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120 results for “bioenergetics”
Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts
<p>Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA</p> <p>All respirometric data that were used for meta-analysis are obtained from the original publications, were converted to SI units, and are available here as a basis for bioenergetic cluster analysis. Inverted regression analysis is illustrated by an example (Figures 1c and d).</p>
Fig. 5 in Seasonal analysis of condition, biochemical and bioenergetic indices of females of Brazilian flathead, Percophis brasiliensis
Fig. 5. Seasonal variation of inorganic matter content (ash) in muscle, gonad and liver of Percophis brasiliensis.
Fig. 1 in Seasonal analysis of condition, biochemical and bioenergetic indices of females of Brazilian flathead, Percophis brasiliensis
Fig. 1. Seasonal variation of mean and standard deviation of hepatosomatic index (HSI), gonadosomatic index (GSI) and condition index (K) estimated for Percophis brasiliensis.
Fig. 4 in Seasonal analysis of condition, biochemical and bioenergetic indices of females of Brazilian flathead, Percophis brasiliensis
Fig. 4. Seasonal variation of water content (moisture) in muscle, gonad and liver of Percophis brasiliensis.
Data for: Combined threats of climate change and contaminant exposure through the lens of bioenergetics
<p>This dataset contains a detailed description of studies identified by a review examining interactive effects of climate change-sensitive environmental variables and chemical contaminant exposure.</p>
2023_ Datasets and R source code of "Allometry Bird Mitochondrial Bioenergetics"
<p>METHODOLOGICAL INFORMATION</p> <p>This dataset contains mitochondrial bioenergetic data and enzymatic activities of our studies from two tissues: skeletal and cardiac muscles, of 13 bird species ranging from 15 g to 160 kg.<br> Methodology: mitochondrial isolation, respiration, enzyme assays, measurement of body mass<br> All analyses were performed in R version 4.2.1 (R Core Team 2022), using phylogenetic comparative analyses.</p> <p><strong>## Description of the Data and file structure "2023_Data_Allometry Bird mitochondrial bioenergetics"</strong></p> <p>The file contains two sheets: one for the skeletal muscle data and the second for the cardiac muscle. <br> For each section you will find: the name of the species studied, the number of individuals, their body mass (in grams), mitochondrial flux measurements (oxygen consumption, ATP synthesis, ROS generation), ratios (RCR, Slope, Mitochondrial efficiency ATP/O...) and enzymatic activity measurements. </p> <p>Missing data correspond to individuals for whom we were unable to collect data (e.g. no heart samples, not enough tissue for analysis...)</p> <p><strong>## Phylogenetic tree " BirdTree_MCMCglmm "</strong></p> <p>The phylogenetic tree combining the 13 species studied was obtained from the BirdTree.org website (Rubolini et al., 2015).The tree source used was Hackett Sequenced Species: a set of 10 000 trees with 6670 OTUs each (Hackett et al., 2008). We performed 1000 simulations to create the most parsimonious tree. The avian tree was summarized using BEAST (v1.10.4, 2002-2018) to create a target tree usable in nexus format in R version 4.2.1 (R Core Team 2022). The parameters used were: burnin as a number of trees (100), maximum clade credibility tree as target tree type, and common ancestor heights.</p>
Raw data related to: Randomised Clinical Trial: Calorie Restriction Regimen with Tomato Juice Supplementation Ameliorates Oxidative Stress and Preserves a Proper Immune Surveillance Modulating Mitochondrial Bioenergetics of T-Lymphocytes in Obese Children Affected by Non-Alcoholic Fatty Liver Disease (NAFLD)
<p><strong>Abstract</strong></p> <p>Fatty liver disease is a serious complication of childhood obesity. Calorie-restricted regimen (RCR) is one of the e ective therapy for this condition. Aim of the study was to evaluate the effect of lycopene-rich tomato sauce with oregano and basil extracts in obese children with fatty liver on RCR. 61 obese children with fatty liver were enrolled, 52 completed the study. A randomized cross over clinical trial was performed. Participants were assigned to RCR alone or with a supplement of lycopene-rich tomato juice for 60 days; subsequently, the groups were switched to the alternative regimen for the next 60 days. Reduction in BMI, HOMA-IR, cholesterol, triglycerides, liver size, and steatosis was more profound in tomato-supplemented group. Leptin decreased in both groups whereas adiponectin raised only after tomato supplementation. RCR is associated with the impaired engagement of T-cells glycolysis and proliferation, tomato-supplementation resulted in glycolytic metabolic activation of T-cells. Tomato juice ameliorates glucose and lipid metabolism in obese children, improve oxidative and inflammatory state and modulates the mitochondrial metabolism of T-cells contributing to a maintenance of a proper immune surveillance in children, impaired by RCR. The addition of tomato to RCR could be considered a protective and preventive support to obese child.</p> <p><strong>Progetto giovani ricercatori </strong>[GR-2016-02363725] dal titolo: "Immune Tolerance, Metabolism and Multiple Sclerosis: Novel Molecular Tools to Monitor Disease Pathogenesis and Progression"</p>
