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opencc-zeroJan 2021View details →

Data from: Association between metabolic syndrome components and the risk of developing nephrolithiasis: Bayesian meta-analysis and meta-regression with dose-response analysis

Nephrolithiasis has shifted to be a systemic disease. As opposed to an isolated urinary metabolic problem, it became determined that nephrolithiasis turned into considerably related to link with systemic diseases such as hypertension, obesity, dyslipidemia, and insulin resistance. The interplay between these four factors defines MetS (metabolic syndrome). In this review we aim to clarify the associations of metabolic syndrome and its components to kidney stone incident. Online databases of EMBASE, MEDLINE, and Google Scholar were searched up to October 2020 to identify observational studies examining the association between metabolic syndrome components and kidney stone incident. Bayesian Random-Effects Meta-Analysis and Meta-Regression were performed to observe the association. Linear dose-response analyses were conducted to shape the direction of the association. Data analysis was performed using STATA, and R statistics. This dataset contains supplementary material and figures as additional analysis of the study.

opencc-zeroDec 2010View details →

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic and environmental influences. We demonstrate how this may be done by comparing the ontogenetic scaling of resting metabolic rate among populations of the same species (the amphipod Gammarus minus) in mid-Appalachian freshwater springs with similar, relatively constant environmental conditions, except for the varying presence of the predatory fish Cottus cognatus. We found that populations of G. minus exhibit significantly lower metabolic scaling slopes (0.54 to 0.62) in three freshwater springs with C. cognatus than in two springs without these fish (0.76 to 0.77). We tested multiple hypothetical causes for these population differences. Our results best supported the hypothesis that metabolic scaling was influenced by the effects of size-selective predation on the ontogeny of growth, a metabolically expensive process. The body-size scaling of growth is significantly less steep in the populations inhabiting springs with versus without fish, thus paralleling the interpopulation differences in metabolic scaling. Prematurational growth of G. minus is as high or higher in the fish springs, whereas postmaturational growth is significantly lower, often approaching zero. Similarly the amphipods in the fish springs tend to have higher metabolic rates at small sizes, but lower metabolic rates at large sizes, compared to those in the fishless springs. Our results do not support other hypothetical causes of the interpopulation variation in metabolic scaling, including differential scaling of cell size or low-metabolism body components (fat and mineralized exoskeleton), or possible effects of other environmental factors associated with the presence of fish. However, fish-induced population differences in adult behavioral activity may influence metabolic scaling in G. minus, a possibility under current study. We conclude that ecological factors may significantly influence metabolic scaling, contrary to common belief.

opencc-zeroDec 2014View details →

Data from: Genetic perturbation of key central metabolic genes extends life span in Drosophila and affects response to dietary restriction

There is a connection between nutrient inputs, energy-sensing pathways, lifespan variation and aging. Despite the role of metabolic enzymes in energy homeostasis and their metabolites as nutrient signals, little is known about how their gene expression impacts lifespan. In this report, we use P-element mutagenesis in Drosophila to study the effect on lifespan of reductions in expression of seven central metabolic enzymes, and contrast the effects on normal diet and dietary restriction. The major observation is that for five of seven genes, the reduction of gene expression extends lifespan on one or both diets. Two genes are involved in redox balance, and we observe that lower activity genotypes significantly extend lifespan. The hexokinases also show extension of lifespan with reduced gene activity. Since both affect the ATP/ADP ratio, this connects with the role of AMP-activated protein kinase as an energy sensor in regulating lifespan and mediating caloric restriction. These genes possess significant expression variation in natural populations, and our experimental genotypes span this level of natural activity variation. Our studies link the readout of energy state with the perturbation of the genes of central metabolism and demonstrate their effect on lifespan.

opencc-zeroDec 2015View details →

Data from: Hormonal and metabolic responses to upper temperature extremes in divergent life-history ecotypes of a garter snake

