线粒体呼吸链复合体Ⅰ

线粒体呼吸链复合体Ⅰ（简称复合体Ⅰ）是呼吸链电子传递的起始复合体,作为电子传递过程的限速酶,复合体Ⅰ的分子量远大于其余的四个呼吸链复合体。复合体Ⅰ相关的疾病发生除了与40余个复合体Ⅰ组成亚基的突变相关外,还同参与其组装的多个组装因子存在密切联系。该文对复合体I的结构以及参与调控复合体Ⅰ组装的各类组装因子进行了综述,旨在为全面了解复合体Ⅰ相关疾病的发生提供具体参考。     

线粒体呼吸链复合体Ⅰ

线粒体呼吸链复合体Ⅰ(简称复合体Ⅰ)是呼吸链电子传递的起始复合体,作为电子传递过程的限速酶,复合体Ⅰ的分子量远大于其余的四个呼吸链复合体。复合体Ⅰ相关的疾病发生除了与40余个复合体Ⅰ组成亚基的突变相关外,还同参与其组装的多个组装因子存在密切联系。该文对复合体I的结构以及参与调控复合体Ⅰ组装的各类组装因子进行了综述,旨在为全面了解复合体Ⅰ相关疾病的发生提供具体参考。     

SSCP和HMA方法在马MHC-Ⅰ类分子基因多态性研究中的应用

文章使用SSCP和HMA两种基于聚丙烯酰胺凝胶电泳的方法对马MHC-Ⅰ类分子基因多态性进行了分析.在应用SSCP法进行分析时,尽管经过实验条件优化,仍未得到对MHC-Ⅰ基因理想的分离效果,提示该方法对分离多态性较高的基因有一定局限性.在对HMA法用参考标准DNA对影响DNA分子构象的温度和变性剂浓度等实验条件进行优化后,获得了对马MHC-Ⅰ类分子基因较好的分离效果.6、7、8、9和10号马的样本在相对应泳道上分别出现了6、5、6、5和7个条带.从凝胶中进行DNA条带回收后克隆测序的结果表明,这一方法可以有效地分离高度多态性的MHC-Ⅰ类分子基因.     

MHC-Ⅰ在特发性炎性肌病患者肌肉组织中表达的研究

目的:探讨MHC-Ⅰ在IIM发生发展中的作用和机制.方法:对收集的15例IIM患者进行肌肉活检,观察其病理结构的改变、MHC-Ⅰ在患者肌肉组织中的分布表达情况,并与非炎症性肌病患者作对照.结果:1.在IIM患者肌肉组织中明确有MHC-Ⅰ类分子的表达,其阳性率为100%;2.虽有6例IIM患者肌纤维中没有明显的炎性细胞浸润,但患者还是出现了临床症状且肌酶异常;3.MHC-Ⅰ在IIM肌肉组织中的表达强弱程度与病人肌酶呈正相关性,且具有统计学意义(P＜0.05).结论:MHC-Ⅰ类分子可以作为IIM早期诊断的指标之一,其表达强弱与患者病情程度有相关性.     

核孔复合体的动态组装

核孔是介导所有大分子入核出核的唯一通道。在整个生命活动中,核孔复合体的组成蛋白总是处于动态变化中。核孔复合体的动态组装改变了核质转运状态,并最终改变了细胞的功能。     

核孔复合体的结构组装及其生理功能

核孔复合体(nuclear pore complex,NPC)介导了大分子物质在细胞质与细胞核之间的穿梭运动。NPC定位于核膜,形成一个疏水通道,使得蛋白质等大分子物质与转运受体结合,进行跨膜转运。这种经核孔复合体进行的跨核膜转运在细胞增殖、细胞分化以及个体发育等生命活动中发挥了重要的生理功能。     

菠菜能量转化复合体的人工组装

从菠菜叶绿体中分离了H~+-ATP酶复合体,其SDS-聚丙烯酰胺凝胶电泳呈九条亚单位带,为纯度较高的酶复合体。将H~+-ATP酶复合体重组于人工膜(脂质体)上,表现出PiATP交换活力。Mg~(++)-ATP酶活力也明显提高。并表现对DCCD,寡霉素的敏感性。 重组H~+-ATP酶复合体表现有ATP诱导的H~+转移。但脂质体也出现类似现象,为此对以pH改变为标准的检测方法提出商榷。     

