1
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Pellizzari J, Soong R, Downey K, Biswas RG, Kock FC, Steiner K, Goerling B, Haber A, Decker V, Busse F, Simpson M, Simpson A. Slice through the water-Exploring the fundamental challenge of water suppression for benchtop NMR systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:463-473. [PMID: 38282484 DOI: 10.1002/mrc.5431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Abstract
Benchtop NMR provides improved accessibility in terms of cost, space, and technical expertise. In turn, this encourages new users into the field of NMR spectroscopy. Unfortunately, many interesting samples in education and research, from beer to whole blood, contain significant amounts of water that require suppression in 1H NMR in order to recover sample information. However, due to the significant reduction in chemical shift dispersion in benchtop NMR systems, the sample signals are much closer to the water resonance compared to those in a corresponding high-field NMR spectrum. Therefore, simply translating solvent suppression experiments intended for high-field NMR instruments to benchtop NMR systems without careful consideration can be problematic. In this study, the effectiveness of several popular water suppression schemes was evaluated for benchtop NMR applications. Emphasis is placed on pulse sequences with no, or few, adjustable parameters making them easy to implement. These fall into two main categories: (1) those based on Pre-SAT including Pre-SAT, PURGE, NOESY-PR, and g-NOESY-PR and (2) those based on binomial inversion including JRS and W5-WATERGATE. Among these schemes, solvent suppression sequences based on Pre-SAT offer a general approach for easy solvent suppression for samples with higher analyte concentrations (sucrose standard and Redbull™). However, for human urine, binomial-like sequences were required. In summary, it is demonstrated that highly efficient water suppression approaches can be implemented on benchtop NMR systems in a simple manner, despite the limited spectral dispersion, further illustrating the potential for widespread implementation of these approaches in education and research.
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Affiliation(s)
| | - Ronald Soong
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Katelyn Downey
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | - Flavio C Kock
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | | | | | | | | | - Myrna Simpson
- University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Andre Simpson
- University of Toronto Scarborough, Toronto, Ontario, Canada
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2
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Ghosh Biswas R, Bermel W, Jenne A, Soong R, Simpson MJ, Simpson AJ. HR-MAS DREAMTIME NMR for Slow Spinning ex Vivo and in Vivo Samples. Anal Chem 2023; 95:17054-17063. [PMID: 37934172 DOI: 10.1021/acs.analchem.3c03800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
HR-MAS NMR is a powerful tool, capable of monitoring molecular changes in intact heterogeneous samples. However, one of the biggest limitations of 1H NMR is its narrow spectral width which leads to considerable overlap in complex natural samples. DREAMTIME NMR is a highly selective technique that allows users to isolate suites of metabolites from congested spectra. This permits targeted metabolomics by NMR and is ideal for monitoring specific processes. To date, DREAMTIME has only been employed in solution-state NMR, here it is adapted for HR-MAS applications. At high spinning speeds (>5 kHz), DREAMTIME works with minimal modifications. However, spinning over 3-4 kHz leads to cell lysis, and if maintaining sample integrity is necessary, slower spinning (<2.5 kHz) is required. Very slow spinning (≤500 Hz) is advantageous for in vivo analysis to increase organism survival; however, sidebands from water pose a problem. To address this, a version of DREAMTIME, termed DREAMTIME-SLOWMAS, is introduced. Both techniques are compared at 2500, 500, and 50 Hz, using ex vivo worm tissue. Following this, DREAMTIME-SLOWMAS is applied to monitor key metabolites of anoxic stress in living shrimp at 500 Hz. Thus, standard DREAMTIME works well under MAS conditions and is recommended for samples reswollen in D2O or spun >2500 Hz. For slow spinning in vivo or intact tissue samples, DREAMTIME-SLOWMAS provides an excellent way to target process-specific metabolites while maintaining sample integrity. Overall, DREAMTIME should find widespread application wherever targeted molecular information is required from complex samples with a high degree of spectral overlap.
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Affiliation(s)
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
| | - Andre J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, ON M1C 1A4, Canada
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3
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O'Connor LE, Robison P, Quesada G, Kerrigan JF, O'Halloran RC, Guerard JJ, Chin YP. Chlorpyrifos fate in the Arctic: Importance of analyte structure in interactions with Arctic dissolved organic matter. WATER RESEARCH 2023; 242:120154. [PMID: 37327545 PMCID: PMC10527095 DOI: 10.1016/j.watres.2023.120154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/17/2023] [Accepted: 05/29/2023] [Indexed: 06/18/2023]
Abstract
The insecticide and current use pesticide chlorpyrifos (CLP) is transported via global distillation to the Arctic where it may pose a threat to this ecosystem. CLP is readily detected in Arctic environmental compartments, but current research has not studied its partitioning between water and dissolved organic matter (DOM) nor the role of photochemistry in CLP's fate in aquatic systems. Here, the partition coefficients of CLP were quantified with various types of DOM isolated from the Arctic and an International Humic Substances Society (IHSS) reference material Suwannee River natural organic matter (SRNOM). While CLP readily partitions to DOM, CLP exhibits a significantly higher binding constant with Arctic lacustrine DOM relative to fluvial DOM or SRNOM. The experimental partitioning coefficients (KDOC) were compared to a calculated value estimated using poly parameter linear free energy relationship (pp-LFER) and was found to be in good agreement with SRNOM, but none of the Arctic DOMs. We found that Arctic KDOC values decrease with increasing SUVA254, but no correlations were observed for the other DOM compositional parameters. DOM also mediates the photodegradation of CLP, with stark differences in photo-kinetics using Arctic DOM isolated over time and space. This work highlights the chemo-diversity of Arctic DOM relative to IHSS reference materials and highlights the need for in-depth characterization of DOM that transcends the current paradigm based upon terrestrial and microbial precursors.
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Affiliation(s)
- Lauren E O'Connor
- Department of Civil and Environmental Engineering, University of Delaware, 127 The Green, Newark, DE 19716, USA
| | - Pippin Robison
- Chemistry Department, United States Naval Academy, Annapolis, MD 21402, USA
| | - Ginna Quesada
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Jill F Kerrigan
- Department of Civil and Environmental Engineering, University of Delaware, 127 The Green, Newark, DE 19716, USA
| | - Robyn C O'Halloran
- Department of Civil and Environmental Engineering, University of Delaware, 127 The Green, Newark, DE 19716, USA
| | - Jennifer J Guerard
- Chemistry Department, United States Naval Academy, Annapolis, MD 21402, USA.
| | - Yu-Ping Chin
- Department of Civil and Environmental Engineering, University of Delaware, 127 The Green, Newark, DE 19716, USA.
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4
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Fondeur F, White TL, Coleman CJ, Diprete DP, Nash CA, Looney BB. Proton nuclear magnetic resonance (1H NMR) of flammable organic chemicals in radioactive high-level supernatant waste at the Savannah River Site (SRS). MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:407-417. [PMID: 36967631 DOI: 10.1002/mrc.5349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 06/09/2023]
Abstract
The Savannah River Site stores approximately 36 million gallons of radioactive and hazardous waste that contains approximately 245 million curies. The waste is sent through various chemical processes to reduce its volume and to separate various components. The facility plans to replace formic acid (a chemical used to reduce soluble mercury) with glycolic acid. Recycle solution with glycolate may flow back to the tank farm, where the glycolate can generate hydrogen gas by thermal and radiolytic mechanisms. The current analytical method for detecting glycolate (ion chromatography) in supernatant requires a large dilution to reduce interference from the nitrate anions. Hydrogen nuclear magnetic resonance is an analytical method that requires less sample dilution. It takes advantage of the CH2 group in glycolate. Liquid samples were spiked with four different levels of glycolate to build a calibration line, as it is recommended in the standard addition method. The detection and quantitation limits determined were 1 and 5 ppm, respectively, for 32 scans, which is well below the process limit of 10 ppm. In one test, 800 scans of a supernatant spiked with 1 ppm glycolate resulted in a -CH2 peak with a signal-to-noise ratio of 36.
