Population divergence of genetic (co)variance matrices in a subdivided plant species,Brassica cretica

Abstract The present study of Brassica cretica had two objectives. First, we compared estimates of population structure (Q_st) for seven phenotypic characters with the corresponding measures for allozyme markers (F_st) to evaluate the supposition that genetic drift is a major determinant of the evolutionary history of this species. Secondly, we compared the genetic (co)variance ( G ) matrices of five populations to examine whether a long history of population isolation is associated with large, consistent differences in the genetic (co)variance structure. Differences between estimates of F_st and Q_st were too small to be declared significant, indicating that stochastic processes have played a major role in the structuring of quantitative variation in this species. Comparison of populations using the common principal component (CPC) method rejected the hypothesis that the G matrices differed by a simple constant of proportionality: most of the variation involved principal component structure rather than the eigenvalues. However, there was strong evidence for proportionality in comparisons using the method of percentage reduction in mean‐square error (MSE), at least when characters with unusually high (co)variance estimates were included in the analyses. Although the CPC and MSE methods provide different, but complementary, views of G matrix variation, we urge caution in the use of proportionality as an indicator of whether genetic drift is responsible for divergence in the G matrix.     

Rarity and threat relationships in the conservation planning of Iberian flora

We analysed the threatened flora of Iberia (including the Balearic Islands) in order to define and explain factors related to levels of rarity and threat. Conservation measures were derived from the relationships observed. We used a random sample of 59 narrowly distributed plant species from the pool (588 species) of potentially endangered flora. Twelve variables were used to classify species into groups based on a multivariate technique: non-parametric principal component analysis. Our results do not indicate a single management model driven by a single mechanism of rarity. Four classes of rare plants were produced from the statistical algorithm: agamospermic species, plants associated with water, endemics, and range-margin (geographical-limit) plants. Some specific strategies for each of these groups are proposed, allowing further discussion and assessment. The overall pattern in conservation practice of threatened Iberian plants seems to be defined by three of the variables in use: ecological specificity, geographical rarity and rate of threat. None of the biological variables in the sample show particularly strong trends in the data.     

Exotic Grasses Potentially Slow Invasion of an N-fixing Tree into a Hawaiian Woodland

This paper examines the effect of an abundant non-native species, Schizachyrium condensatum, on establishment of a later arriving, but very potent invader, Myrica faya, in a seasonally dry forest on the island of Hawaii. Using a replicated removal experiment, we determined that S. condensatum, a perennial C4 grass, reduced recruitment of M. faya, an N-fixing tree species. Recruitment of Myrica was 90% higher in S. condensatum removal plots compared to controls. We believe that because S. condensatum substantially reduces light at the soil surface it reduces germination and early seedling growth of the M. faya. This revised version was published online in July 2006 with corrections to the Cover Date.     

Multivariate analysis of the Vicia sativa L. aggregate

GIL, J. & CUBERO, J. I., 1993. Multivariate analysis of the Vicia sativa L. aggregate . The sativa group of species was studied by using multivariate analysis and karyological analysis. Thirty biometrical characters were studied by using 92 Vicia sativa L. accessions from a variety of geographical sources. The four main taxa analysed were: sativa, macrocarpa, cordata and angustifolia. Principal component analysis provided clear separation among sativa, cordata and angustifolia in terms of the first two components. Karyotype analysis confirmed the PCA results, and by combining both methods, misclassed specimens can be correctly determined. Cluster analyses using the characters which displayed the greatest loads over the first components were performed in order to identify the most valuable characters from the taxonomic point of view. These were flower length, calyx length, pod width, constriction of the pod between seeds, leaf length, leaflet width, seed length and seed width. Our results suggest an early separation of angustifolia from the ancestral stem. The taxon cordata may be useful in future plant breeding programmes not only for crossing with V. saliva to increase the leaflet size of this taxon, but also as a bridge species between sativa and angustifolia.     

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

Alongside the well-studied membrane spanning helices, alpha-helical transmembrane (TM) proteins contain several functionally and structurally important types of substructures. Here, existing 3D structures of transmembrane proteins have been used to define and study the concept of reentrant regions, i.e. membrane penetrating regions that enter and exit the membrane on the same side. We find that these regions can be divided into three distinct categories based on secondary structure motifs, namely long regions with a helix-coil-helix motif, regions of medium length with the structure helix-coil or coil-helix and regions of short to medium length consisting entirely of irregular secondary structure. The residues situated in reentrant regions are significantly smaller on average compared to other regions and reentrant regions can be detected in the inter-transmembrane loops with an accuracy of approximately 70% based on their amino acid composition. Using TOP-MOD, a novel method for predicting reentrant regions, we have scanned the genomes of Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The results suggest that more than 10% of transmembrane proteins contain reentrant regions and that the occurrence of reentrant regions increases linearly with the number of transmembrane regions. Reentrant regions seem to be most commonly found in channel proteins and least commonly in signal receptors.     

