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397 results for “functional interactions”
Data from: Moving from frugivory to seed dispersal: incorporating the functional outcomes of interactions in plant-frugivore networks
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Host-Parasite biogeographic interactions: modelling the distribution of Phyllotis xanthopygus rodents complex and their flea assemblage using the favorability function
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Predator-prey interactions in anurans of the tropical dry forests of the Colombian Caribbean: a functional approach
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Data from: Warming-induced functional shifts in the decomposer community interact with plant community compositional shifts to impact litter decomposition
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Data from: Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish
According to the social decision-making (SDM) network hypothesis, SDM is encoded in a network of forebrain and midbrain structures in a distributed and dynamic fashion, such that the expression of a given social behaviour is better reflected by the overall profile of activation across the different loci rather than by the activity of a single node. This proposal has the implicit assumption that SDM relies on integration across brain regions, rather than on regional specialization. Here we tested the occurrence of functional localization and of functional connectivity in the SDM network. For this purpose we used zebrafish to map different social behaviour states into patterns of neuronal activity, as indicated by the expression of the immediate early genes c-fos and egr-1, across the SDM network. The results did not support functional localization, as some loci had similar patterns of activity associated with different social behaviour states, and showed socially driven changes in functional connectivity. Thus, this study provides functional support to the SDM network hypothesis and suggests that the neural context in which a given node of the network is operating (i.e. the state of its interconnected areas) is central to its functional relevance.
Data from: Interactions between functionally diverse fungal mutualists inconsistently affect plant performance and competition
Plants form mutualistic relationship with a variety of belowground fungal species. Such a mutualistic relationship can enhance plant growth and resistance to pathogens. Yet, we know little about how interactions between functionally diverse groups of fungal mutualists affect plant performance and competition. We experimentally determined the effects of interaction between two functional groups of belowground fungi that form mutualistic relationship with plants, arbuscular mycorrhizal (AM) fungi and Trichoderma, on interspecific competition between pairs of closely related plant species from four different genera. We hypothesized that the combination of two functionally diverse belowground fungal species would allow plants and fungi to partition their symbiotic relationships and relax plant‐plant competition. Our results show that: 1) the AM fungal species consistently outcompeted the Trichoderma species independent of plant combinations; 2) the fungal species generally had limited effects on competitive interactions between plants; 3) however, the combination of fungal species relaxed interspecific competition in one of the four instances of plant–plant competition, despite the general competitive superiority of AM fungi over Trichoderma. We highlight that the competitive outcome between functionally diverse fungal species may show high consistency across a broad range of host plants and their combinations. However, despite this consistent competitive hierarchy, the consequences of their interaction for plant performance and competition can strongly vary among plant communities.
Data from: Three-dimensional reconstructions come to life – interactive 3D PDF animations in functional morphology
Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering.
Data from: Phylogenetic and functional mechanisms of direct and indirect interactions among alien and native plants
Disentangling direct and indirect interactions among alien and native plants is essential to understanding the success of alien plants in multi-species communities, but studies have only focused on direct pairwise interactions. Moreover, it is also essential to explore phylogenetic and functional mechanisms driving these interactions. In a greenhouse experiment, we selected nine groups of alien and native plant species from the herbaceous flora of Germany to disentangle their direct and indirect interactions. Each group had an alien (A) that is common or rare in Germany (i.e. non-native range), two natives that are phylogenetically closely related (Nclose) and distantly related (Ndist) to A respectively, and a distantly related "target" native (T). We grew the four species of each group alone, and in two-species and three-species combinations. Specifically, we tested whether competition is greater between A and Nclose than between A and Ndist, whether presence of Nclose rather than Ndist indirectly alleviates competition of A on T, and whether these interaction patterns depend on commonness of A. Moreover, we tested how intensity of these interactions is explained by phylogenetic distance, functional traits (height, seed mass, SLA, leaf size, specific root length, leaf area ratio, root length ratio (root length/plant mass), shoot weight ratio) and traits-based functional distance. We found A had stronger competition on Nclose than on Ndist. In turn, A was more suppressed by Nclose than by Ndist, but this was only true for rare rather than common A. The presence of Ndist rather than Nclose indirectly reduced competition of A on T. The intensity of the interactions was not explained by phylogenetic or functional distance, but by some of the functional traits. Specifically, a plant experienced stronger competition when it was shorter and had smaller leaves and lower shoot weight ratio, and when its neighbors were taller, had greater SLA, leaf area ratio and shoot weight ratio, and had a lower root length ratio. Synthesis. Functional traits can help explain competitive interactions. While direct competition tended to be stronger between more closely related alien and native plants, this did not indirectly facilitate other co-occurring native plants.
