Skeletal muscle methylome and transcriptome integration reveals profound sex differences related to muscle function and substrate metabolism.

Nearly all human complex traits and diseases exhibit some degree of sex differences, with epigenetics being one of the main contributing factors. Various tissues display sex differences in DNA methylation; however, this has not yet been explored in skeletal muscle, despite skeletal muscle being among the tissues with the most transcriptomic sex differences. For the first time, we investigated the effect of sex on autosomal DNA methylation in human skeletal muscle across three independent cohorts (Gene SMART, FUSION, and GSE38291) using a meta-analysis approach, totalling 369 human muscle samples (222 males and 147 females), and integrated this with known sex-biased transcriptomics. We found 10,240 differentially methylated regions (DMRs) at FDR < 0.005, 94% of which were hypomethylated in males, and gene set enrichment analysis revealed that differentially methylated genes were involved in muscle contraction and substrate metabolism. We then investigated biological factors underlying DNA methylation sex differences and found that circulating hormones were not associated with differential methylation at sex-biased DNA methylation loci; however, these sex-specific loci were enriched for binding sites of hormone-related transcription factors (with top TFs including androgen (AR), estrogen (ESR1), and glucocorticoid (NR3C1) receptors). Fibre type proportions were associated with differential methylation across the genome, as well as across 16% of sex-biased DNA methylation loci (FDR < 0.005). Integration of DNA methylomic results with transcriptomic data from the GTEx database and the FUSION cohort revealed 326 autosomal genes that display sex differences at both the epigenome and transcriptome levels. Importantly, transcriptional sex-biased genes were overrepresented among epigenetic sex-biased genes (p value = 4.6e-13), suggesting differential DNA methylation and gene expression between male and female muscle are functionally linked. Finally, we validated expression of three genes with large effect sizes (FOXO3A, ALDH1A1, and GGT7) in the Gene SMART cohort with qPCR. GGT7, involved in antioxidant metabolism, displays male-biased expression as well as lower methylation in males across the three cohorts. In conclusion, we uncovered 8420 genes that exhibit DNA methylation differences between males and females in human skeletal muscle that may modulate mechanisms controlling muscle metabolism and health.

Intrauterine insemination cycles: prediction of success and thresholds for poor prognosis and futile care.

PURPOSE: We aimed to define intrauterine insemination (IUI) cycle characteristics associated with viable birth, identify thresholds below which IUI treatments are consistent with very poor prognosis and futile care, and develop a nomogram for individualized application. METHODS: This retrospective cohort study evaluated couples using fresh partner ejaculate for IUI from January 2005 to September 2017. Variables included female age, semen characteristics, and ovarian stimulation type. Using cycle-level data, we evaluated the association of these characteristics with the probability of viable birth by fitting generalized regression models for a binary outcome with a logit link function, using generalized estimating equation methodology to account for the correlation between cycles involving the same patient. RESULTS: The cohort consisted of 1117 women with 2912 IUI cycles; viable birth was achieved in 275 (9.4%) cycles. Futile care (viable birth rate < 1%) was identified for women age > 43, regardless of stimulation type or inseminate motility (IM). Very poor prognosis (viable birth rate < 5%) was identified for women using oral medications or Clomid plus gonadotropins who were (1) age < 35 with IM < 49%, (2) age 35-37 with IM < 56%, or (3) age ≥ 38, and (4) women age ≥ 38 using gonadotropins only with IM < 60%. A clinical prediction model and nomogram was developed with an optimism-corrected c-statistic of 0.611. CONCLUSIONS: The present study highlights the impact of multiple clinical factors on IUI success, identifies criteria consistent with very poor prognosis and futile care, and provides a nomogram to individualize counseling regarding the probability of a viable birth.

Enhanced Pyruvate Production in Candida glabrata by Engineering ATP Futile Cycle System.

Energy metabolism plays an important role in the growth and central metabolic pathways of cells. Manipulating energy metabolism is an efficient strategy to improve the formation of target products and to understand the effects of altering intracellular energy levels on global metabolic networks. Candida glabrata, as a dominant yeast strain for producing pyruvate, principally converts glucose to pyruvate through the glycolytic pathway. However, this process can be severely inhibited by a high intracellular ATP content. Here, in combination with the physiological characteristics of C. glabrata, efforts have been made to construct an ATP futile cycle system (ATP-FCS) in C. glabrata to decrease the intracellular ATP level without destroying F0F1-ATPase function. ATP-FCS was capable of decreasing the intracellular ATP level by 51.0% in C. glabrata. The decrease in the ATP level directly led to an increased pyruvate production and glycolysis efficiency. Moreover, we further optimized different aspects of the ATP-FCS to maximize pyruvate accumulation. Combining ATP-FCS with further genetic optimization strategies, we achieved a final pyruvate titer of 40.2 g/L, with 4.35 g pyruvate/g dry cell weight and a 0.44 g/g substrate conversion rate in 500 mL flasks, which represented increases of 98.5%, 322.3%, and 160%, respectively, compared with the original strain. Thus, these strategies hold great potential for increasing the synthesis of other organic acids in microbes.