Extreme temperatures constrain organismal physiology and impose both acute and chronic effects. Additionally, temperature-induced hormone-mediated stress response pathways and energetic trade-offs are important drivers of life-history variation. This study employs an integrative approach to quantify acute physiological responses to high temperatures in divergent life-history ecotypes of the western terrestrial garter snake (Thamnophis elegans). Using wild-caught animals, we measured oxygen consumption rate and physiological markers of hormonal stress response, energy availability, and anaerobic respiration in blood plasma across five ecologically relevant temperatures (24, 28, 32, 35, and 38° C; 3-hour exposure). Corticosterone, insulin, and glucose concentrations all increased with temperature, but with different thermal response curves, suggesting that high temperatures differently affect energy-regulation pathways. Additionally, oxygen consumption rate increased without plateau and lactate concentration did not increase with temperature, challenging the recent hypothesis that oxygen limitation sets upper thermal tolerance limits. Finally, animals had similar physiological thermal responses to high-temperature exposure regardless of genetic background, suggesting that local adaptation has not resulted in fixed differences between ecotypes. Together, these results identify some of the mechanisms by which higher temperatures alter hormonal-mediated energy balance in reptiles and potential limits to the flexibility of this response.

opencc-zeroDec 2014View details →

Data from: Ecological relevance of energy metabolism: transcriptional responses in energy sensing and expenditure to thermal and osmotic stresses in an intertidal limpet

For rocky intertidal species that experience changes in a number of potential stressors seasonally and during the tidal cycle, sensing cellular energy status and modulating it adaptively may be crucial for responding to stressor effects. However, the responses of energy metabolism of intertidal species to multiple sublethal stressors are still unclear. Here, we examined gene expression profiles of biomarkers related to sensing of cellular energy status and regulation of catabolism and energy expenditure in a mid-intertidal limpet Cellana toreuma for elucidating the species' cellular energy responses stresses from high temperature, desiccation and rainfall. Expression levels of genes encoding metabolic regulators [two subunits of AMP-activated protein kinase, ampkα, ampkβ; Fu gene inhibition axis formation, axin; two sirtuins, NAD-dependent deacetylase sirtuin-1 (sirt1); NAD-dependent deacetylase sirtuin-5 (sirt5)], metabolic enzymes (hexokinase, hk; pyruvate kinase, pk; isocitrate dehydrogenase, idh) and heat shock protein 70 (hsp70) were quantified in specimens exposed to different temperatures and aerial/freshwater spray conditions. Based on the gene expression patterns, all individuals could be divided into three groups with divergent cellular energy status, indicating that the selected target genes are appropriate indicators of cellular metabolism. The divergent gene expression patterns indicated a sequence in which individuals from group 1, group 2 and group 3 were faced with increasing energy stress. The frequency distributions of individuals in the three groups were different among different time points and treatments, indicating that high temperature, desiccation, and rainfall, singly or in combination, could cause energy stress. Compared to the high percentage (100%) of individuals placed in the highest-stress group (group 3), after 2 h of freshwater spray at 18 °C, the lower percentage (77·8%) of individuals in group 3 after 2 h of freshwater spray at 30 °C indicated the existence of interactive effects of high temperature and rain; high temperature resulted in a lower response of cellular energy metabolism to rainfall. Sublethal environmental stresses from single stressors such as temperature or osmotic challenges can lead to cellular energy stress. Interactions among stressors may lead to a complex overall effect on cellular energy status in intertidal species.

opencc-zeroDec 2013View details →

Data from: A cross-seasonal perspective on local adaptation: metabolic plasticity mediates responses to winter in a thermal-generalist moth

