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364 results for “Network interaction”
Data from: Logging-induced changes in habitat network connectivity shape behavioral interactions in the wolf-caribou-moose system
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Data from: Frugivore biodiversity and complementarity in interaction networks enhance landscape-scale seed dispersal function
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Data from: The influence of spatial sampling scales on ant-plant interaction network architecture
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Data from: Invariant antagonistic network structure despite high spatial and temporal turnover of interactions
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Interaction network for eleven Cucurbita pepo sites in Guatemala
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Data from: Human-induced biotic invasions and changes in plankton interaction networks
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Data from: Moving from frugivory to seed dispersal: incorporating the functional outcomes of interactions in plant-frugivore networks
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Data from: Differential effects of fertilisers on pollination and parasitoid interaction networks
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Data for: Infectious disease and sickness behaviour: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils
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A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions
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Molecular ecological network analyses: An effective conservation tool for the assessment of biodiversity, trophic interactions, and community structure
<p>Global biodiversity is threatened by the anthropogenic restructuring of animal communities, which rewires species interaction networks in real-time as individuals are extirpated or introduced. Conservation science and adaptive ecosystem management demands more rapid, quantitative, and non-invasive technologies for robustly capturing changing biodiversity and quantifying species interactions. Here we develop molecular ecological network analyses (MENA) as an ecosystem assessment tool to address these needs. To construct the ecological network, we used environmental DNA from feces to identify the plant and mammal diet of two carnivores: puma (<i>Puma concolor</i>) and bobcat (<i>Lynx rufus</i>); two omnivores: coyote (<i>Canis latrans</i>) and gray fox (<i>Urocyon cinereoargenteus</i>); and two herbivores: black-tailed deer (<i>Odocoileus hemionus</i>) and black-tailed jackrabbit (<i>Lepus californicus)</i> in a well-studied Californian reserve<i>. </i>To evaluate MENA as a comprehensive biodiversity tool, we applied our framework to identify the structure of the network, patterns of trophic interactions, key species, and to assess its utility in capturing the biodiversity of the area. The high dietary taxonomic resolution enabled the assessment of species diversity, niche breadth and overlap. The network analysis revealed a dense ecological network with a high diversity of weakly connected species and a community that is highly modular and non-nested. The significant prevalence of tri-trophic chain and exploitative competition patterns indicates (i) the removal or reintroduction of a top predator would trigger a trophic cascade within this community, directly affecting their prey and indirectly the plant communities, and (ii) the potential impact of indirect effects between two predators that consume the same prey. These results suggest that the recent resurgence of puma in the study area may impact the herbaceous and woody vegetation and the population size of other predators. This effect of fluctuating predator populations and plant communities could be predicted through MENA's fine-scale assessment of the diet selection and the identified keystone species. Although just using a subset of species, MENA more rapidly, accurately, and effectively captured the broader biodiversity of the area in comparison to other methodologies. MENA reconstructed and unveiled the hidden complexity in trophic structure and interaction networks within the community, providing a promising toolkit for biodiversity and ecosystem management.</p>
Dataset accompanying "SECAT: Quantifying differential protein-protein interaction states by network-centric analysis"
<p>This repository contains input data, processing parameters and results associated with manuscript "SECAT: Quantifying differential protein-protein interaction states by network-centric analysis".</p> <p>Each archive contains a README.txt file that describes the contents.</p> <p>SECAT_scripts_data.tar.xz is an archive containing the scripts and data to generate the manuscript figures.</p>
Clearcutting and selective logging have inconsistent effects on liana diversity and abundance but not on liana–tree interaction networks
<p class="MsoNoSpacing">Understanding the effects of forest management on lianas and their interaction with trees is an important step towards effective forest management. Our study therefore aimed at quantifying the patterns of liana diversity and abundance, and liana-tree interaction network structure in response to logging disturbance in a moist semi-deciduous forest in Ghana. We sampled lianas (diameter at 1.3 m ≥ 1 cm) and their host trees (diameter at breast height ≥ 5 cm) in 90 20 × 20 m plots among three forest management regimes: clearcut-logged, selectively-logged and old-growth forests. Liana species diversity and abundance in the selectively-logged forest was similar to that of the old-growth forest, while that in clearcut-logged forest was significantly lower than both above-mentioned forest types. Liana-tree interaction networks showed anti-nested structure, which is a form of nonrandom community organization. There were significant modularity and degree of specialization, but no significant connectance in the network structure. Largely, most of the species were peripherals, while a few species acted as structurally important species (i.e. module hubs, network hubs and connectors) in the three networks. A different set of species acted as structurally important species in the different forest management regimes. Our findings call for a re-examination of clearcutting logging in forest management in view of its negative effects on lianas, and we recommend prioritizing important modules in liana-tree network for future conservation.</p>
Data from: Indirect interactions influence contact network structure and diffusion dynamics
Interaction patterns at the individual level influence the behaviour of diffusion over contact networks. Most of the current diffusion models only consider direct interactions, capable of transferring infectious items among individuals, to build transmission networks of diffusion. However, delayed indirect interactions, where a susceptible individual interacts with infectious items after the infected individual has left the interaction space, can also cause transmission events. We define a diffusion model called the same place different time transmission (SPDT) based diffusion that considers transmission links for these indirect interactions. Our SPDT model changes the network dynamics where the connectivity among individuals varies with the decay rates of link infectivity. We investigate SPDT diffusion behaviours by simulating airborne disease spreading on data-driven contact networks. The SPDT model significantly increases diffusion dynamics with a high rate of disease transmission. By making the underlying connectivity denser and stronger due to the inclusion of indirect transmissions, SPDT models are more realistic than SPST models for the study of various airborne diseases outbreaks. Importantly, we also find that the diffusion dynamics including indirect links are not reproducible by the current SPST models based on direct links, even if both SPDT and SPST networks assume the same underlying connectivity. This is because the transmission dynamics of indirect links are different from those of direct links. These outcomes highlight the importance of the indirect links for predicting outbreaks of airborne diseases.