Mass spectrometry data for: A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics
<p><span><strong>Background</strong>:</span> <span>Mitochondria have a central role in cellular functions, aging and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternative open reading frames or altORFs, and they are involved in key biological functions. </span><span>However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed.</span></p> <p><span><strong>Results</strong>:</span> <span>We found a downstream alternative ATG initiation codon in the +3 reading frame of the human mitochondrial <em>nd4</em> gene. This newly characterized altORF encodes a 99-amino acids long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, </span><span>and it impacts cell and mitochondrial physiology. </span></p> <p><span><strong>Conclusions</strong>:</span> <span>Many human-mitochondrial-translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome.</span> <span>Alternative mitochondrial peptides such as MTALTND4 may offer </span><span>a new framework for the investigation of mitochondrial functions and diseases.</span></p>
Telemetry data from: Realized thermal niche approach eliminates temperature bias in 3 bioenergetic model estimates
<h4>Raw data for Ivanova et al paper in Ecology and Evolution</h4><p>Datafile is an .rds file.</p>
Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance
<p>We developed dynamic bioenergetics models to investigate how behavioural responses to anthropogenic disturbance events might affect the population dynamics of three marine mammal species (harbour porpoise, grey seal and harbour seal) with contrasting life-history traits (capital vs income breeders) and movement behaviour (resident vs nomadic). We used these models to analyse how individual vital rates were affected by differences in the probability of disturbance and the duration of any behavioural response, while taking account of uncertainty in the model parameters and heterogeneity in behaviour. The outputs of individual movement models and telemetry data were then used to determine how the probability of exposure might vary among species, individuals, and geographical locations. We then demonstrate how these estimated probabilities of exposure can be translated into probabilities of disturbance. For illustrative purposes, we modelled the potential effects of a temporary decrease in energy assimilation associated with a series of disturbance events that might realistically occur during the construction of an offshore windfarm. Offspring starvation mortality was the vital rate that was most affected by these disturbance events. Monitoring of rates should be considered as standard practice so that populations' responses can be detected as early as possible. Predicted effects on individual vital rates depended on the species' movement behaviour and the likely density of animals where the modelled construction activity was assumed to take place. The magnitude of these effects also depended critically on the assumed duration of the reduction in energy assimilation. No direct estimates of this variable are currently available, but we suggest some ways in which it could be estimated. The described approach could be extended to other species and activities, given sufficient information to parameterise the component models. However, we emphasise the need to account for among-individual heterogeneities and uncertainties in the values of the many model parameters.</p>
Rapid evolution of consumptive and non-consumptive predator effects on prey population densities, bioenergetics and stoichiometry
<p>Predators can strongly influence prey populations not only through consumptive effects (CE) but also through non-consumptive effects (NCE) imposed by predation risk. Yet, the impact of NCE on bioenergetic and stoichiometric body contents of prey, traits that are shaping life histories, population and food web dynamics, is largely unknown. Moreover, the degree to which NCE can evolve and can drive evolution in prey populations is rarely studied. A 6-week outdoor mesocosm experiment with Caged-Fish (NCE) and Free-Ranging-Fish (CE and NCE) treatments was conducted to quantify and compare the effects of CE and NCE on population densities, bioenergetic and stoichiometric body contents of Daphnia magna, a keystone species in freshwater ecosystems. We tested for evolution of CE and NCE by using experimental populations consisting of D. magna clones from two periods of a resurrected natural pond population: a pre-fish period without fish and a high-fish period with high predation pressure. Both