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Se Pu = Chinese Journal of... Feb 2024The occurrence and development of human diseases are influenced by both genetic and environmental factors. Research models that describe disease occurrence only from the... (Review)
Review
The occurrence and development of human diseases are influenced by both genetic and environmental factors. Research models that describe disease occurrence only from the perspective of genetics present certain limitations. In recent years, effects of environment factors on the occurrence and development of diseases have attracted extensive attentions. Exposomics focuses on the measurement of all exposure factors in an individual's life and how these factors are related to disease development. Exposomics provides new ideas to promote studies on the relationship between human health and environmental factors. Environmental exposures are characterized with different physical and chemical properties, as well as very low concentrations in vivo, which contribute great challenges in the comprehensive measurement of chemical residues in the human body. Chromatography-mass spectrometry-based technologies combine the high-efficiency separation ability of chromatography with the high resolution and sensitive detection characteristics of mass spectrometry; the combination of these techniques can achieve the high-coverage, high-throughput, and sensitive detection of environmental exposures, thus providing a powerful tool for measuring chemical exposures. Exposomics-analysis methods based on chromatography-mass spectrometry mainly include targeted quantitative analysis, suspect screening, and non-targeted screening. To explore the relationship between environmental exposure and the occurrence and development of diseases, researchers have developed research paradigms, including exposome wide association study, mixed-exposure study, exposomics and multi-omics (genome, transcriptome, proteome, metabolome)-association study, and so on. The emergence of these methods has brought about unprecedented developments in exposomics studies. In this manuscript, analytical methods based on chromatography-mass spectrometry, exposomics research paradigms, and their relevant prospects are reviewed.
Topics: Humans; Chromatography, Liquid; Environmental Exposure; Mass Spectrometry; Metabolome; Spectrum Analysis
PubMed: 38374591
DOI: 10.3724/SP.J.1123.2023.12001 -
Spectrochimica Acta. Part A, Molecular... Dec 2023Due to the background interference from biological samples, detecting viruses using surface-enhanced Raman scattering (SERS) in clinical samples is challenging. This...
Due to the background interference from biological samples, detecting viruses using surface-enhanced Raman scattering (SERS) in clinical samples is challenging. This study is based on SERS by reducing sodium borohydride and aggregating silver nanoparticles to develop suitable virus detection "hot spot." The monkeypox virus and human papillomavirus fingerprints were quickly obtained, tested, and identified in serum and artificial vaginal discharge, respectively, by combining the principal component analysis method. Therefore, these viruses were successfully identified in the biological background. In addition, the lowest detection limit was 100 copies/mL showing good reproducibility and signal-to-noise ratio. The concentration-dependent curve of the monkeypox virus had a good linear relationship. This method helps solve the SERS signal interference problem in complex biological samples, with low detection limits and high selectivity in virus characterization and quantitative analysis. Therefore, this method has a reasonable prospect of clinical application.
Topics: Humans; Spectrum Analysis, Raman; Metal Nanoparticles; Reproducibility of Results; Silver; Viruses; Limit of Detection
PubMed: 37406546
DOI: 10.1016/j.saa.2023.123087 -
Methods in Molecular Biology (Clifton,... 2024Single-molecule force spectroscopy is a powerful tool to investigate the forces and motions related to interactions of biological molecules. Acoustic force spectroscopy...
Single-molecule force spectroscopy is a powerful tool to investigate the forces and motions related to interactions of biological molecules. Acoustic force spectroscopy (AFS) is a developed measurement tool to study single molecules or cells making use of acoustic standing waves. AFS permits high experimental throughput because many individual molecules can be manipulated and tracked in parallel. Moreover, a wide range of forces can be applied as well as a force loading rate with range of six orders of magnitude. At the same time, AFS stands out because of its simplicity and the compactness of the experimental setup. Even though the AFS setup is simple, it can still be challenging to perform high-quality measurements. Here we describe, in detail, how to setup, perform, and analyze an AFS measurement to determine cell adhesion.
