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Marine dissolved organic matter: a vast and unexplored molecular space. Appl Microbiol Biotechnol 2021; 105:7225-7239. [PMID: 34536106 PMCID: PMC8494709 DOI: 10.1007/s00253-021-11489-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/02/2023]
Abstract
Abstract Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities. Key points • Marine DOM is a vast, unexplored biotechnological resource. • Untargeted bioscreening approaches are emerging for natural product screening. • Perspectives for developing bioscreening platforms for marine DOM are discussed.
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Dhillon SS, Torell F, Donten M, Lundstedt-Enkel K, Bennett K, Rännar S, Trygg J, Lundstedt T. Metabolic profiling of zebrafish embryo development from blastula period to early larval stages. PLoS One 2019; 14:e0213661. [PMID: 31086370 PMCID: PMC6516655 DOI: 10.1371/journal.pone.0213661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/15/2019] [Indexed: 11/18/2022] Open
Abstract
The zebrafish embryo is a popular model for drug screening, disease modelling and molecular genetics. In this study, samples were obtained from zebrafish at different developmental stages. The stages that were chosen were 3/4, 4/5, 24, 48, 72 and 96 hours post fertilization (hpf). Each sample included fifty embryos. The samples were analysed using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). Principle component analysis (PCA) was applied to get an overview of the data and orthogonal projection to latent structure discriminant analysis (OPLS-DA) was utilised to discriminate between the developmental stages. In this way, changes in metabolite profiles during vertebrate development could be identified. Using a GC-TOF-MS metabolomics approach it was found that nucleotides and metabolic fuel (glucose) were elevated at early stages of embryogenesis, whereas at later stages amino acids and intermediates in the Krebs cycle were abundant. This agrees with zebrafish developmental biology, as organs such as the liver and pancreas develop at later stages. Thus, metabolomics of zebrafish embryos offers a unique opportunity to investigate large scale changes in metabolic processes during important developmental stages in vertebrate development. In terms of stability of the metabolic profile and viability of the embryos, it was concluded at 72 hpf was a suitable time point for the use of zebrafish as a model system in numerous scientific applications.
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Affiliation(s)
- Sundeep S. Dhillon
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Frida Torell
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
- Accelerator Lab (ACL), Karlsruhe Institute of Technology, Karlsruhe, Germany
- AcureOmics, Umeå, Sweden
| | | | - Katrin Lundstedt-Enkel
- AcureOmics, Umeå, Sweden
- Environmental toxicology, Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Stefan Rännar
- AcureOmics, Umeå, Sweden
- Corporate Research, Sartorius AG, Göttingen, Germany
| | - Johan Trygg
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
- Corporate Research, Sartorius AG, Göttingen, Germany
- * E-mail:
| | - Torbjörn Lundstedt
- AcureOmics, Umeå, Sweden
- Deparment of Pharmaceutical Bioscience, BMC, Uppsala University, Uppsala, Sweden
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3
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Dickmeis T, Feng Y, Mione MC, Ninov N, Santoro M, Spaink HP, Gut P. Nano-Sampling and Reporter Tools to Study Metabolic Regulation in Zebrafish. Front Cell Dev Biol 2019; 7:15. [PMID: 30873407 PMCID: PMC6401643 DOI: 10.3389/fcell.2019.00015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/31/2019] [Indexed: 01/09/2023] Open
Abstract
In the past years, evidence has emerged that hallmarks of human metabolic disorders can be recapitulated in zebrafish using genetic, pharmacological or dietary interventions. An advantage of modeling metabolic diseases in zebrafish compared to other "lower organisms" is the presence of a vertebrate body plan providing the possibility to study the tissue-intrinsic processes preceding the loss of metabolic homeostasis. While the small size of zebrafish is advantageous in many aspects, it also has shortcomings such as the difficulty to obtain sufficient amounts for biochemical analyses in response to metabolic challenges. A workshop at the European Zebrafish Principal Investigator meeting in Trento, Italy, was dedicated to discuss the advantages and disadvantages of zebrafish to study metabolic disorders. This perspective article by the participants highlights strategies to achieve improved tissue-resolution for read-outs using "nano-sampling" approaches for metabolomics as well as live imaging of zebrafish expressing fluorescent reporter tools that inform on cellular or subcellular metabolic processes. We provide several examples, including the use of reporter tools to study the heterogeneity of pancreatic beta-cells within their tissue environment. While limitations exist, we believe that with the advent of new technologies and more labs developing methods that can be applied to minimal amounts of tissue or single cells, zebrafish will further increase their utility to study energy metabolism.
