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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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2
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Bajo-Fernández M, Montero G, Alonso-Herranz V, Barbas C, Rey-Stolle F, García A. Structural elucidation of derivatives of polyfunctional metabolites after methyl chloroformate derivatization by high-resolution mass spectrometry gas chromatography. Application to microbiota metabolites. J Chromatogr A 2024; 1717:464656. [PMID: 38301332 DOI: 10.1016/j.chroma.2024.464656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/06/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Metabolomics has become an essential discipline in the study of microbiome, emerging gas chromatography coupled to mass spectrometry as the most mature, robust, and reproducible analytical technique. Silylation is the most widely used chemical derivatization strategy, although it has some limitations. In this regard, alkylation by alkyl chloroformate offers some advantages, such as a rapid reaction, milder conditions, better reproducibility, and the generation of more stable derivatives. However, commercial spectral libraries do not include many of the alkyl derivatives, mainly for polyfunctional metabolites, which can form multiple derivatives. That introduces a huge bias in untargeted metabolomics leading to common errors such as duplicates, unknowns, misidentifications, wrong assignations, and incomplete results from which non-reliable findings and conclusions will be retrieved. For this reason, the purpose of this study is to overcome these shortcomings and to expand the knowledge of metabolites in general and especially those closely related to the gut microbiota through the thorough study of the reactivity of the different functional groups in real matrix derivatized by methyl chloroformate, a common representative alkylation reagent. To this end, a systematic workflow has been developed based on exhaustive structural elucidation, along with computational simulation, and taking advantage of the high sensitivity and high-resolution gas chromatography-mass spectrometry. Several empirical rules have been established according to chemically different entities (free fatty acids, amino acids, polyols, sugars, amines, and polyfunctional groups, etc.) to predict the number of derivatives formed from a single metabolite, as well as their elution order and structure. In this work, some methyl chloroformate derivatives not previously reported as well as the mechanisms to explain them are given. Extremely important is the interconversion of E- and Z- geometric isomers of unsaturated dicarboxylic acids (case of fumaric-maleic and case of citraconic-mesaconic acids), or the formation of cycled derivatives for amino acids, as well as common metabolites, as in the case of serine and cysteine, and many others.
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Affiliation(s)
- M Bajo-Fernández
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - G Montero
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - V Alonso-Herranz
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - C Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - F Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain
| | - A García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Spain.
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3
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Nam SL, Giebelhaus RT, Tarazona Carrillo KS, de la Mata AP, Harynuk JJ. Evaluation of normalization strategies for GC-based metabolomics. Metabolomics 2024; 20:22. [PMID: 38347235 DOI: 10.1007/s11306-023-02086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024]
Abstract
INTRODUCTION For many samples studied by GC-based metabolomics applications, extensive sample preparation involving extraction followed by a two-step derivatization procedure of methoximation and trimethylsilylation (TMS) is typically required to expand the metabolome coverage. Performing normalization is critical to correct for variations present in samples and any biases added during the sample preparation steps and analytical runs. Addressing the totality of variations with an adequate normalization method increases the reliability of the downstream data analysis and interpretation of the results. OBJECTIVES Normalizing to sample mass is one of the most commonly employed strategies, while the total peak area (TPA) as a normalization factor is also frequently used as a post-acquisition technique. Here, we present a new normalization approach, total derivatized peak area (TDPA), where data are normalized to the intensity of all derivatized compounds. TDPA relies on the benefits of silylation as a universal derivatization method for GC-based metabolomics studies. METHODS Two sample classes consisting of systematically incremented sample mass were simulated, with the only difference between the groups being the added amino acid concentrations. The samples were TMS derivatized and analyzed using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC-TOFMS). The performance of five normalization strategies (no normalization, normalized to sample mass, TPA, total useful peak area (TUPA), and TDPA) were evaluated on the acquired data. RESULTS Of the five normalization techniques compared, TUPA and TDPA were the most effective. On PCA score space, they offered a clear separation between the two classes. CONCLUSION TUPA and TDPA carry different strengths: TUPA requires peak alignment across all samples, which depends upon the completion of the study, while TDPA is free from the requirement of alignment. The findings of the study would enhance the convenient and effective use of data normalization strategies and contribute to overcoming the data normalization challenges that currently exist in the metabolomics community.
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Affiliation(s)
- Seo Lin Nam
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Ryland T Giebelhaus
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - Kieran S Tarazona Carrillo
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - A Paulina de la Mata
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- The Metabolomics Innovation Centre, Edmonton, AB, Canada
| | - James J Harynuk
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
- The Metabolomics Innovation Centre, Edmonton, AB, Canada.
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4
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Li Y, Kurokawa H, Sekine Y, Kebukawa Y, Nakano Y, Kitadai N, Zhang N, Zang X, Ueno Y, Fujimori G, Nakamura R, Fujishima K, Isa J. Aqueous breakdown of aspartate and glutamate to n-ω-amino acids on the parent bodies of carbonaceous chondrites and asteroid Ryugu. SCIENCE ADVANCES 2023; 9:eadh7845. [PMID: 38100590 PMCID: PMC10848742 DOI: 10.1126/sciadv.adh7845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Amino acids in carbonaceous chondrites may have seeded the origin of life on Earth and possibly elsewhere. Recently, the return samples from a C-type asteroid Ryugu were found to contain amino acids with a similar distribution to Ivuna-type CI chondrites, suggesting the potential of amino acid abundances as molecular descriptors of parent body geochemistry. However, the chemical mechanisms responsible for the amino acid distributions remain to be elucidated particularly at low temperatures (<50°C). Here, we report that two representative proteinogenic amino acids, aspartic acid and glutamic acid, decompose to β-alanine and γ-aminobutyric acid, respectively, under simulated geoelectrochemical conditions at 25°C. This low-temperature conversion provides a plausible explanation for the enrichment of these two n-ω-amino acids compared to their precursors in heavily aqueously altered CI chondrites and Ryugu's return samples. The results suggest that these heavily aqueously altered samples originated from the water-rich mantle of their water/rock differentiated parent planetesimals where protein α-amino acids were decomposed.
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Affiliation(s)
- Yamei Li
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroyuki Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Earth Science and Astronomy, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yasuhito Sekine
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Institute of Nature and Environmental Technology, Japan Kanazawa University, Ishikawa, Kanazawa, Kakumachi 920-1192, Japan
- Planetary Plasma and Atmospheric Research Center, Tohoku University, Aramaki-aza-Aoba 6-3, Aoba, Sendai, Miyagi 980-8578, Japan
| | - Yoko Kebukawa
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogayaku, Yokohama 240-8501, Japan
| | - Yuko Nakano
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Norio Kitadai
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Naizhong Zhang
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Xiaofeng Zang
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Gen Fujimori
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogayaku, Yokohama 240-8501, Japan
| | - Ryuhei Nakamura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa 252-0882, Japan
| | - Junko Isa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Planetary Exploration Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Boutonnet C, Ginies C, Alpha-Bazin B, Armengaud J, Château A, Duport C. S-layer is a key element in metabolic response and entry into the stationary phase in Bacillus cereus AH187. J Proteomics 2023; 289:105007. [PMID: 37730087 DOI: 10.1016/j.jprot.2023.105007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
Bacillus cereus is a food-borne Gram-positive pathogen. The emetic reference strain B. cereus AH187 is surrounded by a proteinaceous surface layer (S-layer) that contributes to its physico-chemical surface properties, and promotes its adhesion in response to starvation conditions. The S-layer produced by B. cereus AH187 is composed of two proteins, SL2 and EA1, which are incorporated at different growth stages. Here, we showed that deletion of the genes encoding SL2 and EA1 produced viable cells, but decreased the glucose uptake rate at the start of growth, and induced extensive reorganization of the cellular and exoproteomes upon entry into the stationary phase. As a consequence, stationary cells were less resistant to abiotic stress. Taken together, our data indicate that the S-layer is crucial but comes at a metabolic cost that modulates the stationary phase response. SIGNIFICANCE: The emetic strains of Bacillus cereus are known to cause severe food poisoning, making it crucial to understand the factors contributing to their selective enrichment in foods. Most emetic strains are surrounded by a crystalline S-layer, which is a costly protein structure to produce. In this study, we used high-throughput proteomics to investigate how S-layer synthesis affects the allocation of cellular resources in the emetic B. cereus strain AH187. Our results demonstrate that the synthesis of the S-layer plays a crucial role in the pathogen's ability to thrive under stationary growth phase conditions by modulating the stress response, thereby promoting its lifestyle as an emetic pathogen. We conclude that the synthesis of the S-layer is a critical adaptation for emetic B. cereus to successfully colonize specific niches.