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Affiliation(s)
| | - Thomas L White
- Savannah River National Laboratory, Aiken, SC, 29841, USA
| | | | | | - Charles A Nash
- Savannah River National Laboratory, Aiken, SC, 29841, USA
| | - Brian B Looney
- Savannah River National Laboratory, Aiken, SC, 29841, USA
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5
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Ronda K, Downey K, Jenne A, Bastawrous M, Wolff WW, Steiner K, Lysak DH, Costa PM, Simpson MJ, Jobst KJ, Simpson AJ. Exploring Proton-Only NMR Experiments and Filters for Daphnia In Vivo: Potential and Limitations. Molecules 2023; 28:4863. [PMID: 37375418 DOI: 10.3390/molecules28124863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Environmental metabolomics provides insight into how anthropogenic activities have an impact on the health of an organism at the molecular level. Within this field, in vivo NMR stands out as a powerful tool for monitoring real-time changes in an organism's metabolome. Typically, these studies use 2D 13C-1H experiments on 13C-enriched organisms. Daphnia are the most studied species, given their widespread use in toxicity testing. However, with COVID-19 and other geopolitical factors, the cost of isotope enrichment increased ~6-7 fold over the last two years, making 13C-enriched cultures difficult to maintain. Thus, it is essential to revisit proton-only in vivo NMR and ask, "Can any metabolic information be obtained from Daphnia using proton-only experiments?". Two samples are considered here: living and whole reswollen organisms. A range of filters are tested, including relaxation, lipid suppression, multiple-quantum, J-coupling suppression, 2D 1H-1H experiments, selective experiments, and those exploiting intermolecular single-quantum coherence. While most filters improve the ex vivo spectra, only the most complex filters succeed in vivo. If non-enriched organisms must be used, then, DREAMTIME is recommended for targeted monitoring, while IP-iSQC was the only experiment that allowed non-targeted metabolite identification in vivo. This paper is critically important as it documents not just the experiments that succeed in vivo but also those that fail and demonstrates first-hand the difficulties associated with proton-only in vivo NMR.
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Affiliation(s)
- Kiera Ronda
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Monica Bastawrous
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - William W Wolff
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katrina Steiner
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Daniel H Lysak
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Peter M Costa
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Myrna J Simpson
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, NL A1C 5S7, Canada
| | - Andre J Simpson
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
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6
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Kida M, Merder J, Fujitake N, Tanabe Y, Hayashi K, Kudoh S, Dittmar T. Determinants of Microbial-Derived Dissolved Organic Matter Diversity in Antarctic Lakes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5464-5473. [PMID: 36947486 PMCID: PMC10077579 DOI: 10.1021/acs.est.3c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Identifying drivers of the molecular composition of dissolved organic matter (DOM) is essential to understand the global carbon cycle, but an unambiguous interpretation of observed patterns is challenging due to the presence of confounding factors that affect the DOM composition. Here, we show, by combining ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, that the DOM molecular composition varies considerably among 43 lakes in East Antarctica that are isolated from terrestrial inputs and human influence. The DOM composition in these lakes is primarily driven by differences in the degree of photodegradation, sulfurization, and pH. Remarkable molecular beta-diversity of DOM was found that rivals the dissimilarity between DOM of rivers and the deep ocean, which was driven by environmental dissimilarity rather than the spatial distance. Our results emphasize that the extensive molecular diversity of DOM can arise even in one of the most pristine and organic matter source-limited environments on Earth, but at the same time the DOM composition is predictable by environmental variables and the lakes' ecological history.
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Affiliation(s)
- Morimaru Kida
- Research
Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute
for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, Oldenburg 26129, Germany
- Soil
Science Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Julian Merder
- Department
of Global Ecology, Carnegie Institution
for Science, 260 Panama Street, Stanford, California 94305, United States
| | - Nobuhide Fujitake
- Soil
Science Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Yukiko Tanabe
- National
Institute of Polar Research, Research Organization of Information
and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
- Department
of Polar Science, SOKENDAI (The Graduate
University for Advanced Studies), 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
| | - Kentaro Hayashi
- Institute
for Agro-Environmental Sciences, NARO, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Sakae Kudoh
- National
Institute of Polar Research, Research Organization of Information
and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
- Department
of Polar Science, SOKENDAI (The Graduate
University for Advanced Studies), 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
| | - Thorsten Dittmar
- Research
Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute
for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, Oldenburg 26129, Germany
- Helmholtz
Institute for Functional Marine Biodiversity (HIFMB) at the University
of Oldenburg, Oldenburg 26129, Germany
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7
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Holderman NR, Ferrer-González FX, Glushka J, Moran MA, Edison AS. Dissolved organic metabolite extraction from high-salt media. NMR IN BIOMEDICINE 2023; 36:e4797. [PMID: 35799308 DOI: 10.1002/nbm.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.
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Affiliation(s)
- Nicole R Holderman
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - John Glushka
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Arthur S Edison
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
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8
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Zhang Z, Ma Y, Li A, Pan Y, Yao Q, Jia X, Zhou Q. Improved fractionation method using amphipathic NDAM for the efficient separation of disinfection by-product precursors in natural organic matter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38174-38184. [PMID: 36576624 DOI: 10.1007/s11356-022-24549-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The hydrophilic substances in natural organic matter (NOM) are the main precursor of disinfection by-products (DBPs) formed during disinfection processes. The fractionation of the components in NOM based on hydrophilicity contributes to elaborating the behavior of NOM during disinfection. However, the traditional NOM fractionation method using two hydrophobic resins of DAX-8 and XAD-4 lays emphasis on the separation of hydrophobic substances, limiting the thorough study of the hydrophilic components in NOM. In this work, the amphiphilic resin NDAM was employed as a replacement of XAD-4 to realize more thorough separation of the hydrophilic substances. Compared with the divinylbenzene (DVB) structure of XAD-4, the NDAM possesses a more hydrophilic skeleton of N-vinylpyrrolidone (NVP) and DVB which favors the adsorption of hydrophilic components in NOM. The two fractionation methods of DAX-8 + XAD-4 and DAX-8 + NDAM were applied to fractionate NOM, and the obtained fractions were characterized via fluorescence spectra, UV spectra, acid-base titration, the partition coefficients of aqueous two-phase systems(ATPs), and 1H nuclear magnetic resonance (1H-NMR). The results showed that the transphilic fractions separated by XAD-4 accounted for 11.09% of NOM, while the proportion increased to 20.33% with the method of NDAM fractionation. Besides, the hydrophilic components enriched by NDAM not only have more π-conjugated systems and more aromatic structure but also contain more oxygen-containing and nitrogen-containing functional groups. In addition, the hydrophilic fractions separated by NDAM contained more DBP precursors. The NDAM separates more NOM which can produce bromine-containing DBPs into HPIA, and the DBP productivity of HPIN is significantly higher than that of XAD-4. In general, the NOM fractionation method proposed in this study utilizing NDAM resin could fractionate the hydrophilic fractions in NOM more thoroughly, showing application potential in the analysis and control of DBPs formed from NOM.
