Find research datasets worth reusing

opencc-zeroNov 2023View details →

Data for: Feeding frequency does not interact with BPA exposure to influence metabolism of behaviour in zebrafish (Danio rerio)

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 (Danio rerio) 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.

opencc-by-4.0Nov 2023View details →

Comparing plasma and skin imprint metabolic profiles in COVID-19 diagnosis and severity assessment_dataset

As SARS-CoV-2 continues to produce new variants, the demand for diagnostics and a better understanding of COVID-19 remain key topics in healthcare. Skin manifestations have been widely reported in cases of COVID-19, but the mechanisms and markers of these symptoms are poorly described. In this cross-sectional study, 101 patients (64 COVID-19 positive patients and 37 controls) were enrolled between April and June 2020, during the first wave of COVID-19, in São Paulo, Brazil. Enrolled patients had skin imprints sampled non-invasively using silica plates; plasma samples were also collected. Samples were used for untargeted lipidomics/metabolomics through high-resolution mass spectrometry. We identified 558 molecular ions, with lipids comprising most of them. We found 245 plasma ions that were significant for COVID-19 diagnosis, compared to 61 from the skin imprints. Plasma samples outperformed skin imprints in distinguishing patients with COVID-19 from controls, with F1-scores of 91.9% and 84.3%, respectively. Skin imprints were excellent for assessing disease severity, exhibiting an F1-score of 93.5% when discriminating between patient hospitalization and home care statuses. Specifically, oleamide and linoleamide were the most discriminative biomarkers for identifying hospitalized patients through skin imprinting, and palmitic amides and N-acylethanolamine 18:0 were also identified as significant biomarkers. These observations underscore the importance of primary fatty acid amides and N-acylethanolamines in immunomodulatory processes and metabolic disorders. These findings confirm the potential utility of skin imprinting as a valuable non-invasive sampling method for COVID-19 screening; a method that may also be applied in the evaluation of other medical conditions.Journal of Molecular Medicine https://doi.org/10.1007/s00109-023-02396-3

opencc-zeroNov 2023View details →

3-(4-Hydroxy-3-methoxyphenyl) propionic acid contributes to improved hepatic lipid metabolism via GPR41

3-(4-hydroxy-3-methoxyphenyl) propionic acid (HMPA) is a metabolite produced by the gut microbiota through the conversion of 4-hydroxy-3-methoxycinnamic acid (HMCA), which is a widely distributed hydroxycinnamic acid-derived metabolite found abundantly in plants. Several beneficial effects of HMPA have been suggested, such as antidiabetic properties, anticancer activities, and cognitive function improvement, in animal models and human studies. However, the intricate molecular mechanisms underlying the bioaccessibility and bioavailability profile following HMPA intake and the substantial modulation of metabolic homeostasis by HMPA require further elucidation. In this study, we effectively identified and characterized HMPA-specific GPR41 receptor, with greater affinity than HMCA. The activation of this receptor plays a crucial role in the anti-obesity effects and improvement of hepatic steatosis by stimulating the lipid catabolism pathway. For the improvement of metabolic disorders, our results provide insights into the development of functional foods, including HMPA, and preventive pharmaceuticals targeting GPR41.

opencc-by-4.0Oct 2023View details →

The metabolic representation of ischemia in rat brain slices: A hyperpolarized 13 C magnetic resonance study

This dataset contains primary data for DOI: 10.1002/nbm.4509NMR in Biomedicine. 2021; 34(7):e4509Title: The metabolic representation of ischemia in rat brain slices: A hyperpolarized 13 C magnetic resonance study Authors: David Shaul , Benjamin Grieb, Gal Sapir, Sivaranjan Uppala, Jacob Sosna, J Moshe Gomori, Rachel Katz-Brull These primary datasets contain data related to the above publication and consist of  31P (thermal equilibrium) and hyperpolarized 13C -NMR spectra. Please consult the Archive Guide.

