面向同源蛋白质探测的一种新型混合深度学习模型

根据蛋白质氨基酸链探测其同源蛋白质,进而预测蛋白质的功能,是生物信息学研究领域的一个重要挑战,也是众多生物医学研究领域的基础研究内容,有着重要的科研价值和广泛的应用需求。其研究难点在于:(1)如何学习对同源蛋白质预测有效、有用的蛋白质特征信息;(2)如何更好地运用蛋白质特征信息,实现同源蛋白质的探测与识别。为了解决同源蛋白质探测与识别研究中的关键难点,本文提出一种基于混合深度学习架构的同源蛋白质探测与识别模型(HDLM-PHP)。通过采用统一的"管道式"深度学习架构,将蛋白质特征学习和探测识别统一为一个整体,提高同源蛋白质探测与识别的效能。采用多组并行的深度卷积神经网络,学习蛋白质的各种属性信息,以期获得丰富的待检测蛋白质和靶蛋白质的高级相关性特征,并通过全连接方式使用多层RBM结构融合和精炼这些相关性特征为全局相关性特征。通过统一的深度网络连接方式,以探测和识别任务为导向,学习到对于同源蛋白质预测最有效、最全面的蛋白质特征信息。在标准数据集SCOPe上,对所提模型进行性能与效率评测,结果表明:本文提出的模型能有效地学习到符合任务导向的蛋白质特征数据,提升同源蛋白质探测与识别的准确度和召回率,优于现有的模型和算法。     

一类高阶自共轭微分算子谱的定量分析

定量研究了一类高阶自共轭微分算子的谱,得到了这类算子的本质谱充满了正实轴,而在负半轴上只有离散谱.     

温度对生命体寿命的影响

综述了温度对生命体寿命的作用，包括温度参与调节特定基因表达和细胞信号传导通路，温度对能量代谢、氧化还原水平、免疫功能和热量限制的影响。介绍了一种将温度系数引入死亡率定律的假设，以此计算温度与寿命之间的关系，为探究温度对寿命的直接影响提供参考和依据。     

家蚕非编码RNA Bm-152功能初探

Bm-152是前期研究中发现的一个在家蚕丝腺中高表达的非编码RNA.采用实时荧光定量PCR技术对Bm-152在家蚕5龄到预蛹期不同发育天数丝腺中的表达谱进行检测.同时,在个体中过表达Bm-152,检测Bm-152可能参与的信号通路.结果显示,Bm-152在家蚕5龄幼虫丝腺发育过程中无明显的变化规律,但在吐丝第1天表达量较高,随后表达量又下降.通过在血淋巴中注射2μg piggyBac[A3-EGFP-A3-Bm-152]过表达载体,48h后发现Bm-152在丝腺组织中无明显过表达,但在非丝腺组织中可实现明显过表达,且表达量上调1.66倍;蜕皮激素信号通路基因Usp在非丝腺组织中上调1.95倍,E75A在非丝腺组织中上调2.26倍,保幼激素信号通路基因Met在非丝腺组织中上调1.79倍.表明非编码RNA Bm-152可能通过蜕皮激素和保幼激素信号通路参与家蚕发育,该结果为进一步探索Bm-152的功能提供了方向.     

由“气韵生动”谈审美活动的符号化显现

审美活动的抽象性特质集中体现在其特殊的形式化特征的显现上。而作为形式化内涵的载体，“符号”的特殊地位就愈发凸显出来。“气韵生动”，这个诞生于我国传统绘画技法当中的审美标尺，就是形式之美的高级实现表述，其可指的对象早已超出绘画的范畴。关于其自身信息传递方式及与我们主体融合对话所呈现出的审美体验的探究，具有非常重要的意义。     

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。     

表现与表达 从计算机辅助制图到辅助设计——以3DMAX为例

通过长期以来对3DMAX的操作、实践、研究与探索,得出了计算机若干辅助生成设计的方法。介绍这些方法,是希望能为计算机辅助设计教学与应用提供一条新的思路,让更多的读者了解普通建模软件不仅可以再现方案——辅助制图,而且能够介入方案设计,进行创作表达。辅助设计的本质是思维方式的转变。