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89 results for “metabolic scaling”
Data from Genome scale metabolic network modelling for metabolic profile predictions
<p>Data used to produce figures 4, 5 and 6 in the paper Genome scale metabolic network modelling for metabolic profile predictions.</p>
Data from: Why does offspring size affect performance? Integrating metabolic scaling with life-history theory
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Data from: Scaling of leaf area with biomass in trees reconsidered: Constant metabolically active sapwood volume per unit leaf area with height growth
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Larval nutrition impacts the scaling of adult metabolic rate with body mass in honeybees
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Data from: Quantifying liver-toxic responses from dose-dependent chemical exposures using a rat genome-scale metabolic model
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Deriving population scaling rules from individual-level metabolism and life history traits - Code and Data
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Scaling of metabolic rate in hibernators: Translation of literature data: For a comment to Nespolo et al. (2022)
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The scaling of metabolic traits differs among larvae and juvenile colonies of scleractinian corals
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Dataset - Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
<p>Models developed for the manuscript “Large-scale kinetic metabolic models of<em> Pseudomonas putida</em> for consistent design of metabolic engineering strategies" by M. Tokic, V. Hatzimanikatis, and L. Miskovic.</p> <ul> <li>Thermodynamically curated and gap-filled genome-scale model of <em>P. putida</em> iJN1411, iJN1411cur. <ul> <li>CuratediJN1411GEM.mat</li> </ul> </li> <li>Three systematically reduced stoichiometric models of <em>P. putida</em>: <ul> <li>D1 model, RedModelD1SminP2.mat</li> <li>D2 model, RedModelD2SminP2.mat - used for the studies performed in the manuscript</li> <li>D3 model, RedModelD3SminP2.mat</li> </ul> </li> </ul> <p> </p>
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>
Age-dependent modulation of bone metabolism in zebrafish scales as new model of male osteoporosis in lower vertebrates
<p>After middle age, in human bone, the resorption usually exceeds formation resulting in bone loss and increased risk of fractures in the aged population. Only few in vivo models in higher vertebrates are available for pathogenic and therapeutic studies about bone aging. Among these, male Danio rerio (zebrafish) can be successfully used as low vertebrate model to study degenerative alterations that affect the skeleton during aging, reducing the role of sex hormones.In this paper, we investigated the early bone aging mechanisms in male zebrafish (3, 6, 9 months old) scales evaluating the physiological changes and the effects of prednisolone, a pro-osteoporotic drug.The results evidentiated an age-dependent reduction of the mineralization rate in the fish scales, as highlighted by growing circle measurements. Indeed, the osteoblastic ALP activity at the matrix deposition site was found progressively downregulated.The higher TRAP activity was found in 63% of 9-month-old fish scales associated with resorption lacunae along the scale border. Gene expression analysis evidentiated that an increase of the tnfrsf1b (homolog of human rank) in aging scales may be responsible for resorption stimulation.Interestingly, prednisolone inhibited the physiological growth of the scale and induced in aged scales a more significant bone resorption compared with untreated fish (3.8% vs 1.02%). Bone markers analysis shown a significant reduction of ALP/TRAP ratio due to a prednisolone-dependent stimulation of tnfsf11 (homolog of human rankl) in scales of older fish.The results evidentiated for the first time the presence of a senile male osteoporosis in lower vertebrate. This new model could be helpful to identify the early mechanisms of bone aging and new therapeutic strategies to prevent age-related bone alterations in humans.</p>
Supplementary material 1 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639
Figures S1–S5. Additional graphs with result analysis and phylogenetical trees used in data analysis
metaGEM: genome scale metabolic models
<p>Genome scale models reconstructed from metagenomes. Please consider citing the original metaGEM <a href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab815/6382386">publication</a> if you use these models in your research.</p>
Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic and environmental influences. We demonstrate how this may be done by comparing the ontogenetic scaling of resting metabolic rate among populations of the same species (the amphipod Gammarus minus) in mid-Appalachian freshwater springs with similar, relatively constant environmental conditions, except for the varying presence of the predatory fish Cottus cognatus. We found that populations of G. minus exhibit significantly lower metabolic scaling slopes (0.54 to 0.62) in three freshwater springs with C. cognatus than in two springs without these fish (0.76 to 0.77). We tested multiple hypothetical causes for these population differences. Our results best supported the hypothesis that metabolic scaling was influenced by the effects of size-selective predation on the ontogeny of growth, a metabolically expensive process. The body-size scaling of growth is significantly less steep in the populations inhabiting springs with versus without fish, thus paralleling the interpopulation differences in metabolic scaling. Prematurational growth of G. minus is as high or higher in the fish springs, whereas postmaturational growth is significantly lower, often approaching zero. Similarly the amphipods in the fish springs tend to have higher metabolic rates at small sizes, but lower metabolic rates at large sizes, compared to those in the fishless springs. Our results do not support other hypothetical causes of the interpopulation variation in metabolic scaling, including differential scaling of cell size or low-metabolism body components (fat and mineralized exoskeleton), or possible effects of other environmental factors associated with the presence of fish. However, fish-induced population differences in adult behavioral activity may influence metabolic scaling in G. minus, a possibility under current study. We conclude that ecological factors may significantly influence metabolic scaling, contrary to common belief.
