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

Critical roles of mTORC1 signaling and metabolic reprogramming for M-CSF-mediated myelopoiesis.

Wed, 09/08/2017 - 13:31
Related Articles Critical roles of mTORC1 signaling and metabolic reprogramming for M-CSF-mediated myelopoiesis. J Exp Med. 2017 Aug 07;: Authors: Karmaus PWF, Herrada AA, Guy C, Neale G, Dhungana Y, Long L, Vogel P, Avila J, Clish CB, Chi H Abstract Myelopoiesis is necessary for the generation of mature myeloid cells during homeostatic turnover and immunological insults; however, the metabolic requirements for this process remain poorly defined. Here, we demonstrate that myelopoiesis, including monocyte and macrophage differentiation, requires mechanistic target of rapamycin complex 1 (mTORC1) signaling and anabolic metabolism. Loss of mTORC1 impaired myelopoiesis under steady state and dampened innate immune responses against Listeria monocytogenes infection. Stimulation of hematopoietic progenitors with macrophage colony-stimulating factor (M-CSF) resulted in mTORC1-dependent anabolic metabolism, which in turn promoted expression of M-CSF receptor and transcription factors PU.1 and IRF8, thereby constituting a feed-forward loop for myelopoiesis. Mechanistically, mTORC1 engaged glucose metabolism and initiated a transcriptional program involving Myc activation and sterol biosynthesis after M-CSF stimulation. Perturbation of glucose metabolism or disruption of Myc function or sterol biosynthesis impaired myeloid differentiation. Integrative metabolomic and genomic profiling further identified one-carbon metabolism as a central node in mTORC1-dependent myelopoiesis. Therefore, the interplay between mTORC1 signaling and metabolic reprogramming underlies M-CSF-induced myelopoiesis. PMID: 28784627 [PubMed - as supplied by publisher]

Mate extract as feed additive for improvement of beef quality.

Wed, 09/08/2017 - 13:31
Related Articles Mate extract as feed additive for improvement of beef quality. Food Res Int. 2017 Sep;99(Pt 1):336-347 Authors: de Zawadzki A, Arrivetti LOR, Vidal MP, Catai JR, Nassu RT, Tullio RR, Berndt A, Oliveira CR, Ferreira AG, Neves-Junior LF, Colnago LA, Skibsted LH, Cardoso DR Abstract Mate (Ilex paraguariensis A.St.-Hil.) is generally recognized as safe (GRAS status) and has a high content of alkaloids, saponins, and phenolic acids. Addition of mate extract to broilers feed has been shown to increase the oxidative stability of chicken meat, however, its effect on beef quality from animals supplemented with mate extract has not been investigated so far. Addition of extract of mate to a standard maize/soy feed at a level of 0.5, 1.0 or 1.5% w/w to the diet of feedlot for cattle resulted in increased levels of inosine monophosphate, creatine and carnosine in the fresh meat. The content of total conjugated linoleic acid increased in the meat as mate extract concentration was increased in the feed. The tendency to radical formation in meat slurries as quantified by EPR spin-trapping decreased as increasing mate extract addition to feed, especially after storage of the meat, indicating higher oxidative stability. Mate supplementation in the diet did not affect animal performance and carcass characteristics, but meat from these animals was more tender and consequently more accepted by consumers. Mate extract is shown to be a promising additive to feedlot diets for cattle to improve the oxidative stability, nutritive value and sensory quality of beef. PMID: 28784491 [PubMed - in process]

Metabolomic Identification of Subtypes of Nonalcoholic Steatohepatitis.