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: Black Queen evolution and trophic interactions determine plasmid survival after the disruption of conjugation network
Mobile genetic elements such as conjugative plasmids are responsible for antibiotic resistant phenotypes in many bacterial pathogens. The ability to conjugate, the presence of antibiotics and ecological interactions all have a notable role in the persistence of plasmids in bacterial populations. Here, we set out to investigate the contribution of these factors when the conjugation network was disturbed by a plasmid-dependent bacteriophage. Phage alone effectively caused the population to lose plasmids, thus rendering them susceptible to antibiotics. Leakiness of the antibiotic resistance mechanism allowing Black Queen evolution (i.e. race to the bottom) was a more significant factor over antibiotic concentration (lethal vs sub-lethal) in determining plasmid prevalence. Interestingly, plasmid loss was also prevented by protozoan predation. These results show that the outcome of attempts to re-sensitize bacterial communities by disrupting the conjugation network are highly dependent on ecological factors and resistance mechanisms.
Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests
1. From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional traits. 2. The objectives of this study were to describe the interaction network topologies of MNs formed between two ectomycorrhizal fungal species, Rhizopogon vesiculosus and R. vinicolor, and interior Douglas-fir trees at the forest stand scale, identify factors leading to this structure and to contrast MN structures between forest plots with xeric versus mesic soil moisture regimes. 3. Tuberculate mycorrhizas were sampled in six 10 × 10 m plots with either xeric or mesic soil moisture regimes. Microsatellite DNA markers were used to identify tree and fungal genotypes isolated from mycorrhizas and for comparison with reference tree boles above-ground. 4. In all six plots, trees and fungal genets were highly interconnected. Size asymmetries between different tree cohorts led to non-random MN topologies, while differences in size and connectivity between Rhizopogon species-specific subnetwork components contributed towards MN nestedness. Large mature trees acted as network hubs with a significantly higher node degree compared to smaller trees. MNs representing trees linked by R. vinicolor genets were mostly nested within larger, more highly connected R. vesiculosus-linked MNs. 5. Attributes of network nodes showed that hub trees were more important to MN topology on xeric than mesic sites, but the emergent structures of MNs were similar in the two soil moisture regimes. 6. Synthesis. This study suggests MNs formed between interior Douglas-fir trees and R. vesiculosus and R. vinicolor genets are resilient to the random loss of participants, and to soil water stress, but may be susceptible to the loss of large trees or fungal genets. Our results regarding the topology of MNs contribute to the understanding of forest stand dynamics and the resilience of forests to stress or disturbance.
Data from: Network structure and local adaptation in coevolving bacteria-phage interactions
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed in community ecology to quantify how the structure of community interaction matrices, so called 'bipartite networks', reflected observed coevolutionary dynamics, and how phages from these communities may or may not have adapted locally to their bacterial hosts. We found a consistent nested network structure for two phage types, one previously demonstrated to exhibit arms race coevolutionary dynamics and the other fluctuating coevolutionary dynamics. Both phages increased their host ranges through evolutionary time, but we found no evidence for a trade off with impact on bacteria. Finally, only bacteria from the arms race phage showed local adaptation, and we provide preliminary evidence that these bacteria underwent (sometimes different) molecular changes in the wzy gene associated with the LPS receptor, while bacteria coevolving with the fluctuating selection phage did not show local adaptation and had partial deletions of the pilF gene associated with Type IV pili. We conclude that the structure of phage-bacteria interaction networks is not necessarily specific to coevolutionary dynamics, and discuss hypotheses for why only one of the two phages was, nevertheless, locally adapted.
Data from: Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions
The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues.
Cheating interactions favor modularity in mutualistic networks
<p>A fundamental fact about mutualisms is that these mutually beneficial interactions often harbor cheaters that benefit from the use of resources and services without providing any positive feedback to the other players. The role of cheaters on the evolutionary dynamics of mutualisms has long been recognized, yet their broader consequences to the community level, and beyond species they interact with, is still poorly understood. Because mutualisms form networks that often involve dozens to hundreds of species, indirect effects generated by cheaters may cascade through the whole community, reshaping trait evolution. Here, we study how harboring cheating interactions can influence coevolution in mutualistic networks. We combine a coevolutionary model, empirical data on animal-plant mutualistic networks, and numerical simulations and show that a higher frequency of cheating interactions in a network can lead to the formation of groups of species phenotypically similar to each other and distinct from other groups, generating higher trait disparity. The resulting clustered trait patterns, in turn, change the patterns of interaction in simulated networks, fostering the formation of modules of interacting species. Our results indicate that cheaters contribute to generate phenotypic clusters in mutualistic networks, counteracting selection for convergence imposed by mutualists, and favoring the emergence of modules of interacting species. Based on these results, we suggest that cheaters might be a fundamental element for our understanding of the evolution of mutualistic networks.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.