Topics: Mechanical Phenomena; Spectrum Analysis; Nanotechnology; Cell Adhesion; Acoustics; Microscopy, Atomic Force
PubMed: 37824018
DOI: 10.1007/978-1-0716-3377-9_22 -
Journal of Natural Products Nov 2023A highly reducing polyketide synthase (HRPKS) gene cluster from the genome of was identified through genome mining. Heterologous expression of this cluster led to the...
A highly reducing polyketide synthase (HRPKS) gene cluster from the genome of was identified through genome mining. Heterologous expression of this cluster led to the production of four new α-pyrone compounds, calcapyrones A () and B (), along with their biosynthetic intermediates calcapyrones C () and D (). The structures of these compounds were elucidated on the basis of extensive spectroscopic experiments, and the absolute configurations of the 7,8-diol moieties in and were assigned using Snatzke's method. The biosynthetic pathway of and was established through and experiments.
Topics: Pyrones; Hypocreales; Spectrum Analysis
PubMed: 37924510
DOI: 10.1021/acs.jnatprod.3c00685 -
Journal of Materials Chemistry. B Jul 2023Snake venoms are complex mixtures of different substances, proteins being their predominant components. To study the composition of venoms, methods based on...
Snake venoms are complex mixtures of different substances, proteins being their predominant components. To study the composition of venoms, methods based on chromatographic separation and mass spectrometric analysis are currently used, requiring the application of a number of sophisticated instruments. To assess the composition of snake venoms, we propose an alternative method based on Raman spectroscopy, which is an express method to study the structural features of different substances, including proteins. The method does not require preliminary preparation of the samples, which are used in small quantities; this makes Raman spectroscopy extremely attractive for venom research. In this work, we have carried out Raman spectroscopic studies on a number of dry venoms from various venomous snakes. Based on the obtained Raman spectra, with the help of mathematical methods of dimensionality reduction and clustering, differentiation of venoms reflecting their composition and the assignment of the venom producing snake to the corresponding family or even genus were performed. The proposed method can be used to analyze both the composition of and variations in venoms of different snake species, including rare and endangered ones.
Topics: Spectrum Analysis, Raman; Snake Venoms; Mass Spectrometry
PubMed: 37350327
DOI: 10.1039/d3tb00829k -
Biological Trace Element Research Sep 2023In this work, microwave-induced plasma optical emission spectrometry was applied for multielement determination in South American wine samples. The analytes were...
In this work, microwave-induced plasma optical emission spectrometry was applied for multielement determination in South American wine samples. The analytes were determined after acid digestion of 47 samples of Brazilian and Argentinian wines. Then, logistic regression, support vector machine, and decision tree for exploratory analysis and comparison of these algorithms in differentiating red wine samples by region of origin were carried out. All wine samples were classified according to their geographical origin. The quantification limits (mg L) were P: 0.06, B: 0.08, K: 0.17, Mn: 0.002, Cr: 0.002, and Al: 0.02. The accuracy of the method was evaluated by analyzing the wine samples by ICP OES for results' comparison. The concentrations in mg L found for each element in wine samples were as follows: Al (< 0.02-1.82), Cr (0.15-0.50), Mn (< 0.002-0.8), P (97-277), B (1.7-11.6), Pb (< 0.06-0.3), Na (8.84-41.57), and K (604-1701), in mg L.
Topics: Wine; Mass Spectrometry; Artificial Intelligence; Spectrum Analysis; Brazil; Trace Elements
PubMed: 36550265
DOI: 10.1007/s12011-022-03529-4 -
Chemphyschem : a European Journal of... Dec 2023OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry...
OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS ) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2'-deoxyadenosine (dA(O)H ), 2'-deoxyadenosine 5'-monophosphate (dAMP(O)H ), 2'-deoxycytidine (dC(O)H ), and 2'-deoxycytidine 5'-monophosphate (dCMP(O)H ) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2'-deoxyadenosine and its monophosphate derivative. For 2'-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C-OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.
