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Soong R, Liaghati Mobarhan Y, Tabatabaei M, Bastawrous M, Biswas RG, Simpson M, Simpson A. Flow-based in vivo NMR spectroscopy of small aquatic organisms. Magn Reson Chem 2020; 58:411-426. [PMID: 32239577 DOI: 10.1002/mrc.4886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/08/2019] [Accepted: 04/28/2019] [Indexed: 06/11/2023]
Abstract
NMR applied to living organisms is arguably the ultimate tool for understanding environmental stress responses and can provide desperately needed information on toxic mechanisms, synergistic effects, sublethal impacts, recovery, and biotransformation of xenobiotics. To perform in vivo NMR spectroscopy, a flow cell system is required to deliver oxygen and food to the organisms while maintaining optimal line shape for NMR spectroscopy. In this tutorial, two such flow cell systems and their constructions are discussed: (a) a single pump high-volume flow cell design is simple to build and ideal for organisms that do not require feeding (i.e., eggs) and (b) a more advanced low-volume double pump flow cell design that permits feeding, maintains optimal water height for water suppression, improves locking and shimming, and uses only a small recirculating volume, thus reducing the amount of xenobiotic required for testing. In addition, key experimental aspects including isotopic enrichment, water suppression, and 2D experiments for both 13 C enriched and natural abundance organisms are discussed.
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Affiliation(s)
- Ronald Soong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Yalda Liaghati Mobarhan
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Maryam Tabatabaei
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Monica Bastawrous
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Rajshree Ghosh Biswas
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Myrna Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andre Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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Liaghati Mobarhan Y, Soong R, Lane D, Simpson AJ. In vivo comprehensive multiphase NMR. Magn Reson Chem 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lane D, Liaghati Mobarhan Y, Soong R, Ning P, Bermel W, Tabatabaei Anaraki M, Wu B, Heumann H, Gundy M, Boenisch H, Jeong TY, Kovacevic V, Simpson MJ, Simpson AJ. Understanding the Fate of Environmental Chemicals Inside Living Organisms: NMR-Based 13C Isotopic Suppression Selects Only the Molecule of Interest within 13C-Enriched Organisms. Anal Chem 2019; 91:15000-15008. [DOI: 10.1021/acs.analchem.9b03596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Lane
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
| | - Yalda Liaghati Mobarhan
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Ronald Soong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Paris Ning
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Maryam Tabatabaei Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Bing Wu
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | | | | | | | - Tae-Yong Jeong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Vera Kovacevic
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
| | - Myrna J. Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
| | - André J. Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
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Lane D, Soong R, Bermel W, Ning P, Dutta Majumdar R, Tabatabaei-Anaraki M, Heumann H, Gundy M, Bönisch H, Liaghati Mobarhan Y, Simpson MJ, Simpson AJ. Selective Amino Acid-Only in Vivo NMR: A Powerful Tool To Follow Stress Processes. ACS Omega 2019; 4:9017-9028. [PMID: 31459990 PMCID: PMC6648361 DOI: 10.1021/acsomega.9b00931] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/09/2019] [Indexed: 05/24/2023]
Abstract
In vivo NMR of small 13C-enriched aquatic organisms is developing as a powerful tool to detect and explain toxic stress at the biochemical level. Amino acids are a very important category of metabolites for stress detection as they are involved in the vast majority of stress response pathways. As such, they are a useful proxy for stress detection in general, which could then be a trigger for more in-depth analysis of the metabolome. 1H-13C heteronuclear single quantum coherence (HSQC) is commonly used to provide additional spectral dispersion in vivo and permit metabolite assignment. While some amino acids can be assigned from HSQC, spectral overlap makes monitoring them in vivo challenging. Here, an experiment typically used to study protein structures is adapted for the selective detection of amino acids inside living Daphnia magna (water fleas). All 20 common amino acids can be selectively detected in both extracts and in vivo. By monitoring bisphenol-A exposure, the in vivo amino acid-only approach identified larger fluxes in a greater number of amino acids when compared to published works using extracts from whole organism homogenates. This suggests that amino acid-only NMR of living organisms may be a very sensitive tool in the detection of stress in vivo and is highly complementary to more traditional metabolomics-based methods. The ability of selective NMR experiments to help researchers to "look inside" living organisms and only detect specific molecules of interest is quite profound and paves the way for the future development of additional targeted experiments for in vivo research and monitoring.
