Special Issue "Selected Papers from 2nd International Electronic Conference on Metabolomics"

A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (30 April 2018)

Special Issue Editors

Guest Editor
A/Prof. Maria Fuller

Genetics and Molecular Pathology, SA Pathology (at Women's and Children's Hospital), Adelaide, Australia
Website | E-Mail
Interests: Cell Biology, Genetics
Guest Editor
Dr. Madhu Basetti

Cancer Research UK Cambridge Institute, University of Cambridge, Robinson way, Cambridge CB2 ORE, UK
Website | E-Mail
Interests: NMR, cancer; metabolomics, bioinformatics, system biology, tumour metabolism
Guest Editor
Prof. Dr. Per Bruheim

Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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Interests: mass spectrometry; metabolomics; metabolic engineering; secondary metabolites; biomakers
Guest Editor
Dr. Clare Daykin

Chemucation Science and Maths Tuition, Heanor, DE75 7UY, UK
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Interests: metabolomics; metabonomics; metabolite-protein interactions; biological sample handling; NMR spectroscopy; chromatography
Guest Editor
Dr. G. A. Nagana Gowda

Northwest Metabolomics Research Center and Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, UW Medicine, University of Washington, Seattle, USA
Website | E-Mail
Interests: Metabolomics, NMR spectroscopy, mass spectrometry, biomarker discovery
Guest Editor
Dr. Basil Nikolau

The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
Website 1 | Website 2 | E-Mail
Interests: biochemistry; molecular biology; regulation of plant lipid metabolism
Guest Editor
Prof. Dr. Georgios Theodoridis

Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University, 541 24 Thessaloniki, Greece
Website | E-Mail
Phone: +30 2310 997718
Fax: +30 2310 997719
Interests: mass spectrometry; metabolomics; biomarker discovery; biomedical applications; nutritional metabolomics; standardising metabolomics; analytical method development

Special Issue Information

Dear Colleagues,

Metabolites held the 2nd International Electronic Conference of Metabolomics (http://sciforum.net/conference/iecm-2) online from 20 November–1 December 2017. The conference covered a wide range of topics in metabolomics. A non-exhaustive list of what were considered comprises is as follows:

  • Neurological Metabolomics
  • Nutrimetabolomics and Pharmaceutical Research
  • Plant and Microbial Metabolomics
  • Clinical Applications of Metabolomics
  • Technological Advances in Metabolomics (including Bioinformatics)

Part of the Special Issue will include selected invited contributions from the 2nd International Electronic Conference on Metabolomics (IECM-2). We also encourage other contributions from the broader metabolomics community.

Dr. Per Bruheim
Assoc. Prof. Maria Fuller
Dr. Clare Daykin
Dr. Basil Nikolau
Prof. Dr. Georgios Theodoridis
Dr. Madhu Basetti
Dr. G. A. Nagana Gowda
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 850 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (2 papers)

