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1.
Caroline Ivanne Le Roy Luke John Mappley Roberto Marcello La Ragione Martin John Woodward Sandrine Paule Claus 《Metabolomics : Official journal of the Metabolomic Society》2016,12(10):157
Introduction
Poultry is one of the most consumed meat in the world and its related industry is always looking for ways to improve animal welfare and productivity. It is therefore essential to understand the metabolic response of the chicken to new feed formulas, various supplements, infections and treatments.Objectives
As a basis for future research investigating the impact of diet and infections on chicken’s metabolism, we established a high-resolution proton nuclear magnetic resonance (NMR)-based metabolic atlas of the healthy chicken (Gallus gallus).Methods
Metabolic extractions were performed prior to 1H-NMR and 2D NMR spectra acquisition on twelve biological matrices: liver, kidney, spleen, plasma, egg yolk and white, colon, caecum, faecal water, ileum, pectoral muscle and brain of 6 chickens. Metabolic profiles were then exhaustively characterized.Results
Nearly 80 metabolites were identified. A cross-comparison of these matrices was performed to determine metabolic variations between and within each section and highlighted that only eight core metabolites were systematically found in every matrice.Conclusion
This work constitutes a database for future NMR-based metabolomic investigations in relation to avian production and health.2.
D. Clark Files Amro Ilaiwy Traci L. Parry Kevin W. Gibbs Chun Liu James R. Bain Osvaldo Delbono Michael J. Muehlbauer Monte S. Willis 《Metabolomics : Official journal of the Metabolomic Society》2016,12(8):134
Introduction
Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more clinically significant in older persons. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation.Objectives
To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice.Methods
Young (2 month), adult (6 month) and old (20 month) male C57Bl6 J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC–MS).Results
Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice.Conclusion
This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.3.
Miaomiao Cheng Peter M. Kopittke Anan Wang Peter W. G. Sale Caixian Tang 《Plant and Soil》2018,430(1-2):219-231
Background and aims
Interactions between Cd and Zn occur in soils and plants but are inconsistent. This study examined how Cd/Zn interactions influence the growth of Carpobrotus rossii (Haw.) and the accumulation of Cd and Zn in plants.Methods
Plants were grown in nutrient solutions containing 5–100 μM Zn and 0, 5 or 15 μM Cd. Plant growth and tissue concentrations were measured, and the speciation of Zn within the plant tissues determined using synchrotron-based X-ray absorption spectroscopy.Results
There was an additive negative interaction between Cd and Zn on root growth. Only the highest level of Zn (100 μM) decreased Cd concentrations in root and shoot tissues (by 40–64%), whilst 100 μM Zn enhanced Cd translocation at 5 μM Cd but decreased it at 15 μM Cd. In contrast, both 5 and 15 μM Cd decreased Zn concentrations in root and shoot tissues but increased Zn translocation by 30–90%. This interaction was not associated with changes in Zn speciation within the plants, with most Zn associated with oxalate (48–87%).Conclusions
The presence of Zn and Cd resulted in an additive negative effect on root growth, but an antagonistic pattern in their accumulation in shoots of C. rossii.4.
Objectives
To evaluate the effects of dexamethasone on the aging of mesenchymal stem cells from human gingiva using next-generation sequencing.Results
Four mRNAs were upregulated and 12 were downregulated when the results of dexamethasone at 24 h were compared with the control at 24 h. Expressions of SIRT1 and IL6 were decreased in dexamethasone at 24 h but expression of EDN1 was increased.Conclusions
Application of dexamethasone reduced the expression of SIRT1 and IL6 but enhanced the expression of EDN1 of stem cells.5.
6.
Piero L. Ipata Rossana Pesi 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):42
Background
A substrate cycle is a metabolic transformation in which a substrate A is phosphorylated to A?P at the expense of ATP (or another “high energy” compound), and A?P is converted back to A by a nucleotidase or a phosphatase. Many biochemists resisted the idea of such an ATP waste. Why a non-phosphorylated metabolite should be converted into a phosphorylated form, and converted back to its non-phosphorylated form through a “futile cycle”?Aim of review
In this Review we aim at presenting our present knowledge on the biochemical features underlying the interrelation between the muscle purine nucleotide cycle and the oxypurine cycle, and on the metabolic responses of the two cycles to increasing intensities of muscle contraction.Key scientific concepts of review
Nowadays it is widely accepted that the substrate cycles regulate many vital functions depending on the expense of large amounts of ATP, including skeletal muscle contraction, so that the expense of some extra ATP and “high energy” compounds, such as GTP and PRPP via substrate cycles, is not surprising. The Review emphasizes the strict metabolic interrelationship between the purine nucleotide cycle and the oxipurine cycle.7.
