根据蛋白质的氨基酸组成实现其快速鉴定

常规进行蛋白质鉴定的方法是测定其氨基酸顺序,它需要蛋白质顺序分析仪,对蛋白质的纯度要求高,费时和花费大,与之相比,蛋白质的氨基酸组成和分子量是容易实验测定的。本文描述了一个基于蛋白质的组成和分子量进行其快速鉴定的方法。其基本出发点是,通过统计蛋白质序列数据库中每个序列的氨基酸组成和分子量,得到一个含蛋白质长度、组成和分子量的数据库,将靶蛋白质的组成等数据与该数据库进行对比,可以检出组成和分子量与之接近的蛋白质。从而对该蛋白质进行初步鉴定。在有些情况下,甚至能相当准确地确定靶蛋白质与数据库中的某个（些）蛋白质相关。根据这一原理本文设计了根据氨基酸组成检索蛋白质组成数据库的程序,通过对胰岛素原、细胞肿瘤抗原Ｐ５３和泛肽等多种蛋白质的组成分析,证实根据氨基酸组成能较好地进行蛋白质鉴定。     

Testing the functional significance of microbial composition in natural communities

Ecologists have long studied the relationship between biotic composition and ecosystem functioning in larger organisms; however, only recently has this relationship been investigated widely in microorganisms. Recent studies are reviewed within a framework of three experimental approaches that are often used to study larger organisms: environmental treatment, common garden, and reciprocal transplant experiments. Although the composition of microorganisms cannot be easily manipulated in the field, applying these approaches to intact microbial communities can begin to tease apart the effects of microbial composition from environmental parameters on ecosystem functioning. The challenges in applying these approaches to microorganisms are highlighted and it is discussed how the experimental approach and duration affects a study's interpretation. In general, long-term environmental treatment experiments identify correlative relationships between microbial composition and ecosystem functioning, whereas short-term common garden experiments demonstrate that microbial composition influences ecosystem functioning. Finally, reciprocal transplants simultaneously test for interactive effects of the environment and composition on functioning. The studies reviewed provide evidence that, at least in some cases, microbial composition influences ecosystem functioning. It is concluded that whole-community experiments offer a way to test whether information about microbial composition will help predict ecosystem responses to global change.     

生物人类学和人体组成学的渊源关系

随着人体组成学中文版的发行和人体组成测量培训班在中国的举行, 中国生物人类学家对人体组成测量方法在科研中的运用有了更大的兴趣。该文对人类学家,如Jindr?ich Matiegka和Stanley MarionGarn在人体组成学发展中的历史贡献做了基本的介绍。此外, 作者还以Garn博士的工作为例, 去激励中国生物人类学家开展人体组成学的研究工作。文章讨论了人体组成成分的测量方法在生物人类学中的用途, 并介绍了人体组成学的基本理论和概念及近年来人体组成学的变化: 如影像技术的发展, 影像技术作为"金标准"对评估其他人体组成测量方法的用途, 双能量x线吸收法的优势, 生物电阻分析法的广泛运用, 和多种人体组成测量方法相辅相成的现象。作者对常用的人体组成测量方法的优缺点做了比较, 并指出人体组成成分测量是人体测量方法的自然延续, 人体组成学和生物人类学的关系渊源已久; 因此中国人类学家应当更多地利用人体组成测量方法对人体差异做更深入的研究, 并注重人体差异同健康疾病和生物医学的关系, 以便让生物人类学更好地为当今社会服务。     

