Journal articles: 'Isotopic 13C NMR'

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Kelleway, J. J., S. M. Trevathan-Tackett, J. Baldock, and L. P. Critchley. "Plant litter composition and stable isotope signatures vary during decomposition in blue carbon ecosystems." Biogeochemistry 158, no. 2 (February 1, 2022): 147–65. http://dx.doi.org/10.1007/s10533-022-00890-3.

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AbstractThe ratio of isotopes of carbon (13C:12C or δ13C) and nitrogen (15N:14N or δ15N) are common indicators of the flow and storage of organic matter in coastal wetland research. Effective use of these indicators requires quantification and understanding of: (1) the variability of isotope signatures of potential organic matter source materials; and (2) the influence of organic matter decomposition on isotopic signatures. While it is well-established that organic matter characteristics change during the decomposition process, there has been little direct quantification of any concurrent shifts in isotope signatures for coastal detritus. In this study, we addressed this by quantifying: (1) shifts in sample composition using solid-state 13C Nuclear Magnetic Resonance (NMR) spectroscopy; and (2) shifts in δ13C and δ15N signatures of coastal plant tissues from field litterbag experiments. We observed significant shifts in 13C NMR spectra across the course of deployment for all four plant tissues assessed (leaves of mangrove Avicennia marina; branchlets of supratidal tree Casuarina glauca; leaf wrack and roots/rhizomes of the seagrass Zostera muelleri), driven largely by the preferential loss of labile constituents and concentration of more resistant macromolecules, such as lignin and leaf waxes. While there were shifts in isotope ratios for all species, these varied in direction and magnitude among species, tissue type and isotopes. This included δ13C enrichments of up to 3.1‰ and 2.4‰ in leaves of A. marina, and branchlets of C. glauca, respectively, but δ13C depletions of up to 4.0‰ for Z. muelleri. Shifts in δ15N varied among species and tissue types, with few clear temporal patterns. Partial least squares regression analyses showed that some tissue isotope signatures can be reliably predicted on the basis of sample composition (13C NMR spectra), however, multiple inter- and intra-species variations preclude a simple explanation of isotopic signature shifts on the basis of plant-material molecular shifts alone. Further, we cannot preclude the potential influence of microbe-associated organic matter on sample composition or isotopic signatures. Our findings emphasise the importance of considering decomposition effects on stable isotope signatures in blue carbon ecosystems. Isotope approaches will remain a valuable tool in coastal ecosystem research, but require robust experimental approaches (including appropriate use of decomposed end-members or fractionation correction factors; quantification of microbial organic matter) and quantification of decomposition dynamics for specific plant tissues and environmental settings.

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Bagga, Puneet, Kevin L. Behar, Graeme F. Mason, Henk M. De Feyter, Douglas L. Rothman, and Anant B. Patel. "Characterization of Cerebral Glutamine Uptake from Blood in the Mouse Brain: Implications for Metabolic Modeling of 13C NMR Data." Journal of Cerebral Blood Flow & Metabolism 34, no. 10 (July 30, 2014): 1666–72. http://dx.doi.org/10.1038/jcbfm.2014.129.

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13C Nuclear Magnetic Resonance (NMR) studies of rodent and human brain using [1-13C]/[1,6-13C2]glucose as labeled substrate have consistently found a lower enrichment (~25% to 30%) of glutamine-C4 compared with glutamate-C4 at isotopic steady state. The source of this isotope dilution has not been established experimentally but may potentially arise either from blood/brain exchange of glutamine or from metabolism of unlabeled substrates in astrocytes, where glutamine synthesis occurs. In this study, the contribution of the former was evaluated ex vivo using 1H-[13C]-NMR spectroscopy together with intravenous infusion of [U-13C5]glutamine for 3, 15, 30, and 60 minutes in mice. 13C labeling of brain glutamine was found to be saturated at plasma glutamine levels > 1.0 mmol/L. Fitting a blood–astrocyte–neuron metabolic model to the 13C enrichment time courses of glutamate and glutamine yielded the value of glutamine influx, VGln(in), 0.036 ± 0.002 μmol/g per minute for plasma glutamine of 1.8 mmol/L. For physiologic plasma glutamine level (~0.6 mmol/L), VGln(in) would be ~0.010 μmol/g per minute, which corresponds to ~6% of the glutamine synthesis rate and rises to ~11% for saturating blood glutamine concentrations. Thus, glutamine influx from blood contributes at most ~20% to the dilution of astroglial glutamine-C4 consistently seen in metabolic studies using [1-13C]glucose.

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Xie, Yimin, Xudong Chen, Kai Zhang, Sheng Cui, and Gongxia Zhang. "Elucidation of lignin and polysaccharide linkages in wheat straw by 2H/13C isotopic tracer." BioResources 18, no. 1 (November 17, 2022): 550–69. http://dx.doi.org/10.15376/biores.18.1.550-569.

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To elucidate chemical linkages between lignin and polysaccharides, the aqueous mixed solutions of coniferin-[α-13C], syringin-[α-13C], D-glucose-[6-2H], and phenylalanine ammonia-lyase inhibitor were injected into a living wheat stalk. Internode tissues with high abundance of 2H-13C were collected. The milled wood lignin, lignin-carbohydrate complex (LCC), and residual LCC (R-LCC) with enrichment of 2H-13C were isolated. The 13C and 2H abundances showed that the lignin and polysaccharides of internode tissues were labeled by 13C and 2H, respectively. Analysis with carbon-13 nuclear magnetic resonance (13C-NMR) showed that ketal and benzyl ether bonds were formed between α-C of lignin and carbohydrates. The R-LCC and LCC were further treated with enzymes to obtain enzymatic degraded R-LCC (ED-R-LCC) and enzymatic degraded LCC (ED-LCC). 13C-NMR spectra of ED-LCC showed that the α-C of lignin side chain was combined with 6-C of carbohydrates by ether, ester, and ketal linkages. 1H-NMR differential spectra of ED-LCCs revealed an LC linkage of benzyl ether bond. Glucan-lignin (En-R-GL) and xylan-lignin (En-R-XL) complexes were separated from ED-R-LCC by ionic liquid. A part of lignin α-C was linked to cellulose 6-C by benzyl ether and α-ketal linkages. 13C-NMR spectra of En-R-XL showed there were α-benzyl ether and α-ketal bonds between lignin and xylan.

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Robinson, Alastair, Peter Richardson, and Meghan Halse. "Hyperpolarised 1H–13C Benchtop NMR Spectroscopy." Applied Sciences 9, no. 6 (March 20, 2019): 1173. http://dx.doi.org/10.3390/app9061173.

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Benchtop NMR spectrometers with sub-ppm spectral resolution have opened up new opportunities for performing NMR outside of the standard laboratory environment. However, the relatively weak magnetic fields of these devices (1–2 T) results in low sensitivity and significant peak overlap in 1H NMR spectra. Here, we use hyperpolarised 13C{1H} NMR to overcome these challenges. Specifically, we demonstrate the use of the signal amplification by reversible exchange (SABRE) parahydrogen-based hyperpolarisation technique to enhance the sensitivity of natural abundance 1D and 2D 13C{1H} benchtop NMR spectra. We compare two detection methods for SABRE-enhanced 13C NMR and observe an optimal 13C{1H} signal-to-noise ratio (SNR) for a refocused INEPT approach, where hyperpolarisation is transferred from 1H to 13C. In addition, we exemplify SABRE-enhanced 2D 13C benchtop NMR through the acquisition of a 2D HETCOR spectrum of 260 mM of 4-methylpyridine at natural isotopic abundance in a total experiment time of 69 min. In theory, signal averaging for over 300 days would be required to achieve a comparable SNR for a thermally polarised benchtop NMR spectrum acquired of a sample of the same concentration at natural abundance.