Topics: Nucleotides; Tandem Mass Spectrometry; Oxygen; DNA; Deoxycytidine; Spectrum Analysis; Spectrophotometry, Infrared
PubMed: 37713246
DOI: 10.1002/cphc.202300534 -
Chemical Society Reviews May 2024Unraveling the cellular and molecular mechanisms underlying tumoral processes is fundamental for the diagnosis and treatment of cancer. In this regard, three-dimensional... (Review)
Review
Unraveling the cellular and molecular mechanisms underlying tumoral processes is fundamental for the diagnosis and treatment of cancer. In this regard, three-dimensional (3D) cancer cell models more realistically mimic tumors compared to conventional 2D cell cultures and are more attractive for performing such studies. Nonetheless, the analysis of such architectures is challenging because most available techniques are destructive, resulting in the loss of biochemical information. On the contrary, surface-enhanced Raman spectroscopy (SERS) is a non-invasive analytical tool that can record the structural fingerprint of molecules present in complex biological environments. The implementation of SERS in 3D cancer models can be leveraged to track therapeutics, the production of cancer-related metabolites, different signaling and communication pathways, and to image the different cellular components and structural features. In this review, we highlight recent progress in the use of SERS for the evaluation of cancer diagnosis and therapy in 3D tumoral models. We outline strategies for the delivery and design of SERS tags and shed light on the possibilities this technique offers for studying different cellular processes, through either biosensing or bioimaging modalities. Finally, we address current challenges and future directions, such as overcoming the limitations of SERS and the need for the development of user-friendly and robust data analysis methods. Continued development of SERS 3D bioimaging and biosensing systems, techniques, and analytical strategies, can provide significant contributions for early disease detection, novel cancer therapies, and the realization of patient-tailored medicine.
Topics: Spectrum Analysis, Raman; Humans; Neoplasms; Animals
PubMed: 38607302
DOI: 10.1039/d3cs01049j -
Advanced Science (Weinheim,... Feb 2024Early clinical diagnosis, effective intraoperative guidance, and an accurate prognosis can lead to timely and effective medical treatment. The current conventional... (Review)
Review
Early clinical diagnosis, effective intraoperative guidance, and an accurate prognosis can lead to timely and effective medical treatment. The current conventional clinical methods have several limitations. Therefore, there is a need to develop faster and more reliable clinical detection, treatment, and monitoring methods to enhance their clinical applications. Raman spectroscopy is noninvasive and provides highly specific information about the molecular structure and biochemical composition of analytes in a rapid and accurate manner. It has a wide range of applications in biomedicine, materials, and clinical settings. This review primarily focuses on the application of Raman spectroscopy in clinical medicine. The advantages and limitations of Raman spectroscopy over traditional clinical methods are discussed. In addition, the advantages of combining Raman spectroscopy with machine learning, nanoparticles, and probes are demonstrated, thereby extending its applicability to different clinical phases. Examples of the clinical applications of Raman spectroscopy over the last 3 years are also integrated. Finally, various prospective approaches based on Raman spectroscopy in clinical studies are surveyed, and current challenges are discussed.
Topics: Spectrum Analysis, Raman; Nanoparticles
PubMed: 38072672
DOI: 10.1002/advs.202300668 -
Journal of Biomolecular Structure &... Dec 20232-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was...
2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (H-NMR and C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV-Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H--H/H--H/C--H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein.Communicated by Ramaswamy H. Sarma.
Topics: Molecular Docking Simulation; Molecular Dynamics Simulation; Spectroscopy, Fourier Transform Infrared; Ligands; Molecular Structure; Quantum Theory; Spectrum Analysis, Raman; Spectrophotometry, Ultraviolet
PubMed: 37942665
DOI: 10.1080/07391102.2023.2180667