Modeling the SED of the AGN inside NGC 4395

We study the broad-band spectral energy distribution (SED) of the prototypical low-mass active galactic nucleus (AGN) in NGC 4395. We jointly model the optical through mid-infrared SED with a combination of galaxy and AGN light, and find that on arcsecond scales, the AGN dominates at most wavelengths. However, there is still some ambiguity about emission from the galaxy, owing partially to the strong short-term variability of the black hole. We investigate the use of smooth and clumpy-torus models in order to disentangle the nuclear infrared emission, as well as exploring the use of poloidal wind emission to account for the blue spectral slope observed in the near-IR. Even when simultaneously fitting the full optical-IR spectral range, we find that degeneracies still remain in the best-fit models. We conclude that high spatial resolution and wider wavelength coverage with the James Webb Space Telescope is needed to understand the mid-infrared emission in this complex highly-variable object, which is the best nearby example to provide a blueprint to finding other low-mass AGN via their mid-infrared emission in the future.Comment: 17 pages, 8 figure

Positive effects of ectomycorrhizal colonization on growth of seedlings of a tropical tree across a range of forest floor light conditions

In a shadehouse experiment we tested the effects of light, nutrients and ectomycorrhizal fungi (EMF) on the growth of Vatica albiramis van Slooten (Dipterocarpaceae) seedlings. We hypothesised that it is more advantageous for plants to form connections with EMF and to trade carbon for nutrients with EMF under high light than low light. The relationship between seedling growth and the proportion of ectomycorrhizal root tips was expected as positive in high light and as negative in low light. Light conditions simulated the forest understory (low; 3% full sunlight), a small gap (medium; 11%) and a large gap (high; 33%) and a fully factorial combination of nutrients (F−/+) and ectomycorrhizal colonization (EMF−/+) treatments were applied within light conditions. The application of EMF and nutrients did significantly alter seedling growth across the range of forest floor light conditions, however the key hypothesis was rejected as seedling growth under low light was not affected by increased EMF colonization of root tips (light:EMF colonization χ2 = 2.97, p = 0.23). In addition, the lack of difference in morphotype abundance across light conditions indicated that light changes may not favour the association to specific EMF in seedlings of this particular dipterocarp species. Our results suggest that antagonistic (non-beneficial to the plant) effects due to ectomycorrhizal colonization under a light constrained environment may not affect seedling growth of Vatica albirami

Weather, Not Climate, Defines Distributions of Vagile Bird Species

Background\ud \ud Accurate predictions of species distributions are essential for climate change impact assessments. However the standard practice of using long-term climate averages to train species distribution models might mute important temporal patterns of species distribution. The benefit of using temporally explicit weather and distribution data has not been assessed. 1We hypothesized that short-term weather associated with the time a species was recorded should be superior to long-term climate measures for predicting distributions of mobile species.\ud \ud Methodology\ud \ud We tested our hypothesis by generating distribution models for 157 bird species found in Australian tropical savannas (ATS) using modelling algorithm Maxent. The variable weather of the ATS supports a bird assemblage with variable movement patterns and a high incidence of nomadism. We developed “weather” models by relating climatic variables (mean temperature, rainfall, rainfall seasonality and temperature seasonality) from the three month, six month and one year period preceding each bird record over a 58 year period (1950–2008). These weather models were compared against models built using long-term (30 year) averages of the same climatic variables.\ud \ud Conclusions\ud \ud Weather models consistently achieved higher model scores than climate models, particularly for wide-ranging, nomadic and desert species. Climate models predicted larger range areas for species, whereas weather models quantified fluctuations in habitat suitability across months, seasons and years. Models based on long-term climate averages over-estimate availability of suitable habitat and species' climatic tolerances, masking species potential vulnerability to climate change. Our results demonstrate that dynamic approaches to distribution modelling, such as incorporating organism-appropriate temporal scales, improves understanding of species distributions

Differential growth responses in seedlings of ten species of Dipterocarpaceae to experimental shading and defoliation

The responses of plants to shade and foliar herbivory jointly affect growth rates and community assembly. We grew 600 seedlings of ten species of the economically important Dipterocarpaceae in experimental gradients of shading (0.3-47.0% of full sunlight) and defoliation (0, 25%, 50% or 75% of leaf area removed). We assessed stem diameters initially, after 2 and 4 mo, and calculated relative growth rates (RGR) with a linear model. Shading interacted with defoliation, reducing RGR by 21.6% in shaded conditions and 8.9% in well-lit conditions. We tested three hypotheses for interspecific trade-offs in growth responses to shading and defoliation. They could be positively related, because both reduce a plant's access to carbon, or inversely related because of trade-offs between herbivore resistance and tolerance. We observed, however, that species varied in their response to shading, but not defoliation, precluding an interspecific trade-off and suggesting that plants tolerate shade and herbivory with differing strategies. Shading most strongly reduced the growth of species with less-dense wood and larger seeds. The strong and variable growth responses to shade, contrasted with the weak and uniform responses to defoliation, suggest that variation in light availability more strongly affects the growth of tropical tree seedlings, and thus community assembly, than does variation in herbivor

