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Makarewicz CA, Winter-Schuh C, Jackson M, Johannesson EG, Amartuvshin C, Honeychurch W. Local circulation of elites punctuated by transregional mobility enabled steppe political consolidation in the Xiongnu nomadic state. PLoS One 2024; 19:e0298593. [PMID: 38557862 PMCID: PMC10984472 DOI: 10.1371/journal.pone.0298593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/28/2024] [Indexed: 04/04/2024] Open
Abstract
The Xiongnu polity (ca. 200 BC- 150 AD) emerged out of indigenous community-centered socio-political structures to forge a powerful state that commanded the Mongolian steppe and beyond. Underpinned by a highly mobile pastoralist population, accustomed to seasonally rhythmic moves and embedded in an equestrian culture that facilitated rapid transport over long-distances, it remains unclear precisely how the movement of commoners, local aristocrats and regional elites abetted the formation and organization of Xiongnu state structures. Here, we evaluate Xiongnu movement and dietary intake through multi-stable isotopic analyses of tooth enamel from directly dated Xiongnu intermediate elites recovered from the mortuary center of Baga Gazaryn Chuluu-a prominent granite outcrop set in the Gobi Desert. Carbon isotope (δ13C) analysis indicates millet was consumed by some individuals, but whether or not this C4 cultivar contributed to the diets of most elites remains ambiguous in this C3/C4 desert-steppe environment. The effectiveness of oxygen isotopes (δ18O) to establish mobility appears much reduced in steppe environments, where geospatially sensitive information appears disrupted by extraordinary seasonality in meteoric water oxygen isotopes, pronounced oxygen isotopic variation in potential drinking water sources, and culturally mediated drinking practices. Most revealing, strontium isotopes (87Sr/86Sr) indicate circulation of local elites around this central place and beyond, a mobility format that helped leaders cement their own position through political consolidation of spatially dispersed mobile pastoralist communities. The consistent presence at Baga Gazaryn Chuluu of extra-local intermediate elites also points toward the importance of transregional mobility in binding together the Xiongnu polity over the vast distances of the eastern steppe.
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Affiliation(s)
- Cheryl A Makarewicz
- Archaeology Stable Isotope Laboratory, University of Kiel, Kiel, Germany
- Institute for Prehistoric and Protohistoric Archaeology, University of Kiel, Kiel, Germany
| | - Christine Winter-Schuh
- Archaeology Stable Isotope Laboratory, University of Kiel, Kiel, Germany
- Institute for Prehistoric and Protohistoric Archaeology, University of Kiel, Kiel, Germany
| | - Meghan Jackson
- Meghan Jackson, Ossifrage Exploration Consulting LLC, Huelva, Spain
| | | | - Chunag Amartuvshin
- Chunag Amartuvshin, Archaeological Research Center, National University of Mongolia, Ulaanbaatar, Mongolia
| | - William Honeychurch
- William Honeychurch, Department of Anthropology, Yale University, New Haven, CT, United States of America
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2
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Kambhampati S, Hubbard AH, Koley S, Gomez JD, Marsolais F, Evans BS, Young JD, Allen DK. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Commun Biol 2024; 7:172. [PMID: 38347116 PMCID: PMC10861564 DOI: 10.1038/s42003-024-05844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
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Affiliation(s)
- Shrikaar Kambhampati
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Allen H Hubbard
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Javier D Gomez
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frédéric Marsolais
- London Research and Development Center, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bradley S Evans
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jamey D Young
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Agricultural Research Service, US Department of Agriculture, St. Louis, MO, 63132, USA.
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3
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Ordaz-Ortiz JJ, Cruz-Narváez Y, Guerrero-Esperanza M, Romero-García NL, Arroyo-Silva A, Gómez-Cruz CY. Carbon and Oxygen Isotopic Ratio Analysis by FT ICR MS for Natural Vanillin Authentication. J Am Soc Mass Spectrom 2023; 34:2755-2763. [PMID: 37983185 DOI: 10.1021/jasms.3c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Vanillin is the main component of vanilla flavor and is naturally produced from an orchid. However, due to the high cost and time-intensive nature of cultivating natural vanilla pods, most of the vanillin is mainly artificially manufactured. Existing methodologies, such as isotope ratio mass spectrometry (IRMS) and site-specific natural isotopic fractionation by nuclear magnetic resonance (SNIF-NMR), are employed to differentiate natural vanillin from other sources based on carbon and hydrogen isotope measurements. Nevertheless, these methods have limitations, as the carbon isotopic ratio can be counterfeited by adding commercially available enriched vanillin. For this research, we purified 1 mg of vanillin from pods from various geographical and botanical sources. We developed a novel method for analyzing 13C/12C and 18O/16O isotopic ratios of vanillin using direct injection analysis coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). This innovative approach enables the examination of bulk vanillin carbon and oxygen isotopic ratios, as well as specific molecular fragments. By analyzing a characteristic vanillin fragment that provides site-specific 18O/16O isotopic ratio data, we achieved superior clustering and discrimination of samples based on their botanical source and geographical origin. Our proposed method holds significant potential for vanillin authentication and can be performed using a mere 20 μg of pure vanillin in just 10 min of analysis time. Subsequent research should focus on acquiring additional vanillin samples from diverse botanical, geographical, and biosynthetic origins while exploring various isotopic ratios to further enhance the reproducibility and reliability of this methodology.
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Affiliation(s)
- José J Ordaz-Ortiz
- Laboratorio de Metabolómica y Espectrometría de Masas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad de Genómica Avanzada, Irapuato, Guanajuato, 36824, Mexico
| | - Yair Cruz-Narváez
- Laboratorio de Posgrado e Investigación de Operaciones Unitarias, Escuela Superior de Ingeniería Química e Industrias Extractivas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - Moisés Guerrero-Esperanza
- Laboratorio de Metabolómica y Espectrometría de Masas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad de Genómica Avanzada, Irapuato, Guanajuato, 36824, Mexico
| | - Nayeli L Romero-García
- Laboratorio de Metabolómica y Espectrometría de Masas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad de Genómica Avanzada, Irapuato, Guanajuato, 36824, Mexico
| | - Anita Arroyo-Silva
- Laboratorio de Metabolómica y Espectrometría de Masas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad de Genómica Avanzada, Irapuato, Guanajuato, 36824, Mexico
| | - Carlos Y Gómez-Cruz
- Laboratorio de Posgrado e Investigación de Operaciones Unitarias, Escuela Superior de Ingeniería Química e Industrias Extractivas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
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4
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Zhao Y, Fan R, Wang C, Xu S, Xie L, Hou J, Lei W, Liu J. Quantification and isotope abundance determination of 13C labeled intracellular sugar metabolites with hydrophilic interaction liquid chromatography. Anal Methods 2023; 15:5666-5673. [PMID: 37855701 DOI: 10.1039/d3ay01178j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Metabolic flux analysis (MFA) using stable isotope labeled tracers is a powerful tool to estimate fluxes through metabolic pathways. It finds applications in studying metabolic changes in diseases, regulation of cellular energetics, and novel strategies for metabolic engineering. Accurate and precise quantification of the concentration of metabolites and their labeling states is critical for correct MFA results. Utilizing an ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) system, an analytical method for simultaneously quantifying the concentration of sugar metabolites and their mass isotopologue distribution (MID) was developed. The method performs with good linearity and coefficient of determination (R2) > 0.99, while the detection limit ranged from 0.1 to 50 mg L-1. Seven sugar metabolites were detected in a labeled Brevibacterium flavum sample using the method. The detected quantities ranged from 6.15 to 3704.21 mg L-1, and 13C abundance was between 12.77% and 66.67% in the fermentation fluid and 16.28% and 91.93% in the bacterial body. Overall, the method is efficient, accurate, and suitable for analysis of labeled sugar metabolites in 13C MFA studies.
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Affiliation(s)
- Yameng Zhao
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Ruoning Fan
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Chuyao Wang
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Sen Xu
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Long Xie
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Jinghua Hou
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Wen Lei
- Shanghai Research Institute of Chemical Industry Co., Ltd, Shanghai, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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5
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Latli B, Hrapchak MJ, Chevliakov M, Samankumara LP, Frutos RP, Lee H. Stable isotope synthesis of glycine transporter 1 inhibitor Iclepertin (BI 425809) and its major metabolites. J Labelled Comp Radiopharm 2023; 66:414-427. [PMID: 37727936 DOI: 10.1002/jlcr.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/26/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
Stable isotope labeled Iclepertin (BI 425809, 1) and its major metabolites are needed as internal standards in bioanalytical studies. BI 425809 consists of two main building blocks, 5-methylsulfonyl-2-[(1R)-2,2,2-trifluoro-1-methyl-ethoxy]benzoic acid (2) and 3-[(1R,5R)-3-azabicyclo[3.1.0]hexan-5-yl]-5-(trifluoromethyl)isoxazole (3) linked to each other via an amide bond. We used fluoro[13 C6 ]benzene as the starting material in the preparation of [13 C6 ]-2. This intermediate was then employed to access carbon 13 labeled Iclepertin ([13 C6 ]-1) and other metabolites. The major metabolite BI 761036 (6), which resulted from cytochrome P450 oxidation and amide hydrolysis of BI 425809, was prepared labeled with carbon 13 and nitrogen 15 via two synthetic routes. In the first route, diethyl [13 C3 ]malonate, [13 C]methyl iodide, and hydroxyl[15 N]amine were used to provide [13 C4 ,15 N]-BI 761036 ([13 C4 ,15 N]-6a) in 13 steps in 6% overall yield, whereas in the second route, [13 C3 ]propargyl alcohol, potassium [13 C]cyanide, and [15 N]ammonia were used to furnish [13 C4 ,15 N]-BI 761036 ([13 C4 ,15 N]-6b) in 11 steps in 1% overall yield. The detailed stable isotope synthesis of 1 and its major metabolites is described.
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Affiliation(s)
- Bachir Latli
- The Radiosynthesis Laboratory, Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Matt J Hrapchak
- The Radiosynthesis Laboratory, Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Maxim Chevliakov
- The Radiosynthesis Laboratory, Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Lalith P Samankumara
- The Radiosynthesis Laboratory, Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Rogelio P Frutos
- The Radiosynthesis Laboratory, Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
| | - Heewon Lee
- The Radiosynthesis Laboratory, Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
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6
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Wu C, Guarnieri M, Xiong W. FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis. ACS Synth Biol 2023; 12:2707-2714. [PMID: 37561998 PMCID: PMC10510750 DOI: 10.1021/acssynbio.3c00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 08/12/2023]
Abstract
13C metabolic flux analysis is a powerful tool for metabolism characterization in metabolic engineering and synthetic biology. However, the widespread adoption of this tool is hindered by limited software availability and computational efficiency. Currently, the most widely accepted 13C-flux tools, such as INCA and 13CFLUX2, are developed in a closed-source environment. While several open-source packages or software are available, they are either computationally inefficient or only suitable for flux estimation at isotopic steady state. To address the need for a time-efficient computational tool for the more complicated flux analysis at an isotopically nonstationary state, especially for understanding the single-carbon substrate metabolism, we present FreeFlux. FreeFlux is an open-source Python package that performs labeling pattern simulation and flux analysis at both isotopic steady state and transient state, enabling a more comprehensive analysis of cellular metabolism. FreeFlux provides a set of interfaces to manipulate the objects abstracted from a labeling experiment and computational process, making it easy to integrate into other programs or pipelines. The flux estimation by FreeFlux is fast and reliable, and its validity has been confirmed by comparison with results from other computational tools using both synthetic and experimental data. FreeFlux is freely available at https://github.com/Chaowu88/freeflux with a detailed online tutorial and documentation provided at https://freeflux.readthedocs.io/en/latest/index.html.
