Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 42 min 46 sec ago

metabolomics; +48 new citations

Tue, 23/02/2021 - 13:22
48 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2021/02/23PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Metformin attenuates post-epidural fibrosis by inhibiting the TGF-β1/Smad3 and HMGB1/TLR4 signaling pathways.

Tue, 23/02/2021 - 10:21
Related Articles Metformin attenuates post-epidural fibrosis by inhibiting the TGF-β1/Smad3 and HMGB1/TLR4 signaling pathways. J Cell Mol Med. 2021 Feb 21;: Authors: Song Z, Wu T, Sun J, Wang H, Hua F, Nicolas YSM, Kc R, Chen K, Jin Z, Liu J, Zhang M Abstract Excessive post-epidural fibrosis is a common cause of recurrent back pain after spinal surgery. Though various treatment methods have been conducted, the safe and effective drug for alleviating post-epidural fibrosis remains largely unknown. Metformin, a medicine used in the treatment of type 2 diabetes, has been noted to relieve fibrosis in various organs. In the present study, we aimed to explore the roles and mechanisms of metformin in scar formation in a mouse model of laminectomy. Post-epidural fibrosis developed in a mouse model of laminectomy by spinous process and the T12-L2 vertebral plate with a rongeur. With the administration of metformin, post-epidural fibrosis was reduced, accompanied with decreased collagen and fibronectin in the scar tissues. Mechanistically, metformin decreased fibronectin and collagen deposition in fibroblast cells, and this effect was dependent on the HMGB1/TLR4 and TGF-β1/Smad3 signalling pathways. In addition, metformin influenced the metabolomics of the fibroblast cells. Taken together, our study suggests that metformin may be a potential option to mitigate epidural fibrosis after laminectomy. PMID: 33611840 [PubMed - as supplied by publisher]

Comparative physiological and metabolic analyses of two Italian ryegrass (Lolium multiflorum) cultivars with contrasting salinity tolerance.

Tue, 23/02/2021 - 10:21
Related Articles Comparative physiological and metabolic analyses of two Italian ryegrass (Lolium multiflorum) cultivars with contrasting salinity tolerance. Physiol Plant. 2021 Feb 21;: Authors: Feng Q, Song S, Yang Y, Amee M, Chen L, Xie Y Abstract Italian ryegrass (Lolium multiflorum) is a widely cultivated forage with high nutritional value and good palatability. Salinity, however, is a negative factor to lessen output and quality in Italian ryegrass. The aim of this study was to elucidate the salt tolerance mechanism of two Italian ryegrass cultivars, 'Abundant' and 'Angus'. Under hydroponic conditions, two cultivars of Italian ryegrass with different salt tolerance were exposed to 0 and 300 mM NaCl solution for one week, respectively. The results showed that salt stress decreased relative growth rate and relative water content, especially in salt-sensitive 'Angus'. The salt-tolerant 'Abundant' cultivar alleviated reactive oxygen species (ROS) induced burst and cell damage. However, 'Angus' exhibited a greater activity of superoxide dismutase (SOD) and peroxidase (POD) than 'Abundant'. Additionally, 'Abundant' exhibited higher photosynthetic efficiency than 'Angus' under salt stress condition. Salt treatment significantly increased the Na/K, Na/Mg and Na/Ca ratios in the leaves and roots of both cultivars, with a pronounced effect in salt-sensitive 'Angus'. The metabolite analysis of leaf polar extracts revealed 41 salt responsive metabolites in both cultivars, mainly consisting of amino acids, organic acids, fatty acids, and sugars. Following exposure to salt conditions, salt-sensitive 'Angus' had a higher level of metabolites and more uniquely up-regulated metabolites were detected. Based on these findings, we conclude that the 'Abundant' cultivar emerged as a favorite in saline-alkali soil, while the 'Angus' cultivar is suitable for planting in normal soil. It appears that the high salt tolerance of 'Abundant' is partly to prevent the plant from ionic homeostasis disruption. This article is protected by copyright. All rights reserved. PMID: 33611798 [PubMed - as supplied by publisher]

Wood profiling by non-targeted high-resolution mass spectrometry: Part 1, Metabolite profiling in Cedrela wood for the determination of the geographical origin.

Tue, 23/02/2021 - 10:21
Related Articles Wood profiling by non-targeted high-resolution mass spectrometry: Part 1, Metabolite profiling in Cedrela wood for the determination of the geographical origin. J Chromatogr A. 2021 Feb 12;1641:461993 Authors: Creydt M, Ludwig L, Köhl M, Fromm J, Fischer M Abstract The determination of the geographical origin of wood can be highly relevant for several reasons: On the one hand, it can help to prevent illegal logging and timber trade, on the other hand, it is of special interest for archaeological artefacts made of wood, as well as for a variety of biological questions. For this reason, different extraction methods were first tested for the analysis of polar and non-polar metabolites using liquid chromatography coupled electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). A two-phase extraction with chloroform, methanol and water proved to be particularly successful. Subsequently, cedrela (Cedrela odorata) samples from South America were measured to distinguish geographic origin. Using multivariate data analysis, numerous origin-dependent differences could be extracted. The identification of the marker substances indicated that several metabolic pathways were affected by the geographical influences, some of them probably indicating pest infections. PMID: 33611119 [PubMed - as supplied by publisher]

Evaluation of a nanoflow interface based on the triple-tube coaxial sheath-flow sprayer for capillary electrophoresis-mass spectrometry coupling in metabolomics.

