Guidelines for the Use of Deuterium Oxide (D2O) in 1H NMR Metabolomics

Quantitative characterization of the crosslinking degree of hydroxypropyl guar gum fracturing fluid by low-field NMR

As a widely used water-based fracturing fluid, the performance of hydroxypropyl guar gum fracturing fluid is closely related to the degree of crosslinking, the quantitative characterization of which can reveal a detailed crosslinking mechanism and guide the preparation of fracturing fluid gels with an excellent performance. However, the commonly used high-temperature rheology method for evaluating the performance of fracturing fluids only qualitatively reflects the degree of crosslinking. In this study, low-field nuclear magnetic resonance (LF-NMR) was used to characterize the degree of crosslinking in guar gum fracturing fluid gels. The spin-spin relaxation time of the H proton in guar gum was molecularly analyzed using LF-NMR. The viscoelastic properties met the requirements when the crosslinking degree of the gel was 88-94 %. The transformation of the linear structure into a membrane structure during the crosslinking process of the guar gum fracturing fluid was confirmed by freeze-drying and scanning electron microscopy (SEM) from a microscopic perspective. The changing trend of the microstructure and viscoelastic properties of the fracturing fluid gel under different crosslinker dosages was consistent with changes in the degree of crosslinking. The LF-NMR test process is non-destructive to the gel structure, and the test results demonstrate good accuracy and repeatability.

Synthesis and Characterization of MOF-Derived Structures: Recent Advances and Future Perspectives

Due to their facile tunability, metal-organic frameworks (MOFs) are employed as precursors and templates to construct advanced functional materials with unique and desired chemical, physical, mechanical, and morphological properties. By tuning MOF precursor composition and manipulating conversion processes, various MOF-derived materials commonly known as MOF derivatives can be constructed. The possibility of controlled and predictable properties makes MOF derivatives a preferred choice for numerous advanced technological applications. The innovative synthetic designs besides the plethora of interdisciplinary characterization approaches applicable to MOF derivatives provide the opportunity to perform a myriad of experiments to explore the performance and offer key insight to develop the next generation of advanced materials. Though there are many published works of literature describing various synthesis and characterization techniques of MOF derivatives, it is still not clear how the synthesis mechanism works and what are the best techniques to characterize these materials to probe their properties accurately. In this review, the recent development in synthesis techniques and mechanisms for a variety of MOF derivates such as MOF-derived metal oxides, porous carbon, composites/hybrids, and sulfides is summarized. Furthermore, the details of characterization techniques and fundamental working principles are summarized to probe the structural, mechanical, physiochemical, electrochemical, and electronic properties of MOF and MOF derivatives. The future trends and some remaining challenges in the synthesis and characterization of MOF derivatives are also discussed.

Quaternization of cassava starch and determination of antimicrobial activity against bacteria and coronavirus

This study describes the novel development of quaternized cassava starch (Q-CS) with antimicrobial and antiviral properties, particularly effective against the MHV-3 coronavirus. The preparation of Q-CS involved the reaction of cassava starch (CS) with glycidyltrimethylammonium chloride (GTMAC) in an alkaline solution. Q-CS physicochemical properties were determined by FTIR, NMR, elemental analysis, zeta potential, TGA, and moisture sorption. FTIR and NMR spectra confirmed the introduction of cationic groups in the CS structure. The elemental analysis revealed a degree of substitution (DS) of 0.552 of the cationic reagent on the hydroxyl groups of CS. Furthermore, Q-CS exhibited a positive zeta potential value (+28.6 ± 0.60 mV) attributed to the high positive charge density shown by the quaternary ammonium groups. Q-CS demonstrated lower thermal stability and higher moisture sorption compared to CS. The antimicrobial activity of Q-CS was confirmed against Escherichia coli (MIC = 0.156 mg mL-1) and Staphylococcus aureus (MIC = 0.312 mg mL-1), along with a remarkable ability to inactivate 99% of MHV-3 coronavirus after only 1 min of direct contact. Additionally, Q-CS showed high cell viability (close to 100%) and minimal cytotoxicity effects, guaranteeing its safe use. Therefore, these findings indicate the potential use of Q-CS as a raw material for antiseptic biomaterials.

Fingerprinting and profiling in metabolomics of biosamples

This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.

