In vivo comprehensive multiphase NMR

Development of a Simple Cost Effective Oxygenation System for In Vivo Solution State NMR in 10 mm NMR Tubes

In vivo NMR is evolving into an important tool to understand biological processes and environmental responses. Current approaches use flow systems to sustain the organisms with oxygenated water and food (e.g., algae) inside the NMR. However, such systems have the potential to leak and clog (potentially damaging costly hardware), require large volumes of media, and multiple expensive HPLC pumps. The proposed "oxygenation system", uses a simple "double slit" adapter and a single air/oxygen flow line into the NMR. The design is especially suited to larger diameter probes given that standard flow systems would require higher flow rates thus amplifying the potential and impact of leaks/clogs. Traditionally, in vivo NMR of small organisms (e.g., Daphnia) have required 2D NMR in combination with 13C enrichment to overcome susceptibility distortions and provide information rich metabolic profiles. Here Daphnia magna, Eisenia fetida and Artemia franciscana are used to demonstrate the potential of the oxygenation system. Survivability tests and 1H time-resolved monitoring were first performed on D. magna, while E. fetida contained enough biomass to permit 1H-13C HSQC, 13C-1H HETCOR and 31P NMR without isotopic enrichment. Finally, STOCSY of 1D 13C NMR was used to follow the growth of A. franciscana (without 13C enrichment) for 48 h after birth, which helps visualize trends across a series of 1D in vivo data. In summary, application of the oxygenation system toward larger diameter probes allows the collection of NMR data without enrichment, offering a promising solution to better understand processes in vivo.

Low-field, not low quality: 1D simplification, selective detection, and heteronuclear 2D experiments for improving low-field NMR spectroscopy of environmental and biological samples

Understanding environmental change is challenging and requires molecular-level tools to explain the physicochemical phenomena behind complex processes. Nuclear magnetic resonance (NMR) spectroscopy is a key tool that provides information on both molecular structures and interactions but is underutilized in environmental research because standard "high-field" NMR is financially and physically inaccessible for many and can be overwhelming to those outside of disciplines that routinely use NMR. "Low-field" NMR is an accessible alternative but has reduced sensitivity and increased spectral overlap, which is especially problematic for natural, heterogeneous samples. Therefore, the goal of this study is to investigate and apply innovative experiments that could minimize these challenges and improve low-field NMR analysis of environmental and biological samples. Spectral simplification (JRES, PSYCHE, singlet-only, multiple quantum filters), selective detection (GEMSTONE, DREAMTIME), and heteronuclear (reverse and CH3/CH2/CH-only HSQCs) NMR experiments are tested on samples of increasing complexity (amino acids, spruce resin, and intact water fleas) at-high field (500 MHz) and at low-field (80 MHz). A novel experiment called Doubly Selective HSQC is also introduced, wherein 1H signals are selectively detected based on the 1H and 13C chemical shifts of 1H-13C J-coupled pairs. The most promising approaches identified are the selective techniques (namely for monitoring), and the reverse and CH3-only HSQCs. Findings ultimately demonstrate that low-field NMR holds great potential for biological and environmental research. The multitude of NMR experiments available makes NMR tailorable to nearly any research need, and low-field NMR is therefore anticipated to become a valuable and widely used analytical tool moving forward.

Improved Photocatalytic Performance of TiO2-Nitrogen-Doped Graphene Quantum Dot Composites Mediated by Heterogeneous Interactions

Photocatalysis is typically monitored via analysis of phases in isolation and focuses on the removal of a target analyte from the solution phase. Here we analyze the photocatalytic action of a TiO2-nitrogen-doped graphene quantum dot (NGQD) composite on a target analyte, phenol, using comprehensive multiphase NMR (CMP-NMR) which observes signals in solid, solution, and gel phases in situ. Phenol preferentially interacts with the composite photocatalyst compared to pure TiO2, increasing its effective concentration near the catalyst surface and its degradation rate. The presence of NGQDs in the composite reduced the fouling of the catalyst surface and caused a reduction of photogenerated intermediates. Increased heterogeneous interactions, likely mediated by π-π interactions, are hypothesized to cause each of these improvements in the observed photocatalytic performance by TiO2-NGQDs. CMP-NMR allows the elucidation of how the photocatalytic mechanism is enhanced via material design and provides a foundation for the development of efficient photocatalysts.

