Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
141
datasets available to search
ShareScore release 0.9.0
Dataset results
141 results for “Metabolic Interactions”
Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism
<p>Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macro aggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in the face of intensifying anthropogenic land-use and climate change.</p>
Data for: The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species
<p>Raw respirometry data and respirometry code</p> <p>Data.xlsx is the data about each fish that was used for all analyses including Stable Isotope values, length, weight, sex, and habitat. This is the data that is used in the R code. </p> <p>Example code of the models used in our analyses</p> <p>TEF_metabolism.xlsx is data on the fish that were kept in the lab for almost a year. </p> <p> </p>
Data from: Status-dependent metabolic effects of social interactions in a group-living fish
<p>Social interactions can sometimes be a source of stress, but social companions can also ameliorate and buffer against stress. Stress and metabolism are closely linked, but the degree to which social companions modulate metabolic responses during stressful situations—and whether such effects differ depending on social rank—is poorly understood. To investigate this question, we studied Neolamprologus pulcher, a group-living cichlid fish endemic to Lake Tanganyika, and measured the metabolic responses of dominant and subordinate individuals when they were either visible or concealed from one another. When individuals could see each other, subordinates had lower maximum metabolic rates and tended to take longer to recover following an exhaustive chase compared to dominants. In contrast, metabolic responses of dominants and subordinates did not differ when individuals could not see one another. These findings suggest that the presence of a dominant individual has negative metabolic consequences for subordinates, even in stable social groups with strong prosocial relationships.</p>
Data for the "Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli"
<p>This dataset contains raw and processed NMR data used in the publication.</p>
Data from: Status-dependent metabolic effects of social interactions in a group-living fish
Open the record for dataset details and reuse information.
Synergistic label-free fluorescence imaging and miRNA studies reveal dynamic human neuron-glial metabolic interactions following injury
Open the record for dataset details and reuse information.
Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism
Open the record for dataset details and reuse information.
Data for: Feeding frequency does not interact with BPA exposure to influence metabolism of behaviour in zebrafish (Danio rerio)
<p><span>Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signaling, and may therefore be impacted by endocrine disrupting compounds (EDCs) such as bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (<em>Danio rerio</em>) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources. </span></p>
Data from: Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages
<p>Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid dysfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridise. Here we use controlled hybrid crosses and high resolution respirometry to provide the first experimental evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two mitodiscordant backcrosses (with mismatched mito-nuclear combinations) differ from one another, although they do not differ significantly from the parental groups or mitoconcordant backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.</p>
Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid
<p>Most insects harbor influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across United States populations of the pea aphid, <em>Acyrthosiphon</em> <em>pisum</em>. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping ~5 out of 9 previously reported co-infection trends. Field data provide a mixture of evidence for symbiont-symbiont synergies, and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. twelve pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts – <em>Serratia</em> <em>symbiotica</em> and <em>Rickettsiella</em> <em>viridis</em>. Applying the expansion network algorithm, through additional use of pea aphid and obligate <em>Buchnera</em> symbiont genomes, <em>Serratia</em> and <em>Rickettsiella</em> emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps within a multi-party mutualism, within their nutrient-limited phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of <em>Serratia</em> and <em>Rickettsiella</em>, raise further questions on the origins of mutualisms and host-symbiont interdependencies.</p>
Designing a Synthetic Microbial Community through Genome Metabolic Modeling to enhance Plant-Microbe Interaction
<p>Supplementary data 1 - <strong>Reconstructed genome-scale metabolic networks from MAGs and Hosts</strong></p> <p>Supplementary data 2 - P<strong>lant growth-promoting traits among members of the minimal community</strong></p> <p> </p> <p>Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynCom, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and a careful selection of compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed an <em>in-silico</em> approach using genome metabolic modeling to design a synthetic microbial community aimed at improving the yield of important crop plants. We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, EPS production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our selection process for the SymCom, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. Our study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.</p>
Interactions Between Cannabinoids and Cytochrome P450-Metabolized Drugs
ClinicalTrials.gov study NCT04201197. IPD Sharing: YES. Countries: 1. Publications: 1.