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Smith, Alan J. R., Richard York, Dušan Uhrín, and Nicholle G. A. Bell. "¹⁹F-centred NMR analysis of mono-fluorinated compounds." RSC Advances 12, no. 16 (2022): 10062–70. http://dx.doi.org/10.1039/d1ra08046f.

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19F is the focal point of broadband, phase-sensitive 2D NMR experiments that provide 1H, 13C and 19F chemical shifts, values of JHF, JHH, and JFC coupling constants and 13C-induced 19F isotopic shifts to elucidate structures of fluorinated molecules.

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Giraudon, Sylvie, Marc Danzart, and Marc H. Merle. "Deuterium Nuclear Magnetic Resonance Spectroscopy and Stable Carbon Isotope Ratio Analysis/Mass Spectrometry of Certain Monofloral Honeys." Journal of AOAC INTERNATIONAL 83, no. 6 (November 1, 2000): 1401–9. http://dx.doi.org/10.1093/jaoac/83.6.1401.

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Abstract Quantitative deuterium nuclear magnetic resonance spectroscopy (NMR) has been used in conjunction with stable carbon isotope ratio analysis/mass spectrometry to refine the detection of sugars that have been added to monofloral honeys. The 13C content of sugars indicates the type of photosynthetic metabolism of the plant that synthesized them; the deuterium content is more characteristic of secondary metabolism and of environmental factors. Consequently, determination of the 13C content of honeys and of proteins extracted from the honeys can be used to detect the addition of C4 plant sugars (cane or corn), but it does not reveal the addition of C3 plant sugars such as beet sugar. Deuterium NMR gives useful information for some monofloral honeys. NMR measurement is performed on ethanol obtained from fermentation of the honey and extracted by distillation. The isotopic composition of the ethanol indicates the nature of the sugars from which it was derived. Various types of monofloral honeys were studied, and the results obtained with commercially available honeys demonstrate the usefulness of isotopic analysis and the need to compile a database of authentic honeys to validate or affirm certain results.

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Bravin, F., R. Duca, N. Loiseau, M. Pean, O. Puel, and M. Delaforge. "Production and use of mycotoxins uniformly enriched with stable isotopes for their dosage in biological samples." World Mycotoxin Journal 1, no. 3 (August 1, 2008): 275–81. http://dx.doi.org/10.3920/wmj2008.x037.

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Due to their low concentrations in biological matrices, mycotoxin analyses often encounter detection and quantification problems, especially for toxicokinetic studies. We have developed a strategy to produce in a single process, several fungi secondary metabolites uniformly enriched with 13C, 15N stable isotopes in their 'natural' composition. This includes: (1) a plant culture in the presence of 10%, 50% or 100% 13CO2 as the only source of carbon, and in the presence or not of 10% 15N-enriched nitrogen salts – as expected wheat or maize uniformlyincorporate enriched isotopes into their bioproducts; (2) a subsequent solid culture of different filamentous fungi on plant biomass led to the production of a 'natural' mixture of isotopes-enriched mycotoxins – these compounds exhibit a characteristic isotopic cluster, which can be easily detected by mass spectrometry. As an example, we achieved 10% uniformly 13C-enriched zearalenone, deoxynivalenol and mycophenolic acid by growing Fusarium graminearum or Penicillium brevicompactum on 10% 13C enriched wheat seeds and 3 to 10% 13C, 15N uniformly enriched fumonisins from Fusarium verticillioides cultures on maize seeds or straw. These compounds were used for metabolism and transport studies in mammals either in vitro or in vivo and analysed by MS and MSn spectra of the isotopic cluster but also by 13C, 15N NMR. Moreover, such isotopic pattern enrichment can be used for quantitative evaluations of mycotoxins transport across mammalian biological membranes, alone or in their 'natural' conditions in the presence of other fungi secondary metabolites. Finally, we used such enriched compounds with high reliabilityin order to study zearalenone metabolism but these enriched compounds would also be used as internal standards to quantify zearalenone or fumonisins in contaminated food samples.

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Matheron, Christelle, Anne-Marie Delort, Geneviève Gaudet, Evelyne Forano, and Tibor Liptaj. "13C and 1H Nuclear Magnetic Resonance Study of Glycogen Futile Cycling in Strains of the Genus Fibrobacter." Applied and Environmental Microbiology 64, no. 1 (January 1, 1998): 74–81. http://dx.doi.org/10.1128/aem.64.1.74-81.1998.

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ABSTRACT We investigated the carbon metabolism of three strains ofFibrobacter succinogenes and one strain ofFibrobacter intestinalis. The four strains produced the same amounts of the metabolites succinate, acetate, and formate in approximately the same ratio (3.7/1/0.3). The four strains similarly stored glycogen during all growth phases, and the glycogen-to-protein ratio was close to 0.6 during the exponential growth phase.13C nuclear magnetic resonance (NMR) analysis of [1-13C]glucose utilization by resting cells of the four strains revealed a reversal of glycolysis at the triose phosphate level and the same metabolic pathways. Glycogen futile cycling was demonstrated by 13C NMR by following the simultaneous metabolism of labeled [13C]glycogen and exogenous unlabeled glucose. The isotopic dilutions of the CH2 of succinate and the CH3 of acetate when the resting cells were metabolizing [1-13C]glucose and unlabeled glycogen were precisely quantified by using 13C-filtered spin-echo difference 1H NMR spectroscopy. The measured isotopic dilutions were not the same for succinate and acetate; in the case of succinate, the dilutions reflected only the contribution of glycogen futile cycling, while in the case of acetate, another mechanism was also involved. Results obtained in complementary experiments are consistent with reversal of the succinate synthesis pathway. Our results indicated that for all of the strains, from 12 to 16% of the glucose entering the metabolic pathway originated from prestored glycogen. Although genetically diverse, the four Fibrobacter strains studied had very similar carbon metabolism characteristics.

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9

Abadie, Cyril, and Guillaume Tcherkez. "13C Isotope Labelling to Follow the Flux of Photorespiratory Intermediates." Plants 10, no. 3 (February 24, 2021): 427. http://dx.doi.org/10.3390/plants10030427.

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Measuring the carbon flux through metabolic pathways in intact illuminated leaves remains challenging because of, e.g., isotopic dilution by endogenous metabolites, the impossibility to reach isotopic steady state, and the occurrence of multiple pools. In the case of photorespiratory intermediates, our knowledge of the partitioning between photorespiratory recycling, storage, and utilization by other pathways is thus rather limited. There has been some controversy as to whether photorespiratory glycine and serine may not be recycled, thus changing the apparent stoichiometric coefficient between photorespiratory O2 fixation and CO2 release. We describe here an isotopic method to trace the fates of glycine, serine and glycerate, taking advantage of positional 13C content with NMR and isotopic analyses by LC–MS. This technique is well-adapted to show that the proportion of glycerate, serine and glycine molecules escaping photorespiratory recycling is very small.

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Pironti, Concetta, Maria Ricciardi, Oriana Motta, Federica Camin, Luana Bontempo, and Antonio Proto. "Application of 13C Quantitative NMR Spectroscopy to Isotopic Analyses for Vanillin Authentication Source." Foods 10, no. 11 (October 30, 2021): 2635. http://dx.doi.org/10.3390/foods10112635.