opencc-by-4.0Dec 2023View details →

Accompanying Data - Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

This repository contains all the data and some of the performed statistical analysis from all the measurements in the following paper: Scott Jr WT, Van Mastrigt O, Block DE, Notebaart RA, Smid EJ. Nitrogenous compound utilization and production of volatile organic compounds among commercial wine yeasts highlight strain-specific metabolic diversity. Microbiology spectrum. 2021 Aug 31;9(1):10-128.Please cite: Scott Jr WT, Van Mastrigt O, Block DE, Notebaart RA, Smid EJ. Nitrogenous compound utilization and production of volatile organic compounds among commercial wine yeasts highlight strain-specific metabolic diversity. Microbiology spectrum. 2021 Aug 31;9(1):10-128.Contact: Dr. William T. Scott (william.scott@wur.nl) or Dr. Eddy J. Smid (eddy.smid@wur.nl) for more information

opencc-by-4.0Dec 2023View details →

Vibrant_metabolic_gene_annotations_vOTUs

Vibrant v. 1.2.0 (default parameters; Kieft, Zhou, and Anantharaman 2020) was used to provide gene annotations for vOTUs that are <10kb or not detected by VirSoter. Although annotation is available for these vOTUs, we chose not to include the data in our results and discussion because of the uncertainty surrounding their validity.

opencc-zeroDec 2023View details →

Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes

Subfamilies of cytochrome P450 proteins have been strongly linked to the metabolism of physiologically disruptive compounds such as alkaloids, terpenoids, and other xenobiotics. Consistent with this function, these genes have adaptively evolved in response to environmental pressures exerted on animals, such as herbivores, that consume elevated amounts of toxic xenobiotics or plant secondary metabolites (PSMs). Theory on evolutionary tradeoffs predicts that highly specialized herbivores should exhibit a relatively narrow toolkit of adaptations to accommodate the concomitantly narrow arrays of PSMs in their diets. The bamboo lemurs of Madagascar (genera Prolemur and Hapalemur) represent an interesting test case for this theory because of their dietary hyper-specialization, as these lemurs consume bamboo and grasses at rates otherwise unseen in the order Primates. To test whether the hyper-specialized folivory of these primates is reflected in a similarly specialized and narrow P450 gene suite, we assembled a dataset of confidently assembled CYP1-3 genes for two species of bamboo lemur and 13 additional lemur species. With this dataset, we tested the predictions that bamboo lemurs would exhibit, first, greater rates of gene loss for xenobiotic-metabolizing P450s and, second, relaxed selection on xenobiotic-metabolizing P450 subfamilies relative to lemurs without such dietary hyper-specialization. We found support for the prediction of gene loss in the CYP2B, CYP2C, CYP2D, CYP2J, and CYP3A subfamilies, all of which encode xenobiotic metabolizers. We inferred relaxation of selection for the CYP1A and CYP2D subfamilies. The CYP2F subfamily exhibited a signal of significant intensification of selection in the bamboo-lemur lineage. The evolution of the P450 genes in bamboo lemurs provides support for the evolutionary tradeoff hypothesis, and we further hypothesize that, rather than adapting to a general array of PSMs, bamboo lemurs have instead adapted to the primary toxin in their diet, the highly potent poison cyanide.

opencc-by-4.0Oct 2023View details →

Real-time influence of intracellular acidification and Na+/H+ exchanger inhibition on in-cell pyruvate metabolism in the perfused mouse heart: A 31P-NMR and hyperpolarized 13C-NMR study

This dataset contains primary data for DOI: 10.1002/nbm.4993 NMR in Biomedicine. 2023; 10;e4993 Title: Real-time influence of intracellular acidification and Na+/H+ exchanger inhibition on in-cell pyruvate metabolism in the perfused mouse heart: A 31P-NMR and hyperpolarized 13C-NMR study Authors: David Shaul, Naama Lev-Cohain, Gal Sapir, Jacob Sosna, J. Moshe Gomori, Leo Joskowicz, Rachel Katz-Brull   Description: These primary datasets contains data presented in the above publication and consist of 31P- (at thermal equilibrium) and hyperpolarized 13C-NMR spectra.  Please consult the Archive Guide.

opencc-zeroDec 2023View details →

Data from: Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas

Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera like Bacillus and Pseudomonas, siderophores are often acclaimed for their function in biocontrol. Here, we set out to determine the functional role of the Bacillus subtilis siderophore bacillibactin in an antagonistic interaction with Pseudomonas marginalis. The presence of bacillibactin strongly influences the outcome of the interaction in an iron-dependent manner. A bacillibactin producer B. subtilis restricts the colony spreading of P. marginalis, repress the transcription of histidine kinase-encoding gene gacS, and thereby abolish production of secondary metabolites such as pyoverdine and viscosin. In contrast, the lack of bacillibactin restricts B. subtilis colony growth in a mechanism reminiscent of a siderophore tug-of-war for iron. Our study identifies a Bacillus-Pseudomonas interaction conserved across fluorescent Pseudomonas spp., expanding our understanding of the interplay between two genera of the most well-studied soil microbes.

