Local Rather than Global Folding Enables the Lead-dependent Activity of the 8-17 Deoxyribozyme: Evidence from Contact Photo-crosslinking

The 8-17 deoxyribozyme is an in vitro selected enzyme capable of sequence-specific cleavage of RNA. While selected to be a magnesium and zinc-utilizing enzyme, the 8-17 DNAzyme has been shown to utilize lead for its catalysis. Fluorescence-based experiments have indicated that the magnesium- and zinc-utilizing versions of the DNAzyme-substrate complex need to form a defined tertiary structure to be active, but no such global folding is required for the lead-mediated activity. Here, we have investigated this phenomenon, including the use of contact photo-crosslinking to map the tertiary fold of the lead-dependent DNAzyme. While our results recapitulate that global folding is not required for the lead activity, they reveal strikingly distinct lead-mediated modes of activity under conditions of low versus moderate solution ionic strength. Even in very low salt buffers, where no global folding of the 8-17 DNAzyme occurs, the active site of the enzyme appears to form a distinct local fold, one that cannot be modelled easily by DNA/RNA constructs that preserve key sequence and secondary structure features of the active site.     

Allelopathy and exotic plant invasion

The primary hypothesis for the astonishing success of many exotics as community invaders relative to their importance in their native communities is that they have escaped the natural enemies that control their population growth – the `natural enemies hypothesis'. However, the frequent failure of introduced biocontrols, weak consumer effects on the growth and reproduction of some invaders, and the lack of consistent strong top-down regulation in many natural ecological systems indicate that other mechanisms must be involved in the success of some exotic plants. One mechanism may be the release by the invader of chemical compounds that have harmful effects on the members of the recipient plant community (i.e., allelopathy). Here, we provide an abbreviated compilation of evidence for allelopathy in general, present a detailed case study for Centaurea diffusa, an invasive Eurasian forb in western North America, and review general evidence for allelopathic effects of invasive plants in native communities. The primary rationale for considering allelopathy as a mechanism for the success of invaders is based on two premises. First, invaders often establish virtual monocultures where diverse communities once flourished, a phenomenon unusual in natural communities. Second, allelopathy may be more important in recipient than in origin communities because the former are more likely to be naïve to the chemicals possessed by newly arrived species. Indeed, results from experiments on C. diffusa suggest that this invader produces chemicals that long-term and familiar Eurasian neighbors have adapted to, but that C. diffusa's new North American neighbors have not. A large number of early studies demonstrated strong potential allelopathic effects of exotic invasive plants; however, most of this work rests on controversial methodology. Nevertheless, during the last 15 years, methodological approaches have improved. Allelopathic effects have been tested on native species, allelochemicals have been tested in varying resource conditions, models have been used to estimate comparisons of resource and allelopathic effects, and experimental techniques have been used to ameliorate chemical effects. We do not recommend allelopathy as a `unifying theory' for plant interactions, nor do we espouse the view that allelopathy is the dominant way that plants interact, but we argue that non-resource mechanisms should be returned to the discussion table as a potential mechanism for explaining the remarkable success of some invasive species. Ecologists should consider the possibility that resource and non-resource mechanisms may work simultaneously, but vary in their relative importance depending on the ecological context in which they are studied. One such context might be exotic plant invasion.     

氧化固醇结合蛋白结构、功能与应用

氧化固醇结合蛋白(oxysterol binding protein,OSBP)是存在于真核细胞内的一类参与脂质代谢的非囊泡运输蛋白质,在哺乳动物中被称为氧化固醇结合蛋白相关蛋白质(oxysterol binding protein-related proteins,ORPs),而在酵母中被称为氧化固醇结合蛋白同源物质(oxysterol-binding protein homologues,OSH）。近年来人们对氧化固醇结合蛋白的研究不断深入,特别是对其同源蛋白质（例如,ORP5/8、Osh3/4、ORP4L等）的结构功能差异和其在信号转导中的作用的相关研究,以及在生物医药方面的应用更成为了本领域的热点。本文综述了关于OSBP及其同源蛋白质结构和功能的相关研究,指出了该领域存在的一些关键问题。与此同时,对OSH和ORPs在细胞内的膜接触位点（membrane contact sites,MCS）进行对比,以及对今后OSBP的研究方向做了展望。     

Choosing between two conflicting scientific hypotheses: The orce dilemmas

How may we choose between conflicting hypotheses when doing a scientific test? Bayesian theory of decision offers a tool to analyse what choosing actually is, preventing us either from giving too much value to rational compounds or from putting aside the scientists’ personal interests and prejudices. Gieres’ cognitive approach to the problem defines the Minimally Open-Minded Scientist’s approach as the right one to dial with the choice dilemma. This approach is used here to give an opinion on the status of the “Orce Man”.     