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The carbon stable isotope ratio (δ13C) is a valuable chemical parameter in the investigation of the geographic origin, quality, and authenticity of foods. The aim of this study is the evaluation of the feasibility of 13C-NMR (Nuclear Magnetic Resonance) spectroscopy to determine the carbon stable isotope ratio, at natural abundance, of small organic molecules, such as vanillin, without the use of IRMS (Isotope Ratio Mass Spectrometry). The determination of vanillin origin is an active task of research, and differentiating between its natural and artificial forms is important to guarantee the quality of food products. To reach our goal, nine vanillin samples were analyzed using both 13C quantitative NMR spectroscopy (under optimized experimental conditions) and IRMS, and the obtained δ13C values were compared using statistical analysis (linear regression, Bland–Altman plot, and ANOVA (analysis of variance)). The results of our study show that 13C-NMR spectroscopy can be used as a valuable alternative methodology to determine the bulk carbon isotope ratio and to identify the origin of vanillin. This makes it attractive for the analysis in the same experiment of site-specific and total isotope effects for testing authenticity, quality, and typicality of food samples. Moreover, the improvement of NMR spectroscopy makes it possible to avoid the influence of additives on carbon stable isotope ratio analysis and to clearly identify fraud and falsification in commercial samples.

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Martin, Gilles G., Valérie Hanote, Michéle Lees, and Yves-Loïc Martin. "Interpretation of Combined H SNIF/NMR and C SIRA/MS Analyses of Fruit Juices To Detect Added Sugar." Journal of AOAC INTERNATIONAL 79, no. 1 (January 1, 1996): 62–72. http://dx.doi.org/10.1093/jaoac/79.1.62.

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Abstract The site-specific natural isotopic fractionation studied by nuclear magnetic resonance (SNIF/NMR) method measures site-specific isotope contents in a variety of organic compounds by deuterium nuclear magnetic resonance spectroscopy. This technique, together with SIRA/MS (stable isotope ratio analysis/mass spectrometry) provides a powerful tool for food authentication and characterization. By using the ethanol resulting from sugar fermentation as a molecular probe, SNIF/NMR (deuterium) and SIRA/MS (13C) have been used together for authentication of fruit juices. The influence of deu terium content of the fermentation water on the iso topic parameters is shown and a means for normal izing the results is proposed. A large number of authentic juices have been analyzed to define the variation of isotopic ratios in natural juices. On the basis of these data, a set of rules was designed to enable interpretation of isotopic parameters in terms of possible adulteration of fruit juices by sugar addition. Results of analyses of Florida orange juice are presented. Orange juice samples from Brazil and Israel are included as 2 extreme cases. Assignment limits for a sample of orange juice of unknown origin also are given. These assignment limits are also provided for apple and grapefruit juices.

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Cohen, David M., and Richard N. Bergman. "Improved estimation of anaplerosis in heart using 13C NMR." American Journal of Physiology-Endocrinology and Metabolism 273, no. 6 (December 1, 1997): E1228—E1242. http://dx.doi.org/10.1152/ajpendo.1997.273.6.e1228.

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Anaplerotic enzymes, such as pyruvate carboxylase or malic enzyme, catalyze reactions that fill up the pools of the citric acid cycle (CAC), thereby increasing the total mass of CAC intermediates. Relative anaplerosis ( y) denotes the ratio of anaplerotic flux to the flux catalyzed by citrate synthase. We examine conventional methods [C. R. Malloy, A. D. Sherry, and F. M. H. Jeffrey. J. Biol. Chem. 263:6964–6971, 1988; C. R. Malloy, A. D. Sherry, and F. M. H. Jeffrey. Am. J. Physiol. 259 ( Heart Circ. Physiol. 28): H987–H995, 1990] of measurement of y using13C-labeled precursors and analysis of [13C]glutamate labeling by nuclear magnetic resonance (NMR) spectroscopy. Through mathematical analysis and computer simulation, we show that isotopic enrichment of the pool of pyruvate that is substrate for anaplerosis will severely decrease the accuracy of estimates of y made with conventional methods no matter how small the mass of the pool of pyruvate. Suppose that the recycling parameter R denotes the fraction of molecules of pyruvate that contain carbons derived from intermediates of the CAC. Each means of estimation of relative anaplerosis in the peer-reviewed literature assumes that R = 0, although this assumption has not been confirmed by experiment. We show that conventional formulas, using either fractional enrichments of carbons or isotopomer analysis, actually estimate at most y ⋅ (1 − R) instead of y during administration of [2-13C]acetate and unlabeled pyruvate. Using a new formula for estimation of y, we recalculate values of y from the literature and find them ∼50% too low. We assume that all anaplerosis is via pyruvate and that the difference in isotopic enrichment between cytosolic and mitochondrial malate is negligible.

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Niu, Hujun, Xudong Chen, Yunbo Zhao, Junyi Zhou, and Yimin Xie. "Exploration of the Linkages between Lignin and Carbohydrates in Kraft Pulp from Wheat Straw Using a 13C/2H Isotopic Tracer." Molecules 28, no. 22 (November 9, 2023): 7493. http://dx.doi.org/10.3390/molecules28227493.

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To further our understanding of the change in association between lignin and carbohydrates after kraft pulping, isotope-labeled kraft pulp (KP) was prepared using 13C and D double-isotope-labeled wheat straw, and it was subjected to enzymatic hydrolysis and ionic liquid treatment to explore the linkages between lignin and carbohydrate complexes in wheat straw. Isotope abundance determination showed that 13C and D abundances in the experimental groups were substantially higher than those in the control group, indicating that the injected exogenous coniferin-[α-13C], coniferin-[γ-13C], and d-glucose-[6-D2] were effectively absorbed and metabolized during wheat internode growth. Solid-state CP/MAS 13C-NMR spectroscopy showed that lignin was mainly linked to polysaccharides via acetal, benzyl ether, and benzyl ester bonds. Kraft pulp (KP) from the labeled wheat straw was degraded by cellulase. The obtained residue was fractionated using the ionic liquid DMSO/TBAH to separate the cellulose–lignin complex (KP-CLC) and xylan–lignin complex (KP-XLC). X-ray diffractometer determination showed that the KP-CLC regenerated cellulose type II from type I after the ionic liquid conversion. The 13C-NMR spectrum of Ac-En-KP-CLC showed that the cellulose–lignin complex structure was chemically bonded between the lignin and cellulose through acetal and benzyl ether bonds. The 13C-NMR spectrum of En-KP-XLC showed a lignin–hemicellulose complex structure, wherein lignin and xylan were chemically bonded by benzyl ether and acetal bonds. These results indicate that the cross-linking between lignin and carbohydrates exists in lignocellulosic fibers even after kraft pulping.

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S, Jana. "Consciousness Energy Healing Treatment and Its Impact on the Structural Properties and Isotopic Abundance Ratios of Thiamine." Medicinal and Analytical Chemistry International Journal 4, no. 1 (February 10, 2020): 1–10. http://dx.doi.org/10.23880/macij-16000154.

