代谢途径数据库简介

复杂的代谢途径分支比线性的基因、基因组和蛋白质序列更难以表示和搜索，介绍了INTERNET上常见的代谢途径数据库，并对其站点、内容和功能以及使用技巧作了简要的阐述。     

Pathway Tools可视化分析水稻基因表达谱

后基因组时代的到来使基因转录组学、蛋白质组学和代谢组学等高通量、多层次的生物研究手段广泛应用于植物科学研究,从海量数据中有效挖掘必要的生物信息成为当今组学研究的瓶颈问题。RiceCyc(http://www.gramene.org/pathway/)及其核心软件Pathway Tools是水稻代谢途径分析的有效工具。通过搜索TIGR(ht-tp://www.tigr.org/tdb/e2k1/osa1/)数据库,用Pathway Tools软件的omics viewer工具将耐盐品种FL478和其不耐盐亲本IR29在盐处理条件相对对照条件下的110个差异表达基因可视化展示在包含362条代谢途径信息的RiceCyc细胞代谢图上,从整体水平上分析了二者对盐胁迫反应的不同。结果表明,在相同的盐胁迫条件下,FL478相对IR29反应明显较快,前者中被诱导的代谢途径主要是能量循环过程如磷酸戊糖途径、糖酵解和三羧酸循环(TCA循环),以及核糖的分解、碳水化合物的利用途径;而后者中表达出现差异的基因主要涉及植物激素的生物合成,细胞结构组分代谢及次级代谢等途径;类黄酮合成途径在IR29中被明显诱导而在FL478中没有变化。     

过氧化物酶和PeroxiBase过氧化物酶数据库

过氧化物酶是存在于生物体中的一大类以过氧化物为电子受体催化底物氧化的酶,在生物体的生命活动中发挥着重要作用.过氧化物酶由多态性丰富的多基因家族所编码,其结构和功能具有多样性.近年来,随着研究和应用的深入,过氧化物酶领域迫切需要建立一个专业的信息交流平台.PeroxiBase数据库收集了大量的过氧化物酶数据,并进行生物信息学加工,为生命科学研究人员免费共享、最大化利用与综合开发过氧化物酶资源搭建了信息平台,在过氧化物酶的研究与应用中发挥着重要作用.     

癌症研究的生物信息学资源

随着癌症研究的发展,生物信息学成为癌症研究的一个非常重要的方法和手段,本文从微阵列芯片数据管理和分析软件、微阵列数据仓库、蛋白质功能预测工具和蛋白质结构预测工具等四个方面介绍癌症研究的生物信息学资源信息,以给相关研究提供帮助.     

植物microRNA的生物信息学预测与分析

microRNAs(miRNAs)是一类广泛存在于真核生物中调控基因转录后表达的非编码小分子RNA。大量研究表明,miRNA在调节多种生物途径中起着重要的作用,采用生物信息学方法预测与分析miRNA是当前发现和鉴定植物miRNA的重要策略之一。研究内容总结了生物信息学预测植物miRNA及其靶基因的方法策略,阐述了生物信息学在植物miRNA研究中的重要作用,为今后的研究奠定了基础。     

基因组尺度分析和代谢工程策略

代谢工程是近年来发展起来的新技术,随着各种组学技术的发展,高通量数据整合方法用于分析细胞的代谢网络,改造代谢途径,以提高目标产物的产量。本文就代谢工程的发展状况,基因组尺度的分析技术,以及代谢工程策略进行了综述。分析了生物信息学和系统生物学方法在代谢途径构建和代谢网络分析中的作用,并就存在的问题和可能的解决途径进行了阐述。     

细胞内信号分子传导的研究进展

近年来有关细胞内信号传导的研究,着重体现在Ca²⁺信号传导途径及相应的蛋白质分子如蛋白激酶C(PKC)、钙调素(CaM)、钙调素激酶Ⅱ(CaMKⅡ),同时也对Ras途径中出现的Vav、Rap、Crk、C3G等蛋白质分子以及cAMP和NF-κB途径作了有益的补充与修改.细胞外信号分子通过以上4种途径及其相互通讯(cross-talk),激活了某些蛋白激酶,调控了基因转录及其他相关功能,其中磷酸化对蛋白激酶及转录因子活性的调节起到了非常重要的作用.     

