Docking of Human Band 3 Anion Transporter Proteins with Their Plasmodium falciparum Interactors Based on Short Linear Motifs

Plasmodium (P.) falciparum is a pathogen that causes severe forms of malaria. Protein interactions have been shown to occur between P. falciparum and human erythrocytes in human blood. The Band 3 Anion Transporter (B3AT) protein is considered the main invasive pathway for the parasite in erythrocytes that causes clinical symptoms for malaria in humans. The interactions between P. falciparum parasites and erythrocytes along this receptor have previously been explored. Short linear motifs (SLIMs) are short linear mediator sequences that involve several biological processes, acting as mediators of protein interactions identifiable by computational tools such as SLiMFinder. For a given protein, the identification of SLIMs allows predicting its interactors. Using the SLIMs approach, protein-protein interaction network analyses between P. falciparum and its human host, were used to identify a tryptophan-rich protein, A5K5E5_PLAVS as an essential interactor of B3AT. To better understand the interaction mechanism, a guided protein-protein docking approach based on SLIM motifs was performed for human B3AT and A5K5E5_PLAVS. The highlights of this important interaction between P. falciparum and its human host have the potential to pave the way to identify new therapeutic candidates.

C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 pathway as a therapeutic target and regulatory mechanism for spinal cord injury

Spinal cord injury involves non-reversible damage to the central nervous system that is characterized by limited regenerative capacity and secondary inflammatory damage.The expression of the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis exhibits significant differences before and after injury.Recent studies have revealed that the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis is closely associated with secondary inflammatory responses and the recruitment of immune cells following spinal cord injury,suggesting that this axis is a novel target and regulatory control point for treatment.This review comprehensively examines the therapeutic strategies targeting the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis,along with the regenerative and repair mechanisms linking the axis to spinal cord injury.Additionally,we summarize the upstream and downstream inflammatory signaling pathways associated with spinal cord injury and the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis.This review primarily elaborates on therapeutic strategies that target the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis and the latest progress of research on antagonistic drugs,along with the approaches used to exploit new therapeutic targets within the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis and the development of targeted drugs.Nevertheless,there are presently no clinical studies relating to spinal cord injury that are focusing on the C-C motif chemokine ligand 2/C-C motif chemokine receptor 2 axis.This review aims to provide new ideas and therapeutic strategies for the future treatment of spinal cord injury.

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。

基于Web Service技术的MotifSampler集成设计

针对MotifSampler生物信息处理程序需要高性能计算机运算及特定系统平台问题,设计实现了基于Web Service技术的分布式处理系统。采用JAVA、JSP、SOAP、XML等技术及三层网络框架实现了MotifSampler程序的运算及数据解析服务。经过测试及实际应用证明该系统实现了高效的跨平台服务,并能提供给远程用户准确的基序分析结果及数据解析结果。

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.

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）.

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.

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.

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.

MORN motifs in plant PIPKs are involved in the regulation of subcellular localization and phospholipid binding

Multiple repeats of membrane occupation and recognition nexus (MORN) motifs were detected in plant phosphatidylinositl monophosphate kinase (PIPK), a key enzyme in PI-signaling pathway. Structural analysis indicates that all the MORN motifs (with varied numbers at ranges of 7-9), which shared high homologies to those of animal ones, were located at N-terminus and sequentially arranged, except those of OsPIPK1 and AtPIPK7, in which the last MORN motif was separated others by an -100 amino-acid "island" region, revealing the presence of two kinds of MORN arrangements in plant PIPKs. Through employing a yeast-based SMET (sequence of membrane-targeting) system, the MORN motifs were shown being able to target the fusion proteins to cell plasma membrane, which were further confirmed by expression of fused MORN-GFP proteins. Further detailed analysis via deletion studies indicated the MORN motifs in OsPIPK 1, together with the 104 amino-acid "island" region are involved in the regulation of differential subcellular localization, i.e. plasma membrane or nucleus, of the fused proteins. Fat Western blot analysis of the recombinant MORN polypeptide, expressed in Escherichia coli, showed that MORN motifs could strongly bind to PA and relatively slightly to PI4P and PI(4,5)P2. These results provide informative hints on mechanisms of subcellular localization, as well as regulation of substrate binding, of plant PIPKs.

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.

Motifs and Impediments for the Harmonization of Accounting Regulations for Small and Medium-Sized Companies in the EU

Small and medium-sized companies in most EU countries form a considerable share in the total number of companies and are also an important development impeller of the entire economy. Therefore, one of the most essential goals of accounting authorities in the EU is accomplishing the harmonization of accounting regulations for these companies. In this paper, the author have discussed and explained the main motifs and impediments for this harmonization. One of the main motifs is a big span and complexity of international standards of financial reports which is allowed and even prescribed in many countries. Some of the main impediments are a lack of uniformity as far as criteria for classification of small and medium-sized companies according to size are concerned as well as the determining of limitations up to which the requirements in accounting standards for small and medium-sized companies should be set.

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 Cooperative Approach for the Extraction of Protein Motifs

By integrating the concept of cooperative approach, an extension of the fast annealing coevolutionary algorithm is presented in this paper. It outperformed the original algorithm in the domain of function optimization, especially in terms of convergence rate. It was also applied to a real optimization problem, protein motif extraction. And a satisfactory result has been obtained with the accuracy of prediction achieving 67.0%, which is in agreement with the result in the PROSITE database.

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.