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Gradient Analysis (gradient + analysis)
Selected AbstractsActin-like protein 1 (ALP1) is a component of dynamic, high molecular weight complexes in Toxoplasma gondii,CYTOSKELETON, Issue 1 2010Jennifer L. Gordon Abstract Apicomplexan parasites, such as Toxoplasma gondii, rely on actin-based motility for cell invasion, yet conventional actin does not appear to be required for cell division in these parasites. Apicomplexans also contain a variety of actin-related proteins (Arps); however, most of these not directly orthologous to Arps in well-studied systems. We recently identified an apicomplexan-specific member of this family called Actin-Like Protein 1, (ALP1), which plays a role in the assembly of vesicular components recruited to the inner membrane complex (IMC) of daughter cells during cell division. In addition to its enrichment at daughter cell membranes, ALP1 is localized throughout the cytoplasm both diffusely distributed and concentrated in clusters that are detected by fluorescence microscopy, suggesting it forms complexes. Using quantitative optical imaging methods, including fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP), we demonstrated that ALP1 is a component of a large complex, and that it readily exchanges between diffusible and complex-bound forms. Sedimentation and density gradient analyses revealed that ALP1 is found in a freely soluble state as well as high molecular weight complexes. During cell division, ALP1 was dynamically associated with the IMC, suggesting it rapidly cycles between freely diffusible and complex forms during daughter cell assembly. © 2009 Wiley-Liss, Inc. [source] Phylogenetic beta diversity: linking ecological and evolutionary processes across space in timeECOLOGY LETTERS, Issue 12 2008Catherine H. Graham Abstract A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity. [source] Quantifying patterns and controls of mire vegetation succession in a southern boreal bog in Finland using partial ordinationsJOURNAL OF VEGETATION SCIENCE, Issue 6 2007E.-S. Tuittila Abstract Question: How do we distinguish between concurrent allogenic and autogenic forcings behind changing patterns in plant community structures during mire development? Location: Lakkasuo raised bog, southern Finland. Methods: Two radiometrically dated peat profiles were studied using high resolution plant macrofossil analysis. A combination of partial direct and indirect gradient analyses (CCA and DCA) was applied to quantify the role of different drivers of vegetation changes. Results: Autogenic hydroseral succession explained 16% of the compositional variation in the vegetation. Disturbance successions initiated by fire explained 15% of the variation in the hummock, but only 9% in the wetter lawn. The early post-disturbance successional stages were characterized by Eriophorum vaginatum. After partialling out the effects of peat depth and time since fire, a moisture gradient explained 29% of variation in the hummock core and 26% in the lawn. The analyses also indicated alternation between species with a similar niche. This interaction gradient explained 26% and 31% of the compositional variation in the hummock and lawn, respectively. The similar order of species replacement from both cores supported the existence of general directional succession in mire vegetation, both during the mire development and after fire events. The autogenic succession was slow and gradual while the disturbance successions were episodic and fast. Conclusion: Our results support the paradigm of the complex nature of mire vegetation dynamics where several interlinked agents have simultaneous effects. The approach of combining partial ordinations developed here appeared to be a useful tool to assess the role of different environmental factors in controlling the vegetation succession. [source] Rejecting the mean: Estimating the response of fen plant species to environmental factors by non-linear quantile regressionJOURNAL OF VEGETATION SCIENCE, Issue 4 2005Henning K. Schröder Abstract Question: Is quantile regression an appropriate statistical approach to estimate the response of fen species to single environmental factors? Background: Data sets in vegetation field studies are often characterized by a large number of zeros and they are generally incomplete in respect to the factors which possibly influence plant species distribution. Thus, it is problematic to relate plant species abundance to single environmental factors by the ordinary least squares regression technique of the conditional mean. Location: Riparian herbaceous fen in central Jutland (Denmark). Methods: Semi-parametric quantile regression was used to estimate the response of 18 plant species to six environmental factors, 95% regression quantiles were chosen to reduce the impact of multiple unmeasured factors on the regression analyses. Results of 95% quantile regression and ordinary least squares regression were compared. Results: The standard regression of the conditional mean underestimated the rates of change of species cover due to the selected factor in comparison to 95% regression quantiles. The fitted response curves