Wed, 09/08/2017 - 13:31
Related Articles Metabolomic Identification of Subtypes of Nonalcoholic Steatohepatitis. Gastroenterology. 2017 May;152(6):1449-1461.e7 Authors: Alonso C, Fernández-Ramos D, Varela-Rey M, Martínez-Arranz I, Navasa N, Van Liempd SM, Lavín Trueba JL, Mayo R, Ilisso CP, de Juan VG, Iruarrizaga-Lejarreta M, delaCruz-Villar L, Mincholé I, Robinson A, Crespo J, Martín-Duce A, Romero-Gómez M, Sann H, Platon J, Van Eyk J, Aspichueta P, Noureddin M, Falcón-Pérez JM, Anguita J, Aransay AM, Martínez-Chantar ML, Lu SC, Mato JM Abstract BACKGROUND & AIMS: Nonalcoholic fatty liver disease (NAFLD) is a consequence of defects in diverse metabolic pathways that involve hepatic accumulation of triglycerides. Features of these aberrations might determine whether NAFLD progresses to nonalcoholic steatohepatitis (NASH). We investigated whether the diverse defects observed in patients with NAFLD are caused by different NAFLD subtypes with specific serum metabolomic profiles, and whether these can distinguish patients with NASH from patients with simple steatosis. METHODS: We collected liver and serum from methionine adenosyltransferase 1a knockout (MAT1A-KO) mice, which have chronically low levels of hepatic S-adenosylmethionine (SAMe) and spontaneously develop steatohepatitis, as well as C57Bl/6 mice (controls); the metabolomes of all samples were determined. We also analyzed serum metabolomes of 535 patients with biopsy-proven NAFLD (353 with simple steatosis and 182 with NASH) and compared them with serum metabolomes of mice. MAT1A-KO mice were also given SAMe (30 mg/kg/day for 8 weeks); liver samples were collected and analyzed histologically for steatohepatitis. RESULTS: Livers of MAT1A-KO mice were characterized by high levels of triglycerides, diglycerides, fatty acids, ceramides, and oxidized fatty acids, as well as low levels of SAMe and downstream metabolites. There was a correlation between liver and serum metabolomes. We identified a serum metabolomic signature associated with MAT1A-KO mice that also was present in 49% of the patients; based on this signature, we identified 2 NAFLD subtypes. We identified specific panels of markers that could distinguish patients with NASH from patients with simple steatosis for each subtype of NAFLD. Administration of SAMe reduced features of steatohepatitis in MAT1A-KO mice. CONCLUSIONS: In an analysis of serum metabolomes of patients with NAFLD and MAT1A-KO mice with steatohepatitis, we identified 2 major subtypes of NAFLD and markers that differentiate steatosis from NASH in each subtype. These might be used to monitor disease progression and identify therapeutic targets for patients. PMID: 28132890 [PubMed - indexed for MEDLINE]

RP-HPLC-DAD-ESI-QTOF-MS based metabolic profiling of the potential Olea europaea by-product "wood" and its comparison with leaf counterpart.

Wed, 09/08/2017 - 13:31
Related Articles RP-HPLC-DAD-ESI-QTOF-MS based metabolic profiling of the potential Olea europaea by-product "wood" and its comparison with leaf counterpart. Phytochem Anal. 2017 May;28(3):217-229 Authors: Ammar S, Contreras MDM, Gargouri B, Segura-Carretero A, Bouaziz M Abstract INTRODUCTION: Olea europaea L. organs such as leaves, stems and roots have been associated with numerous in vivo and in vitro biological activities and used for traditional medicinal purposes. However, tree wood is an untapped resource with little information about their chemical composition. OBJECTIVE: That is why, the objective of this study is to increase the knowledge about phytochemicals from 'Chemlali' olive wood by means of mass spectrometry-based analyses. Its comparison with by-products derived from leaves was also studied. METHODOLOGY: Hydromethanol extracts from wood and leaves with stems of 'Chemlali' olive cultivar were analysed using reversed-phase (RP) high-performance liquid chromatography (HPLC) coupled to two detection systems: diode-array detection (DAD) and quadrupole time-of-flight (QTOF) mass spectrometry (MS) in negative ion mode. Tandem MS experiments were performed to establish the chemical structure of olive phytochemicals. RESULTS: A total of 85 compounds were characterised in the studied olive parts and classified as: sugars (3), organic acids (5), one phenolic aldehyde, simple phenolic acids (6), simple phenylethanoids (5), flavonoids (14), coumarins (3), caffeoyl phenylethanoid derivatives (6), iridoids (5), secoiridoids (32), and lignans (5). To our knowledge, the major part of these metabolites was not previously reported in olive tree wood, and 10 olive chemical constituents were identified for the first time in the Oleaceae family. CONCLUSION: The results presented here demonstrated the usefulness of the methodology proposed, based on RP-HPLC-DAD-ESI-QTOF-MS and MS/MS, to develop an exhaustive metabolic profiling and to recover new biologically active compounds in olive wood with pharmacologic and cosmetic potential. Copyright © 2017 John Wiley & Sons, Ltd. PMID: 28067965 [PubMed - indexed for MEDLINE]

Reverse Iontophoretic Extraction of Metabolites from Living Plants and their Identification by Ion-chromatography Coupled to High Resolution Mass Spectrometry.