Caged-Fish and Free-Ranging-Fish treatments decreased the body size and population densities, especially in Daphnia from the high-fish period. Only the Free-Ranging-Fish treatment affected bioenergetic variables, while both the Caged-Fish and Free-Ranging-Fish treatments shaped body stoichiometry. The effects of CE and NCE were different between both periods indicating their rapid evolution in the natural resurrected population. Both the Caged-Fish and Free-Ranging-Fish treatments changed the clonal frequencies of the experimental Daphnia populations of the pre-fish as well as the high-fish period, indicating that not only CE but also NCE induced clonal sorting, hence rapid evolution during the mesocosm experiment in both periods. Our results demonstrate that CE as well as NCE have the potential to change not only the body size and population density but also the bioenergetic and stoichiometric characteristics of prey populations. Moreover, we show that these responses not only evolved in the studied resurrected population, but that CE and NCE also caused differential rapid evolution in a time frame of 6 weeks (ca. 4-6 generations). As NCE can evolve as well as can drive evolution, they may play an important role in shaping eco-evolutionary dynamics in predator-prey interactions.</p>
Data from: Feeding effects on liver mitochondrial bioenergetics of Boa constrictor (Serpentes: Boidae)
<p>Snakes are interesting examples of overcoming energy metabolism challenges as many species can endure long periods without feeding, and their eventual meals are of reasonably large sizes, thus exhibiting dual extreme adaptations. Consequently, metabolic rate increases considerably to attend to the energetic demand of digestion, absorption and, protein synthesis. These animals should be adapted to transition from these two opposite states of energy fairly quickly, and therefore we investigated mitochondrial function plasticity in these states. Herein we compared liver mitochondrial bioenergetics of the boid snake <i>Boa constrictor</i> during fasting and after meal intake. We fasted the snakes for 60 days, then we fed a subgroup with 30% of their body size and evaluated their maximum postprandial response. We measured liver respiration rates from permeabilized tissue and isolated mitochondria, and from isolated mitochondria, we also measured Ca<sup>2+</sup> retention capacity, the release of H<sub>2</sub>O<sub>2</sub>, and NAD(P) redox state. Mitochondrial respiration rates were maximized after feeding, reaching until 60% increase from fasting levels when energized with complex I-linked substrates. Interestingly, fasting and fed snakes exhibited similar respiratory control ratios and citrate synthase activity. Furthermore, we found no differences in Ca<sup>2+</sup> retention capacity, indicating no increase in susceptibility to mitochondrial permeability transition pore (PTP), or redox state of NAD(P), although fed animals exhibited increases in the release of H<sub>2</sub>O<sub>2</sub>. Thus, we conclude that liver mitochondria from B. constrictor snakes increase the maintenance costs during the postprandial period and quickly improve the mitochondrial bioenergetics capacity without compromising the redox balance.</p>
Turning summer into winter: nutrient dynamics, temperature, density dependence, and invasive species drive bioenergetic processes and growth of a keystone coldwater fish
<p>A combination of global changes such as species invasions, climate change, and nutrient pollution have altered ecosystems, food webs, and the bioenergetic processes that control growth. These changes are especially pronounced in freshwater ecosystems and often lead to rapid variation in fish growth and dependent ecosystems services such as fishery yield. Understanding the mechanisms driving growth responses to environmental change is important for interpreting past dynamics and sustainably managing ecosystems. This study uses integrated bioenergetics and growth modeling to understand how nutrient dynamics, species invasions, and changing temperatures have altered growth of the keystone pelagic whitefish (<em>Coregonus</em> <em>wartmanni</em>) in Lake Constance, Germany from 1925 to 2020. Growth variation was modeled by allowing covariates to alter temperature-dependent consumption, while size-specific metabolism varied only with temperature. Consumption and growth increased strongly to a maximum with phosphorous, and this effect was stronger when intraspecific competition (measured as whitefish biomass) was low. Increasing whitefish biomass reduced growth under mesotrophic conditions, but had no effect under oligotrophic conditions. In contrast, increasing competition with invasive three-spined stickleback (<em>Gasteosteus</em> <em>aculeauts</em>) was predicted to reduce growth even under oligotrophic conditions. The invasion has effectively turned summer into winter for whitefish, with older fish ceasing to grow and younger fish losing up to 10% of their body weight during the normal growing season in subsequent years. Warming is predicted to further reduce whitefish growth due to competition with invasive stickleback, which would further alter zooplankton food availability and reduce already low fishery yields. These results demonstrate the importance of considering biotic interactions and synergistic effects in global change studies, as well as the value of mechanistic-based models for understanding effects. Similar growth responses to ecosystem change are likely within and across ecosystems, and bioenergetic models can help understand effects to support informed ecosystem management.</p>
