Find research datasets worth reusing

opencc-zeroJan 2022View details →

Data from: Using metabolic theory to describe temperature and thermal acclimation effects on parasitic infection

Predicting temperature effects on species interactions can be challenging, especially for parasitism where it is difficult to experimentally separate host and parasite thermal performance curves. Prior authors proposed a possible solution based on the metabolic theory of ecology (MTE), using MTE-based equations to describe the thermal mismatch between host and parasite performance curves and account for thermal acclimation responses. Here we use published infection data, supplemented with experiments measuring metabolic responses to temperature in each species, to show that this modeling framework can successfully describe thermal acclimation effects on two different stages of infection in a tadpole-trematode system. All thermal acclimation effects on host performance manifested as changes in one key model parameter (activation energy), with measurements of host respiration generating similar MTE parameter estimates and acclimation effects compared to measurements of the host's ability to clear encysted parasites. This result suggests that metabolic parameter estimates for whole-body metabolism can sometimes be used to estimate temperature effects on host and parasite performance curves. However, we found different thermal patterns for measurements of host prevention of initial parasite encystment emphasizing potential challenges when applying MTE-based models to complex parasite-host systems with multiple distinct stages of infection.

opencc-by-4.0Feb 2022View details →

Physiological costs of facultative endosymbionts in aphids assessed from energy metabolism

Using the standard metabolic rate (SMR) as a measure of the energy cost of self-maintenance, we investigated whether two common facultative endosymbionts Hamiltonella defensa or Regiella insecticola increase the maintenance cost of the pea aphid Acyrthosiphon pisum and translate into host fitness reduction (‘compensation hypothesis’). In addition, we tested if there was a link between SMR and the aphid fitness and whether it depended on endosymbiont density and aphid energetic reserves. Finally, we measured SMR at different temperatures to assess the impact of suboptimal thermal conditions on physiological cost of endosymbionts.

opencc-by-4.0Mar 2022View details →

Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation.

Original data linked to Lemberg, Martinez de San Vicente, Fróis-Martins, et al., PLoS Pathogens, 2022. Transcriptomic data linked to this paper are deposited on the NCBI BioProject PRJNA491801 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA491801)

opencc-by-4.0Apr 2022View details →

Metabolic data: Inhibition of mitochondrial complex I reverses NOTCH1-driven metabolic reprogramming in T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is commonly driven by activating mutations in NOTCH1 that facilitate glutamine oxidation. Here we identify oxidative phosphorylation (OxPhos) as a critical pathway for leukemia cell survival and demonstrate a direct relationship between NOTCH1, elevated OxPhos gene expression, and acquired chemoresistance in pre-leukemic and leukemic models. Disrupting OxPhos with IACS-010759, an inhibitor of mitochondrial complex I, causes potent growth inhibition through induction of metabolic shut-down and redox imbalance in NOTCH1-mutated and less so in NOTCH1-wt T-ALL cells. Mechanistically, inhibition of OxPhos induces metabolic reprogramming into glutaminolysis. We show that pharmacological blockade of OxPhos combined with inducible knock-down of glutaminase, the key glutamine enzyme, confers synthetic lethality in mice harboring NOTCH1-mutated T-ALL. We leverage this synthetic lethal interaction to demonstrate that IACS-010759 in combination with chemotherapy containing L-asparaginase, an enzyme that uncovers the glutamine dependency of leukemic cells, causes reduced glutaminolysis and profound tumor reduction in pre-clinical models of human T-ALL. In summary, this metabolic dependency of T-ALL on OxPhos provides a rational therapeutic target.

