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Hameed R, Naseer A, Saxena A, Akbar M, Toppo P, Sarkar A, Shukla SK, Nazir A. Functional implications of NHR-210 enrichment in C. elegans cephalic sheath glia: insights into metabolic and mitochondrial disruptions in Parkinson's disease models. Cell Mol Life Sci 2024; 81:202. [PMID: 38691171 PMCID: PMC11063106 DOI: 10.1007/s00018-024-05179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 05/03/2024]
Abstract
Glial cells constitute nearly half of the mammalian nervous system's cellular composition. The glia in C. elegans perform majority of tasks comparable to those conducted by their mammalian equivalents. The cephalic sheath (CEPsh) glia, which are known to be the counterparts of mammalian astrocytes, are enriched with two nuclear hormone receptors (NHRs)-NHR-210 and NHR-231. This unique enrichment makes the CEPsh glia and these NHRs intriguing subjects of study concerning neuronal health. We endeavored to assess the role of these NHRs in neurodegenerative diseases and related functional processes, using transgenic C. elegans expressing human alpha-synuclein. We employed RNAi-mediated silencing, followed by behavioural, functional, and metabolic profiling in relation to suppression of NHR-210 and 231. Our findings revealed that depleting nhr-210 changes dopamine-associated behaviour and mitochondrial function in human alpha synuclein-expressing strains NL5901 and UA44, through a putative target, pgp-9, a transmembrane transporter. Considering the alteration in mitochondrial function and the involvement of a transmembrane transporter, we performed metabolomics study via HR-MAS NMR spectroscopy. Remarkably, substantial modifications in ATP, betaine, lactate, and glycine levels were seen upon the absence of nhr-210. We also detected considerable changes in metabolic pathways such as phenylalanine, tyrosine, and tryptophan biosynthesis metabolism; glycine, serine, and threonine metabolism; as well as glyoxalate and dicarboxylate metabolism. In conclusion, the deficiency of the nuclear hormone receptor nhr-210 in alpha-synuclein expressing strain of C. elegans, results in altered mitochondrial function, coupled with alterations in vital metabolite levels. These findings underline the functional and physiological importance of nhr-210 enrichment in CEPsh glia.
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Affiliation(s)
- Rohil Hameed
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anam Naseer
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ankit Saxena
- Sophisticated Analytical Instrument Facility and Research, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mahmood Akbar
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pranoy Toppo
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arunabh Sarkar
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Sanjeev K Shukla
- Sophisticated Analytical Instrument Facility and Research, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Shukla S, Saxena A, Shukla SK, Nazir A. Modulation of Neurotransmitter Pathways and Associated Metabolites by Systemic Silencing of Gut Genes in C. elegans. Diagnostics (Basel) 2023; 13:2322. [PMID: 37510066 PMCID: PMC10378590 DOI: 10.3390/diagnostics13142322] [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: 05/10/2023] [Revised: 05/28/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The gut is now recognized as the "second brain" of the human body due to its integral role in neuronal health and functioning. Although we know that the gut communicates with the brain via immunological factors, microbial metabolites, and neurotransmitters, the interplay of these systems remains poorly understood. To investigate this interplay, we silenced 48 genes that are exclusively or primarily expressed in the C. elegans intestine. We studied the associated effects on various aspects of neurodegeneration, including proteotoxicity induced by α-Syn expression. We also assayed behaviours, such as mobility and cognition, that are governed by various neurotransmitters. We identified nine gut genes that significantly modulated these events. We further performed HR-MAS NMR-based metabolomics to recognize the metabolic variability induced by the respective RNAi conditions of R07E3.1, C14A6.1, K09D9.2, ZK593.2, F41H10.8, M02D8.4, M88.1, C03G6.15 and T01D3.6. We found that key metabolites such as phenylalanine, tyrosine, inosine, and glutamine showed significant variation among the groups. Gut genes that demonstrated neuroprotective effects (R07E3.1, C14A6.1, K09D9.2, and ZK593.2) showed elevated levels of inosine, phenylalanine, and tyrosine; whereas, genes that aggravated neurotransmitter levels demonstrated decreased levels of the same metabolites. Our results shed light on the intricate roles of gut genes in the context of neurodegeneration and suggest a new perspective on the reciprocal interrelation of gut genes, neurotransmitters, and associated metabolites. Further studies are needed to decipher the intricate roles of these genes in context of neurodegeneration in greater detail.
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Affiliation(s)
- Shikha Shukla
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ankit Saxena
- Sophisticated Analytical Instrumentation Facility and Research Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sanjeev K Shukla
- Sophisticated Analytical Instrumentation Facility and Research Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aamir Nazir
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow 226031, India
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Wong A. A roadmap to high-resolution standard microcoil MAS NMR spectroscopy for metabolomics. NMR IN BIOMEDICINE 2023; 36:e4683. [PMID: 34970795 DOI: 10.1002/nbm.4683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/06/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Current microcoil probe technology has emerged as a significant advancement in NMR applications to biofluids research. It has continued to excel as a hyphenated tool with other prominent microdevices, opening many new possibilities in multiple omics fields. However, this does not hold for biological samples such as intact tissue or organisms, due to the considerable challenges of incorporating the microcoil in a magic-angle spinning (MAS) probe without relinquishing the high-resolution spectral data. Not until 2012 did a microcoil MAS probe show promise in profiling the metabolome in a submilligram tissue biopsy with spectral resolution on par with conventional high-resolution MAS (HR-MAS) NMR. This result subsequently triggered a great interest in the possibility of NMR analysis with microgram tissues and striving toward the probe development of "high-resolution" capable microcoil MAS NMR spectroscopy. This review gives an overview of the issues and challenges in the probe development and summarizes the advancements toward metabolomics.