Geoffrey A. Mueller Peter M. Thompson Eugene F. DeRose Thomas M. O’Connell Robert E. London 《Metabolomics : Official journal of the Metabolomic Society》2016,12(12):187
Background
Studies on ragweed and birch pollen extracts suggested that the adenosine content is an important factor in allergic sensitization. However, exposure levels from other pollens and considerations of geographic and seasonal factors have not been evaluated.Objective
This study compared the metabolite profile of pollen species important for allergic disease, specifically measured the adenosine content, and evaluated exposure to pollen-derived adenosine.Methods
An NMR metabolomics approach was used to measure metabolite concentrations in 26 pollen extracts. Pollen count data was analyzed from five cities to model exposure.Results
A principal component analysis of the various metabolites identified by NMR showed that pollen extracts could be differentiated primarily by sugar content: glucose, fructose, sucrose, and myo-inositol. In extracts of 10 mg of pollen/ml, the adenosine was highest for grasses (45 µM) followed by trees (23 µM) and weeds (19 µM). Pollen count data showed that tree pollen was typically 5–10 times the amount of other pollens. At the daily peaks of tree, grass, and weed season the pollen-derived adenosine exposure per day is likely to be only 1.1, 0.11, and 0.12 µg, respectively. Seasonal models of pollen exposure and respiration suggest that it would be a rare event limited to tree pollen season for concentrations of pollen-derived adenosine to approach physiological levels.Conclusion
Sugar content and other metabolites may be useful in classifying pollens. Unless other factors create localized exposures that are very different from these models, pollen-derived adenosine is unlikely to be a major factor in allergic sensitization.8.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
Introduction
Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.Objectives
In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.Methods
The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.Results
A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.Conclusion
The workflow generated repeatable and informative fingerprints for robust metabolome characterization.9.
Kayoko Yoshida Chiyo K. Imamura Kanako Hara Mayumi Mochizuki Yusuke Tanigawara 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):98
Introduction
Everolimus selectively inhibits mammalian target of rapamycin complex 1 (mTORC1) and exerts an antineoplastic effect. Metabolic disturbance has emerged as a common and unique side effect of everolimus.Objectives
We used targeted metabolomic analysis to investigate the effects of everolimus on the intracellular glycometabolic pathway.Methods
Mouse skeletal muscle cells (C2C12) were exposed to everolimus for 48 h, and changes in intracellular metabolites were determined by capillary electrophoresis time-of-flight mass spectrometry. mRNA abundance, protein expression and activity were measured for enzymes involved in glycometabolism and related pathways.Results
Both extracellular and intracellular glucose levels increased with exposure to everolimus. Most intracellular glycometabolites were decreased by everolimus, including those involved in glycolysis and the pentose phosphate pathway, whereas no changes were observed in the tricarboxylic acid cycle. Everolimus suppressed mRNA expression of enzymes related to glycolysis, downstream of mTOR signaling enzymes and adenosine 5′-monophosphate protein kinases. The activity of key enzymes involved in glycolysis and the pentose phosphate pathway were decreased by everolimus. These results show that everolimus impairs glucose utilization in intracellular metabolism.Conclusions
The present metabolomic analysis indicates that everolimus impairs glucose metabolism in muscle cells by lowering the activities of glycolysis and the pentose phosphate pathway.10.
Objectives
To study the binding of pranlukast to hRKIP and its regulatory role in the Raf1/MEK/ERK signal pathway.Results
NMR and fluorescence experiments demonstrated hRKIP could bind pranlukast with a binding constant of 1016 mM?1. Residues (Y81, S109 and Y181) on the conserved ligand-binding pocket of hRKIP played a crucial role in binding pranlukast, and their mutations reduced the binding affinity more than 85 %. Furthermore, 25 μM pranlukast could up-regulate the ERK phosphorylation by about 17 %.Conclusion
Pranlukast may be used as a potential drug precursor for treating hRKIP involved diseases.11.