Basement Membrane Mimetic Hydrogel Cooperates with Rho-Associated Protein Kinase Inhibitor to Promote the Development of Acini-Like Salivary Gland Spheroids

Successful engineering of functional salivary glands necessitates the creation of cell-instructive environments for ex vivo expansion and lineage specification of primary human salivary gland stem cells (hS/PCs). Herein, basement membrane mimetic hydrogels were prepared using hyaluronic acid, cell adhesive peptides, and hyperbranched polyglycerol (HPG), with or without sulfate groups, to produce "hyperGel+" or "hyperGel", respectively. Differential scanning fluorescence experiments confirmed the ability of the sulphated HPG precursor to stabilize fibroblast growth factor 10. The hydrogels were nanoporous, cytocompatibile and cell-permissive, enabling the development of multicellular hS/PC spheroids in 14 days. Incorporation of sulfated HPG species in the hydrogel enhanced cell proliferation. Culture of hS/PCs in hyperGel+ in the presence of a Rho kinase inhibitor, Y-27632 (Y-27), led to the development of spheroids with a central lumen, increased the expression of acinar marker aquaporin-3 at the transcript level (AQP3), and decreased the expression of ductal marker keratin 7 at both the transcript (KRT7) and the protein levels (K7). Reduced expression of transforming growth factor beta (TGF-β) targets SMAD2/3 was also observed in Y27-treated cultures, suggesting attenuation of TGF-β signaling. Thus, hyperGel+ cooperates with the ROCK inhibitor to promote the development of lumened spheroids with enhanced expression of acinar markers.

Bacteria-Infected Artificial Urine Characterization Based on a Combined Approach Using an Electronic Tongue Complemented with 1H-NMR and Flow Cytometry

The prevailing form of bacterial infection is within the urinary tract, encompassing a wide array of bacteria that harness the urinary metabolome for their growth. Through their metabolic actions, the chemical composition of the growth medium undergoes modifications as the bacteria metabolize urine compounds, leading to the subsequent release of metabolites. These changes can indirectly indicate the existence and proliferation of bacterial organisms. Here, we investigate the use of an electronic tongue, a powerful analytical instrument based on a combination of non-selective chemical sensors with a partial specificity for data gathering combined with principal component analysis, to distinguish between infected and non-infected artificial urine samples. Three prevalent bacteria found in urinary tract infections were investigated, Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis. Furthermore, the electronic tongue analysis was supplemented with 1H NMR spectroscopy and flow cytometry. Bacteria-specific changes in compound consumption allowed for a qualitative differentiation between artificial urine medium and bacterial growth.

Oxidized pullulan exhibits potent antibacterial activity against S. aureus by disrupting its membrane integrity

The capability of bacteria to withstand the misuse of antibiotics leads to the generation of multi-drug resistant strains, posing a new challenge to curb wound infections. The biological macromolecules, due to their biocompatibility, biodegradability, and antimicrobial properties, have been explored for a variety of antimicrobial and therapeutic purposes. This work reports that a single-step oxidation of pullulan polymer leads to the formation of oxidized pullulan (o-pullulan), which shows striking antibacterial and antibiofilm activities against the Gram-positive bacteria, Staphylococcus aureus, implicated in wound-related infections. Oxidation of pullulan generates 28 % aldehyde groups (3.462 mmol/g) which exerted 97 % bactericidal activity against S. aureus by targeting cell wall-associated membrane protein SpA (Staphylococcal protein A). The molecular docking, gene silencing, and fluorescence quenching studies revealed a direct binding of o-pullulan with the B and C domains of SpA, which alters the membrane potential and inhibits Ca2+-Mg2+-ATPase pumps. O-pullulan also exhibited scavenging activity against intracellular reactive oxygen species (ROS), and non-immunotoxic activity and was found to be non-toxic to mammalian cells. Thus, o-pullulan shows great promise as an antimicrobial polymer against S. aureus for chronic wound management.

Rapid characterization of isotopic purity of deuterium-labeled organic compounds and monitoring of hydrogen-deuterium exchange reaction using electrospray ionization-high-resolution mass spectrometry

RATIONALE

Deuterium-labeled organic compounds, reagents, and drugs are widely used in many scientific research fields. Isotopic purity as the feature parameter of deuterated compounds is of great importance. In this article, we used electrospray ionization with high-resolution mass spectrometry (ESI-HRMS) to study isotopic purity of deuterium-labeled organic compounds based on assigning and distinguishing the corresponding H/D (hydrogen-deuterium) isotopolog ions of deuterated compounds.

