Special Issue "Selected Papers from 1st International Electronic Conference on Metabolomics"

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

Deadline for manuscript submissions: closed (30 April 2017)

Special Issue Editors

Guest Editor
Prof. Dr. Daniel Raftery

Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, UW Medicine, South Lake Union, PO Box 358057, 850 Republican St., Seattle, USA
Website | E-Mail
Interests: biomarkers; cancer; metabolic disease; companion diagnostics; NMR; mass spectrometry
Guest Editor
Prof. Dr. James Cox

University of Utah, 20 South 2030 East, Salt Lake City, UT 84112, USA
Website | E-Mail
Interests: yeast metabolism; iron and copper metabolism; metabolomics core; secondary metabolism in antibiotic producing bacteria
Guest Editor
Dr. Katja Dettmer

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
E-Mail
Fax: +49 941 943 5019
Interests: metabolomics; small molecule analysis; seperation science; hyphenated mass spectrometry; sample preparation for metabolomics; cancer
Guest Editor
Dr. Adrian S. Culf

Sussex Research Laboratories, Inc., 100, Sussex Drive, Ottawa, ON, K1A OR6, Canada
E-Mail
Interests: small molecule structure determination, NMR, separation science

Special Issue Information

Dear Colleagues,

This Special Issue will collect some selected, invited and contributed talks during the 1st International Electronic Conference on Metabolomics (IECM-1) which was supported by the Metabolites journal, website http://sciforum.net/conference/iecm-1.

Prof. Dr. Daniel Raftery
Prof. Dr. Daniel Raftery
Prof. Dr. James Cox
Dr. Katja Dettmer
Dr. Adrian S. Culf
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 (1 paper)

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Review

Open AccessReview Metabolic Investigations of the Molecular Mechanisms Associated with Parkinson’s Disease
Metabolites 2017, 7(2), 22; doi:10.3390/metabo7020022
Received: 5 April 2017 / Revised: 16 May 2017 / Accepted: 16 May 2017 / Published: 24 May 2017
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Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by fibrillar cytoplasmic aggregates of α-synuclein (i.e., Lewy bodies) and the associated loss of dopaminergic cells in the substantia nigra. Mutations in genes such as α-synuclein (SNCA) account for only 10% of PD
[...] Read more.
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by fibrillar cytoplasmic aggregates of α-synuclein (i.e., Lewy bodies) and the associated loss of dopaminergic cells in the substantia nigra. Mutations in genes such as α-synuclein (SNCA) account for only 10% of PD occurrences. Exposure to environmental toxicants including pesticides and metals (e.g., paraquat (PQ) and manganese (Mn)) is also recognized as an important PD risk factor. Thus, aging, genetic alterations, and environmental factors all contribute to the etiology of PD. In fact, both genetic and environmental factors are thought to interact in the promotion of idiopathic PD, but the mechanisms involved are still unclear. In this study, we summarize our findings to date regarding the toxic synergistic effect between α-synuclein and paraquat treatment. We identified an essential role for central carbon (glucose) metabolism in dopaminergic cell death induced by paraquat treatment that is enhanced by the overexpression of α-synuclein. PQ “hijacks” the pentose phosphate pathway (PPP) to increase NADPH reducing equivalents and stimulate paraquat redox cycling, oxidative stress, and cell death. PQ also stimulated an increase in glucose uptake, the translocation of glucose transporters to the plasma membrane, and AMP-activated protein kinase (AMPK) activation. The overexpression of α-synuclein further stimulated an increase in glucose uptake and AMPK activity, but impaired glucose metabolism, likely directing additional carbon to the PPP to supply paraquat redox cycling. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Towards standard, accessible and reproducible Metabolomics
Author:
Reza Salek* and Christoph Steinbeck
Affiliations:
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Abstract: Reproducing results in any science is quite challenging. A recent 2016 survey by Nature (http://www.nature.com/news/reality-check-on-reproducibility-1.19961) has shown 2/3 of researchers are concerned about science reproducibility. In the field of metabolomics, for results to become reproducible, descriptions of an investigation in a manuscript are insufficient. To surpass this, and increase the chance of result reproducibility, standard frameworks for data sharing and sharing of experimental data are invaluable. In this presentation, developments in data standards initiatives in metabolomics, including nmrML for NMR raw data (COSMOS initiative) mzTab developments for metabolite identification and qcML for data quality (both joint efforts by MSI and HUPO-PSI) will be discussed. It will also be shown how emerging metabolomics data sharing platforms can promote open, accessible data sharing standards. Finally, our own experiences, as well as community efforts in creating metabolomics data analysis workflows, particularly in Galaxy and KNIME environments which can capture study-specific experimental parameters will be presented. Such workflows would ideally run on a dedicated e-infrastructure platform, such as the ones currently under development by the PhenoMeNal consortium (http://phenomenal-h2020.eu/home/). Such efforts coupled with wider community involvement can pave the way for a greater reproducibility of the results in data analysis, data integration and reuse of data in metabolomics.

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