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11,869 results for “metabolic”
Dataset: Bacterioplankton metabolism of phytoplankton lysates across a cyclone-anticyclone eddy dipole impacts the cycling of semi-labile organic matter in the photic zone
<p>This dataset contains both field data and the results of dilution batch-culture bioassay experiments characterizing bacterioplankton usage of ambient and added dissolved organic matter across a cyclone to anticyclone spatial transect in the North Pacific Subtropical Gyre. Field data include total organic carbon, total nitrogen, bacterioplankton cell abundances, ammonia monooxygenase subunit A gene concentrations, and 16S rRNA gene amplicons. Experimental data include time-resolved changes in total organic carbon, nitrogen species, and bacterioplankton cell abundances.</p>
Top-down and bottom-up vegetal and animal product metabolic profiles for 29 european countries (EU27 + United Kingdom + Norway).
<p>This repository contains the data needed to reproduce the results in:</p> <p>Cadillo-Benalcazar, J.; Renner, A. Giampietro, M. (2020). A multiscale integrated analysis of the factors characterizing the sustainability of food systems in Europe. Journal of Environmental Management. Volume 271, 1 October 2020, 110944. <a href="https://doi.org/10.1016/j.jenvman.2020.110944">https://doi.org/10.1016/j.jenvman.2020.110944</a></p> <p>Renner, A.; Cadillo-Benalcazar, J.; Benini, L., Giampietro, M. (2020). Environmental pressure of the European agricultural system: Anticipating the biophysical consequences of internalization. Ecosystem services. Special Issue: Agro-futures. Volume 46, December 2020, 101195. <a href="https://doi.org/10.1016/j.ecoser.2020.101195">https://doi.org/10.1016/j.ecoser.2020.101195</a></p>
Computed results for Bayesian genome scale modelling temperature effect on yeast metabolism
<p>This repository contains the computed results for reproducing the figures in the manuscript "Li G., et al. Bayesian genome scale modelling identifies thermal determinants of yeast metabolism". The scripts can be found in Github (<a href="https://github.com/Gangl2016/BayesianGEM">https://github.com/Gangl2016/BayesianGEM</a>)</p>
Dataset for the paper "Ripa M, Di Felice LJ, Giampietro M (2021). The energy metabolism of post-industrial economies. A framework to account for externalization across scales. Energy, 214." https://doi.org/10.1016/j.energy.2020.118943
<p>This repository contains the data needed to reproduce the results in: </p> <p>Ripa M, Di Felice LJ, Giampietro M (2021). The energy metabolism of post-industrial economies. A framework to account for externalization across scales. Energy, 214." https://doi.org/10.1016/j.energy.2020.118943</p> <p>The dataset was also used for a case study in "Di Felice L., Dunlop T., Giampietro M., Kovacic Z., Renner A., Ripa M., Velasco-Fernández R. – Report on the Quality Check of the Robustness of the Narrative behind Energy Directives. MAGIC (H2020–GA 689669) Project Deliverable 5.4, 30 November 2018". (link: https://magic-nexus.eu/documents/d54-report-narratives-behind-energy-directives).</p> <p>Sources of data are specified in the dataset (under tab "References")</p>
Gestational Cd exposure in the CD-1 mouse induces sex-specific hepatic insulin insensitivity, obesity and metabolic syndrome in adult female offspring
<p>There is compelling evidence that developmental exposure to some toxic metals increases risk for obesity and obesity-related morbidity including cardiovascular disease and type 2 diabetes in adults. To explore the hypothesis that developmental Cd exposure increased risk of obesity later in life, male and female CD-1 mice were maternally exposed to 500 ppb CdCl<sub>2</sub> in drinking water during a human gestational equivalent period (GD0 - PND10). Hallmark indicators of metabolic disruption, hepatic steatosis, and metabolic syndrome were evaluated prior to birth through adulthood. Blood Cd levels in dams were similar to those observed in human pregnancy cohorts. There were no observed impacts of exposure on dams or pregnancy-related outcomes. Results of glucose and insulin tolerance testing revealed that Cd-exposure impaired glucose homeostasis in young adult offspring. Exposure-related increases in circulating triglycerides and hepatic steatosis were apparent only in females. By PND120, Cd-exposed females had become 30% heavier with 700% more perigonadal