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Affiliation(s)
- Chao Wu
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael Guarnieri
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Wei Xiong
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
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7
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Malloy CR, Sherry AD, Alger JR, Jin ES. Recent progress in analysis of intermediary metabolism by ex vivo 13 C NMR. NMR Biomed 2023; 36:e4817. [PMID: 35997012 DOI: 10.1002/nbm.4817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/03/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Advanced imaging technologies, large-scale metabolomics, and the measurement of gene transcripts or enzyme expression all enable investigations of intermediary metabolism in human patients. Complementary information about fluxes in individual metabolic pathways may be obtained by ex vivo 13 C NMR of blood or tissue biopsies. Simple molecules such as 13 C-labeled glucose are readily administered to patients prior to surgical biopsies, and 13 C-labeled glycerol is easily administered orally to outpatients. Here, we review recent progress in practical applications of 13 C NMR to study cancer biology, the response to oxidative stress, gluconeogenesis, triglyceride synthesis in patients, as well as new insights into compartmentation of metabolism in the cytosol. The technical aspects of obtaining the sample, preparing material for analysis, and acquiring the spectra are relatively simple. This approach enables convenient, valuable, and quantitative insights into intermediary metabolism in patients.
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Affiliation(s)
- Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Veterans Affairs North Texas Healthcare System, Dallas, Texas, USA
| | - A Dean Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Chemistry, University of Texas at Dallas, Richardson, Texas, USA
| | - Jeffry R Alger
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Neurology, Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Eunsook S Jin
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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8
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Jameson E, Taubert M, Angel R, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol 2023; 2555:261-282. [PMID: 36306091 DOI: 10.1007/978-1-0716-2795-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.
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Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martin Taubert
- Aquatic Geochemistry, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Roey Angel
- Soil & Water Research Infrastructure and Institute of Soil Biology, Biology Centre CAS, České Budějovice, Czechia
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Özge Eyice
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK.
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9
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Fan TWM, Sun Q, Higashi RM. Ultrahigh resolution MS 1/MS 2-based reconstruction of metabolic networks in mammalian cells reveals changes for selenite and arsenite action. J Biol Chem 2022; 298:102586. [PMID: 36223837 PMCID: PMC9667311 DOI: 10.1016/j.jbc.2022.102586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Metabolic networks are complex, intersecting, and composed of numerous enzyme-catalyzed biochemical reactions that transfer various molecular moieties among metabolites. Thus, robust reconstruction of metabolic networks requires metabolite moieties to be tracked, which cannot be readily achieved with mass spectrometry (MS) alone. We previously developed an Ion Chromatography-ultrahigh resolution-MS1/data independent-MS2 method to track the simultaneous incorporation of the heavy isotopes 13C and 15N into the moieties of purine/pyrimidine nucleotides in mammalian cells. Ultrahigh resolution-MS1 resolves and counts multiple tracer atoms in intact metabolites, while data independent-tandem MS (MS2) determines isotopic enrichment in their moieties without concern for the numerous mass isotopologue source ions to be fragmented. Together, they enabled rigorous MS-based reconstruction of metabolic networks at specific enzyme levels. We have expanded this approach to trace the labeled atom fate of [13C6]-glucose in 3D A549 spheroids in response to the anticancer agent selenite and that of [13C5,15N2]-glutamine in 2D BEAS-2B cells in response to arsenite transformation. We deduced altered activities of specific enzymes in the Krebs cycle, pentose phosphate pathway, gluconeogenesis, and UDP-GlcNAc synthesis pathways elicited by the stressors. These metabolic details help elucidate the resistance mechanism of 3D versus 2D A549 cultures to selenite and metabolic reprogramming that can mediate the transformation of BEAS-2B cells by arsenite.
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Affiliation(s)
- Teresa W-M Fan
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA.
| | - Qiushi Sun
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky, USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry (CESB), University of Kentucky, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA; Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
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10
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Feng D, Wang D, Wang D, Zhong Q, Li G, Zhang L, Chen N, Lin X, Miao S. Stable isotope ratio analysis of carbon to distinguish sialic acid from freshly stewed bird's nest products. Anal Methods 2022; 14:4386-4392. [PMID: 36281988 DOI: 10.1039/d2ay01152b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Freshly stewed bird's nest products are easily adulterated with exogenous synthetic sialic acid to enhance the grade of the products and sell at high prices. This paper identifies the carbon stable isotope characteristics of sialic acid from natural and commercially synthetic sources using stable isotope ratio mass spectrometry (IRMS). Specifically, an off-line pretreatment technique combined with on-line LC-IRMS was developed to accurately determine δ13C values of sialic acid in a freshly stewed bird's nest. This method has no obvious isotope fractionation and good reproducibility. EA-IRMS was used to determine the δ13C values of commercial sialic acid. The results showed that the δ13C values of sialic acid from natural and synthetic sources were -29.90% ± 0.42% and -16.26% ± 3.91%, respectively, with distinct carbon stable isotope distribution characteristics. By defining a δ13C threshold value of -28.54% for natural SA, additional commercial SA from a minimum of 10% can be identified. Therefore, δ13C was proposed as a suitable tool for verifying the authenticity of fresh stewed bird's nests on the market.
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Affiliation(s)
- Di Feng
- Technology Innovation Center of Light Industrial Consumer Goods Quality and Safety, Beijing 100015, China.
- Sinolight Technology Innovation Center Co. Ltd, Beijing 100015, China
- China National Research Institute of Food and Fermentation Industries, Beijing 100015, China
| | - Daobing Wang
- Technology Innovation Center of Light Industrial Consumer Goods Quality and Safety, Beijing 100015, China.
- Sinolight Technology Innovation Center Co. Ltd, Beijing 100015, China
| | - Dongliang Wang
- Beijing Xiaoxiandun Biotechnology Co., Ltd., Beijing 100020, China
- Hebei Edible Bird's Nest Fresh Stew Technology Innovation Center, Langfang 065700, China
| | - Qiding Zhong
- Technology Innovation Center of Light Industrial Consumer Goods Quality and Safety, Beijing 100015, China.
- Sinolight Technology Innovation Center Co. Ltd, Beijing 100015, China
- China National Research Institute of Food and Fermentation Industries, Beijing 100015, China
- Sinolight Inspection & Certification Co., Ltd., Beijing 100016, China
| | - Guohui Li
- Technology Innovation Center of Light Industrial Consumer Goods Quality and Safety, Beijing 100015, China.
- Sinolight Technology Innovation Center Co. Ltd, Beijing 100015, China
| | - Luoqi Zhang
- Technology Innovation Center of Light Industrial Consumer Goods Quality and Safety, Beijing 100015, China.
- Sinolight Technology Innovation Center Co. Ltd, Beijing 100015, China
| | - Nannan Chen
- Food Industry Promotion Center, Beijing 100015, China
| | - Xiaoxian Lin
- Beijing Xiaoxiandun Biotechnology Co., Ltd., Beijing 100020, China
- Hebei Edible Bird's Nest Fresh Stew Technology Innovation Center, Langfang 065700, China
| | - Shu Miao
- Beijing Xiaoxiandun Biotechnology Co., Ltd., Beijing 100020, China
- Hebei Edible Bird's Nest Fresh Stew Technology Innovation Center, Langfang 065700, China
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11
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Zheng S, Jiang J, Xia J. [Construction and application of natural stable isotope correction matrix in 13C-labeled metabolic flux analysis]. Sheng Wu Gong Cheng Xue Bao 2022; 38:3940-3955. [PMID: 36305420 DOI: 10.13345/j.cjb.220081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable isotope 13C labeling is an important tool to analyze cellular metabolic flux. The 13C distribution in intracellular metabolites can be detected via mass spectrometry and used as a constraint in intracellular metabolic flux calculations. Then, metabolic flux analysis algorithms can be employed to obtain the flux distribution in the corresponding metabolic reaction network. However, in addition to carbon, other elements such as oxygen in the nature also have natural stable isotopes (e.g., 17O, 18O). This makes the isotopic information of elements other than the 13C marker interspersed in the isotopic distribution measured by the mass spectrometry, especially that of the molecules containing many other elements, which leads to large errors. Therefore, it is essential to correct the mass spectrometry data before performing metabolic flux calculations. In this paper, we proposed a method for construction of correction matrix based on Python language for correcting the measurement errors due to natural isotope distribution. The method employed a basic power method for constructing the correction matrix with simple structure and easy coding implementation, which can be directly applied to data pre-processing in 13C metabolic flux analysis. The correction method was then applied to the intracellular metabolic flux analysis of 13C-labeled Aspergillus niger. The results showed that the proposed method was accurate and effective, which can serve as a reliable data correction method for accurate microbial intracellular metabolic flux analysis.
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Affiliation(s)
- Shiyuan Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Junfeng Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin 300308, China
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12
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Lin P, W-M Fan T, Lane AN. NMR-based isotope editing, chemoselection and isotopomer distribution analysis in stable isotope resolved metabolomics. Methods 2022; 206:8-17. [PMID: 35908585 PMCID: PMC9539636 DOI: 10.1016/j.ymeth.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
NMR is a very powerful tool for identifying and quantifying compounds within complex mixtures without the need for individual standards or chromatographic separation. Stable Isotope Resolved Metabolomics (or SIRM) is an approach to following the fate of individual atoms from precursors through metabolic transformation, producing an atom-resolved metabolic fate map. However, extracts of cells or tissue give rise to very complex NMR spectra. While multidimensional NMR experiments may partially overcome the spectral overlap problem, additional tools may be needed to determine site-specific isotopomer distributions. NMR is especially powerful by virtue of its isotope editing capabilities using NMR active nuclei such as 13C, 15N, 19F and 31P to select molecules containing just these atoms in a complex mixture, and provide direct information about which atoms are present in identified compounds and their relative abundances. The isotope-editing capability of NMR can also be employed to select for those compounds that have been selectively derivatized with an NMR-active stable isotope at particular functional groups, leading to considerable spectral simplification. Here we review isotope analysis by NMR, and methods of chemoselection both for spectral simplification, and for enhanced isotopomer analysis.