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Affiliation(s)
| | | | - Béatrice Alpha-Bazin
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, F-84914 Avignon, France
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Ashfaq F, Barkat MA, Ahmad T, Hassan MZ, Ahmad R, Barkat H, Idreesh Khan M, Saad Alhodieb F, Asiri YI, Siddiqui S. Phytocompound screening, antioxidant activity and molecular docking studies of pomegranate seed: a preventive approach for SARS-CoV-2 pathogenesis. Sci Rep 2023; 13:17069. [PMID: 37816760 PMCID: PMC10564957 DOI: 10.1038/s41598-023-43573-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
A global hazard to public health has been generated by the coronavirus infection 2019 (COVID-19), which is spreading quickly. Pomegranate is a strong source of antioxidants and has demonstrated a number of pharmacological characteristics. This work was aimed to analyze the phytochemicals present in ethanolic pomegranate seed extract (PSE) and their in vitro antioxidant potential and further in-silico evaluation for antiviral potential against crystal structure of two nucleocapsid proteins i.e., N-terminal RNA binding domain (NRBD) and C-terminal Domain (CTD) of SARS-CoV-2. The bioactive components from ethanolic extract of PSE were assessed by gas chromatography-mass spectroscopy (GC-MS). Free radical scavenging activity of PSE was determined using DPPH dye. Molecular docking was executed through the Glide module of Maestro software. Lipinski's 5 rule was applied for drug-likeness characteristics using cheminformatics Molinspiration software while OSIRIS Data Warrior V5.5.0 was used to predict possible toxicological characteristics of components. Thirty-two phytocomponents was detected in PSE by GC-MS technique. Free radical scavenging assay revealed the high antioxidant capacity of PSE. Docking analysis showed that twenty phytocomponents from PSE exhibited good binding affinity (Docking score ≥ - 1.0 kcal/mol) towards NRBD and CTD nucleocapsid protein. This result increases the possibility that the top 20 hits could prevent the spread of SARS-CoV-2 by concentrating on both nucleocapsid proteins. Moreover, molecular dynamics (MD) simulation using GROMACS was used to check their binding efficacy and internal dynamics of top complexes with the lowest docking scores. The metrics root mean square deviation (RMSD), root mean square fluctuation (RMSF), intermolecular hydrogen bonding (H-bonds) and radius of gyration (Rg) revealed that the lead phytochemicals form an energetically stable complex with the target protein. Majority of the phytoconstituents exhibited drug-likeness with non-tumorigenic properties. Thus, the PSE phytoconstituents could be useful source of drug or nutraceutical development in SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Fauzia Ashfaq
- Clinical Nutrition Department, Applied Medical Sciences College, Jazan University, Jazan 82817, Saudi Arabia
| | - Md Abul Barkat
- Department of Pharmaceutics, College of Pharmacy, University of Hafr Al-Batin, Al Jamiah, 39524, Hafr Al Batin, Saudi Arabia.
| | - Tanvir Ahmad
- Department of Biotechnology, Era's Lucknow Medical College and Hospital, Lucknow, 226003, India
| | - Mohd Zaheen Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Rumana Ahmad
- Department of Biochemistry, Era's Lucknow Medical College and Hospital, Lucknow, 226003, India
| | - Harshita Barkat
- Department of Pharmaceutics, College of Pharmacy, University of Hafr Al-Batin, Al Jamiah, 39524, Hafr Al Batin, Saudi Arabia
| | - Mohammad Idreesh Khan
- Department of Clinical Nutrition, College of Applied Health Sciences in Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Fahad Saad Alhodieb
- Department of Clinical Nutrition, College of Applied Health Sciences in Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era's Lucknow Medical College and Hospital, Lucknow, 226003, India.
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Zhao Z, Hamid N, Gutierrez-Maddox N, Kam R, Kantono K, Wang K, Young T, Le TT, Lu J. Metabolite profiling identifies chemical markers associated with the cytotoxic properties of roasted fermented avocado seeds. Food Res Int 2023; 172:113131. [PMID: 37689896 DOI: 10.1016/j.foodres.2023.113131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023]
Abstract
Studies have demonstrated avocado seeds are a good source of bioactive compounds. This study investigated the effects of roasting on the metabolites and anticancer activities of fermented avocado seeds. All three anti-cancer activities of fermented avocado seeds were higher at lower roasting temperature and time. The best inhibition effect was found against Hep G2 followed by the MDA-MB-231 and MCF-7 cancer cell lines. Untargeted metabolite profiling using gas chromatography-mass spectrometry resulted in identification of 208 metabolites. In total, 41 metabolites identified had VIP values more than 1 using PLS-R that were related to anticancer activities. All amino acids and most sugars were higher at lower roasting temperature and positively correlated to anticancer activity. The roasting conditions for optimal antioxidant and anticancer activities were determined to be 121 °C for 9 min. Findings showed that fermented avocado seed powder has the potential to become a functional food ingredient with beneficial bioctive properties.
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Affiliation(s)
- Zhiyu Zhao
- Department of Food Science and Microbiology, School of Science, Faculty of Health and Environment Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Nazimah Hamid
- Department of Food Science and Microbiology, School of Science, Faculty of Health and Environment Sciences, Auckland University of Technology, Auckland, New Zealand.
| | - Noemi Gutierrez-Maddox
- Department of Food Science and Microbiology, School of Science, Faculty of Health and Environment Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Rothman Kam
- Department of Food Science and Microbiology, School of Science, Faculty of Health and Environment Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Kevin Kantono
- Department of Food Science and Microbiology, School of Science, Faculty of Health and Environment Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Kelvin Wang
- Department of Environmental Science, School of Science, Faculty of Health & Environmental Sciences, Auckland University of Technology, Auckland 1142, New Zealand
| | - Tim Young
- Department of Environmental Science, School of Science, Faculty of Health & Environmental Sciences, Auckland University of Technology, Auckland 1142, New Zealand
| | - Thao T Le
- Department of Food Science and Microbiology, School of Science, Faculty of Health and Environment Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Jun Lu
- Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand; College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
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8
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Young T, Laroche O, Walker SP, Miller MR, Casanovas P, Steiner K, Esmaeili N, Zhao R, Bowman JP, Wilson R, Bridle A, Carter CG, Nowak BF, Alfaro AC, Symonds JE. Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates. BIOLOGY 2023; 12:1135. [PMID: 37627019 PMCID: PMC10452023 DOI: 10.3390/biology12081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | | | | | - Matthew R. Miller
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | | | | | - Noah Esmaeili
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - John P. Bowman
- Tasmanian Institute of Agricultural Research, University of Tasmania, Hobart 7005, Australia
| | - Richard Wilson
- Central Science Laboratory, Research Division, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
- Blue Economy Cooperative Research Centre, Launceston 7250, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
| | - Jane E. Symonds
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
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Young T, Gale SL, Ragg NLC, Sander SG, Burritt DJ, Benedict B, Le DV, Villas-Bôas SG, Alfaro AC. Metabolic Regulation of Copper Toxicity during Marine Mussel Embryogenesis. Metabolites 2023; 13:838. [PMID: 37512545 PMCID: PMC10385052 DOI: 10.3390/metabo13070838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The development of new tools for assessing the health of cultured shellfish larvae is crucial for aquaculture industries to develop and refine hatchery methodologies. We established a large-volume ecotoxicology/health stressor trial, exposing mussel (Perna canaliculus) embryos to copper in the presence of ethylenediaminetetraacetic acid (EDTA). GC/MS-based metabolomics was applied to identify potential biomarkers for monitoring embryonic/larval health and to characterise mechanisms of metal toxicity. Cellular viability, developmental abnormalities, larval behaviour, mortality, and a targeted analysis of proteins involved in the regulation of reactive oxygen species were simultaneously evaluated to provide a complementary framework for interpretative purposes and authenticate the metabolomics data. Trace metal analysis and speciation modelling verified EDTA as an effective copper chelator. Toxicity thresholds for P. canaliculus were low, with 10% developmental abnormalities in D-stage larvae being recorded upon exposure to 1.10 μg·L-1 bioavailable copper for 66 h. Sublethal levels of bioavailable copper (0.04 and 1.10 μg·L-1) caused coordinated fluctuations in metabolite profiles, which were dependent on development stage, treatment level, and exposure duration. Larvae appeared to successfully employ various mechanisms involving the biosynthesis of antioxidants and a restructuring of energy-related metabolism to alleviate the toxic effects of copper on cells and developing tissues. These results suggest that regulation of trace metal-induced toxicity is tightly linked with metabolism during the early ontogenic development of marine mussels. Lethal-level bioavailable copper (50.3 μg·L-1) caused severe metabolic dysregulation after 3 h of exposure, which worsened with time, substantially delayed embryonic development, induced critical oxidative damage, initiated the apoptotic pathway, and resulted in cell/organism death shortly after 18 h of exposure. Metabolite profiling is a useful approach to (1) assess the health status of marine invertebrate embryos and larvae, (2) detect early warning biomarkers for trace metal contamination, and (3) identify novel regulatory mechanisms of copper-induced toxicity.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | | | | | - Sylvia G. Sander
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
- Marine Mineral Resources Group, Research Division 4: Dynamics of the Ocean Floor, Magmatic and Hydrothermal Systems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148 Kiel, Germany
| | - David J. Burritt
- Department of Botany, University of Otago, 464 Great King St, Dunedin 9016, New Zealand
| | - Billy Benedict
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - Dung V. Le
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- Faculty of Fisheries, Vietnam National University of Agriculture, Hanoi 000084, Vietnam
| | - Silas G. Villas-Bôas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
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10
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Tsermoula P, Rostved Bechshøft M, Friis C, Balling Engelsen S, Khakimov B. Molecular profiling of whey permeate reveals new insights into molecular affinities related to industrial unit operations during lactose production. Food Chem 2023; 420:136060. [PMID: 37086610 DOI: 10.1016/j.foodchem.2023.136060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/07/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Lactose powder production from whey permeate generates various side-streams. Molecular profiling of these side-streams and lactose powder can help to detect minor compounds affecting lactose crystallization, lactose powder properties and document the composition of the underutilized side-streams. In this study, whey permeate, lactose powder and intermediate streams from trial lactose productions were analyzed using gas chromatography-mass spectrometry (GC-MS) and proton nuclear magnetic resonance (1H NMR) spectroscopy. In total, 110 compounds were identified and 49 were quantified. Linking the molecular profiles to in-process steps revealed differential compositional attenuation by the unit operations. Small molecules (e.g. methanol) and a few larger molecules (e.g. fatty acids) permeated reverse osmosis membrane, while twenty-three compounds (e.g. hydroxypyruvic acid, malonic acid, gluconic acid and ribonic acid) co-crystallized with lactose and ended up in lactose power. These results help to better understand and control lactose powder production and highlights possibilities to develop new food ingredients.