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Affiliation(s)
- Thomas Dickmeis
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Yi Feng
- Centre for Inflammation Research, Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland
| | | | - Nikolay Ninov
- DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Herman P. Spaink
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Philipp Gut
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
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4
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Label-free Microarray-based Binding Affinity Constant Measurement with Modified Fluidic Arrangement. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2102-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Abstract
Metabolomics, the characterization of metabolites and their changes within biological systems, has seen great technological and methodological progress over the past decade. Most metabolomic experiments involve the characterization of the small-molecule content of fluids or tissue homogenates. While these microliter and larger volume metabolomic measurements can characterize hundreds to thousands of compounds, the coverage of molecular content decreases as sample sizes are reduced to the nanoliter and even to the picoliter volume range. Recent progress has enabled the ability to characterize the major molecules found within specific individual cells. Especially within the brain, a myriad of cell types are colocalized, and oftentimes only a subset of these cells undergo changes in both healthy and pathological states. Here we highlight recent progress in mass spectrometry-based approaches used for single cell metabolomics, emphasizing their application to neuroscience research. Single cell studies can be directed to measuring differences between members of populations of similar cells (e.g., oligodendrocytes), as well as characterizing differences between cell types (e.g., neurons and astrocytes), and are especially useful for measuring changes occurring during different behavior states, exposure to diets and drugs, neuronal activity, and disease. When combined with other omics approaches such as transcriptomics, and with morphological and physiological measurements, single cell metabolomics aids fundamental neurochemical studies, has great potential in pharmaceutical development, and should improve the diagnosis and treatment of brain diseases.
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Affiliation(s)
- Meng Qi
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Marina C Philip
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ning Yang
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Abstract
The genome revolution represents a complete change on our view of biological systems. The quantitative determination of changes in all major molecular components of the living cells, the "omics" approach, opened whole new fields for all health sciences. Genomics, transcriptomics, proteomics, metabolomics, and others, together with appropriate prediction and modeling tools, will mark the future of developmental toxicity assessment both for wildlife and humans. This is especially true for disciplines, like teratology, which rely on studies in model organisms, as studies at lower levels of organization are difficult to implement. Rodents and frogs have been the favorite models for studying human reproductive and developmental disorders for decades. Recently, the study of the development of zebrafish embryos (ZE) is becoming a major alternative tool to adult animal testing. ZE intrinsic characteristics makes this model a unique system to analyze in vivo developmental alterations that only can be studied applying in toto approaches. Moreover, under actual legislations, ZE is considered as a replacement model (and therefore, excluded from animal welfare regulations) during the first 5 days after fertilization. Here we review the most important components of the zebrafish toolbox available for analyzing early stages of embryotoxic events that could eventually lead to teratogenesis.
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7
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Ortiz-Villanueva E, Navarro-Martín L, Jaumot J, Benavente F, Sanz-Nebot V, Piña B, Tauler R. Metabolic disruption of zebrafish (Danio rerio) embryos by bisphenol A. An integrated metabolomic and transcriptomic approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:22-36. [PMID: 28780062 DOI: 10.1016/j.envpol.2017.07.095] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Although bisphenol A (BPA) is commonly recognized as an endocrine disruptor, the metabolic consequences of its exposure are still poorly understood. In this study, we present a non-targeted LC-MS based metabolomic analysis in combination with a full-genome, high-throughput RNA sequencing (RNA-Seq) to reveal the metabolic effects and the subjacent regulatory pathways of exposing zebrafish embryos to BPA during the first 120 hours post-fertilization. We applied multivariate data analysis methods to extract biochemical information from the LC-MS and RNA-Seq complex datasets and to perform testable predictions of the phenotypic adverse effects. Metabolomic and transcriptomic data revealed a similar subset of altered pathways, despite the large difference in the number of identified biomarkers (around 50 metabolites and more than 1000 genes). These results suggest that even a moderate coverage of zebrafish metabolome may be representative of the global metabolic changes. These multi-omic responses indicate a specific metabolic disruption by BPA affecting different signaling pathways, such as retinoid and prostaglandin metabolism. The combination of transcriptomic and metabolomic data allowed a dynamic interpretation of the results that could not be drawn from either single dataset. These results illustrate the utility of -omic integrative analyses for characterizing the physiological effects of toxicants beyond the mere indication of the affected pathways.
