Novel histone deacetylase 8 ligands without a zinc chelating group: Exploring an ‘upside-down’ binding pose

A novel series of HDAC8 inhibitors without a zinc-chelating hydroxamic acid moiety is reported. Photoaffinity labeling and molecular modeling studies suggest that these ligands are likely to bind in an ‘upside-down’ fashion in a secondary binding site proximal to the main catalytic site. The most potent ligand in the series exhibits an IC₅₀ of 28 μM for HDAC8 and is found to inhibit the deacetylation of H4 but not α-tubulin in SH-SY5Y cell line.     

矮嵩草草甸不同功能群主要植物种生长特征与地表温度的相关性分析

基于国际冻原计划(ITEX)模拟增温效应对植物影响的研究方法,设置温度梯度从物种个体水平研究各功能群主要植物种生长特征与地表温度的相关性,以探讨全球变暖背景下,矮嵩草草甸不同功能群植物种生长特征对地表温度升高的响应。结果显示:(1)莎草科功能群黑褐苔草的高度与地表温度呈线性关系(P<0.01),而分蘖数、叶片数与地表温度呈二次函数关系,但不显著;矮嵩草的分蘖数、叶片数及高度与地表温度均呈二次函数形式变化(P<0.05)。(2)多年生禾本科功能群垂穗披碱草和草地早熟禾的分蘖数、叶片数、高度均与地表温度呈线性正相关关系(P<0.01)。(3)杂类草功能群短穗兔耳草的匍匐茎数与地表温度呈不显著的二次函数关系,而叶片数、高度均与地表温度呈线性相关关系(P<0.01);鸟足毛茛的花蕾数、叶片数、高度均与地表温度呈线性相关关系(P<0.01)。研究表明,不同功能群植物种对地表温度升高的响应是不一致的,地表温度持续升高对禾本科功能群植物种的生长有利,而对莎草科、杂类草功能群植物种均不利。     

煤矿复垦地不同恢复阶段植物群落功能群结构与生物多样性变化

选取黄土高原区黑岱沟露天煤矿不同复垦阶段(1995～2010年)样地4块,以原地貌样地为对照,以时空替代的方法,对煤矿复垦地的植物群落的功能群结构及生物多样性进行研究.结果表明:(1)随着复垦时间的延长,植物群落功能群组成以多年生禾草和多年生杂类草为主,其累积优势度均呈现增加的趋势,而一、二年生草本的累积优势度减小;复垦初期,群落功能群单一、组成种类贫乏,多为一、二年生植物;复垦后期,羊草及冰草逐步出现,复垦地最终形成以克氏针茅、本氏针茅、赖草及糙隐子草为主的植物群落.(2)复垦过程中,中生植物及中旱生植物所占比例逐步增加,而旱生植物比例逐步减少;多年生禾草及多年生杂类草生物量随着复垦时间的增加而递增,而一、二年生草本植物生物量递减;群落总生物量呈先急剧增加、又急剧减少、后缓慢增加的规律.(3)群落的Shan-non-Wiener多样性指数(H)、Patrick丰富度指数(Pa)及Pielou均匀度指数(JP)随着复垦时间延长而增加.     

Microglial LOX-1 reacts with extracellular HSP60 to bridge neuroinflammation and neurotoxicity

Chronic neurodegeneration is in part caused by a vicious cycle of persistent microglial activation and progressive neuronal cell loss. However, the driving force behind this cycle remains poorly understood. In this study, we used medium conditioned by necrotic differentiated-PC12 cells to confirm that damaged neurons can release soluble injury signals, including heat shock protein 60 (HSP60), to efficiently promote the neurotoxic cycle involving microglia. Since lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) has previously been identified as a novel receptor for HSP60, we hypothesize that LOX-1 through binding to extracellular HSP60 promotes microglia-mediated neuroinflammation. In this study, we observed that LOX-1 expression is induced upon toxic microglial activation, and discovered that LOX-1 is necessary in microglia for sensing soluble neuronal injury signal(s) in the conditioned medium to induce generation of pro-inflammatory mediators (IL-1β, TNF-α, NO and ROS) that promote neurotoxicity. Employing a unique eukaryotic HSP60-overexpression method, we further demonstrated that extracellular HSP60 acts on microglial LOX-1 to boost the production of pro-inflammatory factors (IL-1β, NO and ROS) in microglia and to propagate neuronal damage. These results indicate that LOX-1 is essential in microglia for promoting an inflammatory response in the presence of soluble neuronal-injury signals such as extracellular HSP60, thereby linking neuroinflammation and neurotoxicity.     