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11
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Géhin C, Tokarska J, Fowler SJ, Barran PE, Trivedi DK. No skin off your back: the sampling and extraction of sebum for metabolomics. Metabolomics 2023; 19:21. [PMID: 36964290 PMCID: PMC10038389 DOI: 10.1007/s11306-023-01982-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/19/2023] [Indexed: 03/26/2023]
Abstract
INTRODUCTION Sebum-based metabolomics (a subset of "sebomics") is a developing field that involves the sampling, identification, and quantification of metabolites found in human sebum. Sebum is a lipid-rich oily substance secreted by the sebaceous glands onto the skin surface for skin homeostasis, lubrication, thermoregulation, and environmental protection. Interest in sebomics has grown over the last decade due to its potential for rapid analysis following non-invasive sampling for a range of clinical and environmental applications. OBJECTIVES To provide an overview of various sebum sampling techniques with their associated challenges. To evaluate applications of sebum for clinical research, drug monitoring, and human biomonitoring. To provide a commentary of the opportunities of using sebum as a diagnostic biofluid in the future. METHODS Bibliometric analyses of selected keywords regarding skin surface analysis using the Scopus search engine from 1960 to 2022 was performed on 12th January 2023. The published literature was compartmentalised based on what the work contributed to in the following areas: the understanding about sebum, its composition, the analytical technologies used, or the purpose of use of sebum. The findings were summarised in this review. RESULTS Historically, about 15 methods of sampling have been used for sebum collection. The sample preparation approaches vary depending on the analytes of interest and are summarised. The use of sebum is not limited to just skin diseases or drug monitoring but also demonstrated for other systemic disease. Most of the work carried out for untargeted analysis of metabolites associated with sebum has been in the recent two decades. CONCLUSION Sebum has a huge potential beyond skin research and understanding how one's physiological state affects or reflects on the skin metabolome via the sebaceous glands itself or by interactions with sebaceous secretion, will open doors for simpler biomonitoring. Sebum acts as a sink to environmental metabolites and has applications awaiting to be explored, such as biosecurity, cross-border migration, localised exposure to harmful substances, and high-throughput population screening. These applications will be possible with rapid advances in volatile headspace and lipidomics method development as well as the ability of the metabolomics community to annotate unknown species better. A key issue with skin surface analysis that remains unsolved is attributing the source of the metabolites found on the skin surface before meaningful biological interpretation.
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Affiliation(s)
- C Géhin
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - J Tokarska
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - S J Fowler
- Department of Respiratory Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - P E Barran
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - D K Trivedi
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK.
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12
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Dezfooli SM, Nguyen TV, Young T, Gutierrez-Maddox N, Alfaro AC, Seyfoddin A. An evaluation of the growth and immunity of New Zealand black-footed abalone (Haliotis iris) treated with encapsulated feed and probiotics. Anim Feed Sci Technol 2023. [DOI: 10.1016/j.anifeedsci.2023.115639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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13
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Yaroshuk T, Powers RH, Marsico ALM. Evaluating the discriminating power of amino acid ratios on distinguishing dark colored hair samples. J Forensic Sci 2023; 68:416-424. [PMID: 36683150 DOI: 10.1111/1556-4029.15192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023]
Abstract
Human hairs are one of the most commonly encountered items of trace evidence. Currently, conventional methods for hair analysis include microscopic comparison and DNA analysis (nuclear and mitochondrial). Each approach has its own drawbacks. Hair proteins are stable and offer an alternative to DNA testing, as demonstrated with proteomics for distinguishing humans. However, proteomics is complicated and requires identifying peptides to remain intact following harsh sample preparation methods. Alternatively, the actual amino acid content of a hair sample may also offer important identifying information and actually requires proteins and peptides to be broken down completely rather than remaining intact. This study evaluated the discriminating power of using hair amino acid ratios to differentiate hair samples from 10 unrelated individuals with dark colored hair. Hair proteins were digested, derivatized, and analyzed using gas chromatography-mass spectrometry. Amino acid ratios were calculated for each individual and comparisons using ANOVA and post-hoc pairwise t-test with Bonferroni correction were made with amino acid ratios for individuals. Overall, out of the 45 possible pairwise comparisons between all hair samples, 38 (84%) were differentiable. Out of the 36 possible pairwise comparisons between brown haired individuals, 32 (89%) were considered differentiable using univariate statistics. Multivariate statistics were also attempted but, overall, univariate models were sufficient for exclusionary purposes. These results indicate that amino acid ratio analysis can potentially be used as an exclusionary method using hair if DNA analysis cannot be performed, or to corroborate conclusions made following microscopic analysis.
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Affiliation(s)
- Timothy Yaroshuk
- Department of Forensic Science, University of New Haven, West Haven, Connecticut, USA.,Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Robert H Powers
- Department of Forensic Science, University of New Haven, West Haven, Connecticut, USA
| | - Alyssa L M Marsico
- Department of Forensic Science, University of New Haven, West Haven, Connecticut, USA
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Mojsak P, Maliszewska K, Klimaszewska P, Miniewska K, Godzien J, Sieminska J, Kretowski A, Ciborowski M. Optimization of a GC-MS method for the profiling of microbiota-dependent metabolites in blood samples: An application to type 2 diabetes and prediabetes. Front Mol Biosci 2022; 9:982672. [PMID: 36213115 PMCID: PMC9538375 DOI: 10.3389/fmolb.2022.982672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in serum or plasma metabolome may reflect gut microbiota dysbiosis, which is also known to occur in patients with prediabetes and type 2 diabetes (T2DM). Thus, developing a robust method for the analysis of microbiota-dependent metabolites (MDMs) is an important issue. Gas chromatography with mass spectrometry (GC–MS) is a powerful approach enabling detection of a wide range of MDMs in biofluid samples with good repeatability and reproducibility, but requires selection of a suitable solvents and conditions. For this reason, we conducted for the first time the study in which, we demonstrated an optimisation of samples preparation steps for the measurement of 75 MDMs in two matrices. Different solvents or mixtures of solvents for MDMs extraction, various concentrations and volumes of derivatizing reagents as well as temperature programs at methoxymation and silylation step, were tested. The stability, repeatability and reproducibility of the 75 MDMs measurement were assessed by determining the relative standard deviation (RSD). Finally, we used the developed method to analyse serum samples from 18 prediabetic (PreDiab group) and 24 T2DM patients (T2DM group) from our 1000PLUS cohort. The study groups were homogeneous and did not differ in age and body mass index. To select statistically significant metabolites, T2DM vs. PreDiab comparison was performed using multivariate statistics. Our experiment revealed changes in 18 MDMs belonging to different classes of compounds, and seven of them, based on the SVM classification model, were selected as a panel of potential biomarkers, able to distinguish between patients with T2DM and prediabetes.
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Affiliation(s)
- Patrycja Mojsak
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Maliszewska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | | | - Katarzyna Miniewska
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Godzien
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Julia Sieminska
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- *Correspondence: Michal Ciborowski,
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Genome-Scale Metabolic Modeling Combined with Transcriptome Profiling Provides Mechanistic Understanding of Streptococcus thermophilus CH8 Metabolism. Appl Environ Microbiol 2022; 88:e0078022. [PMID: 35924931 PMCID: PMC9477255 DOI: 10.1128/aem.00780-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Streptococcus thermophilus is a lactic acid bacterium adapted toward growth in milk and is a vital component of starter cultures for milk fermentation. Here, we combine genome-scale metabolic modeling and transcriptome profiling to obtain novel metabolic insights into this bacterium. Notably, a refined genome-scale metabolic model (GEM) accurately representing S. thermophilus CH8 metabolism was developed. Modeling the utilization of casein as a nitrogen source revealed an imbalance in amino acid supply and demand, resulting in growth limitation due to the scarcity of specific amino acids, in particular sulfur amino acids. Growth experiments in milk corroborated this finding. A subtle interdependency of the redox balance and the secretion levels of the key metabolites lactate, formate, acetoin, and acetaldehyde was furthermore identified with the modeling approach, providing a mechanistic understanding of the factors governing the secretion product profile. As a potential effect of high expression of arginine biosynthesis genes, a moderate secretion of ornithine was observed experimentally, augmenting the proposed hypothesis of ornithine/putrescine exchange as part of the protocooperative interaction between S. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in yogurt. This study provides a foundation for future community modeling of food fermentations and rational development of starter strains with improved functionality. IMPORTANCEStreptococcus thermophilus is one the main organisms involved in the fermentation of milk and, increasingly, also in the fermentation of plant-based foods. The construction of a functional high-quality genome-scale metabolic model, in conjunction with in-depth transcriptome profiling with a focus on metabolism, provides a valuable resource for the improved understanding of S. thermophilus physiology. An example is the model-based prediction of the most significant route of synthesis for the characteristic yogurt flavor compound acetaldehyde and identification of metabolic principles governing the synthesis of other flavor compounds. Moreover, the systematic assessment of amino acid supply and demand during growth in milk provides insights into the key challenges related to nitrogen metabolism that is imposed on S. thermophilus and any other organism associated with the milk niche.