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Affiliation(s)
- Elena Ortiz-Villanueva
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Laia Navarro-Martín
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Joaquim Jaumot
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Benjamín Piña
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
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Huang SSY, Benskin JP, Veldhoen N, Chandramouli B, Butler H, Helbing CC, Cosgrove JR. A multi-omic approach to elucidate low-dose effects of xenobiotics in zebrafish (Danio rerio) larvae. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 182:102-112. [PMID: 27886581 DOI: 10.1016/j.aquatox.2016.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Regulatory-approved toxicity assays such as the OECD Fish Embryo Toxicity Assay (TG236) allow correlation of chemical exposure to adverse morphological phenotypes. However, these assays are ineffective in assessing sub-lethal (i.e. low-dose) effects, or differentiating between similar phenotypes induced by different chemicals. Inclusion of multi-omic analyses in studies investigating xenobiotic action provides improved characterization of biological response, thereby enhancing prediction of toxicological outcomes in whole animals in the absence of morphological effects. In the current study, we assessed perturbations in both the metabolome and transcriptome of zebrafish (Danio rerio; ZF) larvae exposed from 96 to 120h post fertilization to environmental concentrations of acetaminophen (APAP), diphenhydramine (DH), carbamazepine (CBZ), and fluoxetine (FLX); common pharmaceuticals with known mechanisms of action. Multi-omic responses were evaluated independently and integrated to identify molecular interactions and biological relevance of the responses. Results indicated chemical- and dose-specific changes suggesting differences in the time scale of transcript abundance and metabolite production. Increased impact on the metabolome relative to the transcriptome in FLX-treated animals suggests a stronger post-translational effect of the treatment. In contrast, the transcriptome showed higher sensitivity to perturbation in DH-exposed animals. Integration of 'omic' responses using multivariate approaches provided additional insights not obtained by independent 'omic' analyses and demonstrated that the most distinct overall response profiles were induced following low-dose exposure for all 4 pharmaceuticals. Importantly, changes in transcript abundance corroborated with predictions from metabolomic enrichment analyses and the identified perturbed biological pathways aligned with known xenobiotic mechanisms of action. This work demonstrates that a multi-omic toxicological approach, coupled with a sensitive animal model such as ZF larvae, can help characterize the toxicological relevance of acute low-dose chemical exposures.
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Affiliation(s)
- Susie S Y Huang
- SGS AXYS, Sidney, BC, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Jonathan P Benskin
- Department of Environmental Science and Analytical Chemistry (ACES), Stockholm University, Stockholm, Sweden
| | - Nik Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | | | - Caren C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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9
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Zendong Z, Bertrand S, Herrenknecht C, Abadie E, Jauzein C, Lemée R, Gouriou J, Amzil Z, Hess P. Passive Sampling and High Resolution Mass Spectrometry for Chemical Profiling of French Coastal Areas with a Focus on Marine Biotoxins. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:8522-8529. [PMID: 27463836 DOI: 10.1021/acs.est.6b02081] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Passive samplers (solid phase adsorption toxin tracking: SPATT) are able to accumulate biotoxins produced by microalgae directly from seawater, thus providing useful information for monitoring of the marine environment. SPATTs containing 0.3, 3, and 10 g of resin were deployed at four different coastal areas in France and analyzed using liquid chromatography coupled to high resolution mass spectrometry. Quantitative targeted screening provided insights into toxin profiles and showed that toxin concentrations and profiles in SPATTs were dependent on the amount of resin used. Between the three amounts of resin tested, SPATTs containing 3 g of resin appeared to be the best compromise, which is consistent with the use of 3 g of resin in SPATTs by previous studies. MassHunter and Mass Profiler Professional softwares were used for data reprocessing and statistical analyses. A differential profiling approach was developed to investigate and compare the overall chemical diversity of dissolved substances in different coastal water bodies. Principal component analysis (PCA) allowed for spatial differentiation between areas. Similarly, SPATTs retrieved from the same location at early, medium, and late deployment periods were also differentiated by PCA, reflecting seasonal variations in chemical profiles and in the microalgal community. This study used an untargeted metabolomic approach for spatial and temporal differentiation of marine environmental chemical profiles using SPATTs, and we propose this approach as a step forward in the discovery of chemical markers of short- or long-term changes in the microbial community structure.
