Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis

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Highlights

• •Mechanistic insights into ionic liquids and proteins at molecular level.
• •Extractants prescreen for proteome analysis with MD simulation system.
• •A loss-less sample preparation method developed for in-depth proteome profiling.
• •Over 3,300 proteins were confidently identified from 1,000 HeLa cells in a 1 h run.
• •Label-free quantitative proteome analysis of human liver cancer tissues.

     

沙坡头人工植被变化的动态平衡

沙坡头地处腾格里沙漠的东南缘,属于宁夏回族自治区中卫县。该地区自然条件严酷,沙丘起伏大,沙层深厚,格状沙丘由西北向东南倾斜且呈阶梯状分布。地下水位深达几十甚至10Om以上,有机质、碳酸钙和速效性养分含量都很低,pH值7.14一7.60。     

1:100万中国植被图森林和灌丛群系类型的补充资料

《中华人民共和国植被图(1:1,000,000)》是我国植被研究的最重要数据。受当时研究基础和制图技术限制, 部分植被群系未能体现在中国植被图上。为了给新一代中国植被图的编研提供基础数据, 本文在搜集从20世纪50年代至今的中国植被研究的相关文献的基础上, 提取其中的植被群系名称和分布信息, 采用植物群落学-生态学原则, 以优势种相同作为依据, 合并部分相近的群系类型。与《中华人民共和国植被图(1:1,000,000)》中的森林和灌丛群系进行对比, 本文新增了1,475个森林和灌丛群系。     

Obtaining high sequence coverage in matrix-assisted laser desorption time-of-flight mass spectrometry for studies of protein modification: analysis of human serum albumin as a model

Several approaches were explored for obtaining high sequence coverage in protein modification studies performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Human serum albumin (HSA, 66.5kDa) was used as a model protein for this work. Experimental factors considered in this study included the type of matrix used for MALDI-TOF MS, the protein digestion method, and the use of fractionation for peptide digests prior to MALDI-TOF MS analysis. A mixture of alpha-cyano-4-hydroxycinnamic acid and 2,5-dihydroxybenzoic acid was employed as the final matrix for HSA. When used with a tryptic digest, this gave unique information on only half of the peptides in the primary structure of HSA. However, the combined use of three enzyme digests based on trypsin, endoproteinase Lys-C, and endoproteinase Glu-C increased this sequence coverage to 72.8%. The use of a ZipTip column to fractionate peptides in these digests prior to analysis increased the sequence coverage to 97.4%. These conditions made it possible to examine unique peptides from nearly all of the structure of HSA and to identify specific modifications to this protein (e.g., glycation sites). For instance, Lys199 was confirmed as a glycation site on normal HSA, whereas Lys536 and Lys389 were identified as additional modification sites on minimally glycated HSA.     

Community structure of microorganisms associated with reddish-brown iron-rich snow

Reddish-brown colored snow, containing spherical brown particles, has been observed in several mires in Japan. In order to characterize this remarkable phenomenon, the microbial community and chemical species in snow were analyzed. A core sample of snow which had a colored region was investigated and it revealed vertical shifts in physicochemical characteristics and the microbial community structure. The abundance of particles peaked within the colored layer, and correlated with the amount of reducible Fe(III). The interstitial water of the colored layer was enriched with Fe(II), and characterized by reduced concentration of dissolved methane. The bacterial community in the colored region was characterized by higher relative abundance of iron-reducing bacteria and methanotrophs. Aggregates of the brown particles were found as precipitates in snow melt pools, and were subjected to cloning analyses targeting several different genes. The majority of bacterial 16S rRNA gene clones belonged to the class Betaproteobacteria or the phylum Bacteroidetes. No snow algae were detected in the eukaryotic small subunit rRNA gene clone library. As a possible carbon source to sustain the community in the snow, involvements of carbon dioxide and methane were investigated by analyzing the genes involved in their assimilation. In the analyses of genes for ribulose-1,5-biphosphate carboxylase/oxygenase, clones related to sulfur oxidizers were obtained. The analysis of particulate methane monooxygenase genes indicated dominance of Methylobacter species. These results emphasized the uniqueness of this phenomenon, and iron reducers of the genus Geobacter are suggested to be the key organisms that could be investigated in order to understand the mechanism of this phenomenon.     