生物信息学的研究现状及其发展问题的探讨

结合生物信息学产生的历史条件,对生物信息学的定义进行了介绍;归纳总结了现代生物信息表述、采集、储存、传递、检索的表现形式-生物学数据库的分类与分布;着重介绍了生物信息学的主要研究内容和基本的分析方法,阐明了生物信息的分析和解读模式;强调了生物信息学与其他相关学科的相关性,提出了生物信息学发展的一些亟待解决的问题及其相应的解决方案。     

金铁锁转录因子ptMYC2的克隆和生物信息学分析

金铁锁是 “云南白药”等多种中成药的重要组成,其有效成分为三萜皂苷,MYC类转录因子在调节植物三萜类次生代谢积累中有重要作用。为研究ptMYC2 基因在金铁锁三萜皂苷合成代谢途径的调控机制,该研究基于金铁锁转录组测序数据,克隆得到ptMYC2转录因子的两个全长基因; 通过生物信息学软件对两条转录因子的同源性、理化性质、疏水性、跨膜结构、亚细胞定位、结构域、靶基因结合位点等进行初步预测分析。结果表明:两条转录因子所编码的蛋白属于亲水性蛋白,不存在跨膜区域,均是非分泌蛋白质,且不存在信号肽; 两条转录因子的亚细胞定位于细胞核; 结构域分析显示,两个基因都含有bHLH家族结构域; 预测得到金铁锁三萜皂苷合成途径中HMGR、FPS、SE、β-AS等基因的启动子可能存在与MYC2结合的E-box特异性结合位点。该研究结果将为进一步研究ptMYC2基因在金铁锁三萜皂苷合成代谢途径的调节机制奠定基础。     

国内外生物信息学数据库服务新进展

生物信息学是生命科学中最活跃的领域之一. 各类生物信息学数据库在近年不断出现,其规模呈爆炸趋势增长,同时数据结构日趋复杂. 目前生物信息学数据库服务已实现了高度的计算机和网络化. 算法和软件的进步、数据库的一体化、服务器-客户模式的建立使之成为生物、医药、农业等学科的强有力工具. 在国内北京大学物理化学研究所于1996年建立了第一家生物信息学网络服务器. 现已为国内外科学家提供了7万余次服务,在国际上具有一定影响.     

细菌核糖体的拯救机制

蛋白质翻译过程中,很多因素可能导致核糖体在mRNA上熄火,这对细胞的危害很大,因为这不仅占用了核糖体、氨基酸和tRNA,而且还可能产生有害的蛋白质.细菌进化出了多种核糖体拯救机制,释放熄火的核糖体,清除异常的mRNA,以规避毒害,如：① tmRNA·SmpB介导的拯救机制,又称为反式翻译介导的拯救机制|② ArfA(YhdL)介导的拯救机制|③ YaeJ(ArfB)介导的拯救机制.这些机制对于细菌的生理和繁殖都非常重要,但却在真核生物进化过程中消失了,使这些机制有可能成为抗菌药物靶点.本文主要就细菌核糖体的拯救机制做一概述,并对这些机制的应用前景进行了展望.     

The role of hydrogen-bonding interactions in acidic sugar reaction pathways

Previously, theoretical multiple sugar (β-d-xylose and β-d-glucose) reaction pathways were discovered that depended on the initial protonation site on the sugar molecules using Car-Parrinello-based molecular dynamics (CPMD) simulations [Qian, X. H.; Nimlos, M. R.; Davis, M.; Johnson, D. K.; Himmel, M. E. Carbohydr. Res.2005, 340, 2319-2327]. In addition, simulation results showed that water molecules could participate in the sugar reactions, thus altering the reaction pathways. In the present study, the temperature and water density effects on the sugar degradation pathways were investigated with CPMD. We found that changes in both temperature and water density could profoundly affect the mechanisms and pathways. We attributed these effects to both the strength of hydrogen bonding and proton affinity of water.     

Galectin-3 in apoptosis,a novel therapeutic target

During the past decade, extensive progress has been made toward understanding the molecular basis for the regulation of apoptosis. In mammalian cells undergoing apoptosis, two distinct mechanisms or pathways are operated and are triggered by cell death stimuli from intra- or extra-cellular environments, namely the intrinsic or extrinsic pathways, resulting in mitochondrial membrane depolarization. Several lines of evidence from our laboratories and others have indicated that galectin-3 plays an important role in these pathways by binding to various ligands. Here the authors provide a brief discussion on the role of endogenous or extra-cellular galectin-3 in the regulation of apoptosis and how it could be used as a therapeutic target using natural plant products as its functional inhibitors.     

Alternative respiration pathways in Schwanniomyces castellii

By using cytochrome-deficient mutants of Schwanniomyces castellii found previously, we measured the inhibition constants of azide and SHAM—alone or combined—for the different oxidative pathways, in order to determine the more suitable concentrations of inhibitors. This allowed us to measure the real capacity of each pathway. We calculated their affinity for oxygen, and determined that O₂ was preferencially reduced by the cytochromic pathway, then by the SHAM-sensitive pathway, and finally by the SHAM+AA-insensitive pathway.     