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Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.
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13
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Branscombe T, Lee‐Thorp J, Schulting R, Leng M. Micromilling vs hand drilling in stable isotope analyses of incremental carbonates: The potential for δ 13 C contamination by embedding resin. Rapid Commun Mass Spectrom 2022; 36:e9318. [PMID: 35474593 PMCID: PMC9286849 DOI: 10.1002/rcm.9318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Embedding resins are commonly used to facilitate high-resolution sampling for stable isotope analysis but anomalous δ13 C values have been observed in some cases. Here we compare the results of microsampling strategies for hand-drilled versus resin-embedded micromilled samples from the same marine shells to assess whether resin contamination is implicated in δ13 C spikes. The comparison allows assessment of the relative benefits for spatial resolution, seasonal range for both δ18 O and δ13 C, and sample failure rates. METHODS Hand-drilled samples were obtained from two bivalve shells (Spisula sachalinensis), corresponding to micromilled samples on the same shells where high δ13 C spikes were observed. All carbonate powders were analysed using a dual-inlet Isoprime mass spectrometer and Multiprep device. Results from both sample sets were compared statistically. RESULTS No anomalous high δ13 C values and no failures due to insufficient gas were observed in the hand-drilled samples in contrast to the embedded micromilled sequences. Spatial resolution was reduced (~2.5×) in the former compared with the latter, resulting in a small reduction in the total range observed in the micromilled δ13 C and δ18 O values. Reduced sampling resolution between the two datasets was only significant for δ18 O. CONCLUSIONS For S. sachalinensis (as with other similar bivalves), rapid growth mitigates the reduced sampling resolution of hand drilling and does not significantly impact observed isotopic range and seasonal patterning. Occurrence of anomalous δ13 C values were eliminated and failure rates due to insufficient sample size greatly reduced in the hand-drilled dataset. We can find no other explanation for the occurrence of δ13 C spikes than contamination by the embedding agent. We conclude that the logistical and interpretational benefits of careful hand drilling may be preferable to resin embedding for micromilling in marine shells, corals or speleothems where growth rate is rapid and the highest resolution is not required.
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Affiliation(s)
| | | | | | - Melanie Leng
- National Environmental Isotope FacilityBritish Geological SurveyNottinghamUK
- School of BiosciencesUniversity of NottinghamLoughboroughUK
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14
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Kovatch PY, Ferreira AE, Ghizonni GML, Ambrósio SR, Crotti AEM, Heleno VCG. Detailed 1 H and 13 C NMR structural assignment of ent-polyalthic acid, a biologically active labdane diterpene. Magn Reson Chem 2022; 60:255-260. [PMID: 34510530 DOI: 10.1002/mrc.5217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
In this paper, a complete 1 H and 13 C NMR data assignment of ent-polyalthic acid, a biologically active labdane-type diterpene, is presented. The assignments were carried on the basis of spectroscopic data from 1 H NMR, 13 C{1 H} NMR, gCOSY, gHMQC, and gHMBC experiments. Furthermore, a software-assisted methodology, using FOMSC3_rm_NB and NMR_MultSim programs, supported the detailed and unequivocal assignment of 1 H and 13 C signals, allowing all hydrogen coupling constants to be determined and thus clarifying all hydrogen signal multiplicities.
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Affiliation(s)
- Pedro Y Kovatch
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
| | - Alexsandro E Ferreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
| | - Guilherme M L Ghizonni
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
| | - Sérgio R Ambrósio
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
| | - Antônio E M Crotti
- Departamento de Química da Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Vladimir C G Heleno
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
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15
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Fischer-Rush J, Rochette R, Paton E, Dickey A, Hayden B. An arithmetic correction for the effect of lipid on carbon stable isotope ratios in muscle and digestive glands of the American lobster (Homarus americanus). Rapid Commun Mass Spectrom 2021; 35:e9204. [PMID: 34549474 DOI: 10.1002/rcm.9204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE Lipid correction models use elemental carbon-to-nitrogen ratios to estimate the effect of lipids on δ13 C values and provide a fast and inexpensive alternative to chemically removing lipids. However, the performance of these models varies, especially in whole-body invertebrate samples. The generation of tissue-specific lipid correction models for American lobsters, both an ecologically and an economically important species in eastern North America, will aid ecological research of this species and our understanding of the function of these models in invertebrates. METHOD We determined the δ13 C and δ15 N values before and after lipid extraction in muscle and digestive glands of juvenile and adult lobster. We assessed the performance of four commonly used models (nonlinear, linear, natural logarithm (LN) and generalized linear model (GLM)) at estimating lipid-free δ13 C values based on the non-lipid-extracted δ13 C values and elemental C:N ratios. The accuracy of model predictions was tested using paired t-tests, and the performance of the different models was compared using the Akaike information criterion score. RESULTS Lipid correction models accurately estimated post-lipid-extraction δ13 C values in both tissues. The nonlinear model was the least accurate for both tissues. In muscle, the three other models performed well, and in digestive glands, the LN model provided the most accurate estimates throughout the range of C:N values. In both tissues, the GLM estimates were not independent of the post-lipid-extraction δ13 C values, thus reducing their transferability to other datasets. CONCLUSIONS Whereas previous work found that whole-body models poorly estimated the effect of lipids in invertebrates, we show that tissue-specific lipid correction models can generate accurate and precise estimates of lipid-free δ13 C values in lobster. We suggest that the tissue-specific logarithmic models presented here are the preferred models for accounting for the effect of lipid on lobster isotope ratios.
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Affiliation(s)
- Jonathan Fischer-Rush
- Canadian Rivers Institute, Biology Department, University of New Brunswick, Fredericton, NB, Canada
| | - Rémy Rochette
- University of New Brunswick Saint John, Saint John, NB, Canada
| | - Emily Paton
- University of New Brunswick Saint John, Saint John, NB, Canada
| | - Alexandrea Dickey
- Canadian Rivers Institute, Biology Department, University of New Brunswick, Fredericton, NB, Canada
| | - Brian Hayden
- Canadian Rivers Institute, Biology Department, University of New Brunswick, Fredericton, NB, Canada
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16
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Dai D, Wang X, Liu Y, Yang XL, Glaubitz C, Denysenkov V, He X, Prisner T, Mao J. Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water. Nat Commun 2021; 12:6880. [PMID: 34824218 PMCID: PMC8616939 DOI: 10.1038/s41467-021-27067-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/01/2021] [Indexed: 11/15/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.
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Affiliation(s)
- Danhua Dai
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Xianwei Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang, 310023, China
| | - Yiwei Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xiao-Liang Yang
- Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Clemens Glaubitz
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jiafei Mao
- Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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17
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Abstract
We report two- and three-dimensional (2D and 3D) 13C-17O heteronuclear correlation solid-state NMR experiments under magic-angle spinning (MAS) conditions. These experiments utilize the D-RINEPT (Dipolar-mediated Refocused Insensitive Nuclei Enhanced by Polarization Transfer) scheme with symmetry-based SR412 recoupling blocks for coherence transfer between 13C and 17O nuclei. First, a 2D 17O → 13C correlation experiment was performed for the [1-13C,17O]-Gly/Gly·HCl cocrystal and [U-13C, 1-17O]-α/β-d-glucose samples. Second, a 2D 17O → 13C MQ-D-RINEPT correlation experiment where the indirect dimension incorporates the multiple-quantum MAS (MQMAS) scheme was tested for obtaining isotropic 17O resolution with [U-13C, 1-17O]-α/β-d-glucose. Third, a new 3D 17O → 13C → 13C correlation experiment was demonstrated where 17O → 13C and 13C → 13C correlations are achieved by D-RINEPT and DARR (Dipolar Assisted Rotational Resonance) sequences, respectively (thus termed as a 3D D-RINEPT/DARR OCC experiment). This new 3D 17O NMR experiment is implemented with the aim for site-resolved solid-state 17O NMR studies.
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Affiliation(s)
- Ivan Hung
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
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18
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Gorman D, Skrzypek G, McLaughlin MJ, Bearham D, Vanderklift MA. Gamma-irradiation of common biological samples for stable carbon and nitrogen isotope and elemental analyses. Rapid Commun Mass Spectrom 2021; 35:e9173. [PMID: 34382255 DOI: 10.1002/rcm.9173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE Around the world biosecurity measures are being strengthened to prevent the spread of pests and diseases across national and international borders. Quarantine protocols that involve sample sterilisation have potential effects on sample integrity. The consequences of sterilisation methods such as gamma (γ)-irradiation on the elemental and chemical properties of biological samples have not been widely examined. METHODS We tested the effect of γ-irradiation (50 kGy) on the stable carbon and nitrogen isotope compositions (δ13 C and δ15 N values) and elemental concentrations (C % and N %) of common biological samples (fish, plants and bulk soils). The analysis used a continuous flow system consisting of a Delta V Plus isotope ratio mass spectrometer connected with a Thermo Flash 1112 elemental analyser via a ConFlo IV interface. Results were compared using two one-sided tests (TOST) to test for statistical similarity between paired samples. RESULTS There was no change in the δ15 N values or N % of γ-irradiated samples, and only small changes to the δ13 C values of consumers (range: 0.01‰ to 0.04‰), producers (-0.02‰ to 0.04‰) and sediments (0‰ to 0.07‰). The magnitude of change in δ13 C values was greatest at low carbon concentrations but appeared negligible when measured against replicated sample analysis and the combined analytical uncertainty (i.e., 0.10‰). The C % values of irradiated samples were higher for consumers (0.23%) and lower for producers and sediments (0.04% and 0.05%, respectively) which may have implications for certain types of biological material. CONCLUSIONS Routine γ-irradiation has little effect on the stable carbon and nitrogen isotope compositions of common biological samples and marginal effects on carbon elemental concentrations. This is unlikely to warrant concerns since the observed difference is typically of a magnitude lower than other sources of potential uncertainty.
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Affiliation(s)
- Daniel Gorman
- Commonwealth Scientific and Industrial Research Organisation, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Grzegorz Skrzypek
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - M James McLaughlin
- Commonwealth Scientific and Industrial Research Organisation, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Douglas Bearham
- Commonwealth Scientific and Industrial Research Organisation, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Mathew A Vanderklift
- Commonwealth Scientific and Industrial Research Organisation, Oceans and Atmosphere, Crawley, Western Australia, Australia
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19
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Abstract
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy. To test the limits of this approximation, we systematically study the importance of finite-temperature and quantum nuclear fluctuations for 1H, 13C, and 15N shieldings in polymorphs of three paradigmatic molecular crystals: benzene, glycine, and succinic acid. The effect of quantum fluctuations is comparable to the typical errors of shielding predictions for static nuclei with respect to experiments, and their inclusion improves the agreement with measurements, translating to more reliable assignment of the NMR spectra to the correct candidate structure. The use of integrated machine-learning models, trained on first-principles energies and shieldings, renders rigorous sampling of nuclear fluctuations affordable, setting a new standard for the calculations underlying NMR structure determinations.