自组装短肽对角膜碱烧伤的作用

目的研究自组装短肽材料1%RADAl6-I水溶液对大鼠和兔角膜碱烧伤的作用.方法用1 mol/L NaOH溶液造SD大鼠和兔角膜碱烧伤模型,左眼每口滴加短肽水凝胶10μ1(2次/d),右眼为空白对照.在烧伤后的不同时间段(7、10、14d)处死大鼠,第7 d处死兔,取角膜行HE染色,光学显微镜观察结果.结果短肽水凝胶治疗组角膜上皮重生较快,皮下纤维排列较好,空白对照组皮下仍有较大空洞,皮下纤维排列紊乱,说明短肽材料能促进角膜恢复.     

融合自组装双亲短肽对重组过氧化氢酶酶学性质的影响

【目的】利用融合自组装双亲短肽策略对源自枯草芽孢杆菌(Bacillus subtilis)的过氧化氢酶Kat A进行改性,以强化重组过氧化氢酶在工业中的应用适应性。【方法】将自组装双亲短肽S1vw通过连接肽PT-linker融合在Kat A的N端,构建重组质粒p HT254-S1vw-PT-kat A,将其与携带天然酶基因的p HT254-kat A分别转入枯草芽孢杆菌WB800N中进行分泌表达,之后将分离纯化得到的纯酶进行酶学性质研究。【结果】成功构建出工程菌并将胞外粗酶液通过乙醇沉淀、DEAE阴离子交换层析、疏水层析和凝胶过滤层析4步纯化,最终获得电泳纯的重组酶蛋白。酶学性质研究结果显示,融合酶S1vw-PT-Kat A和天然酶Kat A的最适反应温度均为30°C,最适反应p H值均为11.0。然而,融合酶在p H 12.0下孵育30 min的相对酶活为77.3%,是相同处理条件下天然酶相对酶活的14.9倍,在65°C和70°C下孵育30 min的相对酶活分别为19.8%和17.5%,是相同处理条件下天然酶相对酶活的1.8倍和1.7倍。此外,融合酶在4°C储存14 d后相对酶活为8...     

针对线粒体复合体Ⅰ基因突变的Leigh综合征细胞模型的基因治疗研究

该研究旨在探讨转导酵母NDI1基因对线粒体ND1基因突变的Leigh综合征细胞模型的恢复效果,从而为线粒体复合体I基因突变所致Leigh综合征的基因治疗提供研究基础。已知线粒体复合体Ⅰ的ND1基因的m.3697G>A突变是Leigh综合征的致病突变之一。该研究采用已构建的携带该ND1基因突变的胞质杂合细胞作为线粒体复合体I基因突变的Leigh综合征细胞模型,将酵母NDI1基因的重组慢病毒转导至该细胞模型中表达NDI1蛋白(即酵母复合体I),检测NDI1蛋白对线粒体复合体I各方面功能的恢复效果。酵母NDI1基因转导该细胞模型后能高效表达并定位于线粒体。转导酵母NDI1基因可以恢复复合体I酶活性(外源酵母复合体Ⅰ的补偿)、线粒体有关的氧耗水平、线粒体偶联效率、线粒体有关的ATP水平,并且可以降低线粒体氧化应激水平、线粒体自噬水平。在线粒体复合体Ⅰ基因突变的Leigh综合征细胞模型中,酵母复合体Ⅰ可以替代性补偿线粒体的氧化磷酸化功能,并且可以缓解线粒体的氧化应激和自噬状态。该研究结果可以为线粒体复合体Ⅰ基因突变所致Leigh综合征的基因治疗提供研究基础。     

Dynamics of Major Histocompatibility Complex Class I Association with the Human Peptide-loading Complex