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Thiamine (vitamin B1 ) is an essential water soluble vitamin required in all living cells for many cellular functions. The objective of the study was to investigate the impact of the Trivedi Effect® -Consciousness Energy Healing Treatment on the isotopic abundance ratios (PM+1/PM and PM+2/PM) and structural properties of thiamine hydrochloride using LC-MS, GC-MS, and NMR spectroscopy. Thiamine sample was divided into two parts, one part of the sample was termed as untreated/control thiamine, while the other part of the sample received the Trivedi Effect® -Biofield Energy Healing Treatment remotely by a renowned Biofield Energy Healer, Mr. Mahendra Kumar Trivedi and designated as Biofield Energy Treated thiamine. The LC-ESI-MS analysis of both the thiamine samples showed the mass of parent molecular ion at m/z 265.03 (calcd for C12H17N4 OS+ , 265.11) at the retention times (Rt ) 1.51 minutes with similar fragmentation pattern. But, the relative peak intensities of the treated sample were significantly improved compared to the control sample. The isotopic abundance ratios of PM+1/PM (2 H/1 H or 13C/12C or 15N/14N or 17O/16O or 33S/32S) and PM+2/PM (18O/16O or 34S/32S) were significantly increased by 43.60% and 42.68%, respectively in the treated thiamine compared to the control sample. Therefore, 2 H, 13C, 15N, 17O, and 33S contributions from C12H17N4 OS+ to the isotopic m/z 266 and 18O and 34S contributions to the isotopic m/z 267 was significantly increased in the treated sample compared with the control sample. The GC-MS mass peak intensity of the treated sample (52940.7) was significantly increased by 131.01% compared to the control sample (22917.04). The proton and carbon signals for CH3 , CH2 , NH2 , CH, =C=, and C-OH groups in the 1 H and 13C NMR spectra of the control and treated samples were similar. The increased mass peak intensities and isotopic abundance ratios in thiamine might be due to the Trivedi Effect® -Consciousness Energy Healing Treatment via the possible mediation of neutrinos, which may change the intra-atomic bond strength, its physical stability, kinetic isotope effects of the treated thiamine. Thus, the Trivedi Effect® -Consciousness Energy Healing Treated thiamine would be advantageous for designing better nutraceuticals and pharmaceutical formulations which might provide better therapeutic response against vitamin B1 deficiency and related disorders, including beriberi, Korsakoff’s syndrome, Parkinson’s and Alzheimer’s diseases, maple syrup urine disease, Leigh’s disease, optic neuropathy, alcoholism, and aging.

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Wecksler, Aaron T., Victor Lundin, Ambrose J. Williams, Karthik Veeravalli, Dorothea E. Reilly, and Sung-Hye Grieco. "Bioprocess Development and Characterization of a 13C-Labeled Hybrid Bispecific Antibody Produced in Escherichia coli." Antibodies 12, no. 1 (February 14, 2023): 16. http://dx.doi.org/10.3390/antib12010016.

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Monoclonal antibodies (mAbs) are highly efficacious therapeutics; however, due to their large, dynamic nature, structural perturbations and regional modifications are often difficult to study. Moreover, the homodimeric, symmetrical nature of mAbs makes it difficult to elucidate which heavy chain (HC)-light chain (LC) pairs are responsible for any structural changes, stability concerns, and/or site-specific modifications. Isotopic labeling is an attractive means for selectively incorporating atoms with known mass differences to enable identification/monitoring using techniques such as mass spectrometry (MS) and nuclear magnetic resonance (NMR). However, the isotopic incorporation of atoms into proteins is typically incomplete. Here we present a strategy for incorporating 13C-labeling of half antibodies using an Escherichia coli fermentation system. Unlike previous attempts to generate isotopically labeled mAbs, we provide an industry-relevant, high cell density process that yielded >99% 13C-incorporation using 13C-glucose and 13C-celtone. The isotopic incorporation was performed on a half antibody designed with knob-into-hole technology to enable assembly with its native (naturally abundant) counterpart to generate a hybrid bispecific (BsAb) molecule. This work is intended to provide a framework for producing full-length antibodies, of which half are isotopically labeled, in order to study the individual HC-LC pairs.

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Yin, Zhiyong, and Jeroen S. Dickschat. "Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis." Beilstein Journal of Organic Chemistry 20 (April 5, 2024): 734–40. http://dx.doi.org/10.3762/bjoc.20.67.

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An isotopic labelling method was developed to investigate substrate binding by ketosynthases, exemplified by the second ketosynthase of the polyketide synthase BaeJ involved in bacillaene biosynthesis (BaeJ-KS2). For this purpose, both enantiomers of a 13C-labelled N-acetylcysteamine thioester (SNAC ester) surrogate of the proposed natural intermediate of BaeJ-KS2 were synthesised, including an enzymatic step with glutamate decarboxylase, and incubated with BaeJ-KS2. Substrate binding was demonstrated through 13C NMR analysis of the products against the background of various control experiments.

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Mason, Graeme F., Douglas L. Rothman, Kevin L. Behar, and Robert G. Shulman. "NMR Determination of the TCA Cycle Rate and α-Ketoglutarate/Glutamate Exchange Rate in Rat Brain." Journal of Cerebral Blood Flow & Metabolism 12, no. 3 (May 1992): 434–47. http://dx.doi.org/10.1038/jcbfm.1992.61.

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A mathematical model of cerebral glucose metabolism was developed to analyze the isotopic labeling of carbon atoms C4 and C3 of glutamate following an intravenous infusion of [1-13C]glucose. The model consists of a series of coupled metabolic pools representing glucose, glycolytic intermediates, tricarboxylic acid (TCA) cycle intermediates, glutamate, aspartate, and glutamine. Based on the rate of 13C isotopic labeling of glutamate C4 measured in a previous study, the TCA cycle rate in rat brain was determined to be 1.58 ± 0.41 μmol min−1 g−1 (mean ± SD, n = 5). Analysis of the difference between the rates of isotopic enrichment of glutamate C4 and C3 permitted the rate of exchange between α-ketoglutarate (α-KG) and glutamate to be assessed in vivo. In rat brain, the exchange rate between α-KG and glutamate is between 89 ± 35 and 126 ± 22 times faster than the TCA cycle rate (mean ± SD, n = 4). The sensitivity of the calculated value of the TCA cycle rate to other metabolic fluxes and to concentrations of glycolytic and TCA cycle intermediates was tested and found to be small.

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Matheron, Christelle, Anne-Marie Delort, Genevieve Gaudet, Tibor Liptaj, and Evelyne Forano. "Interactions between Carbon and Nitrogen Metabolism in Fibrobacter succinogenes S85: a 1H and13C Nuclear Magnetic Resonance and Enzymatic Study." Applied and Environmental Microbiology 65, no. 5 (May 1, 1999): 1941–48. http://dx.doi.org/10.1128/aem.65.5.1941-1948.1999.

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ABSTRACT The effect of the presence of ammonia on [1-13C]glucose metabolism in the rumen fibrolytic bacterium Fibrobacter succinogenes S85 was studied by13C and 1H nuclear magnetic resonance (NMR). Ammonia halved the level of glycogen storage and increased the rate of glucose conversion into acetate and succinate 2.2-fold and 1.4-fold, respectively, reducing the succinate-to-acetate ratio. The13C enrichment of succinate and acetate was precisely quantified by 13C-filtered spin-echo difference1H-NMR spectroscopy. The presence of ammonia did not modify the 13C enrichment of succinate C-2 (without ammonia, 20.8%, and with ammonia, 21.6%), indicating that the isotopic dilution of metabolites due to utilization of endogenous glycogen was not affected. In contrast, the presence of ammonia markedly decreased the 13C enrichment of acetate C-2 (from 40 to 31%), reflecting enhanced reversal of the succinate synthesis pathway. The reversal of glycolysis was unaffected by the presence of ammonia as shown by 13C-NMR analysis. Study of cell extracts showed that the main pathways of ammonia assimilation in F. succinogenes were glutamate dehydrogenase and alanine dehydrogenase. Glutamine synthetase activity was not detected. Glutamate dehydrogenase was active with both NAD and NADP as cofactors and was not repressed under ammonia limitation in the culture. Glutamate-pyruvate and glutamate-oxaloacetate transaminase activities were evidenced by spectrophotometry and 1H NMR. When cells were incubated in vivo with [1-13C]glucose, only13C-labeled aspartate, glutamate, alanine, and valine were detected. Their labelings were consistent with the proposed amino acid synthesis pathway and with the reversal of the succinate synthesis pathway.

