Limits to convergence of vegetation during early primary succession

Questions: Primary succession, measured by changes in species composition, is slow, usually forcing a chronose‐quence approach. A unique data set is used to explore spatial and temporal changes in vegetation structure after a 1980 volcanic eruption. On the basis of data from a transect of 20 permanent plots with an altitudinal range of 250 m sampled through 2005, two questions are asked: Do changes along the transect recapitulate succession? Do plots converge to similar composition over time? Location: A ridge between 1218 and 1468 m on Mount St. Helens, Washington, USA. Methods: Repeat sampling of plots for species cover along a 1‐km transect. Floristic changes were characterized by techniques including DCA, clustering and similarity. Results: Species richness and cover increased with time at rates that decreased with increasing elevation. The establishment of Lupinus lepidus accelerated the rate of succession and may control its trajectory. Diversity (H) at first increased with richness, then declined as dominance hierarchies developed. Primary succession was characterized by overlapping phases of species assembly (richness), vegetation maturation (diversity peaks, cover expands) and inhibition (diversity declines). Each plot passed through several community classes, but by 2005, only four classes persisted. Succession trajectories (measured by DCA) became shorter with elevation. Similarity between groups of plots defined by their classification in 2005 did not increase with time. Similarity within plot groups converged slightly at the lower elevations. Despite similarities between temporal and spatial trends in composition, trajectories of higher plots do not recapitulate those of lower plots, apparently because Lupinus was not an early colonist. Any vegetation convergence has been limited to plots that are in close proximity.     

Validation of protein structure models using network similarity score

Accurate structural validation of proteins is of extreme importance in studies like protein structure prediction, analysis of molecular dynamic simulation trajectories and finding subtle changes in very similar structures. The benchmarks for today's structure validation are scoring methods like global distance test‐total structure (GDT‐TS), TM‐score and root mean square deviations (RMSD). However, there is a lack of methods that look at both the protein backbone and side‐chain structures at the global connectivity level and provide information about the differences in connectivity. To address this gap, a graph spectral based method (NSS—network similarity score) which has been recently developed to rigorously compare networks in diverse fields, is adopted to compare protein structures both at the backbone and at the side‐chain noncovalent connectivity levels. In this study, we validate the performance of NSS by investigating protein structures from X‐ray structures, modeling (including CASP models), and molecular dynamics simulations. Further, we systematically identify the local and the global regions of the structures contributing to the difference in NSS, through the components of the score, a feature unique to this spectral based scoring scheme. It is demonstrated that the method can quantify subtle differences in connectivity compared to a reference protein structure and can form a robust basis for protein structure comparison. Additionally, we have also introduced a network‐based method to analyze fluctuations in side chain interactions (edge‐weights) in an ensemble of structures, which can be an useful tool for the analysis of MD trajectories.     

Dynamics alignment: comparison of protein dynamics in the SCOP database

A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculated using the Gaussian network model and the modes of motion are globally aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. The alignment is fast and can be used to analyze large sets of proteins. The methodology is applied to the four major classes of the SCOP database: "all alpha proteins," "all beta proteins," "alpha and beta proteins," and "alpha/beta proteins". We show that different domains may have similar global dynamics. In addition, we report that the dynamics of "all alpha proteins" domains are less specific to structural variations within a given fold or superfamily compared with the other classes. We report that domain pairs with the most similar and the least similar global dynamics tend to be of similar length. The significance of the methodology is that it suggests a new and efficient way of mapping between the global structural features of protein families/subfamilies and their encoded dynamics.     

Fuzzy cluster analysis of molecular dynamics trajectories.