fat than unexposed control females. There was no evidence of dyslipidemia, steatosis, increased weight gain, nor increased adiposity in Cd-exposed male offspring. Hepatic transcriptome analysis at PND1, PND21, and PND42 revealed evidence for female-specific increases in oxidative stress and mitochondrial dysfunction with significant early disruption of retinoic acid signaling and altered insulin receptor signaling consistent with hepatic insulin sensitivity in adult females. The observed steatosis and metabolic syndrome-like phenotypes resulting from exposure to 500 ppb CdCl<sub>2</sub> during the pre- and perinatal period of development equivalent to human gestation indicate that Cd acts developmentally as a sex-specific delayed obesogen.</p>
Data from" Euphotic Zone Metabolism in the North Pacific Subtropical Gyre Based on Oxygen Dynamics"
<p>This data set provides measurements of oxygen to argon molar ratios from discrete samples collected within the mixed layer at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series program, within the North Pacific Subtropical Gyre, between November 2013 and January 2019 (near-monthly cruises). Samples were measured by membrane inlet mass spectrometry following Ferrón et al. (2015). Version 2 had corrected longitude data (in decimal degrees east). Version 3 includes a new file with estimated rates of net community production, gross oxygen production and community respiration for the mixed layer.</p>
Dataset - Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
<p><strong>Dataset simulated for the manuscript "Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities" by Angeles-Martinez and Hatzimanikatis.</strong></p>
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism
<ul> <li>Eight versions of COBRA-compliant SBML files are available for each Recon 2M.1 and Recon 2M.2 depending on the use of: MNXref versus BiGG IDs; Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).</li> <li>892 personal GEMs (only T-GEMs) built with Recon 2.2</li> <li>1,784 personal GEMs (both P-GEMs and T-GEMs) built with Recon 2M.1</li> <li>892 personal GEMs (only T-GEMs) built with Recon 2M.2</li> </ul> <p> </p> <p><strong>Publication</strong></p> <p>Jae Yong Ryu<sup>1</sup>, Hyun Uk Kim<sup>1</sup> & Sang Yup Lee<sup>*</sup>. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism., <em>Proc. Natl. Acad. Sci. U.S.A.</em>, 2017, http://www.pnas.org/content/early/2017/10/23/1713050114</p> <p> </p>
Data for "Combining 13C, 15N, and 2H tracer to measure feeding and metabolic activity in marine, shallow-water sponges – A pilot study"
<p>This dataset includes raw data used in the paper "Combining <sup>13</sup>C, <sup>15</sup>N, and <sup>2</sup>H tracer to measure feeding and metabolic activity in marine, shallow-water sponges – A pilot study" (JEMBE).</p>
Effect of hip abduction assistance on metabolic cost and balance during human walking
<p>The use of wearable robots to provide walking assistance has rapidly grown over the last decade, with significant advances made in robot design and control methods toward reducing physical effort while performing an activity. The reduction in the walking effort has mainly been achieved by assisting forward progression in the sagittal plane. Human gait, however, is a complex movement that combines motions in three planes, not only the sagittal but also the transverse and frontal planes. In the frontal plane, the hip joint plays a key role in gait, including balance. However, wearable robots targeting this motion have rarely been investigated. In this study, we developed a hip abduction assistance wearable robot by formulating the hypothesis that assistance that mimics the biological hip abduction moment or power could reduce the metabolic cost of walking and affect the dynamic balance. We found that hip abduction assistance with a biological moment second peak mimic profile reduced the metabolic cost of walking by 11.6% compared to the normal walking condition (p=0.009). The assistance also influenced balance-related parameters, including the margin of stability. Hip abduction assistance influenced the center-of-mass movement in the mediolateral direction. When the robot assistance was applied as the center of mass moved toward the opposite leg, the assistance replaced some of the efforts that would have otherwise been provided by a human. This indicates that hip abduction assistance can reduce physical effort during human walking while influencing balance.</p>