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Affiliation(s)
- Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette, France
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Sivelli G, Conley GM, Herrera C, Marable K, Rodriguez KJ, Bollwein H, Sudano MJ, Brugger J, Simpson AJ, Boero G, Grisi M. NMR spectroscopy of a single mammalian early stage embryo. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 335:107142. [PMID: 34999310 DOI: 10.1016/j.jmr.2021.107142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
The resolving power, chemical sensitivity and non-invasive nature of NMR have made it an established technique for in vivo studies of large organisms both for research and clinical applications. NMR would clearly be beneficial for analysis of entities at the microscopic scale of about 1 nL (the nanoliter scale), typical of early development of mammalian embryos, microtissues and organoids: the scale where the building blocks of complex organisms could be observed. However, the handling of such small samples (about 100 µm) and sensitivity issues have prevented a widespread adoption of NMR. In this article we show how these limitations can be overcome to obtain NMR spectra of a mammalian embryo in its early stage. To achieve this we employ ultra-compact micro-chip technologies in combination with 3D-printed micro-structures. Such device is packaged for use as plug & play sensor and it shows sufficient sensitivity to resolve NMR signals from individual bovine pre-implantation embryos. The embryos in this study are obtained through In Vitro Fertilization (IVF) techniques, transported cryopreserved to the NMR laboratory, and measured shortly after thawing. In less than 1 h these spherical samples of just 130-190 µm produce distinct spectral peaks, largely originating from lipids contained inside them. We further observe how the spectra vary from one sample to another despite their optical and morphological similarities, suggesting that the method can further develop into a non-invasive embryo assay for selection prior to embryo transfer.
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Affiliation(s)
| | | | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057 Zurich, Switzerland
| | | | - Kyle J Rodriguez
- Microsystems Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057 Zurich, Switzerland
| | - Mateus J Sudano
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jürgen Brugger
- Microsystems Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto, Scarborough Campus, 1265 Military Trail, Toronto M1C1A5, Canada
| | - Giovanni Boero
- Environmental NMR Center, University of Toronto, Scarborough Campus, 1265 Military Trail, Toronto M1C1A5, Canada
| | - Marco Grisi
- Annaida Technologies SA, Lausanne, Switzerland.
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Salzer L, Witting M. Quo Vadis Caenorhabditis elegans Metabolomics-A Review of Current Methods and Applications to Explore Metabolism in the Nematode. Metabolites 2021; 11:metabo11050284. [PMID: 33947148 PMCID: PMC8146106 DOI: 10.3390/metabo11050284] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolomics and lipidomics recently gained interest in the model organism Caenorhabditis elegans (C. elegans). The fast development, easy cultivation and existing forward and reverse genetic tools make the small nematode an ideal organism for metabolic investigations in development, aging, different disease models, infection, or toxicology research. The conducted type of analysis is strongly depending on the biological question and requires different analytical approaches. Metabolomic analyses in C. elegans have been performed using nuclear magnetic resonance (NMR) spectroscopy, direct infusion mass spectrometry (DI-MS), gas-chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) or combinations of them. In this review we provide general information on the employed techniques and their advantages and disadvantages in regard to C. elegans metabolomics. Additionally, we reviewed different fields of application, e.g., longevity, starvation, aging, development or metabolism of secondary metabolites such as ascarosides or maradolipids. We also summarised applied bioinformatic tools that recently have been used for the evaluation of metabolomics or lipidomics data from C. elegans. Lastly, we curated metabolites and lipids from the reviewed literature, enabling a prototypic collection which serves as basis for a future C. elegans specific metabolome database.
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Affiliation(s)
- Liesa Salzer
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
- Correspondence:
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Grisi M, Conley GM, Rodriguez KJ, Riva E, Egli L, Moritz W, Lichtenberg J, Brugger J, Boero G. NMR microsystem for label-free characterization of 3D nanoliter microtissues. Sci Rep 2020; 10:18306. [PMID: 33110145 PMCID: PMC7758329 DOI: 10.1038/s41598-020-75480-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Performing chemical analysis at the nanoliter (nL) scale is of paramount importance for medicine, drug development, toxicology, and research. Despite the numerous methodologies available, a tool for obtaining chemical information non-invasively is still missing at this scale. Observer effects, sample destruction and complex preparatory procedures remain a necessary compromise. Among non-invasive spectroscopic techniques, one able to provide holistic and highly resolved chemical information in-vivo is nuclear magnetic resonance (NMR). For its renowned informative power and ability to foster discoveries and life-saving applications, efficient NMR at microscopic scales is highly sought after, but so far technical limitations could not match the stringent necessities of microbiology, such as biocompatible handling, ease of use, and high throughput. Here we introduce a novel microsystem, which combines CMOS technology with 3D microfabrication, enabling nL NMR as a platform tool for non-invasive spectroscopy of organoids, 3D cell cultures, and early stage embryos. In this study we show its application to microlivers models simulating non-alcoholic fatty liver disease, demonstrating detection of lipid metabolism dynamics in a time frame of 14 days based on 117 measurements of single 3D human liver microtissues.