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Binsl, T., A. De Graaf, K. Venema, J. Heringa, A. Maathuis, P. De Waard, and J. H. Van Beek. "Measuring non-steady-state metabolic fluxes in starch-converting faecal microbiota in vitro." Beneficial Microbes 1, no. 4 (November 1, 2010): 391–405. http://dx.doi.org/10.3920/bm2010.0038.

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This paper explores human gut bacterial metabolism of starch using a combined analytical and computational modelling approach for metabolite and flux analysis. Non-steady-state isotopic labelling experiments were performed with human faecal microbiota in a well-established in vitro model of the human colon. After culture stabilisation, [U-13C] starch was added and samples were taken at regular intervals. Metabolite concentrations and 13C isotopomeric distributions were measured amongst other things for acetate, propionate and butyrate by mass spectrometry and NMR. The vast majority of metabolic flux analysis methods based on isotopomer analysis published to date are not applicable to metabolic non-steady-state experiments. We therefore developed a new ordinary differential equation-based representation of a metabolic model of human faecal microbiota to determine eleven metabolic parameters that characterised the metabolic flux distribution in the isotope labelling experiment. The feasibility of the model parameter quantification was demonstrated on noisy in silico data using a downhill simplex optimisation, matching simulated labelling patterns of isotopically labelled metabolites with measured metabolite and isotope labelling data. Using the experimental data, we determined an increasing net label influx from starch during the experiment from 94±1 µmol/l/min to 133±3 µmol/l/min. Only about 12% of the total carbon flux from starch reached propionate. Propionate production mainly proceeded via succinate with a small contribution via acrylate. The remaining flux from starch yielded acetate (35%) and butyrate (53%). Interpretation of 13C NMR multiplet signals further revealed that butyrate, valerate and caproate were mainly synthesised via cross-feeding, using acetate as a co-substrate. This study demonstrates for the first time that the experimental design and the analysis of the results by computational modelling allows the determination of time-resolved effects of nutrition on the flux distribution within human faecal microbiota in metabolic non-steady-state.

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Gilbert, Alexis, Keita Yamada, and Naohiro Yoshida. "Exploration of intramolecular 13C isotope distribution in long chain n-alkanes (C11–C31) using isotopic 13C NMR." Organic Geochemistry 62 (September 2013): 56–61. http://dx.doi.org/10.1016/j.orggeochem.2013.07.004.

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David, Gabrielle E., D. Brynn Hibbert, Russell D. Frew, and Alan R. Hayman. "Significant Determinants of Isotope Composition During HI/Pred Synthesis of Methamphetamine." Australian Journal of Chemistry 63, no. 1 (2010): 22. http://dx.doi.org/10.1071/ch09429.

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Methamphetamine HCl was synthesized using three variations of the hydriodic acid/red phosphorus (HI/Pred) synthetic route. A Plackett-Burman experimental design was used to determine how reaction parameters affected the isotopic composition of the product. Isotope ratio mass spectrometry results showed only the source of precursor 13C was significant in determining product δ 13C; the manufacturer, reaction temperature, time, scale, and source of HI were not significant. The precursor was also the main determinant of product δ 2H, with smaller contributions from the HI source for one method. From precursor to product, large δ 2H depletion occurred for most samples. Deuterium nuclear magnetic resonance spectroscopy (2H NMR) was used to investigate the specific site of this. Significant fraction of deuterium was observed only at the benzylic position, the site of hydrogen addition during synthesis. Methamphetamine synthesized from ephedrine was shown to be depleted in this position.

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Ahmadipour, Sanaz, and Gavin J. Miller. "6R/S-deutero-α-d-mannopyranoside 1-phosphate." Molbank 2019, no. 3 (June 27, 2019): M1068. http://dx.doi.org/10.3390/m1068.

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6R/S-deutero-α-d-mannopyranoside 1-phosphate was synthesised from a C6 aldehydic mannose thioglycoside donor in four steps. Using NaBD4 as the reductant, isotopic enrichment at C6 was achieved and the resultant C6-deuterated material was converted through to the glycosyl 1-phosphate using a protection/glycosylation/deprotection sequence. The product was fully characterised by 1H, 13C, 31P and 2D NMR, alongside MS analysis.

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Fitzpatrick, Susan M., Hoby P. Hetherington, Kevin L. Behar, and Robert G. Shulman. "The Flux from Glucose to Glutamate in the Rat Brain in vivo as Determined by 1-Observed, 13C-Edited NMR Spectroscopy." Journal of Cerebral Blood Flow & Metabolism 10, no. 2 (March 1990): 170–79. http://dx.doi.org/10.1038/jcbfm.1990.32.

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The rate of incorporation of carbon from [1-13C]glucose into the [4-CH2] and [3-CH2] of cerebral glutamate was measured in the rat brain in vivo by 1H-observed, 13C-edited (POCE) nuclear magnetic resonance (NMR) spectroscopy. Spectra were acquired every 98 s during a 60-min infusion of [1-13C]glucose. Complete time courses were obtained from six animals. The measured intensity of the unresolved [4-13CH2] resonances of glutamate and glutamine increased exponentially during the infusion and attained a steady state in ∼20 min with a first-order rate constant of 0.130 ± 0.010 min−1 (t1/2 = 5.3 ± 0.5 min). The appearance of the [3-13CH2] resonance in the POCE difference spectrum lagged behind that of the [4-13CH2] resonance and had not reached steady state at the end of the 60-min infusion (t1/2 = 26.6 ± 4.1 min). The increase observed in 13C-labeled glutamate represented isotopic enrichment and was not due to a change in the total glutamate concentration. The glucose infusion did not affect the levels of high-energy phosphates or intracellular pH as determined by 31P NMR spectroscopy. Since glucose carbon is incorporated into glutamate by rapid exchange with the tricarboxylic acid (TCA) cycle intermediate α-ketoglutarate, the rate of glutamate labeling provided an estimate of TCA cycle flux. We have determined the flux of carbon through the TCA cycle to be ≈1.4 μmol g−1 min−1. These experiments demonstrate the feasibility of measuring metabolic fluxes in vivo using 13C-labeled glucose and the technique of 1H-observed, 13C-decoupled NMR spectroscopy.

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Joubert, Valentin, Virginie Silvestre, Mathilde Grand, Denis Loquet, Virginie Ladroue, Fabrice Besacier, Serge Akoka, and Gérald S. Remaud. "Full Spectrum Isotopic 13C NMR Using Polarization Transfer for Position-Specific Isotope Analysis." Analytical Chemistry 90, no. 14 (June 18, 2018): 8692–99. http://dx.doi.org/10.1021/acs.analchem.8b02139.

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Kishore, A. I. "Partial 13C isotopic enrichment of nucleoside monophosphates: useful reporters for NMR structural studies." Nucleic Acids Research 33, no. 18 (October 12, 2005): e164-e164. http://dx.doi.org/10.1093/nar/gni165.

