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565 results for “Metabolic response;”
Experimental soil metabolism responses to oxygen availability and carbon pulses
Soil metabolism rates were measured in experimental flow-through reactors (FTRs) in order to assess responses to oxygen availability (i.e., redox conditions) and pulsed inputs of bioavailable carbon. The oxygen and carbon manipulations were meant to simulate patchy conditions in the rhizosphere of Spartina alterniflora marshes. The experiment was conducted over 97 days. During the first 84 days, pulses were applied weekly and metabolic responses were measured 1 and 5 days later. After the final carbon pulse, metabolism responses were followed for another 13 days in order to assess starvation responses. We used soils from Airport marsh on Sapelo Island.
Data in support of 'Mechanistic insights into plant community responses to environmental variables: genome size, cellular nutrient investments, and metabolic trade-offs.'
Data was collected to examine whether and how the plant genome size (GS) influences traits (stomata size, stomata density, cellular and tissue level carbon (C), nitrogen (N), and phosphorus (P) contents) and metabolic-tradeoffs (of photosynthesis, evapotranspiration, water-use, efficiency) of plants in treatment plots in which nothing, N, P, or NP had been annually added. Data was collected from ~500 plants from seven grassland sites that are all part of the Nutrient Network (https://nutnet.org), a globally distributed experiment in which plots have different nutrient amendment treatments that are administered identically to allow cross-site comparisons of the effects of nutrients on biodiversity patterning. The sites chosen varied along a North-South latitude, longitude, mean annual precipitation (MAP) and mean annual temperature (MAT) gradient.
Bone metabolism gene variation and response to bisphosphonate treatment in women with postmenopausal osteoporosis
<p>This repository contains the raw and source data for the manuscript "Bone metabolism gene polymorphism and response to bisphosphonate treatment in women with postmenopausal osteoporosis" submitted to PLOS ONE.</p> <p><strong>Abstract: </strong></p> <p><em>Introduction:</em> Long-term treatment is used in patients with osteoporosis, and bisphosphonates (BPs) are the most commonly prescribed medications. However, in some patients this therapy is not effective, cause different side effects and complications. Unfortunately, at least one year is needed to identify and confirm an ineffectiveness of BPs therapy on bone mineral density (BMD). Among other factors, a response to BPs therapy may also be explained by genetic factors. The aim of this study was to analyze the influence of <em>SOST, PTH, FGF2, FDPS, GGPS1, </em>and<em> LRP5</em> gene polymorphisms on the response to treatment with BPs.</p> <p><em>Materials and methods: </em>Women with postmenopausal osteoporosis were included to this study if they used bisphosphonates for at least 12 months. Exclusion criteria were: persistence on BPs therapy less than 80%, bone metabolic diseases, diseases deemed to affect bone metabolism, malignant tumours, using of any medications influencing BMD. The study protocol was approved by the local ethics committee. The BMD at the lumbar spine and femoral neck were measured using dual x-ray absorptiometry (GE Lunar) before and at least 12 months after treatment with BPs. According to BMD change, patients were divided in two groups – responders and non-responders to BPs terapy. Polymorphic variants in <em>SOST, PTH, FGF2, FDPS, GGPS1, </em>and<em> LRP5</em> genes were determined using PCR analysis with TaqMan probes (Thermo Scientific).</p> <p><em>Results:</em> In total, 201 women with BPs therapy were included in the study. No statistically significant differences were observed in age, age at menopause, weight, height, BMI and baseline BMD levels between responders (122 subjects) and non-responders (79 subjects).</p> <p>As single markers, the <em>SOST </em>rs1234612 T/T (OR=2.3; P=0.02), <em>PTH</em> rs7125774 T/T (OR=2.8, P=0.0009), <em>FDPS</em> rs2297480 G/G (OR=29.3, P=2.2×10<sup>-7</sup>), and <em>GGPS1</em> rs10925503 C/C+C/T (OR=2.9; P=0.003) gene variants were over-represented in non-responders group. No significant association between <em>FGF2</em> rs6854081 and <em>LRP5</em> rs3736228 gene variants and response to BPs treatment was observed. The carriers of T-T-G-C allelic combination (constructed from rs1234612, rs7125774, rs2297480, and rs10925503) were predisposed to negative response to BPs treatment (OR = 4.9, 95% CI 1.7–14.6, P=0.005). The C-C-T-C combination was significantly over-represented in responders (OR = 0.1, 95% CI 0.1–0.5, P=0.006).</p> <p><em>Conclusions:</em> Our findings highlight the importance of identified single gene variants and their allelic combinations for pharmacogenetics of BPs therapy of osteoporosis. Complex screening of these genetic markers could be used as a new strategy for personalized antiresorptive therapy.</p>