HR-MAS DREAMTIME NMR for Slow Spinning ex Vivo and in Vivo Samples

HR-MAS NMR is a powerful tool, capable of monitoring molecular changes in intact heterogeneous samples. However, one of the biggest limitations of 1H NMR is its narrow spectral width which leads to considerable overlap in complex natural samples. DREAMTIME NMR is a highly selective technique that allows users to isolate suites of metabolites from congested spectra. This permits targeted metabolomics by NMR and is ideal for monitoring specific processes. To date, DREAMTIME has only been employed in solution-state NMR, here it is adapted for HR-MAS applications. At high spinning speeds (>5 kHz), DREAMTIME works with minimal modifications. However, spinning over 3-4 kHz leads to cell lysis, and if maintaining sample integrity is necessary, slower spinning (<2.5 kHz) is required. Very slow spinning (≤500 Hz) is advantageous for in vivo analysis to increase organism survival; however, sidebands from water pose a problem. To address this, a version of DREAMTIME, termed DREAMTIME-SLOWMAS, is introduced. Both techniques are compared at 2500, 500, and 50 Hz, using ex vivo worm tissue. Following this, DREAMTIME-SLOWMAS is applied to monitor key metabolites of anoxic stress in living shrimp at 500 Hz. Thus, standard DREAMTIME works well under MAS conditions and is recommended for samples reswollen in D2O or spun >2500 Hz. For slow spinning in vivo or intact tissue samples, DREAMTIME-SLOWMAS provides an excellent way to target process-specific metabolites while maintaining sample integrity. Overall, DREAMTIME should find widespread application wherever targeted molecular information is required from complex samples with a high degree of spectral overlap.

Application of 15N-Edited 1H-13C Correlation NMR Spectroscopy─Toward Fragment-Based Metabolite Identification and Screening via HCN Constructs

Many key building blocks of life contain nitrogen moieties. Despite the prevalence of nitrogen-containing metabolites in nature, 15N nuclei are seldom used in NMR-based metabolite assignment due to their low natural abundance and lack of comprehensive chemical shift databases. However, with advancements in isotope labeling strategies, 13C and 15N enriched metabolites are becoming more common in metabolomic studies. Simple multidimensional nuclear magnetic resonance (NMR) experiments that correlate 1H and 15N via single bond 1JNH or multiple bond 2-3JNH couplings using heteronuclear single quantum coherence (HSQC) or heteronuclear multiple bond coherence are well established and routinely applied for structure elucidation. However, a 1H-15N correlation spectrum of a metabolite mixture can be difficult to deconvolute, due to the lack of a 15N specific database. In order to bridge this gap, we present here a broadband 15N-edited 1H-13C HSQC NMR experiment that targets metabolites containing 15N moieties. Through this approach, nitrogen-containing metabolites, such as amino acids, nucleotide bases, and nucleosides, are identified based on their 13C, 1H, and 15N chemical shift information. This approach was tested and validated using a [15N, 13C] enriched Daphnia magna (water flea) metabolite extract, where the number of clearly resolved 15N-containing peaks increased from only 11 in a standard HSQC to 51 in the 15N-edited HSQC, and the number of obscured peaks decreased from 59 to just 7. The approach complements the current repertoire of NMR techniques for mixture deconvolution and holds considerable potential for targeted metabolite NMR in 15N, 13C enriched systems.