矿质元素及pH值与栀子中栀子苷含量的相关性

为了探讨栀子苷含量与土壤及药材中的矿质元素的相关关系,用主成分分析方法对8个不同产地的栀子土壤中13种矿质元素及pH与药材中12种矿质元素进行了多因素分析.结果表明:Fe和Ni、Fe和Al、Mn和Co之间呈极显著正相关.影响栀子苷含量的Mg和pH贡献率分别为49.614%和20.826%,两者对栀子苷的变异贡献率最大.同时进行了栀子苷含量的变化与主成分的多元相关分析,证实了矿质元素与中药功效之间存在相关性.     

A computational insight into binding modes of inhibitors XD29, XD35, and XD28 to bromodomain-containing protein 4 based on molecular dynamics simulations

In the current work, conformational changes of bromodomain-containing protein 4 (1) (BRD4-1) induced by bindings of inhibitors XD29 (57G), XD35 (57F), and XD28 (L28) were investigated using molecular dynamics (MD) simulations and principal component analysis. The results demonstrate that inhibitor bindings produce significant effect on the motion of ZA loop in BRD4-1. Moreover, to further study binding modes of three inhibitors to BRD4-1, binding free energies of inhibitors to BRD4-1 were also calculated using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The results indicate that van der Waals interactions are main factors to modulate inhibitor bindings. Energy decomposition and hydrogen bond analysis demonstrate that residues Pro82, Leu92, Asn140, and Ile146 play important roles in binding processes of inhibitors to BRD4-1. This study is not only helpful for better understanding function and internal dynamics of BRD4-1, but also can provide a theoretical basis for rational designs of effective anticancer drugs targeting BRD4-1.     

Ethnic groups and biological diversity in medieval Spain: analysis of a Jew Necropolis from Sevilla

The skulls and mandibles of adults individuals from a Jewish necropolis of Sevilla (La Buhayra), (V–IX Cent. A.D.) have been analyzed. The results show that Sevillian Jews, both males and females, present narrow skulls with a notable dolichocrany. Sexual differences in both the height of the skull and the mandible robustness have been found. A comparison between Sevillian Jews and other Iberian samples from different epochs (Neolithic-Bronze to Centuries A.D.) has been carried out by means of a principal component analysis taken only into account the variability between groups. Results of the analysis showed a certain degree of biological differentiation between Sevillian and Catalonian Jews (XI–XIVth Centuries A.D.) which can be justified not only by the geographical distance and the temporal gap between the two groups, but also by the intrinsic heterogeneity of Jews (Nathan, 1961a, b; Nathan et al., 1963; Arensburg et al., 1980). The existence of some degree of biological variability between several ethnic-religious groups (Jew, Christians and Moslems) can be detected although they share a common Mediterranean background. Paper presented at the 4^th congress of the European Anthropology Association (Florence, Sept. 1984).     

Oligochaeta of the middle Po River (Italy): principal component analysis of the benthic data

The application of principal component analysis to two types of habitat (the benthos of macrophytes and of central river bed) enabled us to single out some of the factors that affect the dynamics and the structure of the oligochaete population and its various reactions to environmental conditions. As regards macrophytes, the distribution of the variables on the basis of the first component is correlated, to a certain extent, with a seasonal factor without any significant differences among sites. The largest population is most closely correlated with the summer months. In fact, we found that the Naididae and Tubificidae species generally develop in larger numbers at higher temperatures. For the Tubificidae, we could detect a precise seasonal cycle. In the central river bed habitat, the first component was correlated with the river discharge, which determines the granulometric characteristics of the sediment; we noticed a correlation among the sites that have the same characteristics, regardless of sampling site or date. The species which correlate most closely among themselves are the Tubificidae Limnodrilus hoffmeisteri, Tubifex tubifex, L. udekemianus and L. profundicola, which are very characteristic of environments that contain abundant organic matter. The second component is correlated with temperature, and hence with the availability of oxygen, which determines the presence and the abundance of more sensitive species.     