Data from: What goes in must come out? The metabolic profile of plants and caterpillars, frass, and adults of Asota (Erebidae: Aganainae) feeding on Ficus (Moraceae) in New Guinea
<p>Insect herbivores have evolved a broad spectrum of adaptations in response to the diversity of chemical defences employed by plants. Here we focus on two species of New Guinean Asota and determine how these specialist moths deal with the leaf alkaloids of their fig (Ficus) hosts. As each focal Asota species is restricted to one of three chemically distinct species of Ficus, we also test whether these specialized interactions lead to similar alkaloid profiles in both Asota species. We reared Asota caterpillars on their respective Ficus hosts in natural conditions and analyzed the alkaloid profiles of leaf, frass, caterpillar, and adult moth samples using UHPLC–MS/MS analyses. We identified 43 alkaloids in our samples. Leaf alkaloids showed various fates. Some were excreted in frass or found in caterpillars and adult moths. We also found two apparently novel indole alkaloids likely synthesized de novo by the moths or their microbiota—in both caterpillar and adult tissue but not in leaves or frass. Overall, alkaloids unique or largely restricted to insect tissue were shared across moth species despite feeding on different hosts. This indicates that a limited number of plant compounds have a direct ecological function that is conserved among the studied species. Our results provide evidence for the importance of phytochemistry and metabolic strategies in the formation of plant–insect interactions and food webs in general. Furthermore, we provide a new potential example of insects acquiring chemicals for their benefit in an ecologically relevant insect genus.</p>
Ontogeny of hepatic metabolism in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle
<p>Nutrient availability during early stages of development (embryogenesis and the first week of life) can have long-term effects on physiological functions and bird metabolism. The embryo develops in a closed structure and depends entirely on the nutrients and energy available in the egg. The aim of this study was to describe the ontogeny of pathways governing hepatic metabolism that mediates many physiological functions in the pHu+ and pHu- chicken lines, which are divergently selected for the ultimate pH of meat, a proxy for muscle glycogen stores, and which differ in the nutrient content and composition of eggs. Our study provides the first detailed description of the evolution of different hepatic metabolic pathways during the early development of embryos and post-hatching chicks. We found a metabolic orientation for the pHu+ line towards proteolysis, glycogen degradation, ATP synthesis and autophagy, likely in response to a higher energy requirement compared with pHu- embryos. The metabolic orientations specific to the pHu+ and pHu- lines are established very early, probably in relation with their different genetic background and available nutrients.</p>
Data from : Metabolic footprint of Vero E6 cells highlights the key metabolic routes associated with SARS-CoV-2 infection and response to drug combinations
<p>This dataset contains representative 1D 1H NMR spectra and data used in the manuscript " Metabolic footprint of Vero E6 cells highlights the key metabolic routes associated with SARS-CoV-2 infection and response to drug combinations " . </p><p> </p><p>The present study used Nuclear Magnetic Resonance-based metabolic footprinting to characterize the secreted cellular metabolite levels (exometabolomes) of Vero E6 cells in response to SARS-CoV-2 infection and to two candidate drugs (Remdesivir, RDV and Azithromycin, AZI). </p><p> </p><p><strong>Supplementary File 1.zip = </strong>Representative 1D 1H NMR profiles of examined VE6 esometabolomes, </p><p> </p><p><strong>Supplementary File 2.xlsx</strong> = Average Mean ± Standard Deviations of NMR relative quantified data (integrals, a.u.) from examined VE6 esometabolomes. </p><p> </p><p><strong>Supplementary File 3.csv = </strong>p–values and associated False Discover Rate (FDR) derived from univariate ANOVA with Fischer's LDS post-hoc test comparisons carried out on NMR relative quantified data.</p><p> </p><p><strong>List of Supplementary Files derived from Metabolite Set Enrichment Analysis (MSEA) : </strong></p><p> </p><p><strong>Supplementary File 4.csv </strong>= Tabular Results from MSEA performed on VE6+ VE6- comparison.</p><p><strong>Supplementary File 5.csv </strong>= Tabular Results from MSEA performed on VE6+ RDV vs. VE6+ comparison.</p><p><strong>Supplementary File 6.csv </strong>= Tabular Results from MSEA performed on VE6+ AZI vs. VE6+ comparison.</p><p><strong>Supplementary File 7.csv</strong> = Tabular Results from MSEA performed on VE6+ R+A vs. VE6+ comparison.</p><p> </p>