Exploring Proton-Only NMR Experiments and Filters for Daphnia In Vivo: Potential and Limitations

Environmental metabolomics provides insight into how anthropogenic activities have an impact on the health of an organism at the molecular level. Within this field, in vivo NMR stands out as a powerful tool for monitoring real-time changes in an organism's metabolome. Typically, these studies use 2D ¹³C-¹H experiments on ¹³C-enriched organisms. Daphnia are the most studied species, given their widespread use in toxicity testing. However, with COVID-19 and other geopolitical factors, the cost of isotope enrichment increased ~6-7 fold over the last two years, making ¹³C-enriched cultures difficult to maintain. Thus, it is essential to revisit proton-only in vivo NMR and ask, "Can any metabolic information be obtained from Daphnia using proton-only experiments?". Two samples are considered here: living and whole reswollen organisms. A range of filters are tested, including relaxation, lipid suppression, multiple-quantum, J-coupling suppression, 2D ¹H-¹H experiments, selective experiments, and those exploiting intermolecular single-quantum coherence. While most filters improve the ex vivo spectra, only the most complex filters succeed in vivo. If non-enriched organisms must be used, then, DREAMTIME is recommended for targeted monitoring, while IP-iSQC was the only experiment that allowed non-targeted metabolite identification in vivo. This paper is critically important as it documents not just the experiments that succeed in vivo but also those that fail and demonstrates first-hand the difficulties associated with proton-only in vivo NMR.

SASSY NMR: Simultaneous Solid and Solution Spectroscopy

Synergism between different phases gives rise to chemical, biological or environmental reactivity, thus it is increasingly important to study samples intact. Here, SASSY (SimultAneous Solid and Solution spectroscopY) is introduced to simultaneously observe (and differentiate) all phases in multiphase samples using standard, solid-state NMR equipment. When monitoring processes, the traditional approach of studying solids and liquids sequentially, can lead to information in the non-observed phase being missed. SASSY solves this by observing the full range of materials, from crystalline solids, through gels, to pure liquids, at full sensitivity in every scan. Results are identical to running separate ¹³ C CP-MAS solid-state and ¹³ C solution-state experiments back-to-back but requires only a fraction of the spectrometer time. After its introduction, SASSY is applied to process monitoring and finally to detect all phases in a living freshwater shrimp. SASSY is simple to implement and thus should find application across all areas of research.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Exploring the Applications of Carbon-Detected NMR in Living and Dead Organisms Using a 13C-Optimized Comprehensive Multiphase NMR Probe

Comprehensive multiphase-nuclear magnetic resonance (CMP-NMR) is a non-invasive approach designed to observe all phases (solutions, gels, and solids) in intact samples using a single NMR probe. Studies of dead and living organisms are important to understand processes ranging from biological growth to environmental stress. Historically, such studies have utilized ¹H-based phase editing for the detection of soluble/swollen components and ¹H-detected 2D NMR for metabolite assignments/screening. However, living organisms require slow spinning rates (∼500 Hz) to increase survivability, but at such low speeds, complications from water sidebands and spectral overlap from the modest chemical shift window (∼0-10 ppm) make ¹H NMR challenging. Here, a novel ¹³C-optimized E-Free magic angle spinning CMP probe is applied to study all phases in ex vivo and in vivo samples. This probe consists of a two-coil design, with an inner single-tuned ¹³C coil providing a 113% increase in ¹³C sensitivity relative to a traditional multichannel single-CMP coil design. For organisms with a large biomass (∼0.1 g) like the Ganges River sprat (ex vivo), ¹³C-detected full spectral editing and ¹³C-detected heteronuclear correlation (HETCOR) can be performed at natural abundance. Unfortunately, for a single living shrimp (∼2 mg), ¹³C enrichment was still required, but ¹³C-detected HETCOR shows superior data relative to heteronuclear single-quantum coherence at low spinning speeds (due to complications from water sidebands in the latter). The probe is equipped with automatic-tuning-matching and is compatible with automated gradient shimming─a key step toward conducting multiphase screening of dead and living organisms under automation in the near future.

Microbial metabolites in the marine carbon cycle

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

NMR spectroscopy of wastewater: A review, case study, and future potential

NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (¹³C, ¹⁵N, ¹⁹F, ³¹P, ²⁹Si) as well as other environmentally relevant nuclei and metals such as ²⁷Al, ⁵¹V, ²⁰⁷Pb and ¹¹³Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.