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Affiliation(s)
- Edgar A Engel
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Venkat Kapil
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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20
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van Zijl PCM, Brindle K, Lu H, Barker PB, Edden R, Yadav N, Knutsson L. Hyperpolarized MRI, functional MRI, MR spectroscopy and CEST to provide metabolic information in vivo. Curr Opin Chem Biol 2021; 63:209-218. [PMID: 34298353 PMCID: PMC8384704 DOI: 10.1016/j.cbpa.2021.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
Access to metabolic information in vivo using magnetic resonance (MR) technologies has generally been the niche of MR spectroscopy (MRS) and spectroscopic imaging (MRSI). Metabolic fluxes can be studied using the infusion of substrates labeled with magnetic isotopes, with the use of hyperpolarization especially powerful. Unfortunately, these promising methods are not yet accepted clinically, where fast, simple, and reliable measurement and diagnosis are key. Recent advances in functional MRI and chemical exchange saturation transfer (CEST) MRI allow the use of water imaging to study oxygen metabolism and tissue metabolite levels. These, together with the use of novel data analysis approaches such as machine learning for all of these metabolic MR approaches, are increasing the likelihood of their clinical translation.
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Affiliation(s)
- Peter C M van Zijl
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA.
| | - Kevin Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hanzhang Lu
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
| | - Richard Edden
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
| | - Nirbhay Yadav
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
| | - Linda Knutsson
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medical Radiation Physics, Lund University, Lund, Sweden
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21
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Choi Y, Lee J, Lee H, Song JE, Kim D, Song H. Offset of apparent hyperpolarized 13 C lactate flux by the use of adjuvant metformin in ionizing radiation therapy in vivo. NMR Biomed 2021; 34:e4561. [PMID: 34080736 PMCID: PMC8365667 DOI: 10.1002/nbm.4561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 05/13/2023]
Abstract
An increase in hyperpolarized (HP) [1-13 C]lactate production has been suggested as a biomarker for cancer occurrence as well as for response monitoring of cancer treatment. Recently, the use of metformin has been suggested as an anticancer or adjuvant treatment. By regulating the cytosolic NAD+ /NADH redox state, metformin stimulates lactate production and increases the HP [1-13 C]lactate conversion rate in the kidney, liver, and heart. In general, increased HP [1-13 C]lactate is regarded as a sign of cancer occurrence or tumor growth. Thus, the relationship between the tumor suppression effect of metformin and the change in metabolism monitored by HP [1-13 C]pyruvate MRS in cancer treatment needs to be investigated. The present study was performed using a brain metastasis animal model with MDA-MB-231(BR)-Luc breast cancer cells. HP [1-13 C]pyruvate MRS, T2 -weighted MRI, and bioluminescence imaging were performed in groups treated with metformin or adjuvant metformin and radiation therapy. Metformin treatment alone did not display a tumor suppression effect, and the HP [1-13 C]lactate conversion rate increased. In radiation therapy, the HP [1-13 C]lactate conversion rate decreased with tumor suppression, with a p-value of 0.028. In the adjuvant metformin and radiation treatment, the tumor suppression effect increased, with a p-value of 0.001. However, the apparent HP [1-13 C]lactate conversion rate (Kpl ) was observed to be offset by two opposite effects: a decrease on radiation therapy and an increase caused by metformin treatment. Although HP [1-13 C]pyruvate MRS could not evaluate the tumor suppression effect of adjuvant metformin and radiation therapy due to the offset phenomenon, metabolic changes following only metformin pre-treatment could be monitored. Therefore, our results indicate that the interpretation of HP [1-13 C]pyruvate MRS for response monitoring of cancer treatment should be carried out with caution when metformin is used as an adjuvant cancer therapy.
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Affiliation(s)
- Young‐Suk Choi
- Department of Radiology and Research Institute of Radiological ScienceYonsei University College of MedicineSeoulSouth Korea
| | - Joonsung Lee
- Biomedical Science InstituteYonsei University College of MedicineSeoulSouth Korea
- GE HealthcareSeoulSouth Korea
| | - Han‐Sol Lee
- Department of Electrical and Electronic EngineeringYonsei UniversitySeoulSouth Korea
| | - Jae Eun Song
- Department of Electrical and Electronic EngineeringYonsei UniversitySeoulSouth Korea
| | - Dong‐Hyun Kim
- Department of Electrical and Electronic EngineeringYonsei UniversitySeoulSouth Korea
| | - Ho‐Taek Song
- Department of Radiology and Research Institute of Radiological ScienceYonsei University College of MedicineSeoulSouth Korea
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22
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Šimek M, Nešporová K, Kocurková A, Foglová T, Ambrožová G, Velebný V, Kubala L, Hermannová M. How the molecular weight affects the in vivo fate of exogenous hyaluronan delivered intravenously: A stable-isotope labelling strategy. Carbohydr Polym 2021; 263:117927. [PMID: 33858586 DOI: 10.1016/j.carbpol.2021.117927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/15/2022]
Abstract
There is inconsistent information regarding the size effects of exogenously given hyaluronan on its in vivo fate. The data are often biased by the poor quality of hyaluronan and non-ideal labelling strategies used for resolving exogenous/endogenous hyaluronan, which only monitor the label and not hyaluronan itself. To overcome these drawbacks and establish the pharmacokinetics of intravenous hyaluronan in relation to its Mw, 13C-labelled HA of five Mws from 13.6-1562 kDa was prepared and administered to mice at doses 25-50 mg kg-1. The elimination efficiency increased with decreasing Mw. Low Mw hyaluronan was rapidly eliminated as small hyaluronan fragments in urine, while high Mw hyaluronan exhibited saturable kinetics and complete metabolization within 48 h. All tested Mws exhibited a similar uptake by liver cells and metabolization into activated sugars. 13C-labelling combined with LC-MS provides an excellent approach to elucidating in vivo fate and biological activities of hyaluronan.
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Affiliation(s)
- Matěj Šimek
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic; Department of Analytical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | - Anna Kocurková
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tereza Foglová
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Gabriela Ambrožová
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vladimír Velebný
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Lukáš Kubala
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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23
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Yang J, Zhang G, Wang Z, Meng J, Wen H. Metabolic Study of Stable Isotope Labeled Indolinone Derivative in Hepatocyte Cell by UPLC/Q TOF MS. J Am Soc Mass Spectrom 2021; 32:1538-1544. [PMID: 34028260 DOI: 10.1021/jasms.1c00146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The aggregation process of α-synuclein (α-syn) is substantial in the pathogenesis of Parkinson's disease. Indolinone derivatives are inhibitors of α-syn aggregates and can be used as PET-based radiotracers for imaging α-syn fibrils. However, no investigations on the metabolism of indolinone derivatives have been reported until now. In the present research, a 13C and 15N isotope labeling strategy was developed to synthesize compound [13C2,15N]-(Z)-1-(4-aminobenzyl)-3-((E)-(3-phenyl)allylidene)indolin-2-one (M0'), which was then used in a study of metabolism in hepatocytes. The metabolites were characterized using accurate mass and characteristic ion measurements. In the metabolic system, compound M0' was the main component (accounting for 97.5% of compound-related components) after incubation in hepatocytes for 3 h, which indicated that compound M0' possessed great metabolic stability. Seven metabolites have been successfully verified by UPLC/Q TOF MS in metabolic studies, including hydroxyl M0' (M1'), hydroxyl and methylated M0' (M2'), N-acetylated M0' (M3'), sulfate of hydroxyl M0' (M4'), the glucose conjugate of M0' (M5'), glucuronide conjugate of M0' (M6'), and glucuronide conjugate of hydroxyl M0' (M7'). The study on metabolism provides the important information to develop effective α-syn aggregate inhibitors and new PET-tracer-related indolinone derivatives.
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Affiliation(s)
- Jixia Yang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Fangshan District, Beijing 102488, P.R. China
| | - Gongzheng Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Fangshan District, Beijing 102488, P.R. China
| | - Zhaoyang Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Fangshan District, Beijing 102488, P.R. China
| | - Jian Meng
- Shanghai Institute of Materia Medica Chinese Academy of Sciences, 501 Haike Road, PuDong District, Shanghai 201203, P.R. China
| | - Hongliang Wen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Fangshan District, Beijing 102488, P.R. China
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24
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Perkons NR, Johnson O, Pilla G, Gade TPF. Pharmacodynamics and pharmacokinetics of hyperpolarized [1- 13 C]-pyruvate in a translational oncologic model. NMR Biomed 2021; 34:e4502. [PMID: 33772910 DOI: 10.1002/nbm.4502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
This study investigates the in vivo pharmacokinetics and pharmacodynamics of hyperpolarized [1-13 C]-pyruvate in a translational cancer model in order to inform the application of dynamic nuclear polarization (DNP)-enhanced magnetic resonance spectroscopic imaging (MRSI) as a tool for imaging liver cancer. Intratumoral metabolism within autochthonous hepatocellular carcinomas in male Wistar rats was analyzed by MRSI following hyperpolarized [1-13 C]-pyruvate injections with 80 mM (low dose [LD]) or 160 mM (high dose [HD]) pyruvate. Rats received (i) LD followed by HD injection, (ii) sequential LD injections with or without an interposed lactate dehydrogenase inhibitor (LDHi) injection, or (iii) a single LD injection. A subset of rats in (ii) were sacrificed immediately after imaging, permitting measurement of active LDH concentrations in tumor extracts. Urine and serum were collected before and after injections for rats in (iii). Comparison of LD and HD injections confirmed concentration-dependent variation of intratumoral metabolite fractions and intermetabolite ratios. In addition, quantification of the lactate-to-pyruvate ratio was sensitive to pharmacologic inhibition with intermetabolite ratios correlating with active LDH concentrations in tumor extracts. Finally, comparison of pre- and post-DNP urine collections revealed that pyruvate and the radical source are renally excreted after injection. These data demonstrate that DNP-MRSI facilitates real-time quantification of intratumoral metabolism that is repeatable and reflective of intracellular processes. A translational model system confirmed that interpretation requires consideration of probe dose, administration frequency and excretion.