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Frederick, Kendra K., Vladimir K. Michaelis, Marc A. Caporini, Loren B. Andreas, Galia T. Debelouchina, Robert G. Griffin, and Susan Lindquist. "Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register." Proceedings of the National Academy of Sciences 114, no. 14 (March 22, 2017): 3642–47. http://dx.doi.org/10.1073/pnas.1619051114.

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The yeast prion protein Sup35NM is a self-propagating amyloid. Despite intense study, there is no consensus on the organization of monomers within Sup35NM fibrils. Some studies point to a β-helical arrangement, whereas others suggest a parallel in-register organization. Intermolecular contacts are often determined by experiments that probe long-range heteronuclear contacts for fibrils templated from a 1:1 mixture of 13C- and 15N-labeled monomers. However, for Sup35NM, like many large proteins, chemical shift degeneracy limits the usefulness of this approach. Segmental and specific isotopic labeling reduce degeneracy, but experiments to measure long-range interactions are often too insensitive. To limit degeneracy and increase experimental sensitivity, we combined specific and segmental isotopic labeling schemes with dynamic nuclear polarization (DNP) NMR. Using this combination, we examined an amyloid form of Sup35NM that does not have a parallel in-register structure. The combination of a small number of specific labels with DNP NMR enables determination of architectural information about polymeric protein systems.

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Portaluri, Vincent, Freddy Thomas, Eric Jamin, Serge Akoka, and Gérald S. Remaud. "Authentication of Agave Products through Isotopic Intramolecular 13C Content of Ethanol: Optimization and Validation of 13C Quantitative NMR Methodology." ACS Food Science & Technology 1, no. 7 (July 21, 2021): 1316–22. http://dx.doi.org/10.1021/acsfoodscitech.1c00177.

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Silvestre, Virginie, Vanessa Maroga Mboula, Catherine Jouitteau, Serge Akoka, Richard J. Robins, and Gérald S. Remaud. "Isotopic 13C NMR spectrometry to assess counterfeiting of active pharmaceutical ingredients: Site-specific 13C content of aspirin and paracetamol." Journal of Pharmaceutical and Biomedical Analysis 50, no. 3 (October 2009): 336–41. http://dx.doi.org/10.1016/j.jpba.2009.04.030.

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Takahashi, Hiroki, Sabine Hediger, and Gaël De Paëpe. "Matrix-free dynamic nuclear polarization enables solid-state NMR 13C–13C correlation spectroscopy of proteins at natural isotopic abundance." Chemical Communications 49, no. 82 (2013): 9479. http://dx.doi.org/10.1039/c3cc45195j.

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Portaluri, Vincent, Freddy Thomas, Eric Jamin, Benjamin Lorandel, Virginie Silvestre, Serge Akoka, and Gérald S. Remaud. "Vanillin isotopic intramolecular 13C profile through polarization transfer NMR pulse sequence and statistical modelling." Food Control 130 (December 2021): 108345. http://dx.doi.org/10.1016/j.foodcont.2021.108345.

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Mowery, Daniel M., Roger A. Assink, Dora K. Derzon, Sara B. Klamo, Robert Bernstein, and Roger L. Clough. "Radiation oxidation of polypropylene: A solid-state 13C NMR study using selective isotopic labeling." Radiation Physics and Chemistry 76, no. 5 (May 2007): 864–78. http://dx.doi.org/10.1016/j.radphyschem.2006.06.007.

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Espinosa, Juan Félix, and Teodor Parella. "First experimental determination of two-bond 13C isotopic effects on 1H NMR chemical shifts." Tetrahedron Letters 49, no. 16 (April 2008): 2562–65. http://dx.doi.org/10.1016/j.tetlet.2008.02.097.

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Darwish, Tamim A., Nageshwar Rao Yepuri, Peter J. Holden, and Michael James. "Quantitative analysis of deuterium using the isotopic effect on quaternary 13C NMR chemical shifts." Analytica Chimica Acta 927 (July 2016): 89–98. http://dx.doi.org/10.1016/j.aca.2016.05.003.

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Joubert, Valentin, Virginie Silvestre, Virginie Ladroue, Fabrice Besacier, Paule Blondel, Serge Akoka, Evelyne Baguet, and Gérald S. Remaud. "Forensic application of position-specific isotopic analysis of trinitrotoluene (TNT) by NMR to determine 13C and 15N intramolecular isotopic profiles." Talanta 213 (June 2020): 120819. http://dx.doi.org/10.1016/j.talanta.2020.120819.

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Hannam, K. D., S. A. Quideau, B. E. Kishchuk, S. W. Oh, and R. E. Wasylishen. "Forest-floor chemical properties are altered by clear-cutting in boreal mixedwood forest stands dominated by trembling aspen and white spruce." Canadian Journal of Forest Research 35, no. 10 (October 1, 2005): 2457–68. http://dx.doi.org/10.1139/x05-140.

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Alterations in the chemical properties of the forest floor following clear-cut harvesting may have implications for forest productivity in boreal stands. We used proximate analysis, carbon-13 (13C) isotopic determination, and cross-polarization, magic-angle spinning (CPMAS) 13C nuclear magnetic resonance (NMR) spectroscopy to examine differences in the characteristics of the forest floors from uncut stands and clear-cut stands dominated by white spruce (Picea glauca (Moench) Voss; SPRUCE) and trembling aspen (Populus tremuloides Michx.; ASPEN) in northern Alberta. Proximate analysis revealed no difference in the chemical properties of forest floors from clear-cut and uncut stands in either stand type, but the acid-insoluble residue of forest floors from clear-cut ASPEN stands was enriched in 13C compared with those from uncut ASPEN stands. CPMAS 13C NMR spectroscopy revealed that forest floors from clearcuts were enriched in total aromatic C, particularly in ASPEN stands, and depleted in phenolic C, particularly in SPRUCE stands. These patterns indicate that forest floors from the clearcuts have become more humified, which may reflect stand-type differences in the amount of labile C available to the forest-floor microbial community and reductions in above- and below-ground inputs to the forest floor following clear-cutting in both stand types. Changes in the chemical properties of forest floors from clear-cut SPRUCE and ASPEN stands could exacerbate C limitation in these soils and alter patterns of nutrient cycling.

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Roscoe, R., P. Buurman, B. van Lagen, and E. Velthorst. "Transformations in occluded light fraction organic matter in a clayey oxisol: evidence from 13C-CPMAS-NMR and delta13C Signature." Revista Brasileira de Ciência do Solo 28, no. 5 (October 2004): 811–18. http://dx.doi.org/10.1590/s0100-06832004000500003.

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We hypothesised that, during occlusion inside granular aggregates of oxide-rich soils, the light fraction organic matter would undergo a strong process of decomposition, either due to the slow process of aggregate formation and stabilisation or due to digestion in the macro- and meso-fauna guts. This process would favour the accumulation of recalcitrant materials inside aggregates. The aim of this study was to compare the dynamics and the chemical composition of free and occluded light fraction organic matter in a natural cerrado vegetation (woodland savannah) and a nearby pasture (Brachiaria spp.) to elucidate the transformations during occlusion of light fraction in aggregates of a clayey Oxisol. Nuclear Magnetic Resonance of the 13C, with Cross Polarisation and Magic Angle Spinning (13C-CPMAS-NMR), and 13C/12C isotopic ratio were combined to study organic matter composition and changes in carbon dynamics, respectively. The occluded light fraction had a slower turnover than the free light fraction and the heavy fraction. Organic matter in the occluded fraction also showed a higher degree of decomposition. The results confirm that processes of soil organic matter occlusion in the typical "very fine strong granular" structure of the studied oxide-rich soil led to an intense transformation, selectively preserving stable organic matter. The small amount of organic material stored as occluded light faction, as well as its stability, suggests that this is not an important or manageable sink for sequestration of atmospheric CO2.