Comprehensive Multiphase NMR Probehead with Reduced Radiofrequency Heating Improves the Analysis of Living Organisms and Heat-Sensitive Samples

Comprehensive multiphase (CMP) NMR, first described in 2012, combines all of the hardware components necessary to analyze all phases (solid, gel, and solution) in samples in their natural state. In combination with spectral editing experiments, it can fully differentiate phases and study the transfer of chemical species across and between phases, providing unprecedented molecular-level information in unaltered natural systems. However, many natural samples, such as swollen soils, plants, and small organisms, contain water, salts, and ionic compounds, making them electrically lossy and susceptible to RF heating, especially when using high-strength RF fields required to select the solid domains. While dedicated reduced-heating probes have been developed for solid-state NMR, to date, all CMP-NMR probes have been based on solenoid designs, which can lead to problematic sample heating. Here, a new prototype CMP probe was developed, incorporating a loop gap resonator (LGR) for decoupling. Temperature increases are monitored in salt solutions analogous to those in small aquatic organisms and then tested in vivo on Hyalella azteca (freshwater shrimp). In the standard CMP probe (solenoid), 80% of organisms died within 4 h under high-power decoupling, while in the LGR design, all organisms survived the entire test period of 12 h. The LGR design reduced heating by a factor of ∼3, which allowed 100 kHz decoupling to be applied to salty samples with generally ≤10 °C sample heating. In addition to expanding the potential for in vivo research, the ability to apply uncompromised high-power decoupling could be beneficial for multiphase samples containing true crystalline solids that require the strongest possible decoupling fields for optimal detection.

Ex vivo Comprehensive Multiphase NMR of whole organisms: A complementary tool to in vivo NMR

Nuclear Magnetic Resonance (NMR) spectroscopy is a non-invasive analytical technique which allows for the study of intact samples. Comprehensive Multiphase NMR (CMP-NMR) combines techniques and hardware from solution state and solid state NMR to allow for the holistic analysis of all phases (i.e. solutions, gels and solids) in unaltered samples. This study is the first to apply CMP-NMR to deceased, intact organisms and uses ¹³C enriched Daphnia magna (water fleas) as an example. D. magna are commonly used model organisms for environmental toxicology studies. As primary consumers, they are responsible for the transfer of nutrients across trophic levels, and a decline in their population can potentially impact the entire freshwater aquatic ecosystem. Though in vivo research is the ultimate tool to understand an organism’s most biologically relevant state, studies are limited by conditions (i.e. oxygen requirements, limited experiment time and reduced spinning speed) required to keep the organisms alive, which can negatively impact the quality of the data collected. In comparison, ex vivo CMP-NMR is beneficial in that; organisms do not need oxygen (eliminating air holes in rotor caps and subsequent evaporation); samples can be spun faster, leading to improved spectral resolution; more biomass per sample can be analyzed; and experiments can be run for longer. In turn, higher quality ex vivo NMR, can provide more comprehensive NMR assignments, which in many cases could be transferred to better understand less resolved in vivo signals. This manuscript is divided into three sections: 1) multiphase spectral editing techniques, 2) detailed metabolic assignments of 2D NMR of ¹³C enriched D. magna and 3) multiphase biological changes over different life stages, ages and generations of D. magna. In summary, ex vivo CMP-NMR proves to be a very powerful approach to study whole organisms in a comprehensive manner and should provide very complementary information to in vivo based research.

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Comprehensive Multiphase NMR detects all phases (solid/liquid/gel) in whole samples.

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Deceased organisms are not subjected to the limitations of in vivo NMR studies.

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2D ex vivo NMR offer increased spectral resolution, improving metabolite assignment.

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Holistic analysis shows biological changes in D. magna over different life stages.

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Ex vivo NMR can be a complementary tool for in vivo NMR metabolomic studies.