Wed, 09/08/2017 - 13:31
Related Articles Reverse Iontophoretic Extraction of Metabolites from Living Plants and their Identification by Ion-chromatography Coupled to High Resolution Mass Spectrometry. Phytochem Anal. 2017 May;28(3):195-201 Authors: Sánchez MIG, McCullagh J, Guy RH, Compton RG Abstract INTRODUCTION: The identification and characterisation of cellular metabolites has now become an important strategy to obtain insight into functional plant biology. However, the extraction of metabolites for identification and analysis is challenging and, at the present time, usually requires destruction of the plant. OBJECTIVE: To detect different plant metabolites in living plants with no pre-treatment using the combination of iontophoresis and ion-chromatography with mass spectrometry detection. METHODOLOGY: In this work, the simple and non-destructive method of reverse iontophoresis has been used to extract in situ multiple plant metabolites from intact Ocimum basilicum leaves. Subsequently, the analysis of these metabolites has been performed with ion chromatography coupled directly to high resolution mass spectrometric detection (IC-MS). RESULTS: The application of reverse iontophoresis to living plant samples has avoided the need for complex pre-treatments. With this approach, no less than 24 compounds, including organic acids and sugars as well as adenosine triphosphate (ATP) were successfully detected. CONCLUSION: The research demonstrates that it is feasible to monitor, therefore, a number of important plant metabolites using a simple, relatively fast and non-destructive approach. Copyright © 2016 John Wiley & Sons, Ltd. PMID: 28029194 [PubMed - indexed for MEDLINE]

Cardioprotection and lifespan extension by the natural polyamine spermidine.

Wed, 09/08/2017 - 13:31
Related Articles Cardioprotection and lifespan extension by the natural polyamine spermidine. Nat Med. 2016 Dec;22(12):1428-1438 Authors: Eisenberg T, Abdellatif M, Schroeder S, Primessnig U, Stekovic S, Pendl T, Harger A, Schipke J, Zimmermann A, Schmidt A, Tong M, Ruckenstuhl C, Dammbrueck C, Gross AS, Herbst V, Magnes C, Trausinger G, Narath S, Meinitzer A, Hu Z, Kirsch A, Eller K, Carmona-Gutierrez D, Büttner S, Pietrocola F, Knittelfelder O, Schrepfer E, Rockenfeller P, Simonini C, Rahn A, Horsch M, Moreth K, Beckers J, Fuchs H, Gailus-Durner V, Neff F, Janik D, Rathkolb B, Rozman J, de Angelis MH, Moustafa T, Haemmerle G, Mayr M, Willeit P, von Frieling-Salewsky M, Pieske B, Scorrano L, Pieber T, Pechlaner R, Willeit J, Sigrist SJ, Linke WA, Mühlfeld C, Sadoshima J, Dengjel J, Kiechl S, Kroemer G, Sedej S, Madeo F Abstract Aging is associated with an increased risk of cardiovascular disease and death. Here we show that oral supplementation of the natural polyamine spermidine extends the lifespan of mice and exerts cardioprotective effects, reducing cardiac hypertrophy and preserving diastolic function in old mice. Spermidine feeding enhanced cardiac autophagy, mitophagy and mitochondrial respiration, and it also improved the mechano-elastical properties of cardiomyocytes in vivo, coinciding with increased titin phosphorylation and suppressed subclinical inflammation. Spermidine feeding failed to provide cardioprotection in mice that lack the autophagy-related protein Atg5 in cardiomyocytes. In Dahl salt-sensitive rats that were fed a high-salt diet, a model for hypertension-induced congestive heart failure, spermidine feeding reduced systemic blood pressure, increased titin phosphorylation and prevented cardiac hypertrophy and a decline in diastolic function, thus delaying the progression to heart failure. In humans, high levels of dietary spermidine, as assessed from food questionnaires, correlated with reduced blood pressure and a lower incidence of cardiovascular disease. Our results suggest a new and feasible strategy for protection against cardiovascular disease. PMID: 27841876 [PubMed - indexed for MEDLINE]

Branched-chain and aromatic amino acids, insulin resistance and liver specific ectopic fat storage in overweight to obese subjects.