A mathematical model of fatty acid metabolism and VLDL assembly in human liver

The lipid composition of very-low-density lipoprotein (VLDL) in plasma is crucial for human health. A pre-requisite for the alteration of VLDL composition is a co-ordinated understanding of the complex interactions in VLDL assembly. In order to determine the potential effects of changes in substrate availability on VLDL lipid composition, we constructed, parameterized and evaluated a mechanistic mathematical model of the biosynthesis of triglycerides, phospholipids, and cholesterol esters and the assembly of VLDL in human hepatocytes. Using published data on human liver metabolism, the model was also used to provide insight into the complex process of lipid metabolism and to estimate the affinities of different liver enzymes for different fatty acids (FA). For example, we found that Delta6-desaturase is 19 times more selective for C18:3n-3 than C18:2n-6, stearoyl-CoA-desaturase is 2.7 times more selective for C18:0 than C16:0, Delta5-desaturase desaturates C20:4n-3 preferentially over C20:3n-6 and FA elongase preferentially elongates C18:3n-6. The model was also used to predict the plasma free fatty acid (FFA) composition required to generate a prescribed change in plasma lipoprotein FA composition. Furthermore, the model was tested against a published human feeding trial that investigated the effect of changes in dietary FA composition on human plasma lipid FA composition. The model is a useful tool for predicting the effect of changes in plasma FFA composition on plasma lipoprotein lipid FA composition.     

Seed bank spatial structure in semi-arid environments: beyond the patch-bare area dichotomy

The prevalence of patchy structures in vegetation is a common feature in semi-arid ecosystems. Although the effect of patches on seed density is widely known, we still lack information on how patch features affect seed bank density and composition. Our aim was to answer two basic questions: (1) How do seed bank density and composition vary within and outside patch aboveground physical limits? and (2) Do patch characteristics affect soil seed bank density and composition? We sampled 50 shrub patches in a semi-arid gypsum system in Central Spain, measuring patch size, composition and structure, and seed bank at three locations per shrub (centre, edge and outside). We calculated the effect of interior patch location, patch composition and structure on seed density and composition. Patches acted both as seed sources, increasing seed density in neighbouring areas and as seed sinks by trapping seeds from bare areas. Patch structure (erect perennial cover) had the greatest effect on seed bank density, whereas patch size and microslope had the greatest influence on bare area density. Patch structure, composition and interior location explained the variation in seed bank composition. Patch effect extends to the surrounding bare matrix creating a seed bank gradient in density and composition. This effect is modulated by patch structure and composition and affects seed bank composition. Our results suggest that the spatial structure of gypsum community seed banks may act as a mechanism for a spatial storage effect contributing to the maintenance of high levels of diversity in semi-arid environments     

哺乳动物化石牙齿釉质的碳、氧同位素组成与古气候重建方面的研究进展

哺乳动物化石牙齿釉质能有效地抵抗成岩作用的影响,并保存原始的碳、氧稳定同位素组成信息。通过对食草类哺乳动物化石牙齿釉质同位素组成的分析可以重建这些动物生存时代的古气候。釉质碳酸盐的碳同位素组成响应于取食植物的碳同位素组成,藉此可以恢复陆地生态系统中C3和C4植物的分布比例,这个比例主要受控于大气的CO2水平、气压和光照等因素,与不同的纬度带和气候带有关;釉质磷酸盐的氧同位素组成响应于饮用水的氧同位素组成,饮用水来源于大气降水,其氧同位素组成响应于温度变化,所以釉质的氧同位素组成与气温之间有显著的线性相关,藉此可以计算地史时期的年平均温度、绘制气候的冷暖变化曲线。     

Potential use of the monosaccharide composition of bacteria for their identification

The monosaccharide composition of cell hydrolysates can be used as a criterion for the chemical differentiation of gram-positive bacteria. The monosaccharide composition of six bacterial species belonging to the genus Bacillus has been determined using gas chromatography, mass spectrometry and computers. The qualitative composition was similar, glucose, galactose, ribose and glucosamine being the main components in all of the species. Some Bacillus species differed in their minor components. Although the monosaccharide composition appeared to be homogeneous, bacteria can be identified in terms of their carbohydrate profile using computers. To this end, the monosaccharide composition of bacterial cells is represented as a two-dimensional data file including the qualitative composition of components and the quantity of each component.     