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Affiliation(s)
- Marco Grisi
- Annaida Technologies SA, Lausanne, Switzerland.
| | | | - Kyle J Rodriguez
- Microsystems Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erika Riva
- Service de Gastro-Entérologie et D'hépatologie, CHUV, Epalinges, Switzerland
| | | | | | | | - Jürgen Brugger
- Microsystems Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanni Boero
- Microsystems Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Liaghati Mobarhan Y, Soong R, Lane D, Simpson AJ. In vivo comprehensive multiphase NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:427-444. [PMID: 32239574 DOI: 10.1002/mrc.4832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 06/11/2023]
Abstract
Traditionally, due to different hardware requirements, nuclear magnetic resonance (NMR) has developed as two separate fields: one dealing with solids, and one with solutions. Comprehensive multiphase (CMP) NMR combines all electronics and hardware (magic angle spinning [MAS], gradients, high power Radio Frequency (RF) handling, lock, susceptibility matching) into a universal probe that permits a comprehensive study of all phases (i.e., liquid, gel-like, semisolid, and solid), in intact samples. When applied in vivo, it provides unique insight into the wide array of bonds in a living system from the most mobile liquids (blood, fluids) through gels (muscle, tissues) to the most rigid (exoskeleton, shell). In this tutorial, the practical aspects of in vivo CMP NMR are discussed including: handling the organisms, rotor preparation, sample spinning, water suppression, editing experiments, and finishes with a brief look at the potential of other heteronuclei (2 H, 15 N, 19 F, 31 P) for in vivo research. The tutorial is aimed as a general resource for researchers interested in developing and applying MAS-based approaches to living organisms. Although the focus here is CMP NMR, many of the approaches can be adapted (or directly applied) using conventional high-resolution magic angle spinning, and in some cases, even standard solid-state NMR probes.
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Affiliation(s)
- Yalda Liaghati Mobarhan
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Lane
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andre J Simpson
- Environmental NMR Center, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
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9
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General Guidelines for Sample Preparation Strategies in HR-µMAS NMR-based Metabolomics of Microscopic Specimens. Metabolites 2020; 10:metabo10020054. [PMID: 32019176 PMCID: PMC7073555 DOI: 10.3390/metabo10020054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 11/17/2022] Open
Abstract
The study of the metabolome within tissues, organisms, cells or biofluids can be carried out by several bioanalytical techniques. Among them, nuclear magnetic resonance (NMR) is one of the principal spectroscopic methods. This is due to a sample rotation technique, high-resolution magic angle spinning (HR-MAS), which targets the analysis of heterogeneous specimens with a bulk sample mass from 5 to 10 mg. Recently, a new approach, high-resolution micro-magic angle spinning (HR-μMAS), has been introduced. It opens, for the first time, the possibility of investigating microscopic specimens (<500 μg) with NMR spectroscopy, strengthening the concept of homogeneous sampling in a heterogeneous specimen. As in all bioanalytical approaches, a clean and reliable sample preparation strategy is a significant component in designing metabolomics (or -omics, in general) studies. The sample preparation for HR-μMAS is consequentially complicated by the μg-scale specimen and has yet to be addressed. This report details the strategies for three specimen types: biofluids, fluid matrices and tissues. It also provides the basis for designing future μMAS NMR studies of microscopic specimens.
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Adhikari SS, Zhao L, Dickmeis T, Korvink JG, Badilita V. Inductively coupled magic angle spinning microresonators benchmarked for high-resolution single embryo metabolomic profiling. Analyst 2019; 144:7192-7199. [PMID: 31696868 DOI: 10.1039/c9an01634a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The magic angle coil spinning (MACS) technique has been introduced as a very promising extension for solid state NMR detection, demonstrating sensitivity enhancements by a factor of 14 from the very first time it has been reported. The main beneficiary of this technique is the scientific community dealing with mass- and volume-limited, rare, or expensive samples. However, more than a decade after the first report on MACS, there is a very limited number of groups who have continued to develop the technique, let alone it being widely adopted by practitioners. This might be due to several drawbacks associated with the MACS technology until now, including spectral linewidth, heating due to eddy currents, and imprecise manufacturing. Here, we report a device overcoming all these remaining issues, therefore achieving: (1) spectral resolution of approx 0.01 ppm and normalized limit of detection of approx. 13 nmol s0.5 calculated using the anomeric proton of sucrose at 3 kHz MAS frequency; (2) limited temperature increase inside the MACS insert of only 5 °C at 5 kHz MAS frequency in an 11.74 T magnetic field, rendering MACS suitable to study live biological samples. The wafer-scale fabrication process yields MACS inserts with reproducible properties, readily available to be used on a large scale in bio-chemistry labs. To illustrate the potential of these devices for metabolomic studies, we further report on: (3) ultra-fine 1H-1H and 13C-13C J-couplings resolved within 10 min for a 340 mM uniformly 13C-labeled glucose sample; and (4) single zebrafish embryo measurements through 1H-1H COSY within 4.5 h, opening the gate for the single embryo NMR studies.