Phosphoglycerate kinase acts as a futile cycle at high temperature.

In (hyper)thermophilic organisms metabolic processes have to be adapted to function optimally at high temperature. We compared the gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate at 30 °C and at 70 °C. At 30 °C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 °C, 1,3-bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. When phosphoglycerate kinase was incubated together with glyceraldehyde 3-phosphate dehydrogenase it was possible to convert 3-phosphoglycerate to glyceraldehyde 3-phosphate, both at 30 °C and at 70 °C, however, at 70 °C only low concentrations of product were observed due to thermal instability of glyceraldehyde 3-phosphate. Thus, thermolabile intermediates challenge central metabolic reactions and require special adaptation strategies for life at high temperature.

Futile cycling increases sensitivity toward oxidative stress in Escherichia coli.

Reactive oxygen species (ROS) are toxic molecules utilized by the immune system to combat invading pathogens. Recent evidence suggests that inefficiencies in ATP production or usage can lead to increased endogenous ROS production and sensitivity to oxidative stress in bacteria. With this as inspiration, and knowledge that ATP is required for a number of DNA repair mechanisms, we hypothesized that futile cycling would be an effective way to increase sensitivity to oxidative stress. We developed a mixed integer linear optimization framework to identify experimentally-tractable futile cycles, and confirmed metabolic modeling predictions that futile cycling depresses growth rate, and increases both O2 consumption and ROS production per biomass generated. Further, intracellular ATP was decreased and sensitivity to oxidative stress increased in all actively cycling strains compared to their catalytically inactive controls. This research establishes a fundamental connection between ATP metabolism, endogenous ROS production, and tolerance toward oxidative stress in bacteria.

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3.

The nature of the ammonium import into prokaryotes has been controversial. A systems biological approach makes us hypothesize that AmtB-mediated import must be active for intracellular NH(4)(+) concentrations to sustain growth. Revisiting experimental evidence, we find the permeability assays reporting passive NH(3) import inconclusive. As an inevitable consequence of the proposed NH(4)(+) transport, outward permeation of NH(3) constitutes a futile cycle. We hypothesize that the regulatory protein GlnK is required to fine-tune the active transport of ammonium in order to limit futile cycling whilst enabling an intracellular ammonium level sufficient for the cell's nitrogen requirements.

The Randle cycle revisited: a new head for an old hat.

In 1963, Lancet published a paper by Randle et al. that proposed a "glucose-fatty acid cycle" to describe fuel flux between and fuel selection by tissues. The original biochemical mechanism explained the inhibition of glucose oxidation by fatty acids. Since then, the principle has been confirmed by many investigators. At the same time, many new mechanisms controlling the utilization of glucose and fatty acids have been discovered. Here, we review the known short- and long-term mechanisms involved in the control of glucose and fatty acid utilization at the cytoplasmic and mitochondrial level in mammalian muscle and liver under normal and pathophysiological conditions. They include allosteric control, reversible phosphorylation, and the expression of key enzymes. However, the complexity is formidable. We suggest that not all chapters of the Randle cycle have been written.

Toxoplasma-induced autophagy: a window into nutritional futile cycles in mammalian cells?

The regulation and function of autophagy in response to metabolic signals is not yet well understood. A recent study from our laboratory indicates that an intracellular parasite, Toxoplasma gondii, derives nutritive benefit from the upregulation of host cell autophagy. We discuss this and related findings suggesting that autophagy in infected cells functions as part of a metabolic futile cycle. The hypothesis is presented that endogenous autophagy-based futile cycles may operate in normal mammalian cells, providing a substrate for manipulation by pathogens.

Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae.

