Protein structure determination by conformational space annealing using NMR geometric restraints

We have carried out numerical experiments to investigate the applicability of the global optimization method of conformational space annealing (CSA) to the enhanced NMR protein structure determination over existing PDB structures. The NMR protein structure determination is driven by the optimization of collective multiple restraints arising from experimental data and the basic stereochemical properties of a protein‐like molecule. By rigorous and straightforward application of CSA to the identical NMR experimental data used to generate existing PDB structures, we redetermined 56 recent PDB protein structures starting from fully randomized structures. The quality of CSA‐generated structures and existing PDB structures were assessed by multiobjective functions in terms of their consistencies with experimental data and the requirements of protein‐like stereochemistry. In 54 out of 56 cases, CSA‐generated structures were better than existing PDB structures in the Pareto‐dominant manner, while in the remaining two cases, it was a tie with mixed results. As a whole, all structural features tested improved in a statistically meaningful manner. The most improved feature was the Ramachandran favored portion of backbone torsion angles with about 8.6% improvement from 88.9% to 97.5% (P‐value <10^?17). We show that by straightforward application of CSA to the efficient global optimization of an energy function, NMR structures will be of better quality than existing PDB structures. Proteins 2015; 83:2251–2262. © 2015 Wiley Periodicals, Inc.     

The First Three-Dimensional Structure of Phosphofructokinase from Saccharomyces cerevisiae Determined by Electron Microscopy of Single Particles

Phosphofructokinaseis a key regulatory enzyme of the glycolytic pathway. We have determined the structure of this enzyme from Saccharomyces cerevisiae to a resolution of 2.0 nm. This is the first structure available for this family of enzymes in eukaryotic organisms. Phosphofructokinase is an octamer composed of 4α and 4β subunits arranged in a dihedral point group symmetry D₂. The enzyme has a very open and elongated structure, with dimensions of 24 nm in length and 17 nm in width. The final structure, calculated from 0° tilt projections of the molecule at random orientations using as reference the volume obtained by the random conical reconstruction technique in ice, has allowed us to discern the shapes of the subunits and their mutual arrangement in the octamer.     

内固定拆除前胸腰椎骨折病例矫正曲度丢失的相关因素分析

目的:分析后路短节段复位内固定拆除前的胸腰椎单节段骨折病例矫正曲度丢失的相关因素。方法:纳入于2008.01-2011.01间因胸腰椎单节段骨折于我科接受短节段复位内固定术、影像学资料完整的患者共计87例。于术前、术后及拆除内固定前的胸腰椎侧位X线片上测量伤椎上位椎体和下位椎体所成的Cobb角(α角)、伤椎上终板和上位椎体所成角度(即β角)、伤椎下终板和下位椎体所成角度(γ角)以及伤椎上下终板所成的角度(δ角)。以T检验比较各测量角及改变量,并对α角改变量和各因素进行相关性分析。结果:与术前相比,术后的α角、β角、γ角和δ角均显著增加(p0.05);和术后相比,拆除内固定前α角和δ角均明显减少(p0.05),α角的平均改变量为-2.85度。将α角改变量和各因素进行相关性分析后发现,α角改变量和手术前后矫正曲度(相关系数:-0.342,p=0.026)呈显著负相关,和终板破坏部位(相关系数:0.374,p=0.015)、δ角改变量呈显著正相关(相关系数:0.231,p=0.041)。结论:接受短节段复位内固定的胸腰椎骨折病例内固定拆除前矫正曲度有明显丢失,术后矫正曲度、终板损伤部位和伤椎上下终板所成角度改变量与矫正曲度的丢失有明显相关性。     

Neighbour tolerance,not suppression,provides competitive advantage to non‐native plants

High competitive ability has often been invoked as a key determinant of invasion success and ecological impacts of non‐native plants. Yet our understanding of the strategies that non‐natives use to gain competitive dominance remains limited. Particularly, it remains unknown whether the two non‐mutually exclusive competitive strategies, neighbour suppression and neighbour tolerance, are equally important for the competitive advantage of non‐native plants. Here, we analyse data from 192 peer‐reviewed studies on pairwise plant competition within a Bayesian multilevel meta‐analytic framework and show that non‐native plants outperform their native counterparts due to high tolerance of competition, as opposed to strong suppressive ability. Competitive tolerance ability of non‐native plants was driven by neighbour's origin and was expressed in response to a heterospecific native but not heterospecific non‐native neighbour. In contrast to natives, non‐native species were not more suppressed by hetero‐ vs. conspecific neighbours, which was partially due to higher intensity of intraspecific competition among non‐natives. Heterogeneity in the data was primarily associated with methodological differences among studies and not with phylogenetic relatedness among species. Altogether, our synthesis demonstrates that non‐native plants are competitively distinct from native plants and challenges the common notion that neighbour suppression is the primary strategy for plant invasion success.     

