PBNA： An Improved Probabilistic Biological Network Alignment Method

Biological network alignment is an important research topic in the field of bioinformatics. Nowadays almost every existing alignment method is designed to solve the deterministic biological network alignment problem.However, it is worth noting that interactions in biological networks, like many other processes in the biological realm,are probabilistic events. Therefore, more accurate and better results can be obtained if biological networks are characterized by probabilistic graphs. This probabilistic information, however, increases difficulties in analyzing networks and only few methods can handle the probabilistic information. Therefore, in this paper, an improved Probabilistic Biological Network Alignment（PBNA） is proposed. Based on Iso Rank, PBNA is able to use the probabilistic information. Furthermore, PBNA takes advantages of Contributor and Probability Generating Function（PGF） to improve the accuracy of node similarity value and reduce the computational complexity of random variables in similarity matrix. Experimental results on dataset of the Protein-Protein Interaction（PPI） networks provided by Todor demonstrate that PBNA can produce some alignment results that ignored by the deterministic methods, and produce more biologically meaningful alignment results than Iso Rank does in most of the cases based on the Gene Ontology Consistency（GOC） measure. Compared with Prob method, which is designed exactly to solve the probabilistic alignment problem, PBNA can obtain more biologically meaningful mappings in less time.     

基于全基因组测序的粘绿木霉Gv29-8中分泌蛋白预测

粘绿木霉Gv29-8作为木霉属中重要的生防菌之一,对该菌分泌蛋白进行预测及其特征进行明确具有重要的理论意义。利用SignalP、ProtComp等预测程序对该菌中12427条蛋白质序列进行分泌蛋白找寻,并对上述分泌蛋白的氨基酸分布、信号肽长度大小及切割位点等性质进行分析。粘绿木霉含有分泌蛋白为377个,其氨基酸长度、信号肽长度与植物病原菌不同;信号肽切割位点属于A-X-A类型,与其他已经报道的植物病原真菌、卵菌中分泌蛋白信号肽切割位点一致。     

For whom the bell tolls? DING proteins in health and disease

DING proteins, identified mainly by their eponymous N-terminal sequences, are ubiquitous in living organisms. Amongst bacteria, they are common in pseudomonads, and have been characterised with respect to genetics and structure. They form part of a wider family of phosphate-binding proteins, with emerging roles in phosphate acquisition and pathogenicity. Many DING proteins have been isolated in eukaryotes, in which they have been associated with very diverse biological activities, often in the context of possible signalling roles. Disease states in which DING proteins have been implicated include rheumatoid arthritis, lithiasis, atherosclerosis, some tumours and tumour-associated cachexia, and bacterial and viral adherence. Complete genetic and structural characterisation of eukaryotic DING genes and proteins is still lacking, though the phosphate-binding site seems to be conserved. Whether as bacterial proteins related to bacterial pathogenicity, or as eukaryotic components of biochemical signalling systems, DING proteins require further study. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

糖类遗传与生命起源

从遗传学角度探讨了糖类与生命起源，讨论了遗传学上的再认识，提出糖类在遗传学上扮演着重要、核心的角色、糖类是生命起源物质，基因是糖类衍生物。生命诞生过程可能是：先有糖类、然后有氨基酸和碱基；磷酸及其盐类既是生命物质的组成部分、也是催化剂，阳光或地热为能源，于是诞生了基因。生命体是分子相互作用、有序组合、自我调控的耗散体系。     

SCP-2基因的表达调控研究进展

固醇转运蛋白(SCP-2)是广泛存在于脊椎动物和无脊椎动物中的非特异性脂转运蛋白.任何影响固醇转运蛋白基因表达的因素都会影响甾类激素的合成,进而影响生物体的发育.目前对该基因的转录调控研究较少,主要集中在哺乳动物.环境、激素、转录因子等对SCP-2基因的表达调控均有影响,对SCP-2基因作为害虫防治靶标的可能性进行了初步的探讨.C/EBP蛋白作为调控Sl SCPx基因表达的转录因子,可以调控Sl SCPx基因的表达.推测了C/EBP蛋白成为新的害虫防治的靶标的可能.     