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Affiliation(s)
- Nicholas R Perkons
- Penn Image Guided Interventions Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Omar Johnson
- Penn Image Guided Interventions Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gabrielle Pilla
- Penn Image Guided Interventions Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Terence P F Gade
- Penn Image Guided Interventions Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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25
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Cadelis MM, Gordon H, Grey A, Geese S, Mulholland DR, Weir BS, Copp BR, Wiles S. Isolation of a Novel Polyketide from Neodidymelliopsis sp. Molecules 2021; 26:molecules26113235. [PMID: 34072211 PMCID: PMC8199022 DOI: 10.3390/molecules26113235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 02/02/2023] Open
Abstract
Fungi have become an invaluable source of bioactive natural products, with more than 5 million species of fungi spanning the globe. Fractionation of crude extract of Neodidymelliopsis sp., led to the isolation of a novel polyketide, (2Z)-cillifuranone (1) and five previously reported natural products, (2E)-cillifuranone (2), taiwapyrone (3), xylariolide D (4), pachybasin (5), and N-(5-hydroxypentyl)acetamide (6). It was discovered that (2Z)-cillifuranone (1) was particularly sensitive to ambient temperature and light resulting in isomerisation to (2E)-cillifuranone (2). Structure elucidation of all the natural products were conducted by NMR spectroscopic techniques. The antimicrobial activity of 2, 3, and 5 were evaluated against a variety of bacterial and fungal pathogens. A sodium [1-13C] acetate labelling study was conducted on Neodidymelliopsis sp. and confirmed that pachybasin is biosynthesised through the acetate polyketide pathway.
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Affiliation(s)
- Melissa M. Cadelis
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (H.G.); (B.R.C.)
- Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (A.G.); (S.G.); (D.R.M.)
- Correspondence: (M.M.C.); (S.W.)
| | - Hugo Gordon
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (H.G.); (B.R.C.)
| | - Alex Grey
- Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (A.G.); (S.G.); (D.R.M.)
| | - Soeren Geese
- Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (A.G.); (S.G.); (D.R.M.)
| | - Daniel R. Mulholland
- Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (A.G.); (S.G.); (D.R.M.)
| | - Bevan S. Weir
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland 1142, New Zealand;
| | - Brent R. Copp
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (H.G.); (B.R.C.)
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (A.G.); (S.G.); (D.R.M.)
- Correspondence: (M.M.C.); (S.W.)
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26
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Abstract
The amino-terminal-copper-and-nickel-binding (ATCUN) motif, a tripeptide sequence ending with a histidine, confers important functions to proteins and peptides. Few high-resolution studies have been performed on the ATCUN motifs of membrane-associated proteins and peptides, limiting our understanding of how they stabilize Cu2+/Ni2+ in membranes. Here, we leverage solid-state NMR to investigate metal-binding to piscidin-1 (P1), a host-defense peptide featuring F1F2H3 as its ATCUN motif. Bound to redox ions, P1 chemically and physically damages pathogenic cell membranes. We design 13C/15N correlation experiments to detect and assign the deprotonated nitrogens produced and/or shifted by Ni2+-binding. Occupying multiple chemical states in P1-apo, H3 and the neighboring H4 respond to metalation by populating only the τ-tautomer. H3, as a proximal histidine, directly coordinates the metal, compared to the distal H4. Density functional theory calculations reflect this noncanonical arrangement and point toward cation-π interactions between the F1/F2/H4 aromatic rings and metal. These structural findings, which are relevant to other ATCUN-containing membrane peptides, could help design new therapeutics and materials for use in the areas of drug-resistant bacteria, neurological disorders, and biomedical imaging.
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Affiliation(s)
- Riqiang Fu
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Mary T Rooney
- Department of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
| | - Rongfu Zhang
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, Virginia 23185, United States
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27
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Velayutham M, Poncelet M, Eubank TD, Driesschaert B, Khramtsov VV. Biological Applications of Electron Paramagnetic Resonance Viscometry Using a 13C-Labeled Trityl Spin Probe. Molecules 2021; 26:molecules26092781. [PMID: 34066858 PMCID: PMC8125944 DOI: 10.3390/molecules26092781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/27/2022] Open
Abstract
Alterations in viscosity of biological fluids and tissues play an important role in health and diseases. It has been demonstrated that the electron paramagnetic resonance (EPR) spectrum of a 13C-labeled trityl spin probe (13C-dFT) is highly sensitive to the local viscosity of its microenvironment. In the present study, we demonstrate that X-band (9.5 GHz) EPR viscometry using 13C-dFT provides a simple tool to accurately measure the microviscosity of human blood in microliter volumes obtained from healthy volunteers. An application of low-field L-band (1.2 GHz) EPR with a penetration depth of 1–2 cm allowed for microviscosity measurements using 13C-dFT in the living tissues from isolated organs and in vivo in anesthetized mice. In summary, this study demonstrates that EPR viscometry using a 13C-dFT probe can be used to noninvasively and rapidly measure the microviscosity of blood and interstitial fluids in living tissues and potentially to evaluate this biophysical marker of microenvironment under various physiological and pathological conditions in preclinical and clinical settings.
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Affiliation(s)
- Murugesan Velayutham
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA; (M.V.); (M.P.); (T.D.E.)
- Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Martin Poncelet
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA; (M.V.); (M.P.); (T.D.E.)
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
| | - Timothy D. Eubank
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA; (M.V.); (M.P.); (T.D.E.)
- Department of Microbiology, Immunology & Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Benoit Driesschaert
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA; (M.V.); (M.P.); (T.D.E.)
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
- Correspondence: (B.D.); (V.V.K.); Tel.: +1-304-293-7401 (B.D.); +1-304-293-4470 (V.V.K.)
| | - Valery V. Khramtsov
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA; (M.V.); (M.P.); (T.D.E.)
- Department of Biochemistry, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Correspondence: (B.D.); (V.V.K.); Tel.: +1-304-293-7401 (B.D.); +1-304-293-4470 (V.V.K.)
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28
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Olenginski LT, Dayie TK. Quantifying the effects of long-range 13C- 13C dipolar coupling on measured relaxation rates in RNA. J Biomol NMR 2021; 75:203-211. [PMID: 33914223 PMCID: PMC8131303 DOI: 10.1007/s10858-021-00368-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove 13C-13C dipolar couplings that complicate 13C relaxation analyses. While these phenomena are well documented for sites with adjacent 13C nuclei (e.g. ribose C1'), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) 13C-13C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-13C/15N]-ATP or selectively [2-13C]-ATP labeled RNAs. Our simulations predict non-negligible 13C-13C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R1) relaxation rates in [U-13C/15N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R1 measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-13C/15N]-ATP or [2-13C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range 13C-13C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R1 rates in terms of motional models for large RNAs.
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Affiliation(s)
- Lukasz T Olenginski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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29
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Crane JC, Gordon JW, Chen HY, Autry AW, Li Y, Olson MP, Kurhanewicz J, Vigneron DB, Larson PEZ, Xu D. Hyperpolarized 13 C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed 2021; 34:e4280. [PMID: 32189442 PMCID: PMC7501204 DOI: 10.1002/nbm.4280] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Based on the expanding set of applications for hyperpolarized carbon-13 (HP-13 C) MRI, this work aims to communicate standardized methodology implemented at the University of California, San Francisco, as a primer for conducting reproducible metabolic imaging studies of the prostate and brain. Current state-of-the-art HP-13 C acquisition, data processing/reconstruction and kinetic modeling approaches utilized in patient studies are presented together with the rationale underpinning their usage. Organized around spectroscopic and imaging-based methods, this guide provides an extensible framework for handling a variety of HP-13 C applications, which derives from two examples with dynamic acquisitions: 3D echo-planar spectroscopic imaging of the human prostate and frequency-specific 2D multislice echo-planar imaging of the human brain. Details of sequence-specific parameters and processing techniques contained in these examples should enable investigators to effectively tailor studies around individual-use cases. Given the importance of clinical integration in improving the utility of HP exams, practical aspects of standardizing data formats for reconstruction, analysis and visualization are also addressed alongside open-source software packages that enhance institutional interoperability and validation of methodology. To facilitate the adoption and further development of this methodology, example datasets and analysis pipelines have been made available in the supporting information.
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Affiliation(s)
- Jason C Crane
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - Jeremy W Gordon
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - Hsin-Yu Chen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - Adam W Autry
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - Yan Li
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - Marram P Olson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - John Kurhanewicz
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
| | - Daniel B Vigneron
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
| | - Peder E Z Larson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
| | - Duan Xu
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, USA
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30
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Lassen M, Christensen JB, Balslev-Harder D, Petersen JC. Isotopic gas analysis by means of mid-infrared photoacoustic spectroscopy targeting human exhaled air. Appl Opt 2021; 60:2907-2911. [PMID: 33798172 DOI: 10.1364/ao.418291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
There is a great need for cost-efficient non-invasive medical diagnostic tools for analyzing humanly exhaled air. Compared to present day methods, photoacoustic spectroscopy (PAS) can provide a compact and portable (bedside), sensitive and inexpensive solution. We demonstrate a novel portable photoacoustic spectroscopic platform for isotopic measurements of methane (CH4). We identify and discriminate the 12CH4- and 13CH4 isotopologues and determine their mixing ratio. An Allan deviation analysis shows that the noise equivalent concentration for CH4 is 200 ppt (pmol/mol) at 100 s of integration time, corresponding to a normalized noise equivalent absorption coefficient of 5.1×10-9Wcm-1Hz-1/2, potentially making the PAS sensor a truly disruptive instrument for bedside monitoring using isotope tracers by providing real-time metabolism data to clinical personnel.
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31
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Šturm MB, Smith S, Ganbaatar O, Buuveibaatar B, Balint B, Payne JC, Voigt CC, Kaczensky P. Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi. PLoS One 2021; 16:e0248294. [PMID: 33780458 PMCID: PMC8006982 DOI: 10.1371/journal.pone.0248294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/23/2021] [Indexed: 11/26/2022] Open
Abstract
With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan). Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence. Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.
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Affiliation(s)
- Martina Burnik Šturm
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Steve Smith
- Konrad-Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Oyunsaikhan Ganbaatar
- Great Gobi B Strictly Protected Area Administration, Takhin Tal, Gobi Altai Province, Mongolia
- Department of Zoology, School of Biology and Biotechnology, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | - Boglarka Balint
- Great Gobi B Strictly Protected Area Administration, Takhin Tal, Gobi Altai Province, Mongolia
| | - John C. Payne
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | | | - Petra Kaczensky
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
- Norwegian Institute for Nature Research–NINA, Trondheim, Norway
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32
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Naiyer A, Khan B, Hussain A, Islam A, Alajmi MF, Hassan MI, Sundd M, Ahmad F. Stability of uniformly labeled ( 13C and 15N) cytochrome c and its L94G mutant. Sci Rep 2021; 11:6804. [PMID: 33762670 PMCID: PMC7990917 DOI: 10.1038/s41598-021-86332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
Cytochrome c (cyt c) is widely used as a model protein to study (i) folding and stability aspects of the protein folding problem and (ii) structure-function relationship from the evolutionary point of view. Databases of cyts c now contain 285 cyt c sequences from different organisms. A sequence alignment of all these proteins with respect to horse cyt c led to several important conclusions. One of them is that Leu94 is always conserved in all 30 mammalian cyts c. It is known that mutation L94G of the wild type (WT) horse cyt c is destabilizing and mutant exists as molten globule under the native condition (buffer pH 6 and 25 °C). We have expressed and purified uniformly labeled (13C and 15N) and unlabeled WT horse cyt c and its L94G mutant. We report that labeling does not affect the thermodynamic stability of proteins. To support this conclusion, the secondary and tertiary structure of each protein in labeled and unlabeled forms was determined by conventional techniques (UV-Vis absorption and circular dichroism spectroscopy).
