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Wilkinson DJ, Crossland H, Atherton PJ. Metabolomic and proteomic applications to exercise biomedicine. TRANSLATIONAL EXERCISE BIOMEDICINE 2024; 1:9-22. [PMID: 38660119 PMCID: PMC11036890 DOI: 10.1515/teb-2024-2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024]
Abstract
Objectives 'OMICs encapsulates study of scaled data acquisition, at the levels of DNA, RNA, protein, and metabolite species. The broad objectives of OMICs in biomedical exercise research are multifarious, but commonly relate to biomarker development and understanding features of exercise adaptation in health, ageing and metabolic diseases. Methods This field is one of exponential technical (i.e., depth of feature coverage) and scientific (i.e., in health, metabolic conditions and ageing, multi-OMICs) progress adopting targeted and untargeted approaches. Results Key findings in exercise biomedicine have led to the identification of OMIC features linking to heritability or adaptive responses to exercise e.g., the forging of GWAS/proteome/metabolome links to cardiovascular fitness and metabolic health adaptations. The recent addition of stable isotope tracing to proteomics ('dynamic proteomics') and metabolomics ('fluxomics') represents the next phase of state-of-the-art in 'OMICS. Conclusions These methods overcome limitations associated with point-in-time 'OMICs and can be achieved using substrate-specific tracers or deuterium oxide (D2O), depending on the question; these methods could help identify how individual protein turnover and metabolite flux may explain exercise responses. We contend application of these methods will shed new light in translational exercise biomedicine.
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Affiliation(s)
- Daniel J. Wilkinson
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Hannah Crossland
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Philip J. Atherton
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
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Milone JP, Chakrabarti P, Sagili RR, Tarpy DR. Colony-level pesticide exposure affects honey bee (Apis mellifera L.) royal jelly production and nutritional composition. CHEMOSPHERE 2021; 263:128183. [PMID: 33297150 DOI: 10.1016/j.chemosphere.2020.128183] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 06/12/2023]
Abstract
Honey bees provision glandular secretions in the form of royal jelly as larval nourishment to developing queens. Exposure to chemicals and nutritional conditions can influence queen development and thus impact colony fitness. Previous research reports that royal jelly remains pesticide-free during colony-level exposure and that chemical residues are buffered by the nurse bees. However, the impacts of pesticides can also manifest in quality and quantity of royal jelly produced by nurse bees. Here, we tested how colony exposure to a multi-pesticide pollen treatment influences the amount of royal jelly provisioned per queen and the additional impacts on royal jelly nutritional quality. We observed differences in the metabolome, proteome, and phytosterol compositions of royal jelly synthesized by nurse bees from multi-pesticide exposed colonies, including significant reductions of key nutrients such as 24-methylenecholesterol, major royal jelly proteins, and 10-hydroxy-2-decenoic acid. Additionally, quantity of royal jelly provisioned per queen was lower in colonies exposed to pesticides, but this effect was colony-dependent. Pesticide treatment had a greater impact on royal jelly nutritional composition than the weight of royal jelly provisioned per queen cell. These novel findings highlight the indirect effects of pesticide exposure on queen developmental nutrition and allude to social consequences of nurse bee glandular degeneration.