Hidden transcription in eukaryotes carries a large potential of regulatory functions that are only recently beginning to emerge. Cryptic unstable transcripts (CUTs) are generated by RNA polymerase II (Pol II) and rapidly degraded after transcription in wild-type yeast cells. Whether CUTs or the act of transcription without RNA production have a function is presently unclear. We describe here a nonconventional mechanism of transcriptional regulation that relies on the selection of alternative transcription start sites to generate CUTs or mRNAs. Transcription from TATA box proximal start sites generates unstable transcripts and downregulates expression of the URA2 gene under repressing conditions. Uracil deprivation activates selection of distal start sites, leading to the production of stable mRNAs. We describe the elements that govern degradation of the CUT and activation of mRNA production by downstream transcription initiation. Importantly, we show that a similar mechanism applies to other genes in the nucleotides biogenesis pathway.

Kinetic analysis of a model for double substrate cycling: highly amplified ADP (and/or ATP) quantification.

A mathematical description has been made of an enzyme amplification mechanism involving the coupling of two substrate cycles. In this amplification system one of the noncycling products of a first substrate cycle acts as a trigger molecule that continuously feeds a second substrate cycle. Time-concentration equations describing the evolution of the species involved in the system have been obtained. The model is illustrated by the quantification of nanomolar levels of ADP (and/or ATP) in a continuous assay involving the enzymes L-lactate dehydrogenase and L-lactate oxidase to cycle the pyruvate accumulated in a first enzymatic cycle constituted by the enzymes pyruvate kinase and hexokinase. Progress curves were seen to be parabolic, and, according to the kinetic equations obtained, followed second-order polynomials of the reaction time. Mathematical equations for minimizing the cost of the assays are also given. The model is applicable to the amplified analytical determination of low levels of a metabolite or an enzyme activity, and its amplification capacity, together with the simplicity of determining kinetic parameters, enable it to be employed in enzyme immunoassays to increase the magnitude of the measured response.

[Energy turnover in endurance exercise]. / Energieumsatz bei Ausdauerbelastungen.

During endurance exercise energy derives mainly from oxidation of carbohydrates and fat. Carbohydrates are stored in muscle and liver glycogen, fat is stored in adipose subcutaneous tissue and in intramuscular triglycerides. The intramuscular stores are the preliminary sources of fuel during muscular exercise. The principles of fatloading and carboloading are useful in increasing the intramuscular stores before exercise. The increased muscular reserves enable the athlete to maintain a higher intensity for longer time. During exercise depletion of glycogen may be delayed by ingestion of carbohydrates. Due to the limited resorption and oxidation of carbohydrates, efficacy of ingested carbohydrates is clearly limited. Due to the limitation in energy stores in the muscles and the limitation of energy ingestion during exercise, a considerable energy deficiency in long lasting events over days has to be considered.

Dynamic profiling of the glucose metabolic network in fasted rat hepatocytes using [1,2-13C2]glucose.

Recent studies in metabolic profiling have underscored the importance of the concept of a metabolic network of pathways with special functional characteristics that differ from those of simple reaction sequences. The characterization of metabolic functions requires the simultaneous measurement of substrate fluxes of interconnecting pathways. Here we present a novel stable isotope method by which the forward and reverse fluxes of the futile cycles of the hepatic glucose metabolic network are simultaneously determined. Unlike previous radio-isotope methods, a single tracer [1,2-13C2]D-glucose and mass isotopomer analysis is used. Changes in fluxes of substrate cycles, in response to several gluconeogenic substrates, in isolated fasted hepatocytes from male Wistar rats were measured simultaneously. Incubation with these substrates resulted in a change in glucose-6-phosphatase/glucokinase and glycolytic/gluconeogenic flux ratios. Different net redistributions of intermediates in the glucose network were observed, resulting in distinct metabolic phenotypes of the fasted hepatocytes in response to each substrate condition. Our experimental observations show that the constraints of concentrations of shared intermediates, and enzyme kinetics of intersecting pathways of the metabolic network determine substrate redistribution throughout the network when it is perturbed. These results support the systems-biology notion that network analysis provides an integrated view of the physiological state. Interaction between metabolic intermediates and glycolytic/gluconeogenic pathways is a basic element of cross-talk in hepatocytes, and may explain some of the difficulties in genotype and phenotype correlation.

'Futile cycle' enzymes in the flight muscles of North American bumblebees.

