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。     

利用DGGE法研究不同种植体系中根际微生物群落结构

利用DGGE技术研究不同间作和轮作种植体系对作物根际细菌和真菌群落结构的影响.运用16SrDNA和18SrDNA特异引物对,将土壤中提取的总DNA进行PCR扩增后,通过DGGE技术对PCR产物进行分析,结果表明:玉米-蚕豆轮作对蚕豆根际细菌和真菌群落结构影响明显,二者都与单作蚕豆有较大差异;小麦/蚕豆间作明显改变两种作物根际细菌群落结构和蚕豆根际真菌群落结构;玉米/蚕豆间作明显改变玉米根际细菌、真菌群落结构和蚕豆根际真菌群落结构.     

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     

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/.     

Geographic variation in seed removal of a myrmecochorous herb: influence of variation in functional guild and species composition of the disperser assemblage through spatial and temporal scales

The ecological influence of changes in the functional guild and species composition of ant assemblages on ant‐dispersal mutualisms is still poorly known. Using a multi‐scale approach over an 800 km range within the Iberian Peninsula, we tested the hypothesis that variation in seed removal rate was related to functional guild rather than to species composition variations of disperser assemblages in the myrmecochore herb Helleborus foetidus. At least two premises must be confirmed to validate this hypothesis: 1) ant assemblages that are dissimilar in species composition but with similar functional guild composition will not differ significantly in seed removal, and 2) assemblages with different functional guild composition will render different seed removal services. We conducted 3328 ant‐visitor censuses on 462 individual plants to identify both the species composition and functional guild variation of the ant‐disperser assemblage, and the plant seed removal rate. Functional guild composition of the ant assemblage was determined by the proportion of visits of ants acting as legitimate dispersers, facultative dispersers or elaiosome predators. Results showed that ant‐seed dispersal success seemed to be more sensitive to species composition changes of the ant assemblage than to functional guild shifts. However, this sensitivity was scale‐dependent. Thus, at the fine, inter‐individual scale, seed removal covaried with the species and functional guild composition of the ant assemblages; at the inter‐populational scale, differences in seed removal tended to be related to the dissimilarity of the assemblage species composition rather than the assemblage functional guild; finally, inter‐regional differences in seed removal were unrelated to dissimilarities of the ant assemblage composition or functional guild. Though differences in seed removal and the relative frequency of the legitimate dispersers tended to be positively correlated, none of the above premises were fully confirmed in this study. Therefore, our results did not support in full the hypothesis that the variation in seed removal was explained by shifts in functional guild composition, rather than shifts in species composition.     

Makeup of the extracellular lipids in Rhodotorula glutinis yeasts

The fractional composition of extracellular lipids extracted with hexane and ethanol was studied in the yeast Rhodotorula glutinis 35 by thin-layer chromatography. The two extracts of extracellular lipids were found to be similar in composition though differing in the quantitative content of individual fractions. The fractional composition of extracellular lipids differed from that of intracellular lipids. The peculiarity of the fractional composition of extracellular lipids can be accounted for by the specificity of its fatty acid and alcohol composition.     

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.     

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.     

Identifying drivers of species compositional change in a semi‐natural upland grassland over a 40‐year period

Question: Few long‐term studies exist with integrated vegetation and soil composition data, coupled with detailed environmental driver records. Can changes in community composition in an upland grassland be identified by revisitation after a 40‐year period and allow the main environmental drivers of change to be identified? Location: Snowdon, Wales, UK. Methods: Changes in plant community and soil composition were assessed by resurveying an upland Agrostis–Festuca grassland in 2008, 40 years after the original survey. PCA and ecological indicators were used to determine changes in plant community composition. Redundancy analysis (RDA) allowed the impact of soil chemical composition on the vegetation community to be assessed. Results: A significant shift in community composition was found between years. A 35% reduction in species richness and an increase in the grass:forb ratio, suggest significant ecosystem degradation. Indicator values suggest acidification of the community with an increased acidity preference of species recorded in 2008. However, soil pH measurements showed that soil pH had increased. RDA suggested that the main shifts in species composition were correlated with an increase in pH and a reduction in soil exchangeable base cation concentration. Clear ecosystem responses to climate, land‐use change or nitrogen enrichment were not observed. Conclusions: Shifts in vegetation and soil composition are clearly identifiable after 40 years. The shifts in community composition are consistent with ecosystem degradation due to acidification during the period between surveys. Ecological indicator values and soil chemical composition displayed differing degrees of change. Whilst soils appear to be recovering from historic effects of sulphur deposition, vegetation community composition changes appear to lag behind those in soil chemistry.     

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.     