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Affiliation(s)
- Ziang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Yan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Aimin Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Yang Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Qianqian Yao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Xiaorui Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China
| | - Qing Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, China.
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9
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Alves MR, Coward EK, Gonzales D, Sauer JS, Mayer KJ, Prather KA, Grassian VH. Changes in light absorption and composition of chromophoric marine-dissolved organic matter across a microbial bloom. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1923-1933. [PMID: 36169554 DOI: 10.1039/d2em00150k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Marine chromophoric dissolved organic matter (m-CDOM) mediates many vital photochemical processes at the ocean's surface. Isolating m-CDOM within the chemical complexity of marine dissolved organic matter has remained an analytical challenge. The SeaSCAPE campaign, a large-scale mesocosm experiment, provided a unique opportunity to probe the in situ production of m-CDOM across phytoplankton and microbial blooms. Results from mass spectrometry coupled with UV-VIS spectroscopy reveal production of a chemodiverse set of compounds well-correlated with increases in absorbance after a bacterial bloom, indicative of autochthonous m-CDOM production. Notably, many of the absorbing compounds were found to be enriched in nitrogen, which may be essential to chromophore function. From these results, quinoids, porphyrins, flavones, and amide-like compounds were identified via structural analysis and may serve as important photosensitizers in the marine boundary layer. Overall, this study demonstrates a step forward in identifying and characterizing m-CDOM using temporal mesocosm data and integrated UV-VIS spectroscopy and mass spectrometry analyses.
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Affiliation(s)
- Michael R Alves
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
| | - Elizabeth K Coward
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
| | - David Gonzales
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
| | - Jon S Sauer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
| | - Kathryn J Mayer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Kimberly A Prather
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
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10
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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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11
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Bastawrous M, Gruschke O, Soong R, Jenne A, Gross D, Busse F, Nashman B, Lacerda A, Simpson AJ. Comparing the Potential of Helmholtz and Planar NMR Microcoils for Analysis of Intact Biological Samples. Anal Chem 2022; 94:8523-8532. [DOI: 10.1021/acs.analchem.2c01560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monica Bastawrous
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Oliver Gruschke
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Ronald Soong
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Dieter Gross
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Ben Nashman
- Synex Medical, 2 Bloor Street E, Suite 310, Toronto, Ontario M4W 1A8, Canada
| | - Andressa Lacerda
- Synex Medical, 2 Bloor Street E, Suite 310, Toronto, Ontario M4W 1A8, Canada
| | - Andre J. Simpson
- Environmental NMR Center, Department of Physical and Environmental Science, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
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12
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Cabugao KGM, Gushgari-Doyle S, Chacon SS, Wu X, Bhattacharyya A, Bouskill N, Chakraborty R. Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges. Front Microbiol 2022; 13:864895. [PMID: 35602028 PMCID: PMC9114703 DOI: 10.3389/fmicb.2022.864895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.
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Affiliation(s)
- Kristine Grace M Cabugao
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephany S Chacon
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xiaoqin Wu
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amrita Bhattacharyya
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Bouskill
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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13
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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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
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14
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Xu C, Lin P, Garimella R, Li D, Xing W, Patterson NE, Kaplan DI, Yeager CM, Hatcher PG, Santschi PH. 1H- 13C heteronuclear single quantum coherence NMR evidence for iodination of natural organic matter influencing organo-iodine mobility in the environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152546. [PMID: 34973322 DOI: 10.1016/j.scitotenv.2021.152546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
The complex biogeochemical behavior of iodine (I) isotopes and their interaction with natural organic matter (NOM) pose a challenge for transport models. Here, we present results from iodination experiments with humic acid (HA) and fulvic acid (FA) using 1H-13C heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy. Even though not a quantitative approach, 1H-13C HSQC NMR corroborated that iodination of NOM occurs primarily through aromatic electrophilic substitution of proton by I, and also revealed how iodination chemically alters HA and FA in a manner that potentially affects the mobility of iodinated NOM in the environment. Three types of iodination experiments were conducted with HA and FA: a) non-enzymatic iodination by IO3- (pH 3) and I- (pH 4 and 7), b) addition of lactoperoxidase to promote I--iodination in the presence of the co-substrate, H2O2 (pH 7), and c) addition of laccase for facilitating I--iodination in the presence of O2, with or without a mediator (pH 4). When mediators or H2O2 were present, extracellular oxidases and peroxidases enhanced I- incorporation into NOM by between 54% and 3400%. Iodination of HA, which was less than that of FA, enhanced HA's stability (inferred from increases in aliphatic compounds, decreases in carbohydrate moieties, and thus increased molecular hydrophobicity) yet reduced HA's tendency to incorporate more iodine. As such, HA is expected to act more as a sink for iodine in the environment. In contrast, iodination of FA appeared to generate additional iodine binding sites, which resulted in greater iodine uptake capability and enhanced mobility (inferred from decreases in aliphatic compounds, increases in carbohydrates, and thus decreases in molecular hydrophobicity). These results indicate that certain NOM moieties may enhance while others may inhibit radioiodine mobility in the aqueous environment.
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Affiliation(s)
- Chen Xu
- Department of Marine Science, Texas A & M University at Galveston, Galveston, TX 77551, United States.
| | - Peng Lin
- Department of Marine Science, Texas A & M University at Galveston, Galveston, TX 77551, United States
| | | | - Dien Li
- Savannah River National Laboratory, Aiken, SC 29808, United States
| | - Wei Xing
- Department of Marine Science, Texas A & M University at Galveston, Galveston, TX 77551, United States
| | - Nicole E Patterson
- Department of Marine Science, Texas A & M University at Galveston, Galveston, TX 77551, United States
| | - Daniel I Kaplan
- Savannah River National Laboratory, Aiken, SC 29808, United States
| | - Chris M Yeager
- Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Patrick G Hatcher
- Department of Chemistry, Old Dominion University, Norfolk, VA 23529, United States
| | - Peter H Santschi
- Department of Marine Science, Texas A & M University at Galveston, Galveston, TX 77551, United States
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15
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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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16
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Lamar RT, Monda H, Sleighter R. Use of Ore-Derived Humic Acids With Diverse Chemistries to Elucidate Structure-Activity Relationships (SAR) of Humic Acids in Plant Phenotypic Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:758424. [PMID: 34925408 DOI: 10.3389/fpls.2021.758424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
For legal reasons, the publisher has withdrawn this article from public view. For additional information, please contact the publisher.
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Affiliation(s)
| | - Hiarhi Monda
- Bio Huma Netics, Inc., Gilbert, AZ, United States
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17
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Vione D, Minero C, Carena L. Fluorophores in surface freshwaters: importance, likely structures, and possible impacts of climate change. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1429-1442. [PMID: 34490433 DOI: 10.1039/d1em00273b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluorescence spectroscopy is one of the most useful techniques currently available for the characterisation of organic matter in natural water samples, because it combines easy availability of instrumentation, high sensitivity and limited requirements for sample treatment. The main fluorophores that can be found in natural waters are usually proteins (and/or free amino acids) and humic substances (humic and fulvic acids). The identification of these fluorescent compounds in water samples helps to obtain information about, among others, biological activity in the water body, possible transport of organic matter from soil, and the phenomenon of photobleaching that decreases both the absorbance and (usually) the fluorescence of natural organic matter. Interestingly, all these phenomena can be affected by climate change, which could alter to different extents the ratio between aquagenic and pedogenic fluorophores. Several events induced by warming in natural waters (and especially lake water) could enhance algal growth, thereby also enhancing the production of aquagenic organic matter. Intense precipitation events could increase the export of pedogenic material to surface waters, while photobleaching would be enhanced in the epilimnion of lakes when summer stratification becomes longer and more stable because of higher temperatures. Interestingly, photobleaching affects humic substances to a higher extent compared to protein-like material, thus protein fluorescence signals could be more preserved in stratified waters.