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>
Per capita sperm metabolism is density-dependent
<p>From bacteria to metazoans, higher-density populations have lower <em>per capita</em> metabolic rates than lower-density populations. This relationship between density and metabolism was actually first proposed 100 years ago and was focused on spermatozoa but contemporary studies of sperm metabolism specifically assume that sperm concentration has no effect on metabolism. We did a systematic review to estimate the relationship between sperm aerobic metabolism and sperm concentration, for 203 estimates spanning 49 species, from protostomes to humans from 89 studies. We found strong evidence that <em>per capita </em>metabolic rates are concentration-dependent: both within- and among-species, sperm have lower metabolisms in dense ejaculates but increase their metabolism when diluted. On average, a 10-fold decrease in sperm concentration increased <em>per capita</em> metabolic rate by ~60%. Metabolic plasticity in sperm may be an adaptive response but this requires further testing.</p>
Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system
<p>Diatoms serve as the major link between the marine carbon (C) and silicon (Si) biogeochemical cycles through their contributions to primary productivity and requirement for Si during cell wall formation. Although several culture-based studies have investigated the molecular response of diatoms to Si and nitrogen (N) starvation and replenishment, diatom silicon metabolism has been understudied in natural populations. A series of deckboard Si-amendment incubations were conducted using surface water collected in the California Upwelling Zone near Monterey Bay. Steep concentration gradients in macronutrients in the surface ocean coupled with substantial N and Si utilization led to communities with distinctly different macronutrient states: replete ('healthy'), low N ('N-stressed'), and low N and Si ('N- and Si-stressed'). Biogeochemical measurements of Si uptake combined with metatranscriptomic analysis of communities incubated with and without added Si were used to explore the underlying molecular response of diatom communities to different macronutrient availability. Metatranscriptomic analysis revealed that N-stressed communities exhibited dynamic shifts in N and C transcriptional patterns suggestive of compromised metabolism. Expression patterns in communities experiencing both N and Si stress imply that the presence of Si stress may partially ameliorate N stress and dampen the impact on organic matter metabolism. This response builds upon previous observations that the regulation of C and N metabolism is decoupled from Si limitation status, where Si stress allows the cell to optimize the metabolic machinery necessary to respond to episodic pulses of nutrients. Several well-characterized Si-metabolism associated genes were found to be poor molecular markers of Si physiological status; however, several uncharacterized Si-responsive genes were revealed to be potential indicators of Si stress or silica production.</p>
Dataset for "Structural complexity and benthic metabolism: resolving the links between carbon cycling and biodiversity in restored seagrass meadows"
<p>This dataset accompanies the article "Structural complexity and benthic metabolism: resolving the links between carbon cycling and biodiversity in restored seagrass meadows" accepted for publication in Biogeosciences (https://doi.org/10.5194/bg-2023-173). The dataset includes benthic fluxes and biodiversity data in from bare sediments, restored <em>Zostera marina</em> and a natural <em>Z. marina</em> meadow collected in Gåsö, Sweden (58.2325, 11.3984) between July 05 - July 20, 2022. </p>
Data from: Testing metabolic cold adaptation and the climatic variability hypotheses across the latitudinal range of a widespread, supratidal water beetle