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Affiliation(s)
- Zita Zendong
- Ifremer, Laboratoire Phycotoxines, Rue de l'Ile d'Yeu, 44311 Nantes, France
- LUNAM, Université de Nantes, MMS EA2160 , Faculté de Pharmacie, 9 rue Bias, 44035 Nantes, France
| | - Samuel Bertrand
- LUNAM, Université de Nantes, MMS EA2160 , Faculté de Pharmacie, 9 rue Bias, 44035 Nantes, France
| | - Christine Herrenknecht
- LUNAM, Université de Nantes, MMS EA2160 , Faculté de Pharmacie, 9 rue Bias, 44035 Nantes, France
| | - Eric Abadie
- Ifremer, Laboratoire Environnement Ressources du Languedoc-Roussillon, Centre for Marine Biodiversity, Exploitation and Conservation (MARBEC), CS30171 Sète Cedex 03 34200, France
| | - Cécile Jauzein
- Sorbonne Universités, UPMC Univ Paris 06 , CNRS, LOV, UMR 7093, Observatoire Océanologique de Villefranche/mer, Paris F-06230, France
| | - Rodolphe Lemée
- Sorbonne Universités, UPMC Univ Paris 06 , CNRS, LOV, UMR 7093, Observatoire Océanologique de Villefranche/mer, Paris F-06230, France
| | - Jérémie Gouriou
- Ifremer, Laboratoire Environnement Ressources Bretagne Occidentale (LER-BO), Station de Biologie Marine, Place de la Croi, BP 40537, Concarneau F-29185, France
| | - Zouher Amzil
- Ifremer, Laboratoire Phycotoxines, Rue de l'Ile d'Yeu, 44311 Nantes, France
| | - Philipp Hess
- Ifremer, Laboratoire Phycotoxines, Rue de l'Ile d'Yeu, 44311 Nantes, France
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Roullier C, Bertrand S, Blanchet E, Peigné M, Robiou du Pont T, Guitton Y, Pouchus YF, Grovel O. Time Dependency of Chemodiversity and Biosynthetic Pathways: An LC-MS Metabolomic Study of Marine-Sourced Penicillium. Mar Drugs 2016; 14:md14050103. [PMID: 27213411 PMCID: PMC4882577 DOI: 10.3390/md14050103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/21/2016] [Accepted: 05/11/2016] [Indexed: 12/14/2022] Open
Abstract
This work aimed at studying metabolome variations of marine fungal strains along their growth to highlight the importance of the parameter “time” for new natural products discovery. An untargeted time-scale metabolomic study has been performed on two different marine-derived Penicillium strains. They were cultivated for 18 days and their crude extracts were analyzed by HPLC-DAD-HRMS (High Performance Liquid Chromatography-Diode Array Detector-High Resolution Mass Spectrometry) each day. With the example of griseofulvin biosynthesis, a pathway shared by both strains, this work provides a new approach to study biosynthetic pathway regulations, which could be applied to other metabolites and more particularly new ones. Moreover, the results of this study emphasize the interest of such an approach for the discovery of new chemical entities. In particular, at every harvesting time, previously undetected features were observed in the LC-MS (Liquid Chromatography-Mass Spectrometry) data. Therefore, harvesting times for metabolite extraction should be performed at different time points to access the hidden metabolome.
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Affiliation(s)
- Catherine Roullier
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
| | - Samuel Bertrand
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
| | - Elodie Blanchet
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- Sorbonne Universités, UPMC Université Paris, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer 66650, France.
| | - Mathilde Peigné
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
| | - Thibaut Robiou du Pont
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
| | - Yann Guitton
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), LUNAM Université, Oniris, Nantes 44307, France.