We propose fuzzy clustering as a method to analyze molecular dynamics (MD) trajectories, especially of proteins and polypeptides. A fuzzy cluster analysis locates classes of similar three-dimensional conformations explored during a molecular dynamics simulation. The method can be readily applied to results from both equilibrium and nonequilibrium simulations, with clustering on either global or local structural parameters. The potential of this technique is illustrated by results from fuzzy cluster analyses of trajectories from MD simulations of various fragments of human parathyroid hormone (PTH). For large molecules, it is more efficient to analyze the clustering of root-mean-square distances between conformations comprising the trajectory. We found that the results of the clustering analysis were unambiguous, in terms of the optimal number of clusters of conformations, for the majority of the trajectories examined. The conformation closest to the cluster center can be chosen as being representative of the class of structures making up the cluster, and can be further analyzed, for example, in terms of its secondary structure. The CPU time used by the cluster analysis was negligible compared to the MD simulation time.     

Pteridophyte diversity and species composition in four Amazonian rain forests

Abstract. Local variation in individual density, species composition, species richness and species diversity of terrestrial pteridophytes were studied at four sites in the tropical lowland rain forest of western Amazonia. 15 568 pteridophyte individuals representing 40 species were recorded in four plots. The variability among subplots within the same plot was considerable in all the characteristics measured (number of individuals, number of species, species diversity); the square 1‐ha plot was more homogeneous in these respects than any of the three 5 m by 1300 m transects. Species richness was affected by the density of individuals both within and among plots. Density of individuals was not affected by topographical position within any of the plots, whereas in some of the plots both species richness and species diversity were. Clustering and ordination analyses showed that floristically similar subplots could be found in different plots: although there was a tendency for subplots from the same plot to be floristically similar and therefore to group together, many recognized groups included subplots from two or more plots. Both within and among plots, the floristic differences corresponded to topographic position and were probably related to soil drainage. This was also evident in that the abundance patterns of many species followed the topography.     

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories

More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. The trajectories and analyses are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. Here, we describe the project and the structure and contents of our database, and provide examples of how it can be used to describe the global flexibility properties of proteins. Basic analyses and trajectories stripped of solvent molecules at a reduced resolution level are available from our web server.     

Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein

Protein dynamics make important but poorly understood contributions to molecular recognition phenomena. To address this, we measure changes in fast protein dynamics that accompany the interaction of the arabinose-binding protein (ABP) with its ligand, d-galactose, using NMR relaxation and molecular dynamics simulation. These two approaches present an entirely consistent view of the dynamic changes that occur in the protein backbone upon ligand binding. Increases in the amplitude of motions are observed throughout the protein, with the exception of a few residues in the binding site, which show restriction of dynamics. These counter-intuitive results imply that a localised binding event causes a global increase in the extent of protein dynamics on the pico- to nanosecond timescale. This global dynamic change constitutes a substantial favourable entropic contribution to the free energy of ligand binding. These results suggest that the structure and dynamics of ABP may be adapted to exploit dynamic changes to reduce the entropic costs of binding.     

Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families

Proteins that show similarity in their equilibrium dynamics can be aligned by identifying regions that undergo similar concerted movements. These movements are computed from protein native structures using coarse-grained elastic network models. We show the existence of common large-scale movements in enzymes selected from the main functional and structural classes. Alignment via dynamics does not require prior detection of sequence or structural correspondence. Indeed, a third of the statistically significant dynamics-based alignments involve enzymes that lack substantial global or local structural similarities. The analysis of specific residue-residue correspondences of these structurally dissimilar enzymes in some cases suggests a functional relationship of the detected common dynamic features. Including dynamics-based criteria in protein alignment thus provides a promising avenue for relating and grouping enzymes in terms of dynamic aspects that often, though not always, assist or accompany biological function.     

Cyclone damage to tropical rain forests: Species‐ and community‐level impacts

Abstract Severe Tropical Cyclone ‘Larry’ caused damage to 10 long‐term 0.5 ha monitoring plots in the rain forests of Queensland's Wet Tropics on 20 March 2006. We assessed the community‐level damage and the impact of the cyclone on the most abundant tree species in each plot. Damage was positively correlated with distance from the cyclone eye, though some plots received less damage than predicted owing to topographic shielding. Damage was patchy within plots, which is reflected in the range of damage‐classes recorded for each species, but there are broad trends in the type of response shown by different species. At the plot level, some species were either more susceptible or less susceptible to damage than the rest of the community. Species tended to show similar patterns of damage between plots with different community damage ratings. We discuss these response types in terms of adaptive tolerance to particular wind speeds and the trade‐off between frequently losing canopy volume in light winds, or rarely suffering substantial damage. We suggest that increased frequency of intense cyclones may affect the distribution of some species in the future, with those species most susceptible to high levels of damage at lower wind speeds becoming restricted to leeward‐facing slopes and upland areas away from the coast, and an increased abundance of resilient species in lowland coastal areas.     