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Affiliation(s)
- Abdullah Naiyer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Bushra Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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Mishkovsky M, Gusyatiner O, Lanz B, Cudalbu C, Vassallo I, Hamou MF, Bloch J, Comment A, Gruetter R, Hegi ME. Hyperpolarized 13C-glucose magnetic resonance highlights reduced aerobic glycolysis in vivo in infiltrative glioblastoma. Sci Rep 2021; 11:5771. [PMID: 33707647 PMCID: PMC7952603 DOI: 10.1038/s41598-021-85339-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/28/2021] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive brain tumor type in adults. GBM is heterogeneous, with a compact core lesion surrounded by an invasive tumor front. This front is highly relevant for tumor recurrence but is generally non-detectable using standard imaging techniques. Recent studies demonstrated distinct metabolic profiles of the invasive phenotype in GBM. Magnetic resonance (MR) of hyperpolarized 13C-labeled probes is a rapidly advancing field that provides real-time metabolic information. Here, we applied hyperpolarized 13C-glucose MR to mouse GBM models. Compared to controls, the amount of lactate produced from hyperpolarized glucose was higher in the compact GBM model, consistent with the accepted "Warburg effect". However, the opposite response was observed in models reflecting the invasive zone, with less lactate produced than in controls, implying a reduction in aerobic glycolysis. These striking differences could be used to map the metabolic heterogeneity in GBM and to visualize the infiltrative front of GBM.
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Affiliation(s)
- Mor Mishkovsky
- Laboratory of Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Olga Gusyatiner
- Neuroscience Research Center, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Service of Neurosurgery Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Bernard Lanz
- Laboratory of Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Cristina Cudalbu
- Center for Biomedical Imaging (CIBM), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Irene Vassallo
- Neuroscience Research Center, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Service of Neurosurgery Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Marie-France Hamou
- Neuroscience Research Center, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Service of Neurosurgery Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jocelyne Bloch
- Neuroscience Research Center, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Service of Neurosurgery Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Arnaud Comment
- General Electric Healthcare, Chalfont St Giles, Buckinghamshire, HP8 4SP, UK
| | - Rolf Gruetter
- Laboratory of Functional and Metabolic Imaging, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Biomedical Imaging (CIBM), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Department of Radiology, University of Geneva (UNIGE), Geneva, Switzerland
- Department of Radiology, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Monika E Hegi
- Neuroscience Research Center, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
- Service of Neurosurgery Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
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34
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Tiwari N, Wegner S, Hassan A, Dwivedi N, Rai R, Sinha N. Probing short and long-range interactions in native collagen inside the bone matrix by BioSolids CryoProbe. Magn Reson Chem 2021; 59:99-107. [PMID: 32761649 DOI: 10.1002/mrc.5084] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Solid-state nuclear magnetic resonance is a promising technique to probe bone mineralization and interaction of collagen protein in the native state. However, many of the developments are hampered due to the low sensitivity of the technique. In this article, we report solid-state nuclear magnetic resonance (NMR) experiments using the newly developed BioSolids CryoProbe™ to access its applicability for elucidating the atomic-level structural details of collagen protein in native state inside the bone. We report here approximately a fourfold sensitivity enhancement in the natural abundance 13 C spectrum compared with the room temperature conventional solid-state NMR probe. With the advantage of sensitivity enhancement, we have been able to perform natural abundance 15 N cross-polarization magic angle spinning (CPMAS) and two-dimensional (2D) 1 H-13 C heteronuclear correlation (HETCOR) experiments of native collagen within a reasonable timeframe. Due to high sensitivity, 2D 1 H/13 C HETCOR experiments have helped in detecting several short and long-range interactions of native collagen assembly, thus significantly expanding the scope of the method to such challenging biomaterials.
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Affiliation(s)
- Nidhi Tiwari
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
- Department of Chemistry, Institute of Sciences, Banaras Hindu University, Varanasi, 221005, India
| | | | - Alia Hassan
- Bruker BioSpin Corporation, Fällanden, Switzerland
| | - Navneet Dwivedi
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
- Department of Physics, Integral University, Lucknow, 226026, India
| | - RamaNand Rai
- Department of Chemistry, Institute of Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
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35
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Demény A, Rinyu L, Németh P, Czuppon G, Enyedi N, Makk J, Leél-Őssy S, Kesjár D, Kovács I. Bacterial and abiogenic carbonates formed in caves-no vital effect on clumped isotope compositions. PLoS One 2021; 16:e0245621. [PMID: 33493213 PMCID: PMC7833151 DOI: 10.1371/journal.pone.0245621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022] Open
Abstract
Speleothems (dominated by cave-hosted carbonate deposits) are valuable archives of paleoclimate conditions. As such, they are potential targets of clumped isotope analyses that may yield quantified data about past temperature variations. Clumped isotope analyses of stalagmites, however, seldom provide useful temperature values due to various isotope fractionation processes. This study focuses on the determination of the microbially induced vital effect, i.e., the isotope fractionation processes related to bacterial carbonate production. A cave site with biologically mediated amorphous calcium carbonate precitation was selected as a natural laboratory. Calcite deposits were farmed under a UV lamp to prevent bacterial activity, as well as under control conditions. Microbiological analyses and morphological investigations using scanning electron microscopy showed that the UV lamp treatment effectively reduced the number of bacterial cells, and that bacterial carbonate production strongly influenced the carbonate’s morphology. Stable oxygen isotope analyses of calcite and drip waters, as well as clumped isotope measurements revealed that, although most of the studied carbonates formed close to oxygen isotope equilibrium, clumped isotope Δ47 values varied widely from equilibrium to strongly fractionated data. Site-specific kinetic fractionations played a dominant role in the distribution of Δ47 values, whereas bacterial carbonate production did not result in a detectable clumped isotope effect.
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Affiliation(s)
- Attila Demény
- Institute for Geological and Geochemical Research, Research Centre for Astronomy and Earth Sciences, Budapest, Hungary
- * E-mail:
| | - László Rinyu
- Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Debrecen, Hungary
| | - Péter Németh
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Earth and Environmental Sciences, University of Pannonia, Veszprém, Hungary
| | - György Czuppon
- Institute for Geological and Geochemical Research, Research Centre for Astronomy and Earth Sciences, Budapest, Hungary
| | - Nóra Enyedi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Judit Makk
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Szabolcs Leél-Őssy
- Department of Physical and Applied Geology, Eötvös Loránd University, Budapest, Hungary
| | - Dóra Kesjár
- Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Debrecen, Hungary
| | - Ivett Kovács
- Institute for Geological and Geochemical Research, Research Centre for Astronomy and Earth Sciences, Budapest, Hungary
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36
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Tugarinov V, Karamanos TK, Clore GM. Optimized selection of slow-relaxing 13C transitions in methyl groups of proteins: application to relaxation dispersion. J Biomol NMR 2020; 74:673-680. [PMID: 33006092 PMCID: PMC7704780 DOI: 10.1007/s10858-020-00349-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/18/2020] [Indexed: 05/13/2023]
Abstract
Optimized selection of the slow-relaxing components of single-quantum 13C magnetization in 13CH3 methyl groups of proteins using acute (< 90°) angle 1H radio-frequency pulses, is described. The optimal selection scheme is more relaxation-tolerant and provides sensitivity gains in comparison to the experiment where the undesired (fast-relaxing) components of 13C magnetization are simply 'filtered-out' and only 90° 1H pulses are employed for magnetization transfer to and from 13C nuclei. When applied to methyl 13C single-quantum Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments for studies of chemical exchange, the selection of the slow-relaxing 13C transitions results in a significant decrease in intrinsic (exchange-free) transverse spin relaxation rates of all exchanging species. For exchanging systems involving high-molecular-weight species, the lower transverse relaxation rates translate into an increase in the information content of the resulting relaxation dispersion profiles.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Theodoros K Karamanos
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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37
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Kumar S, Akabayov SR, Kessler N, Cohen LS, Solanki J, Naider F, Kay LE, Anglister J. The methyl 13C-edited/ 13C-filtered transferred NOE for studying protein interactions with short linear motifs. J Biomol NMR 2020; 74:681-693. [PMID: 32997264 DOI: 10.1007/s10858-020-00340-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Many proteins interact with their ligand proteins by recognition of short linear motifs that are often intrinsically disordered. These interactions are usually weak and are characterized by fast exchange. NMR spectroscopy is a powerful tool to study weak interactions. The methods that have been commonly used are analysis of chemicals shift perturbations (CSP) upon ligand binding and saturation transfer difference spectroscopy. These two methods identify residues at the binding interface between the protein and its ligand. In the present study, we used a combination of transferred-NOE, specific methyl-labeling and an optimized isotope-edited/isotope-filtered NOESY experiment to study specific interactions between the 42 kDa p38α mitogen-activated protein kinase and the kinase interaction motif (KIM) on the STEP phosphatase. These measurements distinguished between residues that both exhibit CSPs upon ligand binding and interact with the KIM peptide from residues that exhibit CSPs but do not interact with the peptide. In addition, these results provide information about pairwise interactions that is important for a more reliable docking of the KIM peptide into its interacting surface on p38α. This combination of techniques should be applicable for many protein-peptide complexes up to 80 kDa for which methyl resonance assignment can be achieved.
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Affiliation(s)
- Suresh Kumar
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Sabine R Akabayov
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel.
| | - Naama Kessler
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Leah S Cohen
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, 10314, USA
- The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Jacob Solanki
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, 10314, USA
- The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, 10314, USA
- The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Lewis E Kay
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, M5S1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON, M5S1A8, Canada
- Department of Chemistry, The University of Toronto, Toronto, ON, M5S1A8, Canada
- Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Jacob Anglister
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel.
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38
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Kuan KY, Singleton DA. Vibrationally Hot and Cold Triplets. Sensitizer-Dependent Dynamics and Localized Vibrational Promotion of a Di-π-methane Rearrangement. J Am Chem Soc 2020; 142:19885-19888. [PMID: 33179917 PMCID: PMC8522498 DOI: 10.1021/jacs.0c10468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Large intramolecular 13C kinetic isotope effects (KIEs) for the di-π-methane rearrangement of benzobarrelene fit with statistical expectations from heavy-atom tunneling when a low-energy sensitizer is employed, but much lower KIEs are observed with higher-energy sensitizers. These results in combination with trajectory studies suggest that the excess vibrational energy available from triplet energy transfer leads to hot and nonstatistical dynamics in the rearrangement.
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Affiliation(s)
- Kai-Yuan Kuan
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Daniel A Singleton
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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39
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Jähnigen S, Sebastiani D. Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ. Molecules 2020; 25:E5505. [PMID: 33255423 PMCID: PMC7727823 DOI: 10.3390/molecules25235505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.
