一种快速准确区分III型、IV型分泌效应蛋白的计算方法

通过Ⅲ型、Ⅳ型、Ⅵ型分泌系统,革兰氏阴性菌可将效应蛋白直接注入宿主体内,并导致宿主感染各种疾病.由于Ⅲ型、Ⅳ型分泌效应蛋白均属非经典分泌蛋白,且它们可能具有相似的序列模体或进化保守性,故两者之间难于区分.基于支持向量机和伪位置特异性得分矩阵,本文提出了一种可快速准确识别革兰氏阴性菌Ⅲ型、Ⅳ型效应蛋白的计算方法.测试集实验结果表明,本方法对Ⅲ型、Ⅳ型效应蛋白具有较好的分类效果,可作为辅助工具用于分泌效应蛋白的进一步研究.     

一种快速准确区分Ⅲ型、Ⅳ型分泌效应蛋白的计算方法

通过Ⅲ型、Ⅳ型、Ⅵ型分泌系统,革兰氏阴性菌可将效应蛋白直接注入宿主体内,并导致宿主感染各种疾病.由于Ⅲ型、Ⅳ型分泌效应蛋白均属非经典分泌蛋白,且它们可能具有相似的序列模体或进化保守性,故两者之间难于区分.基于支持向量机和伪位置特异性得分矩阵,本文提出了一种可快速准确识别革兰氏阴性菌Ⅲ型、Ⅳ型效应蛋白的计算方法.测试集实验结果表明,本方法对Ⅲ型、Ⅳ型效应蛋白具有较好的分类效果,可作为辅助工具用于分泌效应蛋白的进一步研究.     

菜豆根瘤菌CFN42全基因组非经典分泌蛋白的预测与分析

为了深入了解生物固氮的分子机理，利用SecretomeP2.0和SignalP4.1对菜豆根瘤菌CFN42全基因组进行预测，结果发现，在5963个蛋白质中，非经典分泌蛋白596个，约占总数的10%，主要涉及底物转运，毒力侵染，物质代谢等方面。在有功能描述的215个分泌蛋白中，识别了I、III、IV型分泌系统，这些蛋白质在侵染和根瘤发育方面发挥了重要作用；在381个假定蛋白中，通过结构域分析，发现了Tad、Cupin、OmPA和CsbD结构域，含有这些结构域的非经典分泌蛋白可能参与了根瘤菌的宿主专一性。在豆科植物-根瘤菌固氮体系中，非经典分泌蛋白发挥了重要作用。     

植物病原丝状真菌分泌蛋白及CAZymes的研究进展

为了明确对植物病原丝状真菌分泌蛋白及CAZymes进一步研究的方向,笔者对丝状真菌分泌蛋白及CAZymes基本特征、分类情况以及预测方法、功能等方面进行综述。基于前人对于植物病原丝状真菌分泌蛋白以及CAZymes的报道,通过文献计量分析方法、SMART保守结构域和motif分析等方法,对丝状真菌分泌蛋白及CAZymes进行了综合分析,统计发现国内关于分泌蛋白的研究较多,对于CAZymes的研究报道较少,诸多分泌蛋白在病原菌侵染致病过程中发挥的功能如何尚未得到全面解析,有关CAZymes的研究也是如此,预测方法基本上是基于生物信息学分析,尚缺少有力的生物学试验验证证据。因此,今后研究需要进一步完善对于分泌蛋白及CAZymes预测的生物信息学分析工具或算法以及开展生物学试验验证; 通过比较植物病原菌与生防菌之间CAZymes数量及功能差异,明确不同菌之间的共性与特性; 此外,学术界应对丝状真菌中CAZymes的分类开展进一步细化研究,以及对比分析不同亚家族的分布情况,更好地解析CAZymes的功能。     

马铃薯青枯病(Ralstonia solanacearum)质粒基因组分泌蛋白信号肽初步分析

应用SignalP 3.0,TMHMM 2.0,THUMBUP,big-PI,TargetP 1.01,Lipop 1.0,TatP 1.0等7种软件分别对马铃薯青枯病菌Ralstonia solanacearum GMI1000质粒基因组1 681个氨基酸序列进行预测分析.结果表明,该物种质粒基因组分泌蛋白有85个,占其基因组编码蛋白的5.1%.通过对质粒分泌蛋白切割位点信号肽类型分析后发现具Ⅰ型信号肽的分泌蛋白有73个,Ⅱ型的有12个,所有分泌蛋白中具RR-motif信号肽结构的有3个,且均为Ⅰ型信号肽.质粒分泌蛋白中,59个具可预测功能,26个为未知功能蛋白.已知功能的分泌蛋白主要集中于细胞代谢,细胞调控及转运,细胞膜结构等领域.在质粒分泌蛋白中发现3个Ⅲ型信号肽分泌蛋白,该类蛋白是由hip基因编码产生,在植物及动物病原细菌中相当保守,负责将效应蛋白分子转运到寄主细胞中从而产生致病作用.这些功能是该物种在长期进化过程中与环境中各种因子发生互作,相互适应的结果.     