Effects of hypoxia and spawning on mitochondrial metabolism and bioenergetics of the blue mussel Mytilus spp. from the Baltic Sea
<p>We studied the effect of short-term hypoxia (7 days) and spawning (pre-spawning, and 3 h and 72 h post-spawning) on mitochondrial respiration, reactive oxygen species (ROS) production, and energy budget of the mussels Mytilus edulis. The data set reports oxygen consumption, efflux of reactive oxygen species (H2O2), fractional electrol leak (ratio of H2O2 efflux to O2 consumption) in isolated mitochondria, as well as the biochemical composition and energy content of the gills and the digestive gland tissues, tissue energy demand (measured as the activity to the electron transport system) and cellular energy allogation (CEA) in the tissues of the mussels.</p>
Data and model code from: Tracing growth patterns in cod (Gadus morhua L.) using bioenergetic modelling
<p><span>Understanding individual growth in commercially exploited fish populations is key to successful stock assessment and informed ecosystem-based fisheries management. Traditionally, growth rates in marine fish are estimated using otolith age-reading in combination with age-length relationships from field samples, or tag-recapture field experiments. However, for some species, otolith-based approaches have been proven unreliable, and tag-recapture experiments suffer from high working effort and costs as well as low recapture rates. An important alternative approach for estimating fish growth is represented by bioenergetic modelling, which, in addition to pure growth estimation, can provide valuable insights into the processes leading to temporal growth changes resulting from environmental and related behavioural changes. We here developed an individual-based bioenergetic model for Western Baltic cod (<em>Gadus</em> <em>morhua</em>), traditionally a commercially important fish species that however collapsed recently and likely suffers from climate change effects. Western Baltic cod is an ideal case study for bioenergetic modelling because of recently gained in-situ process knowledge on spatial distribution and feeding behaviour based on highly resolved data on stomachs and fish distribution. Additionally, physiological processes such as gastric evacuation, consumption, net-conversion efficiency, and metabolic rates have been well studied for cod in laboratory experiments. Our model reliably reproduced seasonal growth patterns observed in the field. </span><span>Importantly, our bioenergetic modelling approach implementing depth-use patterns and food intake allowed us to explain the potentially detrimental effect summer heat periods have on growth of Western Baltic cod that likely will increasingly occur in the future. Hence our model simulations highlighted a potential mechanism of how warming due to climate change affects the growth of a key species that may apply for similar environments elsewhere. </span></p> <p><span>Here we provide access to the individual-based bioenergetic growth model which is set up to model the growth of cod in ages 2 to 4 (<em>Gadus</em> <em>morhua</em> L.) in the Belt Sea (western part of the Western Baltic Sea) on a daily basis within one year. The model incorporates contemporary in-situ process knowledge on food intake and seasonal- and temperate-related spatial distribution of cod and allows us to identify seasonal growth patterns. The model is written in the statistical and programming environment R.<br></span></p>
Effects of Nicotinamide Riboside on Bioenergetics and Oxidative Stress in Mild Cognitive Impairment/Alzheimer's Dementia
ClinicalTrials.gov study NCT04430517. IPD Sharing: YES. Countries: 1. Publications: 0.
Does Improving Vagal Tone Increase Mitochondrial Bioenergetics
ClinicalTrials.gov study NCT03931330. IPD Sharing: NO. Countries: 1. Publications: 3.
Bioenergetic Alterations After Exenatide Administration
ClinicalTrials.gov study NCT00623545. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Bioenergetics and Metabolism in Pediatric Populations
ClinicalTrials.gov study NCT03323294. IPD Sharing: YES. Countries: 1. Publications: 38.
Nitrites, Skeletal Muscle Mitochondrial Bioenergetics, and Physical Activity in Old Age
ClinicalTrials.gov study NCT04405180. IPD Sharing: YES. Countries: 1. Publications: 0.
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