Analysis of the agglutinating activity from unicellular algae

Agglutinating activity often varies both between and within the algal species assayed. However, it is difficulty to interpret such variation without further analysis. We report a statistical analysis of agglutinating activities against human, cow, sheep, and pig erythrocytes, using cell extracts from 43 taxa (strains) of freshwater microalgae. Most of the extracts agglutinated erythrocytes from at least one of the sources, but pig erythrocytes appeared to be most suitable for the detection of agglutination reactions. Chlorella cell extracts preferentially agglutinated human erythrocytes, whereas extracts of other taxa were less active against mammalian erythrocytes. Cluster analysis generated four distinct subclusters of taxa, characterized by different specificities for antigens or carbohydrate receptors on the erythrocytes. Principal component analysis further separated the agglutination characteristics of Chlamydomonas from Chlorella on the first two components. Specificity for pig erythrocytes accounted for most of the clustering or grouping of algal taxa in multivariate analysis. However, clustering or grouping patterns of Chlorella species on haemagglutinating activity resembled that based on DNA sequences, revealing a possible genetic connection of agglutinins and their biochemical characteristics in algal cells. Variability of agglutination reactions among the algae investigated is simplified and interpreted most easily using multivariate analysis.     

适宜印度块菌生长的地形和土壤因子

在云南、四川和西藏印度块菌产区的9个地点进行调查和采样,选择地形因子和土壤因子为评价指标,采用主成分分析法对印度块菌生长适宜性进行综合评价,以确定印度块菌的生长与地形因子和土壤因子的关系.结果表明:1)地形因子和土壤因子15个指标中提取出的5个主成分,累计贡献率达到87.5％.地形因子中坡位对块菌生长的影响最大,坡位越高越不适宜块菌生长,以中坡和中下坡最佳.2)土壤因子中容重、粉粒含量、pH值、全氮含量、交换性钙镁含量是块菌生长的限制因子.容重为0.65～0.82 g· cm-3适宜块菌生长,而容重过高(＞1 g·cm-3)不利于块菌的生长;粉粒含量为30.0％、砂粒含量为55.0％左右适宜块菌的生长,而粘粒含量过高不利于块菌的生长.在土壤化学因子中,pH值在6.40左右、全氮为2.29 ～3.70 g·kg-1、交换性钙为22.91～37.17 cmol·kg-1、交换性镁含量为1.85～2.59 cmol·kg-1的环境条件适宜块菌生长.3)综合评价表明,在9个采集地点,云南省昆明市哨上村和西藏自治区林芝地区江色岗得分较高,其地形和土壤条件最适合块菌生长;而四川省攀枝花市二十九梁子和云南省楚雄州五顶山得分较低,其地形和土壤条件不太适宜印度块菌生长.     

非线性映射法用于鼠尾草属植物的分析鉴定

运用梯度洗脱测定鼠尾草鼠植物中9个主要成分含量的实验数据,对鼠尾草属13个种26个样本进行非线性映射分析鉴定。结合BASICA语言程序,采用主成分分析法给出二维平面上的初始坐标,并运用逐点迭代循环至误差函数E最小,得到各样本的最终坐标,映射到二维空间,进行直观分析。能够直观地将孤隔鼠尾草亚属与荔枝草亚属的样本分离开来,具有一定合理性与实用性。     

The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor

Muscle contraction is driven by a cycle of conformational changes in the myosin II head. After myosin binds ATP and releases from the actin fibril, myosin prepares for the next power stroke by rotating back the converter domain that carries the lever arm by 60 degrees . This recovery stroke is coupled to the activation of myosin ATPase by a mechanism that is essential for an efficient motor cycle. The mechanics of this coupling have been proposed to occur via two distinct and successive motions of the two helices that hold the converter domain: in a first phase a seesaw motion of the relay helix, followed by a piston-like motion of the SH1 helix in a second phase. To test this model, we have determined the principal motions of these structural elements during equilibrium molecular dynamics simulations of the crystallographic end states of the recovery-stroke by using principal component analysis. This reveals that the only principal motions of these two helices that make a large-amplitude contribution towards the conformational change of the recovery stroke are indeed the predicted seesaw and piston motions. Moreover, the results demonstrate that the seesaw motion of the relay helix dominates in the dynamics of the pre-recovery stroke structure, but not in the dynamics of the post-recovery stroke structure, and vice versa for the piston motion of the SH1 helix. This is consistent with the order of the proposed two-phase model for the coupling mechanism of the recovery stroke. Molecular movies of these principal motions are available at http://www.iwr.uni-heidelberg.de/groups/biocomp/fischer.     

Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling

A molecular dynamics study of pig heart citrate synthase is presented that aims to directly address the question of whether, for this enzyme, the ligand-induced closed domain conformation is accessible to the open unliganded enzyme. The approach utilises the technique of essential dynamics sampling, which is used in two modes. In exploring mode, the enzyme is encouraged to explore domain conformations it might not normally sample in free molecular dynamics simulation. In targeting mode, the enzyme is encouraged to adopt the domain conformation of a target structure. Using both modes extensively, it has been found that when the enzyme is prepared from a crystallographic open-domain structure and is in the unliganded state, it is unable to adopt the crystallographic closed-domain conformation of the liganded enzyme. Likewise, when the enzyme is prepared from the crystallographic closed liganded conformation with the ligands removed, it is unable to adopt the crystallographic open domain conformation. Structural investigations point to a common structural difference that is the source of this energy barrier; namely, the shift of alpha-helix 328-341 along its own axis relative to the large domain. Without this shift, the domains are unable to close or open fully. The charged substrate, oxaloacetate, binds near the base of this helix in the large domain and the interaction of Arg329 at the base of the helix with oxaloacetate is one that is consistent with the shift of this helix in going from the crystallographic open to closed structure. Therefore, the results suggest that without the substrate the enzyme remains in a partially open conformation ready to receive the substrate. In this way, the efficiency of the enzyme should be increased over one that is closed part of the time, with its binding site inaccessible to the substrate.     

Assessment of Heavy Metal Contamination in the Sediments of the Shuangtaizi Estuary Using Multivariate Statistical Techniques

In order to assess heavy metal pollution of sediment samples collected from Shuangtaizi estuary, contamination factor (CF) and multivariate statistical analyses, including principal component analysis (PCA), cluster analysis (CA) and correlation analysis, are carried out in this paper. CF confirms that Pb, Cu and Hg concentrations are very low and all fall within the range of background, while Zn and Cd demonstrate moderate contamination (in A10, A13, A15, A16 and A17 sites) and very high contamination (in A10, A13, A15 and A17 sites), respectively. The PCA indicates that four significant principal components (PCs) are extracted, explaining 88.959% of total variance, which suggests that Pb, Cu and Zn are mainly associated with organic carbon (OC). The result from CA is consistent with that obtained from PCA, classifying that the heavy metals in two clusters derive from different sources. Correlation analysis supports the conclusions from PCA and CA, elucidating the relationships between heavy metals and particle sizes of the sediments.     

Restoring Lepidopteran Communities to Oak Savannas: Contrasting Influences of Habitat Quantity and Quality

Ecological restoration is deemed important for the long‐term conservation of biodiversity, but ecologists still lack an understanding of how habitat availability and habitat quality in a restored system interact to determine species diversity. This problem seems particularly apparent in Tallgrass Prairie and savanna ecoregions, where restored management units represent the majority of extant habitat. In this study, we tested three principal hypotheses, each stating that the diversity of Lepidoptera would be greater in (1) patches of savanna habitat that were larger; (2) patches that were of higher habitat quality; and (3) patches that had greater connectivity to management units of similar physiognomy. Lepidoptera were sampled in 2003 from 13 unmanaged woodland remnants within Neal Smith National Wildlife Refuge, a 2,292‐ha prairie and savanna reconstruction project. We also measured 11 environmental variables within each site to assess variation in habitat quantity and quality. Principal components analysis (PCA) was used to identify major gradients of environmental variation among the 13 sites. Our PCA differentiated among woodlands along three environmental gradients, defined by (1) stand size, shape, topography, and oak dominance; (2) degree of disturbance; and (3) isolation. Total lepidopteran species richness, however, was only predicted by variation in the first principal component. Species richness of Lepidoptera known to be oak specialists was significantly affected by variation along all three PCA gradients. Surprisingly, more isolated woodland remnants contained a greater richness of oak feeders. Our results suggest that approaches to restoring oak savannas should emphasize aspects of both habitat quantity and quality. Beyond making individual management units larger, priority sites for restoration should possess a low importance of trees that are indicative of past habitat disturbance (e.g., Honey locust, White mulberry) even if canopy closure is substantial. Connectivity among restored habitats may benefit savanna moth communities only when habitat linkages contain a flora similar in composition to focal patches.     