opencc-by-4.0May 2022View details →

A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast

Computational models and figure data for the publication "A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast" (preprint on <a href="https://doi.org/10.1101/2022.05.04.490403">bioRxiv</a>). Data put together by Pranas Grigaitis, p.grigaitis [at] vu.nl.   Abstract The fission yeast Schizosaccharomyces pombe is a popular eukaryal model organism for cell division and cell cycle studies. With this extensive knowledge of its cell and molecular biology, S. pombe also holds promise for use in metabolism research and industrial applications. However, unlike the baker’s yeast Saccharomyces cerevisiae, a major workhorse in these areas, cell physiology and metabolism of S. pombe remain less explored. One way to advance understanding of organism-specific metabolism is construction of computational models and their use for hypothesis testing. To this end, we leverage existing knowledge of S. cerevisiae to generate a manually-curated high-quality reconstruction of S. pombe’s metabolic network, including a proteome-constrained version of the model. Using these models, we gain insights into the energy demands for growth, as well as ribosome kinetics in S. pombe. Furthermore, we predict proteome composition and identify growth-limiting constraints that determine optimal metabolic strategies under different glucose availability regimes, and reproduce experimentally determined metabolic profiles. Notably, we find similarities in metabolic and proteome predictions of S. pombe with S. cerevisiae, which indicate that similar cellular resource constraints operate to dictate metabolic organization. With these use cases, we show, on the one hand, how these models provide an efficient means to transfer metabolic knowledge from a well-studied to a lesser-studied organism, and on the other, how they can successfully be used to explore the metabolic behaviour and the role of resource allocation in driving different strategies in fission yeast.

opencc-zeroMay 2022View details →

Metabolic syndrome for the prognosis of postoperative complications after open pancreatic surgery in Chinese adult: a propensity score matching study

Background: To investigate the relationship between metabolic syndrome (MS) and postoperative complications in Chinese adults after open pancreatic surgery. Methods: Relevant data were retrieved from the Medicalsystem® database of Changhai hospital (MDCH). All patients who underwent pancreatectomy from January 2017 to May 2019 were included, and relevant data were collected and analyzed. A propensity score matching (PSM) and a multivariate generalized estimating equation were used to investigate the association between MS and composite compositions during hospitalization. Cox regression model was employed for survival analysis. Results: 1481 patients were finally eligible for this analysis. According to diagnostic criteria of Chinese MS, 235 patients were defined as MS, and the other 1246 patients were controls. After PSM, no association was found between MS and postoperative composite complications (OR: 0.958, 95%CI: 0.715-1.282, P=0.958). But MS was associated with postoperative acute kidney injury (OR: 1.730, 95%CI: 1.050-2.849, P=0.031). Postoperative AKI was associated with mortality in 30 days and 90 days after surgery (P<0.001). Conclusions: MS is not an independent risk factor correlated with postoperative composite complications after open pancreatic surgery. But MS is an independent risk factor for postoperative AKI of pancreatic surgery in Chinese population, and AKI is associated with survival after surgery.

opencc-zeroMay 2022View details →

Effects of acute exposure to polystyrene nanoplastics on the channel catfish larvae: Insights from energy metabolism and transcriptomic analysis

Microplastics (nanoplastics) pollution has been a major ecological issue threatening global aquatic ecosystems. However, knowledge of the adverse effects of nanoplastics and the effects on freshwater ecosystems is still limited. To understand the impacts of nanoplastics on freshwater ecosystems, it is essential to reveal the physiological changes caused by nanoplastics in freshwater organisms, especially at their early life-history stages. In the present study, the larval channel catfish Ietalurus punetaus were exposed to gradient concentrations (0, 5, 10, 25 and 50 mg/L) of 75-nm polystyrene nanoplastics (PS-NPs) for 24 h or 48 h, and changes in contents of energy metabolites, metabolic enzyme activities and transcriptome were assessed. The results showed glucose and triglyceride contents increased after 24 h of exposure to 10 or 25 mg/L of PS-NPs but decreased with increased concentrations or prolonged exposure duration. Activities of most metabolic enzymes analyzed decreased in the larvae after 48 h of exposure, especially in 25 or 50 mg/L of PS-NPs. These suggested that PS-NPs caused huge energy consumption and disturbed the energy metabolism in larval fish. Transcriptomic analysis showed that 48 h of exposure to 50 mg/L PS-NPs affected the expression of genes involved in protein digestion and induced response of proteasomes or heat shock proteins in the larval I. punetaus. The genes involved in peroxisome proliferator-activated receptors (PPAR) pathway and biosynthesis of amino acids were activated after the exposure. PS-NPs also depressed the expression of the genes involved in gonad development or muscle contraction in the larval I. punetaus. Overall, acute exposure to 75-nm PS-NPs disrupted the energy metabolism by consuming the energy reserves, and affected a series of molecular pathways which may further affect the development and survival of fish. This study provided the information about adverse effects of nanoplastics on the fish larvae and revealed the molecular pathways for the potential adverse outcomes.

