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150 results for “metabolic phenotype”
Population persistence, phenotypic divergence and metabolic adaptation in yarrow (Achillea millefolium L.) along a climate gradient, CA, 1920 to 2023
This dataset provides insights into the persistence and adaptation of yarrow (Achillea millefolium L.) populations over a 100-year period of climate change. The data include plant height measurements and climatic variables (temperature and precipitation) from historical and resurveyed sites spanning a broad environmental gradient (1–3,200 m a.s.l.), alongside metabolic profiles obtained from a common-garden experiment. The dataset captures phenotypic changes in plant growth, metabolic diversity, and site-specific climatic shifts between 1920 and 2020. These data support analyses of how temperature and precipitation interact to shape plant responses over time and allow for exploring patterns of local adaptation in phenotypic and metabolic traits. This comprehensive dataset is valuable for understanding the ecological and evolutionary mechanisms underlying population persistence and can inform conservation strategies under future climate scenarios.
Data_Figure1(A-D)_AKR1D1 knockout mice develop a sex dependent metabolic phenotype
<p>Data of Fig1 Pannel A-D, “AKR1D1 knockout mice develop a sex dependent metabolic phenotype”</p> <p>The Dataset contains the original figure 1 (Pannel A-D) as PNG-format (10.1530JOE-21-0280_Fig1A-D.PNG). Corresponding raw from LC-MS/MS measurements are provided as one file in CSV format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1.csv), all further experiment related information (meta-data) as one file in TXT format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M1.txt), one file in PDF format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M2.pdf) and one file as CSV format (31003A-179400_10.1530_JOE-21-0280_AKR1D1_SS_DVK_4_Fig1_M3.csv).</p>
Merging metabolomics and genomics provides a catalog of genetic factors that infuence molecular phenotypes in pigs linking relevant metabolic pathways
<h3>Content</h3> <p>Metabolites included in the study. Summary statistics of metabolite levels for the Large White and Duroc pig populations are provided.</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>
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: Metabolic rate shapes phenotypic covariance among physiological, behavioural, and life history traits in honeybees
<p>Metabolic rate is often cited as the fundamental rate that determines the rate of all biological processes by shaping energetic availability for the various behavioral and life history traits that contribute to performance. It has therefore been suggested that metabolic rate drives the widely observed covariance among these different levels of phenotypic traits. However, much of the work on this topic has relied on pairwise correlational analysis, thereby leaving an important gap in our understanding regarding the functional links that shape this phenotypic covariance, often referred to as pace-of-life. Using honeybees as an experimental model, we measured a large number of behavioural, life history and physiological traits in individual bees and used a structural equation model to characterize the phenotypic covariance structure among these traits. Following this with a path analysis, we demonstrate that variation in metabolic rate plays a fundamental proximate role in driving this phenotypic covariance structure in honeybees. We discuss the importance of these findings in the context of how interindividual variation in terms of slow-fast phenotypes may drive the phenotype of a group and the functional role metabolic rate might play in shaping division of labour and social evolution.</p>
Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes
<p>Dataset of multi-well plate reader files related to the analysis of the growth of <em>C. difficile</em> isolates on differnet carbon substrates. </p> <p><strong>Data Collection. </strong>This<strong> </strong>dataset accompanies an <em>mSystems</em> article which is available at <a href="https://doi.org/10.1128/msystems.01075-24">https://doi.org/10.1128/msystems.01075-24</a>. The "Materials and Methods" section in this article fully describes the biological nature of these samples and how the samples were processed and analyzed. </p> <p><strong>Repository Content. </strong>The <em>amiga</em> folders contains both the raw data (see <em>data</em> and <em>mapping </em>sub-folders), intermediate outpus (see <em>dervied</em> sub-folders), and final outputs (see <em>figures</em> and <em>summary</em> sub-folders). Each <em>amiga </em>folder corresponds to a single working directory analyzed by the <a href="https://github.com/firasmidani/amiga"><em>AMiGA</em></a> software. For the <em>amiga-biolog</em> directory, the <em>notes</em> sub-folder also includes text files related to flagging plates and wells for quality issues.</p> <p><strong>Data Organization. </strong>Growth plate data are organized by the following experiments. </p> <ul> <li>biolog</li> <li>validation</li> <li>ribotype-255</li> <li>clade-5</li> <li>yeast-extract-biolog</li> <li>yeast-extract-validation</li> </ul> <p><strong>Data Analysis. </strong>Code used for manipulating and analyzing these samples is also publicly available on GitHub (<a href="https://github.com/firasmidani/cdiff-biolog-growth">https://github.com/firasmidani/cdiff-biolog-growth</a>) under the GNU GPL-3.0 license. The scripts in "analyze-code" can be used to analyze all data and the scripts in the "generate-figures" folder can be used to reproduce all figures included in the manuscript. See the GitHub repository for instructions on how to do so. </p> <p> </p>
Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high elevation hypoxia
<p>In response to a warming climate, many montane species are shifting upslope to track the emergence of preferred temperatures. Characterizing patterns of variation in metabolic, physiological and thermal traits along an elevational gradient, and the plastic potential of these traits, is necessary to understand current and future responses to abiotic constraints at high elevations, including limited oxygen availability. We performed a transplant experiment with the upslope-colonizing common wall lizard (<em>Podarcis</em> <em>muralis</em>) in which we measured nine aspects of thermal physiology and aerobic capacity in lizards from replicate low- (400 m above sea level, ASL) and high-elevation (1700 m ASL) populations. We first measured traits at their elevation of origin and then transplanted half of each group to extreme high elevation (2900 m ASL; above the current elevational range limit of this species), where oxygen availability is reduced by ∼25% relative to sea level. After 3 weeks of acclimation, we again measured these traits in both the transplanted and control groups. The multivariate thermal–metabolic phenotypes of lizards originating from different elevations differed clearly when measured at the elevation of origin. For example, high-elevation lizards are more heat tolerant than their low-elevation counterparts (counter-gradient variation). Yet, these phenotypes converged after exposure to reduced oxygen availability at extreme high elevation, suggesting limited plastic responses under this novel constraint. Our results suggest that high-elevation populations are well suited to their oxygen environments, but that plasticity in the thermal–metabolic phenotype does not pre-adapt these populations to colonize more hypoxic environments at higher elevations.</p>
Supplementary Data to: "A single nucleotide mutation in DUOX2 gene causes some of the panda's unique metabolic phenotypes"
<p>This file contains the data set associated with the manuscript entitled: "A single nucleotide mutation in the dual-oxidase 2 (<em>DUOX2</em>) gene causes some of the panda’s unique metabolic phenotypes", National Science Review, DOI: <a href="http://dx.doi.org/10.1093/nsr/nwab125">10.1093/nsr/nwab125</a></p>
Data from: Phenotypic plasticity of antibiotic resistance, metabolism byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli
<p><span>Although tag-based donation and recognition have well explained how the cooperative individuals are positively assorted if the cooperative individuals possess some signals and are also able to detect such signals, an additional mechanism is required to explain why some individuals pay the costs of evolving such a tag that may not be rewarded subsequently, and how such tag-based cooperative individuals will meet other similar individuals with a very low mutation rate. Here, we show that many and even all<em> Escherichia coli </em>bacteria cells in the increased antibiotic concentration will plastically evolve to be antibiotic resistant individuals who could protect antibiotic sensitive strain from the attack of antibiotics, and the antibiotic resistant strain could reversibly evolve to be antibiotic sensitive in non-antibiotic supplement medium but in a harsher environment with low glucose. A further experiment showed that antibiotic-sensitive <em>E. coli </em>strain could in turn help reduce the concentration of indole produced by the resistant strain. This metabolic product is harmful to the growth of the antibiotic-resistant strain but benefits the antibiotic-sensitive strain by helping turn on the multi-drug exporter to discharge the antibiotic. The utilization of metabolism byproduct indole produced by antibiotic-resistant cells benefits antibiotic-sensitive cells, while the indole-absorbing service of antibiotic sensitive cells unconsciously help in nullifying the indole side effect on antibiotic resistant strain, and a mutual benefit cooperation could therefore evolve.</span></p>
Prandial Metabolic Phenotyping in Sarcopenic Older Adults Comparing Plant Based and Whey Based Protein
ClinicalTrials.gov study NCT06628349. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Prandial Metabolic Phenotype in Adults
ClinicalTrials.gov study NCT05400733. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Data from: Deuterium metabolic imaging phenotypes mouse glioblastoma heterogeneity through glucose turnover kinetics
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Data from: Phenotypic plasticity of antibiotic resistance, metabolism byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli
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Data from: Metabolic rate shapes phenotypic covariance among physiological, behavioural, and life history traits in honeybees
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Switchgrass metabolomics reveals striking genotypic and developmental differences in specialized metabolic phenotypes
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Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high elevation hypoxia