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Research

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Open AccessArticle Stable Isotope-Resolved Metabolomics Shows Metabolic Resistance to Anti-Cancer Selenite in 3D Spheroids versus 2D Cell Cultures
Metabolites 2018, 8(3), 40; https://doi.org/10.3390/metabo8030040
Received: 9 May 2018 / Revised: 29 June 2018 / Accepted: 6 July 2018 / Published: 10 July 2018
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Abstract
Conventional two-dimensional (2D) cell cultures are grown on rigid plastic substrates with unrealistic concentration gradients of O2, nutrients, and treatment agents. More importantly, 2D cultures lack cell–cell and cell–extracellular matrix (ECM) interactions, which are critical for regulating cell behavior and functions.
[...] Read more.
Conventional two-dimensional (2D) cell cultures are grown on rigid plastic substrates with unrealistic concentration gradients of O2, nutrients, and treatment agents. More importantly, 2D cultures lack cell–cell and cell–extracellular matrix (ECM) interactions, which are critical for regulating cell behavior and functions. There are several three-dimensional (3D) cell culture systems such as Matrigel, hydrogels, micropatterned plates, and hanging drop that overcome these drawbacks but they suffer from technical challenges including long spheroid formation times, difficult handling for high throughput assays, and/or matrix contamination for metabolic studies. Magnetic 3D bioprinting (M3DB) can circumvent these issues by utilizing nanoparticles that enable spheroid formation and growth via magnetizing cells. M3DB spheroids have been shown to emulate tissue and tumor microenvironments while exhibiting higher resistance to toxic agents than their 2D counterparts. It is, however, unclear if and how such 3D systems impact cellular metabolic networks, which may determine altered toxic responses in cells. We employed a Stable Isotope-Resolved Metabolomics (SIRM) approach with 13C6-glucose as tracer to map central metabolic networks both in 2D cells and M3DB spheroids formed from lung (A549) and pancreatic (PANC1) adenocarcinoma cells without or with an anti-cancer agent (sodium selenite). We found that the extent of 13C-label incorporation into metabolites of glycolysis, the Krebs cycle, the pentose phosphate pathway, and purine/pyrimidine nucleotide synthesis was largely comparable between 2D and M3DB culture systems for both cell lines. The exceptions were the reduced capacity for de novo synthesis of pyrimidine and sugar nucleotides in M3DB than 2D cultures of A549 and PANC1 cells as well as the presence of gluconeogenic activity in M3DB spheroids of PANC1 cells but not in the 2D counterpart. More strikingly, selenite induced much less perturbation of these pathways in the spheroids relative to the 2D counterparts in both cell lines, which is consistent with the corresponding lesser effects on morphology and growth. Thus, the increased resistance of cancer cell spheroids to selenite may be linked to the reduced capacity of selenite to perturb these metabolic pathways necessary for growth and survival. Full article
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Review

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Open AccessReview Profiling Redox and Energy Coenzymes in Whole Blood, Tissue and Cells Using NMR Spectroscopy
Metabolites 2018, 8(2), 32; https://doi.org/10.3390/metabo8020032
Received: 15 April 2018 / Revised: 10 May 2018 / Accepted: 12 May 2018 / Published: 14 May 2018
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Abstract
Coenzymes of cellular redox reactions and cellular energy, as well as antioxidants mediate biochemical reactions fundamental to the functioning of all living cells. Conventional analysis methods lack the opportunity to evaluate these important redox and energy coenzymes and antioxidants in a single step.
[...] Read more.
Coenzymes of cellular redox reactions and cellular energy, as well as antioxidants mediate biochemical reactions fundamental to the functioning of all living cells. Conventional analysis methods lack the opportunity to evaluate these important redox and energy coenzymes and antioxidants in a single step. Major coenzymes include redox coenzymes: NAD+ (oxidized nicotinamide adenine dinucleotide), NADH (reduced nicotinamide adenine dinucleotide), NADP+ (oxidized nicotinamide adenine dinucleotide phosphate) and NADPH (reduced nicotinamide adenine dinucleotide phosphate); energy coenzymes: ATP (adenosine triphosphate), ADP (adenosine diphosphate) and AMP (adenosine monophosphate); and antioxidants: GSSG (oxidized glutathione) and GSH (reduced glutathione). We show here that a simple 1H NMR experiment can measure these coenzymes and antioxidants in tissue and whole blood apart from a vast pool of other metabolites. In addition, focused on the goal of identification of coenzymes in subcellular fractions, we demonstrate analysis of coenzymes in the cytoplasm using breast cancer cells. Owing to their unstable nature, or low concentrations, most of the coenzymes either evade detection or lose their integrity when established sample preparation and analysis methods are used. To overcome this challenge, here we describe the development of new methods to detect these molecules without affecting the integrity of other metabolites. We used an array of 1D and 2D NMR methods, chemical shift databases, pH measurements and spiking with authentic compounds to establish the identity of peaks for the coenzymes and antioxidants in NMR spectra. Interestingly, while none of the coenzymes and antioxidants were detected in plasma, they were abundant in whole blood. Considering that the coenzymes and antioxidants represent a sensitive measure of human health and risk for numerous diseases, the presented NMR methods to measure them in one step potentially open new opportunities in the metabolomics field. Full article
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