Does habitat structure matter? Spatially explicit population modelling of an Iberian gypsum endemic

Habitat heterogeneity may influence plant demography because conditions for survival, growth, and reproduction vary within a species’ range. We assessed the role of microhabitat spatial structure on the demography of Helianthemum squamatum, a shrubby gypsum specialist endemic to the Iberian Peninsula. We evaluated the demographic effect of microhabitat spatial variation using an approach that combined cellular automata with matrix population models, and included environmental and demographic stochasticty. We collected data on seed bank (2003–2005), seedling emergence (2003–2006), and adult survivorship (2004–2007) for H. squamatum in two independent blocks with different grazing intensity in Belinchón (Cuenca, Spain). We built spatial scenarios for each block based on field data of cover and spatial pattern of four microhabitats: lichenic crust, litter, H. squamatum, and shrub. Seedling survivorship was affected by year, block, and microhabitat, with individuals emerging under conspecifics having the highest survival rate and on litter the lowest in both blocks, whereas the effect of crust and other shrubs differed across blocks. Our models indicated population increase in the block with low grazing, but population decline in the block with intense grazing. We hypothesize that higher pressure of livestock grazing and trampling leads to a shift in relative microhabitat suitability for crust and shrub. This potential effect of grazing on spatial demographic variation opens interesting questions for future research. We emphasize the importance of considering microhabitat spatial structure when evaluating management and conservation strategies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Model for Multi-site Pacing of Fibrillation Using Nonlinear Dynamics Feedback

Traditionally, cardiac defibrillation requires a strong electric shock. Many unwanted side effects of this shock could be eliminated if defibrillation were performed using weak stimuli applied to several locations throughout the heart. Such multi-site pacing algorithms have been shown to defibrillate both experimentally (Pak et al., Am J Physiol 285:H2704–H2711, 2003) and theoretically (Puwal and Roth, J Biol Systems 14:101–112, 2006). Gauthier et al. (Chaos, 12:952–961, 2002) proposed a method to pace the heart using an algorithm based on nonlinear dynamics feedback applied through a single electrode. Our study applies a related but simpler algorithm, which essentially configures each electrode as a demand pacemaker, to simulate the multi-site pacing of fibrillating cardiac tissue. We use the numerical model developed by Fenton et al. (Chaos, 12:852–892, 2002) as the reaction term in a reaction–diffusion equation that we solve over a two-dimensional sheet of tissue. The defibrillation rate after pacing for 3 s is about 30%, which is significantly higher than the spontaneous defibrillation rate and is higher than observed in previous experimental and theoretical studies. Tuning the algorithm period can increase this rate to 45%. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Occurrence and variability of River Habitat Survey features across Europe and the consequences for data collection and evaluation

River Habitat Survey (RHS) data collected for the EU-funded STAR project was used to identify hydromorphological characteristic features of rivers in four European regions namely: lowlands; mountain; the Alps; and the Mediterranean. Using RHS attributes, Habitat Quality Assessment (HQA) – a measure of natural habitat diversity, and Habitat Modification Score (HMS) – a measure of anthropogenic modification, we identified considerable differences in frequency, diversity and evenness of features between the regions. A relatively small subset of features clearly distinguish the hydromorphological characters of lowland, Alpine and southern European rivers. It was more difficult to distinguish mountain rivers from Alpine rivers. The highest statistical differences are observed between Lowland and Mountain region. Within the four regions studied the RHS attributes that most strongly influence the HQA and HMS indices were identified. We conclude that specific effort should be made to ensure these are recorded properly as part of the quality control of RHS data. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Assessing the scale-specific importance of niches and other spatial processes on beta diversity: a case study from a temperate forest