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Metabolic rate shapes phenotypic covariance among physiological, behavioral, and life history traits in honeybees
<p><span>Metabolic rate is often cited as the fundamental rate that determines the rate of all biological processes by shaping energetic availability for the various behavioral and life history traits that contribute to performance. It has therefore been suggested that metabolic rate drives the widely observed covariance among these different levels of phenotypic traits. However, much of the work on this topic has relied on pairwise correlational analysis, thereby leaving an important gap in our understanding regarding the functional links that shape this phenotypic covariance, often referred to as pace-of-life. Using honeybees as an experimental model, we measured a large number of behavioral, life history and physiological traits in individual bees and used a structural equation model to characterize the phenotypic covariance structure among these traits. Following this with a path analysis, we demonstrate that variation in metabolic rate plays a fundamental proximate role in driving this phenotypic covariance structure in honeybees. We discuss the importance of these findings in the context of how interindividual variation in terms of slow-fast phenotypes may drive the phenotype of a group and the functional role metabolic rate might play in shaping division of labor and social evolution.</span></p>
Data from: Ecologically diverse and distinct neighbourhoods trigger persistent phenotypic consequences, and amine metabolic profiling detects them
1.Global change triggers rapid alterations in the composition and diversity of plant communities which may change ecosystem functioning. Do changes in community diversity also change traits persistently, i.e. does coexistence with numerous or functionally or phylogenetically distinct species trigger, in a given focal species, trait shifts that persist? 2.We studied the grass Dactylis glomerata. Dactylis was grown in experimental plots with different species compositions for five years, sampled, cloned and grown in a common garden. We studied amines, regulators integrating growth responses of organisms to their environment. 3.We found that the mean levels and variances of most amines depended on the diversity of the source community, notably the species richness and the phylogenetic and functional distinctness from Dactylis, unbiased by species identity or biomass shifts. 4.Synthesis. Our results suggest that different levels of ambient diversity can, within a few years, select for different genotypes which have different compositions of growth regulators. Our study also suggests that a plant species can evolve in response to the diversity or distinctness of the surrounding plant community. Evolutionary changes of plant phenotypes might mediate an impact of past biological diversity on present ecosystem functioning.
Data from: Untargeted metabolic profiling reveals geography as the strongest predictor of metabolic phenotypes of a cosmopolitan weed
Plants produce a multitude of metabolites that contribute to their fitness and survival, and play a role in local adaptation to environmental conditions. The effects of environmental variation is particularly well studied within the genus Plantago, however, previous studies have largely focused on targeting specific metabolites. Studies exploring metabolome wide changes are lacking, and the effects of natural environmental variation and herbivory on the metabolomes of plants growing in situ remain unknown. An untargeted metabolomic approach using ultra-high performance liquid chromatography-mass spectrometry, coupled with variation partitioning, general linear mixed modelling, and network analysis was used to detect differences in metabolic phenotypes of Plantago major in fifteen natural populations across Denmark. Geographic region, distance, habitat type, phenological stage, soil parameters, light levels, and leaf area, were investigated for their relative contributions to explaining differences in foliar metabolomes. Herbivory effects were further investigated by comparing metabolomes from damaged and undamaged leaves from each plant. Geographic region explained the greatest number of significant metabolic differences. Soil pH had the second largest effect, followed by habitat and leaf area, whilst phenological stage had no effect. No evidence of the induction of metabolic features was found between leaves damaged by herbivores compared to undamaged leaves on the same plant. Differences in metabolic phenotypes explained by geographic factors are attributed to genotypic variation and/or unmeasured environmental factors that differ at the regional level in Denmark. A small number of specialised features in the metabolome may be involved in facilitating the success of a widespread species such as Plantago major into such wide range of environmental conditions, though overall resilience in the metabolome was found in response to environmental parameters tested. Untargeted metabolomic approaches have great potential to improve our understanding of how specialised plant metabolites respond to environmental change and assist in adaptation to local conditions.
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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.