc = 4-（furan-2-yl）-2,6-dimethylpyridine-3,5-dicarboxylate） was synthesized and characterized by single-crystal X-ray analysis. The compound crystallizes in orthorhombic, space group Pbca with a = 12.905（2）, b = 14.774（3）, c = 16.833（3）A, V= 3029.4（10）A^3 Z = 4, Dc = 1.644 g/cm^3, F（000） = 1616, R = 0.0347 and wR = 0.0956 （I 〉 2σ（I））. There exist diverse supramolecular motifs （1-D, 2-D and 3-D） from distinct hydrogen bonds in the crystal structure of the title compound. The furanyl group has obvious contribution to the red-shift in the photoluminescent spectrum of the H2fmpdc ligand. The title compound 1 shows strong photoluminescence with emission maximum at 2 = 402 nm （λex.max = 367 nm）.

Analysis of correlated mutations, stalk motifs, and phylogenetic relationship of the 2009 influenza A virus neuraminidase sequences

The 2009 H1N1 influenza pandemic has attracted worldwide attention. The new virus first emerged in Mexico in April, 2009 was identified as a unique combination of a triple- reassortant swine influenza A virus, composed of genetic information from pigs, hu- mans, birds, and a Eurasian swine influenza virus. Several recent studies on the 2009 H1N1 virus util-ized small datasets to conduct analysis. With new sequences available up to date, we were able to extend the previous research in three areas. The first was finding two networks of co-mutations that may po-tentially affect the current flu-drug binding sites on neuraminidase (NA), one of the two surface proteins of flu virus. The second was discovering a special stalk motif, which was dominant in the H5N1 strains in the past, in the 2009 H1N1 strains for the first time. Due to the high virulence of this motif, the second finding is significant in our current research on 2009 H1N1. The third was updating the phylogenetic an- alysis of current NA sequences of 2009 H1N1 and H5N1, which demonstrated that, in clear contrast to previous findings, the N1 sequences in 2009 are di-verse enough to cover different major branches of the phylogenetic tree of those in previous years. As the novel influenza A H1N1 virus continues to spread globally, our results highlighted the importance of performing timely analysis on the 2009 H1N1 virus.

Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period.

Oscillatory and anti-oscillatory motifs in genetic regulatory networks

Recently, self-sustained oscillatory genetic regulatory networks （GRNs） have attracted significant attention in the biological field. Given a GRN, it is important to anticipate whether the network could generate oscillation with proper parameters, and what the key ingredients for the oscillation are. In this paper the ranges of some function-related parameters which are favorable to sustained oscillations are considered. In particular, some oscillatory motifs appearing with high-frequency in most of the oscillatory GRNs are observed. Moreover, there are some anti-oscillatory motifs which have a strong oscillation repressing effect. Some conclusions analyzing these motif effects and constructing oscillatory GRNs are provided.

Synchronization between different motifs

In this paper, we study the synchronization between different motifs. First, the synchronization between two networks with different topology structures and different dynamical behaviours is studied. With the open-plus-closed-loop（OPCL） method, conditions for two different networks to realize synchronization are given. Then based on the theoretical results achieved, the synchronization between different motifs is studied, which verifies the effectiveness and feasibility of the synchronization scheme.

Dynamics of network motifs in genetic regulatory networks

Network motifs hold a very important status in genetic regulatory networks. This paper aims to analyse the dynamical property of the network motifs in genetic regulatory networks. The main result we obtained is that the dynamical property of a single motif is very simple with only an asymptotically stable equilibrium point, but the combination of several motifs can make more complicated dynamical properties emerge such as limit cycles. The above-mentioned result shows that network motif is a stable substructure in genetic regulatory networks while their combinations make the genetic regulatory network more complicated.

A combined statistical model for multiple motifs search

Transcription factor binding sites （TFBS） play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with definite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite different from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for finding over- represented short sequence segments in different kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from different species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite different, the results show that this model is rather general and sensible.