帽儿山国家森林公园30年前后植物区系比较研究

该研究采用样方结合样线调查的方法,并综合文献资料,于1983年和2013年2次对帽儿山国家森林公园植物种类进行实地调查,并进行了区系特征的对比分析,为评估帽儿山国家森林公园植物保护状况提供依据。结果表明:(1)2013年研究区的植物科数量和组成与1983年相同,但2013年比1983年少20属60种,不同等级科组成差异较小,而不同等级属差异较大。(2)优势科组成差异较小,但2013年兰科(Orchidacea)由优势科变成了非优势科,而藜科(Chenopodiaceae)和松科(Pinaceae)由非优势科变成优势科;优势属组成差异较大,2013年比1983年少了8个优势属。(3)2次调查表征科组成变化较大,但表征属组成差异较小,2013年比1983年少了2个表征属。(4)1983年和2013年科、属、种的分布型均以温带性分布为主;科的分布型完全相同,属的分布型2013年比1983年少了地中海区-西亚至中亚分布型;种的分布型,2013年比1983年多了亚洲-北美-北极分布。研究认为,30年间帽儿山国家森林公园的植物区系构成基本稳定,说明对这一区域的植物保护总体有效,但属和种的数量明显减少,30年间物种多样性显著降低,尤其是某些重要的科,如兰科植物的减少,也说明植物保护现状依然不容乐观。     

The POPPs: clustering and searching using peptide probability profiles

The POPPs is a suite of inter-related software tools which allow the user to discover what is statistically 'unusual' in the composition of an unknown protein, or to automatically cluster proteins into families based on peptide composition. Finally, the user can search for related proteins based on peptide composition. Statistically based peptide composition provides a view of proteins that is, to some extent, orthogonal to that provided by sequence. In a test study, the POPP suite is able to regroup into their families sets of approximately 100 randomised Pfam protein domains. The POPPs suite is used to explore the diverse set of late embryogenesis abundant (LEA) proteins.     

The species composition of zooplankton in waterbodies and watercourses of the great lakes depression

The species composition of zooplankton in lakes, reservoirs, and watercourses of the Great Lakes Depression (Mongolia) is examined. Its changes depending on the type of water objects and water mineralization are shown. Under changes in the climate and the economic situation in Mongolia, the species diversity in fresh waterbodies is seen to increase, which is also due to species that are indicators of eutrophication. The minimum changes in the species composition take place in highly mineralized lakes where zooplankton is characterized by the lowest species diversity. The formation of the zooplankton faunistic composition corresponds to changes that were observed earlier in reservoirs of the Volga cascade. The species composition of zooplankton in watercourses varies significantly and depends on the character of the source of a river and its length.     

COPid: composition based protein identification

In the past, a large number of methods have been developed for predicting various characteristics of a protein from its composition. In order to exploit the full potential of protein composition, we developed the web-server COPid to assist the researchers in annotating the function of a protein from its composition using whole or part of the protein. COPid has three modules called search, composition and analysis. The search module allows searching of protein sequences in six different databases. Search results list database proteins in ascending order of Euclidian distance or descending order of compositional similarity with the query sequence. The composition module allows calculation of the composition of a sequence and average composition of a group of sequences. The composition module also allows computing composition of various types of amino acids (e.g. charge, polar, hydrophobic residues). The analysis module provides the following options; i) comparing composition of two classes of proteins, ii) creating a phylogenetic tree based on the composition and iii) generating input patterns for machine learning techniques. We have evaluated the performance of composition-based (or alignment-free) similarity search in the subcellular localization of proteins. It was found that the alignment free method performs reasonably well in predicting certain classes of proteins. The COPid web-server is available at http://www.imtech.res.in/raghava/copid/.     

Third position codon composition suggests two classes of genes within the Cauliflower mosaic virus genome

The translation of viral mRNAs by host ribosomes is essential for infection. Hence, codon usage of virus genes may influence efficiency of infection. In addition, composition of nucleotides in the third position within codons of genes can reflect evolutionary relationships. In this study, third position codon composition was examined for the seven genes of eight Cauliflower mosaic virus isolates. Genes IV-VII had similar codon composition values and were termed Class 1 genes. Genes I-III possessed corresponding codon composition values and were termed Class 2 genes. The codon composition values of Class 1 and genes differed significantly. Neither Class 1 nor Class 2 genes had codon composition values identical to that of the host plant, Arabidopsis thaliana. However, Class 1 genes possessed codon composition values closer to those of the host than Class 2 genes. Examination of the genomes of three Rous sarcoma virus isolates indicated that codon composition values were similar for the gag, pol, and env genes but these genes differed significantly from the src genes. Since codon composition values for Rous sarcoma virus distinguished a "foreign" gene from the rest of the viral genome, it is possible that the Cauliflower mosaic virus genome is composed of genes from two different sources. Others have suggested that Cauliflower mosaic virus evolved in this manner and our data provide support for this hypothesis.     