Wed, 09/08/2017 - 13:31
Related Articles Branched-chain and aromatic amino acids, insulin resistance and liver specific ectopic fat storage in overweight to obese subjects. Nutr Metab Cardiovasc Dis. 2016 Jul;26(7):637-42 Authors: Haufe S, Witt H, Engeli S, Kaminski J, Utz W, Fuhrmann JC, Rein D, Schulz-Menger J, Luft FC, Boschmann M, Jordan J Abstract BACKGROUND & AIMS: Amino acids may interfere with insulin action, particularly in obese individuals. We hypothesized that increased circulating branched-chain and aromatic amino acids herald insulin resistance and ectopic fat storage, particularly hepatic fat accumulation. METHODS AND RESULTS: We measured fasting branched-chain and aromatic amino acids (tryptophan, tyrosine, and phenylalanine) by mass spectrometry in 111 overweight to obese subjects. We applied abdominal magnetic resonance imaging and spectroscopy to assess adipose tissue distribution and ectopic fat storage, respectively. Plasma branched-chain amino acids concentrations were related to insulin sensitivity and intrahepatic fat independent from adiposity, age and gender, but not to abdominal adipose tissue or intramyocellular fat. CONCLUSIONS: In weight stable overweight and obese individuals, branched-chain amino acid concentrations are specifically associated with hepatic fat storage and insulin resistance. PMID: 27134061 [PubMed - indexed for MEDLINE]

metabolomics; +16 new citations

Tue, 08/08/2017 - 13:15
16 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 2017/08/08PubMed 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.

Elucidating the Structure of N(1)-Acetylisoputreanine: A Novel Polyamine Catabolite in Human Urine.

Mon, 07/08/2017 - 22:00
Related Articles Elucidating the Structure of N(1)-Acetylisoputreanine: A Novel Polyamine Catabolite in Human Urine. ACS Omega. 2017 Jul 31;2(7):3921-3930 Authors: Fitzgerald BL, Mahapatra S, Farmer DK, McNeil MR, Casero RA, Belisle JT Abstract An untargeted metabolomics approach was utilized to determine urinary metabolites that could serve as small-molecule biomarkers for treatment response to standard tuberculosis treatment. However, the majority of metabolites that most accurately distinguished patient samples at the time of diagnosis from those at 1 month after the start of therapy lacked structural identification. The detection of unknown metabolite structures is a well-known limitation of untargeted metabolomics and underscores a need for continued elucidation of novel metabolite structures. In this study, we sought to define the structure of a urine metabolite with an experimentally determined mass of 202.1326 Da, classified as molecular feature (MF) 202.1326. A hypothesized structure of N(1)-acetylisoputreanine was developed for MF 202.1326 using in silico tools and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In the absence of a commercial standard, synthetic N(1)-acetylisoputreanine was generated using enzymatic and chemical syntheses, and LC-MS/MS was used to confirm the structure of MF 202.1326 as N(1)-acetylisoputreanine, a proposed terminal polyamine catabolite that had not been previously detected in biological samples. Further analysis demonstrated that N(1)-acetylisoputreanine and an alternative form of this metabolite, N(1)-acetylisoputreanine-γ-lactam, are both present in human urine and are likely end-products of polyamine metabolism. PMID: 28782053 [PubMed]

New frontiers in metabolomics: from measurement to insight.

Mon, 07/08/2017 - 22:00
Related Articles New frontiers in metabolomics: from measurement to insight. F1000Res. 2017;6:1148 Authors: Riekeberg E, Powers R Abstract Metabolomics is the newest addition to the "omics" disciplines and has shown rapid growth in its application to human health research because of fundamental advancements in measurement and analysis techniques. Metabolomics has unique and proven advantages in systems biology and biomarker discovery. The next generation of analysis techniques promises even richer and more complete analysis capabilities that will enable earlier clinical diagnosis, drug refinement, and personalized medicine. A review of current advancements in methodologies and statistical analysis that are enhancing and improving the performance of metabolomics is presented along with highlights of some recent successful applications. PMID: 28781759 [PubMed]

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

Mon, 07/08/2017 - 22:00
Related Articles ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR. F1000Res. 2017;6: Authors: Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G Abstract ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform's coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR's flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project - a coordinated effort to drive engagement with training in statistics. PMID: 28781748 [PubMed]

Effect of everolimus on the glucose metabolic pathway in mouse skeletal muscle cells (C2C12).

Mon, 07/08/2017 - 22:00
Related Articles Effect of everolimus on the glucose metabolic pathway in mouse skeletal muscle cells (C2C12). Metabolomics. 2017;13(8):98 Authors: Yoshida K, Imamura CK, Hara K, Mochizuki M, Tanigawara Y Abstract 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. PMID: 28781589 [PubMed]

[Metabolomic blood test: purpose, implementation and interpretation of data].

