PubMed

22 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 2019/03/12PubMed 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.

22 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 2019/03/12PubMed 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.

Correction to: Answering biological questions by analysis of the strawberry metabolome. Metabolomics. 2019 Mar 09;15(3):40 Authors: Haugeneder A, Trinkl J, Härtl K, Hoffmann T, Allwood JW, Schwab W Abstract The article Answering biological questions by analysis of the strawberry metabolome, written by Annika Haugeneder, Johanna Trinkl, Katja Härtl, Thomas Hoffman, James William Allwood and Wilfred Schwab, was originally published electronically on the publisher's internet portal (currently SpringerLink) on 26 OCtober, 2018 without open access. After publication in volume 14. Issue 11, Citation Id 145, with the author(s)' decision to opt for Open Choice the copyright of the article changed on 20 December, 2018 to © The Author(s) [Year] and the article is forthwith distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/ ), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. PMID: 30852678 [PubMed - in process]

ColocalizR: An open-source application for cell-based high-throughput colocalization analysis. Comput Biol Med. 2019 Mar 02;107:227-234 Authors: Sauvat A, Leduc M, Müller K, Kepp O, Kroemer G Abstract The microscopic assessment of the colocalization of fluorescent signals has been widely used in cell biology. Although imaging techniques have drastically improved over the past decades, the quantification of colocalization by measures such as the Pearson correlation coefficient or Manders overlap coefficient, has not changed. Here, we report the development of an R-based application that allows to (i) automatically segment cells and subcellular compartments, (ii) measure morphology and texture features, and (iii) calculate the degree of colocalization within each cell. Colocalization can thus be studied on a cell-by-cell basis, permitting to perform statistical analyses of cellular populations and subpopulations. ColocalizR has been designed to parallelize tasks, making it applicable to the analysis of large data sets. Its graphical user interface makes it suitable for researchers without specific knowledge in image analysis. Moreover, results can be exported into a wide range of formats rendering post-analysis adaptable to statistical requirements. This application and its source code are freely available at https://github.com/kroemerlab/ColocalizR. PMID: 30852249 [PubMed - as supplied by publisher]

Resveratrol and other dietary polyphenols are inhibitors of estrogen metabolism in human breast cancer cells. J Steroid Biochem Mol Biol. 2019 Mar 06;: Authors: Poschner S, Maier-Salamon A, Thalhammer T, Jäger W Abstract Polyphenols in foods and dietary supplements are commonly used for the prevention and treatment of a variety of malignancies, including breast cancer. However, daily intake by patients with breast cancer is controversial, as these compounds may stimulate cancer growth. Estrogens serve key roles in breast cancer cell proliferation; therefore, understanding the interaction between endogenous steroid hormones and natural dietary polyphenols is essential. Currently, comprehensive knowledge regarding these effects remains limited. The current review summarizes the dose-dependent in vitro and in vivo interactions of resveratrol and other dietary polyphenols with estrogen precursors, active estrogens, catechol estrogens and their respective glucuronidated, sulfated, glutathionated or O-methylated metabolites in estrogen receptor alpha negative (ERα-) and positive (ERα+) breast cancer. Which estrogen-metabolizing enzymes are affected by polyphenols is also reviewed in detail. Furthermore, the impacts of dose and therapy duration on disease development and progression in patients with breast cancer are discussed. The present article is part of a Special Issue titled 'CSR 2018'. PMID: 30851384 [PubMed - as supplied by publisher]

Interoperable and scalable data analysis with microservices: Applications in Metabolomics. Bioinformatics. 2019 Mar 09;: Authors: Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O Abstract MOTIVATION: Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator. RESULTS: We developed a virtual research environment which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics, and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science. AVAILABILITY AND IMPLEMENTATION: The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the virtual research environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 30851093 [PubMed - as supplied by publisher]

