Selective Amino Acid-Only in Vivo NMR: A Powerful Tool To Follow Stress Processes

Review: Abandoned mines as a resource or liability for wildlife

Abandoned Mine Lands (AMLs) are areas where previous mineral extraction or processing has occurred. Hundreds of thousands of AMLs exist within the United States. Contaminated runoff from AMLs can negatively affect the physiology and ecology of surrounding terrestrial and aquatic habitats and species and can be detrimental to human health. As a response, several U.S. federal and state agencies have launched programs to assess health risks associated with AMLs. In some cases, however, AMLs may be beneficial to specific wildlife taxa. There is a relative paucity of studies investigating the physiological and ecological impacts of AMLs on wildlife. We conducted a systematic review examining published scientific articles that assessed the negative and positive impacts of AMLs across invertebrate and vertebrate taxa. We also offer suggestions on evaluating AMLs to develop effective mitigation strategies that reduce their negative tole on human and wildlife communities. Peer-reviewed publications were screened across WebofScience, PubMed and Google Scholar databases. Abandoned mine lands were generally detrimental to wildlife, with adverse effects ranging from bioaccumulation of heavy metals to decreased ecological fitness. Conversely, AMLs were an overall benefit to imperiled bat populations and could serve as tools for conservation. Studies were unevenly distributed across different wildlife taxa groups, echoing the necessity for additional taxonomically diverse research. We suggest that standardized wildlife survey methods be used to assess how different species utilize AMLs. Federal and state agencies can use these surveys to establish effective remediation plans for individual AML sites and minimize the risks to both wildlife and humans.

A holistic NMR framework to understand environmental impact: Examining the impacts of superparamagnetic iron oxide nanoparticles (SPIONs) in Daphnia magna via imaging, spectroscopy, and metabolomics

Superparamagnetic iron oxide nanoparticles (SPIONs) are a contaminant of emerging interest, often used in the medical field as an imaging contrast agent, with additional uses in wastewater treatment and as food additives. Although the use of SPIONs is increasing, little research has been conducted on the toxic impacts to living organisms beyond traditional lethal concentration endpoints. Daphnia magna are model organisms for aquatic toxicity testing with a well understood metabolome and high sensitivity to SPIONs. Thus, as environmental concentrations continue to increase, it is becoming critical to understand their sub-lethal toxicity. Due to the paramagnetic nature of SPIONs, a range of potential nuclear magnetic resonance spectroscopy (NMR) experiments are possible, offering the potential to probe the physical location (via imaging), binding (via relaxation weighted spectroscopy), and the biochemical pathways impacted (via in vivo metabolomics). Results indicate binding to carbohydrates, likely chitin in the exoskeleton, along with a decrease in energy metabolites and specific biomarkers of oxidative stress. The holistic NMR framework used here helps provide a more comprehensive understanding of SPIONs impacts on D. magna and showcases NMR's versatility in providing physical, chemical, and biochemical insights.

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.

Closing the gap between in vivo and in vitro omics: using QA/QC to strengthen ex vivo NMR metabolomics

Metabolomics aims to achieve a global quantitation of the pool of metabolites within a biological system. Importantly, metabolite concentrations serve as a sensitive marker of both genomic and phenotypic changes in response to both internal and external stimuli. NMR spectroscopy greatly aids in the understanding of both in vitro and in vivo physiological systems and in the identification of diagnostic and therapeutic biomarkers. Accordingly, NMR is widely utilized in metabolomics and fluxomics studies due to its limited requirements for sample preparation and chromatography, its non-destructive and quantitative nature, its utility in the structural elucidation of unknown compounds, and, importantly, its versatility in the analysis of in vitro, in vivo, and ex vivo samples. This review provides an overview of the strengths and limitations of in vitro and in vivo experiments for translational research and discusses how ex vivo studies may overcome these weaknesses to facilitate the extrapolation of in vitro insights to an in vivo system. The application of NMR-based metabolomics to ex vivo samples, tissues, and biofluids can provide essential information that is close to a living system (in vivo) with sensitivity and resolution comparable to those of in vitro studies. The success of this extrapolation process is critically dependent on high-quality and reproducible data. Thus, the incorporation of robust quality assurance and quality control checks into the experimental design and execution of NMR-based metabolomics experiments will ensure the successful extrapolation of ex vivo studies to benefit translational medicine.

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.