| | - Yves François Pouchus
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
| | - Olivier Grovel
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
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Glucose metabolism and gene expression in juvenile zebrafish (Danio rerio) challenged with a high carbohydrate diet: effects of an acute glucose stimulus during late embryonic life. Br J Nutr 2015; 113:403-13. [PMID: 25609020 DOI: 10.1017/s0007114514003869] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Knowledge on the role of early nutritional stimuli as triggers of metabolic pathways in fish is extremely scarce. The objective of the present study was to assess the long-term effects of glucose injection in the yolk (early stimulus) on carbohydrate metabolism and gene regulation in zebrafish juveniles challenged with a high-carbohydrate low-protein (HC) diet. Eggs were microinjected at 1 d post-fertilisation (dpf) with either glucose (2 M) or saline solutions. Up to 25 dpf, fish were fed a low-carbohydrate high-protein (LC) control diet, which was followed by a challenge with the HC diet. Survival and growth of 35 dpf juveniles were not affected by injection or the HC diet. Glucose stimulus induced some long-term metabolic changes in the juveniles, as shown by the altered expression of genes involved in glucose metabolism. On glycolysis, the expression levels of hexokinase 1 (HK1) and phosphofructokinase-6 (6PFK) were up-regulated in the visceral and muscle tissues, respectively, of juveniles exposed to the glucose stimulus, indicating a possible improvement in glucose oxidation. On gluconeogenesis, the inhibition of the expression levels of PEPCK in fish injected with glucose suggested lower production of hepatic glucose. Unexpectedly, fructose-1,6-bisphosphatase (FBP) expression was induced and 6PFK expression reduced by glucose stimulus, leaving the possibility of a specific regulation of the FBP-6PFK metabolic cycle. Glucose metabolism in juveniles was estimated using a [¹⁴C]glucose tracer; fish previously exposed to the stimulus showed lower retention of [¹⁴C]glucose in visceral tissue (but not in muscle tissue) and, accordingly, higher glucose catabolism, in comparison with the saline group. Globally, our data suggest that glucose stimulus at embryo stage has the potential to alter particular steps of glucose metabolism in zebrafish juveniles.
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12
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Rhee JS, Lee JS. Whole genome data for omics-based research on the self-fertilizing fish Kryptolebias marmoratus. MARINE POLLUTION BULLETIN 2014; 85:532-541. [PMID: 24759509 DOI: 10.1016/j.marpolbul.2014.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/24/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
Genome resources have advantages for understanding diverse areas such as biological patterns and functioning of organisms. Omics platforms are useful approaches for the study of organs and organisms. These approaches can be powerful screening tools for whole genome, proteome, and metabolome profiling, and can be used to understand molecular changes in response to internal and external stimuli. This methodology has been applied successfully in freshwater model fish such as the zebrafish Danio rerio and the Japanese medaka Oryzias latipes in research areas such as basic physiology, developmental biology, genetics, and environmental biology. However, information is still scarce about model fish that inhabit brackish water or seawater. To develop the self-fertilizing killifish Kryptolebias marmoratus as a potential model species with unique characteristics and research merits, we obtained genomic information about K. marmoratus. We address ways to use these data for genome-based molecular mechanistic studies. We review the current state of genome information on K. marmoratus to initiate omics approaches. We evaluate the potential applications of integrated omics platforms for future studies in environmental science, developmental biology, and biomedical research. We conclude that information about the K. marmoratus genome will provide a better understanding of the molecular functions of genes, proteins, and metabolites that are involved in the biological functions of this species. Omics platforms, particularly combined technologies that make effective use of bioinformatics, will provide powerful tools for hypothesis-driven investigations and discovery-driven discussions on diverse aspects of this species and on fish and vertebrates in general.
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Affiliation(s)
- Jae-Sung Rhee
- Department of Marine Science, College of Natural Science, Incheon National University, Incheon 406-772, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
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13
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An PNT, Yamaguchi M, Bamba T, Fukusaki E. Metabolome analysis of Drosophila melanogaster during embryogenesis. PLoS One 2014; 9:e99519. [PMID: 25121768 PMCID: PMC4133167 DOI: 10.1371/journal.pone.0099519] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 05/15/2014] [Indexed: 02/02/2023] Open
Abstract
The Drosophila melanogaster embryo has been widely utilized as a model for genetics and developmental biology due to its small size, short generation time, and large brood size. Information on embryonic metabolism during developmental progression is important for further understanding the mechanisms of Drosophila embryogenesis. Therefore, the aim of this study is to assess the changes in embryos’ metabolome that occur at different stages of the Drosophila embryonic development. Time course samples of Drosophila embryos were subjected to GC/MS-based metabolome analysis for profiling of low molecular weight hydrophilic metabolites, including sugars, amino acids, and organic acids. The results showed that the metabolic profiles of Drosophila embryo varied during the course of development and there was a strong correlation between the metabolome and different embryonic stages. Using the metabolome information, we were able to establish a prediction model for developmental stages of embryos starting from their high-resolution quantitative metabolite composition. Among the important metabolites revealed from our model, we suggest that different amino acids appear to play distinct roles in different developmental stages and an appropriate balance in trehalose-glucose ratio is crucial to supply the carbohydrate source for the development of Drosophila embryo.