Related Articles Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space. Proc Natl Acad Sci U S A. 2019 Mar 08;: Authors: Helbert W, Poulet L, Drouillard S, Mathieu S, Loiodice M, Couturier M, Lombard V, Terrapon N, Turchetto J, Vincentelli R, Henrissat B Abstract Over the last two decades, the number of gene/protein sequences gleaned from sequencing projects of individual genomes and environmental DNA has grown exponentially. Only a tiny fraction of these predicted proteins has been experimentally characterized, and the function of most proteins remains hypothetical or only predicted based on sequence similarity. Despite the development of postgenomic methods, such as transcriptomics, proteomics, and metabolomics, the assignment of function to protein sequences remains one of the main challenges in modern biology. As in all classes of proteins, the growing number of predicted carbohydrate-active enzymes (CAZymes) has not been accompanied by a systematic and accurate attribution of function. Taking advantage of the CAZy database, which groups CAZymes into families and subfamilies based on amino acid similarities, we recombinantly produced 564 proteins selected from subfamilies without any biochemically characterized representatives, from distant relatives of characterized enzymes and from nonclassified proteins that show little similarity with known CAZymes. Screening these proteins for activity on a wide collection of carbohydrate substrates led to the discovery of 13 CAZyme families (two of which were also discovered by others during the course of our work), revealed three previously unknown substrate specificities, and assigned a function to 25 subfamilies. PMID: 30850540 [PubMed - as supplied by publisher]

Related Articles Virulence factors produced by Staphylococcus aureus biofilms have a moonlighting function contributing to biofilm integrity. Mol Cell Proteomics. 2019 Mar 08;: Authors: Graf AC, Leonard A, Schäuble M, Rieckmann LM, Hoyer J, Maaß S, Lalk M, Becher D, Pané-Farré J, Riedel K Abstract Staphylococcus aureus is the causative agent of various biofilm-associated infections in humans causing major healthcare problems worldwide. This type of infection is inherently difficult to treat due to a reduced metabolic activity of biofilm-embedded cells and the protective nature of a surrounding extracellular matrix (ECM). However, little is known about S. aureus biofilm physiology and in particular the proteinaceous composition of the ECM. Thus, we cultivated S. aureus biofilms in a flow system and comprehensively profiled intracellular and extracellular (ECM and flow-through (FT)) biofilm proteomes, as well as the extracellular metabolome in comparison to planktonic cultures. Our analyses revealed the expression of many pathogenicity factors within S. aureus biofilms as indicated by a high abundance of capsule biosynthesis proteins along with various secreted virulence factors, including hemolysins, leukotoxins, and lipases as a part of the ECM. The activity of ECM virulence factors was confirmed in a hemolysis assay and a Galleria mellonella pathogenicity model. In addition, we uncovered a so far unacknowledged moonlighting function of secreted virulence factors and ribosomal proteins trapped in the ECM: namely their contribution to biofilm integrity. Mechanistically, it was revealed that this stabilizing effect is mediated by the strong positive charge of alkaline virulence factors and ribosomal proteins in an acidic ECM environment, which is caused by the release of fermentation products like formate, lactate, and acetate as a consequence of oxygen limitation in biofilms. The strong positive charge of these proteins most likely mediates electrostatic interactions with anionic cell surface components, eDNA, and anionic metabolites. In consequence, this leads to strong cell aggregation and biofilm stabilization. Collectively, our study identified a new molecular mechanism during S. aureus biofilm formation and thus significantly widens the understanding of biofilm-associated S. aureus infections - an essential prerequisite for the development of novel antimicrobial therapies. PMID: 30850421 [PubMed - as supplied by publisher]

29 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 2019/03/09PubMed 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.

22 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 2019/03/08PubMed 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.

22 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 2019/03/07PubMed 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.

20 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 2019/03/06PubMed 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.

162 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 2019/03/05PubMed 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.