Shape, membrane morphology, and morphodynamic response of metabolically active human mitochondria revealed by scanning ion conductance microscopy
<p>This contains the hole data set as well as all analysed data for the paper published in Beilstein Journal of Nanotechnology "Shape, membrane morphology and morphodynamic response of metabolically active human mitochondria revealed by Scanning Ion Conductance Microscopy".</p> <p>Most of the images were taken with the SICM. These uncompressed tiff files can be read and processed with the Gwyddion software or other scanning probe image processing software.</p>
Nitrogen cycling and metabolic rates of aquacultured and wild Acropora coral from Guam in response to ammonium loading rates during 2020-2022
Rates from aquacultured corals and coral fragments collected in Guam in response to ammonium loading. These data are from two separate experiments, one using aquacultured corals and artificial seawater and light. The second was done with wild collected Acropora pistillata from two reef sites in Guam. The first site was West Hagåtña Bay (N13.479650, E144.741750; N13.479833, E144.741733) which had more nearby urban influences and was near the sewage outfall for the city (Redding et al. 2013). The second site was Luminao Reef (N13.4652417, E144.6477483; N13.465467, E144.648050) which was a more isolated reef on the seaward side of the breakwater for Guam’s major port. We measured respiration, gross primary production, 15N ammonium uptake to corals, related nitrogen cycling fluxes in the tanks (reminerization, net uptake, nitrification).
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>
Unexpected microbial metabolic responses to elevated temperatures and nitrogen addition in subarctic soils under different land-use
<p>This repository contains all necessary raw data as well as the R code used to conduct statistical analysis and create figures of the publication<br> <br><strong>Unexpected microbial metabolic responses to elevated temperatures and nitrogen addition in subarctic soils under different land-use</strong></p><p>Julia Schroeder1, Tino Peplau1, Edward Gregorich2, Christoph C. Tebbe3, Christopher Poeplau1</p><p>1 Thünen Institute of Climate-Smart Agriculture, Bundesallee 68, 38116 Braunschweig, Germany<br>2 Research and Development Centre, Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada<br>3 Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, Germany</p><p>DOI: https://doi.org/10.1007/s10533-022-00943-7 </p><p>This study investigated how subarctic soils under different land use will respond to warming and increasing N availability to allow for better predictions of C cycling under global change. The short-term temperature sensitivity as well as N-input effects on microbial CUE, respiration, growth and turnover were assessed in a one-day incubation experiment according to the 18O-CUE approach. The warming and N response of SOM decomposition were assessed in a 50-days incubation experiment via measurement of cumulative respiration. Both experiments were conducted with the following three treatments: incubation at 10 °C, incubation at 20 °C, and incubation at 20 °C plus N-fertiliser addition at an amendment rate of 100 kg N ha-1. The response to warming or N addition were expressed as response ratios RRT = 20°C/10°C and RRN = 20°C+N/20°C for warming and N response, respectively.</p><p>The R code was developed under R v3.6.3 and adapted to work under version R v.4.1.2.</p><p>The repository includes the following files:</p><ul><li>general_soil_parameters_per_sample.csv - general soil data for each field sample (n=27)</li><li>general_soil_parameters_per_plot.csv - general soil data assessed on pooled replicated field samples (n=9)</li><li>respiration_over_50d_incubation.csv - respiration rate and cumulative respiration for each time-point and laboratory sample over the 50-days incubation</li><li>sample_data.csv - data measured for each laboratory sample (n=81)</li></ul><p> </p><ul><li>Warming_and_nitrogen_response_of_CUE_in_subarctic_soils.Rproj - Rproject (load project to work on provided scripts and data)</li><li>load_data_script.R - loads required data</li><li>absolute_values_script.R - summary of absolute ranges of parameters per land-use type and site</li><li>absolute_linear_mixed_effects_model_script.R - run statistical analysis</li><li>correlograms_absolute_soil_params_script.R - correlation analysis to identify what drives absolute values</li><li>plot_correlations_absolute_soil_params_script.R - plot drivers of CUE and cumulative respiration</li><li>RRT_RRN_calculation_script.R - calculates response ratios</li><li>plot_RRT_RRN_script.R - plot response ratios</li><li>RRT_RRN_linear_mixed_effects_models_script.R - run statistical analysis</li><li>correlograms_RRT_RRN_soil_param_script.R - correlation analysis to identify drivers of response ratios</li><li>plot_correlations_RRT_RRN_soil_params_script.R - plot drivers of response ratios</li><li>RRT_RRN_resprate_cumulresp_over_time_50d_incubation_script.R - plot response ratios over time course</li></ul>