Data from: Intraspecific scaling of the resting and maximum metabolic rates of the crucian carp (Carassius auratus)
The question of how the scaling of metabolic rate with body mass (M) is achieved in animals is unresolved. Here, we tested the cell metabolism hypothesis and the organ size hypothesis by assessing the mass scaling of the resting metabolic rate (RMR), maximum metabolic rate (MMR), erythrocyte size, and the masses of metabolically active organs in the crucian carp (Carassius auratus). The M of the crucian carp ranged from 4.5 to 323.9 g, representing an approximately 72-fold difference. The RMR and MMR increased with M according to the allometric equations RMR = 0.212M0.776 and MMR = 0.753M0.785. The scaling exponents for RMR (br) and MMR (bm) obtained in crucian carp were close to each other. Thus, the factorial aerobic scope remained almost constant with increasing M. Although erythrocyte size was negatively correlated with both mass-specific RMR and absolute RMR adjusted to M, it and all other hematological parameters showed no significant relationship with M. These data demonstrate that the cell metabolism hypothesis does not describe metabolic scaling in the crucian carp, suggesting that erythrocyte size may not represent the general size of other cell types in this fish and the metabolic activity of cells may decrease as fish grows. The mass scaling exponents of active organs was lower than 1 while that of inactive organs was greater than 1, which suggests that the mass scaling of the RMR can be partly due to variance in the proportion of active/inactive organs in crucian carp. Furthermore, our results provide additional evidence supporting the correlation between locomotor capacity and metabolic scaling.
Data from: Body-size scaling of metabolic rate in the trilobite Eldredgeops rana
We infer the body-size scaling slope of metabolic rate in a trilobite by applying a cell-size model that has been proposed to explain metabolic scaling in living organisms. This application is especially tractable in fossil arthropods with well-preserved compound eyes because the number and size of eye facets appear to be useful proxies for the relative number and size of cells in the body. As a case study, we examined the ontogenetic scaling of facet size and number in a ∼390-Myr-old local assemblage of the trilobite Eldredgeops rana, which has well-preserved compound eyes and a wide body-size range. Growth in total eye lens area resulted from increases in both facet area and number in relatively small (presumably young) specimens, but only from increases in facet area in large (presumably more mature) specimens. These results suggest that early growth in E. rana involved both cell multiplication and enlargement, whereas later growth involved only cell enlargement. If the cell-size model is correct, then metabolic rate scaled allometrically in E. rana, and the scaling slope of log metabolic rate versus log body mass decreased from ∼0.85 to 0.63 as these animals grew. This inferred age-specific change in metabolic scaling is consistent with similar changes frequently observed in living animals. Additional preliminary analyses of literature data on other trilobites also suggest that the metabolic scaling slope was <1 in benthic species, but ∼1 in pelagic species, as has also been observed in living invertebrates. The eye-facet size (EFS) method featured here opens up new possibilities for examining the bioenergetic allometry of extinct arthropods.
Patient-specific genome-scale metabolic models reconstructed for 8 TCGA tumor types
<p>TCGA_reconstructedGEMs: 3,599 cancer patient-specific GEMs for 8 different tumor types reconstructed using the TCGA (The Cancer Genome Atlas) RNA-seq data and generic human GEM 'Recon 2M.2'</p>
Plasticity and evolution shape the scaling of metabolism and excretion along a geothermal temperature gradient
<p>Physiological rates are heavily dependent on temperature and body size. Most current predictions of organisms' response to environmental warming are based on the assumption that key physiological rates like metabolism and excretion scale independently with body size and temperature and will not evolve. However, temperature is a significant driver for phenotypic variability in the allometric scaling and thermal sensitivity of physiological rates within ectotherm species, suggesting that evolution may play a role in shaping these parameters.</p> <p>We common-reared six populations of western mosquitofish that have recently established (~100 years ago) in geothermal springs along a broad thermal gradient (19-33°C) to determine whether these scaling parameters are affected by evolutionary and/or plastic responses to warming over ecological timescales. Each population was reared at four different temperatures (23, 26, 30 and 32°C). We measured routine metabolic and nitrogen excretion rates on mosquitofish across a wide body size range.</p> <p>We found evidence for plasticity, but not evolution, increasing the allometric scaling of metabolic rate with temperature. Plasticity in metabolism allometry reflected a decrease in thermal sensitivity at smaller body sizes.</p> <p>We found evidence for evolution of phenotypic plasticity on the allometry of excretion rate, reflecting evolutionary differences in how thermal sensitivity varies with body size across different populations.</p> <p>Evolutionary differences in excretion rate scaling did not influence the relationship between excretion and metabolism across rearing temperatures, suggesting that warming does not affect the balance between mosquitofish energy demands and nutrient recycling rates.</p>
Data from: Genetic and environmental effects on the scaling of metabolic rate with body size
Metabolic rate (MR) often scales with body mass (BM) following a power function of the form MR = aBMb, where b is the allometric exponent (i.e. slope on a log-log scale). The variational properties of b have been debated, but very few studies have tested for genetic variance in b, and none have tested for a genotype-by-environment (GxE) interaction in b. Consequently, the short-term evolutionary potentials of both b and its phenotypic plasticity remain unknown. Using 10 clones of a population of Daphnia magna, we estimated the genetic variance in b and assessed whether a GxE interaction affected b. We measured metabolic rate on juveniles of different sizes reared and measured at three temperatures (17, 22 and 28&[deg]C). Overall, b decreased with increasing temperature. We found no evidence of genetic variance in b at any temperature, and thus no GxE interaction in b. However, we found a significant GxE interaction in size-specific metabolic rate. Using simulations, we show how this GxE interaction can generate genetic variation in the ontogenetic allometric slopes of animals experiencing directional changes in temperature during growth. This suggests that b can evolve despite having limited genetic variation at constant temperatures.
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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)
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DANDI Archive for NWB datasets
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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.