METHODS

We systematically considered the specific requirements of accuracy and resolution of ESI-HRMS when measuring isotopic purity and demonstrated some actual cases using ESI-HRMS and ultraperformance liquid chromatography (UPLC)-HRMS. Meanwhile, ESI-HRMS/MS of deuterated compounds was performed to obtain more information on deuterium-labeled position characterization.

RESULTS

Two isotopic purity calculation methods based on the relative abundance in ESI-HRMS and UPLC-HRMS of H/D isotopolog ions (D0 -Dn ) were compared, which gave consistent isotopic purity values and were in good agreement with the certified isotopic purity values. We further studied and monitored the H/D exchange reaction of ethyl 3-(4-bromophenyl)-3-oxopropanoate (EBPO) by evaluating the dynamic isotopic purity changes in EBPO-D2 in the H/D exchange reaction in situ.

CONCLUSION

The isotopic purity characterization methods using ESI-HRMS discussed in this article have some outstanding advantages: rapid, highly sensitive, very low sample consumption (even below nanogram level), and deuterated solvent-free. Thus, this low-impact analytical method requires less time and is cost effective and might have good application potential for in-situ isotopic purity analysis and for monitoring the H/D exchange reactions.

Assessing the Acute Toxicological Effects of Annona muricata Leaf Ethanol Extract on Rats: Biochemical, Histopathological, and Metabolomics Analyses

Annona muricata is a common plant used in Africa and South America to manage various types of disease. However, there is insufficient toxicological information or published standard available regarding repeated dose animal toxicity data. As part of the safety assessment, we exposed Sprague Dawley rats to an acute oral toxicity of A. muricata. The intent of the current study was to use advanced proton nuclear magnetic resonance (1H NMR) in serum and urinary metabolomics evaluation techniques to provide the in vivo acute toxicological profile of A. muricata leaf ethanol extract in accordance with the Organization for Economic Co-operation and Development's (OECD) 423 guidelines. A single 2000 mg/kg dose of A. muricata leaf ethanol extract was administered to Sprague Dawley rats over an observational period of 14 days. The toxicity evaluation (physical and behavior observation, body weight, renal function test, liver function test and 1H NMR analysis) showed no abnormal toxicity. Histopathological analysis manifested mild changes, i.e., the treated kidney manifested mild hypercellularity of mesangial cells and mild red blood cell congestion. In addition, there was mild hemorrhage into tissue with scattered inflammatory cells and mild dilated central vein with fibrosis in the liver. However, the changes were very mild and not significant which correlate with other analyses conducted in this study (biochemical test and 1H NMR metabolomic analysis). On the other hand, urinary 1H NMR analysis collected on day 15 revealed high similarity on the metabolite variations for both untreated and treated groups. Importantly, the outcomes suggest that A. muricata leaf ethanol extract can be safely consumed at a dose of 2000 mg/kg and the LD50 must be more than 2000 mg/kg.

Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools

Monkeypox disease is caused by a virus which belongs to the orthopoxvirus genus of the poxviridae family. This disease has recently spread out to several non-endemic countries. While some cases have been linked to travel from endemic regions, more recent infections are thought to have spread in the community without any travel links, raising the risks of a wider outbreak. This state of public health represents a highly unusual event which requires urgent surveillance. In this context, the opportunities and technological challenges of current bio/chemical sensors, nanomaterials, nanomaterial characterization instruments, and artificially intelligent biosystems collectively called "advanced analytical tools" are reviewed here, which will allow early detection, characterization, and inhibition of the monkeypox virus (MPXV) in the community and limit its expansion from endemic to pandemic. A summary of background information is also provided from biological and epidemiological perspective of monkeypox to support the scientific case for its holistic management using advanced analytical tools.

GIPMA: Global Intensity-Guided Peak Matching and Alignment for 2D 1H-13C HSQC-Based Metabolomics