Evolutionary responses of energy metabolism, development, and reproduction to artificial selection for increasing heat tolerance in Drosophila subobscura
<p><span>Adaptation to warming conditions involves increased heat tolerance and metabolic changes to reduce maintenance costs and maximize biological functions close to fitness. Evidence shows that energy metabolism evolves in response to warming conditions, but we know little about how heat stress intensity determines the evolutionary responses of metabolism and life history traits. Here, we evaluated the evolutionary responses of energy metabolism and life-history traits to artificial selection for increasing heat tolerance in Drosophila subobscura, using two protocols to measure and select heat tolerance: slow and fast ramping protocols. We found that the increase in heat tolerance was associated with reduced activity of the enzymes involved in the glucose-6-phosphate branchpoint, but no changes in the metabolic rate in selected lines. We also found that the evolution of increased heat tolerance increased the early fecundity in selected lines and increased the egg-to-adult viability only in the slow-ramping selected lines. This work shows heat tolerance can evolve under different thermal scenarios but with different evolutionary outcomes on associated traits depending on the heat stress intensity. Therefore, spatial and temporal variability of thermal stress intensity should be taken into account to understand and predict the adaptive response to ongoing and future climatic conditions.</span></p>
Dataset: A quantitative 1H NMR approach for evaluating the metabolic response of Saccharomyces cerevisiae to mild heat stress
<p>In this study, the effect of growth temperature on the yeast (<em>Saccharomyces cerevisiae</em>) metabolome has been analyzed by one-dimensional proton NMR spectroscopy (<sup>1</sup>H NMR).</p> <p>Yeast cells were grown either at 30 or 37°C. A non-targeted chemometric evaluation of the spectra was performed in order to detect potential biomarkers. Moreover, an exhaustive assignment for most of the detected NMR signals was carried out, corresponding to 38 identified metabolites. Resonances from these identified metabolites were integrated, and univariate and multivariate data analyses were applied on the matrices of these relative concentrations. Observed changes in metabolite concentrations were consistent with the expected process of temperature acclimation, showing alterations in amino acid cellular pools, nucleotide metabolism and lipid composition.</p>
Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
<p>This dataset supports the article "Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth", which is under minor revision in Journal of Experimental Botany. The study addresses the combined effects of and plant population origin, drought and heat stress on plant growth, plant morphology and the leaf metabolome. The data were assessed in Northern and Southern European individuals of <em>Cakile maritma</em> (See Rocket). An R-script containing all statistical analyses that have been implemented with these data is also provided.</p>
Evolutionary responses of energy metabolism, development, and reproduction to artificial selection for increasing heat tolerance in Drosophila subobscura
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Timing of salinisation and nutrient enrichment drives freshwater microbial community metabolic responses
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Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth
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Data from: Intraspecific variation in metabolic responses of a cool water fish to increasing temperatures
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Local-scale thermal history influences metabolic response of marine invertebrates
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Seagrass ecosystem metabolic carbon capture in response to green turtle grazing across Caribbean meadows, 2016 - 2018
This dataset contains ecosystem metabolism and seagrass meadow data from five locations in the Greater Caribbean and Gulf of Mexico regions at which green turtle populations had established foraging areas. Ecosystem metabolic rates were compared between grazed and adjacent ungrazed areas of seagrass (Thalassia testudinum) to investigate the effects of green turtle grazing on metabolic carbon capture rates in seagrass meadows across a wide geographic area. Seagrass data are provided for site descriptions and drivers of variation in metabolic rates. Ecosystem metabolic rates are also included for meadows of the invasive seagrass Halophila stipulacea from two locations for comparison to rates in the native seagrass meadows where this invasive seagrass is encroaching upon green turtle foraging areas. Data were collected from one location (Little Cayman) in 2016, and from the remaining four locations (Bonaire; St. Croix; Eleuthera, Bahamas; west coast of Florida) in 2018.