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Xue L, Xu J, Feng C, Lu D, Zhou Z. Optimal Normalization Method for GC-MS/MS-Based Large-Scale Targeted Metabolomics. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822030054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Simultaneous Quantification of Organic Acids in Tamarillo ( Solanum betaceum) and Untargeted Chemotyping Using Methyl Chloroformate Derivatisation and GC-MS. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041314. [PMID: 35209098 PMCID: PMC8875926 DOI: 10.3390/molecules27041314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/05/2022]
Abstract
Sixteen organic acids were quantified in peel and pulp of Amber, Laird’s Large and Mulligan cultivars of tamarillo using GC-MS. Fourteen of these compounds had not previously been quantified in tamarillo. An untargeted metabolomics approach was used in parallel to identify and quantify 64 more metabolites relative to the internal standard, indicating abundances of glutamic acid, pro-line, aspartic acid and γ-aminobutyric acid as well as lower concentrations of several other essential fatty acids and amino acids. The main findings were that total organic acid concentration was significantly higher (p < 0.05) in pulp than in peel, with the highest concentration seen in Mulligan pulp (219.7 mg/g DW). Remarkably, after citric acid, the potent bactericide itaconic acid was the second most abundant organic acid. At least 95% of organic acids in tamarillo were one of these two acids, as well as cis-aconitic, malic and 4-toluic acids. Differences between cultivar chemotypes were as substantial as differences between tissues. These results suggest that the bitter flavour of the peel does not result from organic acids. The combination of targeted and untargeted metabolomics techniques for simultaneous qualitative and quantitative investigation of nutrients and flavours is efficient and informative.
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18
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Defining Blood Plasma and Serum Metabolome by GC-MS. Metabolites 2021; 12:metabo12010015. [PMID: 35050137 PMCID: PMC8779220 DOI: 10.3390/metabo12010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.
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Optimized Workflow for On-Line Derivatization for Targeted Metabolomics Approach by Gas Chromatography-Mass Spectrometry. Metabolites 2021; 11:metabo11120888. [PMID: 34940646 PMCID: PMC8703763 DOI: 10.3390/metabo11120888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022] Open
Abstract
Using manual derivatization in gas chromatography-mass spectrometry samples have varying equilibration times before analysis which increases technical variability and limits the number of potential samples analyzed. By contrast, automated derivatization methods can derivatize and inject each sample in an identical manner. We present a fully automated (on-line) derivatization method used for targeted analysis of different matrices. We describe method optimization and compare results from using off-line and on-line derivatization protocols, including the robustness and reproducibility of the methods. Our final parameters for the derivatization process were 20 µL of methoxyamine (MeOx) in pyridine for 60 min at 30 °C followed by 80 µL N-Methyl-N-trimethylsilyltrifluoracetamide (MSTFA) for 30 min at 30 °C combined with 4 h of equilibration time. The repeatability test in plasma and liver revealed a median relative standard deviation (RSD) of 16% and 10%, respectively. Serum samples showed a consistent intra-batch median RSD of 20% with an inter-batch variability of 27% across three batches. The direct comparison of on-line versus off-line demonstrated that on-line was fit for purpose and improves repeatability with a measured median RSD of 11% compared to 17% using the same method off-line. In summary, we recommend that optimized on-line methods may improve results for metabolomics and should be used where available.
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Opekar S, Kvíčala J, Moos M, Pejchal V, Šimek P. Mechanism of Alkyl Chloroformate-Mediated Esterification of Carboxylic Acids in Aqueous Media. J Org Chem 2021; 86:16293-16299. [PMID: 34546734 DOI: 10.1021/acs.joc.1c01546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protection of carboxyl groups by esterification has been the most common method in macroscale and microscale chemistries. The esterification is usually conducted under anhydrous conditions; however, in biological chemistry and related fields, the reaction is of major concern in aqueous environments. Immediate esterification of the carboxyl in aqueous alcoholic media driven by an alkyl chloroformate and pyridine has been such a method which has found widespread use in many research and industrial laboratories. Nevertheless, the reaction mechanism has not yet been investigated, to our knowledge, and is not well understood. Herein, we describe the reaction intermediates and demonstrate that the reaction proceeds via a continual formation of the N-acylpyridinium intermediate decomposed by several reaction channels to the final ester. The understanding of the mechanism could encourage novel laboratory applications of this important esterification method.
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Affiliation(s)
- Stanislav Opekar
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31/1160, České Budějovice 37005, Czech Republic
| | - Jaroslav Kvíčala
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Martin Moos
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31/1160, České Budějovice 37005, Czech Republic
| | - Vladimír Pejchal
- Faculty of Chemical Technology, University of Pardubice, Studentská 95, 53210 Pardubice, Czech Republic
| | - Petr Šimek
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31/1160, České Budějovice 37005, Czech Republic
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Lulijwa R, Alfaro AC, Venter L, Young T, Decker P, Merien F, Meyer J. Haematological and metabolic profiles associated with age and sex in giant kokopu (Galaxias argenteus) (Gmelin 1789) broodstock. JOURNAL OF FISH BIOLOGY 2021; 99:384-395. [PMID: 33715165 DOI: 10.1111/jfb.14726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/13/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
This study characterized selected peripheral blood (PB) haematological parameters, liver, serum and muscle metabolic features in 3- and 5-year-old male and female giant kokopu (Galaxias argenteus) broodstock reared indoor at 16°C. Sex and age did not affect PB total cell count and haematocrit values. Nonetheless, higher erythrocytes in 5-year-old fish, elevated thrombocyte and lymphocyte counts in 3-year-old fish indicate age-specific cellular regulation. Higher thrombocyte counts in female fish suggest sex-specific regulation. At a metabolic level, liver abundance for long chain saturated fatty acids (FAs) was higher in males, whereas females had elevated levels of polyunsaturated FAs. Essential and non-essential amino acids (AAs) in liver and serum were also elevated in females compared to males. These findings suggest differential allocation of FAs and AAs to reflect requirements for gonadal, development and provisioning. Similarly, age significantly resulted in higher liver and serum abundances of some non-essential AAs in 3-year-olds compared to 5-year-old fish, suggesting higher metabolism in younger fish. Overall, results enhance our understanding of sex- and age-based differences in fish haematology, muscle, liver, and serum metabolite profiles in healthy G. argenteus. Future studies should carefully consider potential age- and sex-specific differences in metabolic responses.
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Affiliation(s)
- Ronald Lulijwa
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- National Agricultural Research Organisation (NARO), Rwebitaba Zonal Agricultural Research and Development Institute (Rwebitaba-ZARDI), Fort Portal, Uganda
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Leonie Venter
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Paul Decker
- Mahurangi Technical Institute (MTI), Manāki Premium Marine Technology Facility, Warkworth, New Zealand
| | - Fabrice Merien
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Jill Meyer
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
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A combined targeted/untargeted screening based on GC/MS to detect low-molecular-weight compounds in different milk samples of different species and as affected by processing. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Willacey CC, Karu N, Harms AC, Hankemeier T. Metabolic profiling of material-limited cell samples by dimethylaminophenacyl bromide derivatization with UPLC-MS/MS analysis. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Loyo RM, Zarate E, Barbosa CS, Simoes-Barbosa A. Gas chromatography-mass spectrometry (GC/MS) reveals urine metabolites associated to light and heavy infections by Schistosoma mansoni in mice. Parasitol Int 2020; 80:102239. [PMID: 33157242 DOI: 10.1016/j.parint.2020.102239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 11/17/2022]
Abstract
High-throughput profiling of metabolites has been used to identify metabolic changes in murine models as a response to the infection by the parasitic trematode Schistosoma. These investigations have contributed to our understanding on the pathogenesis of this tropical neglected disease, with a potential of helping diagnosis. Here, our study aimed to investigate the application of gas chromatography-mass spectrometry (GC/MS) on the profiling of urine metabolites from mice carrying infections by Schistosoma mansoni. Two larval infection doses created distinctive infection intensities in mice, whereby the heavily infected animals were found to release 25 times more eggs in faeces than lightly infected animals. Over 200 urine metabolites were identified from these animals by GC/MS, following two complementary derivatisation methods. A list of 14 individual metabolites with altered relative abundances between groups were identified. Most of the altered metabolites showed a trend of increased abundances in response to infection intensity, indicating host-specific metabolic alterations as a result of the disease. Hippurate, a metabolite which concentration is intimately modulated by the gut microbiota, was found to be highly correlated to infection intensity. Our study showed that urine metabolic profiling by GC/MS can distinguish non-infected animals from those carrying light and heavy infections by S. mansoni, revealing metabolites associated to the infection and providing insights on the pathogenesis of schistosomiasis.
