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.

基于Motif的图采样算法

图采样通过对图数据进行约简操作,获得比原图的规模更小的图结构,进而服务于图谱分析、图可视化等下游任务.现有的图采样算法侧重于保留图中显著的结构特征而忽略了节点属性,导致采样图在许多下游任务如频繁模式挖掘等,难以取得预期效果.为此,提出基于Motif的节点有偏采样算法(Motif-Based Node Biased Sampling,MNBS),利用频繁Motif结构重新定义图中节点的重要性,随后进行有偏节点采样,实现融合节点属性与结构特征的采样.为了快速识别频繁Motif模式,设计了具有“提前终止”特性的Motif模式快速发现算法(Fast Motif-Pattern Discovery,FMPD),能高效且准确地发现Motif模式以支持图采样.实验表明,MNBS采样算法在多项指标上优于其他基线算法,其对数归一化累积组相关性指标平均降低0.54,使用包含“提前终止”特性策略的FMPD算法的时间消耗和内存消耗比基线算法分别降低56.1%和29.8%.

基于3D-motif法的刮研表面形貌表征

针对刮研表面微观特性和功能机理研究中缺少表面形貌量化表征方法的问题,采用3D-motif法对刮研表面形貌进行表征。使用LI-3型接触式三维表面形貌测量仪对刮研表面进行测量,并利用三维点云数据生成刮研表面的二维灰度图像。然后,根据3D-motif法中集水盆地的定义,采用分水岭算法对刮研表面的灰度图像进行motif分割与合并。以不同精度等级的刮研表面的整体纹理区域motif分割结果为对象,定义了特征显著度并提取计算了刮研表面在2种不同面积尺度(25 mm^(2)和0.25 mm^(2))上的深度、面积、方向角、各向异性率、扁平系数和特征显著度等6项motif参数。结合部分motif参数的分布情况和motif数量的变化趋势,从形貌特征的尺寸和形态两个方面对刮研表面进行了表征和分析,实现了以较少参数完整表征刮研表面的三维形貌。研究结果可为后续刮研表面微观特性的深入分析提供理论基础。

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.

Multi-layer network embedding on scc-based network with motif

Interconnection of all things challenges the traditional communication methods,and Semantic Communication and Computing(SCC)will become new solutions.It is a challenging task to accurately detect,extract,and represent semantic information in the research of SCC-based networks.In previous research,researchers usually use convolution to extract the feature information of a graph and perform the corresponding task of node classification.However,the content of semantic information is quite complex.Although graph convolutional neural networks provide an effective solution for node classification tasks,due to their limitations in representing multiple relational patterns and not recognizing and analyzing higher-order local structures,the extracted feature information is subject to varying degrees of loss.Therefore,this paper extends from a single-layer topology network to a multi-layer heterogeneous topology network.The Bidirectional Encoder Representations from Transformers(BERT)training word vector is introduced to extract the semantic features in the network,and the existing graph neural network is improved by combining the higher-order local feature module of the network model representation network.A multi-layer network embedding algorithm on SCC-based networks with motifs is proposed to complete the task of end-to-end node classification.We verify the effectiveness of the algorithm on a real multi-layer heterogeneous network.

The Classic Shaping of Typical Female Images by Mulan Motif in Historical Times-Historical Review and Textual Sorting of the Motif

The image of Mulan is well known to the public as an important symbol in the dissemination of Chinese excellent traditional culture.This paper aims to summarise the mother-title from traditional canonical texts,to explore the content and value of sustainable IP development,and to study a large number of derivatives with the image of Mulan as the mother-title,based on the wide circulation of the prototype of the mother-title“The Poem of Mulan”(木兰辞)and the positive values conveyed by the content.Through the processing and imagination of scholars and writers on the mother text in the past generations,the image of Mulan has gradually formed a relatively stable cultural communication theme in the process of dissemination in China’s historical period,and many adaptations with international influence based on the mother title of Mulan have emerged in the foreign dissemination,so through the combing and summarisation of the textual works of various periods both at home and abroad,we will dig out the textual transmission of the mother title of Mulan,which is representative of the mother title of China’s excellent traditional culture,and the development of the Chinese spiritual core.The Development of the Chinese Spiritual Kernel.This paper adopts research methods such as documentary evidence method and discourse analysis to show the textual flow of Mulan’s parent theme in a more diversified form.

Targeting neuronal PAS domain protein 2 and KN motif/ankyrin repeat domains 1:Advances in type 2 diabetes therapy

This editorial summarizes the latest literature on the roles of neuronal PAS domain protein 2 and KN motif/ankyrin repeat domain 1 in type 2 diabetes(T2D).We highlight their involvement inβ-cell dysfunction,explore their potential as therapeutic targets,and discuss the implications for new treatment strategies.We offer valuable insights into relevant gene regulation and cellular mechanisms relevant for the targeted management of T2D.

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 。

基于motif连通性的社区搜索方法

社区搜索的目标是从数据图中得到包含查询顶点的紧密子图,在社会学、生物学等领域有着广泛应用。针对现有基于子图连通性的社区模型的基础连通结构都是完全连通图,无法满足实际应用中用户对社区结构多样性的需求的问题,提出一种基于motif连通性的社区搜索方法,其中包括基于motif连通性的社区(MCC)模型以及两个相应的社区搜索算法——MPCS(Motif-Processed Community Search)算法和基于MP-index的社区搜索算法。MCC模型可以协助用户自由指定社区的基础连通结构,MPCS算法可以用来解决MCC的搜索问题。此外,提出两个分别针对motif实例搜索过程及所属社区判断过程的剪枝优化技术。最后,设计了MP-index以避免社区搜索过程中的冗余遍历操作。在多个真实数据集上进行实验的结果表明:剪枝优化可以使MPCS算法的耗时减少60%~85%,而基于MP-index的社区搜索算法相较于加入剪枝优化的MPCS算法,效率提升普遍达到了2~3个数量级。可见,所提方法在商品推荐和社交网络等问题上有着实际应用价值。

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.