Foliar and sapwood nutritional and metabolic responses to Ca-treatment at the Hubbard Brook Experimental Forest, 2000 – 2015
Background Acidic deposition has caused a depletion of calcium (Ca) in the northeastern forest soils. One time application of wollastonite (CaSiO3 - 1.2 Mg ha-1 of Ca) was done at watershed 1 (WS1) of the Hubbard Brook Experimental Forest (HBEF) in 1999 to evaluate its effects on various functions of the HBEF ecosystem. This rate of application was intended to increase the existing base saturation of the soil from 10% to approximately 19%, and to increase the soil pH to the level that was estimated to exist ~50 years prior to treatment. More details on the treatment can be found at http://www.hubbardbrook.org/research/longterm/calcium/w1_overview/index.html. The overall objective of this study was to evaluate changes in foliar and sapwood metabolic parameters and microbial diversity as indicators of stress and overall health in trees exposed to Ca-supplementation. Raw data from Ca-treated WS1 are compared with WS3 (reference watershed) for cellular metabolites, exchangeable foliar chemistry (not totals) 2000-2015. These watersheds are in close proximity (less than 1.5 Km apart) with similar geology, temperature, soils, and overall climate. For more details see a list of references given below Ca-Supplementation-Metabolic Study (WS1 & along eastern edge of WS3) SUMMARY: The effects of Ca addition on foliar soluble (extractable in 5% HClO4) ions, chlorophyll, polyamines, and amino acids were studied in three hardwood species, namely sugar maple, yellow birch, and American beech. We further analyzed these effects in relation to elevation at Ca-supplemented WS1 and reference WS3 watersheds. During the earlier years foliar soluble Ca increased significantly in all species at mid and high elevations at Ca-supplemented WS1. This was accompanied by increases in soluble P, chlorophyll, and two amino acids, glutamate and glycine. A decrease in known metabolic indicators of physiological stress (i.e. the amino acids, arginine and γ-aminobutyric acid (GABA), and the diamine, pu
Red spruce foliar nutritional and metabolic responses to N, Ca, and N+Ca additions in a plot level study from Hubbard Brook Experimental Forest NH, Adirondack State Park, NY and Groton State Forest, VT from 1997-2000.
Plot Level Ca, N, Ca+N Study Background: Three mature red spruce (Picea rubens Sarg.) – balsam fir (Abies balsamea (L.) Mill.) stands with closed canopies from across the northeastern United States were selected to assess the effects of N and Ca additions on forest growth. These sites included Groton, VT (Groton State Forest), Big Moose Lake, NY (Adirondack State Park) and Watershed 9 in the Hubbard Brook Experimental Forest, NH. Site descriptions can be found in the pdf file included in this dataset. Full site descriptions have been published in Kulmatiski et al, 2007, Nitrogen and calcium additions increase forest growth in northeastern USA spruce–fir forests, Canadian Journal of Forest Research 37: 1574-1585. This publication also provides more in-depth site and soil descriptions. In 1992, three replicate 30 m by 30 m plots were randomly assigned to each of four treatment levels: control (control), Ca addition (Ca), N addition (N), or Ca + N addition (Ca + N) in NY and NH (for a total of 12 plots at each site). In VT, only control and Ca treatments were established due to limited space and research goals (for a total of 6 plots). Beginning in July 1992 through July 2000, N amendments (100 kilograms of NH4NO3-N per hectare per year), Ca amendments (80 kilograms of CaSO4-Ca plus 80 kilograms of CaCl2-Ca per hectare per year), and Ca + N (same dosage as separate applications) amendments were hand broadcast as commercial grade salts. Applications were made in June, July, and August to each plot in each year. SUMMARY: The main objectives of this study were to evaluate changes over time (1997-2000) in foliar metabolism of mature red spruce (Picea rubens Sarg.) trees in response to additions of nitrogen, Ca, or N +Ca supplementation. N was applied as NH4NO3 and Ca was applied as gypsum [CaSO4 .2H2O (2X) + CaCl2 .2H2O (1X)] and Ca + N treatment was a combination of both at the same concentrations Three sites received these treatments; Groton, VT (Groton State Forest), Bi
