Computational fluid dynamics as a tool for testing functional and ecological hypotheses in fossil taxa

Computational fluid dynamics is a method for simulating fluid flows that has been widely used in engineering for decades, and which also has applications for studying function and ecology in fossil taxa. However, despite the possible benefits of this approach, computational fluid dynamics has been used only rarely in palaeontology to date. The theoretical basis underlying the technique is outlined and the main steps involved in carrying out computer simulations of fluid flows are detailed. I also describe previous studies that have applied the method to fossils and discuss their potential for informing future research directions in palaeontology. Computational fluid dynamics can enable large‐scale comparative analyses, as well as exacting tests of hypotheses related to the function and ecology of ancient organisms. In this way, it could transform our understanding of many extinct fossil groups.     

葛根素对糖尿病心肌细胞的保护及其机制研究

观察葛根素（Puerarin）对链脲佐菌素（streptozotocin,STZ）诱导的糖尿病大鼠心肌细胞的保护作用,并探讨血小板反应素1（Thrombospondin-1,TSP-1）的表达改变及其作用。雄性SD大鼠45只随机分为三组（n=15）：糖尿病组和葛根素治疗组采用一次腹腔注射链脲佐菌素（STZ）65mg／kg制备糖尿病模型,其中葛根素治疗组于造模后葛根素腹腔注射4周（100mg/kg/day）,正常对照组仅腹腔注射等量生理盐水（6ml／kg）,同样喂养4周。四周后各组大鼠处死。H—E染色及透射电子显微镜观察三组大鼠心肌细胞纤维显微结构和超微结构的病理改变．免疫组化和实时荧光定量PCR法观察大鼠心肌细胞中TSP-1蛋白和mRNA表达的变化．同时利用Langendorff离体心脏灌流法测定各组大鼠心室肌细胞功能。结果发现葛根素治疗组较糖尿病组大鼠的体重增加明显,同时血糖下降,有显著性差异（P〈0．01）。H—E染色显示糖尿病大鼠多处心肌肌丝紊乱伴少量炎症细胞浸润,电镜下发现有线粒体嵴消失溶解,肌丝排列紊乱等病理改变,而葛根素治疗组大鼠偶见上述病理变化。免疫组化显示葛根素治疗组心肌内TSP-1阳性细胞密度小于糖尿病大鼠,TSP-1 mRNA表达也比糖尿病大鼠要低。此外葛根素治疗组大鼠的左室收缩末压（LVSEP）、左心室舒张末期压（LVEDP）等心功能指标均明显低于正常组（P〈0．01）,但较糖尿病组有显著改善（P〈0．01）。上述结果显示葛根素能保护糖尿病大鼠心肌细胞的高糖损伤和维持心室肌细胞的功能,而该机制可能与抑制心肌细胞TSP-1表达的水平有关。     

Docking and scoring with alternative side-chain conformations

We describe a scoring and modeling procedure for docking ligands into protein models that have either modeled or flexible side-chain conformations. Our methodical contribution comprises a procedure for generating new potentials of mean force for the ROTA scoring function which we have introduced previously for optimizing side-chain conformations with the tool IRECS. The ROTA potentials are specially trained to tolerate small-scale positional errors of atoms that are characteristic of (i) side-chain conformations that are modeled using a sparse rotamer library and (ii) ligand conformations that are generated using a docking program. We generated both rigid and flexible protein models with our side-chain prediction tool IRECS and docked ligands to proteins using the scoring function ROTA and the docking programs FlexX (for rigid side chains) and FlexE (for flexible side chains). We validated our approach on the forty screening targets of the DUD database. The validation shows that the ROTA potentials are especially well suited for estimating the binding affinity of ligands to proteins. The results also show that our procedure can compensate for the performance decrease in screening that occurs when using protein models with side chains modeled with a rotamer library instead of using X-ray structures. The average runtime per ligand of our method is 168 seconds on an Opteron V20z, which is fast enough to allow virtual screening of compound libraries for drug candidates.     