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Hansen, Poul Erik, Yngve Stenstrøm, May-Britt Stjerna, Kjell Undheim, Gyula Wittman, Lajos Gera, Mihály Bartók, István Pelczer, and György Dombi. "Isotopic Perturbation of Equilibrium in 2,6-Dihydroxybenzoyl Compounds. A 13C and 1 H NMR Investigation." Acta Chemica Scandinavica 42b (1988): 423–32. http://dx.doi.org/10.3891/acta.chem.scand.42b-0423.

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Smith, Adam N., Katharina Märker, Sabine Hediger, and Gaël De Paëpe. "Natural Isotopic Abundance 13C and 15N Multidimensional Solid-State NMR Enabled by Dynamic Nuclear Polarization." Journal of Physical Chemistry Letters 10, no. 16 (July 30, 2019): 4652–62. http://dx.doi.org/10.1021/acs.jpclett.8b03874.

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Lapidot, Aviva, and Asher Gopher. "Quantitation of Metabolic Compartmentation in Hyperammonemic Brain by Natural Abundance 13C-NMR Detection of 13C-15N Coupling Patterns and Isotopic Shifts." European Journal of Biochemistry 243, no. 3 (February 1997): 597–604. http://dx.doi.org/10.1111/j.1432-1033.1997.00597.x.

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Galitskaya, P. Yu, S. Yu Selivanovskaya, K. O. Karamova, A. S. Gordeev, P. A. Kuryntseva, and P. Ghorbannezhad. "Transformation of Biochar from Plant Biomass in Gray Forest Soil: Evaluation by Isotopic Labeling Method." Eurasian Soil Science 57, no. 10 (October 2024): 1579–89. http://dx.doi.org/10.1134/s1064229324601598.

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Abstract Pyrolysis is considered to be one of promising methods for processing agricultural waste and for producing fertilizers. The efficiency of the resulting biochar as a fertilizer has been proven, but the preferential way of decomposition of organic substances in it—biotic or abiotic—is still open to argument. The ways of transformation of biochar obtained from corn (a plant of the C4 type of photosynthesis with an increased 13C content) were assessed in this work, using the solid-phase CP/MAS 13C NMR spectroscopy. Biochar was placed into the top layer of a monolith of gray forest soil, and the precipitation regime characteristic of Central Russia was simulated for 90 days. The peak at 129 ppm typical for aromatic compounds increased during the experiment in the obtained NMR spectra of soil samples with biochar in the upper soil layer, but not in other layers. This testifies that biochar particles do not migrate down the soil profile during one season. The intensity of cumulative microbial respiration in the presence of biochar increases from 85.0 g CO2 kg–1 in the control sample to 201.4 g CO2 kg–1 in the sample with biochar (the topsoil). According to the NMR spectra of the salt formed during mineralization of carbon dioxide released from the soil, it contains labeled carbon: there is a peak at 169 ppm characteristic of carbonates. The cumulative volume of CO2 released from the soil with biochar is 1.9 times greater as compared to the control soil. The addition of microorganisms-decomposers caused an additional increase in the CO2 volume: 2.4 times relative to the control, which indicates the role of microorganisms in the destruction of soil organic matter and of biochar. However, based on the stability of the total carbon content in the soil, it can be concluded that only a small proportion of biochar components is susceptible to biotic decomposition.

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Camarasa, Carole, Jean-Philippe Grivet, and Sylvie Dequin. "Investigation by 13C-NMR and tricarboxylic acid (TCA) deletion mutant analysis of pathways for succinate formation in Saccharomyces cerevisiae during anaerobic fermentation." Microbiology 149, no. 9 (September 1, 2003): 2669–78. http://dx.doi.org/10.1099/mic.0.26007-0.

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NMR isotopic filiation of 13C-labelled aspartate and glutamate was used to explore the tricarboxylic acid (TCA) pathway in Saccharomyces cerevisiae during anaerobic glucose fermentation. The assimilation of [3-13C]aspartate led to the formation of [2,3-13C]malate and [2,3-13C]succinate, with equal levels of 13C incorporation, whereas site-specific enrichment on C-2 and C-3 of succinate was detected only with [3-13C]glutamate. The non-random distribution of 13C labelling in malate and succinate demonstrates that the TCA pathway operates during yeast fermentation as both an oxidative and a reductive branch. The observed 13C distribution suggests that the succinate dehydrogenase (SDH) complex is not active during glucose fermentation. This hypothesis was tested by deleting the SDH1 gene encoding the flavoprotein subunit of the SDH complex. The growth, fermentation rate and metabolite profile of the sdh1 mutant were similar to those of the parental strain, demonstrating that SDH was indeed not active. Filiation experiments indicated the reductive branch of the TCA pathway was the main pathway for succinate production if aspartate was used as the nitrogen source, and that a surplus of succinate was produced by oxidative decarboxylation of 2-oxoglutarate if glutamate was the sole nitrogen source. Consistent with this finding, a kgd1 mutant displayed lower levels of succinate production on glutamate than on other nitrogen sources, and higher levels of oxoglutarate dehydrogenase activity were observed on glutamate. Thus, the reductive branch generating succinate via fumarate reductase operates independently of the nitrogen source. This pathway is the main source of succinate during fermentation, unless glutamate is the sole nitrogen source, in which case the oxidative decarboxylation of 2-oxoglutarate generates additional succinate.

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DiNuzzo, Mauro. "Kinetic Analysis of Glycogen Turnover: Relevance to Human Brain 13C-NMR Spectroscopy." Journal of Cerebral Blood Flow & Metabolism 33, no. 10 (June 12, 2013): 1540–48. http://dx.doi.org/10.1038/jcbfm.2013.98.

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A biophysical model of the glycogen molecule is developed, which takes into account the points of attack of synthase and phosphorylase at the level of the individual glucose chain. Under the sole assumption of steric effects governing enzyme accessibility to glucosyl residues, the model reproduces the known equilibrium structure of cellular glycogen at steady state. In particular, experimental data are reproduced assuming that synthase (1) operates preferentially on inner chains of the molecule and (2) exhibits a faster mobility than phosphorylase in translocating from an attacked chain to another. The model is then used to examine the turnover of outer versus inner tiers during the labeling process of isotopic enrichment (IE) experiments. Simulated data are fitted to in vivo13C nuclear magnetic resonance spectroscopy measurements obtained in the human brain under resting conditions. Within this experimental set-up, analysis of simulated label incorporation and retention shows that 7% to 35% of labeled glucose is lost from the rapidly turning-over surface of the glycogen molecule when stimulation onset is delayed by 7 to 11.5 hours after the end of [1-13C]glucose infusion as done in actual procedures. The substantial label washout before stimulation suggests that much of the subsequent activation-induced glycogenolysis could remain undetected. Overall, these results show that the molecular structure significantly affects the patterns of synthesis and degradation of glycogen, which is relevant for appropriate design of labeling experiments aiming at investigating the functional roles of this glucose reserve.