In the flight muscles of European bumblebees, high activities of fructose-1,6-bisphosphatase (FbPase) relative to phosphofructokinase (PFK) have suggested a thermogenic 'futile cycle' important for regional endothermy. We find generally low activities of FbPase (0.7-19.7 units g(-1) thorax) in North American Bombus species, with the exception of Bombus rufocinctus, where activity (43.1 units g(-1) thorax) is comparable with that of European congeners. These data, taken with estimates of maximal rates of heat production by cycling, do not support a significant thermogenic role for the PFK/FbPase cycle. In agreement with earlier studies, both PFK and FbPase activities were found to scale allometrically with body size (allometric exponents -0.18 and -1.33, respectively). The cycle may serve to supplement thermogenesis or amplify glycolytic flux in rest-to-flight transitions, especially in smaller bees.

Glutamine cycling in isolated working rat heart.

To what extent does glutamine turnover keep pace with oxidative metabolism in the rat heart? To address this question, the following groups of substrates were presented to the isolated, working rat heart: 1) glucose (5 mM), insulin (40 microU/ml), and [2-13C]acetate (5 mM; high workload, n = 5); 2) pyruvate (2.5 mM) and [2-13C]acetate (5 mM; normal workload, n = 5); or 3) propionate (1 mM) and [2-13C]acetate (2.5 mM; normal workload, n = 3). In a subset of these experiments, the exchange of glutamate and glutamine was quantified by separation with ion exchange chromatography and analysis by GC-MS. There was an apparent equilibration of mass isotopomers of glutamate and glutamine after 50 min of perfusion, although the extent of equilibration was not determined. The fractional enrichment in glutamine was 31% of the enrichment of glutamate with the three different perfusates. From high-resolution nuclear magnetic resonance spectra, we found a ratio of glutamine to glutamate content of 94.1, 53.4, and 96.9%, respectively, for each experimental group. In experiments for which l-[1-13C]glutamine (5 mM) was included in the perfusate of group 2, [1-13C]glutamine was detected in the heart, but transfer of 13C from glutamine to glutamate was not detected (n = 4). We conclude that, in the perfused working heart, production of glutamine by amidation of glutamate takes place and can be detected, whereas the reverse process, generation of glutamate from glutamine, remains undetected.

Oxígeno y oxidación I: especies reactivasde oxígeno y daño oxidativo de sustratos biológicos / Oxigen and oxidation I: reactive oxigen species and oxidative damage to biological substrates

La mayoría de los organismos eucarióticos necesitan el oxígeno para mantener una suficiente producción de energía para sobrevivir. Sin embargo, durante la utilización del oxígeno se originan especies reactivas intermedias, que resultan dañinas para los sustratos biológicos. Esto es lo que se denomina la paradoja aerobia. En el organismo humano existe un equilibrio entre estas especies reactivas de oxígeno y los sistemas de defensa antioxidante. Cuando este equilibrio se descompensa en favor de las especies reactivas de oxígeno se crea la situación de estrés oxidativo. Este desequilibrio se puede originar por una ingesta deficiente de antioxidantes naturales precedentes de la dieta o por situaciones de exposición a fuentes de especies radicales como son contaminación ambiental, estrés deportivo, enfermedades inflamatorias crónicas, radiaciones, etc. En esta revisión se describen la reactividad y la generación en situaciones fisiológicas de las distintas especies reactivas de oxígeno (el radical superóxido, el peróxido de hidrógeno, el oxígeno en estado triplete o excitado y el radical hidroxilo).Además, se estudia el mecanismo de oxidación de los sustratos biológicos (lípidos, proteínas y ácidos nucleicos) (AU)

Effects of submaximal intensity cycle ergometry for one hour on substrate utilisation in trained prepubertal boys versus trained adults.

AIM: Substrate utilisation during exercise might be different in trained prepubertal boys compared to trained adults, so dietary advice usually given to endurance trained adults may need to be adapted for endurance trained children. EXPERIMENTAL DESIGN: subjects pedalled for 1 hour on an ergocycle at 40% or 60% of Wmax (maximal aerobic power). PARTICIPANTS: 14 boys and 13 adults active in endurance sport (swimming). MEASURES: pulmonary respiratory gas-exchange ratio [RER = VCO(2)/VO(2)], used as the equivalent of the non protein respiratory quotient (RQ), was measured at rest, at the 15(th), 30(th), 45(thv and 60(th) min of exercise in order to calculate energy expenditure. RESULTS: Relative resting energy expenditure was significantly higher in boys than in adults. During exercise, energy expenditure (EE) was significantly lower in children than in adults (p<0.001), whereas fat-free mass relative EE was only influenced by intensity. Relative EE from carbohydrates (EE(CHO)) was lower in children compared to adults, even if the highest intensity involves a higher EE(CHO) in both groups (p<0.05). Boys oxidised more lipid at 40% of Wmax than 60% of Wmax or adults at either intensity. CHO utilisation was significantly increased at 60% vs 40% of Wmax, yet lower in boys than in men (p<0.01). Lipids' use, in g x min(-1) x kg-1)FFM, was significantly higher in boys than in men at 40% of Wmax (p<0.01). CONCLUSION: Trained children, at rest, had greater fat-free mass energy expenditure than adults, which may be linked to growth processes that remain unclear. During exercise, in boys, the main observation was the increase in CHO dependence relative with the intensity. Thus, it appears that CHO feeding is as important in endurance-trained boys as in endurance-trained adults, especially when exercise intensity approaches that of competition or training sessions.