Related Articles Metabolomics profiling and pathway analysis of human plasma and urine reveal further insights into the multifactorial nature of Coronary Artery Disease (CAD). Clin Chim Acta. 2019 Feb 28;: Authors: Amin AM, Mostafa H, Arif NH, Kader MASKA, Hay YK Abstract BACKGROUND: Coronary artery disease (CAD) claims lives yearly. Nuclear magnetic resonance (1H NMR) metabolomics analysis is efficient in identifying metabolic biomarkers which lend credence to diagnosis. We identified CAD metabotypes and its implicated pathways using 1H NMR analysis. METHODS: We analysed plasma and urine samples of 50 stable CAD patients and 50 healthy controls using 1H NMR. Orthogonal partial least square discriminant analysis (OPLS-DA) followed by multivariate logistic regression (MVLR) models were developed to indicate the discriminating metabotypes. RESULTS: Both plasma and urine OPLS-DA models had specificity, sensitivity and accuracy of 100%, 96% and 98%, respectively. Plasma MVLR model had specificity, sensitivity, accuracy and AUROC of 92%, 86%, 89% and 0.96, respectively. The MVLR model of urine had specificity, sensitivity, accuracy and AUROC of 90%, 80%, 85% and 0.92, respectively. 35 and 12 metabolites were identified in plasma and urine metabotypes, respectively. Metabolic pathway analysis revealed that urea cycle, aminoacyl-tRNA biosynthesis and synthesis and degradation of ketone bodies pathways were significantly disturbed in plasma, while methylhistidine metabolism and galactose metabolism pathways were significantly disturbed in urine. The enrichment over representation analysis against SNPs-associated-metabolite sets library revealed that 85 SNPs were significantly enriched in plasma metabotype. CONCLUSIONS: Cardiometabolic diseases, dysbiotic gut-microbiota and genetic variabilities are largely implicated in the pathogenesis of CAD. PMID: 30826371 [PubMed - as supplied by publisher]

Related Articles Environmental cadmium exposure induces alterations in the urinary metabolic profile of pregnant women. Int J Hyg Environ Health. 2019 Feb 27;: Authors: Li H, Huang K, Jin S, Peng Y, Liu W, Wang M, Zhang H, Zhang B, Xia W, Li Y, Lu S, Xu S Abstract Cadmium (Cd) is a well-recognized, hazardous toxic heavy metal, and the adverse effects of high-level Cd exposure on human health have been well documented. However, little is known about the health effects of low-level environmental Cd exposure on pregnant women. The objective of this study was to assess urinary metabolic alterations in pregnant women exposed to environmental Cd, and to identify informative biomarkers. Urine samples from 246 pregnant women in the first trimester of pregnancy were collected, and urinary Cd concentrations were quantified using inductively coupled plasma mass spectrometry (ICP-MS). Urinary metabolomics was analyzed by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS). Cd-related metabolic biomarkers were examined by comparing the samples of the first and third tertiles of Cd exposure classifications, using a partial least-squares discriminant (PLS-DA) model. Five putative biomarkers were identified, including L-cystine, L-tyrosine, dityrosine, histamine, and uric acid, all of which were related to oxidative stress and nephrotoxic effects induced by Cd exposure. The results show that low-level environmental Cd exposure could induce metabolite profile alterations in pregnant women, which might be associated with adverse health effects. Our findings provide new insights into the early molecular events following Cd exposure, and may be valuable for the health risk assessment of Cd exposure during pregnancy. PMID: 30826206 [PubMed - as supplied by publisher]

Metabolomics driven analysis of 11 Portulaca leaf taxa as analysed via UPLC-ESI-MS/MS and chemometrics. Phytochemistry. 2019 Feb 27;161:117-129 Authors: Farag MA, Shakour ZTA Abstract Portulaca oleracea, commonly known as purslane, is a popular plant of considerable value for its nutritive composition as well as traditional medicinal uses. P. oleracea is reported to possess neuroprotective, antimicrobial, antidiabetic, antioxidant, anti-inflammatory, antiulcerogenic, and anticancer activities. Three taxa of P. oleracea L. (P. oleracea, P. rausii and P. granulatostellulata) are grown as mixed populations in several locations in Egypt. The close morphological similarities among these taxa warrants development of methods for their correct identification or classification. We aimed in this study to assess metabolome differences among three P. oleracea taxa via ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) in the context of their genetic diversity and/or geographical origin. A total of 85 metabolites were identified including 6 amino acids, 22 phenolic compounds, 16 alkaloids, and 11 fatty acids characterized based on their MSn and UV spectra. Methoxylated flavone glycosides, O-flavonoids, C-flavonoids and four previously undescribed cyclodopa alkaloids are reported in P. oleracea for the first time. Multivariate data analyses were used for samples classification and revealing that cyclodopa alkaloids (oleracein A, C, K and N) contributed the most for accessions classification. To the best of our knowledge, this study presents the first metabolite profile of Portulaca and its compositional differences that provide chemical based evidence for its nutritive and/or health benefits. PMID: 30825706 [PubMed - as supplied by publisher]