Signalling pathways involved in hypoxia‐induced renal fibrosis

Renal fibrosis is the common pathological hallmark of progressive chronic kidney disease (CKD) with diverse aetiologies. Recent researches have highlighted the critical role of hypoxia during the development of renal fibrosis as a final common pathway in end‐stage kidney disease (ESKD), which joints the scientist's attention recently to exploit the molecular mechanism underlying hypoxia‐induced renal fibrogenesis. The scaring formation is a multilayered cellular response and involves the regulation of multiple hypoxia‐inducible signalling pathways and complex interactive networks. Therefore, this review will focus on the signalling pathways involved in hypoxia‐induced pathogenesis of interstitial fibrosis, including pathways mediated by HIF, TGF‐β, Notch, PKC/ERK, PI3K/Akt, NF‐κB, Ang II/ROS and microRNAs. Roles of molecules such as IL‐6, IL‐18, KIM‐1 and ADO are also reviewed. A comprehensive understanding of the roles that these hypoxia‐responsive signalling pathways and molecules play in the context of renal fibrosis will provide a foundation towards revealing the underlying mechanisms of progression of CKD and identifying novel therapeutic targets. In the future, promising new effective therapy against hypoxic effects may be successfully translated into the clinic to alleviate renal fibrosis and inhibit the progression of CKD.     

Genes acting in longevity-related pathways in the endoparasitoid,Pteromalus puparum

Among insects, lifespans vary over a broad range, from the short-lived mayflies to the 17-year periodical cicadas. Generally, lifespans are determined by a phase in life, the reproductive lifespan, which varies among species. Numerous pathways, such as the insulin/insulin-like growth factor signaling pathway, the target of rapamycin pathway and the mitogen-activated protein kinase/extracellular signal-regulated kinases pathways, influence aging and lifespan. Components of these pathways were identified as lifespan-related genes, including genes mediating growth, metabolism, development, resistance, and other processes. Many age-related genes have been discovered in fruit flies, honeybees, and ants among other insect species. Studies of insect aging and longevity can help understand insect biology and develop new pest management technologies. In this paper, we interrogated the new Pteromalus puparum genome, from which we predicted 133 putative lifespan-related genes based on their homology with known lifespan-related genes of Drosophila melanogaster. These genes function in five signaling pathways and three physiological processes. The conserved domain structures of these genes were predicted and their expression patterns were analyzed. Amino acid sequence alignments and domain structure analysis indicate that most components remain conserved across at least six insect orders. The data in this paper will facilitate future work on parasitoid lifespans, which may have economic value in biocontrol programs.     

Signaling roadmap to epithelial–mesenchymal transition in pterygium,TWIST1 centralized

Pterygium as a complex disease shares common features with other malignant cells in its onset recurrence and especially epithelial–mesenchymal transition (EMT) transition. Although using different approaches including conjunctival autografts, amniotic membrane, radiotherapy, mitomycin C (MMC) has shown promising insights in the inhibition of pterygium recurrence, it needs to be investigated in more details in molecular pathways to present adjuvant target therapy. In this study, we aimed to evaluate the expression of and then illustrate the role of signaling pathways on EMT in pterygium. Using real-time polymerase chain reaction, the twist-related protein 1 (TWIST1) expression was compared in primary pterygium and normal conjunctiva. This study assessed the mRNA expression, as well as the association between the clinicopathological indices and the gene expression level. The expression level of TWIST1 was overexpressed in 36% of our cohort ( n = 76). There was a significant positive correlation between recurrence with grade T, grade V and a significant negative correlation with growth activity. Our vast literature review on different signaling pathways in pterygium showed that EMT has centralization role in recurrence of this disease. Our data confirmed that EMT is important in the recurrence of pterygium samples and different signaling pathways end up activating the EMT markers. It is suggested to evaluate the environmental factors and their correlation with molecular markers to select favorable treatment for this kind of diseases.     

Ganoderma lucidum polysaccharide exerts anti-tumor activity via MAPK pathways in HL-60 acute leukemia cells

In this study, we investigated the anti-tumor activity both in vitro and in vivo of a polysaccharide obtained from Ganoderma lucidum on HL-60 acute myeloid leukemia cells, and focused on its targeting effect on mitogen-activated protein kinase (MAPK) pathways. It was found by the methods such as western blot and flow cytometry (FCM), that G. lucidum polysaccharide (GLP) blocked the extracellular signal-regulated kinase/MAPK signaling pathway, simultaneously activated p38 and JNK MAPK pathways, and therefore regulated their downstream genes and proteins, including p53, c-myc, c-fos, c-jun, Bcl-2, Bax, cleaved caspase-3 and cyclin D1. As a result, cycle arrest and apoptosis of HL-60 cells were induced. Therefore, GLP exerted anti-tumor activity via MAPK pathways in HL-60 acute leukemia cells.     

Genomic pathways database and biological data management

In this paper, we discuss the properties of biological data and challenges it poses for data management, and argue that, in order to meet the data management requirements for 'digital biology', careful integration of the existing technologies and the development of new data management techniques for biological data are needed. Based on this premise, we present PathCase: Case Pathways Database System. PathCase is an integrated set of software tools for modelling, storing, analysing, visualizing and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (i) genomic information integrated with other biological data and presented starting from pathways; (ii) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (iii) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels and to pose exploratory queries; (iv) a wide range of different types of queries including, 'path' and 'neighbourhood queries' and graphical visualization of query outputs; and (v) an implementation that allows for web (XML)-based dissemination of query outputs (i.e. pathways data in BIOPAX format) to researchers in the community, giving them control on the use of pathways data.