蛋白质二级结构预测概率图模型的改进

蛋白质二级结构与蛋白质三级结构及蛋白质功能密切相关,是生物信息学研究的热点,其中概率图模型隐马尔可夫算法(HMM)是该领域研究的重要工具。但是在实际应用中,存在着HMM训练下溢、不同训练集的效果差异较大及参数优化困难等问题。对预测蛋白质二级结构时HMM遇到的训练下溢问题提出了改进方案;首次提出8-状态HMM来预测蛋白质二级结构,并且将参数B改进成为包含状态转移信息的三维参数;为了改进最优HMM模型的确定方法,用每个样本分别对初始HMM模型进行训练,得到一系列新的模型,然后对这些新模型的参数求均值,将求得的均值作为最优模型的参数。这些改进方法提高了HMM预测蛋白质二级结构的准确率,为HMM的进一步优化打下良好的基础。     

环境污染物PFOS可致人脑微血管内皮细胞骨架蛋白改变

目的:探讨全氟辛烷磺酰基化合物(PFOS)引起的人脑微血管内皮细胞(HBMEC)骨架蛋白(F-actin)排列变化.方法:培养正常的人脑毛细血管内皮细胞,不同浓度PFOS作用30分钟,利用免疫荧光染色的方法检测细胞骨架蛋白F-actin的变化.结果:PFOS可使细胞骨架蛋白F-actin发生重排,这与PFOS的浓度有关.     

Serine/threonine protein phosphatases in DNA damage response

DNA damage response (DDR) is among the most important of the mechanisms that maintain genome stability which, when destabilized, predisposes organs to cancer. Reversible phosphorylation mediated by protein kinases and protein phosphatases regulates most, if not all, cellular activities, including DDR. Protein kinase inhibitors have become the main focus of targeted therapy and anticancer drug development. However, our limited knowledge of protein phosphatase function is compromising our capacity to develop therapeutic agents against phosphatases. In this review, we summarize the roles of serine/threonine protein phosphatases involved in DDR and propose that in situ dephosphorylation of phosphoproteins by protein phosphatases, instead of proteasome-mediated degradation of phosphoproteins, is mainly employed by cells.     

抗栓胰岛素原钙调素重组融合蛋白表达条件的摸索

以无活性人胰岛素原突变体为分子支架,在C肽位置嵌合特异拮抗血小板GPⅡbⅢa受体的去整合素活性结构位点序列,构建嵌合人胰岛素原突变体.该突变体相对分子质量大小为7.0×103,与钙调素的C末端融合后形成新型重组融合蛋白质,相对分子质量为24.7×103.构建该重组融合蛋白质的大肠杆菌BL21(DE3)表达系统,尝试在大肠杆菌表达体系中,对该重组融合蛋白质进行高效表达.结果表明,该重组融合蛋白质的表达率约占菌体全蛋白的30%,优化后的表达条件为25℃,50μmol.L-1诱导表达16 h.     

斜纹夜蛾核多角体病毒感染甜菜夜蛾细胞的研究

 研究发现斜纹夜蛾核多角体病毒（Spodoptera litura nucleopolyhedrovirus,SpltNPV）不能成功感染同属甜菜夜蛾（S. exigua,Se）昆虫,为深入研究SpltNPV在离体Se301细胞中的感染进程以及病毒感染失败的原因,对感染后Se301细胞进行DNA复制、病毒基因转录以及病毒蛋白表达等检测。结果显示被感染的Se301细胞中病毒完成了DNA的复制和病毒早、晚期基因转录,但检测不到极晚期基因多角体基因（polyhedrin）的表达,病毒的蛋白表达受阻从而影响了病毒完成复制周期。 研究发现病毒蛋白表达受阻是SpltNPV在Se301细胞中无法形成子代病毒,完成整个病毒复制的主要原因,这为深入研究其感染失败机理奠定了坚实基础。