Modeling compositional heterogeneity

Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.     

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     

Precipitation and elephants,not fire,shape tree community composition in Serengeti National Park,Tanzania

Savannas are spatially diverse, variable and are susceptible to high rates of disturbance from fire and herbivory. There is significant interest in woody cover dynamics in relation to disturbance regimes. Less effort has been devoted to understand processes that drive tree community composition. In this study, tree species composition data collected at the landscape scale in the Serengeti were used to identify key environmental factors driving variation in species composition. A system of 38 plots clustered within 10 sites spanning the mean annual precipitation (MAP) gradient was used to assess the relative role of bottom‐up (precipitation, soil nutrients and soil texture) vs. top‐down factors (fire and elephant herbivory) on tree community composition. We developed candidate models relating tree species composition (based on multivariate community analysis) to different combinations of plot‐level environmental covariates. Results suggest that tree community composition is largely driven by MAP and is associated with elephant population density. Strikingly, we found no evidence that fire influences species compositional turnover. In a second analysis, we used structural equation model (SEM) to explore the possible direction of association between elephant density and tree species composition. We compared a model that included elephant effects on composition to one that included community composition effects on elephant density. Results suggest that variation in elephant population density across space is more likely to drive tree community composition and not vice versa. We propose that precipitation and herbivory, rather than fire, determine tree species composition in Serengeti Acacia tree community.     

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.     

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。     

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.     

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。     

Separation and analysis of acylthioesters from higher plants

The fatty acid composition of acylthioesters, acyl-CoAs and acyl-ACPs, of four plant tissues has been determined. This composition is very different to that presented for the endogenous lipids in each tissue. The composition of acylthioesters in relation to the role of acyl carriers in lipid metabolism is discussed.     

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.     

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.     

Influence of subcutaneous injection of essential fatty acids on the stress-induced modifications of rat platelet aggregation and membrane lipid composition

Membrane lipids play an important role in the function of blood platelets but the mechanisms by which the lipid composition of the platelet membrane is adjusted remain unclear. It has been shown that stress and poly-unsaturated fatty acids modified the lipid composition of blood plasma and platelet lipids, but very little is known about the effect of stress and fatty acids on membrane platelet lipid composition. The purpose of the present investigation was to study the influence of the essential fatty acids: linoleic, linolenic and arachidonic acids on the composition of the platelet membrane lipids of rats assigned to heat and restraint stress. It was shown that injections of polyunsaturated fatty acids decrease or suppress the stress-induced increase in platelet aggregation, suppress the stress-induced modification of the composition of the platelet membrane lipids and modify the fatty acid composition of the platelet membrane phospholipids.     

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。     

Habitat variation in species composition of flea assemblages on small mammals in central Europe

We studied patterns of variation in species composition of flea assemblages on small mammals across different habitats of Slovakia and compared flea species composition within and across host species among habitats. We asked (1) how variable the composition of flea assemblages is among different populations of the same host occurring in different habitats and (2) whether the composition of flea assemblages in a habitat is affected either by species composition of hosts or by environmental affinities of this habitat. Between-habitat similarity in flea species composition increased with an increase in the similarity in host species composition. Species richness of flea assemblages of a host species correlated positively with mean number of cohabitating host species but not with the number of habitats occupied by a host species. Results of the ordination of flea collections from each individual host demonstrated that the first five principal components explained most of the variance in species composition of flea assemblages. The segregation between rodent and insectivore flea assemblages was easily discerned from the ordination diagram when flea assemblages were plotted according to their hosts. When flea assemblages were plotted according to their habitat affinities, the distinction of habitats based on variation in flea composition was not as clear. The results of ANOVA of each principal component showed the significant effect of both host species and habitat type. The variation in each principal component was explained better by the factor of host species compared with the factor of habitat type. Multidimensional scaling of flea assemblages within host species across habitats demonstrated that among-habitat variation in flea composition was manifested differently in different hosts.     

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.     

Pathways to interleukin-6 in healthy males and serious leisure male athletes: physical activity, body composition and age

Physical activity (PA) is beneficial to overall health, in part due to physiological changes that lower risk factors for cardiovascular disease, including reduced inflammation. However, the mechanism by which PA reduces inflammation is unclear. One possible pathway is that PA improves body composition which in turn reduces inflammation. To test this hypothesis, we used structural equation modeling (SEM) to assess PA-body composition -inflammation pathways, as well as influences of age. In a sample of 72 healthy males with a range of PA profiles (age 18-65, mean ± sd = ), we measured PA as metabolic equivalent tasks (as per the International PA Questionnaire), body composition as percent body fat, lean mass, and fat mass, and inflammation as plasma interleukin-6 (IL-6). We treated body composition in the SEM analysis as a latent variable indicated by the three measures. We performed statistical corrections for missing values and one outlier. The model demonstrated significant effects of PA on IL-6 both directly and through body composition. Percent body fat, fat mass, and lean mass were significant indicators of the body composition latent variable. Additionally, age showed an indirect effect on IL-6 through body composition, but no direct effect. The findings suggest that PA does improve inflammatory profile through improving body composition, but that other pathways also exist.     

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/.     

Multiscale analyses of mammal species composition--environment relationship in the contiguous USA

Relationships between species composition and its environmental determinants are a basic objective of ecology. Such relationships are scale dependent, and predictors of species composition typically include variables such as climate, topographic, historical legacies, land uses, human population levels, and random processes. Our objective was to quantify the effect of environmental determinants on U.S. mammal composition at various spatial scales. We found that climate was the predominant factor affecting species composition, and its relative impact increased in correlation with the increase of the spatial scale. Another factor affecting species composition is land-use-land-cover. Our findings showed that its impact decreased as the spatial scale increased. We provide quantitative indication of highly significant effect of climate and land-use-land-cover variables on mammal composition at multiple scales.     

Factors governing macrozoobenthic assemblages in perennial springs in north-western Switzerland

Springs are important freshwater habitats that provide refuge for many rare species. In this study, the fauna and abiotic parameters of 20 perennial springs in north-western Switzerland were investigated. Correlation of abiotic and macrozoobenthos data showed that physicochemical parameters had little impact on macrozoobenthic composition, whereas specific substrate parameters strongly influenced the composition of the macrofauna. Surprisingly, nonmetric multidimensional scaling did not reveal a grouping of springs with similar substrate composition or macrozoobenthic assemblages. However, discharge was identified as the factor significantly determining substrate and the composition of macroinvertebrate assemblages. This justifies the hypothesis that, variation in discharge is the disturbance factor governing the macrofaunal composition temporally and spatially within and between patches. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Associations of physical activity and inactivity with body tissue composition among healthy Polish women and women after mastectomy

The aim of the study is to determine the relationship between physical activity and body composition among healthy women and women who have had mastectomy. This is in order to establish whether physical activity of women after breast cancer treatment improves composition and distribution of body mass components to a degree which will allow to achieve the body composition of healthy women.