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Affiliation(s)
| | - Daniel Sebastiani
- Institut für Chemie, Naturwissenschaftliche Fakultät II, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany;
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40
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Dey A, Charrier B, Martineau E, Deborde C, Gandriau E, Moing A, Jacob D, Eshchenko D, Schnell M, Melzi R, Kurzbach D, Ceillier M, Chappuis Q, Cousin SF, Kempf JG, Jannin S, Dumez JN, Giraudeau P. Hyperpolarized NMR Metabolomics at Natural 13C Abundance. Anal Chem 2020; 92:14867-14871. [PMID: 33136383 PMCID: PMC7705890 DOI: 10.1021/acs.analchem.0c03510] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022]
Abstract
Metabolomics plays a pivotal role in systems biology, and NMR is a central tool with high precision and exceptional resolution of chemical information. Most NMR metabolomic studies are based on 1H 1D spectroscopy, severely limited by peak overlap. 13C NMR benefits from a larger signal dispersion but is barely used in metabolomics due to ca. 6000-fold lower sensitivity. We introduce a new approach, based on hyperpolarized 13C NMR at natural abundance, that circumvents this limitation. A new untargeted NMR-based metabolomic workflow based on dissolution dynamic nuclear polarization (d-DNP) for the first time enabled hyperpolarized natural abundance 13C metabolomics. Statistical analysis of resulting hyperpolarized 13C data distinguishes two groups of plant (tomato) extracts and highlights biomarkers, in full agreement with previous results on the same biological model. We also optimize parameters of the semiautomated d-DNP system suitable for high-throughput studies.
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Affiliation(s)
- Arnab Dey
- Université
de Nantes, CNRS, CEISAM UMR
6230, F-44000 Nantes, France
| | - Benoît Charrier
- Université
de Nantes, CNRS, CEISAM UMR
6230, F-44000 Nantes, France
| | - Estelle Martineau
- Université
de Nantes, CNRS, CEISAM UMR
6230, F-44000 Nantes, France
- SpectroMaitrise,
CAPACITES SAS, F-44000 Nantes, France
| | - Catherine Deborde
- INRAE,
Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, Centre INRAE de Nouvelle Aquitaine-Bordeaux, F-33140 Villenave
d’Ornon, France
- Bordeaux
Metabolome, MetaboHUB, Centre INRAE de Nouvelle
Aquitaine-Bordeaux, F-33140 Villenave d’Ornon, France
| | - Elodie Gandriau
- Université
de Nantes, CNRS, CEISAM UMR
6230, F-44000 Nantes, France
| | - Annick Moing
- INRAE,
Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, Centre INRAE de Nouvelle Aquitaine-Bordeaux, F-33140 Villenave
d’Ornon, France
- Bordeaux
Metabolome, MetaboHUB, Centre INRAE de Nouvelle
Aquitaine-Bordeaux, F-33140 Villenave d’Ornon, France
| | - Daniel Jacob
- INRAE,
Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, Centre INRAE de Nouvelle Aquitaine-Bordeaux, F-33140 Villenave
d’Ornon, France
- Bordeaux
Metabolome, MetaboHUB, Centre INRAE de Nouvelle
Aquitaine-Bordeaux, F-33140 Villenave d’Ornon, France
| | - Dmitry Eshchenko
- Bruker
Biospin, Industriestrasse
26, 8117 Fällanden, Switzerland
| | - Marc Schnell
- Bruker
Biospin, Industriestrasse
26, 8117 Fällanden, Switzerland
| | | | - Dennis Kurzbach
- University
of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Morgan Ceillier
- Université
de Lyon, CNRS, Université Claude
Bernard Lyon 1, ENS de Lyon, Centre de RMN à Très Hauts Champs (CRMN),
FRE 2034, F-69100 Villeurbanne, France
| | - Quentin Chappuis
- Université
de Lyon, CNRS, Université Claude
Bernard Lyon 1, ENS de Lyon, Centre de RMN à Très Hauts Champs (CRMN),
FRE 2034, F-69100 Villeurbanne, France
| | - Samuel F. Cousin
- Université
de Lyon, CNRS, Université Claude
Bernard Lyon 1, ENS de Lyon, Centre de RMN à Très Hauts Champs (CRMN),
FRE 2034, F-69100 Villeurbanne, France
| | - James G. Kempf
- Bruker
Biospin, 15 Fortune Dr., Billerica, Massachusetts 01821, United States
| | - Sami Jannin
- Université
de Lyon, CNRS, Université Claude
Bernard Lyon 1, ENS de Lyon, Centre de RMN à Très Hauts Champs (CRMN),
FRE 2034, F-69100 Villeurbanne, France
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41
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Knipper C, Reinhold S, Gresky J, Berezina N, Gerling C, Pichler SL, Buzhilova AP, Kantorovich AR, Maslov VE, Petrenko VG, Lyakhov SV, Kalmykov AA, Belinskiy AB, Hansen S, Alt KW. Diet and subsistence in Bronze Age pastoral communities from the southern Russian steppes and the North Caucasus. PLoS One 2020; 15:e0239861. [PMID: 33052915 PMCID: PMC7556513 DOI: 10.1371/journal.pone.0239861] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/14/2020] [Indexed: 11/19/2022] Open
Abstract
The flanks of the Caucasus Mountains and the steppe landscape to their north offered highly productive grasslands for Bronze Age herders and their flocks of sheep, goat, and cattle. While the archaeological evidence points to a largely pastoral lifestyle, knowledge regarding the general composition of human diets and their variation across landscapes and during the different phases of the Bronze Age is still restricted. Human and animal skeletal remains from the burial mounds that dominate the archaeological landscape and their stable isotope compositions are major sources of dietary information. Here, we present stable carbon and nitrogen isotope data of bone collagen of 105 human and 50 animal individuals from the 5th millennium BC to the Sarmatian period, with a strong focus on the Bronze Age and its cultural units including Maykop, Yamnaya, Novotitorovskaya, North Caucasian, Catacomb, post-Catacomb and late Bronze Age groups. The samples comprise all inhumations with sufficient bone preservation from five burial mound sites and a flat grave cemetery as well as subsamples from three further sites. They represent the Caucasus Mountains in the south, the piedmont zone and Kuban steppe with humid steppe and forest vegetation to its north, and more arid regions in the Caspian steppe. The stable isotope compositions of the bone collagen of humans and animals varied across the study area and reflect regional diversity in environmental conditions and diets. The data agree with meat, milk, and/or dairy products from domesticated herbivores, especially from sheep and goats having contributed substantially to human diets, as it is common for a largely pastoral economy. This observation is also in correspondence with the faunal remains observed in the graves and offerings of animals in the mound shells. In addition, foodstuffs with elevated carbon and nitrogen isotope values, such as meat of unweaned animals, fish, or plants, also contributed to human diets, especially among communities living in the more arid landscapes. The regional distinction of the animal and human data with few outliers points to mobility radii that were largely concentrated within the environmental zones in which the respective sites are located. In general, dietary variation among the cultural entities as well as regarding age, sex and archaeologically indicated social status is only weakly reflected. There is, however, some indication for a dietary shift during the Early Bronze Age Maykop period.
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Affiliation(s)
- Corina Knipper
- Curt Engelhorn Center Archaeometry, Mannheim, Germany
- * E-mail:
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Julia Gresky
- Department of Natural Sciences, German Archaeological Institute, Berlin, Germany
| | - Nataliya Berezina
- Research Institute and Museum of Anthropology of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Claudia Gerling
- Integrative Prehistory and Archaeological Science IPAS, Basel University, Basel, Switzerland
| | - Sandra L. Pichler
- Integrative Prehistory and Archaeological Science IPAS, Basel University, Basel, Switzerland
| | - Alexandra P. Buzhilova
- Research Institute and Museum of Anthropology of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anatoly R. Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Vladimir E. Maslov
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Sergey V. Lyakhov
- Heritage Organization Ltd, ‘Nasledie’, Stavropol, Russian Federation
| | | | | | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Kurt W. Alt
- Integrative Prehistory and Archaeological Science IPAS, Basel University, Basel, Switzerland
- Center of Natural and Cultural Human History, Danube Private University (DPU), Krems-Stein, Austria
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42
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Sundström Rehal M, Liebau F, Wernerman J, Rooyackers O. Whole-body protein kinetics in critically ill patients during 50 or 100% energy provision by enteral nutrition: A randomized cross-over study. PLoS One 2020; 15:e0240045. [PMID: 33017434 PMCID: PMC7535026 DOI: 10.1371/journal.pone.0240045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/16/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Enteral nutrition (EN) is a ubiquitous intervention in ICU patients but there is uncertainty regarding the optimal dose, timing and importance for patient-centered outcomes during critical illness. Our research group has previously found an improved protein balance during normocaloric versus hypocaloric parenteral nutrition in neurosurgical ICU patients. We now wanted to investigate if this could be demonstrated in a general ICU population with established enteral feeding, including patients on renal replacement therapy. METHODS Patients with EN >80% of energy target as determined by indirect calorimetry were randomized to or 50% or 100% of current EN rate. After 24 hours, whole-body protein kinetics were determined by enteral and parenteral stable isotope tracer infusions. Treatment allocation was then switched, and tracer investigations repeated 24 hours later in a crossover design with patients serving as their own controls. RESULTS Six patients completed the full protocol. During feeding with 100% EN all patients received >1.2 g/kg/day of protein. Mean whole-body protein balance increased from -6.07 to 2.93 µmol phenylalanine/kg/h during 100% EN as compared to 50% (p = 0.044). The oxidation rate of phenylalanine was unaltered (p = 0.78). CONCLUSIONS It is possible to assess whole-body protein turnover using a stable isotope technique in critically ill patients during enteral feeding and renal replacement therapy. Our results also suggest a better whole-body protein balance during full dose as compared to half dose EN. As the sample size was smaller than anticipated, this finding should be confirmed in larger studies.