Predicting the chemical composition of the body and the carcass of hair sheep using body parts and carcass measurements

Determination of the chemical composition in the body and carcass of ruminants is important for both nutritional requirement studies and the meat industry. This study aimed to develop equations to predict the body and carcass chemical composition of hair sheep using the chemical composition of body parts, carcass measurements and shrunk BW as predictors. A database containing 107 individual records for castrated male hair sheep ranging from 24 to 43 kg BW was gathered from two body composition studies. The empty body, carcass and body parts were analyzed for water, ash, fat and protein contents (%). The body parts used to estimate body and carcass composition were fore leg, hind leg and 9–11th rib section. The carcass measurements used were leg length, thoracic circumference, hind circumference, hind width, thoracic width, thoracic depth and chest width. Each model performance was evaluated using a leave-one-out cross-validation. Multiple regression analysis considering the study as a random effect revealed that body parts in association with carcass measurements were significant for predicting the chemical composition in the body of castrate male sheep. However, the use of the chemical composition of hind leg produced the best models for predicting the ash and fat contents in the empty body, whereas the water and protein contents in the empty body were better predicted when using the chemical compositions of 9–11th rib section and fore leg, respectively. Multiple regression analysis also revealed that most body parts were suitable for predicting the carcass composition, except for 9–11th rib section whose chemical composition did not produce significant prediction equations for ash and protein carcass contents. The use of the chemical composition of hind leg in association with carcass measurements produced the best models for predicting the water and fat contents in the carcass, while the ash and protein contents in the carcass were better predicted when using the chemical composition of fore leg. In conclusion, precision, accuracy and goodness-of-fit of the equations drove the selection of the chemical composition of hind leg and carcass measurements in a multivariate approach, as the most suitable predictors of the chemical composition of the body and carcass of hair sheep. However, the chemical composition of fore leg may be used as well. The developed equations could improve the accuracy of the empty body and carcass composition estimations in sheep, optimizing the estimation of nutrient requirements, as well as the carcass quality evaluation for this species.     

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.     

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.     

Biodiversity of stream insects in the Malaysian Peninsula: spatial patterns and environmental constraints

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Seasonal Dynamics of Microbial Community Composition and Function in Oak Canopy and Open Grassland Soils

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (¹³C-PLFA). Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and ¹³C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function.     

How well can the fatty acid content of lake seston be predicted from its taxonomic composition?

1. Results from the few field studies that have tried to relate seston taxonomic and fatty acid (FA) composition suggest that phytoplankton composition only partially explains seston FA composition. However, in these studies, the heterotrophic components of seston (i.e. bacteria and heterotrophic protists) have not been accounted for. 2. The general premise of this article was that including the contribution of heterotrophs to seston biomass can improve understanding of the variability in seston FA composition. This was tested for an oligotrophic clearwater lake, in which the taxonomic and FA compositions of seston, fractionated into three size classes, were monitored every 2 weeks over a growth season. The relationship between seston taxonomic and FA composition was studied using canonical correlation analyses. 3. Because of their relative richness in branched FA and lack of highly unsaturated FAs (HUFA) compared to autotrophs and other protists, the contribution of bacteria to seston biomass was shown to explain an important part of the differences in FA composition between the different seston size classes. Phytoplankton seasonal succession also affected the FA composition of seston but only for size classes that were dominated by autotrophs. 4. The results also indicated that heterotrophic protists such as ciliates and heterotrophic nanoflagellates might substantially influence the seston FA, and especially, HUFA, composition. 5. The per cent of variability in seston FA composition that was explained by its taxonomic composition was still relatively low, even when taking account of heterotrophs. Hence, other possible influences, such as phytoplankton species composition, physiological state and the contribution of terrestrial detritus, need investigation.     

Factors affecting biochemical composition of seston in an eutrophic reservoir (Pampulha Reservoir, Belo Horizonte, MG)

Sestonic biochemical composition (lipids, proteins and carbohydrates) may change with varying environmental fluctuations. These changes and the effects in the nutritional status of algae consists of an actual increasing source of interest. The aims of this work were to establish the relationship between biochemical composition of seston and 1) a range of physical, chemical and climatological factors, and 2) the natural fluctuation in the species composition in phytoplankton assemblages of the Pampulha Reservoir, an urban eutrophic lake located in Belo Horizonte, MG. Seasonal changes in the biochemical composition were observed in this study. None of the considered abiotic factors alone seem to affect the biochemical composition. So the effects could only be understood by interactions among different environmental factors. On the other hand, the dominant algal groups probably have some influence in the observed changes in biochemical composition of seston.     

Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land-use types

Ammonia‐oxidizing bacteria (AOB) perform the rate‐limiting step of nitrification, a key ecosystem process that in part determines the fate of nitrogen in ecosystems. However, little is known about the factors that determine soil AOB diversity or composition, especially in tropical systems. Using a set of study systems in Costa Rica, we examined whether plant diversity or land‐use influenced AOB diversity or composition and whether AOB diversity or composition were associated with nitrification rates. We characterized the molecular diversity and composition of AOB via polymerase chain reaction amplification, cloning, and sequencing of 16S rDNA. We found that AOB diversity or composition did not change significantly across plant diversity treatments. In contrast, AOB differed among land‐use types in some measures of diversity and in composition, and differences in AOB composition among land‐use types were correlated with potential rates of nitrification. Our results suggest that anthropogenic changes of ecosystems can alter microbial communities in ways that may affect the processes they mediate.     

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.     

The Influence of Tropical Plant Diversity and Composition on Soil Microbial Communities

There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.