Tue, 23/02/2021 - 10:21
Related Articles Evaluation of a nanoflow interface based on the triple-tube coaxial sheath-flow sprayer for capillary electrophoresis-mass spectrometry coupling in metabolomics. J Chromatogr A. 2021 Feb 09;1641:461982 Authors: Ferré S, Drouin N, González-Ruiz V, Rudaz S Abstract The performance of an original CE-MS interface that allows the in-axis positioning of the electrospray with respect to the MS inlet was evaluated. The variations in the geometrical alignment of this configuration in the absence of a nebulizing gas afforded a significant reduction in the sheath-liquid flow rate from 3 µL/min to as low as 300 nL/min. The sheath liquid and BGE were respectively composed of H2O-iPrOHCH3COOH 50:50:1 (v/v/v) and 10% acetic acid (pH 2.2). A significant gain in sensitivity was obtained, and it was correlated to the effective mobility of the analytes. Compounds with low mobility values showed a greater sensitivity gain. Special attention was paid to the detection of proteinogenic amino acids. Linear response functions were obtained from 15 ng/mL to 500 ng/mL. The limits of quantification, as low as 34.3 ng/mL, were improved by a factor of up to six compared to the conventional configuration. The in-axis setup was ultimately applied to the absolute quantification of four important amino acids, alanine, tyrosine, methionine and valine, in standard reference material (NIST plasma). The accuracies ranged from 78 to 113%, thus demonstrating the potential of this configuration for metabolomics. PMID: 33611118 [PubMed - as supplied by publisher]

Identification of the metabolites regulated in soybean-Rhizobia symbiosis through solid phase microextraction coupled with LC-MS.

Tue, 23/02/2021 - 10:21
Related Articles Identification of the metabolites regulated in soybean-Rhizobia symbiosis through solid phase microextraction coupled with LC-MS. J Chromatogr A. 2021 Jan 30;1641:461934 Authors: Onat B, Rosales-Solano H, Ferrier L, Pawliszyn J Abstract Legumes provide one of the uniquely nutrient-rich food sources to the population and are one of the primary field crops that play significant roles in agricultural sustainability. Inoculation with Bradyrhizobium japonicum is necessary for the high yield of leguminous crops, i.e. soybean. Nodulation of soybean by Bradyrhizobium japonicum is a complex process that is essential for cultivation of these legumes and external stress factors, such as draught and soil acidity, that influence the nodulation and crop yield. Alterations in the nodule metabolites are known to identify the type of stress that mitigates nodulation and lowers crop yield. Current techniques aimed at understanding the metabolic activities in the symbiont, such as in the case of metabolic regulations in varying nodule growth phases, rely on exhaustive techniques based on the removal of nodules or other plant tissue. Aiming to capture a more in-depth, accurate profile of this system without quenching the metabolic activity in the nodules, or removing the nodules, a workflow was prepared for the metabolite sampling through in vivo solid phase microextraction in thin film format (TF-SPME). This technique was followed by LC-QTOF-MS instrumental analysis with subsequent metabolite annotation and reference standard validation. Our approach is unique in terms of eliminating the effects that arise due to analyte partition coefficients. We show that the symbiont undergoes metabolic regulations throughout the cultivation period, displaying the efficacy of TF-SPME as a non-exhaustive sampling method that can be used as a tool to investigate the metabolic alterations in nodules. These alterations would potentially fingerprint the environmental effects on soybean yield. PMID: 33611117 [PubMed - as supplied by publisher]

Metabolomics analysis reveals the effect of copper on autophagy in myocardia of pigs.