Multivariate analysis of phyto-climatic patterns of the Croatian part of the eastern Adriatic coast

ABSTRACT

The present study analyses the climatic patterns of that part of the eastern Adriatic coast belonging to the Republic of Croatia and the narrow zone of the inlands. This area comprises a part of the Mediterranean phytogeographic region characterised by the Mediterranean climate type, and the transitional area towards the Eurosiberian phytogeographic region influenced by the continental climate type. The analysis was performed using multivariate numerical methods, cluster analysis following by the inertia analysis, and Principal Components Analysis with partitioning, considering the principal local climatic gradients in the data set. Six main climate classes were obtained. The results are biologically more interpretable than those obtained by using either numerical indices or the Walter climate diagram system. This suggests that multivariate numerical methods could be more efficient tools for detecting biologically significant climatic patterns on a small spatial scale.     

Distribution of diatom surface sediment assemblages within Effingham Inlet, a temperate fjord on the west coast of Vancouver Island (Canada)

Twenty-nine surface sediment samples from Effingham Inlet, a small fjord on the west coast of Vancouver Island, British Columbia, were analyzed for diatoms. This fjord has been selected for paleoceanographic investigation due to the presence of laminated sediments resulting from the dysoxic to anoxic bottom water conditions in the inner and outer basins of the inlet. Distributional patterns of the diatom microflora reflected proximity to littoral regions, phytoplankton production, and marine influence from outside the fjord. Principal components and cluster analyses of the microflora established four diatom assemblages with a clear separation between the inner and outer basin diatom floras. Inner basin stations were characterized by elevated absolute abundance with assemblages dominated by spring–early summer bloom taxa including Skeletonema costatum, Thalassiosira nordenskioeldii, and Thalassiosira pacifica. Chaetoceros spp. resting spores were abundant throughout Effingham Inlet, with the exception of the stations closest to the fjord head. Stations located in the outer basin and towards the fjord mouth had relatively lower absolute abundance yet showed a higher relative and absolute abundance of Thalassionema nitzschioides, Rhizosolenia setigera, Coscinodiscus radiatus, Ditylum brightwellii, Odontella longicruris, and Paralia sulcata in relation to the inner basin. Many of these latter taxa are often associated with late summer and autumn conditions in fjords along coastal British Columbia. Oceanographic data for Effingham Inlet suggest that increased offshore penetration is more likely to occur from summer to early fall, with a more restricted offshore influence in the inner basin. Diatom surface sediment assemblages in Effingham Inlet appear to reflect incursions of offshore waters into the fjord. Absolute abundance estimates and the preservation of lightly silicified taxa suggest excellent preservation of fossil material in the sediments of the predominantly anoxic inner basin. Preservation in the outer basin is reduced, reflecting more frequent recharge by oxygenated waters spilling over the outer sill into the basin. Our findings suggest the inner basin should be an optimal site for reconstruction of diatom production, with records from the outer basin providing more consistent information about offshore influence and coastal upwelling conditions over the Holocene. Estimates of diatom abundance within the inner basin sediment may serve as a good proxy of production, although proxy tracers of bottom water conditions and sedimentological analyses must be coupled to the diatom record to ensure depositional conditions were not influencing valve preservation or abundance. Our results suggest that fjords can serve as good environments for paleoceanographic reconstructions of both inshore and offshore conditions although careful site selection and understanding of processes affecting the microfossil record are essential.     

Characterization of Starch Granules from Waxy,Nonwaxy, and Hybrid Seeds of Amaranthus hypochondriacus L.

Perisperm starch granules of the dicotyledonous plant Amaranthus hypochondriacus L. were prepared from two homozygous lines (WxWx and wxwx) and their hybrid (Wxwx). The hybrid line was obtained by natural hybridization. By Sephadex G-75 column chromatography of isoamylase-debranched starches, the amylose content of WxWx starch was 16.9%, that of Wxwx was 10.7, and wxwx was zero. SDS-polyacrylamide gel electrophoresis showed that starch granules from two genotypes (WxWx and Wxwx) contained a Wx protein (MW = 68,000) which was supposed to be a starch granule-bound starch synthase and was associated with amylose synthesis, as observed in nonwaxy maize. The intensities of the stained protein bands were apparently correlated with the number of the Wx alleles. The Wx protein was not detected in the wxwx starch. These findings suggest that the Wx allele produces the Wx protein and amylose in the perisperm of A. hypochondriacus, with incomplete dominance over the wx allele. The Wx allele did not affect the fine structure of amylopectin and had little if any effect on susceptibility to glucoamylase and pasting properties of starch granules from these genotypes.