Niche processes and other spatial processes, such as dispersal, may simultaneously control beta diversity, yet their relative importance may shift across spatial and temporal scales. Although disentangling the relative importance of these processes has been a continuing methodological challenge, recent developments in multi-scale spatial and temporal modeling can now help ecologists estimate their scale-specific contributions. Here we present a statistical approach to (1) detect the presence of a space–time interaction on community composition and (2) estimate the scale-specific importance of environmental and spatial factors on beta diversity. To illustrate the applicability of this approach, we use a case study from a temperate forest understory where tree seedling abundances were monitored during a 9-year period at 40 permanent plots. We found no significant space–time interaction on tree seedling composition, which means that the spatial abundance patterns did not vary over the study period. However, for a given year the relative importance of niche processes and other spatial processes was found to be scale-specific. Tree seedling abundances were primarily controlled by a broad-scale environmental gradient, but within the confines of this gradient the finer scale patchiness was largely due to other spatial processes. This case study illustrates that these two sets of processes are not mutually exclusive and can affect abundance patterns in a scale-dependent manner. More importantly, the use of our methodology for future empirical studies should help in the merging of niche and neutral perspectives on beta diversity, an obvious next step for community ecology. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Spatiotemporal variation in reproductive parameters of yellow-bellied marmots

Spatiotemporal variation in reproductive rates is a common phenomenon in many wildlife populations, but the population dynamic consequences of spatial and temporal variability in different components of reproduction remain poorly understood. We used 43 years (1962–2004) of data from 17 locations and a capture–mark–recapture (CMR) modeling framework to investigate the spatiotemporal variation in reproductive parameters of yellow-bellied marmots (Marmota flaviventris), and its influence on the realized population growth rate. Specifically, we estimated and modeled breeding probabilities of two-year-old females (earliest age of first reproduction), >2-year-old females that have not reproduced before (subadults), and >2-year-old females that have reproduced before (adults), as well as the litter sizes of two-year old and >2-year-old females. Most reproductive parameters exhibited spatial and/or temporal variation. However, reproductive parameters differed with respect to their relative influence on the realized population growth rate (λ). Litter size had a stronger influence than did breeding probabilities on both spatial and temporal variations in λ. Our analysis indicated that λ was proportionately more sensitive to survival than recruitment. However, the annual fluctuation in litter size, abetted by the breeding probabilities, accounted for most of the temporal variation in λ. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ecological relationships between phytoplankton communities and different spatial scales in European reservoirs: implications at catchment level monitoring programmes

Phytoplankton communities are structured by factors acting over temporal and spatial scales. Identifying which factors are driving spatial patterns in aquatic communities is the central aim of ecology. In this study, data sets of phytoplankton communities and environmental data of two Portuguese reservoirs types (lowland “riverine reservoirs” and higher altitude “artificial lake reservoirs”) were used to determine the importance of environmental variables at different spatial (geographical, regional and local) and time scales (seasons, years) on the community structure. In all the data sets, the multivariate ordination technique Canonical Correspondence Analysis (CCA) showed that regional and local scales explained the majority (9–18% and 13–19%, respectively) of the taxa variance. However, for “riverine reservoirs”, time variables were more important, explaining 27% of the variability in phytoplankton assemblages. Variance partitioning was used to assess the individual importance of the three spatial scales and time for the community structure of the two reservoir types. The majority of among-site variability (5.9–21.4%) was accounted for by time variables, with local, regional, and geographical scale variables accounting for 3.3–5.6%, 3.7–4.5% and 2.6–2.9%, respectively. The effects of different spatial scales on phytoplankton communities were clearly interrelated; thus, implying that phytoplankton assemblages are capable of detecting stress from catchment to site scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: J. Padisak     

Controlled Release of Food Lipids Using Monoglyceride Gel Phases Regulates Lipid and Insulin Metabolism in Humans

We describe a solid vegetable oil–water gel structure which is stabilized through the use of low concentrations of monoglycerides, containing no added trans fats or saturated fats. The resulting structure consists of oil droplets encapsulated in self-assembled crystalline monoglyceride multilayers, surrounded by a continuous water phase. Acute ingestion human feeding trials indicated that the serum triglyceride loading was significantly lower after ingestion of the structured gel rather than a simple oil–water mixture, resulting in an attenuated increase in serum insulin. This indicates the effectiveness of encapsulation in modulating blood lipid and insulin response in humans, and suggests a strategy that can be employed for the controlled release of food macronutrients. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Motor pattern selection by combinatorial code of interneuronal pathways