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Affiliation(s)
- Davide Vione
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy.
| | - Claudio Minero
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy.
| | - Luca Carena
- Dipartimento di Chimica, Università di Torino, Via P. Giuria 5, 10125 Torino, Italy.
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18
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Anaraki MT, Lysak DH, Downey K, Kock FVC, You X, Majumdar RD, Barison A, Lião LM, Ferreira AG, Decker V, Goerling B, Spraul M, Godejohann M, Helm PA, Kleywegt S, Jobst K, Soong R, Simpson MJ, Simpson AJ. NMR spectroscopy of wastewater: A review, case study, and future potential. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 126-127:121-180. [PMID: 34852923 DOI: 10.1016/j.pnmrs.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (13C, 15N, 19F, 31P, 29Si) as well as other environmentally relevant nuclei and metals such as 27Al, 51V, 207Pb and 113Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.
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Affiliation(s)
- Maryam Tabatabaei Anaraki
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Flávio Vinicius Crizóstomo Kock
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada; Department of Chemistry, Federal University of São Carlos-SP (UFSCar), São Carlos, SP, Brazil
| | - Xiang You
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Rudraksha D Majumdar
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada; Synex Medical, 2 Bloor Street E, Suite 310, Toronto, ON M4W 1A8, Canada
| | - Andersson Barison
- NMR Center, Federal University of Paraná, CP 19081, 81530-900 Curitiba, PR, Brazil
| | - Luciano Morais Lião
- NMR Center, Institute of Chemistry, Universidade Federal de Goiás, Goiânia 74690-900, Brazil
| | | | - Venita Decker
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | | | - Manfred Spraul
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | | | - Paul A Helm
- Environmental Monitoring & Reporting Branch, Ontario Ministry of the Environment, Toronto M9P 3V6, Canada
| | - Sonya Kleywegt
- Technical Assessment and Standards Development Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON M4V 1M2, Canada
| | - Karl Jobst
- Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada.
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19
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Kida M, Fujitake N, Kojima T, Tanabe Y, Hayashi K, Kudoh S, Dittmar T. Dissolved Organic Matter Processing in Pristine Antarctic Streams. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10175-10185. [PMID: 34240854 DOI: 10.1021/acs.est.1c03163] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accelerated glacier melt and runoff may lead to inputs of labile dissolved organic matter (DOM) to downstream ecosystems and stimulate the associated biogeochemical processes. However, still little is known about glacial DOM composition and its downstream processing before entering the ocean, although the function of DOM in food webs and ecosystems largely depends on its composition. Here, we employ a set of molecular and optical techniques (UV-vis absorption and fluorescence spectroscopy, 1H NMR, and ultrahigh-resolution mass spectrometry) to elucidate the composition of DOM in Antarctic glacial streams and its downstream change. Glacial DOM consisted largely of a mixture of small microbial-derived biomolecules. 1H NMR analysis of bulk water revealed that these small molecules were processed downstream into more complex, structurally unrecognizable molecules. The extent of processing varied between streams. By applying multivariate statistical (compositional data) analysis of the DOM molecular data, we identified molecular compounds that were tightly associated and moved in parallel in the glacial streams. Lakes in the middle of the flow paths enhanced water residence time and allowed for both more DOM processing and production. In conclusion, downstream processing of glacial DOM is substantial in Antarctica and affects the amounts of biologically labile substrates that enter the ocean.
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Affiliation(s)
- Morimaru Kida
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Street 9-11, Oldenburg 26129, Germany
| | - Nobuhide Fujitake
- Soil Science Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Taichi Kojima
- Soil Science Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Yukiko Tanabe
- National Institute of Polar Research, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
- Department of Polar Science, SOKENDAI (The Graduate University for Advanced Studies), 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
| | - Kentaro Hayashi
- Institute for Agro-Environmental Sciences, NARO, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Sakae Kudoh
- National Institute of Polar Research, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
- Department of Polar Science, SOKENDAI (The Graduate University for Advanced Studies), 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Street 9-11, Oldenburg 26129, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB) at the University of Oldenburg, Carl-von-Ossietzky-Street 9-11, Oldenburg 26129, Germany
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20
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Whitty SD, Waggoner DC, Cory RM, Kaplan LA, Hatcher PG. Direct noninvasive 1 H NMR analysis of stream water DOM: Insights into the effects of lyophilization compared with whole water. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:540-553. [PMID: 31429120 DOI: 10.1002/mrc.4935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is widely used in the field of aquatic biogeochemistry to examine the chemical structure of dissolved organic matter (DOM). Most aquatic DOM analyzed by proton NMR (1 H NMR) is concentrated mainly by freeze-drying prior to analysis to combat low concentrations, frequently <100 μM C, and eliminate interference from water. This study examines stream water with low dissolved organic carbon content by 1 H NMR with a direct noninvasive analysis of whole water using a water-suppression technique. Surface waters, collected from the headwaters of the Rio Tempisquito, Costa Rica, were examined directly, and the spectral characteristics were compared with those of the traditional preanalysis freeze-drying approach revealing significant differences in the relative intensity of peaks between the whole water and freeze-dried DOM. The freeze-dried DOM required less time to obtain quality spectra, but several peaks were missing compared with the spectra of whole water DOM; notably the most dominant peak in the spectrum constituting roughly 10% of the DOM. The stream water DOM showed an increase in the relative intensity of aliphatic methyl and methylene groups and a decrease in carbonyl, carboxyl, and carbohydrate functionalities after freeze-drying. The results of this study show that freeze-drying alters the original composition of DOM and thus freeze-dried DOM may not represent the original DOM. The information gained from whole water analysis of stream water DOM in a noninvasive fashion outweighs the attraction of reduced analysis times for preconcentrated samples, particularly for studies interested in investigating the low molecular weight fraction of DOM.