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Affiliation(s)
- Rodrigo Moraes Loyo
- Laboratory and reference service on Schistosomiasis, Aggeu Magalhães Institute, Oswaldo Cruz foundation (Fiocruz), Recife, PE, Brazil; School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Erica Zarate
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Constança Simões Barbosa
- Laboratory and reference service on Schistosomiasis, Aggeu Magalhães Institute, Oswaldo Cruz foundation (Fiocruz), Recife, PE, Brazil.
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Kovačič A, Gys C, Gulin MR, Kosjek T, Heath D, Covaci A, Heath E. The migration of bisphenols from beverage cans and reusable sports bottles. Food Chem 2020; 331:127326. [DOI: 10.1016/j.foodchem.2020.127326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/26/2020] [Accepted: 06/10/2020] [Indexed: 01/03/2023]
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Görg LM, Gallinger J, Gross J. The phytopathogen ‘Candidatus Phytoplasma mali’ alters apple tree phloem composition and affects oviposition behavior of its vector Cacopsylla picta. CHEMOECOLOGY 2020. [DOI: 10.1007/s00049-020-00326-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractApple proliferation disease is caused by the phloem-dwelling bacterium ‘Candidatus Phytoplasma mali’, inducing morphological changes in its host plant apple, such as witches’ broom formation. Furthermore, it triggers physiological alterations like emission of volatile organic compounds or phytohormone levels in the plant. In our study, we assessed phytoplasma-induced changes in the phloem by sampling phloem sap from infected and non-infected apple plants. In infected plants, the soluble sugar content increased and the composition of phloem metabolites differed significantly between non-infected and infected plants. Sugar and sugar alcohol levels increased in diseased plants, while organic and amino acid content remained constant. As ‘Ca. P. mali’ is vectored by the phloem-feeding insect Cacopsylla picta (Foerster, 1848), we assessed whether the insect–plant interaction was affected by ‘Ca. P. mali’ infection of the common host plant Malus domestica Borkh. Binary-choice oviposition bioassays between infected and non-infected apple leaves revealed C. picta’s preference for non-infected leaves. It is assumed and discussed that the changes in vector behavior are attributable to plant-mediated effects of the phytoplasma infection.
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Mojsak P, Rey-Stolle F, Parfieniuk E, Kretowski A, Ciborowski M. The role of gut microbiota (GM) and GM-related metabolites in diabetes and obesity. A review of analytical methods used to measure GM-related metabolites in fecal samples with a focus on metabolites' derivatization step. J Pharm Biomed Anal 2020; 191:113617. [PMID: 32971497 DOI: 10.1016/j.jpba.2020.113617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
Abstract
Disruption of gut microbiota (GM) composition is increasingly related to the pathogenesis of various metabolic diseases. Additionally, GM is responsible for the production and transformation of metabolites involved in the development of metabolic disorders, such as obesity and type 2 diabetes mellitus (T2DM). The current state of knowledge regarding the composition of GM and GM-related metabolites in relation to the progress and development of obesity and T2DM is presented in this review. To understand the relationships between GM-related metabolites and the development of metabolic disorders, their accurate qualitative and quantitative measurement in biological samples is needed. Feces represent a valuable biological matrix which composition may reflect the health status of the lower gastrointestinal tract and the whole organism. Mass spectrometry (MS), mainly in combination with gas chromatography (GC) or liquid chromatography (LC), is commonly used to measure fecal metabolites. However, profiling metabolites in such a complex matrix as feces is challenging from both analytical chemistry and biochemistry standpoints. Chemical derivatization is one of the most effective methods used to overcome these problems. In this review, we provide a comprehensive summary of the derivatization methods of GM-related metabolites prior to GC-MS or LC-MS analysis, which have been published in the last five years (2015-2020). Additionally, analytical methods used for the analysis of GM-related metabolites without the derivatization step are also presented.
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Affiliation(s)
- Patrycja Mojsak
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ewa Parfieniuk
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland.
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Li S, Alfaro AC, Nguyen TV, Young T, Lulijwa R. An integrated omics approach to investigate summer mortality of New Zealand Greenshell™ mussels. Metabolomics 2020; 16:100. [PMID: 32915338 DOI: 10.1007/s11306-020-01722-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Green-lipped mussels, commercially known as Greenshell™ mussels (Perna canaliculus Gmelin 1791), contribute > $300 million to New Zealand's aquaculture exports. However, mortalities during summer months and potential pathogenic outbreaks threaten the industry. Thermal stress mechanisms and immunological responses to pathogen infections need to be understood to develop health assessment strategies and early warning systems. METHODS P. canaliculus were collected during a mortality event at a commercial aquaculture farm in Firth of Thames, New Zealand. Gill tissues from six healthy and six unhealthy mussels were excised and processed for metabolomic (GC-MS) and label-free proteomic (LC-MS) profiling. Univariate analyses were conducted separately on each data layer, with data being integrated via sparse multiple discriminative canonical correlation analysis. Pathway enrichment analysis was used to probe coordinated changes in functionally related metabolite sets. RESULTS Findings revealed disruptions of the tricarboxylic acid (TCA) cycle and fatty acid metabolism in unhealthy mussels. Metabolomics analyses also indicated oxidative stress in unhealthy mussels. Proteomics analyses identified under-expression of proteins associated with cytoskeleton structure and regulation of cilia/flagellum in gill tissues of unhealthy mussels. Integrated omics revealed a positive correlation between Annexin A4 and CCDC 150 and saturated fatty acids, as well as a negative correlation between 2-aminoadipic acid and multiple cytoskeletal proteins. CONCLUSIONS Our study demonstrates the ability of using integrative omics to reveal metabolic perturbations and protein structural changes in the gill tissues of stressed P. canaliculus and provides new insight into metabolite and protein interactions associated with incidences of summer mortality in this species.
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Affiliation(s)
- Siming Li
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Thao V Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Ronald Lulijwa
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
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Engel B, Suralik P, Marchetti‐Deschmann M. Critical considerations for trimethylsilyl derivatives of 24 primary metabolites measured by gas chromatography–tandem mass spectrometry. SEPARATION SCIENCE PLUS 2020. [DOI: 10.1002/sscp.202000025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Benedikt Engel
- Institute of Chemical Technologies and Analytics TU Wien Vienna Austria
| | - Peter Suralik
- Institute of Chemical Technologies and Analytics TU Wien Vienna Austria
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Grandiosa R, Young T, Van Nguyen T, Mérien F, Alfaro AC. Immune response in probiotic-fed New Zealand black-footed abalone (Haliotis iris) under Vibrio splendidus challenge. FISH & SHELLFISH IMMUNOLOGY 2020; 104:633-639. [PMID: 32569712 DOI: 10.1016/j.fsi.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/26/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Vibriosis disease is a major constraint for sustainable molluscan aquaculture. Development of strategies to enhance disease resistance during grow out would greatly reduce stock mortality and boost production yields. In this study, New Zealand black-footed abalone (Haliotis iris) were fed a commercial diet enhanced with multi-strain probiotics (Exiguobacterium JHEb1, Vibrio JH1 and Enterococcus JHLDc) for four months, then challenged with an injection of pathogenic Vibrio splendidus. Host immune responses in haemocytes were characterized using flow cytometry by measuring total haemocyte counts (THC) and viability, degree of apoptosis, and production of reactive oxygen species (ROS) 48 h post-challenge. Probiotic-fed abalone had significantly higher survival rates compared to control animals after the bacterial challenge. Infected probiotic-fed abalone also had significantly higher haemocyte viabilities, slightly lower proportions of haemocytes undergoing early apoptosis, and lower proportions of ROS-producing haemocytes compared to infected control-fed abalone. In addition, metabolite profiles of muscle tissues generated via gas chromatography-mass spectrometry (GC-MS) delivered complimentary evidence to support a perturbed ROS-regulatory system in infected abalone through changes in key metabolites associated with glutathione biosynthesis. The results of this study provide valuable information to assist in farm management practices, leading to enhance production and sustainability of the New Zealand abalone aquaculture industry.
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Affiliation(s)
- Roffi Grandiosa
- Faculty of Fisheries and Marine Science, Padjadjaran University, Indonesia; AUT Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand.
| | - Tim Young
- AUT Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand; The Centre for Biomedical and Chemical Science, School of Science, Auckland University of Technology, Auckland, New Zealand.
| | - Thao Van Nguyen
- AUT Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand; NTT Hi-Tech Institute, Nguyen Tat Thanh University, Viet Nam.
| | - Fabrice Mérien
- AUT Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand; AUT-Roche Diagnostics Laboratory, School of Science, Auckland University of Technology, Auckland, New Zealand.
| | - Andrea C Alfaro
- AUT Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand.