opencc-zeroAug 2022View details →

Data from: Metabolic changes associated with two endocrine abnormalities in dogs: elevated fructosamine and low thyroxine

Metabolomics studies in canine endocrine abnormalities are sparse and basic information on these abnormalities must be generated. This dataset includes the 1H NMR metabolic profiling results of 151 dog serum samples. The samples have been collected in an ethical way, being leftovers of clinical diagnostic samples. The sample set includes 25 control samples based on unremarkable routine clinical chemistry and hematology, 79 samples exhibiting high fructosamine which reflects poor glycemic control, and 47 samples with low thyroxine, a metabolically important thyroid hormone. The metabolite data and metadata were utilized in the study: Ottka et al. Metabolic changes associated with two endocrine abnormalities in dogs: elevated fructosamine and low thyroxine. The control group results were utilized also in: Ottka et al. Serum NMR metabolomics uncovers multiple metabolic changes in phenobarbital-treated dogs.

opencc-zeroMay 2022View details →

Senescent preosteoclast secretome promotes metabolic syndrome-associated osteoarthritis through COX2-PGE2

Metabolic syndrome–associated osteoarthritis (MetS-OA) is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. Here, we report that humans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. MetS-OA mice exhibited a rapid increase in joint subchondral bone plate and trabecular thickness before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence at the pre- or early-osteoarthritis stage and acquire a unique secretome to stimulate osteoblast differentiation and inhibit osteoclast differentiation. Antagonizing preosteoclast senescence markedly mitigates pathological subchondral alterations and osteoarthritis progression in MetS-OA mice. At the molecular level, preosteoclast secretome activates COX2-PGE2, resulting in stimulated differentiation of osteoblast progenitors for subchondral bone formation. Administration of a selective COX2 inhibitor attenuated subchondral bone alteration and osteoarthritis progression in MetS-OA mice. Longitudinal analyses of the human Osteoarthritis Initiative (OAI) cohort dataset also revealed that COX2 inhibitor use, relative to non-selective nonsteroidal anti-inflammatory drug use, is associated with less progression of osteoarthritis and subchondral bone marrow lesion worsening in participants with MetS-OA. Our findings suggest a central role of a senescent preosteoclast secretome-COX2/PGE2 axis in the pathogenesis of MetS-OA.

opencc-by-4.0May 2022View details →

Strain specific genome scale metabolic models for 1011 Saccharomyces cerevisiae

This is generated strain-specific genome scale metabolic models for 1011 S.cerevisiae. This is linked with the paper: Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). <a href="https://doi.org/10.1038/s41467-019-11581-3">doi:10.1038/s41467-019-11581-3</a>

opencc-zeroJun 2022View details →

The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach

The plant genus Oenothera has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 Oenothera species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section Oenothera exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to Oenothera diversification and rapid gene family evolution.

opencc-zeroJun 2022View details →

Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period

Aim: Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period. Methods: Aged C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses, quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period. Results: Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (Htr1a, Rims1, Ezh2, etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (Gpld1, Sirt1, Cry2, etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (Mmp2, Itpr1, Nrf1, etc.). Conclusion: The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.

opencc-zeroJun 2022View details →

The metabolic hormone adiponectin affects the correlation between nutritional status and pneumococcal vaccine response in vulnerable indigenous children