Exercise Training Effects on Metabolic Syndrome: Interactions With Medication
ClinicalTrials.gov study NCT03019796. IPD Sharing: NO. Countries: 1. Publications: 27.
Data from: Interactive effects of temperature acclimation and dietary fatty acids on metabolic rate and body composition of zebra finches (Taeniopygia guttata)
Open the record for dataset details and reuse information.
Data from: Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages
Open the record for dataset details and reuse information.
Data for: Feeding frequency does not interact with BPA exposure to influence metabolism of behaviour in zebrafish (Danio rerio)
Open the record for dataset details and reuse information.
Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid
Open the record for dataset details and reuse information.
Large-scale metabolic interaction network of the mouse and human gut microbiota
<p>The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.</p>
Temperature and predator cues interactively affect ontogenetic metabolic scaling of aquatic amphipods
<p>A common belief is that body-mass scaling of metabolic rate results chiefly from intrinsic body-design constraints. However, several studies have shown that multiple ecological factors affect metabolic scaling. The mechanistic basis of these effects is largely unknown. Here, we explore whether abiotic and biotic environmental factors have interactive effects on metabolic scaling. To address this question, we studied the simultaneous effects of temperature and predator cues on the ontogenetic metabolic scaling of amphipod crustaceans inhabiting two different aquatic ecosystems, a freshwater spring and a saltwater lagoon. We assessed effects of phenotypic plasticity on metabolic scaling by exposing amphipods in the laboratory to water with and without fish-cues at multiple temperatures. Temperature interacts significantly with predator cues to affect metabolic scaling. Our results suggest that metabolic scaling is highly malleable in response to short-term acclimation. The interactive effects of temperature and predators show the importance of studying effects of global warming in realistic ecological contexts.</p>
Intraspecific interaction of host plants leads to concentrated distribution of a specialist herbivore through metabolic alterations in the leaves
<p>1. Recent studies suggest that changes in leaf traits due to interactions between plants affect resource utilisation by and the distribution of herbivores. However, this has not yet been confirmed experimentally. Here, we investigated the effects of phenotypic plasticity in leaf traits of <i>Rumex obtusifolius</i> (host plant) in response to intra- and interspecific interaction on the distribution of two leaf beetles, <i>Gastrophysa atrocyanea</i> (specialist herbivore) and <i>Galerucella grisescens</i> (generalist herbivore).</p> <p>2. We investigated the local population density of <i>R. obtusifolius</i> plants and the presence of leaf beetles on the plants at five study sites. Leaf chemicals (condensed tannins and total phenolics) were compared between aggregated and solitary <i>R. obtusifolius</i> plants. To clarify the effects of the interaction environment of <i>R. obtusifolius</i> plants on their leaf traits and on resource utilisation by the leaf beetles, we compared leaf chemicals and preferences of adult leaf beetles among treatments where <i>R. obtusifolius</i> experienced intraspecific interaction, interspecific interaction, or no interaction in cultivation experiments. Finally, we evaluated the independent and combined effects of patch size and intraspecific interaction on leaf beetle distribution in mesocosm experiments.</p> <p>3. In the field, the presence of the specialist leaf beetle <i>G. atrocyanea</i> was positively correlated with the local population density (rosette overlap ratio) of <i>R. obtusifolius</i> plants; however, there was no correlation in the case of the generalist leaf beetle <i>G. grisescens</i>. In the cultivation experiments, plants in the intraspecific interaction treatment increased their leaf contents of condensed tannins and total phenolics, and <i>G. atrocyanea</i> consumed more of these leaves than leaves in other treatments. Similar results were observed in the field. In the mesocosm experiments, larger numbers of <i>G. atrocyanea</i> were distributed on <i>R. obtusifolius</i> plants exposed to below-ground intraspecific interaction than on plants not exposed to intraspecific interaction.</p> <p>4. Our results provide experimental evidence that leaf-trait changes in response to intraspecific interaction between host plants influence specialist herbivore distribution. This highlights the need to integrate plant–plant interactions into our understanding of plant–animal interactions. </p>
ScienceDex guides
Understand access before you commit
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.