Tue, 23/02/2021 - 10:21
Related Articles Metabolomics analysis reveals the effect of copper on autophagy in myocardia of pigs. Ecotoxicol Environ Saf. 2021 Feb 18;213:112040 Authors: Li Q, Liao J, Lei C, Shi J, Zhang H, Han Q, Guo J, Hu L, Li Y, Pan J, Tang Z Abstract Among different synthetic compounds copper (Cu) is persistently and frequently used as growth promoter, antibacterial, antifungal and antiparasitic agent and has become common environmental pollutant. Therefore, this study explores the cardio-toxic effects of control group (10 mg/kg bw Cu) and treatment group (125 and 250 mg/kg bw Cu), and it association with process of autophagy and metabolomics in myocardium of pigs kept in three different experimental treatments for a period of 80 days. The results of serum biochemical parameters showed a significantly increase in creatinine kinase (CK), creatine kinase-MB (CK-MB), high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol (LDL-C) and aspartate aminotransferase (AST) in pigs exposed to 125 mg/kg bw and 250 mg/kg bw Cu. Meanwhile, the severe structural abnormalities in cardiomyocytes were found when exposed to 250 mg/kg Cu at day 80. In addition, the mRNA and proteins (Beclin1, ATG5 and LC3II) expression levels were significantly increased and p62 was significantly decreased in cardiomyocytes exposed to 250 mg/kg Cu at day 80 of the trial. Further, UPLC-QTOF/MS technique showed that 7 metabolites were up-regulated and 37 metabolites were down-regulated in cardiomyocytes after 250 mg/kg Cu treatment, with a principal impact on the metabolic pathways including glycerophospholipid metabolism, one carbon pool by folate, fatty acid elongation and fatty acid degradation, which were related to autophagy. Overall, our study identified the autophagy processes and metabolites in metabolic pathways in Cu-induced myocardium injury, which provided useful evidence of myocardium toxicity caused by Cu exposure via metabolomics and multiple bioanalytic methods. PMID: 33610943 [PubMed - as supplied by publisher]

M. tuberculosis curli pili (MTP) is associated with alterations in carbon, fatty acid and amino acid metabolism in a THP-1 macrophage infection model.

Tue, 23/02/2021 - 10:21
Related Articles M. tuberculosis curli pili (MTP) is associated with alterations in carbon, fatty acid and amino acid metabolism in a THP-1 macrophage infection model. Microb Pathog. 2021 Feb 18;:104806 Authors: Ashokcoomar S, Loots DT, Beukes D, van Reenen M, Pillay B, Pillay M Abstract The initial host-pathogen interaction is crucial for the establishment of infection. An improved understanding of the pathophysiology of Mycobacterium tuberculosis (M. tuberculosis) during macrophage infection can aid the development of intervention therapeutics against tuberculosis. M. tuberculosis curli pili (MTP) is a surface located adhesin, involved in the first point-of-contact between pathogen and host. This study aimed to better understand the role of MTP in modulating the intertwined metabolic pathways of M. tuberculosis and its THP-1 macrophage host. Metabolites were extracted from pelleted wet cell mass of THP-1 macrophages infected with M. tuberculosis wild-type V9124 (WT), Δmtp-deletion mutant and the mtp-complemented strains, respectively, via a whole metabolome extraction method using a 1:3:1 ratio of chloroform:methanol:water. Metabolites were detected by two-dimensional gas chromatography time-of-flight mass spectrometry. Significant metabolites were determined through univariate and multivariate statistical tests and online pathway databases. Relative to the WT, a total of nine and ten metabolites were significantly different in the Δmtp and complement strains, respectively. All nine significant metabolites were found in elevated levels in the Δmtp relative to the WT. Additionally, of the ten significant metabolites, eight were detected in lower levels and two were detected in higher levels in the complement relative to the WT. The absence of the MTP adhesin resulted in reduced virulence of M. tuberculosis leading to alterations in metabolites involved in carbon, fatty acid and amino acid metabolism during macrophage infection, suggesting that MTP plays an important role in the modulation of host metabolic activity. These findings support the prominent role of the MTP adhesin as a virulence factor as well as a promising biomarker for possible diagnostic and therapeutic intervention. PMID: 33610716 [PubMed - as supplied by publisher]

Metabolism response of grazing yak to dietary concentrate supplementation in warm season.

Tue, 23/02/2021 - 10:21
Related Articles Metabolism response of grazing yak to dietary concentrate supplementation in warm season. Animal. 2021 Feb 17;:100175 Authors: Xue BC, Zhang JX, Wang ZS, Wang LZ, Peng QH, Da LC, Bao SK, Kong XY, Xue B Abstract Supplementary feeding has a significant effect on the growth performance of grazing yaks. However, as far as is known, little information is available concerning how energy or protein feed supplementation affects the serum metabolome of grazing yaks during the warm season. We investigated the effects of supplementation with two different concentrates on the serum metabolome in grazing yaks using nuclear magnetic resonance spectroscopy in conjunction with multivariate data analysis. Twenty-four 2-year-old female yaks (133.04 ± 6.52 kg BW) were randomly divided into three groups and fed three different regimes (n = 8 per group): (1) grazing plus hull-less barley (HLB) supplementation, (2) grazing plus rapeseed meal (RSM) supplementation, and (3) grazing without supplementation. Both HLB and RSM supplementation significantly increased the average daily gain (ADG), and ADG under HLB supplementation was 11.9% higher (P < 0.05) than that of the RSM group. Supplementation markedly altered glucose, lipid, and protein metabolism, with the difference manifested as increased levels of some amino acids, acetyl-glycoproteins, low-density lipoproteins, and very low-density lipoproteins . Furthermore, the levels of 3-hydroxybutyrate, acetoacetate, and lactate metabolism were decreased. Serum metabolite changes in yaks in the HLB supplementation treatment differed from those in the RSM supplementation treatment; the difference was primarily manifested in lipid- and protein-related metabolites. We conclude that both the energy supplementation (HLB) and the protein supplementation (RSM) could remarkably promote the growth of yak heifers during the warm season, and the effect of energy supplementation was superior. Supplementary feeding changed the serum metabolite levels of yak heifers, indicating that such feeding could improve glucose's energy-supply efficiency and increase the metabolic intensity of lipids and proteins. Supplementation of yaks with HLB was more efficient in the promotion of yak glucose and protein anabolism compared to supplementation with RSM, while having a lesser effect on lipid metabolism. PMID: 33610519 [PubMed - as supplied by publisher]