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Affiliation(s)
- Shyam S Adhikari
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Li Zhao
- Voxalytic GmbH, Rosengarten 3, 76228, Karlsruhe, Germany
| | - Thomas Dickmeis
- Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Jan G Korvink
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Vlad Badilita
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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Monte GG, Nani JV, de Almeida Campos MR, Dal Mas C, Marins LAN, Martins LG, Tasic L, Mori MA, Hayashi MAF. Impact of nuclear distribution element genes in the typical and atypical antipsychotics effects on nematode Caenorhabditis elegans: Putative animal model for studying the pathways correlated to schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:19-30. [PMID: 30578843 DOI: 10.1016/j.pnpbp.2018.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/18/2022]
Abstract
The nuclear distribution element genes are conserved from fungus to humans. The nematode Caenorhabditis elegans expresses two isoforms of nuclear distribution element genes, namely nud-1 and nud-2. While nud-1 was functionally demonstrated to be the worm nudC ortholog, bioinformatic analysis revealed that the nud-2 gene encodes the worm ortholog of the mammalian NDE1 (Nuclear Distribution Element 1 or NudE) and NDEL1 (NDE-Like 1 or NudEL) genes, which share overlapping roles in brain development in mammals and also mediate the axon guidance in mammalian and C. elegans neurons. A significantly higher NDEL1 enzyme activity was shown in treatment non-resistant compared to treatment resistant SCZ patients, who essentially present response to the therapy with atypical clozapine but not with typical antipsychotics. Using C. elegans as a model, we tested the consequence of nud genes suppression in the effects of typical and atypical antipsychotics. To assess the role of nud genes and antipsychotic drugs over C. elegans behavior, we measured body bend frequency, egg laying and pharyngeal pumping, which traits are controlled by specific neurons and neurotransmitters known to be involved in SCZ, as dopamine and serotonin. Evaluation of metabolic and behavioral response to the pharmacotherapy with these antipsychotics demonstrates an important unbalance in serotonin pathway in both nud-1 and nud-2 knockout worms, with more significant effects for nud-2 knockout. The present data also show an interesting trend of mutant knockout worm strains to present a metabolic profile closer to that observed for the wild-type animals after the treatment with the typical antipsychotic haloperidol, but which was not observed for the treatment with the atypical antipsychotic clozapine. Paradoxically, behavioral assays showed more evident effects for clozapine than for haloperidol, which is in line with previous studies with rodent animal models and clinical evaluations with SCZ patients. In addition, the validity and reliability of using this experimental animal model to further explore the convergence between the dopamine/serotonin pathways and neurodevelopmental processes was demonstrated here, and the potential usefulness of this model for evaluating the metabolic consequences of treatments with antipsychotics is also suggested.
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Affiliation(s)
- Gabriela Guilherme Monte
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP) São Paulo, Brazil
| | - João V Nani
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP) São Paulo, Brazil
| | | | - Caroline Dal Mas
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP) São Paulo, Brazil
| | - Lucas Augusto Negri Marins
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP) São Paulo, Brazil
| | - Lucas Gelain Martins
- Chemical Biology Laboratory, Department of Organic Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Ljubica Tasic
- Chemical Biology Laboratory, Department of Organic Chemistry, Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Marcelo A Mori
- Departament of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mirian A F Hayashi
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP) São Paulo, Brazil.
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Lucas-Torres C, Wong A. Current Developments in µMAS NMR Analysis for Metabolomics. Metabolites 2019; 9:metabo9020029. [PMID: 30736341 PMCID: PMC6410107 DOI: 10.3390/metabo9020029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/02/2019] [Accepted: 02/02/2019] [Indexed: 12/30/2022] Open
Abstract
Analysis of microscopic specimens has emerged as a useful analytical application in metabolomics because of its capacity for characterizing a highly homogenous sample with a specific interest. The undeviating analysis helps to unfold the hidden activities in a bulk specimen and contributes to the understanding of the fundamental metabolisms in life. In NMR spectroscopy, micro(µ)-probe technology is well-established and -adopted to the microscopic level of biofluids. However, this is quite the contrary with specimens such as tissue, cell and organism. This is due to the substantial difficulty of developing a sufficient µ-size magic-angle spinning (MAS) probe for sub-milligram specimens with the capability of high-quality data acquisition. It was not until 2012; a µMAS probe had emerged and shown promises to µg analysis; since, a continuous advancement has been made striving for the possibility of µMAS to be an effective NMR spectroscopic analysis. Herein, the mini-review highlights the progress of µMAS development—from an impossible scenario to an attainable solution—and describes a few demonstrative metabolic profiling studies. The review will also discuss the current challenges in µMAS NMR analysis and its potential to metabolomics.
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Affiliation(s)
| | - Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France.
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13
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Jouda M, Fuhrer E, Silva P, Korvink JG, MacKinnon N. Automatic Adaptive Gain for Magnetic Resonance Sensitivity Enhancement. Anal Chem 2019; 91:2376-2383. [PMID: 30608654 DOI: 10.1021/acs.analchem.8b05148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The decaying nature of magnetic resonance (MR) signals results in a decreasing signal-to-quantization noise ratio (SQNR) over the acquisition time. Here we describe a method to enhance the SQNR, and thus the overall signal-to-noise ratio (SNR), by dynamically adapting the gain of the receiver before analog-to-digital conversion (ADC). This is in contrast to a standard experiment in which the gain is fixed for a single data acquisition and is thus adjusted only for the first points of the signal. The gain adjustment in our method is done automatically in a closed loop fashion by using the envelope of the MR signal as the control signal. Moreover, the method incorporates a robust mechanism that runs along with signal acquisition to monitor the gain modulation, enabling precise recovery of the signals. The automatic adaptive gain (AGAIN) method requires minimal additional hardware and is thus general and can be implemented in the signal path of any commercial spectrometer system. We demonstrate an SNR enhancement factor of 2.64 when applied to a custom spectrometer, while a factor of 1.4 was observed when applied to a commercial spectrometer.