以工程素质培养为导向的生物工程专业核心课程改革

探讨以注重综合素质、强化工程能力和工程素质的培养、完善知识结构为重点的生物工程专业核心课程的教学改革。阐明生物工程师应具备的以五种能力和五种意识为核心的工程素质内涵,明确培养工程素质实施的核心课程;充分利用产学研平台,建设素质精良的"双师型"教师队伍;以工程能力培养为主线,建立以生物工厂设计和工艺改进的教学特色课程群;实施启发式、分组讨论法、比较归纳法和案例式的教学方法改革,提高了教学效果,强化了生物工程专业学生工程素质的培养。     

Lipid hydration and mobility: an interplay between fluorescence solvent relaxation experiments and molecular dynamics simulations

Fluorescence solvent relaxation experiments are based on the characterization of time-dependent shifts in the fluorescence emission of a chromophore, yielding polarity and viscosity information about the chromophore’s immediate environment. A chromophore applied to a phospholipid bilayer at a well-defined location (with respect to the z-axis of the bilayer) allows monitoring of the hydration and mobility of the probed segment of the lipid molecules. Specifically, time-resolved fluorescence experiments, fluorescence quenching data and molecular dynamic (MD) simulations show that 6-lauroyl-2-dimethylaminonaphthalene (Laurdan) probes the hydration and mobility of the sn-1 acyl groups in a phosphatidylcholine bilayer. The time-dependent fluorescence shift (TDFS) of Laurdan provides information on headgroup compression and expansion induced by the addition of different amounts of cationic lipids to phosphatidylcholine bilayers. Those changes were predicted by previous MD simulations. Addition of truncated oxidized phospholipids leads to increased mobility and hydration at the sn-1 acyl level. This experimental finding can be explained by MD simulations, which indicate that the truncated chains of the oxidized lipid molecules are looping back into aqueous phase, hence creating voids below the glycerol level. Fluorescence solvent relaxation experiments are also useful in understanding salt effects on the structure and dynamics of lipid bilayers. For example, such experiments demonstrate that large anions increase hydration and mobility at the sn-1 acyl level of phosphatidylcholine bilayers, an observation which could not be explained by standard MD simulations. If polarizability is introduced into the applied force field, however, MD simulations show that big soft polarizable anions are able to interact with the hydrophilic/hydrophobic interface of the lipid bilayer, penetrating to the level probed by Laurdan, and that they expand and destabilize the bilayer making it more hydrated and mobile.     

Shoot Proliferation and Leaf Malformation of Celosia argentea and Celosia spicata Caused by a Phytoplasma of the 16SrIII‐J Group

Ornamental plants of Celosia argentea L. and Celosia spicata L. displaying typical phytoplasma‐induced symptoms were observed in Piracicaba, State of São Paulo, south‐eastern Brazil. Our aim was to identify the possible phytoplasma involved. PCR revealed the association of phytoplasma with diseased plants of both species. Based on actual and virtual RFLP analysis and phylogenetic analysis, the phytoplasma was characterized as a member of the 16SrIII‐J subgroup. Transmission of the pathogen by dodder supported the evidence that the symptoms observed in naturally diseased plants were induced by a phytoplasma. Our results show that C. spicata is a new host for phytoplasma and that this is the first report of a 16SrXIII‐J phytoplasma infecting plants of C. argentea and C. spicata in Brazil.     

How many ionizable groups can sit on a protein hydrophobic core?

Full or partial burial of ionizable groups in the hydrophobic interior of proteins underlies the large modulation in group properties (modified pK value, high nucleophilicity, enhanced capability of interaction with chemical moieties of the substrate, etc.) linked to biological function. Indeed, the few internal ionizable residues found in proteins are known to play important functional roles in catalysis and, in general, in energy transduction processes. However, ionizable‐group burial is expected to be seriously disruptive and, it is important to note, most functional sites contain not just one, but several ionizable residues. Hence, the adaptations involved in the development of function in proteins (through in vitro engineering or during the course of natural evolution) are not fully understood. Here, we explore experimentally how proteins respond to the accumulation of hydrophobic‐to‐ionizable residue substitutions. For this purpose, we have constructed a combinatorial library targeting a hydrophobic cluster in a consensus‐engineered, stabilized form of a small model protein. Contrary to naïve expectation, half of the variants randomly selected from the library are soluble, folded, and active, despite including up to four mutations. Furthermore, for these variants, the dependence of stability with the number of mutations is not synergistic and catastrophic, but smooth and approximately linear. Clearly, stabilized protein scaffolds may be robust enough to withstand many disruptive hydrophobic‐to‐ionizable residue mutations, even when they are introduced in the same region of the structure. These results should be relevant for protein engineering and may have implications for the understanding of the early evolution of enzymes. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Thermal coefficients of the methyl groups within ubiquitin

Physiological processes such as protein folding and molecular recognition are intricately linked to their dynamic signature, which is reflected in their thermal coefficient. In addition, the local conformational entropy is directly related to the degrees of freedom, which each residue possesses within its conformational space. Therefore, the temperature dependence of the local conformational entropy may provide insight into understanding how local dynamics may affect the stability of proteins. Here, we analyze the temperature dependence of internal methyl group dynamics derived from the cross-correlated relaxation between dipolar couplings of two CH bonds within ubiquitin. Spanning a temperature range from 275 to 308 K, internal methyl group dynamics tend to increase with increasing temperature, which translates to a general increase in local conformational entropy. With this data measured over multiple temperatures, the thermal coefficient of the methyl group order parameter, the characteristic thermal coefficient, and the local heat capacity were obtained. By analyzing the distribution of methyl group thermal coefficients within ubiquitin, we found that the N-terminal region has relatively high thermostability. These results indicate that methyl groups contribute quite appreciably to the total heat capacity of ubiquitin through the regulation of local conformational entropy.