A bestiary of non-linear functions for growth analysis

Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions and ecosystem functioning.
A challenge in modeling plant growth is that growth rates almost universally decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear models that are more appropriate for modeling plant growth than are the traditional, linear, models.
Ecological inference is frequently based on growth rates, rather than model parameters. Traditional calculations of absolute and relative growth rates assume that they are invariant with respect to time or biomass, which is almost never valid. We advocate and demonstrate the calculation of function-derived growth rates, which highlight the time- and biomass-varying nature of growth. We further show how uncertainty in estimated parameter values can be propagated to express uncertainty in absolute and relative growth rates. 
The use of non-linear models and function-derived growth rates can facilitate testing novel hypotheses in population and community ecology. Even so, we acknowledge that fitting non-linear models can be tricky. To foster the spread of these methods, we make many recommendations for ecologists to follow when their hypotheses lead them into the subject of plant growth. 
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A trait-based trade-off between growth and mortality: Evidence from 15 tropical tree species using size-specific relative growth rates

A life-history trade-offbetween low mortality in the dark and rapid growth in the light is one of the most widely accepted mechanisms underlying plant ecological strategies in tropical forests. Differences in plant functional traits are thought to underlie these distinct ecological strategies; however, very few studies have shown relationships between functional traits and demographic rates within a functional group. We present 8 years of growth and mortality data from saplings of 15 species of Dipterocarpaceae planted into logged-over forest in Malaysian Borneo, and the relationships between these demographic rates and four key functional traits: wood density, specific leaf area (SLA), seed mass, and leaf C:N ratio. Species-specific differences in growth rates were separated from seedling size effects by fitting nonlinear mixed-effects models, to repeated measurements taken on individuals at multiple time points. Mortality data were analyzed using binary logistic regressions in a mixed-effects models framework. Growth increased and mortality decreased with increasing light availability. Species differed in both their growth and mortality rates, yet there was little evidence for a statistical interaction between species and light for either response. There was a positive relationship between growth rate and the predicted probability of mortality regardless of light environment, suggesting that this relationship may be driven by a general trade-offbetween traits that maximize growth and traits that minimize mortality, rather than through differential species responses to light. Our results indicate that wood density is an important trait that indicates both the ability of species to grow and resistance to mortality, but no other trait was correlated with either growth or mortality. Therefore, the growth mortality trade-offamong species of dipterocarp appears to be general in being independent of species crossovers in performance in different light environments. © 2014 The Authors

Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats

The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity\u27s effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity\u27s effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups

Preliminary Assessment of Sponge Biodiversity on Saba Bank, Netherlands Antilles

Background Saba Bank Atoll, Netherlands Antilles, is one of the three largest atolls on Earth and provides habitat for an extensive coral reef community. To improve our knowledge of this vast marine resource, a survey of biodiversity at Saba Bank included a multi-disciplinary team that sampled fishes, mollusks, crustaceans, macroalgae, and sponges. Methodology/Principal Findings A single member of the dive team conducted surveys of sponge biodiversity during eight dives at six locations, at depths ranging from 15 to 30 m. This preliminary assessment documented the presence of 45 species pooled across multiple locations. Rarefaction analysis estimated that only 48 to 84% of species diversity was sampled by this limited effort, clearly indicating a need for additional surveys. An analysis of historical collections from Saba and Saba Bank revealed an additional 36 species, yielding a total of 81 sponge species recorded from this area. Conclusions/Significance This observed species composition is similar to that found on widespread Caribbean reefs, indicating that the sponge fauna of Saba Bank is broadly representative of the Caribbean as a whole. A robust population of the giant barrel sponge, Xestospongia muta, appeared healthy with none of the signs of disease or bleaching reported from other Caribbean reefs; however, more recent reports of anchor chain damage to these sponges suggests that human activities can have dramatic impacts on these communities. Opportunities to protect this extremely large habitat should be pursued, as Saba Bank may serve as a significant reservoir of sponge species diversity

Crystal Structures of Native and Inactivated cis-3-Chloroacrylic Acid Dehalogenase. Structural Basis for Substrate Specificity and Inactivation by (R)-Oxirane-2-Carboxylate

The bacterial degradation pathways for the nematocide 1,3-dichloropropene rely on hydrolytic dehalogenation reactions catalyzed by cis- and trans-3-chloroacrylic acid dehalogenases (cis-CaaD and CaaD, respectively). X-ray crystal structures of native cis-CaaD and cis-CaaD inactivated by (R)-oxirane-2-carboxylate were elucidated. They locate four known catalytic residues (Pro-1, Arg-70, Arg-73, and Glu-114) and two previously unknown, potential catalytic residues (His-28 and Tyr-103'). The Y103F and H28A mutants of these latter two residues displayed reductions in cis-CaaD activity confirming their importance in catalysis. The structure of the inactivated enzyme shows covalent modification of the Pro-1 nitrogen atom by (R)-2-hydroxypropanoate at the C3 position. The interactions in the complex implicate Arg-70 or a water molecule bound to Arg-70 as the proton donor for the epoxide ring-opening reaction and Arg-73 and His-28 as primary binding contacts for the carboxylate group. This proposed binding mode places the (R)-enantiomer, but not the (S)-enantiomer, in position to covalently modify Pro-1. The absence of His-28 (or an equivalent) in CaaD could account for the fact that CaaD is not inactivated by either enantiomer. The cis-CaaD structures support a mechanism in which Glu-114 and Tyr-103' activate a water molecule for addition to C3 of the substrate and His-28, Arg-70, and Arg-73 interact with the C1 carboxylate group to assist in substrate binding and polarization. Pro-1 provides a proton at C2. The involvement of His-28 and Tyr-103' distinguishes the cis-CaaD mechanism from the otherwise parallel CaaD mechanism. The two mechanisms probably evolved independently as the result of an early gene duplication of a common ancestor