Liang Hu Fei Han Lin Chen Xie Peng Daiwen Chen De Wu Lianqiang Che Keying Zhang 《Genes & nutrition》2018,13(1):23
Background
Intrauterine growth-restricted (IUGR) neonates impair postnatal skeletal muscle growth. The aim of this study was to investigate whether high nutrient intake (HNI) during the suckling period could improve muscle growth and metabolic status of IUGR pigs.Methods
Twelve pairs of IUGR and normal birth weight (NBW) pigs (7 days old) were randomly assigned to adequate nutrient intake and HNI formula milk groups. Psoas major (PM) muscle sample was obtained after 21 days of rearing.Results
IUGR decreased cross-sectional areas (CSA) and myofiber numbers, activity of lactate dehydrogenase (LDH), and mRNA expression of insulin-like growth factor 1 (IGF-1), IGF-1 receptor (IGF-1R), mammalian target of rapamycin (mTOR), ribosomal protein s6 (RPS6), eukaryotic translation initiation factor 4E (eIF4E), protein expression of phosphorylated mTOR (P-mTOR), and phosphorylated protein kinase B (P-Akt) in the PM muscle of pigs. Irrespective of birth weight, HNI increased muscle weight and CSA, the concentration of RNA, and ratio of RNA to DNA, as well as ratio of LDH to β-hydroxy-acyl-CoA-dehydrogenase in the PM muscle of pigs. Furthermore, HNI increased percentages of MyHC IIb, mRNA expression of IGF-1, IGF-1R, Akt, mTOR, RPS6, and eIF4E, as well as protein expression of P-mTOR, P-Akt, P-RPS6, and P-eIF4E in the PM muscle of pigs.Conclusion
The present findings suggest that high nutrient intake during the suckling period could improve skeletal muscle growth and maturity, which is associated with increasing the expression of protein deposition-related genes and accelerating the development of glycolytic-type myofiber in pigs.12.
Xiaofan Yang Pingping Xue Xin Liu Xiang Xu Zhenbing Chen 《Cell communication and signaling : CCS》2018,16(1):97
Background
Transforming growth factor beta 1 (TGF-β1) is a classical modulator of skeletal muscle and regulates several processes, such as myogenesis, regeneration and muscle function in skeletal muscle diseases. Skeletal muscle atrophy, characterized by the loss of muscle strength and mass, is one of the pathological conditions regulated by TGF-β1, but the underlying mechanism involved in the atrophic effects of TGF-β1 is not fully understood.Methods
Mice sciatic nerve transection model was created and gastrocnemius were analysed by western blot, immunofluorescence staining and fibre diameter quantification after 2 weeks. Exogenous TGF-β1 was administrated and high-mobility group box-1 (HMGB1), autophagy were blocked by siRNA and chloroquine (CQ) respectively to explore the mechanism of the atrophic effect of TGF-β1 in denervated muscle. Similar methods were performed in C2C12 cells.Results
We found that TGF-β1 was induced in denervated muscle and it could promote atrophy of skeletal muscle both in vivo and in vitro, up-regulated HMGB1 and increased autophagy activity were also detected in denervated muscle and were further promoted by exogenous TGF-β1. The atrophic effect of TGF-β1 could be inhibited when HMGB1/autophagy pathway was blocked.Conclusions
Thus, our data revealed that TGF-β1 is a vital regulatory factor in denervated skeletal muscle in which HMGB1/ autophagy pathway mediates the atrophic effect of TGF-β1. Our findings confirmed a new pathway in denervation-induced skeletal muscle atrophy and it may be a novel therapeutic target for patients with muscle atrophy after peripheral nerve injury.13.