Sampling Techniques Influence Understory Plant Trajectories After Restoration: An Example from Ponderosa Pine Restoration

Abstract Although there is no one correct technique for sampling vegetation, the sampling design chosen may greatly influence the conclusions researchers can draw from restoration treatments. Considerations when designing vegetation sampling protocol include determining what sampling attributes to measure, the size and shape of the sampling plot, the number of replicates and their location within the study area, and the frequency of sampling. We installed 20 point‐intercept transects (50‐m long), 8 belt transects (10 × 50 m), 10 adapted Daubenmire transects (four 0.5 × 2‐m plots), and 4 modified‐Whittaker plots (20 × 50 m with smaller nested plots) in treatment and control units to measure understory herbaceous response in a forest restoration experiment that tested different treatments. Point‐intercept transects on average recorded at least twice as much plant cover as did adapted Daubenmire transects and modified‐Whittaker plots taken at the same location for all control and treatment units. Point‐intercept transects and adapted Daubenmire plots on average captured fewer rare and exotic species in the control and treatment units in comparison with the belt transects and modified‐Whittaker plots. Modified‐Whittaker plots captured the highest species richness in all units. Early successional understory response to restoration treatments was likely masked by the response of the herbaceous community to yearly climatic variation (dry vs. wet years). Species richness and abundance were higher in wet years than dry years for all control and treatment units. Our results illustrate that sampling techniques can greatly influence perceptions of understory plant trajectories and therefore the interpretation of whether restoration goals have been achieved. In addition, our results suggest that restoration monitoring needs to be conducted for a sufficient length of time so that restoration treatment responses can be detected.     

Plot sizes used for phytosociological sampling of European vegetation

Abstract. In European phytosociology, variable plot sizes are traditionally used for sampling different vegetation types. This practice may generate problems in current vegetation or habitat survey projects based on large data sets, which include relevés made by many authors at different times. In order to determine the extent of variation in plot sizes used in European phytosociology, we collected a data set of 41 174 relevés with an indication of plot size, published in six major European journals focusing on phytosociology from 1970 to 2000. As an additional data set, we took 27 365 relevés from the Czech National Phytosociological Database. From each data set, we calculated basic statistical figures for plot sizes used to sample vegetation of various phytosociological classes. The results show that in Europe the traditionally used size of vegetation plots is roughly proportional to vegetation height; however, there is a large variation in plot size, both within and among vegetation classes. The effect of variable plot sizes on vegetation analysis and classification is not sufficiently known, but use of standardized plot sizes would be desirable in future projects of vegetation or habitat survey. Based on our analysis, we suggest four plot sizes as possible standards. They are 4 m² for sampling aquatic vegetation and low‐grown herbaceous vegetation, 16 m² for most grassland, heathland and other herbaceous or low‐scrub vegetation types, 50 m² for scrub, and 200 m² for woodlands. It has been pointed out that in some situations, sampling in either small or large plots may result in assignment of relevés to different phytosociological classes or habitat types. Therefore defining vegetation and habitat types as scale‐dependent concepts is needed.     

