Robustness of Taylor’s law under spatial hierarchical groupings of forest tree samples

Testing how well Taylor's law (TL) describes spatial variation of the population density of a species requires grouping sampling areas (patches of habitat) into blocks so that a mean and a variance of the population density can be calculated over the patches in each block. The relationship between specific groupings and TL remains largely unknown. Here, using tree counts from a deciduous forest, we studied the effect of four biological methods of grouping sampling areas into blocks on the form and parameters of TL. Regardless of the method of grouping, the species-specific basal area densities obeyed TL, and the estimated slopes were not significantly different from one grouping method to another. Surprisingly, TL remained valid when four kinds of randomizations were performed to the biological groupings and tree census. These randomizations randomly assigned sampling areas to blocks, and/or randomized the species composition within or across sampling areas. We found that the form of TL was robust to different grouping methods and species randomizations, but its parameter values depended significantly on species compositions at sampling areas.     

Area‐wide monitoring of potato tuberworm (Phthorimaea operculella) by pheromone trapping in Northern Italy: phenology,spatial distribution and relationships between catches and tuber damage

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Measures of precision for dissimilarity‐based multivariate analysis of ecological communities

Ecological studies require key decisions regarding the appropriate size and number of sampling units. No methods currently exist to measure precision for multivariate assemblage data when dissimilarity‐based analyses are intended to follow. Here, we propose a pseudo multivariate dissimilarity‐based standard error (MultSE) as a useful quantity for assessing sample‐size adequacy in studies of ecological communities. Based on sums of squared dissimilarities, MultSE measures variability in the position of the centroid in the space of a chosen dissimilarity measure under repeated sampling for a given sample size. We describe a novel double resampling method to quantify uncertainty in MultSE values with increasing sample size. For more complex designs, values of MultSE can be calculated from the pseudo residual mean square of a permanova model, with the double resampling done within appropriate cells in the design. R code functions for implementing these techniques, along with ecological examples, are provided.     

Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations

The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ～45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg(2)ATP, a monomer with bound Mg(2)ATP, and a homodimer with bound Mg(2)ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg(2)ATP. For the dimer with Mg(2)ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg(2)ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg(2)ATP is only approximately 2k(B)T higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg(2)ATP are much smaller than the overall reaction time, which is on the order of seconds.     

Activity budget of inshore Indo‐Pacific bottlenose dolphins (Tursiops aduncus): A critical evaluation of methods and comparison among other populations

Activity budgets are widely used to compare behavior patterns but sampling methods vary, rendering comparisons difficult. The two main methods used are instantaneous and continuous sampling. Their comparability was examined by applying them to data obtained from bottlenose dolphins in the Port River estuary, South Australia. They gave comparable results for activity budgets, but instantaneous sampling did not detect most of the behavioral events. Individual differences in behavior and/or follow duration influenced results. Variability in activity definitions and categories among studies makes comparative analysis difficult. Comparison of the Port River dolphin's activity budget with other inshore populations indicated the former spent more time feeding and resting, and less time traveling. The greater feeding time seemed to be due to small prey size rather than reduced abundance or unpredictable distribution. The reduced traveling time, possibly the result of low predation pressure and/or evenly distributed prey, gave them more time to rest. They traveled mostly at 2.5 kn or less, consistent with studies from other shallow areas. Most feeding was individual, probably on demersal species. Surface feeding incorporated physical barriers rather than cooperative behavior. Activity durations ranged from 2 s to 2.9 h, with mean durations varying from 7.8 to 22.9 min.     

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster

An enhanced conformational sampling method, multicanonical molecular dynamics (McMD), was applied to the ab intio folding of the 57-residue first repeat of human glutamyl- prolyl-tRNA synthetase (EPRS-R1) in explicit solvent. The simulation started from a fully extended structure of EPRS-R1 and did not utilize prior structural knowledge. A canonical ensemble, which is a conformational ensemble thermodynamically probable at an arbitrary temperature, was constructed by reweighting the sampled structures. Conformational clusters were obtained from the canonical ensemble at 300 K, and the largest cluster (i.e., the lowest free-energy cluster), which contained 34% of the structures in the ensemble, was characterized by the highest similarity to the NMR structure relative to all alternative clusters. This lowest free-energy cluster included native-like structures composed of two anti-parallel α-helices. The canonical ensemble at 300 K also showed that a short Gly-containing segment, which adopts an α-helix in the native structure, has a tendency to be structurally disordered. Atomic-level analyses demonstrated clearly that inter-residue hydrophobic interactions drive the helix formation of the Gly-containing segment, and that increasing the hydrophobic contacts accompanies exclusion of water molecules from the vicinity of this segment. This study has shown, for the first time, that the free-energy landscape of a structurally well-ordered protein of about 60 residues is obtainable with an all atom model in explicit water without prior structural knowledge.     