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Affiliation(s)
- Stephanie D Whitty
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Derek C Waggoner
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Rose M Cory
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
| | | | - Patrick G Hatcher
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
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21
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Edison AS, Colonna M, Gouveia GJ, Holderman NR, Judge MT, Shen X, Zhang S. NMR: Unique Strengths That Enhance Modern Metabolomics Research. Anal Chem 2020; 93:478-499. [DOI: 10.1021/acs.analchem.0c04414] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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22
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Ali S, Badshah G, Da Ros Montes D’Oca C, Ramos Campos F, Nagata N, Khan A, de Fátima Costa Santos M, Barison A. High-Resolution Magic Angle Spinning (HR-MAS) NMR-Based Fingerprints Determination in the Medicinal Plant Berberis laurina. Molecules 2020; 25:E3647. [PMID: 32796509 PMCID: PMC7465263 DOI: 10.3390/molecules25163647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 01/10/2023] Open
Abstract
Berberis laurina (Berberidaceae) is a well-known medicinal plant used in traditional medicine since ancient times; however, it is scarcely studied to a large-scale fingerprint. This work presents a broad-range fingerprints determination through high-resolution magical angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy, a well-established flexible analytical method and one of most powerful "omics" platforms. It had been intended to describe a large range of chemical compositions in all plant parts. Beyond that, HR-MAS NMR allowed the direct investigation of botanical material (leaves, stems, and roots) in their natural, unaltered states, preventing molecular changes. The study revealed 17 metabolites, including caffeic acid, and berberine, a remarkable alkaloid from the genus Berberis L. The metabolic pattern changes of the leaves in the course of time were found to be seasonally dependent, probably due to the variability of seasonal and environmental trends. This metabolites overview is of great importance in understanding plant (bio)chemistry and mediating plant survival and is influenceable by interacting environmental means. Moreover, the study will be helpful in medicinal purposes, health sciences, crop evaluations, and genetic and biotechnological research.
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Affiliation(s)
- Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil; (G.B.); (C.D.R.M.D.); (N.N.); (M.d.F.C.S.)
| | - Gul Badshah
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil; (G.B.); (C.D.R.M.D.); (N.N.); (M.d.F.C.S.)
| | - Caroline Da Ros Montes D’Oca
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil; (G.B.); (C.D.R.M.D.); (N.N.); (M.d.F.C.S.)
| | | | - Noemi Nagata
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil; (G.B.); (C.D.R.M.D.); (N.N.); (M.d.F.C.S.)
| | - Ajmir Khan
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Maria de Fátima Costa Santos
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil; (G.B.); (C.D.R.M.D.); (N.N.); (M.d.F.C.S.)
| | - Andersson Barison
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil; (G.B.); (C.D.R.M.D.); (N.N.); (M.d.F.C.S.)
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Lane D, Bermel W, Ning P, Jeong TY, Martin R, Soong R, Wu B, Tabatabaei-Anaraki M, Heumann H, Gundy M, Boenisch H, Adamo A, Arhonditsis G, Simpson AJ. Targeting the Lowest Concentration of a Toxin That Induces a Detectable Metabolic Response in Living Organisms: Time-Resolved In Vivo 2D NMR during a Concentration Ramp. Anal Chem 2020; 92:9856-9865. [DOI: 10.1021/acs.analchem.0c01370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Paris Ning
- 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
| | - Richard Martin
- IMicrosolder, 57 Marshall Street West, Meaford, Ontario, Canada N4L 1E4
| | - Ronald Soong
- 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
| | - Maryam Tabatabaei-Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | | | | | | | - Antonio Adamo
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - George Arhonditsis
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
| | - 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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Song C, Shan S, Yang C, Zhang C, Zhou X, Ma Q, Yrjälä K, Zheng H, Cao Y. The comparison of dissolved organic matter in hydrochars and biochars from pig manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137423. [PMID: 32325561 DOI: 10.1016/j.scitotenv.2020.137423] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) has an important effect on soil fertility, activity of microorganisms and transport of contaminants. In this study, DOM released by the hydrochar and biochar prepared under various conditions from pig manure, was assessed using a combination of UV-Visible spectroscopy, fluorescence excitation-emission (EEM) spectrophotometry and 1H-nuclear magnetic resonance (1H NMR). The dissolved organic carbon (DOC) extracted from the hydrochar and biochar ranged from 3.34-11.96% and 0.38-0.48%, respectively, and the highest DOM was released by HCK0.5 (180 °C and 0.5% KOH). The aliphatic compounds were most common in DOM which mainly included three humic acid-like and one protein-like substance. The hydrochar-DOM had a larger molecular weight and lower aromaticity than biochar-DOM, but the effect of temperature on the DOM characteristics of hydrochar and biochar was opposite. The acidic treatment increased the content of functional groups containing oxygen and nitrogen in hydrochar-DOM, and alkaline treatment increased the content of aliphatic compounds. The results obtained are beneficial to select carbonation process and guide the rational application of hydrochar and biochar from pig manure in soil remediation field.
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Affiliation(s)
- Chengfang Song
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China
| | - Shengdao Shan
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Chao Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Cheng Zhang
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaoqing Zhou
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China
| | - Qi Ma
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China
| | - Kim Yrjälä
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China; Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Huabao Zheng
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yucheng Cao
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, Zhejiang A&F University, Hangzhou 311300, China
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25
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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. MAGNETIC RESONANCE IN CHEMISTRY : MRC 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] [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. 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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27
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Makowka A, Nichelmann L, Schulze D, Spengler K, Wittmann C, Forchhammer K, Gutekunst K. Glycolytic Shunts Replenish the Calvin-Benson-Bassham Cycle as Anaplerotic Reactions in Cyanobacteria. MOLECULAR PLANT 2020; 13:471-482. [PMID: 32044444 DOI: 10.1016/j.molp.2020.02.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/16/2019] [Accepted: 01/10/2020] [Indexed: 05/07/2023]
Abstract
The recent discovery of the Entner-Doudoroff (ED) pathway as a third glycolytic route beside Embden-Meyerhof-Parnas (EMP) and oxidative pentose phosphate (OPP) pathway in oxygenic photoautotrophs requires a revision of their central carbohydrate metabolism. In this study, unexpectedly, we observed that deletion of the ED pathway alone, and even more pronounced in combination with other glycolytic routes, diminished photoautotrophic growth in continuous light in the cyanobacterium Synechocystis sp. PCC 6803. Furthermore, we found that the ED pathway is required for optimal glycogen catabolism in parallel to an operating Calvin-Benson-Bassham (CBB) cycle. It is counter-intuitive that glycolytic routes, which are a reverse to the CBB cycle and do not provide any additional biosynthetic intermediates, are important under photoautotrophic conditions. However, observations on the ability to reactivate an arrested CBB cycle revealed that they form glycolytic shunts that tap the cellular carbohydrate reservoir to replenish the cycle. Taken together, our results suggest that the classical view of the CBB cycle as an autocatalytic, completely autonomous cycle that exclusively relies on its own enzymes and CO2 fixation to regenerate ribulose-1,5-bisphosphate for Rubisco is an oversimplification. We propose that in common with other known autocatalytic cycles, the CBB cycle likewise relies on anaplerotic reactions to compensate for the depletion of intermediates, particularly in transition states and under fluctuating light conditions that are common in nature.
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Affiliation(s)
- Alexander Makowka
- Department of Biology, Botanical Institute, University Kiel, 24118 Kiel, Germany
| | - Lars Nichelmann
- Department of Biology, Botanical Institute, University Kiel, 24118 Kiel, Germany
| | - Dennis Schulze
- Institute for Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Katharina Spengler
- Department of Biology, Botanical Institute, University Kiel, 24118 Kiel, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Karl Forchhammer
- Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, University Tübingen, 72076 Tübingen, Germany
| | - Kirstin Gutekunst
- Department of Biology, Botanical Institute, University Kiel, 24118 Kiel, Germany.