Heat treatment of bovine colostrum: effects on colostrum metabolome and serum metabolome of calves.

Tue, 23/02/2021 - 10:21
Related Articles Heat treatment of bovine colostrum: effects on colostrum metabolome and serum metabolome of calves. Animal. 2021 Feb 17;:100180 Authors: Xu W, Mann S, Curone G, Kenéz Á Abstract Bovine colostrum is important for neonates' health due to its nutritive and non-nutritive components. Heat treatment of colostrum is a well-established management tool, but it may influence colostrum components and affect the health status of calves. In our previous studies, we had shown that colostrum proteome and serum proteome of calves were altered by heat treatment to different degrees. Our objectives in this study were to investigate the effects of heat treatment on colostrum metabolome and the effect of feeding heat-treated colostrum on the serum metabolome of newborn calves. Further, the changes in serum metabolome from before to after colostrum feeding were characterized. Newborn Holstein female calves (n = 10) were randomized within pairs and fed heat-treated (n = 5; 60 °C, 60 min) or raw (n = 5) colostrum at 8.5% of birth BW by esophageal feeder within 1 h of birth. After a single colostrum feeding, calves were not fed until after the 8 h time point. Blood samples were taken immediately prior to feeding (0 h) and 8 h after feeding. The colostrum and serum metabolome were first analyzed using reverse-phase chromatography and tandem MS, and serum metabolome was then further analyzed using hydrophilic interaction chromatography and tandem MS. In colostrum metabolome, 458 features were identified and 328 were annotated and a trend of separation between raw and heat-treated colostrum could be observed through multivariate analysis. In serum metabolome, 3 360 features were identified and 1 439 were annotated, but no trend of separation was observed between the two groups of calves fed raw colostrum vs. heat-treated colostrum. The serum metabolome presented substantial differences comparing before (0 h) and after colostrum feeding (8 h); in particular, a tripeptide, β-homovaline-β-homoalanine-β-homoleucine, and 1-(2-acetamido-2-deoxy-α-d-glucopyranosyl)-1D-myo-inositol had higher concentrations after colostrum feeding than before, along with other metabolites that were not fully annotated. Based on a relatively small sample size, our findings point to the effect of heat treatment on the change of colostrum metabolome, but not on the change of serum metabolome of calves fed raw colostrum vs. heat-treated colostrum. Further studies using larger sample size and complementary analytical techniques are warranted to further explore potential heat treatment-induced alterations in colostrum metabolome. PMID: 33610513 [PubMed - as supplied by publisher]

Relaxometric learning: a pattern recognition method for T2 relaxation curves based on machine learning supported by an analytical framework.

Tue, 23/02/2021 - 10:21
Related Articles Relaxometric learning: a pattern recognition method for T2 relaxation curves based on machine learning supported by an analytical framework. BMC Chem. 2021 Feb 20;15(1):13 Authors: Date Y, Wei F, Tsuboi Y, Ito K, Sakata K, Kikuchi J Abstract Nuclear magnetic resonance (NMR)-based relaxometry is widely used in various fields of research because of its advantages such as simple sample preparation, easy handling, and relatively low cost compared with metabolomics approaches. However, there have been no reports on the application of the T2 relaxation curves in metabolomics studies involving the evaluation of metabolic mixtures, such as geographical origin determination and feature extraction by pattern recognition and data mining. In this study, we describe a data mining method for relaxometric data (i.e., relaxometric learning). This method is based on a machine learning algorithm supported by the analytical framework optimized for the relaxation curve analyses. In the analytical framework, we incorporated a variable optimization approach and bootstrap resampling-based matrixing to enhance the classification performance and balance the sample size between groups, respectively. The relaxometric learning enabled the extraction of features related to the physical properties of fish muscle and the determination of the geographical origin of the fish by improving the classification performance. Our results suggest that relaxometric learning is a powerful and versatile alternative to conventional metabolomics approaches for evaluating fleshiness of chemical mixtures in food and for other biological and chemical research requiring a nondestructive, cost-effective, and time-saving method. PMID: 33610164 [PubMed]

Short- and medium-term exposures of diazepam induce metabolomic alterations associated with the serotonergic, dopaminergic, adrenergic and aspartic acid neurotransmitter systems in zebrafish (Danio rerio) embryos/larvae.