Should reference conditions be drawn from a single 10 ha plot? Assessing representativeness in a 10,000 ha old‐growth European beech forest

The management targets of modern forestry are often dictated by a desire to restore natural conditions, largely considered to be those found in contemporary reference sites. Beech reference sites are usually subjectively placed plots located in old‐growth reserves. Given the inherent variability in old‐growth, the validity of using a single such plot to guide restoration efforts is questionable. We therefore applied 3 methods to assess the representativeness of a 10 ha research plot in an old‐growth European beech (Fagus sylvatica L.) forest in Ukraine compared to an inventory of the entire 10,282 ha forest reserve. We compared the research plot to the 500‐m² inventory plots using (1) permutation tests of structure metrics, (2) synthetic multivariate structural condition, and (3) functional condition via the proportion of area assigned to 8 forest development phases. Despite up to 82% distributional overlap for some metrics, both the averages and distributions of individual structural metrics (e.g. basal area, tree diameters) differed significantly between the RP and the inventory, as did the synthetic structural condition and the proportion of late optimal and decay phases. Extrapolations from this subjectively placed plot to the surrounding old‐growth matrix would overestimate several stereotypical “old‐growth” structures. These results support the need to draw on multiple reference sites and metrics and to select restoration target conditions that account for the variability associated with naturally dynamic ecosystems. A lack of absolute representativeness does not, however, necessarily preclude the generalizability of process‐based dynamics from old‐growth remnants.     

Right‐ and left‐handed three‐helix proteins. II. Similarity and differences in mechanical unfolding of proteins

Here, we study mechanical properties of eight 3‐helix proteins (four right‐handed and four left‐handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right‐handed three‐helix domains are more mechanically resistant than the left‐handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps^?1, T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right‐handed domains have a larger number of contacts per residue and the radius of cross section than the left‐handed domains. Proteins 2014; 82:90–102. © 2013 Wiley Periodicals, Inc.     

Interactive Data Visualization for HIV Cohorts: Leveraging Data Exchange Standards to Share and Reuse Research Tools

Objective

To develop and disseminate tools for interactive visualization of HIV cohort data.

Design and Methods

If a picture is worth a thousand words, then an interactive video, composed of a long string of pictures, can produce an even richer presentation of HIV population dynamics. We developed an HIV cohort data visualization tool using open-source software (R statistical language). The tool requires that the data structure conform to the HIV Cohort Data Exchange Protocol (HICDEP), and our implementation utilized Caribbean, Central and South America network (CCASAnet) data.

Results

This tool currently presents patient-level data in three classes of plots: (1) Longitudinal plots showing changes in measurements viewed alongside event probability curves allowing for simultaneous inspection of outcomes by relevant patient classes. (2) Bubble plots showing changes in indicators over time allowing for observation of group level dynamics. (3) Heat maps of levels of indicators changing over time allowing for observation of spatial-temporal dynamics. Examples of each class of plot are given using CCASAnet data investigating trends in CD4 count and AIDS at antiretroviral therapy (ART) initiation, CD4 trajectories after ART initiation, and mortality.

Conclusions

We invite researchers interested in this data visualization effort to use these tools and to suggest new classes of data visualization. We aim to contribute additional shareable tools in the spirit of open scientific collaboration and hope that these tools further the participation in open data standards like HICDEP by the HIV research community.     

Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilisation

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change – fertilisation and herbivore loss – are affected by species pool size and spatial compositional heterogeneity. Fertilisation led to higher rates of local extinction, whereas turnover in herbivore exclusion plots was driven by species replacement. Overall, sites with more spatially heterogeneous composition showed significantly higher rates of annual turnover, independent of species pool size and treatment. Taking into account spatial biodiversity aspects will therefore improve our understanding of consequences of global and anthropogenic change on community dynamics.     

Floristic and functional affiliations of woody plants with climate in western Amazonia