indicated a general broad tolerance of the studied fen species to different flooding durations but a narrower range concerning groundwater amplitude. The cover of all species was related to soil exchangeable phosphate and base-richness. A relationship between soil exchangeable potassium and species cover was only found for 11 species. Conclusion: Considering the characteristics of data sets in vegetation science, non-linear quantile regression is a useful method for gradient analyses. [source] Fish assemblages as influenced by environmental factors in streams in protected areas of the Czech RepublicECOLOGY OF FRESHWATER FISH, Issue 1 2006M. Humpl Abstract,,, Three streams of comparable size located in different landscape-protected areas were selected for studying the effect of environmental factors on fish assemblages using indirect (detrended correspondence analysis, DCA) and direct (canonical correspondence analysis, CCA) gradient analysis. DCA of species showed well a gradient of assemblage changes in the longitudinal profile. DCA of sites stressed the variability between the fish assemblages of the three streams. This pattern was then confirmed by the highly significant between-stream CCA. In the within-site CCA, environmental factors explained 50.7% variability for presence,absence data and 58.3% for the relative abundance data. The analysis revealed that number of ponds and land use are the most influential factors of the strongest environmental gradient. However, in the partial CCAs, factor substratum type explained the largest proportion of the variability affecting fish in their habitat choice. Generally, presence,absence and relative abundance data of fish gave similar results in both DCA and CCA analyses; the same environmental factors proved to be important in both data type analyses. The environmental factors explain more variability than the regional (between-stream) one. The total proportion of variability explained by the presence,absence data analysis was 71.9% and in the relative abundance analysis even 80.8%. The environmental factors measured during the field survey explain 2.1- and 3.4-times more assemblages' variability than factors measured from a hydrological map. Resumen 1. Tres ríos de tamaño comparable localizados en diferentes áreas de paisaje protegido de la República Checa fueron seleccionados para estudiar el efecto de factores ambientales sobre los ensamblajes de peces. Para ello, utilizando análisis de gradientes indirectos (DCA) y directos (CCA). 2. El DCA para las especies enfatizó la variabilidad entre los ensamblajes de peces de los tres ríos. Este patrón fue confirmado por un CCA altamente significativo. Para la variabilidad dentro de la localidad, un CCA reveló que los factores ambientales explicaron un 50.7% para datos de presencia-ausencia y un 58.3% para las abundancias relativas. 3. Los análisis revelaron que el número de pozas y el uso del suelo fueron los factores de mayor influencia en el gradiente ambiental. Sin embargo, en el CCA parcial, el tipo de sustrato explicó la mayor proporción de la variabilidad que afecta a los peces en la elección de hábitat. 4. Generalmente los datos de presencia-ausencia y abundancia relativa produjeron resultados similares tanto en los análisis DCA como en los CCA; los mismos factores ambientales probaron ser importantes en los análisis de ambos tipos de datos. Los factores ambientales explicaron mas variabilidad que los regionales (entre ríos). La proporción total de variabilidad explicada por el análisis de los datos de presencia-ausencia fue 71.9% mientras que para las abundancias relativas fue de 80.8%. Los factores ambientales medidos durante los muestreos de campo explicaron 2.1 y 3.4 veces mas variabilidad que los factores medidos sobre mapas hidrológicos. [source] Herbage mass and nutritive value of herbage of extensively managed temperate grasslands along a gradient of shrub encroachmentGRASS & FORAGE SCIENCE, Issue 3 2009S. Kesting Abstract Semi-natural grasslands often serve as important reserves of biodiversity. In Europe extensive grazing by livestock is considered an appropriate management to conserve biodiversity value and to limit shrub encroachment. However, little is known about the influence of shrubs on agronomic values. A gradient analysis of shrub-invaded temperate grasslands (from shrub-free to pioneer forest) in Germany was carried out to test the hypothesis that herbage mass and variables describing nutritive value of herbage decrease with increasing shrub encroachment. The herbage mass of dry matter (DM), variables describing the nutritive value of herbage, composition of the vegetation and mean of Ellenberg's indicator values were analysed with respect to the extent of shrubs. There was a reduction of herbage mass of DM from 3570 to 210 kg ha,1 with increasing shrub encroachment. Metabolizable energy concentration of herbage ranged from 8·9 to 10·2 MJ kg,1 DM and crude protein concentration from 72 to 171 g kg,1 DM, both measures being positively correlated with shrub occurrence. Increasing shrub occurrence was associated with a decrease in water-soluble carbohydrates concentration (from 151 to 31 g kg,1) and a reduction in the