We use a modeling approach to examine ideas derived from physiological network analyses, pertaining to the switch of a motor control network between two opposite control modes. We studied the femur–tibia joint control system of the insect leg, and its switch between resistance reflex in posture control and “active reaction” in walking, both elicited by the same sensory input. The femur–tibia network was modeled by fitting the responses of model neurons to those obtained in animals. The strengths of 16 interneuronal pathways that integrate sensory input were then assigned three different values and varied independently, generating a database of more than 43 million network variants. We demonstrate that the same neural network can produce the two different behaviors, depending on the combinatorial code of interneuronal pathways. That is, a switch between behaviors, such as standing to walking, can be brought about by altering the strengths of selected sensory integration pathways. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Influences of Wildfire and Channel Reorganization on Spatial and Temporal Variation in Stream Temperature and the Distribution of Fish and Amphibians

Abstract Wildfire can influence a variety of stream ecosystem properties. We studied stream temperatures in relation to wildfire in small streams in the Boise River Basin, located in central Idaho, USA. To examine the spatio-temporal aspects of temperature in relation to wildfire, we employed three approaches: a pre–post fire comparison of temperatures between two sites (one from a burned stream and one unburned) over 13 years, a short-term (3 year) pre–post fire comparison of a burned and unburned stream with spatially extensive data, and a short-term (1 year) comparative study of spatial variability in temperatures using a “space for time” substitutive design across 90 sites in nine streams (retrospective comparative study). The latter design included streams with a history of stand-replacing wildfire and streams with severe post-fire reorganization of channels due to debris flows and flooding. Results from these three studies indicated that summer maximum water temperatures can remain significantly elevated for at least a decade following wildfire, particularly in streams with severe channel reorganization. In the retrospective comparative study we investigated occurrence of native rainbow trout (Oncorhynchus mykiss) and tailed frog larvae (Ascaphus montanus) in relation to maximum stream temperatures during summer. Both occurred in nearly every site sampled, but tailed frog larvae were found in much warmer water than previously reported in the field (26.6°C maximum summer temperature). Our results show that physical stream habitats can remain altered (for example, increased temperature) for many years following wildfire, but that native aquatic vertebrates can be resilient. In a management context, this suggests wildfire may be less of a threat to native species than human influences that alter the capacity of stream-living vertebrates to persist in the face of natural disturbance. Electronic supplementary material: The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of Historical and Likely Future Scenarios of Land Use on Above- and Belowground Vegetation Carbon Stocks of an Alpine Valley

Long-term trends including depopulation and shifts in agricultural policies and management have led to large-scale land-use changes throughout the European Alps which are likely to affect the size of carbon (C) stocks of the respective land-use types. This article analyzes landscape-scale changes of C-stocks present in the vegetation in relation to historical land use (1865), current land use (2003), and three contrasting scenarios of future land use (2020) in the Stubai Valley, Austria. Results show that more than 47% of the total valley area and more than 90% of the usable agricultural area have undergone a change in land use during the last approximately 140 years. Changes of land use were seen to peak between 1954 and 1973 and slow down there after. Phytomass and C-stocks in 1865 amounted to 63.1 Mg ha⁻¹ and 30.8 Mg C ha⁻¹, and increased until 2003 to 75.8 Mg ha⁻¹ and 37.2 Mg C ha⁻¹, respectively. Evaluations along an altitudinal gradient indicate the highest C gain to be in the sub-Alpine belt (more than doubling of the C-stock) due to the abandonment of pastures and hay meadows. All future scenarios project only a minor increase in phytomass (0.3–2.8 Mg ha⁻¹) and C-stocks (0.2–1.4 Mg C ha⁻¹) because major elements of the landscape (forests, rocks, screes) will be either largely unaffected or are unimportant in their spatial extent (built environment). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The evolution of cyclodextrin glucanotransferase product specificity