基于全基因组序列的尖孢镰刀菌分泌蛋白预测及其特征分析

尖孢镰刀菌是一种以土壤习居为主要特征的植物病原菌,广泛分布于世界各地,且寄主广泛,能引起豆科、茄科、葫芦科等科100多种植物根腐、茎腐、茎基腐等病害,严重时造成植株萎蔫死亡,严重影响着植物的产量和品质.同时,目前生产上对于该菌的防治多使用甲霜灵·锰锌、多菌灵、百菌清等化学药剂,然而,防治效果不佳,急需开发针对该菌新的作用靶标的药剂.前人已经明确植物病原真菌分泌蛋白在侵染、操控植物等过程中发挥着重要功能,然而,学术界尚未见有关该菌中分泌蛋白的报道.本研究以尖孢镰刀菌菌株(Fusarium oxysporumf.sp.lycopersici 4287)的蛋白序列为基础数据,以分泌蛋白所具有的N-端含有信号肽、不含有跨膜结构域、没有GPI锚定位点、将蛋白分泌在胞外4大特征为依据,利用生物信息学在线分析程序明确该菌中含有778个分泌蛋白,并对上述蛋白开展特征分析,明确上述蛋白的氨基酸长度主要集中在101～400aa、氨基酸组成中以G,T,S,A较多,信号肽长度主要集中在16～21aa、信号肽氨基酸组成中以P,S,A,T,G较多,信号肽切割位点为T-X-T类型.为今后进一步开展尖孢镰刀菌的分泌蛋白功能解析和开发新型药剂靶标提供了重要的理论基础.     

松砂直剪试验中的经典与非经典场量数值分析

采用改进的离散元商业软件PFC2D,通过大量的模拟分析了松散砂土直剪试验中的经典与非经典场量。经典场量包括应力、应变、速度场以及应力路径;非经典场量包括转动场、组构和配位数等。不仅分析了剪切过程中经典与非经典场量的变化规律,而且探讨了两种常量之间的联系。研究结果表明,应力应变状态等经典变量与配位数、组构以及颗粒运动状态之间是相互联系的,非经典变量是经典变量的微观本质体现。     

大鼠呼吸系统表面活性蛋白SP-A和SP-D分泌细胞的分布研究

为了揭示表面活性蛋白SP-A和SP-D分泌细胞在呼吸系统中的分布.使用大鼠鼻腔到肺的各部位组织冰冻切片,进行免疫组织化学染色.结果显示,从鼻腔到小支气管的小颗粒细胞和杯状细胞细呈SP-D阳性;在喉腺和气管腺及其导管上皮呈SP-D强阳性;在细支气管克拉拉细胞和肺Ⅱ型细胞均呈SP-A和SP-D阳性.揭示了在大鼠呼吸系统中SP-D分泌细胞比SP-A分泌细胞更广泛分布,SP-A与SP-D对于维持肺部无菌环境起到重要免疫防御作用.     

RGD-拖丝蛋白基因的构建及其在毕赤酵母中的分泌表达

根据天然拖丝蛋白的高度重复性序列,引入与细胞黏附有关的精氨酸-甘氨酸-天冬氨酸(RGD)三肽序列,以毕赤酵母偏好的密码子化学合成RGD-拖丝蛋白基因单体,通过"头尾相连"的多聚化策略,倍加成16聚体与32聚体基因.分别将这两种多聚体与分泌型表达载体pPIC9K连接,转化毕赤酵母GS115,用G418筛选毕赤酵母重组菌.通过甲醇诱导表达,培养液上清的SDS-PAGE分析表明RGD-重组拖丝蛋白获得分泌型表达.     

结核分枝杆菌分泌蛋白调控巨噬细胞自噬诱导持续性感染

巨噬细胞的自噬作用能够保护宿主抵抗结核分枝杆菌的感染;而持续性感染的MTB(Mycobacterium tuberculosis)可以从自噬体中逃逸或抑制自噬的发生,从而在宿主体内长期存活。尽管相关机制不明确,但胞内存活的MTB分泌蛋白在持续性感染时发挥了重要作用。它可以通过抑制巨噬细胞自噬维持蛋白质稳定性和在胞内长期存活,导致LTBI(latent TB infection)的发生。综述了MTB的四种分泌蛋白(Eis、Pkn G、Sap M和Hsp16. 3)在持续性感染中调节巨噬细胞自噬的作用,可能为发现LTBI新的生物标志物和药物新靶点提供有效思路。     

Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains.