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28
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The influence of the stereochemistry and C-end chemical modification of dermorphin derivatives on the peptide-phospholipid interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183066. [PMID: 31634444 DOI: 10.1016/j.bbamem.2019.183066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/24/2019] [Accepted: 09/11/2019] [Indexed: 11/23/2022]
Abstract
In this work the conformation of dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2, an opioid peptide and its analogues with different stereochemistry of alanine and different C-terminus is studied in aqueous and membrane environments. Using two-dimensional NMR techniques we demonstrate that in D2O/H2O peptides with D-alanine have extended conformation, while for the L-isomers more compact conformation is preferred. The analysis of ROESY HR MAS spectra of the peptides interacting with the DMPC bilayer indicates that both stereoisomers have still more extended conformation compared to aqueous phase, as shown by much weaker intermolecular interactions. The influence of Ala residue stereochemistry is also reflected in the interactions of the studied peptides with model membranes, as shown by the 31P NMR static spectra, in which the shapes of the phosphorus NMR signals originating from D-isomers correspond to spherically shaped vesicles in the presence of external magnetic field, in comparison to a more elongated ones observed for L-isomers, while TEM photographs shows that upon addition of D-isomers larger lipid vesicles are formed, in contrast to smaller ones for L-isomers. The location of aromatic fragments of dermorphins in the membrane is determined based on static 2H NMR and 1H1H RFDR MAS experiments. All aromatic rings were found to be inserted in the hydrophobic part of the bilayer, with the exception of the Tyr5 rings of D-Ala dermorphins. The influence of the C-terminal modification was found to be almost imperceptible.
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29
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Benchtop flow NMR spectroscopy as an online device for the in vivo monitoring of lipid accumulation in microalgae. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101624] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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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] [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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31
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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: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [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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32
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Tomar D, Chaudhary S, Jena KC. Self-assembly of l-phenylalanine amino acid: electrostatic induced hindrance of fibril formation. RSC Adv 2019; 9:12596-12605. [PMID: 35515878 PMCID: PMC9063664 DOI: 10.1039/c9ra00268e] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/11/2019] [Indexed: 11/21/2022] Open
Abstract
Nanostructure morphology originating from the self-assembly of molecules has attracted substantial attention due to its role in toxic amyloid fibril formation and immense potential in the design and fabrication of novel biomaterials. This study presents the role of intermolecular electrostatic interaction on the self-assembly process of l-phenylalanine (L-Phe) amino acid. We have employed attenuated total reflection Fourier transform infrared spectroscopy to probe the existence of different ionization states of the amino acid in various pH aqueous solutions. The self-assembly process of L-Phe in the aqueous phase is explored by using circular dichroism absorption and nuclear magnetic resonance spectroscopic tools. The observed spectral features have shown the signature of higher order structures and possible perturbation in the π-π stacking aromatic interactions for the cationic and anionic states of the amino acid. Scanning electron microscopy is used to probe the self-assembled morphology of the L-Phe amino acid dried samples prepared from the same pH aqueous solutions. We find that for the case of zwitterionic states the self-assembly nanostructures are dominated by the presence of fibrillar morphology, however interestingly for cationic and anionic states the morphology is dominated by the presence of flakes. Our finding demonstrates the potential influence of intermolecular electrostatic interaction over the aromatic π-π stacking interaction in hindering the fibril formation.
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Affiliation(s)
- Deepak Tomar
- Department of Physics, Indian Institute of Technology Ropar Rupnagar Punjab-140001 India +91-1881-242166
| | - Shilpi Chaudhary
- Department of Physics, Indian Institute of Technology Ropar Rupnagar Punjab-140001 India +91-1881-242166
| | - Kailash Chandra Jena
- Department of Physics, Indian Institute of Technology Ropar Rupnagar Punjab-140001 India +91-1881-242166
- Center for Biomedical Engineering, Indian Institute of Technology Ropar Rupnagar Punjab-140001 India
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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. JOURNAL OF BIOMOLECULAR 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] [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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34
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Anaraki MT, Lane D, Bastawrous M, Jenne A, Simpson AJ. Metabolic Profiling Using In Vivo High Field Flow NMR. Methods Mol Biol 2019; 2037:395-409. [PMID: 31463857 DOI: 10.1007/978-1-4939-9690-2_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In vivo NMR (nuclear magnetic resonance) has the potential to monitor and record metabolic flux in close to real time, which is essential for better understanding the toxic mode of action of a contaminant and deciphering complex interconnected stress-induced pathways impacted inside an organism. Here, we describe how to construct and use a simple flow system to keep small aquatic organisms alive inside the NMR spectrometer. In living organisms, magnetic susceptibility distortions lead to severe broadening in conventional NMR. Two main approaches can be employed to overcome this issue: (1) use a pulse sequence to reduce the distortions, or (2) employ multidimensional NMR in combination with isotopic enrichment to provide the spectral dispersion required to separate peaks from overlapping resonances. Both approaches are discussed, and protocols for both approaches are provided here in the context of small aquatic organisms.
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Affiliation(s)
- Maryam Tabatabaei Anaraki
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Daniel Lane
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON, Canada
| | - Monica Bastawrous
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Amy Jenne
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON, Canada
| | - André J Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
- Department of Chemistry, University of Toronto Scarborough, Toronto, ON, Canada.
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Hassan Q, Dutta Majumdar R, Wu B, Lane D, Tabatabaei-Anraki M, Soong R, Simpson MJ, Simpson AJ. Improvements in lipid suppression for 1 H NMR-based metabolomics: Applications to solution-state and HR-MAS NMR in natural and in vivo samples. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 57:69-81. [PMID: 30520113 DOI: 10.1002/mrc.4814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Proton nuclear magnetic resonance (NMR) spectra of intact biological samples often show strong contributions from lipids, which overlap with signals of interest from small metabolites. Pioneering work by Diserens et al. demonstrated that the relative differences in diffusivity and relaxation of lipids versus small metabolites could be exploited to suppress lipid signals, in high-resolution magic angle spinning (HR-MAS) NMR spectroscopy. In solution-state NMR, suspended samples can exhibit very broad water signals, which are challenging to suppress. Here, improved water suppression is incorporated into the sequence, and the Carr-Purcell-Meiboom-Gill sequence (CPMG) train is replaced with a low-power adiabatic spinlock that reduces heating and spectral artefacts seen with longer CPMG filters. The result is a robust sequence that works well in both HR-MAS as well as static solution-state samples. Applications are also extended to include in vivo organisms. For solution-state NMR, samples containing significant amount of fats such as milk and hemp hearts seeds are used to demonstrate the technique. For HR-MAS, living earthworms (Eisenia fetida) and freshwater shrimp (Hyalella azteca) are used for in vivo applications. Lipid suppression techniques are essential for non-invasive NMR-based analysis of biological samples with a high-lipid content and adds to the suite of experiments advantageous for in vivo environmental metabolomics.