Sun, 21/02/2021 - 13:01
Related Articles Short- and medium-term exposures of diazepam induce metabolomic alterations associated with the serotonergic, dopaminergic, adrenergic and aspartic acid neurotransmitter systems in zebrafish (Danio rerio) embryos/larvae. Comp Biochem Physiol Part D Genomics Proteomics. 2021 Feb 16;38:100816 Authors: Markin PA, Brito A, Moskaleva NE, Tagliaro F, Tarasov VV, La Frano MR, Savitskii MV, Appolonova SA Abstract INTRODUCTION: Diazepam is a well-known psychoactive drug widely used worldwide for the treatment of anxiety, seizures, alcohol withdrawal syndrome, muscle spasms, sleeplessness, agitation, and pre/post-operative sedation. It is part of the benzodiazepine family, substances known to primarily act by binding and enhancing gamma-aminobutyric acid (GABAA) receptors. The objective of the present work was to investigate the influence of short and medium-term diazepam exposures on neurotransmitters measured through targeted metabolomics using a zebrafish embryo model. METHODS: Short-term (2.5 h) and medium-term (96 h) exposures to diazepam were performed at drug concentrations of 0.8, 1.6, 16, and 160 μg/L. Intervention groups were compared with a vehicle control group. Each group consisted of 20 zebrafish eggs/larvae. Metabolites related with neurotransmission were determined by ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). RESULTS: Thirty-six compounds were quantified. Significantly increased tryptophan and serotonin concentrations were found in the intervention groups receiving higher doses of diazepam in 2.5 h exposure (p < 0.05 control versus intervention groups). Tyrosine concentrations were higher (p < 0.05) at higher concentrations in 2.5 h exposure, but lower (p < 0.05) at higher concentrations in 96 h exposure. Both phenylalanine and aspartic acid concentrations were higher (p < 0.05) at higher doses in 2.5 h and 96 h exposure. CONCLUSIONS: Short- and medium-term exposures to diazepam induce dose- and time-dependent metabolomic alterations associated with the serotonergic, dopaminergic/adrenergic, and aspartic acid neurotransmitter systems in zebrafish. PMID: 33610025 [PubMed - as supplied by publisher]

Tissue-based metabolomics reveals metabolic biomarkers and potential therapeutic targets for esophageal squamous cell carcinoma.

Sun, 21/02/2021 - 13:01
Related Articles Tissue-based metabolomics reveals metabolic biomarkers and potential therapeutic targets for esophageal squamous cell carcinoma. J Pharm Biomed Anal. 2021 Feb 05;197:113937 Authors: Chen Z, Gao Y, Huang X, Yao Y, Chen K, Zeng S, Mao W Abstract Prognosis for esophageal squamous cell carcinoma (ESCC) is poor, so it is essential to develop a more complete understanding of the disease. The purpose of this study was to explore metabolic biomarkers and potential therapeutic targets for ESCC. An ultra-high-performance liquid chromatography coupled with high resolution mass (UPLC/MS)-based metabolomic analysis was performed in 141 ESCC cancerous tissue samples and 70 non-cancerous counterparts. The results showed that 41 differential metabolites were annotated in the training set, and 37 were validated in the test set. Single-metabolite-based receiver operating characteristic (ROC) curves as well as metabolite-based machine learning models, including Partial Least Squares (PLS), Support Vector Machine (SVM), and Random Forest (RF), were investigated for cancerous and non-cancerous tissue classification. Six most prevalent diagnostic metabolites-adenylsuccinic acid, UDP-GalNAc, maleylacetoacetic acid, hydroxyphenylacetylglycine, galactose, and kynurenine-showed testing predictive accuracies of 0.89, 0.95, 0.97, 0.89, 0.84, and 0.84, respectively. Moreover, the metabolite-based models (PLS, SVM, and RF) had testing predictive accuracies of 0.95, 0.95, and 1.00, respectively. Kaplan-Meier survival analysis and Cox proportional hazards regression analysis demonstrated that 2-hydroxymyristoylcarnitine (HR: 0.55, 95 % CI: 0.32 to 0.92), 3-hydroxyhexadecanoylcarnitine (HR: 0.49, 95 % CI: 0.29 to 0.83), and 2,3-Dinor-TXB1 (HR: 0.56, 95 % CI: 0.33 to 0.95) to be significantly associated with OS. Based on the observation of accumulation in amino acids, immunohistochemistry (IHC) staining revealed that the amino acid transporters SLC7A5/LAT1, SLC1A5/ASCT2, and SLC16A10/MCT10 were up-regulated in ESCC cancerous tissues when compared to non-cancerous equivalents. Consistently, the same panel of amino acids were downregulated in cells with SLC1A5 knockdown. Herein, it is concluded that this study not only identified several metabolites with diagnostic and/or prognostic value, but also provided accurate metabolite-based prediction models for ESCC tissue classification. Furthermore, the three up-regulated amino acid transporters were identified as potential therapeutic targets for ESCC, especially SLC1A5. PMID: 33609949 [PubMed - as supplied by publisher]

Metabolic pathways of Chlorella sp. cells induced by exogenous spermidine against nitric oxide damage from coal-fired flue gas.