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Sergeyev, Ivan V., Caitlin M. Quinn, Jochem Struppe, Angela M. Gronenborn, and Tatyana Polenova. "Competing transfer pathways in direct and indirect dynamic nuclear polarization magic anglespinning nuclear magnetic resonance experiments on HIV-1 capsid assemblies: implications for sensitivity and resolution." Magnetic Resonance 2, no. 1 (April 27, 2021): 239–49. http://dx.doi.org/10.5194/mr-2-239-2021.

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Abstract. Dynamic nuclear polarization (DNP)-enhanced magic angle spinning (MAS) nuclear magnetic resonance (NMR) of biological systems is a rapidly growing field. Large signal enhancements make the technique particularly attractive for signal-limited cases, such as studies of complex biological assemblies or at natural isotopic abundance. However, spectral resolution is considerably reduced compared to ambient-temperature non-DNP spectra. Herein, we report a systematic investigation into sensitivity and resolution of 1D and 2D 13C-detected DNP MAS NMR experiments on HIV-1 CA capsid protein tubular assemblies. We show that the magnitude and sign of signal enhancement as well as the homogeneous line width are strongly dependent on the biradical concentration, the dominant polarization transfer pathway, and the enhancement buildup time. Our findings provide guidance for optimal choice of sample preparation and experimental conditions in DNP experiments.

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Lozhko, D. M., I. Yu Zhukov, and A. I. Kornelyuk. "Bacterial expression and 13C/15N isotopic labeling of EMA PII cytokine for structural studies by NMR spectroscopy." Biopolymers and Cell 27, no. 4 (July 20, 2011): 273–78. http://dx.doi.org/10.7124/bc.000109.

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Kamal, Ghulam Mustafa, Jalal Uddin, Abdullatif Bin Muhsinah, Xiaohua Wang, Ayesha Noreen, Asma Sabir, and Syed Ghulam Musharraf. "1H NMR-Based metabolomics and 13C isotopic ratio evaluation to differentiate conventional and organic soy sauce." Arabian Journal of Chemistry 15, no. 1 (January 2022): 103516. http://dx.doi.org/10.1016/j.arabjc.2021.103516.

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Jackalin, Lukas, Boris B. Kharkov, Andrei V. Komolkin, and Sergey V. Dvinskikh. "Experimental strategies for 13C–15N dipolar NMR spectroscopy in liquid crystals at the natural isotopic abundance." Physical Chemistry Chemical Physics 20, no. 34 (2018): 22187–96. http://dx.doi.org/10.1039/c8cp04161j.

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Höhener, Patrick, Virginie Silvestre, Anaïs Lefrançois, Denis Loquet, Eliot P. Botosoa, Richard J. Robins, and Gérald S. Remaud. "Analytical model for site-specific isotope fractionation in 13C during sorption: Determination by isotopic 13C NMR spectrometry with vanillin as model compound." Chemosphere 87, no. 5 (April 2012): 445–52. http://dx.doi.org/10.1016/j.chemosphere.2011.12.023.

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Norris, C. E., S. A. Quideau, J. S. Bhatti, R. E. Wasylishen, and M. D. MacKenzie. "Influence of fire and harvest on soil organic carbon in jack pine sites." Canadian Journal of Forest Research 39, no. 3 (March 2009): 642–54. http://dx.doi.org/10.1139/x08-207.

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Boreal forest soils represent a considerable reservoir of carbon on a global basis. The objective of this study was to compare the response of soil organic carbon (OC) to disturbance along two jack pine ( Pinus banksiana Lamb.) chronosequences of either fire or harvest origin. Total OC stocks were determined for the A and B horizons, and results indicated a recovery to predisturbance levels by 30 years in both chronosequences. To further characterize OC composition at all sites, we used a combination of physical fractionation of soil OC pools, 13C isotopic determination, and cross-polarization magic-angle spinning 13C nuclear magnetic resonance (NMR) spectroscopy. OC within all soils was dominated by a labile pool associated with the coarse-sand fraction. The relative importance of this labile pool increased with time since disturbance along both chronosequences. However, the fire and harvested sites differed in terms of the macromolecular composition of soil OC as determined by NMR. In particular, spectra of the forest floors from the two younger fire sites showed a high aromatic OC intensity that may be attributed to the presence of char. Interestingly, our results also indicated that with increasing time since fire, this char was transferred from the forest floors to the A horizons.

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Winnike, Jason H., Delisha A. Stewart, Wimal W. Pathmasiri, Susan L. McRitchie, and Susan J. Sumner. "Stable Isotope-Resolved Metabolomic Differences between Hormone-Responsive and Triple-Negative Breast Cancer Cell Lines." International Journal of Breast Cancer 2018 (September 30, 2018): 1–12. http://dx.doi.org/10.1155/2018/2063540.

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Purpose. To conduct an exploratory study to identify mechanisms that differentiate Luminal A (BT474 and MCF-7) and triple-negative (MDA-MB-231 and MDA-MB-468) breast cancer (BCa) cell lines to potentially provide novel therapeutic targets based on differences in energy utilization. Methods. Cells were cultured in media containing either [U-13C]-glucose or [U-13C]-glutamine for 48 hours. Conditioned media and cellular extracts were analyzed by 1H and 13C NMR spectroscopy. Results. MCF-7 cells consumed the most glucose, producing the most lactate, demonstrating the greatest Warburg effect-associated energy utilization. BT474 cells had the highest tricarboxylic acid cycle (TCA) activity. The majority of energy utilization patterns in MCF-7 cells were more similar to MDA-MB-468 cells, while the patterns for BT474 cells were more similar to MDA-MB-231 cells. Compared to the Luminal A cell lines, TNBC cell lines consumed more glutamine and less glucose. BT474 and MDA-MB-468 cells produced high amounts of 13C-glycine from media [U-13C]-glucose which was integrated into glutathione, indicating de novo synthesis. Conclusions. Stable isotopic resolved metabolomics using 13C substrates provided mechanistic information about energy utilization that was difficult to interpret using 1H data alone. Overall, cell lines that have different hormone receptor status have different energy utilization requirements, even if they are classified by the same clinical BCa subtype; and these differences offer clues about optimizing treatment strategies.

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Sönnichsen, Frank D., Peter L. Davies, and Brian D. Sykes. "NMR structural studies on antifreeze proteins." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 284–93. http://dx.doi.org/10.1139/o98-052.

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Antifreeze proteins (AFPs) are a structurally diverse class of proteins that bind to ice and inhibit its growth in a noncolligative manner. This adsorption-inhibition mechanism operating at the ice surface results in a lowering of the (nonequilibrium) freezing point below the melting point. A lowering of ~1°C, which is sufficient to prevent fish from freezing in ice-laden seawater, requires millimolar AFP levels in the blood. The solubility of AFPs at these millimolar concentrations and the small size of the AFPs (typically 3-15 kDa) make them ideal subjects for NMR analysis. Although fish AFPs are naturally abundant, seasonal expression, restricted access to polar fishes, and difficulties in separating numerous similar isoforms have made protein expression the method of choice for producing AFPs for structural studies. Expression of recombinant AFPs has also facilitated NMR analysis by permitting isotopic labeling with 15N and 13C and has permitted mutations to be made to help with the interpretation of NMR data. NMR analysis has recently solved two AFP structures and provided valuable information about the disposition of ice-binding side chains in a third. The potential exists to solve other AFP structures, including the newly described insect AFPs, and to use solid-state NMR techniques to address fundamental questions about the nature of the interaction between AFPs and ice.Key words: NMR spectroscopy, antifreeze, ice-binding affinity, review.

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Journal articles on the topic 'Isotopic 13C NMR'

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