与分子对话——分子信息学及其应用

设计合成具有预期功能和实用价值的复杂分子体系,在今天已经不再是幻想 有效地获取和利用分子信息学方面的数据,有助于加快化学、生物学和材料科学等领域的科研创新 作为分子科学中的一个重要部分。

化学组学及其信息学探索研究和初步应用

提出诸如烷烯炔组、醇酚醚组、醛酮醌组、生物碱组、抗生素组、黄酮[醇]组、多寡肽组、萜组、合成药物组、天然药物组、环境激素组、代谢物质组、环境激素组等化学组学新颖概念,犹如基因组、蛋白质组、糖组等生物组学概念一样,对于化学研究与应用具有重要意义,通过大量物质组分子多样性结构表达和化学性能预测,阐述了化学组学方法与技术的广阔应用前景。

黄瓜PP2-A1蛋白的生物信息学分析

韧皮部蛋白2(PP2)是植物特异性的韧皮部蛋白,通过参与植物调控其细胞内基因表达水平和产物活性来应对自然界中的各种胁迫,对于维持植物株体形态、体内物质运转和保护愈合植物伤口有重要意义。以前期克隆得到的黄瓜(Cucumis sativus) PP2-A1蛋白序列为对象,利用生物信息学方法,对黄瓜PP2-A1蛋白序列进行生物学功能分析。结果表明,黄瓜PP2-A1蛋白具有亲水性,比较不稳定,半衰期短,无信号肽段,没有跨膜结构,是定位在胞质的非分泌蛋白;结合对其二级结构和三级结构的预测分析,得出PP2-A1是以无规则卷曲和延伸链为主的片层结构;构建PP2的系统发育树,发现其与香瓜亲缘关系最近,同时预测其结构功能域,发现其具有1个典型的PP2结构功能域。

生物信息资源的应用与二次开发

概述了利用计算机及分子生物学信息资源进行文献检索、序列分析、蛋白质分子结构模建、药物设计等工作的方法。

基于中药分子机制的生物信息学在线分析归芪白术方辅助治疗胃癌的作用机制

目的利用中药分子机制的生物信息学在线分析工具(BATMAN-TCM)预测中药复方归芪白术方潜在的分子靶点,并基于京都基因与基因组百科全书(KEGG)通路进行富集分析,探讨归芪白术方辅助治疗胃癌的作用机制。方法将归芪白术方中的7味药物按照君、臣、佐、使依次输入BATMAN-TCM,检索筛选归芪白术方活性成分及对应的潜在靶点。结果君、臣、佐、使共有10个目标基因;君、臣、佐、使配伍均富集的生物学通路共47条,其中有多条与胃癌相关的信号通路;君、臣、佐、使配伍均富集的疾病共49种,其中与胃癌相关的疾病有非特异性癌症、肿瘤、炎症、疼痛等。结论在归芪白术方中发现了多个与胃癌相关的作用靶点、KEGG通路及作用疾病,为临床治疗胃癌及今后进一步深入研究归芪白术方辅助治疗胃癌的作用机制提供了思路。

物理学新技术与生命科学前沿研究

物理学新技术对现代生命科学取得的巨大成就发挥了极其重要的作用 ;生命科学和医学的需要又促进了物理新技术和仪器的发展 .本文介绍了在生命科学一些前沿研究领域中应用物理学新技术取得的成果 ,并展望了 2 1世纪的发展前景 ,包括 :单分子动力学、结构生物学、纳米技术和生物技术、分子细胞信息学、脑科学和神经信息学 .

基于深度学习的全新药物分子设计:原理、工具与实践

利用深度学习方法设计具有全新结构的药物分子可以突破传统计算机辅助药物设计的技术瓶颈,已经成为药物设计新技术研究的前沿,在药物研发实践中展现了巨大潜力。本文从深度学习驱动的全新分子设计的基本原理出发,简要介绍了深度分子生成技术和计算工具,分析了若干代表性成功案例,最后对该技术的未来发展方向和应用前景进行了展望。本综述将为新技术研究提供思路,为应用该技术开展新药研发实践提供借鉴。

Identification of a Novel snoRNA Gene in Arabidopsis thaliana L.