Background: Almost 200 million children worldwide are either undernourished or overweight. Only a few studies have addressed the effect of variation in nutritional status on vaccine response. We previously demonstrated an association between stunting and an increased post-vaccination 13-valent pneumococcal conjugate vaccine (PCV13) response. In this prospective study, we assessed to what extent metabolic hormones may be a modifier in the association between nutritional status and PCV13 response. Methods: Venezuelan children aged 6 weeks to 59 months were vaccinated with a primary series of PCV13. Nutritional status and serum levels of leptin, adiponectin and ghrelin were measured upon vaccination and their combined effect on serum post-vaccination antibody concentrations was assessed by generalized estimating equations multivariable regression analysis. Results: A total of 210 children were included, of whom 80 were stunted, 81 had a normal weight and 49 were overweight. Overweight children had lower post-vaccination antibody concentrations than normal weight children (regression coefficient -1.15, 95% CI -2.22 – -0.072). Additionally, there was a significant adiponectin-nutritional status interaction. In stunted children, higher adiponectin serum concentrations were associated with lower post-PCV13 antibody concentrations (regression coefficient -0.19, 95% CI -0.24 – -0.14) while the opposite was seen in overweight children (regression coefficient 0.14, 95% CI 0.049 – 0.22). Conclusion: Metabolic hormones, in particular adiponectin, may modify the effect of nutritional status on pneumococcal vaccine response. These findings emphasize the importance of further research to better understand the immunometabolic pathways underlying vaccine response and enable a future of optimal personalized vaccination schedules.

opencc-by-4.0Mar 2022View details →

Data of Mitochondrial respirometric data of adult males of Octopus maya: supporting the method to evaluate heart metabolic activity

Mitochondrial respirometry is key to understanding how environmental factors model energetic cellular processes. Until now, no reports have shown temperature effects and other environmental variables on cephalopod mitochondria activity because of the lack of a method to evaluate mitochondrial respiratory parameters on those groups of species. In this sense and for the first time, it showed the mitochondrial respirometry data of adult Octopus maya’s heart. Following the protocol is illustrated a step-by-step procedure to get the corresponding respiratory parameters.

opencc-by-4.0Jul 2022View details →

Comprehensive Context-specific Genome-scale Metabolic Models for Mus Musculus

Comprehensive Context-specific Genome-scale Metabolic Models for  Mus Musculus. The data consists of 28 models for the combination 2 mouse strains (WT and Ob/Ob), 2 diets (WT and HFD) and 7 tissues (Aorta, Heart, Liver, Skeletal Muscle, Hippocampus, Hypothalamus and Epididymal fat).

Resting metabolic rate of Sceloporus grammicus at intermediate and native elevations

Body maintenance energy requirements are measured as minimal metabolic rate (RMR) of inactive, postabsorptive individuals in the laboratory. For mountain-dwelling species, translocation to the laboratory can mean a change in elevation and thus oxygen pressure, which may affect metabolic rates. Here we present resting metabolic rate (RMR) of three populations of the Mesquite lizard (Sceloporus grammicus) at their native elevations (i.e., 2600, 3200 and 4100 m) and at an intermediate elevation (3100 m). Each lizard was tested at 15, 25, 30 and 35ºC. For each test RMR is given in VCO2 ml/min. Data also includes sex, snout vent length (SVL), body mass, and throat color morph.

Warm acclimation alters antioxidant defences but not metabolic capacities in the Antarctic fish, Notothenia coriiceps

The Southern Ocean surrounding the Western Antarctic Peninsula region is rapidly warming. Survival of members of the dominant suborder of Antarctic fishes, the Notothenioidei, will likely require thermal plasticity and adaptive capacity in key traits delimiting thermal tolerance. Herein, we have assessed the thermal plasticity of several cellular and biochemical pathways, many of which are known to be associated with thermal tolerance in notothenioids, including mitochondrial function, activities of aerobic and anaerobic enzymes, antioxidant defences,protein ubiquitination and degradation in cardiac, oxidative skeletal muscles and gill of Notothenia coriiceps warm acclimated to 4◦C for 22 days or 5◦C for 42 days. Levels of triacylglycerol (TAG) were measured in liver and oxidative and glycolytic skeletal muscles, and glycogen in liver and glycolytic muscle to assess changes in energy stores. Metabolic pathways displayed minimal thermal plasticity, yet antioxidant defences were lower in heart and oxidative skeletal muscles of warm-acclimated animals compared with animals held at ambient temperature. Despite higher metabolic rates at elevated temperature, energy storage depots of TAG and glycogen increase in liver and remain unchanged in muscle with warm acclimation. Overall, our studies reveal that N. coriiceps displays thermal plasticity in some key traits thatmay contribute to their survival as the Southern Ocean continues to warm.