A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor

MOTIVATION: Knowledge of how proteomic amino acid composition has changed over time is important for constructing realistic models of protein evolution and increasing our understanding of molecular evolutionary history. The proteomic amino acid composition of the Last Universal Ancestor (LUA) of life is of particular interest, since that might provide insight into the early evolution of proteins and the nature of the LUA itself. RESULTS: We introduce a method to estimate ancestral amino acid composition that is based on expectation-maximization. On simulated data, the approach was found to be very effective in estimating ancestral amino acid composition, with accuracy improving as the number of residues in the dataset was increased. The method was then used to infer the amino acid composition of a set of proteins in the LUA. In general, as compared with the modern protein set, LUA proteins were found to be richer in amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those believed to have been unavailable or scarce. Additionally, we found the inferred amino acid composition of this protein set in the LUA to be more similar to the observed composition of the same set in extant thermophilic species than in extant mesophilic species, supporting the idea that the LUA lived in a thermophilic environment. AVAILABILITY: The program is available at http://compbio.cs.princeton.edu/ancestralaa     

Prediction of protein secondary structure content using amino acid composition and evolutionary information

Knowing protein structure and inferring its function from the structure are one of the main issues of computational structural biology, and often the first step is studying protein secondary structure. There have been many attempts to predict protein secondary structure contents. Previous attempts assumed that the content of protein secondary structure can be predicted successfully using the information on the amino acid composition of a protein. Recent methods achieved remarkable prediction accuracy by using the expanded composition information. The overall average error of the most successful method is 3.4%. Here, we demonstrate that even if we only use the simple amino acid composition information alone, it is possible to improve the prediction accuracy significantly if the evolutionary information is included. The idea is motivated by the observation that evolutionarily related proteins share the similar structure. After calculating the homolog-averaged amino acid composition of a protein, which can be easily obtained from the multiple sequence alignment by running PSI-BLAST, those 20 numbers are learned by a multiple linear regression, an artificial neural network and a support vector regression. The overall average error of method by a support vector regression is 3.3%. It is remarkable that we obtain the comparable accuracy without utilizing the expanded composition information such as pair-coupled amino acid composition. This work again demonstrates that the amino acid composition is a fundamental characteristic of a protein. It is anticipated that our novel idea can be applied to many areas of protein bioinformatics where the amino acid composition information is utilized, such as subcellular localization prediction, enzyme subclass prediction, domain boundary prediction, signal sequence prediction, and prediction of unfolded segment in a protein sequence, to name a few.     

Composition of corn and distillers dried grains with solubles from dry grind ethanol processing

Increase in the demand for ethanol has resulted in growth in the dry grind (DG) ethanol industry. In DG processing, the whole corn kernel is fermented, resulting in two main coproducts, ethanol and distillers dried grains with solubles (DDGS). Marketing of DDGS is critical to the economic stability of DG plants. The composition of DDGS can vary considerably; this reduces market value. Factors that cause variation in composition need to be evaluated. The objective was to determine the relationship between composition of corn and composition of DDGS. Samples of corn and DDGS were obtained from a DG ethanol plant and analyzed for protein, fat, starch and other nutrients. Concentrations of protein, fiber and starch were similar to published data for corn but were higher for DDGS. Coefficients of variation for protein fat and fiber concentrations were similar for corn and DDGS. There were no significant correlations between concentrations of components in corn and those in DDGS. Variation in the composition of DDGS was not related to variation in corn composition and probably was due to variation in processing streams or processing techniques. This implies that reducing the variation in composition of DDG will require modification of processing strategies.     