Metabolomic analysis predicted changes in growth rate in Daphnia magna exposed to acetaminophen

As urbanization and the global population increases, pollutants associated with municipal wastewater such as pharmaceuticals are becoming more prevalent in aquatic environments. Acetaminophen (paracetamol) is a widely used drug worldwide and one of the most frequently detected pharmaceuticals in freshwater ecosystems. This study investigated the impact of acetaminophen on the metabolite profile of Daphnia magna at two life stages; and used these metabolomic findings to hypothesize a potential impact at a higher organismal level which was subsequently tested experimentally. Targeted polar metabolite analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to measure changes in the concentration of 51 metabolites in the neonate (> 24 h old) and adult (8 day-old) daphnids following a 48-h exposure to sub-lethal concentrations of acetaminophen. The impact of acetaminophen on the metabolic profile of neonates was widely different from adults. Also, acetaminophen exposure perturbed the abundance of nucleotides more extensively than other metabolites. The acute metabolomic experimental results led to the hypotheses that exposure to sub-lethal concentrations of acetaminophen upregulates protein synthesis in D. magna and subsequently increases growth during early life stages and has an opposite impact on adults. Accordingly, a 10 day growth rate experiment indicated that exposure to acetaminophen elevated biomass production in neonates but not in adults. These novel findings demonstrate that a targeted analysis and interpretation of the changes in the polar metabolic profile of organisms in response to environmental stressors could be used as a tool to predict changes at higher biological levels. As such, this study further emphasizes the incorporation of molecular-level platforms as critical and robust tools in environmental assessment frameworks and biomonitoring of aquatic ecosystems.

Simultaneous identification and quantification of amino acids in biofluids by reactive 19F-tags

A robust method to identify and quantify amino acids close to physiological conditions by 1D ¹⁹F NMR was established. Each ¹⁹F-derivatized amino acid has its characteristic chemical-shift profile that is readily identified in the mixture of amino acids or in biofluids including fetal bovine serum and cell lysates. The method shows great potential in metabolomics and biochemical analysis.

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.

Metabolomics Reveals That Bisphenol Pollutants Impair Protein Synthesis-Related Pathways in Daphnia magna

Bisphenols are used in the production of polycarbonate plastics and epoxy resins. Bisphenol A (BPA) has been widely studied and is believed to act as an endocrine disruptor. Bisphenol F (BPF) and bisphenol S (BPS) have increasingly been employed as replacements for BPA, although previous studies suggested that they yield similar physiological responses to several organisms. Daphnia magna is a common model organism for ecotoxicology and was exposed to sub-lethal concentrations of BPA, BPF, and BPS to investigate disruption to metabolic profiles. Targeted metabolite analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to measure polar metabolites extracted from D. magna, which are linked to a range of biochemical pathways. Multivariate analyses and individual metabolite changes showed similar non-monotonic concentration responses for all three bisphenols (BPA, BPF, and BPS). Pathway analyses indicated the perturbation of similar and distinct pathways, mostly associated with protein synthesis, amino acid metabolism, and energy metabolism. Overall, we observed responses that can be linked to a chemical class (bisphenols) as well as distinct responses that can be related to each individual bisphenol type (A, F, and S). These findings further demonstrate the need for using metabolomic analyses in exposure assessment, especially for chemicals within the same class which may disrupt the biochemistry uniquely at the molecular-level.

Spatial variation in the amino acid profile of four macroinvertebrate taxa along a highly polluted river

Acid mine drainage (AMD) is one of the major environmental problems impacting aquatic ecosystems globally. We studied changes in the community composition of macroinvertebrates and amino acid (AA) profiles of dominant taxa along an AMD contamination gradient within the Dee River, Queensland, Australia to understand how AMD can affect the biomolecular composition of macroinvertebrates. Taxa richness and community composition of macroinvertebrates changed widely along the AMD gradient with significantly lower taxa richness recorded at the polluted sites compared to upstream and downstream sites. The Dipteran families: Chironomidae and Ceratopogonidae, the Odonata family Gomphidae, and the Coleoptera family Dytiscidae were the only families found at all sampling sites and were used here for AA analysis. There were significant variations in the AA profiles among the studied taxa. The AA profile of each taxon also varied among upstream, polluted and downstream sites suggesting that contamination of a river system with acid mine drainage not only alters the overall macroinvertebrate community composition but also significantly influences the AA profile of organisms that are tolerant to AMD. This study highlights the potential of using AA profiling to study the response of aquatic organisms to contamination gradients such as those associated with AMD.

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.

Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective

The tumor microenvironment (TME) comprises complex interactions of multiple cell types that determines cell behavior and metabolism such as nutrient competition and immune suppression. We discuss the various types of heterogeneity that exist in solid tumors, and the complications this invokes for studies of TME. As human subjects and in vivo model systems are complex and difficult to manipulate, simpler 3D model systems that are compatible with flexible experimental control are necessary for studying metabolic regulation in TME. Stable Isotope Resolved Metabolomics (SIRM) is a valuable tool for tracing metabolic networks in complex systems, but at present does not directly address heterogeneous metabolism at the individual cell level. We compare the advantages and disadvantages of different model systems for SIRM experiments, with a focus on lung cancer cells, their interactions with macrophages and T cells, and their response to modulators in the immune microenvironment. We describe the experimental set up, illustrate results from 3D cultures and co-cultures of lung cancer cells with human macrophages, and outline strategies to address the heterogeneous TME.

NMR assignment of the in vivo daphnia magna metabolome

Daphnia (freshwater fleas) are among the most widely used organisms in regulatory aquatic toxicology/ecology, while their recent listing as an NIH model organism is stimulating research for understanding human diseases and processes.