[ Objective] To identify a novel snoRNA gene in Arabidopsis thalianan. [ Method ] Genome sequence of Arabidopsis thalianan was screened by using bioinformatics methods, and the sequence structure, organization form and function of typical candidate gene were analyzed. [ Result] The identified snR95 box H/ACA snoRNA had conservative component and structural features of box C/D snoRNA family, possessed two more than 10 nt long rRNA antisense elements. The result revealed that the novel snoRNA is a partial counterpart of the rice Z270, named box C/D snoRNA -AthZ270. [ Conclusion ] Z270 snoRNA in Arabidopsis thalianan has different function with common snoRNA.

日本扩大ERATO研究计划

报道说日本ERATO研究计划补充了四项新的子项计划．即《人脑活动过程动态研究》（领头组织一人智力活动实验室．负责执行人三雄河田）．《光敏遗传学》（领头组织一大阪大学．负责执行人美久井上教授）．《分子信息学》（领头组织一东京大学科学研究系．负责执行人成之横山教授）．仓脊椎神经组织》（领头组织一京都大学医学系．负责执行人章一郎筑田教授）。每个子项研究期限规定为五年。为了实现子项研究计划．每个负责执行人将挑选15名日本和其他国家的青年学者。

Cloning and Identification of A New Na^+/H^+ Antiporter Gene ZmSOS1 in Maize(Zea mays L.)

[ Objective] The study aimed to clone and identify Na^＋/H^＋ antiporter genes in maize, and provided the information for characterizing the function of such genes in abiotic stress tolerance of maize. Method The in silico cloning, RT-PCR, and bioinformatics analysis were used in this study. Result By in sifico cloning, a plasma membrane Na^＋/H^＋ antiporter gene, named as ZmSOS1 （EMBL accession No. BN001309）, was cloned from maize （ Zea mays L. ）. ZmSOS1 has an open reading frame （ORF） of 3 411 bp which encoded a protein of 1 136 amino acids. By multiple sequence alignment analysis, it showed the predicated peptide of ZmSOS1 were 61% and 82% identities in amino acids to the plasma membrane Na^＋/H^＋ antiporter AtSOS1 and OsSOS1, respectively. The RT-PCR analysis revealed that ZmSOS1 could be significantly up-regulated by salt stress, which indicated ZmSOS1 might play a role in salt tolerance of maize. Conclusion ZmSOS1 is a putative plasma membrane Na^＋/H^＋ antiporter gene and may play a role in abiotic stress tolerance of maize.

Asymmetrical Quantum Encryption Protocol Based on Quantum Search Algorithm

Quantum cryptography and quantum search algorithm are considered as two important research topics in quantum information science.An asymmetrical quantum encryption protocol based on the properties of quantum one-way function and quantum search algorithm is proposed.Depending on the no-cloning theorem and trapdoor one-way functions of the publickey,the eavesdropper cannot extract any private-information from the public-keys and the ciphertext.Introducing key-generation randomized logarithm to improve security of our proposed protocol,i.e.,one privatekey corresponds to an exponential number of public-keys.Using unitary operations and the single photon measurement,secret messages can be directly sent from the sender to the receiver.The security of the proposed protocol is proved that it is informationtheoretically secure.Furthermore,compared the symmetrical Quantum key distribution,the proposed protocol is not only efficient to reduce additional communication,but also easier to carry out in practice,because no entangled photons and complex operations are required.

Bioinformatics Analysis of VOZ Gene Family in Populus trichocarpa

To explore the biological characteristics of Vascular plant One-Zinc finger(VOZ)gene family in Populus trichocarpa,this paper used bioinformatics to analyze the nucleotide sequences and protein sequences of four members of VOZ gene family of P.trichocarpa.The results showed that the four PtVOZ genes of P.trichocarpa were evenly distributed on four chromosomes.The length and molecular weight of the encoded protein were almost the same,and the subcellular localization was located in the nucleus,belonging to the unstable acidic hydrophilic non-aliphatic soluble protein.The gene structures were all in the patterns of 4 exons and 3 introns.The proportion order of PtVOZ transcription factor secondary structure components was random coil>αhelix>extended strand>βsheets,and the tertiary structure was very similar in spatial conformation.The phylogenetic tree analysis showed that P.trichocarpa was more closely related to VOZ transcription factors of dicotyledons.The four PtVOZ genes of P.trichocarpa were expressed in seedlings and different tissues,but there were differences in the expression intensity.This study provided a necessary theoretical basis for further exploring the molecular biological function of PtVOZ genes.