Although the human peptide-loading complex (PLC) is required for optimal major histocompatibility complex class I (MHC I) antigen presentation, its composition is still incompletely understood. The ratio of the transporter associated with antigen processing (TAP) and MHC I to tapasin, which is responsible for MHC I recruitment and peptide binding optimization, is particularly critical for modeling of the PLC. Here, we characterized the stoichiometry of the human PLC using both biophysical and biochemical approaches. By means of single-molecule pulldown (SiMPull), we determined a TAP/tapasin ratio of 1:2, consistent with previous studies of insect-cell microsomes, rat-human chimeric cells, and HeLa cells expressing truncated TAP subunits. We also report that the tapasin/MHC I ratio varies, with the PLC population comprising both 2:1 and 2:2 complexes, based on mutational and co-precipitation studies. The MHC I-saturated PLC may be particularly prevalent among peptide-selective alleles, such as HLA-C4. Additionally, MHC I association with the PLC increases when its peptide supply is reduced by inhibiting the proteasome or by blocking TAP-mediated peptide transport using viral inhibitors. Taken together, our results indicate that the composition of the human PLC varies under normal conditions and dynamically adapts to alterations in peptide supply that may arise during viral infection. These findings improve our understanding of the quality control of MHC I peptide loading and may aid the structural and functional modeling of the human PLC.     

Assembly and Function of the Major Histocompatibility Complex (MHC) I Peptide-loading Complex Are Conserved Across Higher Vertebrates

Antigen presentation to cytotoxic T lymphocytes via major histocompatibility complex class I (MHC I) molecules depends on the heterodimeric transporter associated with antigen processing (TAP). For efficient antigen supply to MHC I molecules in the ER, TAP assembles a macromolecular peptide-loading complex (PLC) by recruiting tapasin. In evolution, TAP appeared together with effector cells of adaptive immunity at the transition from jawless to jawed vertebrates and diversified further within the jawed vertebrates. Here, we compared TAP function and interaction with tapasin of a range of species within two classes of jawed vertebrates. We found that avian and mammalian TAP1 and TAP2 form heterodimeric complexes across taxa. Moreover, the extra N-terminal domain TMD0 of mammalian TAP1 and TAP2 as well as avian TAP2 recruits tapasin. Strikingly, however, only TAP1 and TAP2 from the same taxon can form a functional heterodimeric translocation complex. These data demonstrate that the dimerization interface between TAP1 and TAP2 and the tapasin docking sites for PLC assembly are conserved in evolution, whereas elements of antigen translocation diverged later in evolution and are thus taxon specific.     

Polypeptide Components of Telomere Nucleoprotein Complex

Chromosome telomeres of humans and many model organisms contain a structure called a t-loop, which is maintained by TERF, TINF2, Pot1, and other proteins. Increase in TERF1 concentration prevents telomere elongation by telomerase. Decrease in TERF2 concentration (preventing t-loop formation) is accompanied by blockade of proliferation and appearance of other signs of cellular senescence in experiments. Natural regulation of TERF1 involves tankyrase, ATM protein kinase, and fluctuations of the protein level across a cell cycle. The telomere nucleoprotein complex also interacts with various polypeptide macromolecules (e.g., Sir2, PinX1, Rap1, Ku, Rad50/Mre11/Nbs1) responsible for heterochromatin formation, modulation of telomerase activity, DNA repair, and signaling to other cell compartments about telomere state. Study of structure and functioning of telomere nucleoprotein complex may contribute to elucidation of poorly understood mechanisms of aging and processes of tumor transformation of cells.     

RNA诱导沉默复合体中的生物大分子及其装配

在RNA干扰机制中,双链RNA诱导同源RNA降解的过程依赖于RNA诱导沉默复合体（RISC）的活性。RISC由Dicer酶,Argonaute蛋白,siRNA等多种生物大分子装配而成,对这些大分子的结构和功能进行深入细致的研究,有助于进一步了解RISC的形成过程、作用方式,以及阐明整个RNAi过程的作用机制。研究表明,RISC中的Dicer具有RNaseIII结构域,在RNAi的起始阶段负责催化siRNA的产生,在RISC装配过程中起稳定RISC中间体结构和功能的作用;Argonaute蛋白是RISC中的核心蛋白,有PAZ和PIWI两个主要的结构域,前者为siRNA的传递提供结合位点,后者是RISC中的酶切割活性中心;siRNA是RISC完成特异性切割作用的向导,在成熟的RISC中虽然只包含siRNA的一条链,但siRNA在RISC形成过程中的双链结构是保证RNAi效应的决定因素。尽管RISC中还存在其他一些功能未知的蛋白质,但在RISC组分结构及功能研究方面取得的进展为建立一个可能的RISC装配模型提供了理论基础。     