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Affiliation(s)
- Qusai Hassan
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | | | - Bing Wu
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Lane
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Maryam Tabatabaei-Anraki
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Ronald Soong
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andre J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
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Perminova IV, Shirshin EA, Konstantinov AI, Zherebker A, Lebedev VA, Dubinenkov IV, Kulikova NA, Nikolaev EN, Bulygina E, Holmes RM. The Structural Arrangement and Relative Abundance of Aliphatic Units May Effect Long-Wave Absorbance of Natural Organic Matter as Revealed by 1H NMR Spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12526-12537. [PMID: 30296078 DOI: 10.1021/acs.est.8b01029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The objective of this study was to shed light on structural features which underlay intensity of long wave absorbance of natural organic matter (NOM) using 1H NMR spectroscopy. For this purpose, a set of the NOM samples was assembled from arctic and nonarctic sampling sites (the Kolyma river basin and Moscow region, respectively). It was to ensure a substantial difference in the humification degree of the isolated organic matter-the biogeochemical proxy of the long-wave absorbance of NOM. The assembled NOM set was analyzed using solution-state 1H NMR spectroscopy. The distribution of both backbone and exchangeable protons was determined using acquisition of spectra in three different solvents. The substantially higher contribution of nonfunctionalized aliphatic moieties CHn (e.g., materials derived from linear terpenoids, MDLT) in the arctic NOM samples was revealed as compared to the nonarctic ones. The latter were characterized with the higher content of CHα protons adjacent to electron-withdrawing groups which belong to carboxyl rich alicyclic moieties (CRAMs) or to aromatic constituents of NOM. We have calculated a ratio of CHn to CHα protons as a structural descriptor which showed significant inverse correlation to intensity of long wave absorbance assessed with a use of E4/ E6 ratio and the slope of absorption spectrum. The steric hindrance of aromatic chromophoric groups of the NOM ensemble by bulky nonfunctionalized aliphatic moieties (e.g., MDLT) was set as a hypothesis for explanation of this phenomenon. The bulky aliphatics might increase a distance between the interacting groups resulting in inhibition of electronic (e.g., charge-transfer) interactions in the NOM ensemble. The obtained relationships were further explored using Fourier transform mass spectrometry as complementary technique to 1H NMR spectroscopy. The data obtained on correlation of molecular composition of NOM with 1H NMR data and optical properties were very supportive of our hypothesis that capabilities of NOM ensemble of charge transfer interactions can be dependent on structural arrangement and relative abundance of nonabsorbing aliphatic moieties.
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Affiliation(s)
- I V Perminova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
| | - E A Shirshin
- Department of Physics , Lomonosov Moscow State University , Leninskie Gory 1-2 , 119991 Moscow , Russia
| | - A I Konstantinov
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
| | - A Zherebker
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
- Skolkovo Institute of Science and Technology , 143025 Skolkovo, Moscow region , Russia
- Institute for Energy Problems of Chemical Physics of RAS , Leninskij pr. 38-2 , 119334 Moscow , Russia
| | - V A Lebedev
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
- Department of Materials Science , Lomonosov Moscow State University , Leninskie Gory 1-73 , 199991 Moscow , Russia
| | - I V Dubinenkov
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
| | - N A Kulikova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
- Department of Soil Science , Lomonosov Moscow State University , Leninskie Gory 1-12 , 199991 Moscow , Russia
- Bach Institute of Biochemistry of RAS , Federal Research Center "Biotechnology" , Leninskij pr. 33-2 , 119071 Moscow , Russia
| | - E N Nikolaev
- Skolkovo Institute of Science and Technology , 143025 Skolkovo, Moscow region , Russia
- Institute for Energy Problems of Chemical Physics of RAS , Leninskij pr. 38-2 , 119334 Moscow , Russia
| | - E Bulygina
- Woods Hole Research Center , 149 Woods Hole Rd , Falmouth , Massachusetts 02540 , United States
| | - R M Holmes
- Woods Hole Research Center , 149 Woods Hole Rd , Falmouth , Massachusetts 02540 , United States
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Yellowstone Hot Springs are Organic Chemodiversity Hot Spots. Sci Rep 2018; 8:14155. [PMID: 30237444 PMCID: PMC6147864 DOI: 10.1038/s41598-018-32593-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/11/2018] [Indexed: 11/08/2022] Open
Abstract
Yellowstone National Park hydrothermal springs were investigated according to their organic geochemistry with a special focus on the Yellowstone hot spring dissolved organic matter (YDOM) that was solid-phase extracted. Here we show that YDOM has a unique chemodiversity that has not yet been observed anywhere else in aquatic surface environments and that Yellowstone hot springs are organic chemodiversity hot spots. Four main geochemically classified hot spring types (alkaline-chloride, mixed alkaline-chloride, acid-chloride-sulfate and travertine-precipitating) exhibited distinct organic molecular signatures that correlated remarkably well with the known inorganic geochemistry and manifested themselves in excitation emission matrix fluorescence, nuclear magnetic resonance, and ultrahigh resolution mass spectra. YDOM contained thousands of molecular formulas unique to Yellowstone of which 80% contained sulfur, even in low hydrogen sulfide containing alkaline-chloride springs. This unique YDOM reflects the extreme organic geochemistry present in the hydrothermal features of Yellowstone National Park.
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38
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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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Brenner T, Chen J, Stait-Gardner T, Zheng G, Matsukawa S, Price WS. Jump-and-return sandwiches: A new family of binomial-like selective inversion sequences with improved performance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 288:100-108. [PMID: 29448232 DOI: 10.1016/j.jmr.2018.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 06/08/2023]
Abstract
A new family of binomial-like inversion sequences, named jump-and-return sandwiches (JRS), has been developed by inserting a binomial-like sequence into a standard jump-and-return sequence, discovered through use of a stochastic Genetic Algorithm optimisation. Compared to currently used binomial-like inversion sequences (e.g., 3-9-19 and W5), the new sequences afford wider inversion bands and narrower non-inversion bands with an equal number of pulses. As an example, two jump-and-return sandwich 10-pulse sequences achieved 95% inversion at offsets corresponding to 9.4% and 10.3% of the non-inversion band spacing, compared to 14.7% for the binomial-like W5 inversion sequence, i.e., they afforded non-inversion bands about two thirds the width of the W5 non-inversion band.
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Affiliation(s)
- Tom Brenner
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan.
| | - Johnny Chen
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Tim Stait-Gardner
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Gang Zheng
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia.
| | - Shingo Matsukawa
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Minato, Konan 4-5-7, Tokyo 108-8477, Japan
| | - William S Price
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
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40
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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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41
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Simpson AJ, Simpson MJ, Soong R. Environmental Nuclear Magnetic Resonance Spectroscopy: An Overview and a Primer. Anal Chem 2017; 90:628-639. [PMID: 29131590 DOI: 10.1021/acs.analchem.7b03241] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy is a versatile tool for the study of structure and interactions in environmental media such as air, soil, and water as well as monitoring the metabolic responses of living organisms to an ever changing environment. Part review, part perspective, and part tutorial, this Feature is aimed at nonspecialists who are interested in learning more about the potential and impact of NMR spectroscopy in environmental research.
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Affiliation(s)
- André J Simpson
- Environmental NMR Centre and Department of Physical & Environmental Sciences, University of Toronto Scarborough , Toronto, Ontario, Canada , M1C 1A4
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical & Environmental Sciences, University of Toronto Scarborough , Toronto, Ontario, Canada , M1C 1A4
| | - Ronald Soong
- Environmental NMR Centre and Department of Physical & Environmental Sciences, University of Toronto Scarborough , Toronto, Ontario, Canada , M1C 1A4
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42
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Dutta Majumdar R, Bliumkin L, Lane D, Soong R, Simpson M, Simpson AJ. Analysis of DOM phototransformation using a looped NMR system integrated with a sunlight simulator. WATER RESEARCH 2017; 120:64-76. [PMID: 28478296 DOI: 10.1016/j.watres.2017.04.067] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Photochemical transformation plays an important role in functionalizing and degrading dissolved organic matter (DOM), producing one of the most complex mixtures known. In this study, using a flow-based design, nuclear magnetic resonance (NMR) spectroscopy is directly interfaced with a sunlight simulator enabling the study of DOM photodegradation in situ with high temporal resolution over 5 days. Samples from Suwannee River (Florida), Nordic Reservoir (Norway), and Pony Lake (Antarctic) are studied. Phototransformation of DOM is dominated by the degradation of aromatics and unsaturated structures (many arising from lignin) into carboxylated and hydroxylated products. To assess longer term changes, the samples were continuously irradiated for 17.5 days, followed by the identification a wide range of compounds and assessment of their fate using off-line 2D-NMR. This study demonstrates the applicability of the looped system to follow degradation in a non-targeted fashion (the mixture as a whole) and target analysis (tracing specific metabolites), which holds great potential to study the fate and transformation of contaminants and nutrients in the presence of DOM. It also demonstrates that components that remain unresolved in 1D NMR can be identified using 2D methods.