Partitioning the effects of environmental and spatial heterogeneity on distribution of plant diversity in the Yellow River Estuary

For successful conservation and restoration of biodiversity, it is important to understand how diversity is regulated. In the ecological research community, a current topic of interest is how much of the variation in plant species richness and composition is explained by environmental variation (niche-based model), relative to spatial processes (neutral theory). The Yellow River Estuary (YRE) is a newly formed and fragile wetland ecosystem influenced by both the Yellow River and Bohai Bay. Here, we applied variance partitioning techniques to assess the relative effects of spatial and environmental variables on species richness and composition in the YRE. We also conducted a species indicator analysis to identify characteristic species for three subestuaries within the YRE. Partial redundancy analysis showed that the variations in species richness and composition were explained by both environmental and spatial factors. The majority of explained variation in species richness and composition was attributable to local environmental factors. Among the environmental variables, soil salinity made the greatest contribution to species abundance and composition. Soil salinity was the most important factor in the Diaokou subestuary, while soil moisture was the most important factor influencing species richness in the Qingshui and Chahe subestuaries. The combined effects of soil salinity and moisture determined species richness and composition in the wetlands. These results increase our understanding of the organization and assembly of estuarine plant communities.     

中国桫椤科植物叶、孢子和孢子囊环带元素的X-射线微区成分分析

用扫描电镜和X ray微区分析方法测定和分析了中国产的13种及变种的桫椤科植物的叶、孢子和孢子囊环带中元素组成和平均质量分数。结果表明这13种及变种植物在叶、孢子和孢子囊环带的元素组成上彼此均有一定的差异;在元素的平均质量分数上,差异更加明显;同一植物的叶、孢子和孢子囊环带元素组成大多不完全相同,在叶中的元素种类均多于孢子和孢子囊环带的元素;并且同一植物的叶、孢子和孢子囊环带中元素的平均质量分数差异也较大;13种及变种植物叶、孢子和孢子囊环带元素的的平均质量分数最高的大多为K元素,而孢子中质量分数最高的为Si元素。13种及变种的桫椤科植物在元素组成和平均质量分数上的差异可能与其结构、生理和生态环境有关。     

Using Pair-Coupled Amino Acid Composition to Predict Protein Secondary Structure Content

The pair-coupled amino acid composition is introduced to predict the secondary structure contents of a protein. Compared with the existing methods all based on singlewise amino acid composition as defined in a 20D (dimensional) space, this represents a step forward to the consideration of the sequence coupling effect. The test results indicate that the introduction of the pair-coupled amino acid composition can significantly improve the prediction quality. It is anticipated that the concept of the pair-coupled amino acid composition can be used to simplify the formulation of sequence coupling (or sequence order) effects and to study many other features of proteins as well.     

Nutrient limitation and nutrient‐driven shifts in plant species composition in a species‐rich fen meadow

Question: We studied the development and persistence of the effects of nutrient pulses on biomass production and species composition in a fen meadow. Location: Nature reserve, central Netherlands, 5 m a.s.l. Methods: Single pulse fertilization with N and P in a factorial design on an undrained central and a drained margin site in a species‐rich fen meadow (Cirsio dissecti‐Molinietum). Biomass production and species composition were monitored during four years. Results: At the central site, N addition boosted biomass production, but only during one year. The species composition was not changed. P fertilization increased the biomass production and changed the species composition from a vegetation dominated by Carex panicea to a grassland community with abundant Holcus lanatus, but not before the second year. At the margin site, P fertilization changed the species composition in a similar way, but biomass production was not increased. N fertilization had no effect. At both sites the P induced shift in species composition persisted for four years although the P effect declined during the experiment. Conclusions: The biomass responses show that N was limiting in the central site. Another nutrient, besides N and P (probably K) must have been limiting in the marginal site. The fast decline of the N effect on biomass is ascribed to increased denitrification and biomass removal. The delay in the P effect on biomass and species composition and the persistence of the P effect on species composition are ascribed to fast immobilisation and subsequent slow release of fertilizer P in the peat soil. Recurrence of the P pulses is expected to cause permanent changes in species composition.