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Affiliation(s)
- Mazin Jouda
- Institute of Microstructure Technology (IMT) , Karlsruhe Institute of Technology (KIT) , Karlsruhe , Baden-Württemberg 76131 , Germany
| | - Erwin Fuhrer
- Institute of Microstructure Technology (IMT) , Karlsruhe Institute of Technology (KIT) , Karlsruhe , Baden-Württemberg 76131 , Germany
| | - Pedro Silva
- Institute of Microstructure Technology (IMT) , Karlsruhe Institute of Technology (KIT) , Karlsruhe , Baden-Württemberg 76131 , Germany
| | - Jan G Korvink
- Institute of Microstructure Technology (IMT) , Karlsruhe Institute of Technology (KIT) , Karlsruhe , Baden-Württemberg 76131 , Germany
| | - Neil MacKinnon
- Institute of Microstructure Technology (IMT) , Karlsruhe Institute of Technology (KIT) , Karlsruhe , Baden-Württemberg 76131 , Germany
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14
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Bastawrous M, Jenne A, Tabatabaei Anaraki M, Simpson AJ. In-Vivo NMR Spectroscopy: A Powerful and Complimentary Tool for Understanding Environmental Toxicity. Metabolites 2018; 8:E35. [PMID: 29795000 PMCID: PMC6027203 DOI: 10.3390/metabo8020035] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
Abstract
Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning. With in-vivo NMR it is possible to use the same organisms for control and exposure studies (controls are the same organisms prior to exposure inside the NMR). As such individual variability can be reduced while continual data collection over time provides the temporal resolution required to discern complex interconnected response pathways. When multidimensional NMR is combined with isotopic labelling, a wide range of metabolites can be identified in-vivo providing a unique window into the living metabolome that is highly complementary to more traditional metabolomics studies employing extracts, tissues, or biofluids.
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Affiliation(s)
- Monica Bastawrous
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Amy Jenne
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Maryam Tabatabaei Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - André J Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
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15
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Montinaro E, Grisi M, Letizia MC, Pethö L, Gijs MAM, Guidetti R, Michler J, Brugger J, Boero G. 3D printed microchannels for sub-nL NMR spectroscopy. PLoS One 2018; 13:e0192780. [PMID: 29742104 PMCID: PMC5942786 DOI: 10.1371/journal.pone.0192780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
Nuclear magnetic resonance (NMR) experiments on subnanoliter (sub-nL) volumes are hindered by the limited sensitivity of the detector and the difficulties in positioning and holding such small samples in proximity of the detector. In this work, we report on NMR experiments on liquid and biological entities immersed in liquids having volumes down to 100 pL. These measurements are enabled by the fabrication of high spatial resolution 3D printed microfluidic structures, specifically conceived to guide and confine sub-nL samples in the sub-nL most sensitive volume of a single-chip integrated NMR probe. The microfluidic structures are fabricated using a two-photon polymerization 3D printing technique having a resolution better than 1 μm3. The high spatial resolution 3D printing approach adopted here allows to rapidly fabricate complex microfluidic structures tailored to position, hold, and feed biological samples, with a design that maximizes the NMR signals amplitude and minimizes the static magnetic field inhomogeneities. The layer separating the sample from the microcoil, crucial to exploit the volume of maximum sensitivity of the detector, has a thickness of 10 μm. To demonstrate the potential of this approach, we report NMR experiments on sub-nL intact biological entities in liquid media, specifically ova of the tardigrade Richtersius coronifer and sections of Caenorhabditis elegans nematodes. We show a sensitivity of 2.5x1013 spins/Hz1/2 on 1H nuclei at 7 T, sufficient to detect 6 pmol of 1H nuclei of endogenous compounds in active volumes down to 100 pL and in a measurement time of 3 hours. Spectral resolutions of 0.01 ppm in liquid samples and of 0.1 ppm in the investigated biological entities are also demonstrated. The obtained results may indicate a route for NMR studies at the single unit level of important biological entities having sub-nL volumes, such as living microscopic organisms and eggs of several mammalians, humans included.