尼龙膜cDNA阵列的图像处理和表达量化

高密度的cDNA阵列是大规模基因组织表达谱研究的重要技术。目标细胞的cDNA样品用同位素标记时,尼龙膜cDNA阵列对杂交信号探测的灵敏度高、线性范围大,对低表达量的cDNA也能进行有效分析。但是同位素标记的杂交样点也存在易污染、易扩散和表达量取值误差大等问题。为此,首先按同位素辐射感光原理建立严格的样点理论模型,然后对样点进行精确定位、饱和补偿、干扰校正处理,实现了样点表达量的精确提取,显著提高了量化结果的重复性。     

基于多源遥感影像的盐碱地治理效果

将Landsat-8 OLI影像与Sentinel-2号影像结合,利用光合有效辐射比率（FPAR）,构建适用于MODIS植被总初级生产力（GPP）影像空间分辨率提高的逐层逐像元修正因子,实现内蒙古巴彦淖尔市赵贵圪旦组盐碱地农田改良前后的植被长势监测,同时结合不同深度土壤的含盐量数据,采用转移矩阵方法与热点分析方法分别分析了全局土壤含盐量变化与植被长势变化的局部差异。结果表明：（1）12-20号地块内土壤含盐量改良效果最明显,且研究区改良效果随土壤深度增加而逐渐降低。土壤深度0-20cm,盐土向中度盐土转入面积最大;土壤深度20-40cm,强度盐土向中度盐土转入面积最大;土壤深度40-60cm,强度盐土与盐土的转入面积大于转出面积,其他土壤的转入面积小于转出面积。（2）研究区内,GPP提升区域比降低区域面积约多60.36hm²,占研究区面积的42.88%;同时,对改良前植被GPP低值区域提高效果更明显。（3） GPP提升区域中热点区域集中分布在12-17、25-27、34号地块内,该区域改良效果显著;GPP降低区域中冷点区域集中分布在6、12-14、22-23、27-28、30-31号地块内,该区域改良效果差。     

Confocal Raman microspectroscopy on excised human skin: uncertainties in depth profiling and mathematical correction applied to dermatological drug permeation

Confocal Raman microspectroscopy represents the advantage of giving structural and conformational information on samples without any destructive treatment. Recently, several studies were achieved to study the skin hydration, endogenous and exogenous molecules repartition in the skin using the confocal feature of this technique. Meanwhile, when working through a material boundary with a different refractive index, the main limitation remains the spatial precision, especially the distortion in the depth and the depth resolution. Recently, several authors described mathematical models to correct the depth and the resolution values. In this study, we combined theoretical approaches, proposed by different authors with experimental measurements to try to find out the most appropriate approach for correction. We then applied the corrections on in‐depth profiles tracking the penetration of Metronidazole, a drug produced by Galderma for rosacea treatment, through excised human skin. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

In defense of Louis Pasteur: Critique of Gerald Geison's deconstruction of Pasteur's discovery of molecular chirality

Louis Pasteur discovered the phenomenon of molecular chirality, based on his studies of tartrate crystals. His finding remains one of the most important discoveries in the history of chemistry and a fundamentally important chemical phenomenon, with essential implications in biology. In his 1995 book The Private Science of Louis Pasteur, the eminent historian of science Gerald L. Geison (1943‐2001) was highly critical of much of Pasteur's work including his discovery of molecular chirality. The in‐depth analysis provided in this article indicates, however, that the negative assessment of Pasteur's chirality work by Geison is entirely without scientific basis. Criticisms of Pasteur in the book for other “transgressions” in his chirality work, such as supposed influences of his personal biases and stubbornly held a priori notions, misrepresentation of his scientific work in his publications and lectures, and unethical and career‐minded conduct, are also not supported by the evidence. Other troubling features of the book include a broad failure to assure accuracy in a variety of fundamental and important information, including errors in names, dates, events, referencing, indexing, and French‐language text.