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Metabolites
Special Issues
Integrated Systems Biology: Challenges and Future Perspectives
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Integrated Systems Biology: Challenges and Future Perspectives

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Metabolomics".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 7970

Special Issue Editors

Dr. David J. Beale

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Guest Editor
Environmental Metabolomics and Proteomics, Land & Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecoscience Precinct, Dutton Park, QLD 4160, Australia
Interests: metabolomics; environmental multi-omics; pesticide analysis; systems biology; environmental science
Special Issues, Collections and Topics in MDPI journals
Dr. Katie E. Hillyer

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Guest Editor
Environmental Systems Biology, Land & Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecoscience Precinct, Dutton Park, QLD 4160, Australia
Interests: metabolomics; environmental multi-omics; systems biology; environmental science
Dr. Andrew Bissett

E-Mail
Guest Editor
Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organization (CSIRO), Hobart, TAS 7000, Australia
Interests: metagenomics; microbial ecology; systems biology; environmental science
Dr. Pâmela A. Alexandre

E-Mail Website
Guest Editor
Animal Genomics, Livestock & Aquaculture, Agriculture & Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Queensland Bioscience Precinct, Dutton Park, QLD 4160, Australia
Interests: transcriptomics; computational multi-omics; systems biology; co-expression networks; livestock production
Dr. Annette McGrath

E-Mail Website
Guest Editor
Life Science Informatics, Data61, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecoscience Precinct, Dutton Park, QLD 4160, Australia
Interests: metagenomics; systems biology; bioinformatics; multi-omics
Dr. James A. Broadbent

E-Mail Website
Guest Editor
Livestock and Aquaculture, Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
Interests: proteomics; machine learning; network biology; agriculture science

Special Issue Information

Dear Colleagues,

The CSIRO ‘Cutting-edge Symposium on Integrated Systems Biology: Challenges and Future Perspectives’ is a chance to learn about the most recent developments in integrated systems biology and its applications. The Symposium will cover all aspects of metabolites and metabolism relevant to the fields of metabolomics, metabolic biochemistry, computational and systems biology, biotechnology and medicine that encompass multi-omics integration. It will also offer a forum to identify and then work together to address the challenges associated with computational advances relevant to understanding metabolic processes and metabolic networks via integrated systems biology research. This forum will aim to take the community forward to develop truly integrative systems biology research approached and tools that maximize the utility of this practice and the impact that it can help to deliver.

The symposium encompasses six podium presentation themes, posters, lightning plenary session, and a half-day workshop. The six major themes encompass synthetic biology, environmental sciences and ecosystem surveillance, industrial technology, health and precision medicine, food and agriculture, and machine learning and artificial intelligence.

For this Special Issue, we particularly, but not exclusively, welcome papers presented at or resulting from the Cutting-Edge Symposium on Integrated Systems Biology: Challenges and Future Perspectives, held 25–27 October 2021 at the Brisbane Convention and Exhibition Centre and a community workshop at the CSIRO Ecosciences Precinct (October 27), with a focus related to integrated systems biology.

More information about the Cutting-Edge Symposium on Integrated Systems Biology: Challenges and Future Perspectives can be found at: https://wp.csiro.au/sisb/

We look forward to reading your papers!

Dr. David J. Beale
Dr. Katie E. Hillyer
Dr. Andrew Bissett
Dr. Pâmela A. Alexandre
Dr. Annette McGrath
Dr. James A. Broadbent
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.

Keywords

  • synthetic biology
  • environmental sciences
  • industrial technology
  • health and precision medicine
  • food and agriculture
  • machine learning and artificial intelligence

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Published Papers (3 papers)