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Affiliation(s)
- Phan Nguyen Thuy An
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Insect Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- * E-mail:
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Rocha F, Dias J, Engrola S, Gavaia P, Geurden I, Dinis MT, Panserat S. Glucose overload in yolk has little effect on the long-term modulation of carbohydrate metabolic genes in zebrafish (Danio rerio). ACTA ACUST UNITED AC 2013; 217:1139-49. [PMID: 24363414 DOI: 10.1242/jeb.095463] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Some fish show a low metabolic ability to use dietary carbohydrates. The use of early nutritional stimuli to program metabolic pathways in fish is ill defined. Therefore, studies were undertaken with zebrafish to assess the effect of high glucose levels during the embryonic stage as a lifelong modulator of genes involved in carbohydrate metabolism. Genes related to carbohydrate metabolism were expressed at low levels at 0.2 and 1 day post-fertilization (dpf). However, from 4 dpf onwards there was a significant increase on expression of all genes, suggesting that all analysed pathways were active. By microinjection, we successfully enriched zebrafish egg yolk with glucose (a 43-fold increase of basal levels). Acute effects of glucose injection on gene expression were assessed in larvae up to 10 dpf, and the programming concept was evaluated in juveniles (41 dpf) challenged with a hyperglucidic diet. At 4 dpf, larvae from glucose-enriched eggs showed a downregulation of several genes related to glycolysis, glycogenolysis, lipogenesis and carbohydrate digestion in comparison with control (saline-injected) embryos. This inhibitory regulation was suppressed after 10 dpf. At the juvenile stage, and upon switching from a low to a high digestible carbohydrate diet, early glucose enrichment had no significant effect on most analysed genes. However, these same fish showed altered expression of the genes for cytosolic phosphoenolpyruvate carboxykinase, sodium-dependent glucose cotransporter 1 and glycogen synthase, suggesting changes to the glucose storage capacity in muscle and glucose production and transport in viscera. Overall, supplementation of egg yolk with high glucose levels had little effect on the long-term modulation of carbohydrate metabolic genes in zebrafish.
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Affiliation(s)
- Filipa Rocha
- CCMAR/CIMAR, Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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15
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Pre-symptomatic activation of antioxidant responses and alterations in glucose and pyruvate metabolism in Niemann-Pick Type C1-deficient murine brain. PLoS One 2013; 8:e82685. [PMID: 24367541 PMCID: PMC3867386 DOI: 10.1371/journal.pone.0082685] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/26/2013] [Indexed: 11/19/2022] Open
Abstract
Niemann-Pick Type C (NPC) disease is an autosomal recessive neurodegenerative disorder caused in most cases by mutations in the NPC1 gene. NPC1-deficiency is characterized by late endosomal accumulation of cholesterol, impaired cholesterol homeostasis, and a broad range of other cellular abnormalities. Although neuronal abnormalities and glial activation are observed in nearly all areas of the brain, the most severe consequence of NPC1-deficiency is a near complete loss of Purkinje neurons in the cerebellum. The link between cholesterol trafficking and NPC pathogenesis is not yet clear; however, increased oxidative stress in symptomatic NPC disease, increases in mitochondrial cholesterol, and alterations in autophagy/mitophagy suggest that mitochondria play a role in NPC disease pathology. Alterations in mitochondrial function affect energy and neurotransmitter metabolism, and are particularly harmful to the central nervous system. To investigate early metabolic alterations that could affect NPC disease progression, we performed metabolomics analyses of different brain regions from age-matched wildtype and Npc1-/- mice at pre-symptomatic, early symptomatic and late stage disease by 1H-NMR spectroscopy. Metabolic profiling revealed markedly increased lactate and decreased acetate/acetyl-CoA levels in Npc1-/- cerebellum and cerebral cortex at all ages. Protein and gene expression analyses indicated a pre-symptomatic deficiency in the oxidative decarboxylation of pyruvate to acetyl-CoA, and an upregulation of glycolytic gene expression at the early symptomatic stage. We also observed a pre-symptomatic increase in several indicators of oxidative stress and antioxidant response systems in Npc1-/- cerebellum. Our findings suggest that energy metabolism and oxidative stress may present additional therapeutic targets in NPC disease, especially if intervention can be started at an early stage of the disease.