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Zhou H, Bae HY, Leutzsch M, Kennemur JL, Bécart D, List B. The Silicon-Hydrogen Exchange Reaction: A Catalytic σ-Bond Metathesis Approach to the Enantioselective Synthesis of Enol Silanes. J Am Chem Soc 2020; 142:13695-13700. [PMID: 32786813 PMCID: PMC7426905 DOI: 10.1021/jacs.0c06677] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The use of chiral enol silanes in fundamental transformations such as Mukaiyama aldol, Michael, and Mannich reactions as well as Saegusa-Ito dehydrogenations has enabled the chemical synthesis of enantiopure natural products and valuable pharmaceuticals. However, accessing these intermediates in high enantiopurity has generally required the use of either stoichiometric chiral precursors or stoichiometric chiral reagents. We now describe a catalytic approach in which strongly acidic and confined imidodiphosphorimidates (IDPi) catalyze highly enantioselective interconversions of ketones and enol silanes. These "silicon-hydrogen exchange reactions" enable access to enantiopure enol silanes via tautomerizing σ-bond metatheses, either in a deprotosilylative desymmetrization of ketones with allyl silanes as the silicon source or in a protodesilylative kinetic resolution of racemic enol silanes with a carboxylic acid as the silyl acceptor.
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Affiliation(s)
- Hui Zhou
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Han Yong Bae
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.,Department of Chemistry, Sungkyunkwan University, 16419, Suwon, Korea
| | - Markus Leutzsch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Jennifer L Kennemur
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Diane Bécart
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Benjamin List
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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Khodadadi M, Pourfarzam M. A review of strategies for untargeted urinary metabolomic analysis using gas chromatography-mass spectrometry. Metabolomics 2020; 16:66. [PMID: 32419109 DOI: 10.1007/s11306-020-01687-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Human urine gives evidence of the metabolism in the body and contains different metabolites at various concentrations. A number of analytical techniques including mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been used to obtain metabolites levels in urine samples. However, gas chromatography-mass spectrometry (GC-MS) is one of the most widely used techniques for urinary metabolomics studies due to its higher sensitivity, resolution, reproducibility, reliability, relatively low cost and ease of operation compared to liquid chromatography-mass spectrometry and NMR. AIM OF REVIEW This review looks at various aspects of urine preparation prior to analysis by GC-MS including sample storage, urease pretreatment, derivatization, use of internal standard and quality control samples for data correction. In addition, most common types of inlet liners, ionization techniques and columns are discussed and a summary of mass analyzers are also highlighted. Lastly, the role of retention index in metabolite identification and data normalization methods are presented. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is summarizing methods of sample storage, pretreatment, and GC-MS analysis that are mostly used in urine metabolomics studies. Specific emphasis is given to the critical steps within the GC-MS urine metabolomics that those new to this field need to be aware of and the remaining challenges that require further attention and studies.
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Affiliation(s)
- Mohammad Khodadadi
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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Lulijwa R, Alfaro AC, Merien F, Burdass M, Meyer J, Venter L, Young T. Metabolic and immune responses of Chinook salmon (Oncorhynchus tshawytscha) smolts to a short-term poly (I:C) challenge. JOURNAL OF FISH BIOLOGY 2020; 96:731-746. [PMID: 31995234 DOI: 10.1111/jfb.14266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Polyinosinic:polycytidylic acid [poly (I:C)] was administered in vivo to Chinook salmon (Oncorhynchus tshawytscha) post-smolts to determine the immune responses on haematological and cellular functional parameters, including spleen (SP), head kidney (HK) and red blood cell (RBC) cytokine expression, as well as serum metabolomics. Poly (I:C) in vivo (24 h exposure) did not affect fish haematological parameters, leucocyte phagocytic activity and phagocytic index, reactive oxygen species and nitric oxide production. Gas chromatography-mass spectrometry-based metabolomics revealed that poly (I:C) significantly altered the serum biochemistry profile of 25 metabolites. Metabolites involved in the branched-chain amino acid/glutathione and transsulphuration pathways and phospholipid metabolism accumulated in poly (I:C)-treated fish, whereas those involved in the glycolytic and energy metabolism pathways were downregulated. At cytokine transcript level, poly (I:C) induced a significant upregulation of antiviral ifnγ in HK and Mx1 protein in HK, SP and RBCs. This study provides evidence for poly (I:C)-induced, immune-related biomarkers at metabolic and molecular levels in farmed O. tshawytscha in vivo. These findings provide insights into short-term effects of poly (I:C) at haematological, innate and adaptive immunity and metabolic levels, setting the stage for future studies.
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Affiliation(s)
- Ronald Lulijwa
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- National Agricultural Research Organisation (NARO), Rwebitaba Zonal Agricultural Research and Development Institute (Rwebitaba-ZARDI), Fort Portal, Uganda
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Fabrice Merien
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Mark Burdass
- Nelson Marlborough Institute of Technology (NMIT), Nelson, New Zealand
| | - Jill Meyer
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Leonie Venter
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
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Comparative Investigation of Amino Acids Content in the Dry Extracts of Juno bucharica, Gladiolus Hybrid Zefir, Iris Hungarica, Iris Variegata and Crocus Sativus Raw Materials of Ukrainian Flora. Sci Pharm 2020. [DOI: 10.3390/scipharm88010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The aim of this research was the comparative study of the amino acids content in the dry extracts of Iridaceae plants of Ukrainian flora: Juno bucharica leaves and corms, Gladiolus hybrid Zefir leaves, Iris hungarica and Iris variegata rhizomes, and Crocus sativus stigmas, flowers, leaves and corms. A gas chromatography–mass spectrometry (GC–MS) method has been used. Separation of amino acids in the samples was carried out using a Shimadzu GC-MS-QP2010 equipped with an Rxi-5ms (Restek Corporation capillary column (30 m long, 0.25 mm outer diameter and 0.25 µm) with a liquid stationary phase (5% diphenyl and 95% polysiloxane) after derivatization with N-(t-butyldimethylsilyl)-N109 methyltrifluoroacetamide (MTBSTFA) reagent. The results obtained have shown that extracts from the aerial parts of plants investigated have a higher amino acid content and more diverse composition than the underground organs. Experimental data showed that Crocus leaves and Juno leaves extracts contain the highest general content of amino acids—31.99 mg/g and 14.65 mg/g respectively. All samples showed a high content of L-pyroglutamic acid (0.33–12.35 mg/g). Moreover, Crocus leaves and Juno leaves extracts had the most suitable amino acids composition and are prospective for further pharmacological studies.
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Brunetto MDR, Gallignani M, Orozco W, Clavijo S, Delgado Y, Ayala C, Zambrano A. The effect of fermentation and roasting on free amino acids profile in Criollo cocoa (Theobroma cacao L.) grown in Venezuela. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2020. [DOI: 10.1590/1981-6723.15019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract The development of cocoa flavor and aroma is a complex phenomenon that depends on how the fermentation and roasting processes are carried out. During fermentation, the formation of some compounds so-called “aroma and flavor precursors” takes place, which are finally expressed during the roasting stage. Therefore, the evaluation of aroma precursors such as the amino acids formed during fermentation is crucial in order to determine the quality of the cocoa. In this context, we developed and validated a method for the study of these compounds in cocoa samples. The amino acids were quantitatively converted into their trimethylsilyl derivatives before their determination by gas chromatography with mass spectrometry detection. The results were verified performing precision and accuracy studies. The inter and intra assay coefficients of variation (C.V, n = 5) were lower than 4.7% and 4%, respectively. The analytical recoveries (95% to 108% with C.V < 4.2, n = 5) demonstrated the high performance of the extraction procedure. The method was successfully applied to the analysis of the amino acids in 110 samples of Venezuelan Criollo cocoa during the three days of fermentation and roasting (110 °C for 25 min). All samples had an appreciable content of free amino acids ranging between 3.87 and 5.97 g/kg in the absence of fermentation. We observed degradation of the acidic amino acids during the first day of fermentation, while the rest of amino acids increased progressively during the fermentation process with a predominance of the hydrophobic ones, mainly leucine, phenylalanine, valine, alanine and isoleucine. Additionally, during the roasting stage a fraction of the amino acids, especially the hydrophobic ones, was partially degraded through Maillard reaction to form the compounds associated with the cocoa aroma and flavor.