The physiological and ecological impact of the thermal environment across life-stages can result in trade-offs that determine fitness and population dynamics. Understanding mechanisms and consequences of local adaptation for any organism that overwinters requires taking a cross-seasonal perspective. We used a trait-based approach to distinguish variation among ecotypes in ecological and physiological responses to overwintering conditions. We used fall webworms (Hyphantria cunea; Lepidoptera: Arctiidae) from Ottawa, Ontario and Columbus Ohio, representing the centre and periphery of the native range. We hypothesised that populations would be locally adapted to their overwintering environments, with fitness maximised under natal overwintering conditions. We predicted that this local adaptation would result from modulation of rates of energy use, growth and development. Each ecotype had higher overwinter survival in their natal compared to non-natal winter environment, and this was associated with larger pupal mass, size and carbohydrate reserves at the end of winter. This suggests that the ecotypes are locally adapted to winter conditions. Larger adults laid more eggs, but there was no effect of ecotype or environment on fecundity. Pupae overwintering at warm, energetically demanding southern temperatures suppressed metabolic rates in autumn, and developed more quickly in the spring, compensating for energetic demands of warmer winters. Northern ecotypes had lower thermal sensitivity of metabolism, leading to higher metabolic rates at cool temperatures that correlated with faster post-winter development. Local adaptation to winter conditions suggests performance of peripheral populations may not be enhanced by warming winters. Decoupling of winter and growing season temperatures may negatively impact ectotherms.

opencc-by-4.0Jul 2024View details →

Transcriptome analysis and functional study of phospholipase A2 in Galleria mellonella larvae lipid metabolism in response to envenomation by an ectoparasitoid, Iseropus kuwanae

The file is the raw data of "Transcriptome analysis and functional study of phospholipase A2 in Galleria mellonella larvae lipid metabolism in response to envenomation by an ectoparasitoid, Iseropus kuwanae".

opencc-zeroJun 2021View details →

Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature

This dataset contains pre-processed untargeted GC-MS metabolomics and direct shotgun proteomics from a microcosm woodblock experiment described in the paper "Rawlings et al (2021) Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature. Ecology." The experiment investigates the effect of diurnal cycling of temperature on the metabolism of two wood decay species, Mucidula mucida and Exidia glandulosa. We colonised beech woodblocks with the two species (separate microcosms) and exposed them to either a diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. After 8 weeks we extracted the full complement of metabolites and proteins in the wood to examine the extent to which the abundances of metabolic products were altered. The main results of the experiment were that products linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely E. glandulosa showed little differential response to the experimental treatments which may be linked with its preference for habitats exhibiting abiotic stress.

opencc-zeroJul 2021View details →

Membrane lipid metabolism, heat shock response, and energy costs mediate the interaction between acclimatization and heat hardening response

Thermal plasticity on different timescales, including acclimation/acclimatization and heat hardening response – a rapid adjustment for thermal tolerance after a nonlethal thermal stress, can interact on organisms to improve the resilience to thermal stress. However, little is known about the physiological mechanisms mediating this interaction. To investigate underpinnings of heat hardening responses after acclimatization in warm season, we measured thermal tolerance plasticity, compared transcriptomic and metabolomic changes after heat hardening at 33 or 37oC followed by recovery of 3 h or 24 h in an intertidal bivalve Sinonovacula constricta. The clams showed explicit heat hardening responses after acclimatization in warm season. The higher inducing temperature (37oC) caused a less effective heat hardening effect than the inducing temperature that was closer to seasonal maximum temperature (33oC). Metabolomic analysis highlighted the elevated contents of membrane glyceropholipids in all heat hardened clams, which may help to maintain structure and function of membrane. Heat shock proteins (HSPs) tended to be up-regulated after heat hardening at 37oC but not at 33oC, indicating that there was no complete dependency of heat hardening effects on up-regulated HSPs. Enhanced energy metabolism and decreased energy reserves were observed after heat hardening at 37oC, suggesting more energy costs during exposure to higher inducing temperature which may restrict heat hardening effects. These results highlighted the mediating role of membrane lipid metabolism, heat shock responses and energy costs in the interaction of heat hardening response and seasonal acclimatization, and benefit the mechanistic understanding of evolutionary change and thermal plasticity during global climate change.

opencc-zeroNov 2022View details →

Metabolic phenotype mediates the outcome of competitive interactions in a response-surface field experiment