甲虫抗冻蛋白热滞活性的二维吸附结合模型

甲虫抗冻蛋白是一种具有规则结构的昆虫抗冻蛋白。在相同浓度条件下,甲虫抗冻蛋白比鱼类抗冻蛋白有更高的热滞活性,目前已成为人们重点研究的一类抗冻蛋白。根据甲虫抗冻蛋白的结构特点及其在冰晶表面的吸附模式,应用二维吸附结合模型计算分析了具有6￣11个β-螺旋(β-helix)结构片段的甲虫抗冻蛋白变体分子,得到了它们的热滞活性随溶液浓度变化的规律,特别是热滞活性与甲虫抗冻蛋白的β-螺旋结构片段数的关系。结果显示,抗冻蛋白在冰晶表面的覆盖度是一个影响其热滞活性的重要因素。     

Spatial variation in the demography and population dynamics of a perennial shrub (Atriplex vesicaria) under sheep grazing in semi‐arid Australian rangelands

Atriplex vesicaria Heward ex Benth. (Chenopodiaceae) is a widespread perennial shrub in southern Australia's chenopod rangelands but is sensitive to grazing. A detailed investigation of the demography and population dynamics of A. vesicaria under sheep grazing was conducted over 6.5 years at a range of sites across a typical paddock to assess the long‐term effects of grazing on the species and elucidate the mechanisms of population change under grazing. The effects of rainfall on recruitment and mortality were also examined. Six‐monthly censuses of all A. vesicaria individuals were conducted in permanent grazed and ungrazed plots at sites located across an 1100‐ha paddock. Grazing increased adult shrub mortality close to water and reduced recruitment over a broader area of the paddock, but seedling survival did not appear to be affected by grazing. As a result of these changes, the population declined on grazed plots up to 2200 m from water during the study, but the decline was greatest closer to water. The population was most dynamic at the sites furthest from the water point where it was unaffected by grazing because of the greater recruitment and mortality of young plants, but because these processes balanced out over time, population density was effectively unchanged by the end of the study. Although statistical models indicated that six‐monthly rainfall did not explain temporal variation in recruitment or mortality, rainfall nevertheless has a central role in both processes. In particular, longer periods of favourable rainfall and drought appear to have an important influence on recruitment and mortality, respectively, with heavy grazing during a drought period increasing mortality. Occasional shortages of seed or rains occurring during the warmer months when seed germination is limited possibly explain poor recruitment at sites unaffected by grazing following good rainfall.     

Identification of the spectral characteristics of submerged plant Vallisneria spiralis

The relationship between land features and their spectral characteristics is important for the interpretation of remote sensing images. In this study, the spectral characteristics of a submerged plant Vallisneria spiralis with varied coverage was measured with a ground sensor/radiometer, FieldSpec^TM Pro JR Spectroradiometer in the laboratory and in the constructed wetland of “Mengqingyuan”, Shanghai, China. The results showed that the reflectance rate of Vallisneria spiralis rose with its increasing coverage, which was exhibited both at the visible band (500–650 nm) and the near infrared band (700–900 nm). Water quality influenced the reflectance rate with the primary differences between the laboratory and field experiments mainly occurring at the near-infrared band (700–900 nm). A regression analysis was carried out respectively between the coverage of Vallisneria spiralis and the reflectance rate at the wavelengths of Quick Bird 4 bands where the coverage responded to the strongest. These results of regression analyses showed a clear linear relationship, by which the coverage of Vallisneria spiralis could be quantitatively deduced from the reflectance rate measured in situ. The implications in terms of the ability of hyperspectral remote sensing to distinguish and monitor the distribution and dynamics of submerged vegetation on a large scale are discussed.