Two-dimensional (2D) ¹H-¹³C heteronuclear single quantum coherence (HSQC) has been increasingly applied to metabolomics studies because it can greatly improve the resolving capability compared with one-dimensional (1D) ¹H NMR. However, preprocessing methods such as peak matching and alignment tools for 2D NMR-based metabolomics have lagged behind similar methods for 1D ¹H NMR-based metabolomics. Correct matching and alignment of 2D NMR spectral features across multiple samples are particularly important for subsequent multivariate data analysis. Considering different intensity dynamic ranges of a variety of metabolites and the chemical shift variation across the spectra of multiple samples, here, we developed an efficient peak matching and alignment algorithm for 2D ¹H-¹³C HSQC-based metabolomics, called global intensity-guided peak matching and alignment (GIPMA). In GIPMA, peaks identified in all spectra are pooled together and sorted by intensity. Chemical shift of a stronger peak is regarded to be more accurate and reliable than that of a weaker peak. The strongest undesignated peak is chosen as the reference of a new cluster if it is not located within the chemical shift tolerance of any existing peak cluster (PC), or otherwise it is matched to an existing PC and the aligned chemical shift of the PC is updated as the intensity-weighted average of the chemical shifts of all peaks in the cluster. Setting an optimum chemical shift tolerance (Δδ_o) is critical for the peak matching and alignment across multiple samples. GIPMA dynamically searches for and intelligently selects the Δδ_o for peak matching to maximize the number of valid peak clusters (vPC), that is, spectral features, among multiple samples. By GIPMA, fully automatic peakwise matching and alignment do not require any spectrum as initial reference, while the chemical shift of each PC is updated as the intensity-weighted average of the chemical shifts of all peaks in the same PC, which is warranted to be statistically more accurate. Accurate chemical shifts for each representative spectral feature will facilitate subsequent peak assignment and are essential for correct metabolite identification and result interpretation. The proposed method was demonstrated successfully on the spectra of six model mixtures consisting of seven typical metabolites, yielding correct matching of all known spectral features. The performance of GIPMA was also demonstrated on 2D ¹H-¹³C HSQC spectra of 87 real extracts of 29 samples of five Dendrobium species. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) of the 87 matched and aligned spectra by GIPMA generates correct classification of the 29 samples into five groups. In summary, the proposed algorithm of GIPMA provided a practical peak matching and alignment method to facilitate 2D NMR-based metabolomics studies.

Pharmacometabolomics for the Study of Lipid-Lowering Therapies: Opportunities and Challenges

Lipid-lowering therapies are widely used to prevent the development of atherosclerotic cardiovascular disease (ASCVD) and related mortality worldwide. "Omics" technologies have been successfully applied in recent decades to investigate the mechanisms of action of these drugs, their pleiotropic effects, and their side effects, aiming to identify novel targets for future personalized medicine with an improvement of the efficacy and safety associated with the treatment. Pharmacometabolomics is a branch of metabolomics that is focused on the study of drug effects on metabolic pathways that are implicated in the variation of response to the treatment considering also the influences from a specific disease, environment, and concomitant pharmacological therapies. In this review, we summarized the most significant metabolomic studies on the effects of lipid-lowering therapies, including the most commonly used statins and fibrates to novel drugs or nutraceutical approaches. The integration of pharmacometabolomics data with the information obtained from the other "omics" approaches could help in the comprehension of the biological mechanisms underlying the use of lipid-lowering drugs in view of defining a precision medicine to improve the efficacy and reduce the side effects associated with the treatment.

Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part III: Implementations for the Diagnosis of Non-Cancerous Disorders, Both Oral and Systemic

This communication represents Part III of our series of reports based on the applications of human saliva as a useful and conveniently collectable medium for the discovery, identification and monitoring of biomarkers, which are of some merit for the diagnosis of human diseases. Such biomarkers, or others reflecting the dysfunction of specific disease-associated metabolic pathways, may also be employed for the prognostic pathological tracking of these diseases. Part I of this series set the experimental and logistical groundwork for this report, and the preceding paper, Part II, featured the applications of newly developed metabolomics technologies to the diagnosis and severity grading of human cancer conditions, both oral and systemic. Clearly, there are many benefits, both scientific and economic, associated with the donation of human saliva samples (usually as whole mouth saliva) from humans consenting to and participating in investigations focused on the discovery of biomolecular markers of diseases. These include usually non-invasive collection protocols, relatively low cost when compared against blood sample collection, and no requirement for clinical supervision during collection episodes. This paper is centred on the employment and value of 'state-of-the-art' metabolomics technologies to the diagnosis and prognosis of a wide range of non-cancerous human diseases. Firstly, these include common oral diseases such as periodontal diseases (from type 1 (gingivitis) to type 4 (advanced periodontitis)), and dental caries. Secondly, a wide range of extra-oral (systemic) conditions are covered, most notably diabetes types 1 and 2, cardiovascular and neurological diseases, and Sjögren's syndrome, along with a series of viral infections, e.g., pharyngitis, influenza, HIV and COVID-19. Since the authors' major research interests lie in the area of the principles and applications of NMR-linked metabolomics techniques, many, but not all, of the studies reviewed were conducted using these technologies, with special attention being given to recommended protocols for their operation and management, for example, satisfactory experimental model designs; sample collection and laboratory processing techniques; the selection of sample-specific NMR pulse sequences for saliva analysis; and strategies available for the confirmation of resonance assignments for both endogenous and exogenous molecules in this biofluid. This article also features an original case study, which is focussed on the use of NMR-based salivary metabolomics techniques to provide some key biomarkers for the diagnosis of pharyngitis, and an example of how to 'police' such studies and to recognise participants who perceive that they actually have this disorder but do not from their metabolic profiles and multivariate analysis pattern-based clusterings. The biochemical and clinical significance of these multidimensional metabolomics investigations are discussed in detail.

