基于SVM的microRNA计算识别方法研究

microRNA(简称miRNA)是近年来发现的一类新的长约19-24nt的内源性非编码RNA,在动物和植物中发挥着重要而广泛的调控功能。它的发现主要有cDNA克隆预测和计算发现两条途径。由于cDNA克隆预测方法受miRNA表达的时间和组织特异性以及表达水平的影响,而计算发现可以弥补其不足,因此miRNA的计算方法受到了广泛的重视。支持向量机作为一种优异的机器学习方法,因其良好的主动学习能力可应用于miRNA的预测。本文利用支持向量机方法对线虫miRNA进行预测,结果表明,该方法具有良好的正确率和敏感性。     

隐马尔可夫模型在生物信息学中的应用

结合DNA序列分析例子,介绍了HMMs与其的解码、估计、学习3个计算问题。综述了HMMs在生物信息学中的应用情况,同时对HMMs在生物信息学中可能的发展方向进行了展望。     

变形假单胞菌吡咯喹啉醌合成基因簇的克隆与分析

从变形假单胞菌JUIM01中克隆到吡咯喹啉醌(PQQ)合成基因簇,阐明了其基因组成和生物学信息。根据已报道的假单胞菌的基因组进行简并引物设计,采用LA-PCR技术克隆变形假单胞菌的PQQ合成基因簇,对克隆的基因片段进行测序并使用生物信息学方法进行综合分析。结果表明:克隆到的基因片段全长为11 659 bp,其中包括pqqF、pqqA、pqqB、pqqC、pqqD、pqqE、pqqM、pqqH和pqqI共9个基因,编码PQQ生物合成的前体短肽PqqA和合成途径的相关酶;这些基因与荧光假单胞菌Pf0-1的PQQ合成基因簇的基因组成类似,相应基因的序列一致性达41%～94%。本研究中首次从变形假单胞菌中克隆到PQQ合成基因簇,并对其进行生物信息学分析,为变形假单胞菌的PQQ生物合成途径和胞内再生机制的研究奠定了基础,进而为提高2KGA的生产强度提供了理论支撑。     

纳米金与细胞相互作用机理的蛋白质组学研究

应用蛋白质组学结合生物信息学方法研究纳米金与人皮肤成纤维细胞(HDF-f )的作用机理.首先采用柠檬酸钠还原氛金酸法制备20nm的纳米金,然后应用MTT法和流式细胞术评价纳米金的细胞毒性及对细胞周期和细胞凋亡的影响.接着应用蛋白质组学技术和生物信息学方法筛选纳米金作用后细胞发生差异表达的蛋白质并进行基因本体论分析.MT...     

State of the art in silico tools for the study of signaling pathways in cancer

In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical events that occur during cellular signaling, as well as the number of interactions within a signaling pathway, make these systems complex to study. In silico resources are tools used to aid the understanding of cellular signaling pathways. Systems approaches have provided a deeper knowledge of diverse biochemical processes, including individual metabolic pathways, signaling networks and genome-scale metabolic networks. In the future, these tools will be enormously valuable, if they continue to be developed in parallel with growing biological knowledge. In this study, an overview of the bioinformatics resources that are currently available for the analysis of biological networks is provided.     

Stereospecific Reduction of Methyl o‐Chlorobenzoylformate at 300 g⋅L−1 without Additional Cofactor using a Carbonyl Reductase Mined from Candida glabrata

In order to search for oxidoreductases suitable for the preparation of methyl (R)‐o‐chloromandelate [(R)‐CMM], the key intermediate for clopidogrel, the homologous proteins of Gre2p were expressed in Escherichia coli, among which CgKR1 showed the most satisfactory activity and stereoselectivity towards methyl o‐chlorobenzoylformate (CBFM). Using the crude enzyme of CgKR1 and glucose dehydrogenase (GDH), as much as 300 g⋅L⁻¹ of CBFM was almost stoichiometrically converted to (R)‐CMM with excellent enantiomeric excess (98.7% ee). More importantly, the reaction could be performed without external addition of an expensive cofactor. The substrate profile indicates that keto esters serve as the most suitable substrate, which was confirmed by gram‐scale preparations. Homology modeling and docking analysis revealed the molecular basis for the high stereoselectivity of CgKR1. These demonstrate not only the feasibility of in silico mining of novel enzymes based on sequence homology but also the applicability of this new reductase for the practical production of optically active (R)‐CMM.     

Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research

Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement strategies. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. Genomic and functional genomic studies in crops still lag far behind similar studies in humans and other animals. In this review, we summarize some useful genomics and bioinformatics resources available to crop scientists. In addition, we also discuss the major challenges and advancements in the “-omics” studies, with an emphasis on their possible impacts on crop stress research and crop improvement.