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re‐ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re‐ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

浮游动物昼夜垂直迁移机理的主要假说及其研究进展

对有关浮游动物昼夜垂直迁移(DVM)机理的实验、假说以及理论模型方面的研究进.展进行了综述。昼夜垂直迁移通常指常规迁移(傍晚上升,拂晓下降),其行为过程不仅影响浮游动物的垂直分布,而且也间接地影响其水平分布及生活史特征,对浮游动物在一定水域的种群维持和补充具有重要的意义。与垂直迁移机理有关的假说主要有光驱动假说、逃避捕食者假说、能量和资源利用假说等,其中逃避捕食者假说已得到大量的实验证实。其理论模型研究一般在两个时间尺度上进行,一个是短期的行为机制研究,另一个从长期的生活史策略的角度考虑。随着实验技术的进步和理论及建模工具的发展,这两个时间尺度的研究正逐渐统一到一个框架下进行。     

Relationship between functional diversity and productivity in meadow and marsh plant communities

功能多样性-生产力关系研究结果支持质量比假说和多样性假说, 但对于这两种假说的适用条件尚有争议。通过对吉林省西部草甸和沼泽植物群落的地上生物量、2个物种多样性指标(物种丰富度和Shannon-Weaver指数)、7种植物性状的两类功能多样性指标(群落权重均值和Rao二次熵), 以及土壤环境因子进行调查测量, 研究了群落功能多样性与生产力的关系。结果表明: 1)功能多样性与生产力的关系比物种多样性与生产力的关系更为密切; 2)功能群落权重均值解释生产力变异的能力好于Rao二次熵, 即优势物种对群落生产力的影响作用更大; 3)水淹条件影响着功能多样性与生产力的关系, 以群落权重均值为基础的质量比假说适于解释草甸群落功能多样性与生产力的关系, 而以Rao二次熵为基础的多样性假说适于解释有强烈环境筛(水淹)的沼泽群落功能多样性与生产力的关系。     

石菖蒲提取物对四种储粮害虫的生物活性研究

研究了石菖蒲4种溶剂无水乙醇、丙酮、乙酸乙酯、石油醚提取物对玉米象、谷蠹、长角扁谷盗和锯谷盗4种储粮害虫的驱避作用和触杀作用。结果表明：石菖蒲4种溶剂提取物对4种试虫均有明显的驱避作用和触杀作用,处理60 h的平均驱避等级均达到Ⅲ级以上,对4种试虫的触杀死亡率均达到41.11%以上。     

中国蔷薇属植物物种丰富度分布格局及其与环境因子的关系

物种丰富度的大尺度地理格局及其成因是宏观生态学及生物地理学的中心议题之一。蔷薇属(Rosa L.)植物具有很高的经济价值和生态价值,探讨中国蔷薇属植物的丰富度分布格局及其影响因素可为该属植物资源的保护和合理开发利用乃至其系统进化研究提供重要依据。基于蔷薇属植物在中国的15451条分布数据和11种地理、气候等环境因子进行了物种丰富度分析和相关性分析,研究结果显示:(1)蔷薇属植物在中国分布不均匀。在水平方向上,蔷薇属植物于26.19°—34.29°N带内有较高的物种丰富度,之后随着纬度的增加而降低,且随着经度的增加表现为先增加后减少,于99.10°—108.47°E间存在明显的峰值;在垂直方向上,蔷薇属植物的物种丰富度随海拔的增加表现为先增加后减少,956.46—3518.60m范围内的丰富度最高。西南横断山区为蔷薇属物种分布的中心地区,新疆北部及东北长白山周边地区为局部聚集区。(2)蔷薇属物种丰富度与各能量、水分和生境异质性因子均呈正相关关系,与气候稳定性因子呈负相关关系。表明中国蔷薇属植物在水分和热量条件好、气候季节性变化小且生境异质性程度高的地方,有着更高的物种丰富度。(3)蔷薇属...     

两种雀形目鸟类的窝雏数处理实验:检验Lack假说

于1997—1999年在位于青海省北部的中国科学院海北高寒草甸生态系统定位站进行。选择地面筑巢的小云雀(Alauda gulgula)和灌丛筑巢的黄嘴朱顶雀(Acanthis flavirostris)为代表进行窝雏数处理实验。根据Lack假说的预报检验(1)常见窝卵数是否是最大生产力窝卵数;(2)窝雏数处理对雏鸟质量和亲鸟投入是否产生影响;(3)两种鸟的响应方式是否相同。其结果如下：①小云雀和黄嘴朱顶雀的常见窝卵数分别是3和5枚。年间变化不明显,用幼鸟出飞率作为生产力,两种鸟的扩增窝幼鸟出飞率下降,常见窝卵数(分布频率最高)等同于最大生产力窝卵数;②小云雀的幼鸟的生长参数不随窝雏数的改变而变化．而黄嘴朱顶雀有明显变化．说明窝雏数处理对后者幼鸟质量有明显影响。③用递食率作为亲鸟投资指标,小云雀亲鸟的递食率随窝雏数的增加而增加,但雏期不变;而黄嘴朱顶雀递食率不变,但雏期延长。④扩增窝雏数后,两种亲鸟表现出不同的响应方式,小云雀表现为提高单位时间递食次数,而黄嘴朱顶雀延长育幼时间。这两种方式不是通过影响雏鸟质量就是通过影响亲鸟存活率来降低子代和亲代的适合度。结果支持了自然选择将窝卵数调节到亲鸟能喂活最大数量子代的限度。即常见窝卵数就是最大生产力窝卵数的Lack假说。