Mon, 07/08/2017 - 22:00
Related Articles [Metabolomic blood test: purpose, implementation and interpretation of data]. Biomed Khim. 2017 May;63(3):232-240 Authors: Lokhov PG, Lisitsa AV, Archakov AI Abstract The human body is an open system that receives a variety of xenobiotics in the course of dietary route or respiration and in the form of the drugs. As a lump sum scores of toxic and potentially toxic substances are detected in a human body that significantly affect health and human lifespan. There are also thousands of diseases, dozens of which latently occur in the body of each person. Traditional diagnosis is not able to screen all the variety of xenobiotics and potential human diseases. For this purpose metabolomic blood test is available which is of non-targeted (review) nature. The test can reveal all the diversity of low molecular weight substances in blood, including tens of thousands of xenobiotics and markers of different diseases. Detection of xenobiotics in the blood, directional detoxification and subsequent monitoring of "body's chemical purity" together with the control of "normality" of all biochemical processes in the organism, using metabolomics blood tests is a necessary and presumably a sufficient condition in the implementation of inherent human genotype longevity. This article describes the purpose, implementation and interpretation of metabolomic blood test facilitating the implementation of this method in the Russian Federation, in order to significantly increase the average life expectancy. PMID: 28781256 [PubMed - in process]

Investigation of metabolites for estimating blood deposition time.

Mon, 07/08/2017 - 22:00
Related Articles Investigation of metabolites for estimating blood deposition time. Int J Legal Med. 2017 Aug 05;: Authors: Lech K, Liu F, Davies SK, Ackermann K, Ang JE, Middleton B, Revell VL, Raynaud FJ, Hoveijn I, Hut RA, Skene DJ, Kayser M Abstract Trace deposition timing reflects a novel concept in forensic molecular biology involving the use of rhythmic biomarkers for estimating the time within a 24-h day/night cycle a human biological sample was left at the crime scene, which in principle allows verifying a sample donor's alibi. Previously, we introduced two circadian hormones for trace deposition timing and recently demonstrated that messenger RNA (mRNA) biomarkers significantly improve time prediction accuracy. Here, we investigate the suitability of metabolites measured using a targeted metabolomics approach, for trace deposition timing. Analysis of 171 plasma metabolites collected around the clock at 2-h intervals for 36 h from 12 male participants under controlled laboratory conditions identified 56 metabolites showing statistically significant oscillations, with peak times falling into three day/night time categories: morning/noon, afternoon/evening and night/early morning. Time prediction modelling identified 10 independently contributing metabolite biomarkers, which together achieved prediction accuracies expressed as AUC of 0.81, 0.86 and 0.90 for these three time categories respectively. Combining metabolites with previously established hormone and mRNA biomarkers in time prediction modelling resulted in an improved prediction accuracy reaching AUCs of 0.85, 0.89 and 0.96 respectively. The additional impact of metabolite biomarkers, however, was rather minor as the previously established model with melatonin, cortisol and three mRNA biomarkers achieved AUC values of 0.88, 0.88 and 0.95 for the same three time categories respectively. Nevertheless, the selected metabolites could become practically useful in scenarios where RNA marker information is unavailable such as due to RNA degradation. This is the first metabolomics study investigating circulating metabolites for trace deposition timing, and more work is needed to fully establish their usefulness for this forensic purpose. PMID: 28780758 [PubMed - as supplied by publisher]

The use of LC predicted retention times to extend metabolites identification with SWATH data acquisition.

Mon, 07/08/2017 - 22:00
Related Articles The use of LC predicted retention times to extend metabolites identification with SWATH data acquisition. J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Jul 19;: Authors: Bruderer T, Varesio E, Hopfgartner G Abstract The application of predicted LC retention time to support metabolite identification was evaluated for a metabolomics MS/MS database containing 532 compounds representative for the major human metabolite classes. LC retention times could be measured for two C18 type columns using a mobile phase of pH=3.0 for positive ESI mode (n=337, 228) and pH=8.0 for negative ESI mode (n=410, 233). A QSRR modelling was applied with a small set of model compound selected based on the Kennard-Stone algorithm. The models were implemented in the R environment and can be applied to any library. The prediction model was built with two molecular descriptors, LogD2 and the molecular volume. A limited set of model compounds (LC CalMix, n=16) could be validated on two different C18 reversed phase LC columns and with comparable prediction accuracy. The CalMix can be used to compensate for different LC systems. In addition, LC retention prediction was found, in combination with SWATH-MS, to be attractive to eliminate false positive identification as well as for ranking purpose different metabolite isomeric forms. PMID: 28780068 [PubMed - as supplied by publisher]

Metabolic disruption of zebrafish (Danio rerio) embryos by bisphenol A. An integrated metabolomic and transcriptomic approach.