Cyclodextrin glucanotransferases (CGTases) have attracted major interest from industry due to their unique capacity of forming large quantities of cyclic α-(1,4)-linked oligosaccharides (cyclodextrins) from starch. CGTases produce a mixture of cyclodextrins from starch consisting of 6 (α), 7 (β) and 8 (γ) glucose units. In an effort to identify the structural factors contributing to the evolutionary diversification of product specificity amongst this group of enzymes, we selected nine CGTases from both mesophilic, thermophilic and hyperthermophilic organisms for comparative product analysis. These enzymes displayed considerable variation regarding thermostability, initial rates, percentage of substrate conversion and ratio of α-, β- and γ-cyclodextrins formed from starch. Sequence comparison of these CGTases revealed that specific incorporation and/or substitution of amino acids at the substrate binding sites, during the evolutionary progression of these enzymes, resulted in diversification of cyclodextrin product specificity. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Hans Leemhuis acknowledges financial support from the Netherlands Organization for Scientific Research (NWO).     

Evidence of chemical exchange in recombinant Major Urinary Protein and quenching thereof upon pheromone binding

The internal dynamics of recombinant Major Urinary Protein (rMUP) have been investigated by monitoring transverse nitrogen-15 relaxation using multiple-echo Carr–Purcell–Meiboom–Gill (CPMG) experiments. While the ligand-free protein (APO-rMUP) features extensive evidence of motions on the milliseconds time scale, the complex with 2-methoxy-3-isobutylpyrazine (HOLO-rMUP) appears to be much less mobile on this time scale. At 308 K, exchange rates k _ex = 500–2000 s⁻¹ were typically observed in APO-rMUP for residues located adjacent to a β-turn comprising residues 83–87. These residues occlude an entry to the binding pocket and have been proposed to be a portal for ligand entry in other members of the lipocalin family, such as the retinol binding protein and the human fatty-acid binding protein. Exchange rates and populations are largely uncorrelated, suggesting local ‘breathing’ motions rather than a concerted global conformational change. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Binding of HIV-1 TAR mRNA to a peptide nucleic acid oligomer and its conjugates with metal-ion-binding multidentate ligands

A peptide nucleic acid (PNA) oligomer and a series of PNA conjugates featuring covalently attached pendant 1,4,7,10-tetraazacyclododecane (cyclen) or bis((pyridin-2-yl)methyl)amine (DPA) moieties have been synthesized that are complementary to regions of the HIV-1 TAR messenger RNA stem-loop. Thermal denaturation studies, in conjunction win with native gel shift assays, suggest that the PNAs “invade” TAR to produce a mixture of two 1:1 PNA–TAR adducts, tentatively assigned as an “open-duplex” structure, in which the TAR stem-loop dissociates and the PNA hybridizes with its RNA complement via Watson–Crick base-pairing, and a triplex-type structure, in which the initially displaced RNA segment is bound to the PNA:RNA duplex through Hoogsteen base-pairing. Thermal denaturation experiments with the TAR sequence and single-stranded RNA and DNA oligonucleotides, both in the presence and in the absence of Zn²⁺ ions, show that the introduction of cyclen or DPA ligand arms into the PNA oligomer leads to a small but reproducible increase in the T _m values. This is attributed to hydrogen-bonding and/or electrostatic interactions between protonated forms of cyclen/DPA and the cognate RNA or DNA oligonucleotide targets. Contrary to expectations, the addition of Zn²⁺ ions did not further enhance duplex formation through binding of Zn(II)–cyclen or Zn(II)–DPA moieties to the complementary RNA or DNA. Native gel shift assays further confirmed the stability increase of the metal-free cyclen- and DPA-modified PNA hybrids as compared with a control PNA sequence. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Modeling the effect of fire on the demography of <Emphasis Type="Italic">Dicerandra frutescens</Emphasis> ssp. <Emphasis Type="Italic">frutescens</Emphasis> (Lamiaceae), an endangered plant endemic to Florida scrub