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Affiliation(s)
- Rudraksha Dutta Majumdar
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Liora Bliumkin
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Myrna Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada.
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43
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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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44
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Zheng G, Torres AM, Price WS. WaterControl: self-diffusion based solvent signal suppression enhanced by selective inversion. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:447-451. [PMID: 26923534 DOI: 10.1002/mrc.4420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
Selective inversion/excitation based solvent signal suppression techniques are widely used in various NMR experiments because of their high efficiency and general applicability. However, these techniques generate a 'null'/suppression region containing (non-quantitatively) degraded solvent and desired resonances because of their reliance on the rejection of the coherence transfer pathway corresponding to all the resonances within the suppression region. To address this issue, the WaterControl technique was developed by inserting a (pulsed gradient - selective inversion pulse - pulsed gradient) unit into each 'transverse' period of a standard stimulated echo pulse sequence so that the coherence transfer pathways corresponding to both the suppression and non-suppression regions can be selected in one transient. The new sequence affords a diffusion based and quantifiable solvent signal suppression with no or minimal loss of features of interest. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Gang Zheng
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Allan M Torres
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - William S Price
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
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45
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Chen J, Zheng G, Price WS. A new phase modulated binomial-like selective-inversion sequence for solvent signal suppression in NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:115-119. [PMID: 27549075 DOI: 10.1002/mrc.4505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/05/2016] [Accepted: 08/18/2016] [Indexed: 06/06/2023]
Abstract
A new 8-pulse Phase Modulated binomial-like selective inversion pulse sequence, dubbed '8PM', was developed by optimizing the nutation and phase angles of the constituent radio-frequency pulses so that the inversion profile resembled a target profile. Suppression profiles were obtained for both the 8PM and W5 based excitation sculpting sequences with equal inter-pulse delays. Significant distortions were observed in both profiles because of the offset effect of the radio frequency pulses. These distortions were successfully reduced by adjusting the inter-pulse delays. With adjusted inter-pulse delays, the 8PM and W5 based excitation sculpting sequences were tested on an aqueous lysozyme solution. The 8 PM based sequence provided higher suppression selectivity than the W5 based sequence. Two-dimensional nuclear Overhauser effect spectroscopy experiments were also performed on the lysozyme sample with 8PM and W5 based water signal suppression. The 8PM based suppression provided a spectrum with significantly increased (~ doubled) cross-peak intensity around the suppressed water resonance compared to the W5 based suppression. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Johnny Chen
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Gang Zheng
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - William S Price
- Nanoscale Organisation and Dynamics Group, School of Science and Health, Western Sydney University, Penrith, NSW, Australia
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46
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Pander III JE, Ren D, Yeo BS. Practices for the collection and reporting of electrocatalytic performance and mechanistic information for the CO2reduction reaction. Catal Sci Technol 2017. [DOI: 10.1039/c7cy01785e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work discusses how to best perform experiments and report data for the electrochemical reduction of carbon dioxide.
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Affiliation(s)
- James E. Pander III
- Department of Chemistry
- Faculty of Science
- National University of Singapore
- Singapore 117543
| | - Dan Ren
- Department of Chemistry
- Faculty of Science
- National University of Singapore
- Singapore 117543
| | - Boon Siang Yeo
- Department of Chemistry
- Faculty of Science
- National University of Singapore
- Singapore 117543
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47
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Fugariu I, Soong R, Lane D, Fey M, Maas W, Vincent F, Beck A, Schmidig D, Treanor B, Simpson AJ. Towards single egg toxicity screening using microcoil NMR. Analyst 2017; 142:4812-4824. [DOI: 10.1039/c7an01339f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Planar NMR microcoils are evaluated, their application to single eggs is demonstrated, and their potential for studying smaller single cells is discussed.
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Affiliation(s)
- I. Fugariu
- Dept. of Chemistry and Dept. Phys. Env. Sci
- University of Toronto at Scarborough
- Scarborough
- Canada
| | - R. Soong
- Dept. of Chemistry and Dept. Phys. Env. Sci
- University of Toronto at Scarborough
- Scarborough
- Canada
| | - D. Lane
- Dept. of Chemistry and Dept. Phys. Env. Sci
- University of Toronto at Scarborough
- Scarborough
- Canada
| | - M. Fey
- Bruker Biospin
- Billerica
- USA
| | | | | | - A. Beck
- Bruker Biospin
- 8117 Fällanden
- Switzerland
| | | | - B. Treanor
- Dept. of Biological Science
- University of Toronto at Scarborough
- Scarborough
- Canada
| | - A. J. Simpson
- Dept. of Chemistry and Dept. Phys. Env. Sci
- University of Toronto at Scarborough
- Scarborough
- Canada
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48
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Colloidal Mobilization and Fate of Trace Heavy Metals in Semi-Saturated Artificial Soil (OECD) Irrigated with Treated Wastewater. SUSTAINABILITY 2016. [DOI: 10.3390/su8121257] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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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] [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 (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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Bliumkin L, Dutta Majumdar R, Soong R, Adamo A, Abbatt JPD, Zhao R, Reiner E, Simpson AJ. Development of an in Situ NMR Photoreactor To Study Environmental Photochemistry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5506-5516. [PMID: 27172272 DOI: 10.1021/acs.est.6b00361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photochemistry is a key environmental process directly linked to the fate, source, and toxicity of pollutants in the environment. This study explores two approaches for integrating light sources with nuclear magnetic resonance (NMR) spectroscopy: sample irradiation using a "sunlight simulator" outside the magnet versus direct irradiation of the sample inside the magnet. To assess their applicability, the in situ NMR photoreactors were applied to a series of environmental systems: an atmospheric pollutant (p-nitrophenol), crude oil extracts, and groundwater. The study successfully illustrates that environmentally relevant aqueous photochemical processes can be monitored in situ and in real time using NMR spectroscopy. A range of intermediates and degradation products were identified and matched to the literature. Preliminary measurements of half-lives were also obtained from kinetic curves. The sunlight simulator was shown to be the most suitable model to explore environmental photolytic processes in situ. Other light sources with more intense UV output hold potential for evaluating UV as a remediation alternative in areas such as wastewater treatment plants or oil spills. Finally, the ability to analyze the photolytic fate of trace chemicals at natural abundance in groundwater, using a cryogenic probe, demonstrates the viability of NMR spectroscopy as a powerful and complementary technique for environmental applications in general.
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Affiliation(s)
- Liora Bliumkin
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | | | | | | | - Jonathan P D Abbatt
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | - Ran Zhao
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | - Eric Reiner
- Ontario Ministry of the Environment , Toronto, Ontario M9P 3 V6, Canada
| | - André J Simpson
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
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