Sun, 21/02/2021 - 13:01
Related Articles Metabolic pathways of Chlorella sp. cells induced by exogenous spermidine against nitric oxide damage from coal-fired flue gas. Bioresour Technol. 2021 Feb 11;328:124827 Authors: Wang Z, Cheng J, Zhang X, Chen L, Liu J Abstract To protect microalgae that are used for photosynthetic CO2 fixation against high NO concentrations from coal-fired flue gas, 500 μM exogenous spermidine was added into Chlorella sp. solution resulting in an elevation of biomass yield by 30.5% under 327 ppm NO. Metabolomics, proteomics and enzyme activities were analyzed, revealing three effects of spermidine on Chlorella sp. resistance to NO stress. First, spermidine induced NO fixation in amino acids and their metabolites, mainly in form of 5-oxoproline (1.51-fold), which occurred through intracellular conversion reactions between citrulline and arginine. Accordingly, cellular respiration was strengthened along with a weakened NO inhibition, which enhanced active transport with ATP consumption. Second, spermidine guarded Chlorella sp. against peroxidation damage by improving activity of antioxidant enzymes. Finally, it protected the photosynthetic system of Chlorella sp. by increasing abundance of related enzymes to enhance carbon fixation. Thus exogenous spermidine improved biomass production against NO environment. PMID: 33609886 [PubMed - as supplied by publisher]

The elucidation of the biodegradation of nitrobenzene and p-nitrophenol of nitroreductase from Antarctic psychrophile Psychrobacter sp. ANT206 under low temperature.

Sun, 21/02/2021 - 13:01
Related Articles The elucidation of the biodegradation of nitrobenzene and p-nitrophenol of nitroreductase from Antarctic psychrophile Psychrobacter sp. ANT206 under low temperature. J Hazard Mater. 2021 Feb 11;413:125377 Authors: Wang Y, Hou Y, Wang Q, Wang Y Abstract Psychrobacter is one important typical strain in the Antarctic environment. In our previous study, Psychrobacter sp. ANT206 from Antarctica with novel cold-adapted nitroreductase (PsNTR) could biodegrade nitrobenzene and p-nitrophenol in low temperature environment. In this study, the in-frame deletion mutant of psntr (Δpsntr-ANT206) that displayed well genetic stability and kanamycin resistance stability was constructed using allelic replacement method. Additionally, Δpsntr-ANT206 was more sensitive to nitrobenzene and p-nitrophenol in the comparison of heat and hyperosmolarity, suggesting that psntr gene participated in the regulation of the tolerance against nitro-aromatic compounds (NACs). Further analysis was conducted by integrated gas chromatography-mass spectrometry (GC-MS), and several metabolites were identified. Among them, ethylbenzene, L-Alanine, citric acid, aniline, 4-aminophenol and other metabolites were different between the wild-type strain and Δpsntr-ANT206 under nitrobenzene and p-nitrophenol stress at different time periods under low temperature, respectively. These data could increase the knowledge of the construction of deletion mutant strains and biodegradation mechanism of NACs of typical strains Psychrobacter from Antarctica, which would also provide the basis of the molecular technique on the regulation of bioremediation of the contaminants under low temperature in the future. PMID: 33609870 [PubMed - as supplied by publisher]

Metabolite profiling, histological and oxidative stress responses in the grey mullet, Mugil cephalus exposed to the environmentally relevant concentrations of the heavy metal, Pb (NO3)2.

Sun, 21/02/2021 - 13:01
Related Articles Metabolite profiling, histological and oxidative stress responses in the grey mullet, Mugil cephalus exposed to the environmentally relevant concentrations of the heavy metal, Pb (NO3)2. Comp Biochem Physiol C Toxicol Pharmacol. 2021 Feb 17;:109004 Authors: Hajirezaee S, Ajdari A, Azhang B Abstract In this study, a metabolomics approach was applied to investigate the metabolic responses of grey mullet, Mugil cephalus to toxicity induced by heavy metal, Pb (NO3)2. In addition, the study was followed by assessing the peroxidation index and histology of liver as supplementary data. Pb (NO3)2 exposure affected the plasma metabolome, especially four group metabolites including amino acids, methylated metabolites, energetic metabolites and citric acid intermediates. Pb (NO3)2 in medium and high concentrations (15 and 25 μg/l) increased the levels of plasma amino acids compared to control (P < 0.01). In contrast, Pb (NO3)2 decreased the plasma levels of methylated metabolites (P < 0.01). The ketogenic metabolites and glycerol levels significantly elevated in fish exposed to 25 μg/l Pb (NO3)2 (P < 0.01). The plasma glucose levels increased in treatment, 5 μg/l Pb (NO3)2 and after a decline in treatment 15 μg/l Pb (NO3)2 elevated again in treatment 25 μg/l Pb (NO3)2 (P < 0.01).The plasma levels of lactate significantly increased in fish exposed to 5 and 15 μg/l Pb (NO3)2 and then declined to initial levels in treatment, 25 μg/l Pb (NO3)2 (P < 0.01). The plasma levels of TCA cycle intermediates significantly elevated in treatments 15 and 25 μg/l Pb (NO3)2 (P < 0.01). As a biomarker of oxidative stress, the plasma levels of malondialdehyde (MDA) showed significant increases in Pb (NO3)2 exposed fish (P < 0.01). During exposure period, wide ranges of liver tissue damages were also observed in Pb (NO3)2 exposed fish. In conclusion, exposure to Pb (NO3)2 affected the metabolome content of blood in grey mullet, mainly through inducing the biochemical pathways related to the metabolism of the amino acids, energetic metabolites and methylated metabolites. Our results may help to understand the effects of heavy metals on fish hematology from a molecular point of view. PMID: 33609749 [PubMed - as supplied by publisher]