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19 pages, 3328 KiB  
Article
Exposure to Environmentally Relevant Levels of PFAS Causes Metabolic Changes in the Freshwater Amphipod Austrochiltonia subtenuis
by Georgia M. Sinclair, Sara M. Long, Navneet Singh, Timothy L. Coggan, Matthew P. J. Askeland and Oliver A. H. Jones
Metabolites 2022, 12(11), 1135; https://doi.org/10.3390/metabo12111135 - 18 Nov 2022
Cited by 4 | Viewed by 2643
Abstract
Per and polyfluoroalkyl substances (PFAS) are of concern to environmental regulators due to their widespread occurrence, persistence and reported toxicity. However, little data exist on the effects of PFAS at environmentally relevant concentrations. The development of molecular markers for PFAS exposure would therefore [...] Read more.
Per and polyfluoroalkyl substances (PFAS) are of concern to environmental regulators due to their widespread occurrence, persistence and reported toxicity. However, little data exist on the effects of PFAS at environmentally relevant concentrations. The development of molecular markers for PFAS exposure would therefore be useful to better understand the environmental risks of these compounds. In this study, we assessed if such markers could be developed using Gas Chromatography–Mass Spectrometry-based metabolomics. We exposed the freshwater amphipod Austrochiltonia subtenuis to a range of environmentally relevant concentrations of perfluoro-octane sulfonic acid (PFOS), hexafluoropropylene oxide dimer acid (GenX) and perfluorohexanesulphonic acid (PFHxS) for 7 days at five concentrations. A metabolic response was detected in all concentrations and treatments even though the survival rates only differed significantly at the highest exposure levels. The metabolic response differed between compounds but all three PFAS induced changes in the levels of amino acids, fatty acids, and cholesterol, in line with the literature. PFOS was found to bioaccumulate. Both GenX and PFHxS were eliminated from the amphipods, but PFHxS was eliminated at a slower rate than GenX. This information improves our understanding of the sublethal effects of PFAS as well as their environmental fate and behaviour. Full article
(This article belongs to the Special Issue Integrated Systems Biology: Challenges and Future Perspectives)
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19 pages, 3397 KiB  
Article
Multi-Omics, an Integrated Approach to Identify Novel Blood Biomarkers of Alzheimer’s Disease
by Maxime François, Avinash V. Karpe, Jian-Wei Liu, David J. Beale, Maryam Hor, Jane Hecker, Jeff Faunt, John Maddison, Sally Johns, James D. Doecke, Stephen Rose and Wayne R. Leifert
Metabolites 2022, 12(10), 949; https://doi.org/10.3390/metabo12100949 - 6 Oct 2022
Cited by 11 | Viewed by 3128
Abstract
The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer’s disease (AD) is poorly understood, and the relationships between systemic abnormalities in metabolism and AD/MCI pathogenesis is unclear. This study compared the metabolomic and proteomic signature of plasma from cognitively normal [...] Read more.
The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer’s disease (AD) is poorly understood, and the relationships between systemic abnormalities in metabolism and AD/MCI pathogenesis is unclear. This study compared the metabolomic and proteomic signature of plasma from cognitively normal (CN) and dementia patients diagnosed with MCI or AD, to identify specific cellular pathways and new biomarkers altered with the progression of the disease. We analysed 80 plasma samples from individuals with MCI or AD, as well as age- and gender-matched CN individuals, by utilising mass spectrometry methods and data analyses that included combined pathway analysis and model predictions. Several proteins clearly identified AD from the MCI and CN groups and included plasma actins, mannan-binding lectin serine protease 1, serum amyloid A2, fibronectin and extracellular matrix protein 1 and Keratin 9. The integrated pathway analysis showed various metabolic pathways were affected in AD, such as the arginine, alanine, aspartate, glutamate and pyruvate metabolism pathways. Therefore, our multi-omics approach identified novel plasma biomarkers for the MCI and AD groups, identified changes in metabolic processes, and may form the basis of a biomarker panel for stratifying dementia participants in future clinical trials. Full article
(This article belongs to the Special Issue Integrated Systems Biology: Challenges and Future Perspectives)
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4 pages, 200 KiB  
Commentary
The Importance of Sharing Data in Systems Biology
by Elisha M. Wood-Charlson
Metabolites 2023, 13(1), 99; https://doi.org/10.3390/metabo13010099 - 7 Jan 2023
Viewed by 1315
Abstract
Systems biology research spans a range of biological scales and science domains, and often requires a collaborative effort to collect and share data so that integration is possible. However, sharing data effectively is a challenging task that requires effort and alignment between collaborative [...] Read more.
Systems biology research spans a range of biological scales and science domains, and often requires a collaborative effort to collect and share data so that integration is possible. However, sharing data effectively is a challenging task that requires effort and alignment between collaborative partners, as well as coordination between organizations, repositories, and journals. As a community of systems biology researchers, we must get better at efficiently sharing data, and ensuring that shared data comes with the recognition and citations it deserves. Full article
(This article belongs to the Special Issue Integrated Systems Biology: Challenges and Future Perspectives)
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