Glial Cell Line-Derived Neurotrophic Factor-Loaded CMCht/PAMAM Dendrimer Nanoparticles for Peripheral Nerve Repair

(1) Background: Peripheral nerve injuries represent a major clinical challenge. If nerve ends retract, there is no spontaneous regeneration and grafts are required to proximate the nerve ends and give continuity to the nerve. (2) Methods: GDNF-loaded NPs were characterized physicochemically. For that, NPs stability at different pH’s was assessed, and GDNF release was studied through ELISA. In vitro studies are performed with Schwann cells, and the NPs are labeled with fluorescein-5(6)-isothiocyanate for uptake experiments with SH-SY5Y neural cells. (3) Results: GDNF-loaded NPs are stable in physiological conditions, releasing GDNF in a two-step profile, which is beneficial for nerve repair. Cell viability is improved after 1 day of culture, and the uptake is near 99.97% after 3 days of incubation. (4) Conclusions: The present work shows the efficiency of using CMCht/PAMAM NPs as a GDNF-release system to act on peripheral nerve regeneration.

Determination of Isotope Abundance for Deuterium-labeled Compounds by Quantitative 1 H NMR + 2 H NMR

Deuterated reagents have been used in many research fields. Isotope abundance, as the feature parameter of deuterated reagents, the precise quantification is of great importance. Based on quantitative nuclear magnetic resonance technology, a novel method that combines ¹ H NMR + ² H NMR was systematically established to determine the isotopic abundance of deuterated reagents. The results showed that the isotopic abundance of partially labeled and fully labeled compounds calculated by this new method was even more accurate than that calculated by classical ¹ H NMR and MS methods. In brief, this new method is a robust strategy for the determination of isotope abundance in large-scale deuterated reagents.

Three- and four-site models for heavy water: SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW

Heavy water or deuterium oxide, D₂O, is used as a solvent in various biophysical and chemical experiments. To model such experiments with molecular dynamics simulations, effective pair potentials for heavy water are required, which reproduce the well-known physicochemical differences relative to light water. We present three effective pair potentials for heavy water, denoted SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW. The models were parameterized by modifying the widely used three- and four-site models for light water, with the aim of maintaining the specific characteristics of the light water models. At room temperature, SPC/E-HW and TIP3P-HW capture the modulations relative to light water of the mass and electron densities, heat of vaporization, diffusion coefficient, and water structure. TIP4P/2005-HW captures, in addition, the density of heavy water over a wide temperature range.

Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications

Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape for biomedical metabolomics, which is not available to other techniques. Furthermore, the non-destructive nature of NMR-based metabolomics allows for multidimensional analysis of biomarkers that facilitates unambiguous assignment and quantification of metabolites in complex biofluids.

Effect of daunorubicin on acute promyelocytic leukemia cells using nuclear magnetic resonance spectroscopy-based metabolomics

The aim of this study was to determine several key metabolites as potential biomarkers of daunorubicin (DNR) treatment of acute promyelocytic leukemia (APL) using APL blasts and NB4 cells. Samples which were obtained from 16 newly diagnosed APL patients and human APL NB4 cell lines were exposed to increasing concentrations of DNR (0 μM, 0.1 μM, 0.5 μM and 1.0 μM). Electron microscopy and Nuclear Magnetic Resonance (NMR) spectroscopy confirmed that there were clear differences between controls and DNR-treated groups, with the resultant models having excellent predictive and discriminative abilities. Four metabolites meeting the biomarker requirements were identified. KEGG analyses revealed that these biomarkers were associated with the metabolism of fat, choline, and glucose. These findings offered vital information about the effects of chemotherapies on the whole body biochemistry which might be important for monitoring apoptosis and injury to cells in order to reduce chemotherapies-induced side effects.