The thermal performance curve for aerobic metabolism of a flying endotherm

Performance benefits of stable, warm muscles are believed to be important for the evolution of endothermy in mammals, birds, and flying insects. However, thermal performance curves have never been measured for a free-flying endotherm, as it is challenging to vary body temperatures of these animals, and maximal flight performance is difficult to elicit. We varied air temperatures and gas densities to manipulate thoracic temperatures of flying honey bees from 29-44°C, with low air densities used to increase flight metabolic rates to maximal values. Honey bees showed a clear thermal performance curve with an optimal temperature of 39°C. Maximal flight metabolic rates increased by ~2% per 1°C increase in thoracic temperature at suboptimal thoracic temperatures, but decreased ~5% per 1°C increase as the bees continued to heat up. This study provides the first quantification of the maximal metabolic performance benefit of thermoregulation in an endotherm. These data directly support aerobic capacity models for benefits of thermoregulation in honey bees, and suggest that improved aerobic capacity likely contributes to the multiple origins of endothermic heterothermy in bees and other insects.

Predictors of metabolic syndrome among adults in Ethiopia

Background Available evidence showed that metabolic syndrome in the adult population is persistently elevated due to nutrition transition, genetic predisposition, individual-related lifestyle factors, and other environmental risks. However, in developing nations, the burden and scientific evidence on the pattern, and risk exposures for the development of the metabolic syndrome were not adequately investigated. Thus, the study aimed to measure the prevalence of metabolic syndrome and to identify specific risk factors among adult populations who visited Dessie Comprehensive Specialized Hospital, Ethiopia. Methods A hospital-based cross-sectional study was conducted among randomly selected 419 adults attending Dessie Comprehensive Specialized Hospital from January 25 to February 29, 2020. We used the WHO STEP-wise approach for non-communicable disease surveillance to assess participants' disease condition. Metabolic syndrome was measured using the harmonized criteria recommended by the International Diabetes Federation Task Force in 2009. Data were explored for missing values, outliers, and multicollinearity before presenting the summary statistics and regression results. Multivariable logistic regression was used to disentangle statistically significant predictors of metabolic syndrome expressed using an odds ratio with a 95% of uncertainty interval. All statistical tests were managed using SPSS version 26. A non-linear dose-response analysis was performed to show the relationships between metabolic syndrome with potential risk factors. Results The overall prevalence of metabolic syndrome among adults was 35.0 %( 95% CI, (30.5, 39.8)). Women were more affected than men (i.e. 40.3% vs 29.4%). After adjusting for other variables, being female [OR=1.85; 95% CI (1.01, 3.38)], urban residence [OR=1.94; 95% CI (1.08, 3.24)], increased age [OR= 18.23; 95% CI (6.66, 49.84)], shorter sleeping durations [OR= 4.62; 95% CI (1.02, 20.98)], sedentary behaviour[OR=4.05; 95% CI (1.80, 9.11)], obesity[OR=3.14; 95% CI (1.20, 8.18) and alcohol drinking[OR=2.85; 95% CI (1.27,6.39)] were positively associated with the adult metabolic syndrome. Whilst have no formal education [OR=0.30; 95% CI (0.12, 0.74)] was negatively associated with metabolic syndrome. Conclusions The prevalence of the adult metabolic syndrome is found to be high. Metabolic syndrome has linear relationships with BMI, physical activity, sleep duration, and level of education. The demographic and behavioral factors are strongly related to the risk of metabolic syndrome. Since most of the factors are modifiable, there should be urgent large-scale community intervention programs focusing on increased physical activity, healthy sleep, weight management, minimizing behavioral risk factors, and healthier food interventions targeting a lifecycle approach. The existing policy should be evaluated whether due attention has been given to prevention strategies of NCDs.