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Affiliation(s)
- Daniel Lane
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Ronald Soong
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Wolfgang Bermel
- Bruker
BioSpin GmbH, Silberstreifen 4, Rheinstetten, Germany
| | - Paris Ning
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Rudraksha Dutta Majumdar
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
- Bruker
Canada Ltd, 2800 High
Point Drive, Milton, Ontario, Canada L9T 6P4
| | - Maryam Tabatabaei-Anaraki
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | | | | | | | - Yalda Liaghati Mobarhan
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - Myrna J. Simpson
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - André J. Simpson
- Environmental
NMR Centre, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
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Lane D, Skinner TE, Gershenzon NI, Bermel W, Soong R, Dutta Majumdar R, Liaghati Mobarhan Y, Schmidt S, Heumann H, Monette M, Simpson MJ, Simpson AJ. Assessing the potential of quantitative 2D HSQC NMR in 13C enriched living organisms. J Biomol NMR 2019; 73:31-42. [PMID: 30600417 DOI: 10.1007/s10858-018-0221-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/17/2018] [Indexed: 05/22/2023]
Abstract
In vivo Nuclear Magnetic Resonance (NMR) spectroscopy has great potential to interpret the biochemical response of organisms to their environment, thus making it an essential tool in understanding toxic mechanisms. However, magnetic susceptibility distortions lead to 1D NMR spectra of living organisms with lines that are too broad to identify and quantify metabolites, necessitating the use of 2D 1H-13C Heteronuclear Single Quantum Coherence (HSQC) as a primary tool. While quantitative 2D HSQC is well established, to our knowledge it has yet to be applied in vivo. This study represents a simple pilot study that compares two of the most popular quantitative 2D HSQC approaches to determine if quantitative results can be directly obtained in vivo in isotopically enriched Daphnia magna (water flea). The results show the perfect-HSQC experiment performs very well in vivo, but the decoupling scheme used is critical for accurate quantitation. An improved decoupling approach derived using optimal control theory is presented here that improves the accuracy of metabolite concentrations that can be extracted in vivo down to micromolar concentrations. When combined with 2D Electronic Reference To access In vivo Concentrations (ERETIC) protocols, the protocol allows for the direct extraction of in vivo metabolite concentrations without the use of internal standards that can be detrimental to living organisms. Extracting absolute metabolic concentrations in vivo is an important first step and should, for example, be important for the parameterization as well as the validation of metabolic flux models in the future.
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Affiliation(s)
- Daniel Lane
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Thomas E Skinner
- Department of Physics, Wright State University, Dayton, OH, 45735, USA
| | - Naum I Gershenzon
- Department of Physics, Wright State University, Dayton, OH, 45735, USA
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, Rheinstetten, Germany
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Rudraksha Dutta Majumdar
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Bruker Ltd., 2800 Highpoint Drive, Milton, ON, L9T 6P4, Canada
| | - Yalda Liaghati Mobarhan
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | | | | | - Martine Monette
- Bruker Ltd., 2800 Highpoint Drive, Milton, ON, L9T 6P4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
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Mobarhan YL, Fortier-McGill B, Soong R, Maas WE, Fey M, Monette M, Stronks HJ, Schmidt S, Heumann H, Norwood W, Simpson AJ. Comprehensive multiphase NMR applied to a living organism. Chem Sci 2016; 7:4856-4866. [PMID: 30155133 PMCID: PMC6016732 DOI: 10.1039/c6sc00329j] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/17/2016] [Indexed: 12/23/2022] Open
Abstract
Comprehensive Multiphase NMR provides an overview as to all components (liquids, gels, solids) in a living organism.
Comprehensive multiphase (CMP) NMR is a novel technology that integrates all the hardware from solution-, gel- and solid-state into a single NMR probe, permitting all phases to be studied in intact samples. Here comprehensive multiphase (CMP) NMR is used to study all components in a living organism for the first time. This work describes 4 new scientific accomplishments summarized as: (1) CMP-NMR is applied to a living animal, (2) an effective method to deliver oxygen to the organisms is described which permits longer studies essential for in-depth NMR analysis in general, (3) a range of spectral editing approaches are applied to fully differentiate the various phases solutions (metabolites) through to solids (shell) (4) 13C isotopic labelling and multidimensional NMR are combined to provide detailed assignment of metabolites and structural components in vivo. While not explicitly studied here the multiphase capabilities of the technique offer future possibilities to study kinetic transfer between phases (e.g. nutrient assimilation, contaminant sequestration), molecular binding at interfaces (e.g. drug or contaminant binding) and bonding across and between phases (e.g. muscle to bone) in vivo. Future work will need to focus on decreasing the spinning speed to reduce organism stress during analysis.
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Affiliation(s)
- Yalda Liaghati Mobarhan
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
| | - Blythe Fortier-McGill
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
| | - Ronald Soong
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
| | - Werner E Maas
- Bruker BioSpin Corp. , 15 Fortune Drive , Billerica , Massachusetts , USA 01821-3991
| | - Michael Fey
- Bruker BioSpin Corp. , 15 Fortune Drive , Billerica , Massachusetts , USA 01821-3991
| | - Martine Monette
- Bruker BioSpin Canada , 555 Steeles Avenue East , Milton , ON , Canada L9T 1Y6
| | - Henry J Stronks
- Bruker BioSpin Canada , 555 Steeles Avenue East , Milton , ON , Canada L9T 1Y6
| | | | | | - Warren Norwood
- Environment Canada , 867 Lakeshore Rd. , Burlington , ON , Canada L7R 4A6
| | - André J Simpson
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
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