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Nguyen M, Yang E, Neelkantan N, Mikhaylova A, Arnold R, Poudel MK, Stewart AM, Kalueff AV. Developing 'integrative' zebrafish models of behavioral and metabolic disorders. Behav Brain Res 2013; 256:172-87. [PMID: 23948218 DOI: 10.1016/j.bbr.2013.08.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 07/31/2013] [Accepted: 08/03/2013] [Indexed: 02/09/2023]
Abstract
Recently, the pathophysiological overlap between metabolic and mental disorders has received increased recognition. Zebrafish (Danio rerio) are rapidly becoming a popular model organism for translational biomedical research due to their genetic tractability, low cost, quick reproductive cycle, and ease of behavioral, pharmacological or genetic manipulation. High homology to mammalian physiology and the availability of well-developed assays also make the zebrafish an attractive organism for studying human disorders. Zebrafish neurobehavioral and endocrine phenotypes show promise for the use of zebrafish in studies of stress, obesity and related behavioral and metabolic disorders. Here, we discuss the parallels between zebrafish and other model species in stress and obesity physiology, as well as outline the available zebrafish models of weight gain, metabolic deficits, feeding, stress, anxiety and related behavioral disorders. Overall, zebrafish demonstrate a strong potential for modeling human behavioral and metabolic disorders, and their comorbidity.
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Affiliation(s)
- Michael Nguyen
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA; Thomas Jefferson High School for Science and Technology, 6560 Braddock Road, Alexandria, VA 22312, USA
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17
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Abstract
Zebrafish offer a unique vertebrate model for research areas such as drug development, disease modeling and other biological exploration. There is significant conservation of genetics and other cellular networks among zebrafish and other vertebrate models, including humans. Here we discuss the recent work and efforts made in different fields of biology to explore the potential of zebrafish. Along with this, we also reviewed the concept of systems biology. A biological system is made up of a large number of components that interact in a huge variety of combinations. To understand completely the behavior of a system, it is important to know its components and interactions, and this can be achieved through a systems biology approach. At the end of the paper we present a concept of integrating zebrafish into the systems biology approach.
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Affiliation(s)
- Mian Yahya Mushtaq
- a Natural Products Laboratory, Institute of Biology, Leiden University , Leiden , The Netherlands
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18
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Basu S, Sachidanandan C. Zebrafish: a multifaceted tool for chemical biologists. Chem Rev 2013; 113:7952-80. [PMID: 23819893 DOI: 10.1021/cr4000013] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sandeep Basu
- Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology (CSIR-IGIB) , South Campus, New Delhi 110025, India
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19
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Huang SM, Xu F, Lam SH, Gong Z, Ong CN. Metabolomics of developing zebrafish embryos using gas chromatography- and liquid chromatography-mass spectrometry. MOLECULAR BIOSYSTEMS 2013; 9:1372-80. [DOI: 10.1039/c3mb25450j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Goulitquer S, Potin P, Tonon T. Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. Mar Drugs 2012; 10:849-880. [PMID: 22690147 PMCID: PMC3366679 DOI: 10.3390/md10040849] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/13/2012] [Accepted: 03/21/2012] [Indexed: 01/01/2023] Open
Abstract
Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated.
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Affiliation(s)
- Sophie Goulitquer
- Plate-forme MetaboMER, CNRS & UPMC, FR2424, Station Biologique, 29680 Roscoff, France
| | - Philippe Potin
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
| | - Thierry Tonon
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
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Zhang A, Sun H, Han Y, Yuan Y, Wang P, Song G, Yuan X, Zhang M, Xie N, Wang X. Exploratory urinary metabolic biomarkers and pathways using UPLC-Q-TOF-HDMS coupled with pattern recognition approach. Analyst 2012; 137:4200-8. [DOI: 10.1039/c2an35780a] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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