Serum Metabolomic Profiling Correlated with ISS and Clinical Outcome for Multiple Myeloma Patients Treated with High-dose Melphalan and Autologous Stem Cell Transplantation.

Sun, 21/02/2021 - 13:01
Related Articles Serum Metabolomic Profiling Correlated with ISS and Clinical Outcome for Multiple Myeloma Patients Treated with High-dose Melphalan and Autologous Stem Cell Transplantation. Exp Hematol. 2021 Feb 17;: Authors: Veskovski L, Andersson PO, Turesson I, Malmodin D, Pedersen A, Mellqvist UH Abstract The metabolome, which is the final down-stream global product of metabolic processes in organisms, is not sufficiently described in multiple myeloma (MM) patients. The aim of this study was, therefore, to study the serum metabolomic profile using proton nuclear magnetic resonance (1H-NMR) spectroscopy, and its relationship to clinical characteristics and patient outcome. Serum samples, which were taken at diagnosis, from 201 MM patients who underwent high-dose melphalan followed by autologous stem cell transplantation (ASCT) as the first-line therapy, were analyzed. We found that the metabolomic profile differed between patients with different MM International Staging System (ISS) stages. The profile showed increased levels of cholesterol, phospholipids, high-density lipoprotein (HDL), low-density lipoprotein (LDL), apolipoproteins A1 and A2, valine, and leucine in ISS I patients compared with ISS III patients. The metabolomic profile also differed between patients with IgA and IgG paraprotein, predominantly because of higher levels of LDL and HDL subfractions in IgA patients. The exact pathway of metabolism leading to accumulation of these metabolites is still elusive, but this study shows an area of interest for further investigation in the search for new therapy targets and prognostic markers for this disease. PMID: 33609593 [PubMed - as supplied by publisher]

LC-MS untargeted metabolomics assesses the delayed response of glufosinate treatment of transgenic glufosinate resistant (GR) buffalo grasses (Stenotaphrum secundatum L.).

Sun, 21/02/2021 - 13:01
Related Articles LC-MS untargeted metabolomics assesses the delayed response of glufosinate treatment of transgenic glufosinate resistant (GR) buffalo grasses (Stenotaphrum secundatum L.). Metabolomics. 2021 Feb 20;17(3):28 Authors: Boonchaisri S, Rochfort S, Stevenson T, Dias DA Abstract INTRODUCTION: Glufosinate resistant (GR) buffalo grasses were genetically modified to resist the broad-spectrum herbicide, glufosinate by inserting a novel pat gene into its genome. This modification results in a production of additional phosphinothricin acetyltransferase (PAT) to detoxify the deleterious effects of glufosinate. The GR grasses and its associated herbicide form a modern, weeding program, to eradicate obnoxious weeds in turf lawn without damaging the grasses at relatively low costs and labor. As with several principal crops which are genetically modified to improve agricultural traits, biosafety of the GR buffalo grasses is inevitably expected to become a public concern. For the first time, we had previously examined the metabolome of glufosinate-resistant buffalo grasses, using a GC-MS untargeted approach to assess the risk of GR as well as identify any pleotropic effects arising from the genetically modification process. In this paper, an untargeted high-resolution LC-MS (LC-HRMS) untargeted metabolomics approach was carried out to complement our previous findings with respect to GR and wild type (WT) buffalo grasses. OBJECTIVE: One of the major aims of this present work was to compare GR to WT buffalo grasses by including the detection of the secondary metabolome and determine any unprecedented metabolic changes. METHODS: Eight-week old plants of 4 GR buffalo grasses, (93-1A, 93-2B, 93-3 C and 93-5A) and 3 wild type varieties (WT 8-4A, WT 9-1B and WT 9-1B) were submerged in either 5 % v/v of glufosinate or distilled water 3 days prior to a LC-HRMS based untargeted metabolomics analysis (glufosinate-treated or control, samples, respectively). An Ultra-High-Performance Liquid Chromatography (UHPLC) system coupled to a Velos Pro Orbitrap mass spectrometer system was employed to holistically measure the primary and secondary metabolome of both GR and WT buffalo grasses either treated with or without glufosinate and subsequently apply several bioinformatic tools including the automated pathway analysis algorithm, mummichog. RESULTS: LC-HRMS untargeted based metabolomics clearly identified that the global metabolite pools of both GR and WT cultivars were highly similar, providing strong, supporting evidence of substantial equivalence between the GR and WT varieties. These findings indicate that if any associated risks to these GR grasses were somehow present, the risk would be within those acceptable ranges present in the WT. Additionally, mummichog-based pathway analysis indicated that phenylalanine metabolism and the TCA cycle were significantly impacted by glufosinate treatment in the WT cultivar. It was possible that alterations in the relative concentrations of several intermediates in these pathways were likely due to glufosinate-induced production of secondary metabolites to enhance plant defense mechanisms against herbicidal stress at the expense of primary metabolism. CONCLUSIONS: GR buffalo grasses were found to be near identical to its WT comparator based on this complementary LC-HRMS based untargeted metabolomics. Therefore, these results further support the safe use of these GR buffalo grasses with substantial evidence. Interestingly, despite protected by PAT, GR buffalo grasses still demonstrated the response to glufosinate treatment by up-regulating some secondary metabolite-related pathways. PMID: 33609206 [PubMed - as supplied by publisher]