Members of the Frizzled family of seven-pass transmembrane proteins serve as receptors for Wnt signalling proteins. Wnt proteins have important roles in the differentiation and patterning of diverse tissues during animal development, and inappropriate activation of Wnt signalling pathways is a key feature of many cancers. An extracellular cysteine-rich domain (CRD) at the amino terminus of Frizzled proteins binds Wnt proteins, as do homologous domains in soluble proteins-termed secreted Frizzled-related proteins-that function as antagonists of Wnt signalling. Recently, an LDL-receptor-related protein has been shown to function as a co-receptor for Wnt proteins and to bind to a Frizzled CRD in a Wnt-dependent manner. To investigate the molecular nature of the Wnt signalling complex, we determined the crystal structures of the CRDs from mouse Frizzled 8 and secreted Frizzled-related protein 3. Here we show a previously unknown protein fold, and the design and interpretation of CRD mutations that identify a Wnt-binding site. CRDs exhibit a conserved dimer interface that may be a feature of Wnt signalling. This work provides a framework for studies of homologous CRDs in proteins including muscle-specific kinase and Smoothened, a component of the Hedgehog signalling pathway.     

Cytokine-induced pseudopodial protrusion is coupled to tumour cell migration

Pseudopodia protrusion is a prominent feature of actively motile cells in vitro and invading tumour cells in vivo; however, the function and regulation of pseudopodia are poorly understood. Tumour autocrine motility factor (AMF) represents a new class of cytokines which are secreted by tumour cells and embryonic cells and induce random motility in the producer cells or in heterologous cells with appropriate receptors. Here we report that a major effect of this factor is to induce the extension of cell pseudopodia before cell translocation. Using a new method to quantify and isolate pseudopodia, we find that human breast carcinoma cell AMF (at concentrations of 1 nM or below) stimulates random pseudopodia formation in a dose-dependent and time-dependent manner. Anti-AMF antibodies inhibit pseudopodia protrusion and cell motility, showing the importance of pseudopodia formation during locomotion. AMF-stimulated motility and pseudopodia formation occur on a wide variety of adhesive substrata which suggests that certain intrinsic motility events are independent of the attachment mechanism. Induced pseudopodia show a prominent axial actin network in the electron microscope. The number of laminin receptor and fibronectin RGD recognition sites is increased by a factor of 20 in the induced pseudopodia when compared to the average distribution in unstimulated cells. Exploratory pseudopodia regulated by cell-derived motility factors contain receptors for matrix proteins and could serve as 'senseorgans' essential to the process of cell locomotion.     

基于SVM的视频中闪光灯的检测方法

在分析大量实验数据基础上,比较镜头切变、字幕突现或消失、光照突变等与闪光灯具有类似特征的情况后,提出了构造符号特征值的方法.符号特征值能够使得闪光灯与其他类似情况的区别更明显.在符号特征值的基础上提出了构造基于SVM的闪光灯检测器的方法,该检测器在实验中表现良好.     

Secretion of immunoglobulin M assembly intermediates in the presence of reducing agents

There are several demonstrations that misfolded or unassembled proteins are not transported along the secretory pathway, but are retained intracellularly, generally in the endoplasmic reticulum. For instance, B lymphocytes synthesize but do not secrete IgM, and only the polymeric form of IgM is secreted by plasma cells. The C-terminal cysteine of the mu heavy chain of secreted IgM (residue 575) is involved in the intracellular retention of unpolymerized IgM subunits. Here we report that the addition of reducing agents to the culture medium, at concentrations which do not affect cell viability, terminal glycosylation, or retention of proteins in the endoplasmic reticulum through the KDEL mechanism, induces secretion of IgM assembly intermediates by both B and plasma cells. Free joining (J) chains, which are not normally secreted by plasma cells unless as part of IgM or IgA, are also secreted in the presence of reducing agents. We propose a role for free thiol groups in preventing the unhindered transport of proteins through the secretory pathway. Under the scheme, assembly intermediates interact through their thiol groups between themselves and/or with unknown proteins of the endoplasmic reticulum. Such interactions may be prevented by altering the intracellular redox potential or by site-directed mutagenesis of the relevant cysteine residue(s).     

