(Pre)Clinical Metabolomics Analysis.

Metabolomics is the scientific field with the eager goal to comprehensively analyze the entirety of all small molecules of a biological system, i.e., the metabolome. Over the last few years, metabolomics has matured to become an analytical cornerstone of life science research across diverse fields, from fundamental biochemical applications to preclinical studies, including biomarker discovery and drug development. In this chapter, we provide an introduction to (pre)clinical metabolomics. We define key metabolomics aspects and provide the basis to thoroughly understand the relevance of this field in a biological and clinical context. We present and explain state-of-the-art analytical technologies devoted to metabolomic analysis as well as emerging technologies, discussing both strengths and weaknesses. Given the ever-increasing demand for handling complex datasets, the role of bioinformatics approaches in the context of metabolomic analysis is also illustrated.

Research on the quality evaluation of crude drugs.

As crude drugs are natural products, their quality may vary. However, the degradation of the active ingredients in the compositional changes that occur during processing and preparation also affects the medicinal properties of the Kampo formula, which uses herbal medicines; therefore, a detailed investigation of the effects of compositional changes during preparation is required. Plant constituents vary in content depending on the year of cultivation and the plant part; however, detailed studies have rarely been reported for some crude drugs. Liquid chromatography-nuclear magnetic resonance/mass spectrometry revealed the degradation process of saponins, which are unstable components of the crude drug "Achyranthes root." The presence of diterpenes unstable with respect to drying temperature in the leaves of the crude drug "Leonurus herb" was revealed and their structures were elucidated. At the examination stage of the degradation process of perillaldehyde, the characteristic aromatic component of Perilla herb, it was elucidated that some specimens contained a small amount of perillaldehyde and that they contained more α-asarone. A trend toward lower ephedrine content was observed toward the tip of the above-ground branching of the Ephedra herb. Multivariate analysis was also introduced into the quality assessment of crude drugs and was established as a tool to identify bioactive compounds using the component diversity of crude drugs and to elucidate component differences due to the cultivation environment.

Mechanistic Insights into the Removal of Surfactant-Like Contaminants on Mesoporous Polydopamine Nanospheres from Complex Wastewater Matrices.

The detrimental environmental effects of surfactant-like contaminants (SLCs) with distinctive amphiphilic structures have garnered significant attention, particularly since perfluorooctanesulfonate was classified as a persistent organic pollutant. Despite the numerous absorbents developed for SLCs removal, the underlying interaction mechanisms remain speculative and lack experimental validation. To address this research gap, we elucidate the mechanistic insights into the selective removal of SLCs using mesoporous polydopamine nanospheres (MPDA) fabricated via a novel soft-template method. We employed low-field nuclear magnetic resonance to quantitatively characterize the hydrophilicity of the absorbents using water molecules as probes. The results demonstrated that MPDA with uniform mesopores exhibited a remarkable threefold enhancement in SLCs' adsorption capacity compared to conventional polydopamine particles via intraparticle diffusion. We further demonstrated the dominant effects of electrostatic and hydrophobic interactions on the selective removal of SLCs with MPDA by regulating the isoelectric pH value and performing a comparative analysis. The mechanism-inspired SLC-removal strategy achieved an average removal rate of 76.3% from highly contaminated wastewater. Our findings offer new avenues for applying MPDA as an efficient adsorbent and provide innovative and mechanistic insights for targeted SLC removal in complex wastewater matrices.

Cryo-EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils.

The tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.

Backbone assignments of the biotin carboxyl carrier protein domain of Propionyl CoA carboxylase of Leishmania major and its interaction with its cognate Biotin protein ligase.

