A Cooperative Approach for the Extraction of Protein Motifs

Many problems in chemistry depend on the ability to identify the global solution of a function, which can be a minimum or a maximum. Because the number of local optima grows exponentially with the complexity of the problems, finding the global optimum tur…     

Cooperative Hairpin Dimers for Recognition of DNA by Pyrrole–Imidazole Polyamides

A doubling of the length of binding site for the same size of ligand is achieved by the title compound by formation of a cooperative hairpin dimer on binding to DNA (depicted schematically below) . The binding affinity and selectivity are unaffected by this new binding pattern. Circles represent heterocyclic rings, and diamonds and curved lines represent β-alanine and (R)-2,4-diaminobutyric acid residues, respectively.     

Aptamer-Mediated Reversible Transactivation of Gene Expression by Light

The investigation and manipulation of cellular processes with subcellular resolution requires non-invasive tools with spatiotemporal precision and reversibility. Building on the interaction of the photoreceptor PAL with an RNA aptamer, we describe a variation of the CRISPR/dCAS9 system for light-controlled activation of gene expression. This platform significantly reduces the coding space required for genetic manipulation and provides a strong on-switch with almost no residual activity in the dark. It adds to the current set of modular building blocks for synthetic biological circuit design and is broadly applicable.     

基于Gene Ontology的表达谱与基因功能相似性的相关性研究

聚类是芯片数据分析中被广泛使用的方法。未知基因的功能通常通过其与已知基因在不同生物状态下具有表达相似性来进行预测。然而，还未有人就这种通过表达相似性来进行功能注释的方法的可靠性进行评估。本文利用Gene Ontology对表达相似性和基因功能相似性的相关关系进行了全面的研究。研究表明，尽管表达谱的相似性和基因功能相似性之间有一定的依赖关系，但相关性较弱。在Gene Ontology的三大类中，相对生物过程和分子功能，基因表达谱的相似性更有助于细胞组分的注释。本文的研究结果对于基因功能的预测有一定的指导意义。     

Cooperative conformational changes in globular proteins

In globular proteins, the complicated steric arrangement of the polypeptide chain is determined by several interdependent cooperative interactions. These macromolecules are capable of reacting to changes in the environmental conditions such as temperature and pressure or the concentration of a wide range of compounds by changing their conformation and hence their biological and chemical properties. They are thus suitable for regulation processes or information storage in solution with a wide range of time constants. Environmental effects of this kind can be followed and explained in part at the molecular level by investigation of the time-dependent reversible unfolding of a number of proteins that can be described to a good approximation by a strongly cooperative “all-or-none” transition between two states.     

化学修饰的寡核营酸作为基因表达的反义抑制剂

本文综述了反义寡核普酸作为墓因表达抑制剂的原理和作用机理,作为人类疾病治疗剂的寡核普酸必须具备的性质。介绍了化学修饰的寡核普酸的种类、性质和目前已达到的研究及应用水平。     

aprE基因表达的分子生物学和微量热法分析

利用分子生物学方法(SDS-PAGE和酶活检测法)未检测到所克隆的aprE基因在大肠杆菌中的表达产物(碱性蛋白酶), 而微量热法检测结果发现: 重组菌株的生长代谢产热曲线之间存在明显的差异. 根据这些差异, 分析了该基因的上、下游调控序列对该基因在大肠杆菌中表达的重要作用, 从而进一步对该基因进行了亚克隆, 得到了生物学方法可检测到的表达产物. 由此推测, 微量热技术有可能为检测外源基因表达及其调控, 以及为指导进一步基因工程操作提供一种新的快速灵敏的技术和方法.     

Clustering of time-course gene expression data using functional data analysis

Clustering of gene expression data collected across time is receiving growing attention in the biological literature since time-course experiments allow one to understand dynamic biological processes and identify genes governed by the same processes. It is believed that genes demonstrating similar expression profiles over time might give an informative insight into how underlying biological mechanisms work. In this paper, we propose a method based on functional data analysis (FNDA) to cluster time-dependent gene expression profiles. Consideration of clustering problems using the FNDA setting provides ways to take time dependency into account by using basis function expansion to describe the partially observed curves. We also discuss how to choose the number of bases in the basis function expansion in FNDA. A synthetic cycle data and a real data are used to demonstrate the proposed method and some comparisons between the proposed and existing approaches using the adjusted Rand indices are made.     