Metabolic footprint of aging and obesity in red blood cells.

Sun, 21/02/2021 - 13:01
Related Articles Metabolic footprint of aging and obesity in red blood cells. Aging (Albany NY). 2021 Feb 19;13: Authors: Domingo-Ortí I, Lamas-Domingo R, Ciudin A, Hernández C, Herance JR, Palomino-Schätzlein M, Pineda-Lucena A Abstract Aging is a physiological process whose underlying mechanisms are still largely unknown. The study of the biochemical transformations associated with aging is crucial for understanding this process and could translate into an improvement of the quality of life of the aging population. Red blood cells (RBCs) are the most abundant cells in humans and are involved in essential functions that could undergo different alterations with age. The present study analyzed the metabolic alterations experienced by RBCs during aging, as well as the influence of obesity and gender in this process. To this end, the metabolic profile of 83 samples from healthy and obese patients was obtained by Nuclear Magnetic Resonance spectroscopy. Multivariate statistical analysis revealed differences between Age-1 (≤45) and Age-2 (>45) subgroups, as well as between BMI-1 (<30) and BMI-2 (≥30) subgroups, while no differences were associated with gender. A general decrease in the levels of amino acids was detected with age, in addition to metabolic alterations of glycolysis, the pentose phosphate pathway, nucleotide metabolism, glutathione metabolism and the Luebering-Rapoport shunt. Obesity also had an impact on the metabolomics profile of RBCs; sometimes mimicking the alterations induced by aging, while, in other cases, its influence was the opposite, suggesting these changes could counteract the adaptation of the organism to senescence. PMID: 33609087 [PubMed - as supplied by publisher]

A metabolomics approach to evaluate post-fermentation enhancement of daidzein and genistein in a green okara extract.

Sun, 21/02/2021 - 13:01
Related Articles A metabolomics approach to evaluate post-fermentation enhancement of daidzein and genistein in a green okara extract. J Sci Food Agric. 2021 Feb 19;: Authors: Gupta S, Chen WN Abstract BACKGROUND: Okara is a major agri-industrial by-product of the tofu and soymilk industries. Employing food-wastes as substrates for the green production of natural functional compounds is a recent trend that addresses the dual concepts of sustainable production and a zero-waste ecosystem. RESULTS: Extracts of unfermented okara and okara fermented with Rhizopus oligosporus were obtained using ethanol as extraction solvent, coupled with ultrasound sonication for enhanced extraction. Fermented extracts yielded significantly better results for TPC and TFC than unfermented extracts. A qualitative LCQTOF/MS analysis revealed a shift from glucoside forms to respective aglycone forms of the detected isoflavones, post fermentation. Since the aglycone forms have been associated with numerous health benefits, a quantitative HPLC analysis was performed. Fermented okara extracts had daidzein and genistein concentrations of 11.782 ± 0.325 μg/mL and 10.125 ± 1.028 μg/mL, as opposed to that of 6.7 ± 2.42 μg/mL and 4.55 ± 0.316 μg/mL in raw okara extracts respectively. Lastly, the detected isoflavones were mapped to their metabolic pathways, to understand the biochemical reactions triggered during the fermentation process. CONCLUSION: Fermented okara may be implemented as a sustainable solution for production of natural bioactive isoflavonoids genistein and daidzein. This article is protected by copyright. All rights reserved. PMID: 33608899 [PubMed - as supplied by publisher]

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