Phosphatidylinositol transfer proteins: sequence motifs in structural and evolutionary analyses

Phosphatidylinositol transfer proteins (PITP) are a family of monomeric proteins that bind and transfer phosphatidylinositol and phosphatidylcholine between membrane compartments. They are required for production of inositol and diacylglycerol second messengers, and are found in most metazoan organisms. While PITPs are known to carry out crucial cell-signaling roles in many organisms, the structure, function and evolution of the majority of family members remains unexplored;primarily because the ubiquity and diversity of the family thwarts traditional methods of global alignment. To surmount this obstacle, we instead took a novel approach, using MEME and a parsimony-based analysis to create a cladogram of conserved sequence motifs in 56 PITP family proteins from 26 species. In keeping with previous functional annotations, three clades were supported within our evolutionary analysis;two classes of soluble proteins and a class of membrane-associat- ed proteins. By, focusing on conserved regions, the analysis allowed for in depth queries regarding possible functional roles of PITP proteins in both intra- and extra- cellular signaling.

Comparison of Mythological Motifs between Chinese and Western Meteorological Films

Meteorological films generally refer to those that suffer from the influence of natural disasters including meteorological factors,resulting in great violence and casualties.Meteorological disaster films contain a large number of traditional mythological motifs.The meteorological mythology composed of Chinese and Western meteorological mythological motifs is the"meta story"model of modern meteorological films,which establishes the logical starting point of its dissemination.Meanwhile,as a cultural resource,meteorological mythology has also completed the creative transformation in modern times.If the differences between Chinese and Western meteorological films on the motif from the perspective of mythology is compared,it can explore the collective memory and cultural genes of different nations from the original civilization.The motif of punishment in Western meteorological films comes from the collective unconsciousness of human fear of disaster and the collective values of deep deity worship;the motif of disaster management in Chinese meteorological films comes from the realistic tradition of resisting nature and the moralization of myth,which will be a good perspective for comparative study of Chinese and Western meteorological films bearing Chinese and Western cultures.

The Comparison between Random Forest and Support Vector Machine Algorithm for Predicting β-Hairpin Motifs in Proteins

Based on the research of predictingβ-hairpin motifs in proteins, we apply Random Forest and Support Vector Machine algorithm to predictβ-hairpin motifs in ArchDB40 dataset. The motifs with the loop length of 2 to 8 amino acid residues are extracted as research object and thefixed-length pattern of 12 amino acids are selected. When using the same characteristic parameters and the same test method, Random Forest algorithm is more effective than Support Vector Machine. In addition, because of Random Forest algorithm doesn’t produce overfitting phenomenon while the dimension of characteristic parameters is higher, we use Random Forest based on higher dimension characteristic parameters to predictβ-hairpin motifs. The better prediction results are obtained;the overall accuracy and Matthew’s correlation coefficient of 5-fold cross-validation achieve 83.3% and 0.59, respectively.

Synergistic effect of oxygen vacancies and edging/corner-connected MnOs structural motifs in multi-dimensional manganese oxides to enhance OvOCs catalytic oxidation

The structure-activity relationships for vinyl acetate catalytic oxidation are challenging to explore at the atomic scale due to the ambiguity of the structural defect types and sites of manganese oxides.Our work elaborates,at the atomic level,through in-situ experimental and theoretical methods,the synergistic effects of two types of structural defect sites of Vo-e(edge-sharing oxygen)and Vo-c(corner-sharing oxygen)and MnO6 structural motifs of manganese oxides.Multi-dimensional manganese oxides,namely those with corner-connected MnOs structural motifs and Vo-c structural oxygen defect sites,significantly improved the activation of vinyl acetate.Enhancement of enol structure formation,acetate and formate intermediate species,and tautomerism between enol structure and acetaldehyde were detected when oxygen vacancies of manganese oxides were present in combination with corner/edge-connected MnO6.Moreover,the activation of chemical bonds and deep catalytic oxidation of vinyl acetate depend on the presence of a redox couple,surface oxygen species,and weakened Mn-O bonds.It provides a valuable notion for investigating and designing catalytic systems and reaction processes for the purpose of emission reduction and the management of environmental contaminants.