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Untargeted Serum Metabolic Profiling by Comprehensive Two-Dimensional Gas Chromatography–High-Resolution Time-of-Flight Mass Spectrometry. J Proteome Res 2019; 19:1013-1028. [DOI: 10.1021/acs.jproteome.9b00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Edouard Louis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
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Serrano J, Kolanczyk RC, Tapper MA, Lahren T, Dongari N, Hammermeister DE, Kosian PA, Schmieder PK, Sheedy BR, Challis K, Kubátová A. Characterization and analysis of estrogenic cyclic phenone metabolites produced in vitro by rainbow trout liver slices using GC-MS, LC-MS and LC-TOF-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1126-1127:121717. [PMID: 31437775 DOI: 10.1016/j.jchromb.2019.121717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/18/2019] [Accepted: 07/12/2019] [Indexed: 11/25/2022]
Abstract
Cyclic phenones are chemicals of interest to the USEPA and international organizations due to their potential for endocrine disruption to aquatic and terrestrial species. The metabolic conversion of cyclic phenones by liver hepatocytes and the structure of main metabolites yielded have not been assessed in fish species. As part of a larger project, in this study we investigated the structure of metabolites produced in vitro by rainbow trout (rt) liver slices after exposure to the model cyclic phenones benzophenone (DPK), cyclobutyl phenyl ketone (CBP) and cyclohexyl phenyl ketone (CPK). While only one distinct metabolite was detected for DPK and CBP (benzhydrol and CBPOH, respectively), CPK yielded nine positional isomers (M1-M9) as products. In absence of standards, improved inference of CPK metabolites tentative structures was achieved by combining GC-MS with and without derivatization, LC with tandem MS, LC with high resolution time of flight (TOF) MS and LC fractionation data with CPK phase II conjugative metabolism information. Data supported that CPK is metabolized by phase I oxidation of the cyclohexyl ring and not the phenyl group as predicted by metabolism simulators. CPK metabolites M1 and M2 (MW 186), were proposed to be cyclohexenyl-derivatives. Also, M6-M9 were proposed to be hydroxylated metabolites (MW 204), with the potential for undergoing phase II conjugative metabolism to glucuronides and sulfates. Finally, M3, M4 and M5 were proposed as cyclohexanone-derivatives of CPK (MW 202), resulting from the limited redox-interconversion of their hydroxylated pairs M8, M6 and M7, respectively. Assessment of metabolite role in biological responses associated with endocrine disruption will advance the development of methods for species extrapolation and the understanding of differential sensitivity of species to chemical exposure.
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Affiliation(s)
- Jose Serrano
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA.
| | - Richard C Kolanczyk
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Mark A Tapper
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Tylor Lahren
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Nagaraju Dongari
- University of North Dakota, Department of Chemistry, 151 Cornell Street Stop 9024, Grand Forks, ND, USA
| | - Dean E Hammermeister
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Patricia A Kosian
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Patricia K Schmieder
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Barbara R Sheedy
- USEPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Katie Challis
- Student Services Contractor, Mid-Continent Ecology Division, 6201 Congdon Boulevard, Duluth, MN, USA
| | - Alena Kubátová
- University of North Dakota, Department of Chemistry, 151 Cornell Street Stop 9024, Grand Forks, ND, USA
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Young T, Walker SP, Alfaro AC, Fletcher LM, Murray JS, Lulijwa R, Symonds J. Impact of acute handling stress, anaesthesia, and euthanasia on fish plasma biochemistry: implications for veterinary screening and metabolomic sampling. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1485-1494. [PMID: 31240506 DOI: 10.1007/s10695-019-00669-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Impacts of pre-sampling practices on fish plasma biochemistry may bias the outcome of a study if not considered within the general sampling strategy. Acute handling stresses can be imposed on fish during capture, and it is common practice to immobilise fish via sedation prior to obtaining blood samples for non-lethal extraction purposes, and/or to reduce stress, pain, or suffering before being euthanised. We investigated these potential influences using a Chinook salmon model (Oncorhynchus tshawytscha) by measuring levels of 119 biochemical targets comprising ions, metabolites, and enzymes in plasma. Multivariate analyses showed that 2 min of confinement with mild handling manipulation led to a significant departure from baseline metabolism, which was further exasperated during a prolonged 5-min challenge. These changes were characterised by a disruption in osmoregulation, a switch towards anaerobic metabolism, and shifts in ammonia recycling, among others. Sedation of fish with clove oil and AQUI-S® had major impacts on plasma biochemical profiles, with alterations signalling changes in glycolytic metabolism, respiratory modes, carbon flux through the TCA cycle, and lipid compartmentalisation. Sedation also enhanced levels of plasma amino acids, revealing a key difference between responses to handling stress and sedation. These results demonstrate that pre-harvest practices should be carefully managed during fish sampling for biochemical/metabolomic-based analyses, and if manipulations are essential, they should be standardised.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | | | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | | | | | - Ronald Lulijwa
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- Rwebitaba Zonal Agricultural Research and Development Institute (Rwebitaba-ZARDI), National Agricultural Research Organisation (NARO), P. O. Box 96, Fort Portal, Uganda
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Beale DJ, Pinu FR, Kouremenos KA, Poojary MM, Narayana VK, Boughton BA, Kanojia K, Dayalan S, Jones OAH, Dias DA. Review of recent developments in GC-MS approaches to metabolomics-based research. Metabolomics 2018; 14:152. [PMID: 30830421 DOI: 10.1007/s11306-018-1449-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC-MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and 'in house' metabolite databases available. AIM OF REVIEW This review provides an overview of developments in GC-MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC-MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is to both highlight and provide an update on GC-MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC-MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.
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Affiliation(s)
- David J Beale
- Land and Water, Commonwealth Scientific & Industrial Research Organization (CSIRO), P.O. Box 2583, Brisbane, QLD, 4001, Australia.
| | - Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Trajan Scientific and Medical, 7 Argent Pl, Ringwood, 3134, Australia
| | - Mahesha M Poojary
- Chemistry Section, School of Science and Technology, University of Camerino, via S. Agostino 1, 62032, Camerino, Italy
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Vinod K Narayana
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | - Komal Kanojia
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, GPO Box 2476, Melbourne, 3001, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, 3083, Australia.
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Grandiosa R, Mérien F, Young T, Van Nguyen T, Gutierrez N, Kitundu E, Alfaro AC. Multi-strain probiotics enhance immune responsiveness and alters metabolic profiles in the New Zealand black-footed abalone (Haliotis iris). FISH & SHELLFISH IMMUNOLOGY 2018; 82:330-338. [PMID: 30125709 DOI: 10.1016/j.fsi.2018.08.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 06/08/2023]
Abstract
We assessed whether dietary administration of a multi-strain probiotic (Exiguobacterium JHEb1, Vibrio JH1 and Enterococcus JHLDc) lead to enhanced immune responsiveness in juvenile New Zealand black-footed abalone (Haliotis iris). Two groups of abalone were fed (1% body weight per day) over a four-month period with different diets. The control diet consisted of a standard commercial pellet feed (AbMax 16), whereas the treatment diet was additionally enriched with the probiotic mix. At the end of the experiment, probiotic-fed animals showed improved growth compared with control-fed abalone in length (32.3% vs 22.3%), width (31.9% vs 20.7%) and wet weight (109.6% vs 72.8%), respectively. Haemolymph sampling was conducted at the beginning of the experiment and after 2 and 4 months. Haemolymph samples were analysed for total haemocyte count (THC) and viability, presence of apoptotic cells and production of Reactive Oxygen Species (ROS). Compared with control abalone, probiotic-fed abalone had significantly higher THC (1.9 × 106 vs 5.6 × 105 cells), higher viability (90.8% vs 75.6%), higher percentage of ROS-positive cells (19.4% vs 0.5%) and higher numbers of non-apoptotic cells (88.0% vs 78.0%), respectively. These results indicate that the probiotic-enriched diet enhanced the immunostimulatory mechanisms, with a simultaneous low-level up-regulation of ROS production as a priming mechanism of the antibacterial defence system. Metabolomics-based profiling of foot muscle tissue additionally revealed that probiotic-fed abalone differentially expressed 17 unique metabolites, including amino acids, fatty acids and TCA cycle related compounds. These data suggest that the probiotic-supplemented diet can also alter central carbon metabolic processes, which may improve the survival, as well as the growth of abalone.
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Affiliation(s)
- Roffi Grandiosa
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Fabrice Mérien
- AUT-Roche Diagnostics Laboratory, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Thao Van Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Noemi Gutierrez
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Eileen Kitundu
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Auckland, New Zealand.
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El Sheikha AF, Hu DM. Molecular techniques reveal more secrets of fermented foods. Crit Rev Food Sci Nutr 2018; 60:11-32. [DOI: 10.1080/10408398.2018.1506906] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Aly Farag El Sheikha
- Jiangxi Agricultural University, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Nanchang, China
- McMaster University, Department of Biology, Hamilton, Ontario, Canada
- Minufiya University, Faculty of Agriculture, Department of Food Science and Technology, Shibin El Kom, Minufiya Government, Egypt
| | - Dian-Ming Hu
- Jiangxi Agricultural University, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Nanchang, China
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42
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Nguyen TV, Alfaro AC, Young T, Ravi S, Merien F. Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:396-409. [PMID: 29611031 DOI: 10.1007/s10126-018-9804-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Vibrio coralliilyticus is a bacterial pathogen which can affect a range of marine organisms, such as corals, fish and shellfish, with sometimes devastating consequences. However, little is known about the mechanisms involved in the host-pathogen interaction, especially within molluscan models. We applied gas chromatography-mass spectrometry (GC-MS)-based metabolomics to characterize the physiological responses in haemolymph of New Zealand Greenshell™ mussels (Perna canaliculus) injected with Vibrio sp. DO1 (V. coralliilyticus/neptunius-like isolate). Univariate data analyses of metabolite profiles in Vibrio-exposed mussels revealed significant changes in 22 metabolites at 6 h post-infection, compared to non-exposed mussels. Among them, 10 metabolites were up-regulated, while 12 metabolites were down-regulated in infected mussels. Multivariate analyses showed a clear distinction between infected and non-infected mussels. In addition, secondary pathway analyses indicated perturbations of the host innate immune system following infection, including oxidative stress, inflammation and disruption of the TCA cycle, change in amino acid metabolism and protein synthesis. These findings provide new insights into the pathogenic mechanisms of Vibrio infection of mussels and demonstrate our ability to detect detailed and rapid host responses from haemolymph samples using a metabolomics approach.