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Affiliation(s)
- Joseph P Milone
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Ramesh R Sagili
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - David R Tarpy
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
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Miehle F, Möller G, Cecil A, Lintelmann J, Wabitsch M, Tokarz J, Adamski J, Haid M. Lipidomic Phenotyping Reveals Extensive Lipid Remodeling during Adipogenesis in Human Adipocytes. Metabolites 2020; 10:metabo10060217. [PMID: 32466532 PMCID: PMC7361991 DOI: 10.3390/metabo10060217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 12/15/2022] Open
Abstract
Differentiation of preadipocytes into mature adipocytes is a highly complex cellular process. At lipidome level, the adipogenesis remains poorly characterized. To investigate the lipidomic changes during human adipogenesis, we used the LipidyzerTM assay, which quantified 743 lipid species from 11 classes. The undifferentiated human SGBS cell strain showed a heterogeneous lipid class composition with the most abundant classes, phosphatidylethanolamines (PE), phosphatidylcholines (PC), and sphingomyelins (SM). The differentiation process was accompanied by increased ceramide concentrations. After completion of differentiation around day 4, massive lipid remodeling occurred during maturation, characterized by substantial synthesis of diacylglycerols (DAG), lysophosphatidylethanolamines (LPE), PC, PE, SM, and triacylglycerols (TAG). Lipid species composition became more homogeneous during differentiation to highly concentrated saturated and monounsaturated long-chain fatty acids (LCFA), with the four most abundant being C16:0, C16:1, C18:0, and C18:1. Simultaneously, the amount of polyunsaturated and very long-chain fatty acids (VLCFA) markedly decreased. High negative correlation coefficients between PE and PC species containing VLCFA and TAG species as well as between ceramides and SM imply that PE, PC, and ceramides might have served as additional sources for TAG and SM synthesis, respectively. These results highlight the enormous remodeling at the lipid level over several lipid classes during adipogenesis.
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Affiliation(s)
- Florian Miehle
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Gabriele Möller
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
| | - Alexander Cecil
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
| | - Jutta Lintelmann
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, 89075 Ulm, Germany;
| | - Janina Tokarz
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, 85764 Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Mark Haid
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; (F.M.); (G.M.); (A.C.); (J.L.); (J.T.); (J.A.)
- Correspondence: ; Tel.: +49-893-187-3234
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Xu J, Martien J, Gilbertson C, Ma J, Amador-Noguez D, Park JO. Metabolic flux analysis and fluxomics-driven determination of reaction free energy using multiple isotopes. Curr Opin Biotechnol 2020; 64:151-160. [PMID: 32304936 DOI: 10.1016/j.copbio.2020.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/08/2020] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
Metabolite concentrations, fluxes, and free energies constitute the basis for understanding and controlling metabolism. Mass spectrometry and stable isotopes are integral tools in quantifying these metabolic features. For absolute metabolite concentration and flux measurement, 13C internal standards and tracers have been the gold standard. In contrast, no established methods exist for comprehensive thermodynamic quantitation under physiological environments. Recently, using high-resolution mass spectrometry and multi-isotope tracing, flux quantitation has been increasingly adopted in broader metabolism. The improved flux quantitation led to determination of Gibbs free energy of reaction (ΔG) in central carbon metabolism using a relationship between reaction reversibility and thermodynamic driving force. Here we highlight recent advances in multi-isotope tracing for metabolic flux and free energy analysis.
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Affiliation(s)
- Jimmy Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Julia Martien
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cole Gilbertson
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Junyu Ma
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Danchin A. Isobiology: A Variational Principle for Exploring Synthetic Life. Chembiochem 2020; 21:1781-1792. [DOI: 10.1002/cbic.202000060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Antoine Danchin
- Stellate TherapeuticsInstitut Cochin 24 rue du Faubourg Saint-Jacques 75014 Paris France
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Balcells C, Foguet C, Tarragó-Celada J, de Atauri P, Marin S, Cascante M. Tracing metabolic fluxes using mass spectrometry: Stable isotope-resolved metabolomics in health and disease. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Rothman JA, Leger L, Kirkwood JS, McFrederick QS. Cadmium and Selenate Exposure Affects the Honey Bee Microbiome and Metabolome, and Bee-Associated Bacteria Show Potential for Bioaccumulation. Appl Environ Microbiol 2019; 85:e01411-19. [PMID: 31471302 PMCID: PMC6803295 DOI: 10.1128/aem.01411-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 08/26/2019] [Indexed: 01/12/2023] Open
Abstract