Mon, 07/08/2017 - 22:00
Related Articles Metabolic disruption of zebrafish (Danio rerio) embryos by bisphenol A. An integrated metabolomic and transcriptomic approach. Environ Pollut. 2017 Aug 03;231(Pt 1):22-36 Authors: Ortiz-Villanueva E, Navarro-Martín L, Jaumot J, Benavente F, Sanz-Nebot V, Piña B, Tauler R Abstract Although bisphenol A (BPA) is commonly recognized as an endocrine disruptor, the metabolic consequences of its exposure are still poorly understood. In this study, we present a non-targeted LC-MS based metabolomic analysis in combination with a full-genome, high-throughput RNA sequencing (RNA-Seq) to reveal the metabolic effects and the subjacent regulatory pathways of exposing zebrafish embryos to BPA during the first 120 hours post-fertilization. We applied multivariate data analysis methods to extract biochemical information from the LC-MS and RNA-Seq complex datasets and to perform testable predictions of the phenotypic adverse effects. Metabolomic and transcriptomic data revealed a similar subset of altered pathways, despite the large difference in the number of identified biomarkers (around 50 metabolites and more than 1000 genes). These results suggest that even a moderate coverage of zebrafish metabolome may be representative of the global metabolic changes. These multi-omic responses indicate a specific metabolic disruption by BPA affecting different signaling pathways, such as retinoid and prostaglandin metabolism. The combination of transcriptomic and metabolomic data allowed a dynamic interpretation of the results that could not be drawn from either single dataset. These results illustrate the utility of -omic integrative analyses for characterizing the physiological effects of toxicants beyond the mere indication of the affected pathways. PMID: 28780062 [PubMed - as supplied by publisher]

Endocrinology Meets Metabolomics: Achievements, Pitfalls, and Challenges.

Mon, 07/08/2017 - 22:00
Related Articles Endocrinology Meets Metabolomics: Achievements, Pitfalls, and Challenges. Trends Endocrinol Metab. 2017 Aug 02;: Authors: Tokarz J, Haid M, Cecil A, Prehn C, Artati A, Möller G, Adamski J Abstract The metabolome, although very dynamic, is sufficiently stable to provide specific quantitative traits related to health and disease. Metabolomics requires balanced use of state-of-the-art study design, chemical analytics, biostatistics, and bioinformatics to deliver meaningful answers to contemporary questions in human disease research. The technology is now frequently employed for biomarker discovery and for elucidating the mechanisms underlying endocrine-related diseases. Metabolomics has also enriched genome-wide association studies (GWAS) in this area by providing functional data. The contributions of rare genetic variants to metabolome variance and to the human phenotype have been underestimated until now. PMID: 28780001 [PubMed - as supplied by publisher]

The metabolomics window into diabetic complications.

Sun, 06/08/2017 - 15:01
Related Articles The metabolomics window into diabetic complications. J Diabetes Investig. 2017 Aug 05;: Authors: Wu T, Qiao S, Shi C, Wang S, Ji G Abstract Diabetes has become a major global health problem. The elucidation of characteristic metabolic alterations during the diabetic progression is critical for better understanding its pathogenesis and identifying potential biomarkers and drug targets. Metabolomics is a promising tool to reveal the metabolic changes and the underlying mechanism involved in the pathogenesis of diabetic complications. The present review provides an update on the application of metabolomics in diabetic complications, including diabetic coronary artery disease, diabetic nephropathy, diabetic retinopathy, and diabetic neuropathy, and this review provides notes on the prevention and prediction of diabetic complications. This article is protected by copyright. All rights reserved. PMID: 28779528 [PubMed - as supplied by publisher]

metabolomics; +27 new citations

Sat, 05/08/2017 - 17:16
27 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 2017/08/05PubMed 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.

metabolomics; +21 new citations

Thu, 03/08/2017 - 13:40
21 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 2017/08/03PubMed 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.

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