Aim To test whether a direct relationship exists between the relative abundance of woody plant genera and precipitation regime along the north–south climate gradient of the western Amazon. Location Lowland rain forests in the western Amazon. Methods Floristic data on 91 woody plant genera, from 39 0.1‐ha plots across the western Amazon, and precipitation data from a 0.5° global data set were used to test for correlations between plant relative abundance (defined as percentage number of stems ≥ 2.5 cm diameter at breast height for each woody plant genus per plot) and derived dry‐season variables. Moisture preference was then assessed in terms of pioneer and shade‐tolerant life‐history strategy. Results There were significant associations between the distribution of plant relative abundances and seasonal precipitation variables in 34% of genera analysed. Significant differences were identified in size‐class distribution between dry affiliates and generalists. Dry affiliates were not dominant in any size class in any plot type, whereas climate generalists dominated most of the size classes in the dry plots and the mid‐range size classes in the wet plots. Dry‐affiliate genera were a minority, even in dry forests. Wet‐affiliate genera were correlated with shade tolerance, whereas genera with no rainfall affiliation were often pioneers. Main conclusions The results suggest that moisture variable seasonality influences community composition in a manner that can be related to the life‐history trade‐off between shade tolerance and pioneer ranking. One possible reason for higher diversity in wetter forests is that high rainfall amplifies the niche space available to shade‐tolerant plants. Determining which plant groups are constrained by which environmental variables can contribute to our understanding of how forest composition may be changing now, and how it may change under future climate: if shade‐tolerant trees are also drought‐intolerant, community structure in wet forests may be more vulnerable to future increases in moisture stress.     

Shifts in mollusc traits following floodplain reconnection: Testing the response of functional diversity components

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Smoluchowski dynamics of the vnd/NK‐2 homeodomain from Drosophila melanogaster: First‐order mode‐coupling approximation

This work is the first in a series devoted to applying mode coupling diffusion theory to the derivation of local dynamics properties of proteins in solution. The first‐order mode‐coupling approximation, or optimized Rouse–Zimm local dynamics (ORZLD), is applied here to derive the rotational dynamics of the bonds and compare the calculated with the experimental nmr ¹⁵N spin–lattice relaxation time behavior of the vnd/NK‐2 homeodomain from Drosophila melanogaster. The starting point for the calculations is the experimental three‐dimensional structure of the homeodomain determined by multidimensional nmr spectroscopy. The results of the computations are compared with experimentally measured ¹⁵N spin–lattice relaxation times T₁, at 34.5 and 60.8 MHz, to check the first‐order approximation. To estimate the relative importance of internal and overall rotation, both rigid and fluctuating dynamic models are examined, with fluctuations evaluated using molecular dynamics (MD) simulations. The correlation times for the fundamental bond vector time correlation function and for the second‐order bond orientational TCF are obtained as a function of the residue number for vnd/NK‐2. The stability of the corresponding local dynamics pattern for the fluctuating structure as a function of the length of the MD trajectory is presented. Diffusive dynamics, which is essentially free of model parameters even at first order in the mode‐coupling diffusion approach, confirm that local dynamics of proteins can be described in terms of rotational diffusion of a fluctuating quasi‐rigid structure. The comparison with the nmr data shows that the first‐order mode coupling diffusion approximation accounts for the correct order of magnitude of the results and of important qualitative aspects of the data sensitive to conformational changes. Indications are obtained from this study to efficiently extend the theory to higher order in the mode‐coupling expansion. These results demonstrate the promise of the mode‐coupling approach, where the local dynamics of proteins is described in terms of rotational diffusion of a fluctuating quasi‐rigid structure, to analyze nmr spin–lattice relaxation behavior. © 1999 John Wiley & Sons, Inc. Biopoly 49: 235–254, 1999     

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

Although the highly dynamic and mosaic organization of the plasma membrane is well-recognized, depicting a resolved, global view of this organization remains challenging. We present an analytical single-particle tracking (SPT) method and tool, multiple-target tracing (MTT), that takes advantage of the high spatial resolution provided by single-fluorophore sensitivity. MTT can be used to generate dynamic maps at high densities of tracked particles, thereby providing global representation of molecular dynamics in cell membranes. Deflation by subtracting detected peaks allows detection of lower-intensity peaks. We exhaustively detected particles using MTT, with performance reaching theoretical limits, and then reconnected trajectories integrating the statistical information from past trajectories. We demonstrate the potential of this method by applying it to the epidermal growth factor receptor (EGFR) labeled with quantum dots (Qdots), in the plasma membrane of live cells. We anticipate the use of MTT to explore molecular dynamics and interactions at the cell membrane.