Identification and bioinformatics analysis of micro RNAs from the sporophyte and gametophyte of Pyropia haitanensis

Pyropia haitanensis(T.J.Chang et B.F.Zheng) N.Kikuchi et M.Miyata( Porphyra haitanensis) is an economically important genus that is cultured widely in China.P.haitanensis is cultured on a larger scale than Pyropia yezoensis,making up an important part of the total production of cultivated Pyropia in China.However,the majority of molecular mechanisms underlying the physiological processes of P.haitanensis remain unknown.P.haitanensis could utilize inorganic carbon and the sporophytes of P.haitanensis might possess a PCK-type C 4-like carbon-fixation pathway.To identify micro RNAs and their probable roles in sporophyte and gametophyte development,we constructed and sequenced small RNA libraries from sporophytes and gametophytes of P.haitanensis.Five micro RNAs were identified that shared no sequence homology with known micro RNAs.Our results indicated that P.haitanensis might posses a complex s RNA processing system in which the novel micro RNAs act as important regulators of the development of different generations of P.haitanensis.

Polyploid organisms

Polyploids are organisms with three or more complete chromosome sets. Polyploidization is widespread in plants and animals, and is an important mechanism of speciation. Genome sequencing and related molecular systematics and bioinformatics studies on plants and animals in recent years support the view that species have been shaped by whole genome duplication during evolution. The stability of polyploids depends on rapid genome recombination and changes in gene expression after formation. The formation of polyploids and subsequent diploidization are important aspects in long-term evolution. Polyploids can be formed in various ways. Among them, hybrid organisms formed by distant hybridization could produce unreduced gametes and thus generate offspring with doubled chromosomes, which is a fast, efficient method of polyploidization. The formation of fertile polyploids not only promoted the interflow of genetic materials among species and enriched the species diversity, but also laid the foundation for polyploidy breeding. The study of polyploids has both important theoretical significance and valuable applications. The production and application of polyploidy breeding have brought remarkable economic and social benefits.

Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures

Microarray and deep sequencing technologies have provided unprecedented opportunities for mapping genome mutations,RNA transcripts,transcription factor binding,and histone modifications at high resolution at the genome-wide level.This has revolutionized the way in which transcriptomes,regulatory networks and epigenetic regulations have been studied and large amounts of heterogeneous data have been generated.Although efforts are being made to integrate these datasets unbiasedly and efficiently,how best to do this still remains a challenge.Here we review major impacts of high-throughput genome-wide data generation,their relevance to human diseases,and various bioinformatics approaches for data integration.Finally,we provide a case study on inflammatory diseases.

The molecular dynamics of neural metabolism during the action potential

Neural information processing is tightly coupled to both energy consumption and derivation from substrates.In this study,the energy function of the neuron during the action potential(AP)is described and analyzed.It has been observed that energy consumption during the AP does not match predictions of the conventional theory of neural energy dynamics.On short time scales,neural energy expenditure shifts between positive and negative phases.During the AP,the energy source switches from neuronal stores(positive expenditure or net consumption)to exploitation of external substrates,specifically the glucose and oxygen carried in cerebral blood(the negative consumption phase).Based on the idea of reductionism,this paper demonstrates how ion channels,membrane pumps and transporters,ionotropic and metabotropic receptor signaling pathways,astrocyte glycolysis and the production lactate,and the glutamate-glutamine cycle all serve to relate cerebral blood flow and neuronal metabolism to neuronal activity and so maintain neuronal energy charge during the AP.

Rapid progress of DNA replication studies in Archaea,the third domain of life

Archaea,the third domain of life,are interesting organisms to study from the aspects of molecular and evolutionary biology.Archaeal cells have a unicellular ultrastructure without a nucleus,resembling bacterial cells,but the proteins involved in genetic information processing pathways,including DNA replication,transcription,and translation,share strong similarities with those of Eukaryota.Therefore,archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells.Moreover,the hyperthermophilic archaea provide very stable proteins,which are especially useful for the isolation of replisomal multicomplexes,to analyze their structures and functions.This review focuses on the history,current status,and future directions of archaeal DNA replication studies.