SPAP2基因的克隆、融合表达及分离纯化

本文构建的表达载体pGex-2T-SPAP2CT在大肠杆菌中表达出可融性蛋白, 其分子量为46 000, 经纯化后得到产率为10%、 纯度大于90%的GST-SPAP2CT蛋白.     

HZSM-5分子筛中邻近酸中心上的协同催化作用

总结了HZSM-5分子筛中邻近的酸中心协同催化作用的研究进展, 包括布朗斯特酸(B酸)和路易斯酸 (L酸)的协同催化、 B酸和B酸的协同催化作用. 综述了通过多种表征手段下协同催化作用机理的研究进展, 以及实验与理论计算相结合并相互验证的研究结果, 对邻近酸中心协同作用下反应分子的共同吸附、 活化与转化路径的特点进行了分析与总结, 提出了对邻近酸中心协同催化作用进行深入研究的关键科学问题和可能的解决方案.     

化合物结构特征与其基因表达信息的互补性研究

化合物分子指纹在化合物相似性比较、生物芯片技术在分子标记识别中都有着重要的应用, 因而受到广泛的重视. 但是由于这两个研究对象依传统的观点, 分属于化学信息学和生物信息学两个不同的研究领域, 因此一直未能在同一研究对象中同时得到应用. 近年来, 小分子刺激的生物芯片数据的大量出现, 使得联合化合物的结构特征及其基因表达谱信息共同的用于药物筛选成为可能. 为此, 根据本质和外延互补的哲学思想, 提出了综合运用这两种数据来共同描述化合物的新方法. 通过(1)只利用化合物分子指纹, (2)只利用化合物基因表达谱信息和(3)前面两种方法互补等三种方法在化合物相似性比较的研究中, 发现本文提出的互补方法比前两种方法的查询结果更准确: (1)使结构和功能两方面均相似的化合物之间的相似性更高, (2)并且能有效使那些仅在某一方面表现非常特殊的化合物能够暴露出来, 而得到有效地排除. 本研究给化学信息者和生物信息者重新审视以往的数据, 联合致力于药物的筛选提供了线索. 化合物分子指纹(本质)和基因表达谱(外延)的互补原理则为药物的筛选提供更有效的依据, 并最终加快药物的研发进程.     

基于基因表达式编程预测醛类化合物急性毒性

对大鼠急性毒性的定量构效关系模型提出了一种新的算法:基因表达式编程,其核心是种群的进化.种群由染色体构成,染色体是由结构正确的基因组合而成,包含头部和尾部,对种群中染色体的基因进行特定的操作便形成了进化.本实验以启发式方法筛选的8个关键描述符为建模参数,应用基因表达式编程建立了88种醛类化合物分子结构对大鼠急性毒性的定量构关系模型,模型交互检验相关系数为0.947,均方误差为0.037.通过与支持向量机方法的比较表明:基因表达式编程建立的定量构效关系模型能够更好地预测醛类化合物对大鼠急性毒性的半效致死量,且具有较强的稳定性.     

Cross‐Platform DNA Encoding for Single‐Cell Imaging of Gene Expression

Integration of imaging data across different molecular target types can provide in‐depth insight into cell physiology and pathology, but remains challenging owing to poor compatibility between target‐type‐specific labeling methods. We show that cross‐platform imaging analysis can be readily achieved through DNA encoding of molecular targets, which translates the molecular identity of various target types into a uniform in situ array of ssDNA tags for subsequent labeling with complementary imaging probes. The concept was demonstrated through multiplexed imaging of mRNAs and their corresponding proteins with multicolor quantum dots. The results reveal heterogeneity of cell transfection with siRNA and outline disparity in RNA interference (RNAi) kinetics at the level of both the mRNA and the encoded protein.     