Flying, nectar-loaded honey bees conserve water and improve heat tolerance by reducing wingbeat frequency and metabolic heat production

Heat waves are becoming increasingly common due to climate change, making it crucial to identify and understand the capacities for insect pollinators, such as honey bees, to avoid overheating. We examined the effects of hot, dry air temperatures on the physiological and behavioral mechanisms that honey bees use to fly when carrying nectar loads, to assess how foraging is limited by overheating or desiccation. We found that flight muscle temperatures increased linearly with load mass at air temperatures of 20 or 30°C, but, remarkably, there was no change with increasing nectar loads at an air temperature of 40°C. Flying, nectar-loaded bees were able to avoid overheating at 40°C by reducing their flight metabolic rates and increasing evaporative cooling. At high body temperatures, bees apparently increase flight efficiency by lowering their wingbeat frequency and increasing stroke amplitude to compensate, reducing the need for evaporative cooling. However, even with reductions in metabolic heat production, desiccation likely limits foraging at temperatures well below bees' critical thermal maxima in hot, dry conditions.

Feasibility and metabolic outcomes of a well-formulated ketogenic diet as an adjuvant therapeutic intervention for women with stage IV metastatic breast cancer: The Keto-CARE trial

Purpose: Ketogenic diets may positively influence cancer through pleiotropic mechanisms, but only a few small and short-term studies have addressed feasibility and efficacy in cancer patients. The primary goals of this study were to evaluate the feasibility and the sustained metabolic effects of a personalized well-formulated ketogenic diet (WFKD) designed to achieve consistent blood beta-hydroxybutyrate (βHB) >0.5 mM in women diagnosed with stage IV metastatic breast cancer (MBC) undergoing chemotherapy. Methods: Women (n = 20) were enrolled in a six-month two-phase, single-arm WFKD intervention (NCT03535701). Phase I was a highly-supervised, ad libitum, personalized WFKD, where women were provided with ketogenic-appropriate food daily for three-months. Phase II transitioned women to a self-administered WFKD with ongoing coaching for an additional three-months. Fasting capillary βHB and glucose were collected daily; weight, body composition, plasma insulin, and insulin resistance were collected at baseline, three- and six-months. Results: Capillary βHB indicated women achieved nutritional ketosis (Phase I mean: 0.8 mM (n = 15); Phase II mean: 0.7 mM (n = 9)). Body weight decreased 10% after three-months, primarily from body fat. Fasting plasma glucose, plasma insulin, and insulin resistance also decreased significantly after three-months (p < 0.01), an effect that persisted at six-months. Conclusions: Women diagnosed with MBC undergoing chemotherapy can safely achieve and maintain nutritional ketosis, while improving body composition and insulin resistance, out to six-months.

Data from: anterior pituitary transcriptomics following a high fat diet: impact of oxidative stress on cell metabolism

Anterior pituitary cells are highly active with regards to protein synthesis and secretion, processes which depend heavily on mitochondrial ATP production and functional endoplasmic reticula. It is well known that obesity adds an allostatic overload to tissues, requiring them to adapt to inflammation and oxidative stress. Therefore, we hypothesized that the pituitary is highly vulnerable to the stress of high fat diet-induced weight gain. In this study, we utilized a 10-15 week high fat diet (HFD, 60%) plus a thermoneutral housing paradigm, testing both male and female FVB.129P mice. We quantified serum hormones and cytokines, characterized the metabolic phenotype, and defined changes in the pituitary transcriptome using single-cell RNA-seq. Weight gain was significant by 3 weeks in HFD mice, and by 10 weeks all HFD groups had gained 20 g. HFD females (15 weeks) had increased energy expenditure and decreased activity. All HFD groups showed increases in serum leptin, Il-6, resistin, MCP-1, and TNFα. HFD males had increased insulin; both HFD males and females had increased TSH, and HFD females had decreased serum prolactin and growth hormone (GH) pulse amplitude. Pituitary scRNA-seq revealed modest or no changes in pituitary cell gene expression in the different cell types from HFD males after 10 or 15 weeks or HFD females after 10 weeks. However, females exposed to a HFD for 15 weeks showed significant numbers of differentially expressed genes in lactotropes and stem cells. Pathway analyses identified a reduction in pathways that supported protein translation, ribosome biogenesis, and oxidative phosphorylation, indicating mitochondrial dysfunction. Collectively, these studies reveal that pituitary cells from males are more resilient to the oxidative stress of obesity than females and identify the most vulnerable pituitary cell populations in females.