Data from: Independent and interactive effects of immune activation and larval diet on adult immune function, growth and development in the greater wax moth (Galleria mellonella)
Organisms in the wild are likely to face multiple immune challenges as well as additional ecological stressors, yet their interactive effects on immune function are poorly understood. Insects are found to respond to cues of increased infection risk by enhancing their immune capacity. However, such adaptive plasticity in immune function may be limited by physiological and environmental constraints. Here, we investigated the effects of two environmental stressors – poor larval diet and an artificial parasite-like immune challenge at the pupal stage – on adult immune function, growth and development in the greater wax moth (Galleria mellonella). Males whose immune system was activated with an artificial parasite-like immune challenge had weaker immune response – measured as strength of encapsulation response – as adults compared to the control groups, but only when raised in highnutrition larval diet. Immune activation did not negatively affect adult immune response in males reared in low-nutrition larval diet, indicating that poor larval diet improved the capacity of the insects to respond to repeated immune challenges. Low-nutrition larval diet also had a positive independent effect on immune capacity in females, yet it negatively affected development time and adult body mass in both sexes. As in the nature immune challenges are rarely isolated, and adverse nutritional environment may indicate an elevated risk of infection, resilience to repeated immune challenges as a response to poor nutritional environment could provide a significant fitness advantage. This study highlights the importance of considering environmental context when investigating the effects of immune activation in insects.
Raw data associated to the paper "Analysis of species pair associations combined with functional traits reveals the effects of environmental filtering and biotic interactions in an unmanaged temperate forest"
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Common protein interactions explain variant oncofusion function and predict a novel oncofusion in rhabdomyosarcoma
<p>Original Westerns from publications</p>
Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4
<p>This dataset contains coordinate files, scripts and input parameters to run and analyse molecular dynamics simulations of membrane bound CYP 2B4.</p> <p> </p> <p>The associated study is described in: </p> <p>data - containes input data & last simulation frames for all of the described MD simulations and analyses described in the manuscript</p> <p>Structures_used_for_figures - contains .pdb and .pse files of all protein structures depicted in the manuscript</p>
A mechanistic model of functional response provides new insights into indirect interactions among arctic tundra prey
Prey handling processes are considered a dominant mechanism leading to short-term positive indirect effects between prey that share a predator. However, a growing body of research indicates that predators are not necessarily limited by such processes in the wild. Density-dependent changes in predator foraging behavior can also generate positive indirect effects but they are rarely included as explicit functions of prey densities in functional response models. With the aim of untangling proximate mechanisms of species interactions in natural communities and improving our ability to quantify interaction strength, we extended the multi-prey version of the Holling disk equation by including density-dependent changes in predator foraging behavior. Our model, based on species traits and behavior, was inspired by the vertebrate community of the arctic tundra, where the main predator (the arctic fox) is an active forager feeding primarily on cyclic small rodent (lemming) and eggs of various tundra-nesting bird species. Short-term positive indirect effects of lemmings on birds have been documented over the circumpolar Arctic but the underlying mechanisms remain poorly understood. We used a unique data set, containing high-frequency GPS tracking, accelerometer, behavioral, and experimental data to parameterize the multi-prey model, and a 15-year time series of prey densities and bird nesting success to evaluate interaction strength between species. We found that: (i) prey handling processes play a minor role in our system and (ii) changes in arctic fox daily activity budget and distance traveled can partly explain the predation release on birds observed during lemming peaks. These adjustments in predator foraging behavior with respect to the main prey density thus appear as the dominant mechanism leading to positive indirect effects commonly reported among arctic tundra prey. Density-dependent changes in functional response components have been little studied in natural vertebrate communities and deserve more attention to improve our ability to quantify the strength of species interactions.