Propionyl CoA carboxylase (PCC) is a multimeric enzyme composed of two types of subunits, α and ß arranged in α6ß6 stoichiometry. The α-subunit consists of an N-terminal carboxylase domain, a carboxyl transferase domains, and a C-terminal biotin carboxyl carrier protein domain (BCCP). The ß-subunit is made up of an N- and a C- carboxyl transferase domain. During PCC catalysis, the BCCP domain plays a central role by transporting a carboxyl group from the α-subunit to the ß-subunit, and finally to propionyl CoA carboxylase, resulting in the formation of methyl malonyl CoA. A point mutation in any of the subunits interferes with multimer assembly and function. Due to the association of this enzyme with propionic acidemia, a genetic metabolic disorder found in humans, PCC has become an enzyme of wide spread interest. Interestingly, unicellular eukaryotes like Leishmania also possess a PCC in their mitochondria that displays high sequence conservation with the human enzyme. Thus, to understand the function of this enzyme at the molecular level, we have initiated studies on Leishmania major PCC (LmPCC). Here we report chemical shift assignments of LmPCC BCCP domain using NMR. Conformational changes in LmPCC BCCP domain upon biotinylation, as well as upon interaction with its cognate biotinylating enzyme (Biotin protein ligase from L. major) have also been reported. Our studies disclose residues important for LmPCC BCCP interaction and function.

Assessing Mechanochemical Properties of Acrylonitrile Butadiene Styrene (ABS) Items in Cultural Heritage Through a Multimodal Spectroscopic Approach.

A multimodal spectroscopic approach is proposed to correlate the mechanical and chemical properties of plastic materials in art and design objects, at both surface and subsurface levels, to obtain information about their conservation state and to monitor their degradation. The approach was used to investigate the photo-oxidation of acrylonitrile butadiene styrene (ABS), a plastic commonly found in many artistic and design applications, using ABS-based LEGO bricks as model samples. The modifications of the chemical and viscoelastic properties of ABS during photoaging were monitored by correlative Brillouin and Raman microspectroscopy (BRaMS), combined with portable and noninvasive broad-range external reflection infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) relaxometry, directly applicable in museums. BRaMS enabled combined measurements of Brillouin light scattering and Raman spectroscopy in a microspectroscopic setup, providing for the coincident probe of the chemical and mechanical changes of ABS at the sample surface. NMR relaxometry allowed for noninvasive measurements of relaxation times and depth profiles which are directly related to the molecular mobility of the material. Complementary chemical information was acquired by external reflection IR spectroscopy. The simultaneous probe of the chemical and mechanical properties by this multimodal spectroscopic approach enabled us to define a decay model of ABS in terms of compositional changes and variation of stiffness and rigidity occurring with photodegradation. The knowledge acquired on LEGO samples has been used to rate the conservation state of ABS design objects noninvasively investigated by external reflection Fourier transform IR spectroscopy and NMR relaxometry offered by the MObile LABoratory (MOLAB) platform of the European Research Infrastructure of Heritage Science.

Influence of electrohydrodynamics on the drying characteristics, microstructure and volatile composition of apricot abalone mushroom (Pleurotus eryngii).

The study explored the use of current fluid dynamics drying technology for apricot abalone mushroom, examining how different output voltages (15, 25, and 35 kV) affected drying characteristics, microstructure, and volatile components. Comparisons were made with samples dried using hot air drying (HAD) and natural air drying (AD). Results revealed that HAD had the fastest drying rate at 0.29664(g·h-1). However, apricot abalone mushroom treated with electrohydrodynamic drying (EHD) maintained a color closer to fresh samples, exhibited a 21% increase in the ordered structure of protein secondary structure, a 12.5-fold increase in bound water content, and the most stable cell structure compared to HAD and AD treatments. A total of 83 volatile organic compounds were identified in the apricot abalone mushroom, with alcohols and aldehydes being the most prominent in terms of threshold and relative content, peaking in the 35 kV treatment group. These findings provide both experimental and theoretical insights into applying current fluid dynamics for drying apricot abalone mushroom.

Enzymatic Synthesis of a Novel Antioxidant Octacosanol Lipoate and Its Antioxidant Potency in Sunflower Oil.

