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Metabolites
Special Issues
Selected Papers from 2nd International Electronic Conference on Metabolomics
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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) | Viewed by 15184

Special Issue Editors

Dr. Maria Fuller

E-Mail Website
Guest Editor
1. Genetics and Molecular Pathology, SA Pathology (at Women's and Children's Hospital), North Adelaide 5006, Australia
2. Adelaide Medical School, University of Adelaide, Adelaide 5005, Australia
Interests: lysosomal storage disorders; diagnosis of inborn errors of metabolism; understanding and treating inherited neurodegenerative disease
Special Issues, Collections and Topics in MDPI journals
Dr. Madhu Basetti

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

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

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

E-Mail Website
Guest Editor
Northwest Metabolomics Research Center and Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, UW Medicine, University of Washington, Seattle, WA 98109, USA
Interests: metabolomics; NMR spectroscopy; mass spectrometry; biomarker discovery
Dr. Basil Nikolau

E-Mail Website1 Website2
Guest Editor
1. The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
2. Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
Interests: biochemistry; molecular biology; regulation of plant lipid metabolism
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Prof. Dr. Georgios Theodoridis

E-Mail Website
Guest Editor
1. Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
2. Biomic_AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 10th km Thessaloniki-Thermi Rd, 57001 Thessaloniki, Greece
Interests: metabonomic/metabolomic analysis for biomarker discovery; bioanalysis and biological mass spectrometry (LC-MS, GC-MS); exploitation of molecular recognition mechanisms in analytical separations (immunoaffinity chromatography, molecular imprinting); novel sample pretreatment techniques (solid phase extraction-microextraction, chromatographic techniques in bioanalysis, pharmaceutical-toxicological analysis)
Special Issues, Collections and Topics in MDPI journals

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 submissions that pass pre-check are 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 monthly 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 2700 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.

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Published Papers (2 papers)

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Research

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16 pages, 3179 KiB  
Article
Stable Isotope-Resolved Metabolomics Shows Metabolic Resistance to Anti-Cancer Selenite in 3D Spheroids versus 2D Cell Cultures
by Teresa W.-M. Fan, Salim S. El-Amouri, Jessica K. A. Macedo, Qing Jun Wang, Huan Song, Teresa Cassel and Andrew N. Lane
Metabolites 2018, 8(3), 40; https://doi.org/10.3390/metabo8030040 - 10 Jul 2018
Cited by 39 | Viewed by 7607
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
(This article belongs to the Special Issue Selected Papers from 2nd International Electronic Conference on Metabolomics)
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Review

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11 pages, 5315 KiB  
Review
Profiling Redox and Energy Coenzymes in Whole Blood, Tissue and Cells Using NMR Spectroscopy
by G. A. Nagana Gowda
Metabolites 2018, 8(2), 32; https://doi.org/10.3390/metabo8020032 - 14 May 2018
Cited by 12 | Viewed by 6421
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
(This article belongs to the Special Issue Selected Papers from 2nd International Electronic Conference on Metabolomics)
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