Yuliya V. Kuzmicheva Aleksander I. Shaposhnikov Svetlana N. Petrova Natalia M. Makarova Irina L. Tychinskaya Jan V. Puhalsky Nikolay V. Parahin Igor A. Tikhonovich Andrey A. Belimov 《Plant and Soil》2017,413(1-2):83-95
Aims
It has been increasingly recognized that only distal lower order roots turn over actively within the <2 mm fine root system of trees. This study aimed to estimate fine root production and turnover rate based on lower order fine roots and their relations to soil variables in mangroves.Methods
We conducted sequential coring in five natural mangrove forests at Dongzhai Bay, China. Annual fine root production and turnover rate were calculated based on the seasonal variations of the biomass and necromass of lower order roots or the whole fine root system.Results
Annual fine root production and turnover rate ranged between 571 and 2838 g m?2 and 1.46–5.96 yr?1, respectively, estimated with lower order roots, and they were increased by 0–30 % and reduced by 13–48 %, respectively, estimated with the whole fine root system. Annual fine root production was 1–3.5 times higher than aboveground litter production and was positively related to soil carbon, nitrogen and phosphorus concentrations. Fine root turnover rate was negatively related to soil salinity.Conclusions
Mangrove fine root turnover plays a more important role than aboveground litter production in soil C accumulation. Sites with higher soil nutrients and lower salinity favor fine root production and turnover, and thus favor soil C accumulation.14.
Objectives
To assess the effects of light intensity and quality on the growth and phycobiliproteins (PBP) accumulation in Nostoc sphaeroides Kützing (N. sphaeroides).Results
Dry weights, dry matter, protein, chlorophyll and PBP contents were higher under 90 μmol m?2 s?1 than under other intensities (both higher and lower). Phycocyanin and allophycocyanin increased with light intensity while phycoerythrin decreased. Fresh weights, protein and PBP contents increased at the highest rates under blue light. Red light resulted in higher values of dry matter, phycocyanin and chlorophyll a.Conclusion
White light at 90 μmol m?2 s?1 or blue light 30 μmol m?2 s?1 were optimal for the growth and phycobiliprotein accumulation in N. sphaeroides.15.
Background
Xanthurenic acid is an endogenous molecule produced by tryptophan degradation, produced in the cytoplasm and mitochondria. Its accumulation can be observed in aging-related diseases, e.g. senile cataract and infectious disease. We previously reported that xanthurenic acid provokes apoptosis, and now present a study of the response of mitochondria to xanthurenic acid.Results
Xanthurenic acid at 10 or 20 μM in culture media of human aortic smooth muscle cells induces translocation of the proteins Bax, Bak, Bclxs, and Bad into mitochondria. In 20 μM xanthurenic acid, Bax is also translocated to the nucleus. In isolated mitochondria xanthurenic acid leads to Bax and Bclxs oligomerization, accumulation of Ca2+, and increased oxygen consumption.Conclusion
Xanthurenic acid interacts directly with Bcl-2 family proteins, inducing mitochondrial pathways of apoptosis and impairing mitochondrial functions.16.
M. O. Versteylen M. Manca I. A. Joosen D. E. Schmidt M. Das L. Hofstra H. J. Crijns E. A. Biessen B. L. Kietselaer 《Netherlands heart journal》2016,24(12):722-729
Background
CC chemokine ligands (CCLs) are elevated during acute coronary syndrome (ACS) and correlate with secondary events. Their involvement in plaque inflammation led us to investigate whether CCL3-5-18 are linked to the extent of coronary artery disease (CAD) and prognostic for primary events during follow-up.Methods
We measured CCL3-5-18 serum concentrations in 712 patients with chest discomfort referred for cardiac CT angiography. Obstructive CAD was defined as ≥50?% stenosis. The extent of CAD was measured by calcium score and segment involvement score (number of coronary segments with any CAD, range 0–16). Patients were followed up for all-cause mortality, ACS and revascularisation, for a mean 26 ± 7 months.Results
Patients with obstructive CAD had significantly higher CCL5 (p = 0.02), and borderline significantly elevated CCL18 plasma levels as compared with patients with <50?% stenosis (p = 0.06). CCL18 levels were associated with coronary calcification (p = 0.002) and segment involvement score (p = 0.007). Corrected for traditional risk factors, only CCL5 provided independent predictive value for obstructive CAD: odds ratio (OR) 1.27 (1.02–1.59), p = 0.04. CCL5 provided independent predictive value for primary events during follow-up: OR 1.62 (1.03–2.57), p = 0.04.Conclusions
While CCL18 serum levels correlated with extent of CAD, CCL5 demonstrated an independent association with the presence of obstructive CAD, and occurrence of primary cardiac events.17.