α-Lipoic acid possesses remarkable antioxidant activity; however, its poor lipid solubility greatly restricts its practical utilization. The present study was the first (i) to synthesize a novel lipophilic antioxidant of octacosanol lipoate and (ii) to assess its antioxidant potency in sunflower oil by hydrogen nuclear magnetic resonance (1H NMR) spectroscopy. In brief, octacosanol lipoate was successfully synthesized using octacosanol and lipoic acid as substrates and Candida sp. 99-125 lipase as a catalyst. The conversion of octacosanol lipoate could reach as high as 98.1% within merely 2 h, with an overall yield of 87.9%. The hydrophobicity of lipoic acid was significantly enhanced upon esterification with octacosanol. Interestingly, both traditional methods and 1H NMR analysis consistently indicated that octacosanol lipoate exhibited superior antioxidant activity compared with butyl hydroxytoluene at high temperatures. It was concluded that octacosanol lipoate has the potential to be developed into a safe and efficient natural antioxidant which can be utilized not only in daily cooking oils but also in frying oils.

An integrative characterisation of proline cis and trans conformers in a disordered peptide.

Intrinsically disordered proteins (IDPs) often contain proline residues, which undergo cis/trans isomerisation. While molecular dynamics (MD) simulations have the potential to fully characterise the proline cis and trans sub-ensembles, they are limited by the slow timescales of isomerisation and force field inaccuracies. Nuclear magnetic resonance (NMR) spectroscopy can report on ensemble-averaged observables for both the cis-proline and trans-proline states, but a full atomistic characterisation of these conformers is challenging. Given the importance of proline cis/trans isomerisation for influencing the conformational sampling of disordered proteins, we employed a combination of all-atom MD simulations with enhanced sampling (metadynamics), NMR, and small-angle X-ray scattering (SAXS) to characterise the two sub-ensembles of the ORF6 C-terminal region (ORF6CTR) from SARS-CoV-2 corresponding to the proline-57 (P57) cis and trans states. We performed MD simulations in three distinct force fields: AMBER03ws, AMBER99SB-disp, and CHARMM36m, which are all optimised for disordered proteins. Each simulation was run for an accumulated time of 180-220 µs until convergence was reached, as assessed by blocking analysis. A good agreement between the cis-P57 populations predicted from metadynamic simulations in AMBER03ws was observed with populations obtained from experimental NMR data. Moreover, we observed good agreement between the radius of gyration predicted from the metadynamic simulations in AMBER03ws and that measured using SAXS. Our findings suggest that both the cis-P57 and trans-P57 conformations of ORF6CTR are extremely dynamic and that interdisciplinary approaches combining both multi-scale computations and experiments offer avenues to explore highly dynamic states that cannot be reliably characterised by either approach in isolation.

The Use of Nuclear Magnetic Resonance Spectroscopy (NMR) to Characterize Bitumen Used in the Road Pavements Industry: A Review.

Bitumen, a vital component in road pavement construction, exhibits complex chemo-mechanical properties that necessitate thorough characterization for enhanced understanding and potential modifications. Nuclear Magnetic Resonance (NMR) spectroscopy emerges as a valuable technique for probing the structural and compositional features of bitumen. This review presents an in-depth exploration of the role of NMR spectroscopy in bitumen characterization, highlighting its diverse applications in determining bitumen content, group composition, molecular dynamics, and interaction with additives. Various NMR techniques, including free induction decay (FID), Carr-Purcell-Meilboom-Gill (CPMG), and Pulsed Field Gradient Stimulated Echo (PFGSE), are discussed in the context of their utility in bitumen analysis. Case studies, challenges, and limitations associated with NMR-based bitumen characterization are critically evaluated, offering insights into potential future research directions. Overall, this review provides a comprehensive overview of the current state-of-the-art in NMR-based bitumen characterization and identifies avenues for further advancement in the field.