Metabolic responses of Plectus murrayi across a temperature gradient, McMurdo Dry Valleys, Antarctica, 2016-2017
Populations of Plectus murrayi, a mesophilic nematode, have been increasing in the McMurdo Dry Valleys, Antarctica over the past three decades. In contrast, most other Antarctic nematode species, including Scottnema lindsayae, have experienced constant population declines over the same time period due to climate change related increases in summer temperatures and wetting occurrences. To determine why P. murrayi populations are outperforming other Antarctic nematode species, we performed a laboratory experiment to measure their metabolic responses to increasing temperatures. For this experiment, P. murrayi were cultured from soils collected in Taylor Valley during the austral summers of 2016 and 2017 as part of the McMurdo Dry Valleys Long Term Ecological Research (LTER) Project. Using a TAM IV Isothermal Microcalorimeter, we measured the metabolic heat rates of these cultured P. murrayi populations in six sealed 4 mL vials. Three of these vials also contained 200 µl ampoules of 0.4 M NaOH. NaOH reacts with CO2 produced from metabolic processes to release a known amount of heat (108.5 kJ/mol CO2). The difference in metabolic heat rate produced in vials containing NaOH and those without NaOH is proportional to CO2 produced from P. murrayi metabolism. Consequently, this method allowed us to track metabolic heat rates as well as CO2 production rates. O2 consumption was calculated from vials without NaOH using Thornton's rule (455 kJ of metabolic heat/mol O2). P. murrayi metabolic heat rates were compared to C. elegans for reference, and baseline measurements included heat rates of E. coli and blank agar.
Data from: Developmental nutrition modulates metabolic responses to projected climate change
<ol> <li>Current policy has the world on track to experience around 3°C of warming by 2100. The responses of organisms to our warming world will be mediated by changes in physiological processes, including metabolic rate. Metabolic rate represents the energetic cost of living, and is fundamental to understanding the energy required to sustain populations. Current evidence indicates that animals have a limited capacity to adapt to warmer environments by reducing their metabolic rate. Consequently, animals may be more reliant on metabolic plasticity to ameliorate the thermodynamic effect of rising temperatures on physiological rates. However, metabolic plasticity is influenced by other environmental factors, including the nutritional quality of food. Elevated levels of atmospheric CO<sub>2</sub> are expected to reduce the protein and increase the carbohydrate concentration in plants, but we do not know how this will affect the response of metabolic rate to climate warming.</li> <li>Here we test the interactive effects of developmental dietary protein and carbohydrate concentrations on the metabolic plasticity of adult <i>Drosophila melanogaster</i> in response to a 3°C increase in temperature while accounting for variation associated with body mass and activity (resting metabolic rate).</li> <li>We show that the thermal sensitivity of resting metabolic rate is modulated by developmental nutrition with animals reared on nutritionally poor, low-protein diets showing the greatest increase in resting metabolic rate in response to simulated climate warming. We also show that if the nutritional quality of resources is unaffected by climate change, then temperature-induced increases in resting metabolic rate will be offset by decreases in mass, but the absolute energy requirements of animals will be elevated relative to current conditions despite this. If, on the other hand, temperatures rise and resources become more calorie-dense and carbohydrate-rich, then the resting metabolic rate of animals will remain relatively unchanged, but decreases in mass and activity may drive down the absolute energy requirements of animals.</li> <li>In the absence of evolutionary adaptation, these findings suggest that the combined plastic response of physiological, morphological, and behavioural traits to temperature and nutrition may be an important determinant of the ultimate outcome of climate change for populations.</li> </ol>
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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.