indicator ,forage value'. The results indicate a potentially large agronomic value for shrub-encroached temperate grasslands. [source] Use of [125I]4,-iodoflavone as a tool to characterize ligand-dependent differences in Ah receptor behaviorJOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 6 2002Hollie I. Swanson Abstract We have synthesized [125I]4,-iodoflavone to study Ah receptor (AhR),ligand interactions by a class of AhR ligands distinct from the prototypic ligand 2,3,7,8-tetrachlorodibenzo- p -dioxin (TCDD). This radioligand allows the comparison of AhR,ligand interactions using a ligand that differs in AhR affinity, and yet has the same radiospecific activity as [125I]2-iodo-7,8-dibromodibenzo- p -dioxin. Specific binding of [125I]4,-iodoflavone with the AhR was detected as a single radioactive peak (,9.7 S) following density sucrose gradient analysis. Cytosolic extracts from both Hepa 1 and HeLa cells were used as the source of mouse and human AhR, respectively. A ,6.7 S form of radioligand-bound Ah receptor was detected in the high salt nuclear extracts of both cell lines. In HeLa cells approximately twofold more [125I]4,-iodoflavone,AhR 6 S complex, compared with [125I]2-iodo-7,8-dibromodibenzo- p -dioxin, was recovered in nuclear extracts. A comparison of the ability of 4,-iodoflavone and TCDD to cause time-dependent translocation of AhR-yellow fluorescent protein revealed that 4,-iodoflavone was more efficient at enhancing nuclear accumulation of the receptor. These results suggest that [125I]4,-iodoflavone is a particularly useful and easily synthesized ligand for studying the AhR. © 2002 Wiley Periodicals, Inc. J Biochem Mol Toxicol 16:298,310, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.10053 [source] The drought tolerance limit of Fagus sylvatica forest on limestone in southwestern GermanyJOURNAL OF VEGETATION SCIENCE, Issue 6 2008Stefanie Gärtner Abstract Question: What components of drought influence the drought limit of Fagus sylvatica forests? This study contributes to the ongoing discussion regarding the future of Fagus as a major component of central European forests. Location: The drought limit of F. sylvatica at its ecotone with forest dominated by Quercus pubescens, Q. petraea and their hybrids in two limestone regions (Klettgau, Schwäbische Alb) in southwestern Germany was compared. Methods: Vegetation relevés were classified and a gradient analysis was performed. The vegetation pattern was analysed with several drought relevant variables. Classification trees were used to determine the drought limits of the Fagus forest. Results: The Fagus, Quercus and the ecotone forests were floristically characterized. The lower humidity in the submontane Klettgau, compared to the montane Schwäbische Alb, was compensated for by greater soil moisture (ASWSC). Therefore, Fagus forest in the Schwäbische Alb grew on sites with ASWSC values similar to those of ecotone forest in Klettgau. Conclusions: The interaction between climatic and edaphic drought related factors demonstrates that drought is a complex edaphic-climatic factor. Both components contribute to limiting the distribution of Fagus. For the two regions in southwestern Germany, and under the existing climatic conditions, it could be shown that Fagus is able to dominate forests on soils with very low ASWSC (, 68 l.m -2). [source] Environment, disturbance history and rain forest composition across the islands of Tonga, Western PolynesiaJOURNAL OF VEGETATION SCIENCE, Issue 2 2006Janet Franklin Abstract Questions: How do forest types differ in their distinctiveness among islands in relation to environmental and anthropogenic disturbance gradients? Are biogeographic factors also involved? Location: Tonga, ca. 170 oceanic islands totalling 700 km2 spread across 8° of latitude in Western Polynesia. Method Relative basal area was analysed for 134 species of woody plants in 187 plots. We used clustering, indirect gradient analysis, and indicator species analysis to identify continuous and discontinuous variation in species composition across geographical, environmental and disturbance gradients. Partial DCA related environmental to compositional gradients for each major forest type after accounting for locality. CCA and partial CCA partitioned observed compositional variation into components explained by environment/disturbance, locality and covariation between them. Results: Differences among forest types are related to environment and degree of anthropogenic disturbance. After accounting for inter-island differences, compositional variation (1) in coastal forest types is related to substrate, steepness and proximity to coast; (2) in early-successional, lowland rain forest to proximity to the coast, steepness and cultivation disturbance; (3) in late-successional, lowland forest types to elevation. For coastal/littoral forests, most of the compositional variation (71%) is explained by disturbance and environmental variables that do not covary with island while for both early and late-successional forests there is a higher degree of compositional variation reflecting covariation between disturbance/environment and island. Conclusions: There are regional