Interactions between soil properties,soil microbes and plants in remnant-grassland and old-field areas: a reciprocal transplant approach 总被引:1,自引:0,他引:1
Background and Aims
Biological soil crusts cover about one third of the terrestrial soil surfaces in drylands, fulfilling highly important ecosystem services. Their relevance to global carbon cycling, however, is still under debate.Methods
We utilized CO2 gas exchange measurements to investigate the net photosynthetic response of combined cyanobacteria/cyanolichen-, chlorolichen- and moss-dominated biocrusts and their isolated photoautotrophic components to light, temperature, and water. The results were compared with field studies to evaluate their compatibility.Results
Different biocrust types responded similarly, being inhibited by limited and excess water, saturated by increasing light intensities, and having optimum temperatures. Cyanobacteria/cyanolichen-dominated biocrusts reached their water optimum at lowest contents (0.52–0.78 mm H2O), were saturated at highest light intensities, and had a comparably high temperature optimum at 37 °C. Chlorolichen-dominated crusts had a medium water optimum (0.75–1.15 mm H2O), medium saturating light intensities and a moderate temperature optimum of 22 °C. Moss-dominated biocrusts had the highest water optimum (1.76–2.38 mm H2O), lowest saturating light intensities, and a similar temperature optimum at 22 °C. Isolated photoautotrophs responded similar to complete crusts, only isolated moss stems revealed much lower respiration rates compared to complete crusts.Conclusions
In addition to their overall functional similarities, cyanobacteria/cyanolichen-dominated biocrusts appeared to be best adapted to predicted climate change of increasing temperatures and smaller precipitation events, followed by chlorolichen-dominated biocrusts. Moss-dominated biocrusts needed by far the largest amounts of water, thus likely being prone to anticipated climate change.18.
Kumaraswamy Naidu Chitrala Xiaoming Yang Prakash Nagarkatti Mitzi Nagarkatti 《BMC structural biology》2018,18(1):15
Background
Aryl hydrocarbon receptor (AhR) ligands may act as potential carcinogens or anti-tumor agents. Understanding how some of the residues in AhR ligand binding domain (AhRLBD) modulate their interactions with ligands would be useful in assessing their divergent roles including toxic and beneficial effects. To this end, we have analysed the nature of AhRLBD interactions with 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), 6-formylindolo[3,2-b]carbazole (FICZ), indole-3-carbinol (I3C) and its degradation product, 3,3′-diindolylmethane (DIM), Resveratrol (RES) and its analogue, Piceatannol (PTL) using molecular modeling approach followed by molecular dynamic simulations.Results
Results showed that each of the AhR ligands, TCDD, FICZ, I3C, DIM, RES and PTL affect the local and global conformations of AhRLBD.Conclusion
The data presented in this study provide a structural understanding of AhR with its ligands and set the basis for its functions in several pathways and their related diseases.19.
Shayne Mason Karin Terburgh Roan Louw 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):74
Introduction
The analysis of limited-quantity samples remains a challenge associated with mouse models, especially for multi-platform metabolomics studies. Although inherently insensitive, the highly specific characteristics of nuclear magnetic resonance (NMR) spectroscopy make it an advantageous platform for global metabolite profiling, particularly in mitochondrial disease research.Objectives
Show method equivalency between a well-established standard operating protocol (SOP) and our novel miniaturized 1H-NMR method.Method
The miniaturized method was performed in a 2 mm NMR tube on a standard 500 MHz NMR spectrometer with a 5 mm triple-resonance inverse TXI probe at room temperature.Results
Firstly, using synthetic urine spiked with low (50 µM), medium (250 µM) and high (500 µM) levels (n?=?10) of nine standards, both the SOP and miniaturized method were shown to have acceptable precision (CV?<?15%), relative accuracy (80–120%), and linearity (R2?>?0.95), except for taurine. Furthermore, statistical equivalence was shown using the two one-sided test. Secondly, pooled mouse quadriceps muscle extract was used to further confirm method equivalence (n?=?3), as well as explore the analytical dynamics of this novel approach by analyzing more-concentrated versions of samples (up to 10× concentration) to expand identification of metabolites qualitatively, with quantitative linearity. Lastly, we demonstrate the new technique’s application in a pilot metabolomics study using minute soleus muscle tissue from a mouse model of Leigh syndrome using Ndufs4 KO mice.Conclusion
We demonstrate method equivalency, supporting our novel miniaturized 1H-NMR method as a financially feasible alternative to cryoprobe technology—for limited-quantity biological samples in metabolomics studies that requires a volume one-tenth of the SOP.20.