Emergent global patterns of ecosystem structure and function from a mechanistic general ecosystem model

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures

GABA Maintains the Proliferation of Progenitors in the Developing Chick Ciliary Marginal Zone and Non-Pigmented Ciliary Epithelium

GABA is more than the main inhibitory neurotransmitter found in the adult CNS. Several studies have shown that GABA regulates the proliferation of progenitor and stem cells. This work examined the effects of the GABAA receptor system on the proliferation of retinal progenitors and non-pigmented ciliary epithelial (NPE) cells. qRT-PCR and whole-cell patch-clamp electrophysiology were used to characterize the GABAA receptor system. To quantify the effects on proliferation by GABAA receptor agonists and antagonists, incorporation of thymidine analogues was used. The results showed that the NPE cells express functional extrasynaptic GABAA receptors with tonic properties and that low concentration of GABA is required for a baseline level of proliferation. Antagonists of the GABAA receptors decreased the proliferation of dissociated E12 NPE cells. Bicuculline also had effects on progenitor cell proliferation in intact E8 and E12 developing retina. The NPE cells had low levels of the Cl–transporter KCC2 compared to the mature retina, suggesting a depolarising role for the GABAA receptors. Treatment with KCl, which is known to depolarise membranes, prevented some of the decreased proliferation caused by inhibition of the GABAA receptors. This supported the depolarising role for the GABAA receptors. Inhibition of L-type voltage-gated Ca2+ channels (VGCCs) reduced the proliferation in the same way as inhibition of the GABAA receptors. Inhibition of the channels increased the expression of the cyclin-dependent kinase inhibitor p27KIP1, along with the reduced proliferation. These results are consistent with that when the membrane potential indirectly regulates cell proliferation with hyperpolarisation of the membrane potential resulting in decreased cell division. The increased expression of p27KIP1 after inhibition of either the GABAA receptors or the L-type VGCCs suggests a link between the GABAA receptors, membrane potential, and intracellular Ca2+ in regulating the cell cycle

Modular Mass Spectrometric Tool for Analysis of Composition and Phosphorylation of Protein Complexes

The combination of high accuracy, sensitivity and speed of single and multiple-stage mass spectrometric analyses enables the collection of comprehensive sets of data containing detailed information about complex biological samples. To achieve these properties, we combined two high-performance matrix-assisted laser desorption ionization mass analyzers in one modular mass spectrometric tool, and applied this tool for dissecting the composition and post-translational modifications of protein complexes. As an example of this approach, we here present studies of the Saccharomyces cerevisiae anaphase-promoting complexes (APC) and elucidation of phosphorylation sites on its components. In general, the modular concept we describe could be useful for assembling mass spectrometers operating with both matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) ion sources into powerful mass spectrometric tools for the comprehensive analysis of complex biological samples

Effect of Pictorial Depth Cues, Binocular Disparity Cues and Motion Parallax Depth Cues on Lightness Perception in Three-Dimensional Virtual Scenes

Surface lightness perception is affected by scene interpretation. There is some experimental evidence that perceived lightness under bi-ocular viewing conditions is different from perceived lightness in actual scenes but there are also reports that viewing conditions have little or no effect on perceived color. We investigated how mixes of depth cues affect perception of lightness in three-dimensional rendered scenes containing strong gradients of illumination in depth.Observers viewed a virtual room (4 m width x 5 m height x 17.5 m depth) with checkerboard walls and floor. In four conditions, the room was presented with or without binocular disparity (BD) depth cues and with or without motion parallax (MP) depth cues. In all conditions, observers were asked to adjust the luminance of a comparison surface to match the lightness of test surfaces placed at seven different depths (8.5-17.5 m) in the scene. We estimated lightness versus depth profiles in all four depth cue conditions. Even when observers had only pictorial depth cues (no MP, no BD), they partially but significantly discounted the illumination gradient in judging lightness. Adding either MP or BD led to significantly greater discounting and both cues together produced the greatest discounting. The effects of MP and BD were approximately additive. BD had greater influence at near distances than far.These results suggest the surface lightness perception is modulated by three-dimensional perception/interpretation using pictorial, binocular-disparity, and motion-parallax cues additively. We propose a two-stage (2D and 3D) processing model for lightness perception

How Spatial Heterogeneity of Cover Affects Patterns of Shrub Encroachment into Mesic Grasslands