similarities, across islands, among littoral/coastal forest types dominated by widespread seawater-dispersed species. The early-successional species that dominate secondary forests are distributed broadly across islands and environmental gradients, consistent with the gradient-in-time model of succession. Among-island differences in early-successional forest may reflect differences in land-use practices rather than environmental differences or biogeographical history. In late-successional forests, variation in composition among islands can be partly explained by differences among islands and hypothesized tight links between species and environment. Disentangling the effects of anthropogenic disturbance history versus biogeographic history on late-successional forest in this region awaits further study. [source] Use of the ,-function to estimate the skewness of species responsesJOURNAL OF VEGETATION SCIENCE, Issue 6 2003Branko Karad Abstract. Response of a species to an environmental variable may be modeled and predicted using a wide spectrum of different functions. Contrary to other functions (Gaussian, polynomial etc), all parameters of the ,-function are interpretable in ecological terms. However, computational difficulties in the determination of the ,-function parameters initiated controversial debates on the applicability and usefulness of this function in vegetation modelling and gradient analysis. We propose a simple algorithm for fitting the ,-function to observed data. Analytic properties of the algorithm (its ability to recover the known species responses along gradients) are tested using a series of simulated data. In most cases the algorithm correctly estimated parameters of the simulated responses. [source] Fagus sylvatica forest vegetation in Greece: Syntaxonomy and gradient analysisJOURNAL OF VEGETATION SCIENCE, Issue 1 2001Erwin Bergmeier Abstract. This is the first comprehensive study on Fagus sylvatica s.l. forest communities in Greece. It is based on the multivariate analysis of more than 1100 relevés throughout the distribution area of Fagus in Greece, 60 % of which have been sampled within the last 15 years. The data were compiled from all relevant literature and from unpublished field studies. Prior to data analysis, taxonomic and floristic inaccuracies in older literature have been corrected, and some taxa aggregated. Status and distribution of Fagus in Greece, as well as historical and silvicultural aspects, are outlined. Classification resulted in 16 vegetation types defined by species composition, of which 10 units are ranked as association (of which two were described as new) or community, with six subcommunities included. Synonyms from the literature are given to all types. The floristic structure of the data set is displayed by a synoptic table and by DCA ordination. Community differentiation follows a complex edaphic-climatic-phytogeographic pattern. Apart from Fagus sylvatica ssp. orientalis forests of warm and dry habitats and low to medium altitudes which are related to deciduous Quercus forests, four Fagion community groups are distinguished which represent different habitat types: (1) cool, humid, mesotrophic; (2) cool, acidic; (3) high altitude, calcareous; (4) medium altitude, moderately warm and dry. The communities may be assigned to three regional suballiances, viz. (a) Doronico orientalis-Fagenion at medium altitudes of North-Central and East-Central Greece; (b) Doronico columnae-Fagenion in the far north and at high altitudes southward to East-Central Greece; (c) Geranio striati-Fagenion in the Northwest. Various types of thermophilous beech forest are assigned to (a) and (c), acidic forest to (b), and mesic Fagus forest to (b) and (c). [source] The effect of stationary phase on lipophilicity determination of , -blockers using reverse-phase chromatographic systemsBIOMEDICAL CHROMATOGRAPHY, Issue 10 2005Tomasz Welerowicz Abstract Evaluation of lipophilicity parameters for basic compounds using different chromatographic stationary phases is presented. An HPLC method for determination of lipophilic molecule,stationary phase interactions was based on gradient analysis. Differences in correlation between the lipophilicity of compounds and experimental chromatographic results obtained in pseudo-membrane systems showed a strong influence of stationary phase structure and physico-chemical properties. , -Blocker drugs with varying lipophilicity and bio-activity were chosen as test compounds. The stationary phases used for the study were monolithic rod-structure C18 and silica gel octadecyl phase SG-C18 as reference material. The second group was silica gel-based polar-embedded alkylamide and cholesterolic phases. The mobile phase was composed of acetonitrile or methanol with ammonium acetate, and a linear gradient of methanol and acetonitrile in mobile phase was performed. A linear correlation of plots of log kg = f(log P) was observed, especially for polar-embedded phases, and this allowed log PHPLC to be calculated. The behavior of stationary phases in methanol and acetonitrile buffer showed differences between obtained log PHPLC values. Copyright © 2005 John Wiley & Sons, Ltd. [source] | ||||||||||||||||