Coral community metabolism during year-long exposure to experimental elevated CO2 conditions

The implications of ocean acidification are acute for calcifying organisms, notably tropical reef corals, for which accretion generally is depressed and dissolution enhanced at reduced seawater pH. We describe year-long experiments in which back reef and fore reef (17-m depth) communities from Moorea, French Polynesia, were incubated outdoors under pCO2 regimes reflecting endpoints of representative concentration pathways (RCPs) expected by the end the century. Incubations were completed in 3–4 flumes (5.0 × 0.3 m, 500 L) in which seawater was refreshed and circulated at 0.1 m s-1, and the response of the communities was evaluated monthly by measurements of net community calcification (NCC) and net community photosynthesis (NCP). For both communities, NCC (but not NCP) was affected by treatments and time, with NCC declining with increasing pCO2, and for the fore reef, becoming negative (i.e., dissolution was occurring) at the highest pCO2 (1067–1433 µatm, RCP8.5). There was scant evidence of community adjustment to reduce the negative effects of ocean acidification, and inhibition of NCC intensified in the back reef as the abundance of massive Porites spp. declined. These results highlight the risks of dissolution under ocean acidification for coral reefs and suggest these effects will be most acute in fore reef habitats. Without signs of amelioration of the negative effects of ocean acidification during year-long experiments, it is reasonable to expect that the future of coral reefs in acidic seas can be predicted from their current known susceptibility to ocean acidification.

opencc-zeroFeb 2024View details →

Increased ladybird predation and metabolism do not counterbalance increased field aphid population growth under experimental warming

<ol> <li>Climate change may have diverse and complex impacts on species interactions, destabilizing food webs and ecosystem services. The effects of warming on the top-down biological control of crop pests have been considerably less studied than bottom-up effects through crop physiological changes.</li> <li>We studied the effect of a 2 °C warming in the laboratory and in wheat fields on the predation and metabolism of Harmonia axyridis on wheat aphids using molecular gut content analysis. We also measured the effects of warming on the predation rate and functional response of H. axyridis on each aphid species in the laboratory, as well as on DNA degradation rate.</li> <li>Field densities of Sitobion avenae and Rhopalosiphum padi, the two most abundant wheat aphid species, were increased by 2 and 2.5 times, respectively, under experimental warming, but densities of H. axyridis were not. Field predation rate of H. axyridis on these two aphids was found to be about 25% lower under elevated temperature. This could have been due to faster prey digestion, since degradation of the preferred aphid species, Sitobion avenae, was 1.5 times faster under elevated temperature. However, the functional response of H. axyridis larvae on these two species was 1.5 times higher under warming over the range of prey densities tested (50 to 250 over 24 h). The total predation rate of H. axyridis larvae on a mixture of S. avenae, R. padi and Schizaphis graminum aphid prey was also increased by 1.4 times, but consumption of R. padi aphids was increased while that of S. graminum was decreased under warming.</li> <li>Overall, our results show that global warming could strongly increase pest outbreaks and destabilize biological pest control, which would likely result in accrued yield losses. </li> </ol>

opencc-by-4.0Feb 2024View details →

Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled scRNAseq

During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.   This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.

Fifteen physiological traits related to osmoregulation and reactive oxygen species metabolism in two life form aquatic plants under a natural water salinity gradient on the Tibetan Plateau and Northwest China

Aquatic plants, as the primary producers, determine the community structure and ecological function of freshwater ecosystems. However, salinization threatens inland freshwater wetlands and thus the survival of aquatic plants. Exploring the plant physiological responses to increasing water salinity could enhance our understandings of plant adaptive strategies under future climate change regimes in wetlands. We measured 15 physiological traits of 49 aquatic plant species along a large environmental gradient in alpine and arid regions of western China, to explore the physiological adaptions and compare the similarities and differences in adaptive strategies between the two life forms to natural water salinity. We found that both water salinity and low temperature were key factors affecting aquatic plants in alpine and arid regions. Aquatic plants adapt to saline habitats by accumulating proline and sulfur (S) concentrations, and to cold habitats by increasing ascorbate peroxidase activity. Plant trait network analysis showed that the hub trait in emergent plants was S, but in submerged plants was proline, suggesting that emergent plants balanced osmoregulation and reactive oxygen metabolism via S-containing compounds, while submerged plants prioritizing the regulation of osmotic balance via proline.