Honey bees are important insect pollinators used heavily in agriculture and can be found in diverse environments. Bees may encounter toxicants such as cadmium and selenate by foraging on plants growing in contaminated areas, which can result in negative health effects. Honey bees are known to have a simple and consistent microbiome that conveys many benefits to the host, and toxicant exposure may impact this symbiotic microbial community. We used 16S rRNA gene sequencing to assay the effects that sublethal cadmium and selenate treatments had over 7 days and found that both treatments significantly but subtly altered the composition of the bee microbiome. Next, we exposed bees to cadmium and selenate and then used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to show that chemical exposure changed the bees' metabolite profiles and that compounds which may be involved in detoxification, proteolysis, and lipolysis were more abundant in treatments. Finally, we exposed several strains of bee-associated bacteria in liquid culture and found that each strain removed cadmium from its medium but that only Lactobacillus Firm-5 microbes assimilated selenate, indicating the possibility that these microbes may reduce the metal and metalloid burden on their host. Overall, our report shows that metal and metalloid exposure can affect the honey bee microbiome and metabolome and that strains of bee-associated bacteria can bioaccumulate these toxicants.IMPORTANCE Bees are important insect pollinators that may encounter environmental pollution when foraging upon plants grown in contaminated areas. Despite the pervasiveness of pollution, little is known about the effects of these toxicants on honey bee metabolism and their symbiotic microbiomes. Here, we investigated the impact of selenate and cadmium exposure on the gut microbiome and metabolome of honey bees. We found that exposure to these chemicals subtly altered the overall composition of the bees' microbiome and metabolome and that exposure to toxicants may negatively impact both host and microbe. As the microbiome of animals can reduce mortality upon metal or metalloid challenge, we grew bee-associated bacteria in media spiked with selenate or cadmium. We show that some bacteria can remove these toxicants from their media in vitro and suggest that bacteria may reduce metal burden in their hosts.
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Affiliation(s)
- Jason A Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Laura Leger
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California, Riverside, Riverside, California, USA
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Chakrabarti P, Morré JT, Lucas HM, Maier CS, Sagili RR. The omics approach to bee nutritional landscape. Metabolomics 2019; 15:127. [PMID: 31538263 PMCID: PMC6753177 DOI: 10.1007/s11306-019-1590-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/11/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Significant annual honey bee colony losses have been reported in the USA and across the world over the past years. Malnutrition is one among several causative factors for such declines. Optimal nutrition serves as the first line of defense against multiple stressors such as parasites/pathogens and pesticides. Given the importance of nutrition, it is imperative to understand bee nutrition holistically, identifying dietary sources that may fulfill bee nutritional needs. Pollen is the primary source of protein for bees and is critical for brood rearing and colony growth. Currently, there is significant gap in knowledge regarding the chemical and nutritional composition of pollen. METHODS Targeted sterol analysis and untargeted metabolomics were conducted on five commercially available crop pollens, three bee-collected crop pollens, three vegetable oils (often added to artificial protein supplements by beekeepers), and one commonly used artificial protein supplement. RESULTS This study reports key phytosterols and metabolites present across a spectrum of bee diets, including some of the major bee-pollinated crop pollens in the western United States. Significant differences were observed in sterol concentrations among the dietary sources tested. Among all quantified sterols, the highest concentrations were observed for 24-methylenecholesterol and further, pollen samples exhibited the highest 24-methylenecholesterol among all diet sources that were tested. Also, 236 metabolites were identified across all dietary sources examined. CONCLUSION Information gleaned from this study is crucial in understanding the nutritional landscape available to all bee pollinators and may further assist in future efforts to develop comprehensive database of nutrients and metabolites present in all bee diets.
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Affiliation(s)
| | - Jeffery T Morré
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Hannah M Lucas
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Ramesh R Sagili
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
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Zachleder V, Vítová M, Hlavová M, Moudříková Š, Mojzeš P, Heumann H, Becher JR, Bišová K. Stable isotope compounds - production, detection, and application. Biotechnol Adv 2018; 36:784-797. [PMID: 29355599 DOI: 10.1016/j.biotechadv.2018.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/14/2022]
Abstract
Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.
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Affiliation(s)
- Vilém Zachleder
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Milada Vítová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Monika Hlavová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Šárka Moudříková
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | | | | | - Kateřina Bišová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic.
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