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Affiliation(s)
- E. Montinaro
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Microsystems, Lausanne, Switzerland
| | - M. Grisi
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Microsystems, Lausanne, Switzerland
| | - M. C. Letizia
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Microsystems, Lausanne, Switzerland
| | - L. Pethö
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Laboratory for Mechanics of Materials and Nanostructures, Thun, Switzerland
| | - M. A. M. Gijs
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Microsystems, Lausanne, Switzerland
| | - R. Guidetti
- University of Modena and Reggio Emilia, Department of Life Sciences, Modena, Italy
| | - J. Michler
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Laboratory for Mechanics of Materials and Nanostructures, Thun, Switzerland
| | - J. Brugger
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Microsystems, Lausanne, Switzerland
| | - G. Boero
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory for Microsystems, Lausanne, Switzerland
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16
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Shiokawa Y, Date Y, Kikuchi J. Application of kernel principal component analysis and computational machine learning to exploration of metabolites strongly associated with diet. Sci Rep 2018; 8:3426. [PMID: 29467421 PMCID: PMC5821832 DOI: 10.1038/s41598-018-20121-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022] Open
Abstract
Computer-based technological innovation provides advancements in sophisticated and diverse analytical instruments, enabling massive amounts of data collection with relative ease. This is accompanied by a fast-growing demand for technological progress in data mining methods for analysis of big data derived from chemical and biological systems. From this perspective, use of a general “linear” multivariate analysis alone limits interpretations due to “non-linear” variations in metabolic data from living organisms. Here we describe a kernel principal component analysis (KPCA)-incorporated analytical approach for extracting useful information from metabolic profiling data. To overcome the limitation of important variable (metabolite) determinations, we incorporated a random forest conditional variable importance measure into our KPCA-based analytical approach to demonstrate the relative importance of metabolites. Using a market basket analysis, hippurate, the most important variable detected in the importance measure, was associated with high levels of some vitamins and minerals present in foods eaten the previous day, suggesting a relationship between increased hippurate and intake of a wide variety of vegetables and fruits. Therefore, the KPCA-incorporated analytical approach described herein enabled us to capture input–output responses, and should be useful not only for metabolic profiling but also for profiling in other areas of biological and environmental systems.
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Affiliation(s)
- Yuka Shiokawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan. .,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. .,Graduate School of Bioagricultural Sciences and School of Agricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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17
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Kikuchi J, Ito K, Date Y. Environmental metabolomics with data science for investigating ecosystem homeostasis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:56-88. [PMID: 29405981 DOI: 10.1016/j.pnmrs.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 05/08/2023]
Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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18
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Wong A, Lucas-Torres C. High-resolution Magic-angle Spinning (HR-MAS) NMR Spectroscopy. NMR-BASED METABOLOMICS 2018. [DOI: 10.1039/9781782627937-00133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Since the beginning of high-resolution magic-angle spinning (HR-MAS) NMR spectroscopy in 1990s, we have witnessed tremendous instrumentation and methodological advancements in the HR-MAS NMR technique for semisolids. With HR-MAS, it is now possible to acquire reliable high-quality spectra in a routine and high-throughput fashion, and it has become a well-integrated metabolic screening tool for ex vivo biospecimens such as tissue biopsies, cells and organisms for NMR-based metabolomics research. This chapter provides the basic principles of HR-MAS and describes a few recent noteworthy developments that could strengthen the role of HR-MAS as a frontline NMR technique for metabolomics.
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Affiliation(s)
- Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette France
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19
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Duong NT, Yamato M, Nakano M, Kume S, Tamura Y, Kataoka Y, Wong A, Nishiyama Y. Capillary-Inserted Rotor Design for HRµMASNMR-Based Metabolomics on Mass-Limited Neurospheres. Molecules 2017; 22:E1289. [PMID: 28771206 PMCID: PMC6152061 DOI: 10.3390/molecules22081289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 07/30/2017] [Indexed: 11/17/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique and has been widely used in metabolomics. However, the intrinsic low sensitivity of NMR prevents its applications to systems with limited sample availabilities. In this study, a new experimental approach is presented to analyze mass-scarce samples in limited volumes of less than 300 nL with simple handling. The sample is loaded into the glass capillary, and this capillary is then inserted into a Kel-F rotor. The experimental performance of the capillary-inserted rotor (capillary-insert) is investigated on an isotropic solution of sucrose by the use of a high-resolution micro-sized magic angle spinning (HRµMAS) probe. The acquired NMR signal's sensitivity to a given sample amount is comparable or even higher in comparison to that recorded by the standard solution NMR probe. More importantly, this capillary-insert coupled with the HRµMAS probe allows in-depth studies of heterogeneous samples as the MAS removes the line broadening caused by the heterogeneity. The NMR analyses of mass-limited cultured neurospheres have been demonstrated, resulting in high quality spectra where numerous metabolites are unambiguously identified.
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Affiliation(s)
- Nghia Tuan Duong
- Advanced Solid-State NMR Unit, RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan.
| | - Masanori Yamato
- Multi-Modal Microstructure Analysis Unit, RIKEN CLST-JEOL Collaboration Center, RIKEN, Kobe, Hyogo 650-0047, Japan.
- Cellular Function Imaging Team, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan.
| | - Masayuki Nakano
- Cellular Function Imaging Team, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan.
- Department of Physiology, Osaka City University Graduate School of Medicine, Abeno-ku, Osaka 545-8585, Japan.
| | - Satoshi Kume
- Multi-Modal Microstructure Analysis Unit, RIKEN CLST-JEOL Collaboration Center, RIKEN, Kobe, Hyogo 650-0047, Japan.
- Cellular Function Imaging Team, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan.
| | - Yasuhisa Tamura
- Multi-Modal Microstructure Analysis Unit, RIKEN CLST-JEOL Collaboration Center, RIKEN, Kobe, Hyogo 650-0047, Japan.
- Cellular Function Imaging Team, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan.
| | - Yosky Kataoka
- Multi-Modal Microstructure Analysis Unit, RIKEN CLST-JEOL Collaboration Center, RIKEN, Kobe, Hyogo 650-0047, Japan.