Control Centrality and Hierarchical Structure in Complex Networks

We introduce the concept of control centrality to quantify the ability of a single node to control a directed weighted network. We calculate the distribution of control centrality for several real networks and find that it is mainly determined by the network’s degree distribution. We show that in a directed network without loops the control centrality of a node is uniquely determined by its layer index or topological position in the underlying hierarchical structure of the network. Inspired by the deep relation between control centrality and hierarchical structure in a general directed network, we design an efficient attack strategy against the controllability of malicious networks.     

Jerarca: Efficient Analysis of Complex Networks Using Hierarchical Clustering

Background

How to extract useful information from complex biological networks is a major goal in many fields, especially in genomics and proteomics. We have shown in several works that iterative hierarchical clustering, as implemented in the UVCluster program, is a powerful tool to analyze many of those networks. However, the amount of computation time required to perform UVCluster analyses imposed significant limitations to its use.

Methodology/Principal Findings

We describe the suite Jerarca, designed to efficiently convert networks of interacting units into dendrograms by means of iterative hierarchical clustering. Jerarca is divided into three main sections. First, weighted distances among units are computed using up to three different approaches: a more efficient version of UVCluster and two new, related algorithms called RCluster and SCluster. Second, Jerarca builds dendrograms based on those distances, using well-known phylogenetic algorithms, such as UPGMA or Neighbor-Joining. Finally, Jerarca provides optimal partitions of the trees using statistical criteria based on the distribution of intra- and intercluster connections. Outputs compatible with the phylogenetic software MEGA and the Cytoscape package are generated, allowing the results to be easily visualized.

Conclusions/Significance

The four main advantages of Jerarca in respect to UVCluster are: 1) Improved speed of a novel UVCluster algorithm; 2) Additional, alternative strategies to perform iterative hierarchical clustering; 3) Automatic evaluation of the hierarchical trees to obtain optimal partitions; and, 4) Outputs compatible with popular software such as MEGA and Cytoscape.     

综合性状及其分量的多元条件分析

提出基于混合线性模型的多元条件分析方法,用于分析复杂综合性状的分量对其目标性状的贡献。定义了贡献率和贡献遗传效应两个概念,贡献率测定给定分量性状的遗传变异对目标性状的贡献比率,贡献遗传效应衡量给定分量性状的遗传效应对目标性状的贡献值。运用所提出的新方法分析了棉花籽棉产量的3个分量对产量的贡献。     

De Novo Evolution of Complex, Global and Hierarchical Gene Regulatory Mechanisms

Gene regulatory networks exhibit complex, hierarchical features such as global regulation and network motifs. There is much debate about whether the evolutionary origins of such features are the results of adaptation, or the by-products of non-adaptive processes of DNA replication. The lack of availability of gene regulatory networks of ancestor species on evolutionary timescales makes this a particularly difficult problem to resolve. Digital organisms, however, can be used to provide a complete evolutionary record of lineages. We use a biologically realistic evolutionary model that includes gene expression, regulation, metabolism and biosynthesis, to investigate the evolution of complex function in gene regulatory networks. We discover that: (i) network architecture and complexity evolve in response to environmental complexity, (ii) global gene regulation is selected for in complex environments, (iii) complex, inter-connected, hierarchical structures evolve in stages, with energy regulation preceding stress responses, and stress responses preceding growth rate adaptations and (iv) robustness of evolved models to mutations depends on hierarchical level: energy regulation and stress responses tend not to be robust to mutations, whereas growth rate adaptations are more robust and non-lethal when mutated. These results highlight the adaptive and incremental evolution of complex biological networks, and the value and potential of studying realistic in silico evolutionary systems as a way of understanding living systems.