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Affiliation(s)
- Martin Sundström Rehal
- Department of Perioperative Medicine and Intensive Care (PMI), Karolinska University Hospital Huddinge, Stockholm, Sweden
- Division of Anesthesia and Intensive Care, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Felix Liebau
- Department of Perioperative Medicine and Intensive Care (PMI), Karolinska University Hospital Huddinge, Stockholm, Sweden
- Division of Anesthesia and Intensive Care, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Jan Wernerman
- Division of Anesthesia and Intensive Care, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Olav Rooyackers
- Department of Perioperative Medicine and Intensive Care (PMI), Karolinska University Hospital Huddinge, Stockholm, Sweden
- Division of Anesthesia and Intensive Care, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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43
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Tiziani R, Pii Y, Celletti S, Cesco S, Mimmo T. Phosphorus deficiency changes carbon isotope fractionation and triggers exudate reacquisition in tomato plants. Sci Rep 2020; 10:15970. [PMID: 32994443 PMCID: PMC7524771 DOI: 10.1038/s41598-020-72904-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/06/2020] [Indexed: 11/28/2022] Open
Abstract
Plant roots are able to exude vast amounts of metabolites into the rhizosphere in response to phosphorus (P) deficiency. Causing noteworthy costs in terms of energy and carbon (C) for the plants. Therefore, it is suggested that exudates reacquisition by roots could represent an energy saving strategy of plants. This study aimed at investigating the effect of P deficiency on the ability of hydroponically grown tomato plants to re-acquire specific compounds generally present in root exudates by using 13C-labelled molecules. Results showed that P deficient tomato plants were able to take up citrate (+ 37%) and malate (+ 37%), particularly when compared to controls. While glycine (+ 42%) and fructose (+ 49%) uptake was enhanced in P shortage, glucose acquisition was not affected by the nutritional status. Unexpectedly, results also showed that P deficiency leads to a 13C enrichment in both tomato roots and shoots over time (shoots-+ 2.66‰, roots-+ 2.64‰, compared to control plants), probably due to stomata closure triggered by P deficiency. These findings highlight that tomato plants are able to take up a wide range of metabolites belonging to root exudates, thus maximizing C trade off. This trait is particularly evident when plants grew in P deficiency.
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Affiliation(s)
- Raphael Tiziani
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy.
| | - Youry Pii
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Silvia Celletti
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy.
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Abstract
A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square #2, 16206 Prague, Czech Republic;
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Lacharity JJ, Mailyan AK, Chen KY, Zakarian A. Concise Synthesis of (+)-[ 13 C 4 ]-Anatoxin-a by Dynamic Kinetic Resolution of a Cyclic Iminium Ion. Angew Chem Int Ed Engl 2020; 59:11364-11368. [PMID: 32304178 PMCID: PMC7409530 DOI: 10.1002/anie.202004464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/17/2020] [Indexed: 11/11/2022]
Abstract
An asymmetric total synthesis of [13 C4 ]-anatoxin-a ([13 C4 ]-1) has been developed from commercially available ethyl [13 C4 ]-acetoacetate ([13 C4 ]-15). The unique requirements associated with isotope incorporation inspired a new, robust, and highly scalable route, providing access to 0.110 g of this internal standard for use in the detection and precise quantification of anatoxin-a in freshwater. A highlight of the synthesis is a method that leverages a cyclic iminium ion racemization to achieve dynamic kinetic resolution in an enantioselective Morita-Baylis-Hillman (MBH) cyclization.
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Affiliation(s)
- Jacob J Lacharity
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106-9510, USA
| | - Artur K Mailyan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106-9510, USA
| | - Karen Y Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106-9510, USA
| | - Armen Zakarian
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106-9510, USA
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Kraus J, Gupta R, Lu M, Gronenborn AM, Akke M, Polenova T. Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter. Chemphyschem 2020; 21:1436-1443. [PMID: 32363727 PMCID: PMC8080305 DOI: 10.1002/cphc.202000249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Indexed: 01/07/2023]
Abstract
Chemical shift tensors obtained from solid-state NMR spectroscopy are very sensitive reporters of structure and dynamics in proteins. While accurate 13 C and 15 N chemical shift tensors are accessible by magic angle spinning (MAS) NMR, their quantum mechanical calculations remain challenging, particularly for 15 N atoms. Here we compare experimentally determined backbone 13 Cα and 15 NH chemical shift tensors by MAS NMR with hybrid quantum mechanics/molecular mechanics/molecular dynamics (MD-QM/MM) calculations for the carbohydrate-binding domain of galectin-3. Excellent agreement between experimental and computed 15 NH chemical shift anisotropy values was obtained using the Amber ff15ipq force field when solvent dynamics was taken into account in the calculation. Our results establish important benchmark conditions for improving the accuracy of chemical shift calculations in proteins and may aid in the validation of protein structure models derived by MAS NMR.
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Affiliation(s)
- Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Department of Chemistry, The College of Staten Island, 2800 Victory Blvd, Staten Island, NY 10314
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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Abstract
Carbon stable isotope analysis can provide information about the origin and synthetic pathways that produce organic molecules, with applications in chemical, medical and (bio)geochemical sciences. The 13C/12C isotope ratios of organics such as amino acids are most commonly obtained as whole molecule averages. In this study, we apply proton nuclear magnetic resonance spectroscopy to conduct position-specific carbon isotope analyses of L-/D-alanine, L-threonine and L-histidine from different sources, in addition to molecule average stable isotope analyses obtained via mass spectrometry. Our results demonstrate that carbon isotope ratios can vary significantly between the individual carbon positions within an amino acid. For example, the β- and γ- carbons of L-threonine can differ in 13C/12C ratio by > 20 ‰. Comparisons of the position-specific and whole molecule average stable isotope abundances show that whole molecule analyses can mask the intramolecular isotope variation. These results provide the first experimentally measured position-specific isotope ratios for alpha and side chain carbons of alanine, threonine and histidine. Comparison with previous ab initio calculations of intramolecular equilibrium fractionation shows that the carbon isotope distributions are not at equilibrium, thus kinetic isotope effects play a significant role in amino acid synthesis. We hypothesize that position-specific 13C/12C isotope ratios provide an "isotopic fingerprint" that can give insight into the origin or synthesis pathway that formed an amino acid, and that this emerging analytical field will be a valuable addition to traditional stable isotope analysis.
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Affiliation(s)
- Cornelia Rasmussen
- Institute for Geophysics and Department of Geological Sciences, Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA.
- University of Texas Center for Planetary Systems Habitability, Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA.
| | - David W Hoffman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- University of Texas Center for Planetary Systems Habitability, Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
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Bazzer SK, Kaler AS, Ray JD, Smith JR, Fritschi FB, Purcell LC. Identification of quantitative trait loci for carbon isotope ratio (δ 13C) in a recombinant inbred population of soybean. Theor Appl Genet 2020; 133:2141-2155. [PMID: 32296861 DOI: 10.1007/s00122-020-03586-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/31/2020] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE QTL analysis identified 16 QTLs, grouped in eight loci on seven soybean chromosomes that were associated with carbon isotope ratio (δ13C) in a biparental recombinant inbred population. Drought is a major limitation to soybean yield, and the frequency of drought stress is likely to increase under future climatic scenarios. Water use efficiency (WUE) is associated with drought tolerance, and carbon isotope ratio (δ13C) is positively correlated with WUE. In this study, 196 F6-derived recombinant inbred lines from a cross of PI 416997 (high WUE) × PI 567201D (low WUE) were evaluated in four environments to identify genomic regions associated with δ13C. There were positive correlations of δ13C values between different environments (0.67 ≤ r ≤ 0.78). Genotype, environment, and genotype × environment interactions had significant effects on δ13C. Narrow sense heritability of δ13C was 90% when estimated across environments. There was a total of 16 QTLs on seven chromosomes with individual QTLs explaining between 2.5 and 29.9% of the phenotypic variation and with additive effects ranging from 0.07 to 0.22‰. These 16 QTLs likely identified eight loci based on their overlapping confidence intervals. Of these eight loci, two loci on chromosome 20 (Gm20) were detected in at least three environments and were considered as stable QTLs. Additive QTLs on Gm20 showed epistatic interactions with 10 QTLs present across nine chromosomes. Five QTLs were identified across environments and showed significant QTL × environment interactions. These findings demonstrate that additive QTLs and QTL × QTL interactions play significant roles in genetic control of the δ13C trait. Markers flanking identified QTLs may facilitate marker-assisted selection to accumulate desirable QTLs to improve WUE and drought tolerance in soybean.
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Affiliation(s)
- Sumandeep K Bazzer
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Avjinder S Kaler
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Jeffery D Ray
- Agricultural Research Service, Crop Genetics Research Unit, USDA, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - James R Smith
- Agricultural Research Service, Crop Genetics Research Unit, USDA, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, 1-13 Agriculture Building, Columbia, MO, 65211, USA
| | - Larry C Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA.
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49
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Reijerse E, Birrell JA, Lubitz W. Spin Polarization Reveals the Coordination Geometry of the [FeFe] Hydrogenase Active Site in Its CO-Inhibited State. J Phys Chem Lett 2020; 11:4597-4602. [PMID: 32420744 PMCID: PMC7309315 DOI: 10.1021/acs.jpclett.0c01352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
The active site of [FeFe] hydrogenase features a binuclear iron cofactor Fe2ADT(CO)3(CN)2, where ADT represents the bridging ligand aza-propane-dithiolate. The terminal diatomic ligands all coordinate in a basal configuration, and one CO bridges the two irons leaving an open coordination site at which the hydrogen species and the competitive inhibitor CO bind. Externally supplied CO is expected to coordinate in an apical configuration. However, an alternative configuration has been proposed in which, due to ligand rotation, the CN- bound to the distal Fe becomes apical. Using selective 13C isotope labeling of the CN- and COext ligands in combination with pulsed 13C electron-nuclear-nuclear triple resonance spectroscopy, spin polarization effects are revealed that, according to density functional theory calculations, are consistent with only the "unrotated" apical COext configuration.
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50
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Iwayama K, Onishi T, Maruyama K, Takahashi H. Diurnal variation in the glycogen content of the human liver using 13 C MRS. NMR Biomed 2020; 33:e4289. [PMID: 32157774 DOI: 10.1002/nbm.4289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Glycogen in tissues functions not only as carbohydrate reserves, but also as molecular sensors capable of activating signaling pathways in response to physical activity. While glycogen in the skeletal muscles is mainly a local energy substrate, glycogen in the liver serves as a glucose reserve to maintain normal blood glucose levels in the body, even during the sleep state. The aim of this study is to compare the diurnal variation of glycogen in the muscle and liver of human subjects under normal conditions. The glycogen content was measured in the muscle and liver of 10 young, healthy, male volunteers using 13 C MRS, a non-invasive technique. The subjects remained sedentary, and glycogen concentration was measured six times daily. Experimental meals were provided to achieve individual energy balance, estimated according to the energy requirement guideline for patients from Japan. The largest variation in muscle glycogen compared with 1 h after supper (20:00 on Day 1) was 3.1 ± 8.2 mmol/L (16:00 on Day 2). In the liver, however, the glycogen content decreased by 80.6 ± 40.4 mmol/L through the overnight fasting period (07:00 on Day 2). This study demonstrated that the glycogen content in the liver was significantly lower in the morning, while the glycogen content in the calf muscles underwent minimal diurnal variation. The overnight fast is a characteristic daily condition, in which liver glycogen content is low, whereas muscle glycogen content is relatively unaffected.
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Affiliation(s)
- Kaito Iwayama
- Faculty of Budo and Sport Studies, Tenri University, Nara, Japan
| | - Takahiro Onishi
- Medical Center, Japan Institute of Sports Sciences, Tokyo, Japan
| | - Katsuya Maruyama
- MR Research & Collaboration Department, Siemens Healthcare K.K., Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Sport Research, Japan Institute of Sports Sciences, Tokyo, Japan
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