Accelerated substrate cycling: a new energy-wasting role for leptin in vivo.

Simultaneous lipolysis and reesterification form the triacylglycerol/fatty acid (TAG/FA) cycle, a substrate cycle commonly used for thermogenesis. Its rate was measured in vivo by indirect calorimetry and continuous infusion of [2-(3)H]glycerol and [1-(14)C]palmitate, after injection of leptin or vehicle saline in rabbits. Leptin stimulated in vivo lipolysis from 9.66 +/- 0.62 to 14.78 +/- 0.93 micromol x kg(-1) x min(-1), the rate of appearance of FA from 20.69 +/- 2.14 to 29.03 +/- 3.03 micromol x kg(-1) x min(-1), and TAG/FA cycling from 24.82 +/- 1.73 to 37.09 +/- 2.49 micromol FA x kg(-1) x min(-1). This large increase in total cycling was caused by an 85% rise in primary cycling (reesterification without transit in the circulation) and accounted for 14% of the difference in metabolic rate between the controls and the leptin-treated animals. This study shows that leptin causes a strong activation of TAG/FA cycling, lipolysis, and FA oxidation, shifting fuel preference from carbohydrates to lipids. Therefore, the acceleration of substrate cycling is a new mechanism triggered by leptin to increase metabolic rate, besides the known induction of uncoupling proteins.

Regulation of the futile cycle of fructose phosphate in sea mussel.

Carbohydrate metabolism in mussels shows two phases separated seasonally. During summer and linked to food supply, carbohydrates, mainly glycogen, are accumulated in the mantle tissue. During winter, mantle glycogen decreases concomitantly with an increase in triglyceride synthesis. In spring, after spawning, the animals go in to metabolic rest until the beginning of a new cycle. This cycle is regulated by the futile cycle of fructose phosphate that implicates PFK-1 and FBPase-1 activities. These enzymes and the bifunctional PFK-2/FBPase-2 that regulates the Fru-2,6-P2 levels, are seasonally modulated by covalent phosphorylation/dephosphorylation mechanisms, as a response to unknown factors. The futile cycle of the fructose phosphates also controls the transition from physiological aerobiosis to hypoxia. The process is independent of the phosphorylation state. In this sense, a pH decrease triggers a small Pasteur effect during the first 24 h of aerial exposure. Variations in the concentration of Fru-2,6-P2 and AMP are the sole factor responsible for this effect. Longer periods of hypoxia induce a metabolic depression characterized by a decrease in Fru-2,6-P2 which is hydrolyzed by drop in the pH. In this review, the authors speculate on the two regulation processes.

Energy-wasteful total Ca(2+) handling underlies increased O(2) cost of contractility in canine stunned heart.

Postischemic myocardial stunning halved left ventricular contractility [end-systolic maximum elastance (E(max))] and doubled the O(2) cost of E(max) in excised cross-circulated canine heart. We hypothesized that this increased O(2) cost derived from energy-wasteful myocardial Ca(2+) handling consisting of a decreased internal Ca(2+) recirculation, some futile Ca(2+) cycling, and a depressed Ca(2+) reactivity of E(max). We first calculated the internal Ca(2+) recirculation fraction (RF) from the exponential decay component of postextrasystolic potentiation. Stunning significantly accelerated the decay and decreased RF from 0.63 to 0. 43 on average. We then combined the decreased RF with the halved E(max) and its doubled O(2) cost and analyzed total Ca(2+) handling using our recently developed integrative method. We found a decreased total Ca(2+) transport and a considerable shift of the relation between futile Ca(2+) cycling and Ca(2+) reactivity in an energy-wasteful direction in the stunned heart. These changes in total Ca(2+) handling reasonably account for the doubled O(2) cost of E(max) in stunning, supporting the hypothesis.