Competition and metabolism should be linked. Intraspecific variation in metabolic rates and, hence, resource demands covary with competitive ability. The effects of metabolism on conspecific interactions, however, have mostly been studied under laboratory conditions. We used a trait-specific response-surface design to test for the effects of metabolism on pairwise interactions of the marine colonial invertebrate, Bugula neritina in the field. Specifically, we compared the performance (survival, growth, and reproduction) of focal individuals, both in the presence and absence of a neighbour colony, both of which had their metabolic phenotype characterised. Survival of focal colonies depended on the metabolic phenotype of the neighbouring individual, and on the combination of both the focal and neighbour colony metabolic phenotypes that were present. Surprisingly, we found pervasive effects of neighbour metabolic phenotypes on focal colony growth and reproduction, though the sign and strength of these effects showed strong microenvironmental variability. Overall, we find that the metabolic phenotype changes the strength of competitive interactions, but these effects are highly contingent on local conditions. We suggest future studies explore how variation in metabolic rate affects organisms beyond the focal organism alone, particularly under field conditions.

Fig. 7 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 7. Phylogenetic relationship of the five FnTPS candidates with other known terpene synthases and a sequence alignment showing the conserved protein motifs. (A) A maximum-likelihood tree of the TPS proteins depicting the TPS-a, TPS-b, TPS-d, TPS-e/f, and TPS-g clades, with bootstrap values greater than 50% shown for the branching. The scale bar corresponds to 6% amino acid substitution. The five F. nilgerrensis proteins are in red. Selected proteins with available three-dimensional structural data are shown in bold using their PDB code followed by the abbreviated species name. The known enzymatic products are in light blue followed with the UniProt Accession numbers of the proteins. (B) Alignment of the five candidates FnTPSs with α-farnesene synthase from apple (Malus domestica) and α-bergamotene synthase from Lavender (Lavandula Angustifolia). The DxDD motif of typical class II terpene synthases in FnTPS6 is boxed and the highly conserved class I DDxxD as well as the lesser conserved RRx8W and NSE/DTE motifs are indicated. The color regime of amino acids is set in Bioedit version 7.2.6. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 3. Most enriched metabolic pathways of the DEGs during the first 18 hpi with C. gloeosporioides. Only significant pathways with a Q-value below 1 are shown. Terpene metabolism clusters are highlighted.

Fig. 1 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 1. Determination of terpenoids in leaves challenged with C. gloeosporioides. (A) Total contents of monoterpenes and sesquiterpenes, (B–C) The contents of individual monoterpene and sesquiterpene identified. Data are average of two independent experiments.

Fig. 4 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 2. Global differentially-expressed-genes (DEG) in leaves of F. nilgerrensis after challenged by C. gloeosporioides. (A) DEG heatmap depicts clustering of the early upregulated genes (up to 18-h post challenge) and the late respondents (>24 h) in the upper and lower parts, respectively, with top GO terms indicated. (B) Major GO term enrichment in an early responsive gene cluster 7 showing that terpenoid biosynthesis genes are co-expressed with antipathogen immune-responsive pathway genes. Each time-point contains 2 biological replications and the expression data was zero-normalized before hierarchical clustering is performed (Pearson uncentered metric, average linkage ordering) using Cluster 3.0 version 1.58. Heatmap was examined and generated using Java Tree- View version 1.1.6r4. Gene Ontology (GO) enrichment analysis of the DEGs is implemented by the topGO R package-based Kolmogorov–Smirnov test.

Fig. 5 in Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis

Fig. 5. Heat maps depicting the transcript levels of terpenoid biosynthesis genes from F. nilgerrensis leaf transcriptome in response to C. gloeosporioides. (A) Fifty-six MVA and MEP pathway-associated genes. Annotation of the unigenes by homologous are listed in Table S4. (B) Fifty-nine terpene synthase-like or related genes. Annotation of the unigenes by homologous are listed in Table S5. Average FPKM (n = 2) were log2 transformed. The heatmap was generated by Prism GraphPad version 7.04.