- Cellular Function Imaging Team, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan.
- Department of Physiology, Osaka City University Graduate School of Medicine, Abeno-ku, Osaka 545-8585, Japan.
| | - Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | - Yusuke Nishiyama
- Advanced Solid-State NMR Unit, RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan.
- Engineering Division, JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
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20
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Effective combined water and sideband suppression for low-speed tissue and in vivo MAS NMR. Anal Bioanal Chem 2017. [DOI: 10.1007/s00216-017-0450-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Grisi M, Vincent F, Volpe B, Guidetti R, Harris N, Beck A, Boero G. NMR spectroscopy of single sub-nL ova with inductive ultra-compact single-chip probes. Sci Rep 2017; 7:44670. [PMID: 28317887 PMCID: PMC5357791 DOI: 10.1038/srep44670] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/13/2017] [Indexed: 11/28/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy enables non-invasive chemical studies of intact living matter. However, the use of NMR at the volume scale typical of microorganisms is hindered by sensitivity limitations, and experiments on single intact organisms have so far been limited to entities having volumes larger than 5 nL. Here we show NMR spectroscopy experiments conducted on single intact ova of 0.1 and 0.5 nL (i.e. 10 to 50 times smaller than previously achieved), thereby reaching the relevant volume scale where life development begins for a broad variety of organisms, humans included. Performing experiments with inductive ultra-compact (1 mm2) single-chip NMR probes, consisting of a low noise transceiver and a multilayer 150 μm planar microcoil, we demonstrate that the achieved limit of detection (about 5 pmol of 1H nuclei) is sufficient to detect endogenous compounds. Our findings suggest that single-chip probes are promising candidates to enable NMR-based study and selection of microscopic entities at biologically relevant volume scales.
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Affiliation(s)
- Marco Grisi
- Microengineering Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Franck Vincent
- Bruker BioSpin AG, Industriestrasse 26, Fällanden, 8116, Switzerland
| | - Beatrice Volpe
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, 41125, Italy
| | - Nicola Harris
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Armin Beck
- Bruker BioSpin AG, Industriestrasse 26, Fällanden, 8116, Switzerland
| | - Giovanni Boero
- Microengineering Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
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22
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Moran RF, Dawson DM, Ashbrook SE. Exploiting NMR spectroscopy for the study of disorder in solids. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1256604] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Robert F. Moran
- School of Chemistry, EaStCHEM and St Andrews Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Daniel M. Dawson
- School of Chemistry, EaStCHEM and St Andrews Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Sharon E. Ashbrook
- School of Chemistry, EaStCHEM and St Andrews Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
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23
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Kapranas A, Snart CJP, Williams H, Hardy ICW, Barrett DA. Metabolomics of aging assessed in individual parasitoid wasps. Sci Rep 2016; 6:34848. [PMID: 27713504 PMCID: PMC5054366 DOI: 10.1038/srep34848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/02/2016] [Indexed: 11/09/2022] Open
Abstract
Metabolomics studies of low-biomass organisms, such as small insects, have previously relied on the pooling of biological samples to overcome detection limits, particularly using NMR. We show that the differentiation of metabolite profiles of individual 1 mg parasitoid wasps of different ages is possible when using a modified sample preparation and a combination of untargeted NMR and LC-MS based metabolomics. Changes were observed between newly emerged and older wasps in glycerolipids, amino acids and circulatory sugars. This advance in chemical profiling has important implications for the study of the behaviour and ecology of parasitoids and many other species of small organisms because predictions and observations are typically made at the level of the individual. Thus, the metabolomic state of low-biomass individuals can now be related to their behaviour and ecological performance. We discuss specifically the utility of age-related metabolomic profiling but our new approach can be applied to a wide range of biological research.
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Affiliation(s)
| | - Charles J. P. Snart
- School of Biosciences, University of Nottingham, LE12 5RD, UK
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Huw Williams
- School of Chemistry, University of Nottingham, NG7 2RD, UK
| | - Ian C. W. Hardy
- School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - David A. Barrett
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, NG7 2RD, UK
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24
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Misawa T, Wei F, Kikuchi J. Application of Two-Dimensional Nuclear Magnetic Resonance for Signal Enhancement by Spectral Integration Using a Large Data Set of Metabolic Mixtures. Anal Chem 2016; 88:6130-4. [DOI: 10.1021/acs.analchem.6b01495] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Takuma Misawa
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Feifei Wei
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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25
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Zhang T, Zhang A, Qiu S, Yang S, Wang X. Current Trends and Innovations in Bioanalytical Techniques of Metabolomics. Crit Rev Anal Chem 2015; 46:342-51. [DOI: 10.1080/10408347.2015.1079475] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Bingol K, Brüschweiler R. Two elephants in the room: new hybrid nuclear magnetic resonance and mass spectrometry approaches for metabolomics. Curr Opin Clin Nutr Metab Care 2015; 18:471-7. [PMID: 26154280 PMCID: PMC4533976 DOI: 10.1097/mco.0000000000000206] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review describes some of the advances made over the past year in NMR-based metabolomics for the elucidation of known and unknown compounds, including new ways of how to combine this information with high-resolution mass spectrometry. RECENT FINDINGS A new method allows the back-calculation of mass spectra from NMR spectra that have been queried against databases improving the accuracy of the identified compounds by validation and consistency analysis. For the de-novo characterization of unknown compounds, an algorithm has been introduced that predicts all viable NMR spectra from accurate masses allowing, by comparison with experimental NMR data, the determination of the structures of new metabolites in complex mixtures. SUMMARY Recent advances in NMR and mass spectrometry-based metabolomics and their synergistic use promises to significantly improve metabolomics sample characterization both in terms of identification and quantitation, and accelerate metabolite discovery.