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Affiliation(s)
- Thao V Nguyen
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Sridevi Ravi
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Fabrice Merien
- AUT-Roche Diagnostics Laboratory, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
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43
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Lai Z, Fiehn O. Mass spectral fragmentation of trimethylsilylated small molecules. MASS SPECTROMETRY REVIEWS 2018; 37:245-257. [PMID: 27580014 DOI: 10.1002/mas.21518] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometry-based untargeted metabolomics detects many peaks that cannot be identified. While advances have been made for automatic structure annotations in LC-electrospray-MS/MS, no open source solutions are available for hard electron ionization used in GC-MS. In metabolomics, most compounds bear moieties with acidic protons, for example, amino, hydroxyl, or carboxyl groups. Such functional groups increase the boiling points of metabolites too much for use in GC-MS. Hence, in GC-MS-focused metabolomics, derivatization of these groups is essential and has been employed since the 1960s. Specifically, trimethylsilylation is known as mild and universal method for GC-MS analysis. Here, we comprehensively compile accurate mass fragmentation rules and pathways of trimethylsilylated small molecules from 80 research articles over the past 5 decades, including diagnostic fragment ions, neutral losses, and typical ion ratios, for alcohols, carboxylic acids, amines, amino acids, sugars, steroids, thiols, and phosphates. These fragmentation rules were subsequently validated by specificity and sensitivity assessments using the NIST 14 nominal mass library and a new in-house GC-QTOF MS library containing 589 accurate mass spectra. From 556 tested fragmentation patterns, 228 rules yielded true positive hits within 4 mDa mass accuracy. These rules can be applied to assign substructures for mass spectra computation and unknown identification. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:245-257, 2018.
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Affiliation(s)
- Zijuan Lai
- West Coast Metabolomics Center, University of California Davis, Davis, CA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 2018; 149:74-84. [PMID: 29705211 DOI: 10.1016/j.ymeth.2018.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/10/2018] [Accepted: 04/22/2018] [Indexed: 12/12/2022] Open
Abstract
There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease.
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Affiliation(s)
- Pamela Pruski
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK; Queen Charlotte's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Julian R Marchesi
- Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Centre for Digestive and Gut Health, Surgery and Cancer, Imperial College London, London W2 1NY, UK
| | - Phillip R Bennett
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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Berkov S, Georgieva L, Sidjimova B, Nikolova M. Metabolite Profiling of In Vitro Plant Systems. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-3-319-54600-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Cruz-Munoz M, Petrone JR, Cohn AR, Munoz-Beristain A, Killiny N, Drew JC, Triplett EW. Development of Chemically Defined Media Reveals Citrate as Preferred Carbon Source for Liberibacter Growth. Front Microbiol 2018; 9:668. [PMID: 29675013 PMCID: PMC5895721 DOI: 10.3389/fmicb.2018.00668] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
Liberibacter crescens is the closest cultured relative of four important uncultured crop pathogens. Candidatus L. asiaticus, L. americanus, and L. africanus are causal agents of citrus greening disease, otherwise known as huanglongling (HLB). Candidatus L. solanacearum is responsible for potato Zebra chip disease. Cultures of L. crescens grow slowly on BM-7 complex medium, while attempts to culture the Ca. Liberibacter pathogens in BM-7 have failed. Developing a defined medium for the growth of L. crescens will be useful in the study of Liberibacter metabolism and will improve the prospects for culturing the Ca. Liberibacter pathogens. Here, M15 medium is presented and described as the first chemically defined medium for the growth of L. crescens cultures that approaches the growth rates obtained with BM-7. The development of M15 was a four step process including: (1) the identification of Hi-Graces Insect medium (Hi-GI) as an essential, yet undefined component in BM-7, for the growth of L. crescens, (2) metabolomic reconstruction of Hi-GI to create a defined medium for the growth of L. crescens cultures, and (3) the discovery of citrate as the preferred carbon and energy source for L. crescens growth. The composition of M15 medium includes inorganic salts as in the Hi-GI formula, amino acids derived from the metabolomic analyses of Hi-GI, and a 10-fold increase in vitamins compared to the Hi-GI formula, with exception choline chloride, which was increased 5000-fold in M15. Since genome comparisons of L. crescens and the Ca. Liberibacter pathogens show that they are very similar metabolically. Thus, these results imply citrate and other TCA cycle intermediates are main energy sources for these pathogens in their insect and plant hosts. Thus, strategies to reduce citrate levels in the habitats of these pathogens may be effective in reducing Ca. Liberibacter pathogen populations thereby reducing symptoms in the plant host.
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Affiliation(s)
- Maritsa Cruz-Munoz
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Joseph R Petrone
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Alexa R Cohn
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Alam Munoz-Beristain
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Nabil Killiny
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jennifer C Drew
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Eric W Triplett
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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Cooray ST, Chen WN. Valorization of brewer’s spent grain using fungi solid-state fermentation to enhance nutritional value. J Funct Foods 2018. [DOI: 10.1016/j.jff.2017.12.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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48
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Mhlongo MI, Piater LA, Madala NE, Labuschagne N, Dubery IA. The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:112. [PMID: 29479360 PMCID: PMC5811519 DOI: 10.3389/fpls.2018.00112] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/22/2018] [Indexed: 05/21/2023]
Abstract
Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant-plant and plant-microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground 'signalomics', and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial - and priming events.
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Affiliation(s)
- Msizi I. Mhlongo
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nico Labuschagne
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
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Hušek P, Švagera Z, Hanzlíková D, Karlínová I, Řimnáčová L, Zahradníčková H, Šimek P. GC-MS Metabolomic Profiling of Protic Metabolites Following Heptafluorobutyl Chloroformate Mediated Dispersive Liquid Microextraction Sample Preparation Protocol. Methods Mol Biol 2018; 1738:159-181. [PMID: 29654589 DOI: 10.1007/978-1-4939-7643-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A simple analytical workflow is described for gas chromatographic-mass spectrometry (GC-MS)-based metabolomic profiling of protic metabolites, particularly amino-carboxylic species in biological matrices. The sample preparation is carried out directly in aqueous samples and uses simultaneous in situ heptafluorobutyl chloroformate (HFBCF) derivatization and dispersive liquid-liquid microextraction (DLLME), followed by GC-MS analysis in single-ion monitoring (SIM) mode. The protocol involves ten simple pipetting steps and provides quantitative analysis of 132 metabolites by using two internal standards. A comment on each analytical step and explaining notes are provided with particular attention to the GC-MS analysis of 112 physiological metabolites in human urine.
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Affiliation(s)
- Petr Hušek
- University Hospital Ostrava, Institute of Laboratory Diagnostics, Department of Biochemistry, Ostrava, Czech Republic
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Analytical Biochemistry & Metabolomics, České Budějovice, Czech Republic
| | - Zdeněk Švagera
- University Hospital Ostrava, Institute of Laboratory Diagnostics, Department of Biochemistry, Ostrava, Czech Republic
| | - Dagmar Hanzlíková
- University Hospital Ostrava, Institute of Laboratory Diagnostics, Department of Biochemistry, Ostrava, Czech Republic
| | - Iva Karlínová
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Analytical Biochemistry & Metabolomics, České Budějovice, Czech Republic
| | - Lucie Řimnáčová
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Analytical Biochemistry & Metabolomics, České Budějovice, Czech Republic
| | - Helena Zahradníčková
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Analytical Biochemistry & Metabolomics, České Budějovice, Czech Republic
| | - Petr Šimek
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Analytical Biochemistry & Metabolomics, České Budějovice, Czech Republic.
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50
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Cheng J, Lan W, Zheng G, Gao X. Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration. Methods Mol Biol 2018. [PMID: 29536449 DOI: 10.1007/978-1-4939-7717-8_16] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metabolomics aims to quantitatively measure small-molecule metabolites in biological samples, such as bodily fluids (e.g., urine, blood, and saliva), tissues, and breathe exhalation, which reflects metabolic responses of a living system to pathophysiological stimuli or genetic modification. In the past decade, metabolomics has made notable progresses in providing useful systematic insights into the underlying mechanisms and offering potential biomarkers of many diseases. Metabolomics is a complementary manner of genomics and transcriptomics, and bridges the gap between genotype and phenotype, which reflects the functional output of a biological system interplaying with environmental factors. Recently, the technology of metabolomics study has been developed quickly. This review will discuss the whole pipeline of metabolomics study, including experimental design, sample collection and preparation, sample detection and data analysis, as well as mechanism interpretation, which can help understand metabolic effects and metabolite function for living organism in system level.
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Affiliation(s)
- Jing Cheng
- Department of Medical Instrument, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Wenxian Lan
- State Key Laboratory of Bio-Organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Guangyong Zheng
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Xianfu Gao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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