Spatial patterns of plant diversity below-ground as revealed by DNA barcoding

Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.     

Why replication is important in landscape genetics: American black bear in the Rocky Mountains

We investigated how landscape features influence gene flow of black bears by testing the relative support for 36 alternative landscape resistance hypotheses, including isolation by distance (IBD) in each of 12 study areas in the north central U.S. Rocky Mountains. The study areas all contained the same basic elements, but differed in extent of forest fragmentation, altitude, variation in elevation and road coverage. In all but one of the study areas, isolation by landscape resistance was more supported than IBD suggesting gene flow is likely influenced by elevation, forest cover, and roads. However, the landscape features influencing gene flow varied among study areas. Using subsets of loci usually gave models with the very similar landscape features influencing gene flow as with all loci, suggesting the landscape features influencing gene flow were correctly identified. To test if the cause of the variability of supported landscape features in study areas resulted from landscape differences among study areas, we conducted a limiting factor analysis. We found that features were supported in landscape models only when the features were highly variable. This is perhaps not surprising but suggests an important cautionary note - that if landscape features are not found to influence gene flow, researchers should not automatically conclude that the features are unimportant to the species' movement and gene flow. Failure to investigate multiple study areas that have a range of variability in landscape features could cause misleading inferences about which landscape features generally limit gene flow. This could lead to potentially erroneous identification of corridors and barriers if models are transferred between areas with different landscape characteristics.     

Histamine and H1 -histamine receptors faster venous circulation

The study has analysed the action of histamine in the rabbit venous system and evaluated its potential role in contraction during increased venous pressure. We have found that a great variety exists in histamine sensitivity and H(1) -histamine receptor expression in various types of rabbit veins. Veins of the extremities (saphenous vein, femoral vein, axillary vein) and abdomen (common iliac vein, inferior vena cava) responded to histamine by a prominent, concentration-dependent force generation, whereas great thoracic veins (subclavian vein, superior vena cavas, intrathoracic part of inferior vena cava) and a pelvic vein (external iliac vein) exhibited slight sensitivity to exogenous histamine. The lack of reactivity to histamine was not due to increased activity of nitric oxide synthase (NOS) or heme oxygenase-1. H(1) -histamine receptor expression of veins correlated well with the histamine-induced contractions. Voltage-dependent calcium channels mediated mainly the histamine-induced force generation of saphenous vein, whereas it did not act in the inferior vena cava. In contrast, the receptor-operated channels were not involved in this response in either vein. Tyrosine phosphorylation occurred markedly in response to histamine in the saphenous vein, but not in the inferior vena cava. Histamine induced a prominent ρ kinase activation in both vessels. Protein kinase C and mitogen-activated protein kinase (MAPK) were not implicated in the histamine-induced intracellular calcium sensitization. Importantly, transient clamping of the femoral vein in animals caused a short-term constriction, which was inhibited by H(1) -histamine receptor antagonist in vivo. Furthermore, a significantly greater histamine immunopositivity was detected in veins after stretching compared to the resting state. We conclude that histamine receptor density adapts to the actual requirements of the circulation, and histamine liberated by the venous wall during increased venous pressure contributes to the contraction of vessels, providing a force for the venous return.     

Quantifying soil organic carbon in complex landscapes: an example of grassland undergoing encroachment of woody plants

The invasion of woody plants into grass‐dominated ecosystems has occurred worldwide during the past century with potentially significant impacts on soil organic carbon (SOC) storage, ecosystem carbon sequestration and global climate warming. To date, most studies of tree and shrub encroachment impacts on SOC have been conducted at small scales and results are equivocal. To quantify the effects of woody plant proliferation on SOC at broad spatial scales and to potentially resolve inconsistencies reported from studies conducted at fine spatial scales, information regarding spatial variability and uncertainty of SOC is essential. We used sequential indicator simulation (SIS) to quantify spatial uncertainty of SOC in a grassland undergoing shrub encroachment in the Southern Great Plains, USA. Results showed that both SOC pool size and its spatial uncertainty increased with the development of woody communities in grasslands. Higher uncertainty of SOC in new shrub‐dominated communities may be the result of their relatively recent development, their more complex above‐ and belowground architecture, stronger within‐community gradients, and a greater degree of faunal disturbance. Simulations of alternative sampling designs demonstrated the effects of spatial uncertainty on the accuracy of SOC estimates and enabled us to evaluate the efficiency of sampling strategies aimed at quantifying landscape‐scale SOC pools. An approach combining stratified random sampling with unequal point densities and transect sampling of landscape elements exhibiting strong internal gradients yielded the best estimates. Complete random sampling was less effective and required much higher sampling densities. Results provide novel insights into spatial uncertainty of SOC and its effects on estimates of carbon sequestration in terrestrial ecosystem and suggest effective protocol for the estimating of soil attributes in landscapes with complex vegetation patterns.