<p>Temperature significantly impacts ectotherm physiology, with thermal and metabolic traits varying with latitude but the drivers of this variation remain unclear, despite obvious consequences in the face of ongoing global change. This study explores metabolic cold adaptation (MCA) and the climatic variability hypothesis (CVH) to evaluate local adaptation and phenotypic plasticity of metabolic rates and thermal limits in two populations of the supratidal rockpool beetle <em>Ochthebius lejolisii</em> from localities experiencing contrasting thermal variability. Reciprocal acclimation was conducted under spring temperature regimes of both localities, incorporating local diurnal variation. Metabolic rates were measured by closed respirometry, and thermal tolerance limits estimated through thermography. In line with MCA, the northern population (colder climate) showed higher metabolic rates and Q10s at lower temperatures than the southern population. As predicted by the CVH, the southern population (more variable climate) showed higher upper thermal tolerance but only the northern population was able to acclimate upper thermal limits. This pattern suggests the existence of trade-offs in thermal adaptation in this species, likely increasing the vulnerability of populations on Mediterranean coasts to the projected increases in extreme temperatures under ongoing climate change.</p>
Supplementary dataset for "Phenylacetic acid metabolism in land plants: novel pathways and metabolites"
<p>Supplementary dataset with measured data for publication "Phenylacetic acid metabolism in land plants: novel pathways and metabolites"</p>
GC-MS raw data_Figure 6E_Lysophosphatidic Acid Shifts Metabolic and Transcriptional Landscapes to Induce a Distinct Cellular State in Human Pluripotent Stem Cells
<p><strong>Sample name</strong></p> <p>hESCs (H1 cells) were given treatments for two days and then collected for GC-MS analysis.</p> <p>E8: E8 medium</p> <p>AX: E8 + 1.6% AlbuMAX;</p> <p>BSA: E8 + 1% albumin;</p> <p>BSA+hCDL: E8 + 1% albumin + 0.1% hCDL;</p> <p>LPA+BSA: E8 + 1 μM LPA + 1% albumin;</p> <p>LPA+BSA+hCDL: E8 + 1 μM LPA + 1% albumin + 0.1% hCDL</p> <p>STD: standard lipids mixture used as reference</p> <p><strong>Extraction and Methylation</strong></p> <p>Sample preparation was conducted according to the previously reported method (Araujo et al., 2008) with the modification. Briefly, spent medium was removed, and cells were rinsed with 1 mL/well 0.9% (w/v) saline twice. Then 0.5 mL/well -80°C 80% methanol was added to quench the metabolism. Five wells of cells (from 6-well plate) were scrapped off into a glass screw-cap tube. Then 4 mL heptadecanoate containing chloroform (4 μg/mL, internal standard for fatty acids) was added into the tube. Vortex, and then centrifuge at 2000 rpm for 5 min. Cellular debris was carefully removed, and nitrogen blow the solution till dry. Add 1.5 mL hexane and 1.5 mL 14% boron trifluoride (BF<sub>3</sub>)/methanol solution. Seal the tube with nitrogen gas, heat it at 100°C for 1 h using MK200-2 dry bath incubator (Aosheng), and then cool down to room temperature. Add 1 mL water into the tube, vortex and then centrifuge at 3000 rpm for 10 min. The upper layer was transferred into a new 1.5-mL eppendorf tube and evaporated by nitrogen gas. The residue was re-dissolved in 100 μL hexane for GC-MS analysis.</p> <p><strong>GC-MS method</strong></p> <p>Samples were analyzed using an Agilent GC-MS system (Agilent) consisting of a 6890 gas chromatography and a 5973 mass spectrometer. Fatty acid methyl esters were separated by an Omegawax™ 250 fused silica capillary column (30 m × 0.25 mm i.d., 0.25 μm film thickness, Supelco, Bellefonte, PA). The optimized oven temperature program was: initial temperature set at 180°C and held for 3 min; ramped to 206°C at 2°C/min and held at 206°C for 25 min, then, ramped to 240°C at 10°C/min and held for 5 min. Overall, the total run time was 50 min. Carrier gas was high-purity helium at a flow rate of 1.5 mL/min. Injector temperature was set at 250°C. Injection volume was 2 μL with a split ratio of 1:15. The mass spectrometer was operated in electron-impact (EI) mode at 70 eV ionization energy. The temperatures of quadrupole and ionization source were set at 150°C and 280°C, respectively. The spectra from 3 to 50 min were acquired with the <em>m/z</em> range of 35–550 at a scan rate of 0.34 s per scan.</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.