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Affiliation(s)
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio, USA
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Nagato EG, Lankadurai BP, Soong R, Simpson AJ, Simpson MJ. Development of an NMR microprobe procedure for high-throughput environmental metabolomics of Daphnia magna. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:745-53. [PMID: 25891518 DOI: 10.1002/mrc.4236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 11/21/2014] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Nuclear magnetic resonance (NMR) is the primary platform used in high-throughput environmental metabolomics studies because its non-selectivity is well suited for non-targeted approaches. However, standard NMR probes may limit the use of NMR-based metabolomics for tiny organisms because of the sample volumes required for routine metabolic profiling. Because of this, keystone ecological species, such as the water flea Daphnia magna, are not commonly studied because of the analytical challenges associated with NMR-based approaches. Here, the use of a 1.7-mm NMR microprobe in analyzing tissue extracts from D. magna is tested. Three different extraction procedures (D2O-based buffer, Bligh and Dyer, and acetonitrile : methanol : water) were compared in terms of the yields and breadth of polar metabolites. The D2O buffer extraction yielded the most metabolites and resulted in the best reproducibility. Varying amounts of D. magna dry mass were extracted to optimize metabolite isolation from D. magna tissues. A ratio of 1-1.5-mg dry mass to 40 µl of extraction solvent provided excellent signal-to-noise and spectral resolution using (1)H NMR. The metabolite profile of a single daphnid was also investigated (approximately 0.2 mg). However, the signal-to-noise of the (1)H NMR was considerably lower, and while feasible for select applications would likely not be appropriate for high-throughput NMR-based metabolomics. Two-dimensional NMR experiments on D. magna extracts were also performed using the 1.7-mm NMR probe to confirm (1)H NMR metabolite assignments. This study provides an NMR-based analytical framework for future metabolomics studies that use D. magna in ecological and ecotoxicity studies.
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Affiliation(s)
- Edward G Nagato
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Brian P Lankadurai
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
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28
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Metabolite localization in living drosophila using High Resolution Magic Angle Spinning NMR. Sci Rep 2015; 5:9872. [PMID: 25892587 PMCID: PMC4402646 DOI: 10.1038/srep09872] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/06/2015] [Indexed: 11/17/2022] Open
Abstract
We have developed new methods enabling in vivo localization and identification of metabolites through their 1H NMR signatures, in a drosophila. Metabolic profiles in localized regions were obtained using HR-MAS Slice Localized Spectroscopy and Chemical Shift Imaging at high magnetic fields. These methods enabled measurement of metabolite contents in anatomic regions of the fly, demonstrated by a decrease in β-alanine signals in the thorax of flies showing muscle degeneration.
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29
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Larive CK, Barding GA, Dinges MM. NMR spectroscopy for metabolomics and metabolic profiling. Anal Chem 2014; 87:133-46. [PMID: 25375201 DOI: 10.1021/ac504075g] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cynthia K Larive
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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30
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André M, Dumez JN, Rezig L, Shintu L, Piotto M, Caldarelli S. Complete protocol for slow-spinning high-resolution magic-angle spinning NMR analysis of fragile tissues. Anal Chem 2014; 86:10749-54. [PMID: 25286333 DOI: 10.1021/ac502792u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
High-resolution magic-angle spinning (HR-MAS) nuclear magnetic resonance (NMR) is an essential tool to characterize a variety of semisolid systems, including biological tissues, with virtually no sample preparation. The "non-destructive" nature of NMR is typically compromised, however, by the extreme centrifugal forces experienced under conventional HR-MAS frequencies of several kilohertz. These features limit the usefulness of current HR-MAS approaches for fragile samples. Here, we introduce a full protocol for acquiring high-quality HR-MAS NMR spectra of biological tissues at low spinning rates (down to a few hundred hertz). The protocol first consists of a carefully designed sample preparation, which yields spectra without significant spinning sidebands at low spinning frequency for several types of sample holders, including the standard disposable inserts classically used in HR-MAS NMR-based metabolomics. Suppression of broad spectral features is then achieved using a modified version of the recently introduced PROJECT experiment with added water suppression and rotor synchronization, which deposits limited power in the sample and which can be suitably rotor-synchronized at low spinning rates. The performance of the slow HR-MAS NMR procedure is demonstrated on conventional (liver tissue) and very delicate (fish eggs) samples, for which the slow-spinning conditions are shown to preserve the structural integrity and to minimize intercompartmental leaks of metabolites. Taken together, these results expand the applicability and reliability of HR-MAS NMR spectroscopy. These results have been obtained at 400 and 600 MHz and suggest that high-quality slow HR-MAS spectra can be expected at higher magnetic fields using the described protocol.
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Affiliation(s)
- Marion André
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301 , Avenue de la Terrasse, 91190 Gif sur Yvette, France
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