Construction and characteristics of a transformed lepidopteran cell clone expressing baculovirus p35

A transformed cell line was constructed from Mythimna separata cells Ms7311 by lipofection method. TMs7311 cells were generated using a double selection technique involving a selection in the antibiotic Zeocin, followed by a second round of selection by exhibiting cell characterization. A cell clone expressing p35 was obtained with high level of AcMNPV and recombinant proteins. Compared with wild type Ms7311 cells, the cell clone showed increased resistance to Actinamycin D-induced apoptosis and a profound resistance to nutrient development （PBS）. When the cell clone was infected with recombinant baculoviruses expressing secreted alkaline phosphatase （SEAP） and β-galactosidase, expression of the recombinant proteins from TMs7311 cells exceeded that from parental Ms7311 cells. Production of budded virus and occlusion body was significantly higher than that from parental ceils Ms7311.     

基于LVQ神经网络的植物种类识别

提出一种基于学习矢量量化（LVQ）神经网络的计算机植物种类识别新方法. 使用2-D不变矩、 多尺度2-D Gabor滤波器等多种方法分别提取了叶片的几何特征和纹理特征, 应用LVQ神经网络识别植物种类. 实验结果表明, 该方法对植物种类的识别效率较高.     

The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla

Hedgehog (Hh) proteins specify tissue pattern in metazoan embryos by forming gradients that emanate from discrete sites of expression and elicit concentration-dependent cellular differentiation or proliferation responses. Cellular responses to Hh and the movement of Hh through tissues are both precisely regulated, and abnormal Hh signalling has been implicated in human birth defects and cancer. Hh signalling is mediated by its amino-terminal domain (HhN), which is dually lipidated and secreted as part of a multivalent lipoprotein particle. Reception of the HhN signal is modulated by several cell-surface proteins on responding cells, including Patched (Ptc), Smoothened (Smo), Ihog (known as CDO or CDON in mammals) and the vertebrate-specific proteins Hip (also known as Hhip) and Gas1 (ref. 11). Drosophila Ihog and its vertebrate homologues CDO and BOC contain multiple immunoglobulin and fibronectin type III (FNIII) repeats, and the first FNIII repeat of Ihog binds Drosophila HhN in a heparin-dependent manner. Surprisingly, pull-down experiments suggest that a mammalian Sonic hedgehog N-terminal domain (ShhN) binds a non-orthologous FNIII repeat of CDO. Here we report biochemical, biophysical and X-ray structural studies of a complex between ShhN and the third FNIII repeat of CDO. We show that the ShhN-CDO interaction is completely unlike the HhN-Ihog interaction and requires calcium, which binds at a previously undetected site on ShhN. This site is conserved in nearly all Hh proteins and is a hotspot for mediating interactions between ShhN and CDO, Ptc, Hip and Gas1. Mutations in vertebrate Hh proteins causing holoprosencephaly and brachydactyly type A1 map to this calcium-binding site and disrupt interactions with these partners.     

一种改进的基于子带谱熵的语音激活检测方法

语音信号的激活检测(voice activity detection,VAD)是变速率语音编码的关键技术,用来检测通信时是否有语音片存在。在有噪环境下对语音信号的激活检测是非常重要而困难的。对传统子带谱熵算法进行了改进,提出了一种能够用于语音激活检测的新算法。该算法利用语音谱熵和噪声谱熵分布的不同,将信号的数字特征(方差、均值等)与传统子带谱熵相结合,用于区分语音段和非语音段。计算机仿真结果表明,在高斯白噪声环境下,改进后的子带谱熵算法能很好地区分说话人的语音段和非语音段,在某种程度上解决了传统语音激活检测算法结构复杂、参数难调、易受噪声影响等问题。     

Study on interleukin-18 gene transfer into human breast cancer cells to prevent tumorigenicity

To study the effect of interleukin-18 gene transfection on the tumorigenesis of breast cancer cell line Bacp37, human breast cancer cell line Bcap37 were transfected with Lipofectamine and selected by G418. The biological expression of rhIL-18 was tested by RT-PCR and ELISA method; nude mice were injected with Bcap37 cell with or without the hIL-18 gene. The hIL-18 cDNA was successfully integrated into Bcap37 cell; 126.3+/-4.5 pg hIL-18 secreted by one million transduced cells in 24 hours. Nude mice injected with IL-18 gene engineered Bcap37 cell had no tumor growth. These findings indicated that human breast cancer cells were successfully modified by the gene of IL-18 cytokine; the IL-18 gene engineered Bcap37 cells secreted hIL-18 and lost their tumorigenicity. The Bcap37 cells transduced with IL-18 gene may be used as breast cancer vaccine.     

一种基于小波能量分析的目标识别方法

针对坦克目标与主要干扰(金属废弃物和可能出现的水面)的毫米波辐射特性在时域内难以区分的问题,采用小波分解的方法提取毫米波信号在不同尺度上的能量信息,以概貌分量能量和细节集中特征能量层为识别依据,通过统计的方法设计了识别门限.理论分析及仿真结果表明,该方法是有效可行的.