K-means Find Density Peaks in Molecular Conformation Clustering

Performing cluster analysis on molecular conformation is an important way to find the representative conformation in the molecular dynamics trajectories. Usually, it is a critical step for interpreting complex conformational changes or interaction mechanisms. As one of the density-based clustering algorithms, find density peaks (FDP) is an accurate and reasonable candidate for the molecular conformation clustering. However, facing the rapidly increasing simulation length due to the increase in computing power, the low computing efficiency of FDP limits its application potential. Here we propose a marginal extension to FDP named K-means find density peaks (KFDP) to solve the mass source consuming problem. In KFDP, the points are initially clustered by a high efficiency clustering algorithm, such as K-means. Cluster centers are defined as typical points with a weight which represents the cluster size. Then, the weighted typical points are clustered again by FDP, and then are refined as core, boundary, and redefined halo points. In this way, KFDP has comparable accuracy as FDP but its computational complexity is reduced from O\begin{document}$(n^2)$\end{document} to O\begin{document}$(n)$\end{document}. We apply and test our KFDP method to the trajectory data of multiple small proteins in terms of torsion angle, secondary structure or contact map. The comparing results with K-means and density-based spatial clustering of applications with noise show the validation of the proposed KFDP.     

Cooperative Hydrogen Bonding and Enzyme Catalysis

An important contribution to enzyme catalysis may be made by cooperative effects—which are induced by the interactions of a negatively charged ligand L with peptide hydrogen bond networks—through stabilization of charge formation along the reaction pathway. This has been found from density functional calculations on model systems for peptide hydrogen bond networks (an example is shown in the picture).     

Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation

Radiotherapy (RT) is a common cancer treatment approach that accounts for nearly 50% of patient treatment; however, tumor relapse after radiotherapy is still a major issue. To study the crucial role of tumor-associated macrophages (TAMs) in the regulation of tumor progression post-RT, microarray experiments comparing TAM gene expression profiles between unirradiated and irradiated tumors were conducted to discover possible roles of TAMs in initiation or contribution to tumor recurrence following RT, taking into account the relationships among gene expression, tumor microenvironment, and immunology. A single dose of 25 Gy was given to TRAMP C-1 prostate tumors established in C57/B6 mice. CD11b-positive macrophages were extracted from the tumors at one, two and three weeks post-RT. Gene ontology (GO) term analysis using the DAVID database revealed that genes that were differentially expressed at one and two weeks after irradiation were associated with biological processes such as morphogenesis of a branching structure, tube development, and cell proliferation. Analysis using Short Time-Series Expression Miner (STEM) revealed the temporal gene expression profiles and identified 13 significant patterns in four main groups of profiles. The genes in the upregulated temporal profile have diverse functions involved in the intracellular signaling cascade, cell proliferation, and cytokine-mediated signaling pathway. We show that tumor irradiation with a single 25-Gy dose can initiate a time-series of differentially expressed genes in TAMs, which are associated with the immune response, DNA repair, cell cycle arrest, and apoptosis. Our study helps to improve our understanding of the function of the group of genes whose expression changes temporally in an irradiated tumor microenvironment.     

Hyperbranched Polylysine: A Versatile,Biodegradable Transfection Agent for the Production of Recombinant Proteins by Transient Gene Expression and the Transfection of Primary Cells

The feasibility of a new transfection agent, HBPL, for the production of recombinant IgG antibody via TGE as well as for the transfection of primary cells is studied. Under the conditions investigated, transfection of CHO‐DG44 cells using HBPL results in IgG yields that are comparable to those obtained with PEI. In experiments with CHO‐K1 cells and MEFs the use of HPBL allows to achieve transfection efficiencies comparable to or better than those obtained with PEI or Fugene®. HBPL‐mediated transfection does not require complex pre‐formation, works well in serum‐containing media and is biodegradable, which may prevent cumulative cytotoxicity and facilitates downstream processing.

     

丙三醇浓溶液Tg附近协同松弛的量热研究

利用差示扫描量热法测量了丙三醇水溶液Tg前后的比热容. 通过曲线拟合获得AGF模型参数. 研究结果表明, 该模型很好地预测了(Tg+20 K)以下体系的结构松弛时间. 协同重排活化能(Δμ')和协同重排域尺寸(z*)的分析结果表明, 只有选择比聚合物大得多的某一协同重排位形数, 用AGF方法得到的z*才具有物理意义. 作为材料常数的Δμ' 随体系水含量的增加而逐渐降低. 用Donth方法得到的丙三醇水溶液的协同重排域长度尺度(ξCRR)随着水含量的增加逐渐降低, 且其变化趋势可与Δμ'的分析结果相符. 但用AGF方法和Donth方法得到的协同重排域尺寸不能统一.