We used a multi-method approach to analyze the spatial patterns of shrubs and cover types (plant species, litter or bare soil) in grassland-shrubland ecotones. This approach allows us to assess how fine-scale spatial heterogeneity of cover types affects the patterns of Cytisus balansae shrub encroachment into mesic mountain grasslands (Catalan Pyrenees, Spain). Spatial patterns and the spatial associations between juvenile shrubs and different cover types were assessed in mesic grasslands dominated by species with different palatabilities (palatable grass Festuca nigrescens and unpalatable grass Festuca eskia). A new index, called RISES (“Relative Index of Shrub Encroachment Susceptibility”), was proposed to calculate the chances of shrub encroachment into a given grassland, combining the magnitude of the spatial associations and the surface area for each cover type. Overall, juveniles showed positive associations with palatable F. nigrescens and negative associations with unpalatable F. eskia, although these associations shifted with shrub development stage. In F. eskia grasslands, bare soil showed a low scale of pattern and positive associations with juveniles. Although the highest RISES values were found in F. nigrescens plots, the number of juvenile Cytisus was similar in both types of grasslands. However, F. nigrescens grasslands showed the greatest number of juveniles in early development stage (i.e. height<10 cm) whereas F. eskia grasslands showed the greatest number of juveniles in late development stages (i.e. height>30 cm). We concluded that in F. eskia grasslands, where establishment may be constrained by the dominant cover type, the low scale of pattern on bare soil may result in higher chances of shrub establishment and survival. In contrast, although grasslands dominated by the palatable F. nigrescens may be more susceptible to shrub establishment; current grazing rates may reduce juvenile survival

The Brightness of Colour

Background: The perception of brightness depends on spatial context: the same stimulus can appear light or dark depending on what surrounds it. A less well-known but equally important contextual phenomenon is that the colour of a stimulus can also alter its brightness. Specifically, stimuli that are more saturated (i.e. purer in colour) appear brighter than stimuli that are less saturated at the same luminance. Similarly, stimuli that are red or blue appear brighter than equiluminant yellow and green stimuli. This non-linear relationship between stimulus intensity and brightness, called the Helmholtz-Kohlrausch (HK) effect, was first described in the nineteenth century but has never been explained. Here, we take advantage of the relative simplicity of this 'illusion' to explain it and contextual effects more generally, by using a simple Bayesian ideal observer model of the human visual ecology. We also use fMRI brain scans to identify the neural correlates of brightness without changing the spatial context of the stimulus, which has complicated the interpretation of related fMRI studies.Results: Rather than modelling human vision directly, we use a Bayesian ideal observer to model human visual ecology. We show that the HK effect is a result of encoding the non-linear statistical relationship between retinal images and natural scenes that would have been experienced by the human visual system in the past. We further show that the complexity of this relationship is due to the response functions of the cone photoreceptors, which themselves are thought to represent an efficient solution to encoding the statistics of images. Finally, we show that the locus of the response to the relationship between images and scenes lies in the primary visual cortex (V1), if not earlier in the visual system, since the brightness of colours (as opposed to their luminance) accords with activity in V1 as measured with fMRI.Conclusions: The data suggest that perceptions of brightness represent a robust visual response to the likely sources of stimuli, as determined, in this instance, by the known statistical relationship between scenes and their retinal responses. While the responses of the early visual system (receptors in this case) may represent specifically the statistics of images, post receptor responses are more likely represent the statistical relationship between images and scenes. A corollary of this suggestion is that the visual cortex is adapted to relate the retinal image to behaviour given the statistics of its past interactions with the sources of retinal images: the visual cortex is adapted to the signals it receives from the eyes, and not directly to the world beyond

Motives and comprehension in a public goods game with induced emotions

This study analyses the sensitivity of public goods contributions through the lens of psychological motives. We report the results of a public goods experiment in which subjects were induced with the motives of care and anger through autobiographical recall. Subjects' preferences, beliefs, and perceptions under each motive are compared with those of subjects experiencing a neutral autobiographical recall control condition. We find, but only for those subjects with the highest comprehension of the game, that care elicits significantly higher contributions than anger, with the control treatment in between. This positive influence of the care motive on unconditional giving is accounted for partly by preferences for giving and partly by the beliefs concerning greater contributions by others. Anger also affects attention to own and other's payoffs (using mouse tracking) and perceptions of the game's incentive structure (cooperative or competitive)