Related Articles The role of neurotransmitters and neuromodulators in the pathogenesis of cluster headache: a review. Neurol Sci. 2019 Mar 02;: Authors: D'Andrea G, Gucciardi A, Perini F, Leon A Abstract The pathogenesis underlying cluster headache remains an unresolved issue. Although both the autonomic system and the hypothalamus play a central role, the modality of their involvement remains largely unknown. It is, also, unknown why the duration of the pain attacks is so brief and why their onset and termination are abrupt and extremely painful. This review summarizes the evidence to date accumulated in favor of a possible role of anomalies in the metabolism of tyrosine, tryptophan, and arginine in these unresolved issues. PMID: 30825019 [PubMed - as supplied by publisher]

Related Articles Time-resolved decoding of metabolic signatures of in vitro growth of the hemibiotrophic pathogen Colletotrichum sublineolum. Sci Rep. 2019 Mar 01;9(1):3290 Authors: Tugizimana F, Djami-Tchatchou AT, Fahrmann JF, Steenkamp PA, Piater LA, Dubery IA Abstract Metabolomics has emerged as a powerful approach to comprehensively interrogate cellular biochemistry. As such, we applied an untargeted liquid chromatography-mass spectrometry metabolomic strategy to elucidate metabolome changes in the anthracnose-causing hemibiotrophic sorghum pathogen, Colletotrichum sublineolum. An in vitro batch culture study model with different carbon sources, glucose, arabinose and rhamnose, were used to support fungal growth over a period of twelve days. Metabolites representing the intracellular and extracellular (secreted) metabolomes were extracted with methanol and subjected to LC-MS analyses. Chemometric modelling revealed a metabolic variation trajectory, comprising three distinct stages that metabolically describe the adaptation of the fungus to diminishing nutrients. Selected marker gene expression indicated stage one (0-3 d.p.i) as corresponding to the early logarithmic phase. Stage two can be interpreted as an intermediate transitionary stage with stage three corresponding to the stationary phase (9-12 d.p.i). Stage one was characterised by up-regulation of endo-metabolites such as ferricrocin, fatty acids and flavone-conjugates, while stage three was characterised by the secretion of phytotoxins, including colletotrichin and colletotric acid. Ultimately, results from our in vitro model reveal previously unknown insights into the dynamic aspects of metabolome reprogramming in the growth phases of Colletotrichum spp as determined by nutrients obtainable from plant cell walls. PMID: 30824820 [PubMed - in process]

Related Articles Luigi Maiuri: un Grande Uomo - a Great Spirit. Cell Death Dis. 2019 Mar 01;10(3):209 Authors: Piacentini M, Kroemer G Abstract PMID: 30824687 [PubMed - in process]

Related Articles Twenty Years on: Metabolomics in Helminth Research. Trends Parasitol. 2019 Feb 26;: Authors: Kokova D, Mayboroda OA Abstract This contribution makes a critical assessment of the metabolomics application to helminthic infection research. To ensure a cross-comparison of the results published by different laboratories over a period of almost two decades, we restrict the discussion to only the publications where nuclear magnetic resonance (NMR) spectroscopy is used as the analytical platform. We review the metabolites consistently reported for the body fluids of animals infected with the parasitic helminths and the characteristic metabolic patterns, arguing that the field needs a complete integration of metabolomics into research lines that examine host-helminth interactions. PMID: 30824203 [PubMed - as supplied by publisher]