毛竹的异质性空间点格局分析

毛竹是一种重要的经济用材,研究其空间分布格局有益于对其空间发生进行预测。选取了一块空间肥量分布不均的毛竹样地,使用异质性空间点格局分析方法对毛竹的空间分布进行了研究,结果发现毛竹在给定的距离尺度下呈现出显著的泊松分布,而并不是聚集分布。同时选用二元二次方程拟合观察的数据,发现对毛竹强度的拟合优度较高。研究揭示出异质性空间环境中毛竹的分布特点,潜在地表明土壤肥量的空间分布对毛竹空间分布的影响,对毛竹的集约化经营具有重要的指导意义;同时,鉴于国内生态研究中较少采用异质性空间点格局分析方法,研究对于推动这种方法在国内生态学研究中的普及还具有一定的参考价值。     

Ⅰ型蛋白磷酸酶研究进展

Ⅰ型蛋白磷酸酶(PP1)属丝/苏氨酸磷酸酶的一种,在生物体中广泛存在,参与调节多种重要的生理功能,包括转录、翻译、代谢、细胞生长及分化等.PP1分子结构表面的3个凹槽及β 12-β 13 Loop环结构,它在底物与抑制剂的结合方面起决定作用.近期研究发现,Loop环结构除了是抑制剂的结合部位之外,对整个酶分子的结构和性质都起重要作用.功能研究也证明PP1还参与HIV-1转录过程的调节,并且与老年性痴呆等多种疾病密切相关.主要对PP1的组织分布、分子结构、酶学特性、催化机制以及生物学功能等方面进行了相应的综述.     

加纳籽中5-羟基色氨酸的研究进展

5-羟基色氨酸主要存在于豆科植物中,尤其在加纳籽中含量居多。在体内,5-羟基色氨酸是5-羟色胺的前体,是一类重要的神经类药物。对5-羟基色氨酸的生物学作用、检测、生产方面的最新研究进行了概述,并对5-羟基色氨酸资源匮乏的问题提出了建议。     

Is there a ‘plenhaptic’ function?

One approach to gauge the complexity of the computational problem underlying haptic perception is to determine the number of dimensions needed to describe it. In vision, the number of dimensions can be estimated to be seven. This observation raises the question of what is the number of dimensions needed to describe touch. Only with certain simplified representations of mechanical interactions can this number be estimated, because it is in general infinite. Organisms must be sensitive to considerably reduced subsets of all possible measurements. These reductions are discussed by considering the sensing apparatuses of some animals and the underlying mechanisms of two haptic illusions.     

我国生态补偿研究中的科学问题

我国生态补偿的研究始于20世纪80年代对生态学意义上生态补偿的探讨和经济学意义上生态补偿的摸索;联合国环境与发展大会后,进入主动的基于环境损失赔偿的理论探讨阶段;随着生态保护的加强、生态工程的实施以及保护和发展矛盾的加剧,生态补偿涵义拓展到对生态环境保护者进行补偿,进入理论和实践相结合的阶段,并成为国内社会各界的热点问题。但是目前生态补偿的涵义、理论依据和补偿标准等生态补偿研究的核心问题仍然存在不确定性。我国生态补偿涵义经历了从生态学意义到经济学意义的发展历程,目前阶段的生态补偿涵义与国际上的"生态系统服务付费"比较接近。理清生态补偿费与环境费、资源费的关系是生态补偿定位的关键,主要是确定与后者的包含或者补充关系;生态补偿的环境经济学理论来源是基本一致的,即环境外部成本内部化原理和公共物品理论,但是生态系统服务作为生态补偿的理论依据还存在基于效益补偿还是基于价值补偿的争论;生态补偿标准确定主要包括基于生态系统服务量化、成本(机会成本)或通过供需双方的博弈等方法,目前仍然处于探索阶段。上述科学问题是决定生态补偿实施的可行性和有效性的关键性问题,需要从我国的实际出发,从不同区域的现实出发结合理论探讨和实践需求进行研究,建议日后加强以下几个方面的研究:(1)与现实需求一致的生态补偿概念的确定和科学定位;(2)以现实有效性为基础的理论依据和补偿标准计算;(3)基于利益相关方多方参与的生态补偿机制研究;(4)生态系统服务研究与生态补偿研究的结合。