Data for: Effects of biotic interactions on plant fecundity depend on spatial and functional structure of communities and time since disturbance
<p><span>Biotic interactions in plant communities affect individual fitness and community dynamics. Interactions between plants vary in space, over time and with organisational complexity. Yet it is challenging to quantify temporal, spatial and functional determinants of different types of interactions between long-lived perennial plant species and their effect on lifetime fecundity. We studied how plant-plant, pollinator- and seed predator-mediated interactions affect year-to-year variation in three fecundity components (cone production, seed set and seed survival) during post-fire recovery. Age-stratified data on the three fecundity components were collected in 19 even-aged communities comprising 20 serotinous <em>Protea </em>shrub species in the South African Fynbos. We analyse data on these fecundity components with neighbourhood models to infer the sign and strength of interactions throughout post-disturbance recovery, the neighbour plant traits that shape them and the spatial scale at which interactions take place. For each fecundity component, these models describe how neighbourhood effects change over time and with spatial distance between plants. For each focal plant, we then predicted neighbourhood effects on individual fecundity components and cumulative reproductive output at different post-fire stand ages. Competitive effects on cone production and seed set increased with post-fire stand age as biomass and floral resources for pollinators build up. In contrast, neighbourhood effects on seed survival were weak throughout post-disturbance recovery. Plant-plant interactions were shaped by neighbour traits related to resource acquisition, whereas animal-mediated interactions depended on neighbour traits related to resource availability for pollinators and seed predators. The spatial scale of the interactions increased from plant-plant over predator-mediated to pollinator-mediated interactions. The joint effect of these interactions on cumulative reproductive output caused the proportion of focal plants experiencing competition to increase with time since fire. We show that temporal changes in biotic interactions throughout post-disturbance recovery of perennial plant communities depend on functional traits and can be integrated to neighbourhood effects on lifetime fecundity. Studying the temporal, spatial and functional determinants of neighbourhood effects on lifetime fecundity is important for predicting not only individual plant fitness, but also population and community dynamics in changing environments. </span></p>
Figure 1a from: Eisenhauer N (2018) Aboveground-belowground interactions drive the relationship between plant diversity and ecosystem function. Research Ideas and Outcomes 4: e23688. https://doi.org/10.3897/rio.4.e23688
Figure 1a - Importance of the duration of the experiment for its outcome. <br> The effect of plant diversity on plant productivity and on the performance of decomposers increases over time. Regression between the R² of the relationship between plant diversity and plant productivity and the R² of the relationship between plant diversity and decomposer biomass/density. Data from the Jena Experiment from different years [plant productivity in 2003 – 2009; microbial biomass in 2003 – 2009 (white circles); meso- (gray circles) and macroinvertebrate densities (black circles) in 2004, 2006 and 2008].
Figure 3 from: Eisenhauer N (2018) Aboveground-belowground interactions drive the relationship between plant diversity and ecosystem function. Research Ideas and Outcomes 4: e23688. https://doi.org/10.3897/rio.4.e23688
Figure 3 - Plant diversity effects on soil microbes more pronounced at elevated [CO2]. Microbial biomass (µg Cmic g-1 soil dry mass) and basal respiration (BR; µl O2 h-1 g-1 soil dry mass) as affected by plant species richness (SR) and CO2 concentrations. Dashed lines indicate ambient CO2 levels, solid lines elevated CO2 levels (+180 ppm). SR x CO2 for Cmic: p=0.007; SR x CO2 for BR: p=0.03). Data from August 2010. Means with SE. Redrawn after Eisenhauer et al. (2013).
Figure 4 from: Eisenhauer N (2018) Aboveground-belowground interactions drive the relationship between plant diversity and ecosystem function. Research Ideas and Outcomes 4: e23688. https://doi.org/10.3897/rio.4.e23688
Figure 4 - Conceptual figure showing how global change drivers like temperature increase and drought may increase plant diversity–ecosystem function relationships.
Figure 2 from: Eisenhauer N (2018) Aboveground-belowground interactions drive the relationship between plant diversity and ecosystem function. Research Ideas and Outcomes 4: e23688. https://doi.org/10.3897/rio.4.e23688
Figure 2 - Conceptual scheme of how aboveground–belowground interactions may influence the positive relationship between plant diversity and ecosystem functioning. The left part of the scheme illustrates how lower quantity and quality of plant inputs to the soil in species-poor plant communities (being low in resource use complementarity) may induce negative soil feedback effects. The right part of the scheme shows that higher quantity and quality of plant inputs in species-rich plant communities (being high in resource use complementarity) may cause the dominance of positive soil feedback effects. Mutualists will decrease (Wurst et al. 2008, Latz et al. 2012) and/or superimpose (Eisenhauer et al. 2012a) detrimental effects of antagonists on plants. The four proposed projects complement each other to explore the underlying mechanisms of this scheme across different experimental contexts.
Figure 1b from: Eisenhauer N (2018) Aboveground-belowground interactions drive the relationship between plant diversity and ecosystem function. Research Ideas and Outcomes 4: e23688. https://doi.org/10.3897/rio.4.e23688
Figure 1b - Importance of the duration of the experiment for its outcome. <br> Long-term plant diversity studies on soil biota are rare. Relationship between sampling time since the establishment of the biodiversity experiment, number of studies investigating soil biota and percentage of significant plant diversity effects on soil biota (Eisenhauer et al. 2012a). Size of the bubbles and respective numbers indicate percentage of significant plant diversity effects (regression between number of studies and time: R²=0.56, p=0.033, between time and significant plant diversity effects: R²=0.66, p=0.014, n=20 studies).
Supplementary material 1 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.