Managing populations, either for conservation, harvesting, or control, requires a mechanistic or semi-mechanistic understanding of population dynamics. Here, we investigate how time-since-fire affects demographic transitions in an endangered plant, Dicerandra frutescens ssp. frutescens (Lamiaceae), which is specialized to gaps created by fire. We used a hierarchical Bayesian model to estimate transition probabilities (i.e., the elements of population projection matrices) as a function of time-since-fire and random effects, from 13 years of data on marked individuals in five populations. Using a standard Bayesian criterion to compare models, we find that death becomes increasingly probable and progression increasingly improbable with time-since-fire. The magnitude of some of the time-since-fire effects is substantial: death is 3–5 times more likely for flowering plants >6 years versus 3–6 years post-fire, 3-step progression is almost 7 times less likely, and large flowering plants are more than 6 times more likely to stop flowering. These insights inspire new hypotheses about the underlying cause of decline with time-since-fire, and how it can be managed. Our approach can be used by others who wish to model the effect of an exogenous factor on demography, while rigorously accounting for uncertainty and variability. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Comparative Plasmonic Study of Nanoporous and Evaporated Gold Films

Previously, we have reported that nanoporous gold (NPG) films prepared by a chemical dealloying method have distinctive plasmonic properties, i.e., they can simultaneously support localized and propagating surface plasmon resonance modes (l-SPR and p-SPR, respectively). In this study, the plasmonic properties of NPG are quantified through direct comparison with thermally evaporated gold (EG) films. Cyclic voltammetry and electrochemical impedance spectroscopy experiments reveal that the NPG films have 4–8.5 times more accessible surface area than EG films. Assemblies of streptavidin–latex beads generate p-SPR responses on both NPG and EG films that correlate well with the bead density obtained from scanning electron microscopy (SEM) images. A layer-by-layer assembly experiment on NPG involving biotinylated anti-avidin IgG and avidin, studied by l-SPR and SEM, shows that the l-SPR signal is directly linked to the accessibility of the interior of the NPG porosity, an adjustable experimental parameter that can be set by the dealloying condition and time. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Deuterium isotope effects on <Superscript>15</Superscript>N backbone chemical shifts in proteins

Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the ¹⁵N chemical shift of backbone amides of proteins, ¹Δ¹⁵N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for ¹Δ¹⁵N(D) including the backbone dihedral angles, Φ and Ψ, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N–H bond length. Another contributing factor is the effect of increased anharmonicity of the N–H stretching vibrational state upon hydrogen bonding, which results in an altered N–H/N–D equilibrium bond length ratio. The N–H stretching anharmonicity contribution falls off with the cosine of the N–H···O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, ¹Δ¹⁵N(D) can provide insights into hydrogen bonding geometries. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The influence of flood cycle and fish predation on invertebrate production on a restored California floodplain

Although floodplains are known to be tightly controlled by the flood cycle, we know comparatively little about how flooding influences predators and their consumption of secondary production, particularly in highly seasonal floodplains typical of Mediterranean climates. In this study, we investigate how the seasonal dynamics of a central California floodplain influence the timing and magnitude of fish predation and the abundance and composition of invertebrates. For 3 years (2000–2002), we compared changes in abundances and size distributions of invertebrates through the flood season (January–June) with seasonal changes in the abundance of larval and juvenile fishes. Using diet analysis of fishes and manipulative feeding experiments with fishes in field enclosures, we link specific changes in invertebrate populations directly to feeding preferences of seasonally abundant fish. Early in the flood season prior to March, we found little influence of fish predation, consistent with the near absence of larval and juvenile fishes during this period. Coinciding with the midseason increase in the abundance of larval and juvenile fishes in April, we found significant declines in zooplankton abundance as well as declines in the size of zooplankton consistent with fish feeding preferences. Our results were consistent with results from feeding enclosure experiments that showed that fish rapidly depressed populations of larger cladocerans with much less effect on smaller cladocerans and calanoid copepods. At the end of the flood season, zooplankton abundances rapidly increased, consistent with a switch in the feeding of juvenile fish to aquatic insects and subsequent fish mortality. We also found that zooplankton biomass on the floodplain reached a maximum 2–3 weeks after disconnection with the river. We suggest that floodplain restoration in this region should consider management strategies that would ensure repeated flooding every 2–3 weeks during periods that would best match the peaks in abundance of native fishes. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.