Drp1 controls Complex II assembly and skeletal muscle metabolism by Sdhaf2 action on mitochondria

The Dynamin-related GTPase, Drp1 (encoded by Dnm1l) plays a central role in mitochondrial fission and is requisite for numerous cellular processes however its role in muscle metabolism remains unclear. Herein, we show that among human tissues, the highest number of gene correlations with DNM1L are in skeletal muscle. Knockdown of Drp1 (Drp1-KD) promoted mitochondrial hyperfusion in the muscle of male mice. Reduced fatty acid oxidation and impaired insulin action along with increased muscle succinate was observed in Drp1-KD muscle. Muscle Drp1-KD reduced Complex II assembly and activity as a consequence of diminished mitochondrial translocation of succinate dehydrogenase assembly factor 2 (Sdhaf2). Restoration of Sdhaf2 normalized Complex II activity, lipid oxidation, and insulin action in Drp1-KD myocytes. Drp1 is critical in maintaining mitochondrial Complex II assembly, lipid oxidation, and insulin sensitivity, suggesting a mechanistic link between mitochondrial morphology and skeletal muscle metabolism, which is clinically relevant in combatting metabolic-related diseases.

Data from: thyroid hormone concentrations in female baboons: metabolic consequences of living in a highly seasonal environment

How female mammals adapt metabolically in response to environmental variation remains understudied in the wild, because direct measures of metabolic activity are difficult to obtain in wild populations. However, recent advances in the non-invasive measurement of fecal thyroid hormones, triiodothyronine (T3), an important regulator of metabolism, provide an opportunity to understand how female baboons living in the harsh Amboseli ecosystem in southern Kenya adapt to environmental variability and escape strict reproductive seasonality. Specifically, we assessed how a female's activity budget, diet, and concentrations of fecal T3 metabolites (mT3) changed over the course of the year and between years. We then tested which of several environmental variables (season, rainfall, and temperature) and behavioral variables (female activity budget and diet) best predicted mT3 concentrations. Finally, we determined if two important reproductive events – onset of ovarian cycling and conception of an offspring – were preceded by changes in female mT3 concentrations. We found female baboons' mT3 concentrations varied markedly across the year and between years as a function of environmental conditions. Further, changes in a female's behavior and diet only partially mediated the metabolic response to the environment. Finally, mT3 concentrations increased in the weeks prior to menarche and cycling resumption, regardless of the month or season in which cycling started. This pattern indicates that metabolic activation may be an indicator of reproductive readiness in female baboons as their energy balance is restored.

opencc-by-4.0Mar 2024View details →

Cortese et al. 2024. The effect of metabolism on cognitive performance varies with task complexity in common minnows Phoxinus phoxinus

These datasets have been used to produce the figures and results of the manuscript entitled "The effect of metabolism on cognitive performance varies with task complexity in common minnows Phoxinus phoxinus" by Cortese D, Munson A, Storm Z, Jones NAR and Killen SS (2024).

A thermal performance curve perspective explains decades of disagreements over how air temperature affects the flight metabolism of honey bees

While multiple studies have shown that honey bees and some other flying insects lower their flight metabolic rates when flying at high air temperatures, critics have suggested such patterns result from poor experimental methods as, theoretically, air temperature should not appreciably affect aerodynamic force requirements. Here, we show that apparently contradictory studies can be reconciled by considering the thermal performance curve of flight muscle. We show that prior studies that found no effects of air temperature on flight metabolism of honey bees achieved flight muscle temperatures that were near or on equal, opposite sides of the thermal performance curve. Honey bees vary their wing kinematics and metabolic heat production to thermoregulate, and how air temperature affects the flight metabolic rate of honey bees is predictable using a non-linear thermal performance perspective of honey bee flight muscle.