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Metabolites
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Determination and Analysis of Known and Unknown Metabolites in NMR-Based...
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Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Metabolomic Profiling Technology".

Deadline for manuscript submissions: closed (20 October 2023) | Viewed by 9107

Special Issue Editors

Dr. Cheng Wang

E-Mail Website
Guest Editor
Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250002, China
Interests: metabolomics; machine learning; bioinformatics; biomedical networks
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Donghai Lin

E-Mail Website
Guest Editor
Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
Interests: NMR-based metabolomics; LC-MS-based metabolomics; biomolecular NMR; structural biology; cancer cachexia; muscular atrophy; sarcopenia; metabolic regulation; allosteric effect
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolites are the phenotypic outcomes of genomic and enzymatic activities in a cell or organism. Accurate determination and analysis of metabolites are critical for understanding biochemical pathways and their roles in health and disease. NMR-based metabolomics (metabonomics) offers a highly accurate and reproductive approach for metabolic profiling of complex metabolite mixtures. However, the identification of unknown metabolites remains a key bottleneck in NMR-based metabolomics. An increasing number of NMR-based metabolomic studies have been conducted in a variety of research areas, such as disease pathology, tumor metabolism, pharmaceutics, nutrition, food, plant, and microbiology as well as physical exercise and sports. This Special Issue of Metabolites, “Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics”, will be dedicated to publishing a wide range of methods and applications of NMR-Based Metabolomics to various research fields with an emphasis on improving the performance of the determination and analysis of known and unknown metabolites. Highly desired researches also include those on experimental and computational approaches to improve the identification and analysis of known and unknown metabolites using hybrid LC-MS/NMR methods.

Dr. Cheng Wang
Prof. Dr. Donghai Lin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolites
  • NMR
  • hybrid LC-MS/NMR
  • metabolomics
  • metabonomics
  • metabolite identification
  • bioinformatics
  • biomarker discovery
  • metabolic pathway
  • metabolism
  • metabolome

Published Papers (5 papers)

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Research

13 pages, 2859 KiB  
Article
Clinical Efficacy and Metabolomics Modifications Induced by Polyphenol Compound Supplementation in the Treatment of Residual Dizziness following Semont Maneuver in Benign Paroxysmal Positional Vertigo (BPPV) of the Posterior Semicircular Canal (PSC): Preliminary Results
by Augusto Pietro Casani, Roberto Albera, Cristina Piras, Andrea Albera, Antonio Noto, Nicola Ducci, Luigi Atzori, Sergio Lucisano, Michele Mussap and Vassilios Fanos
Metabolites 2024, 14(2), 86; https://doi.org/10.3390/metabo14020086 - 25 Jan 2024
Viewed by 1143
Abstract
Benign paroxysmal positional vertigo (BPPV) represents the most frequent cause of peripheral vertigo. In most cases, it is successfully treated using the canalith repositioning procedure, but it is often followed by continuous lightheadedness in the absence of vertigo or nystagmus (residual dizziness, RD). [...] Read more.
Benign paroxysmal positional vertigo (BPPV) represents the most frequent cause of peripheral vertigo. In most cases, it is successfully treated using the canalith repositioning procedure, but it is often followed by continuous lightheadedness in the absence of vertigo or nystagmus (residual dizziness, RD). Our aim is to describe the clinical effectiveness and the urine metabolomics profile of treating these patients with polyphenol compound supplementation. We enrolled 30 patients reporting RD after BPPV of the posterior semicircular canal (PSC) successfully treated using the Semont maneuver. Supplementation with a polyphenol compound was administered for 60 days, and patients were evaluated after 30 and 60 days of treatment using self-administered questionnaires (Visual Analog Scales for Dizziness and Nausea, Dizziness Handicap Inventory, DHI) and urine metabolomics analysis performed using 1H-NMR spectroscopy and multivariate followed by univariate analysis. Most patients reported excellent or good efficacy in the treatment of RD with a significant decrease in VAS and DHI values. The metabolomics analysis identified six significant metabolites related to the treatment, namely 1-methylnicotinamide, anserine, hippurate, lysine, methyl succinate and urea, indicating the inflammatory activities and antioxidant properties of the polyphenol compound. These preliminary data suggest that supplementation with a polyphenol compound could induce some metabolic changes that can help in recovery from RD. However, future steps will require confirmation with a more significant cohort of patients and an extension of the metabolomics evaluation to other problems concerning the different clinical aspects of BPPV, such as the high rate of relapse. Full article
(This article belongs to the Special Issue Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics)
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33 pages, 8353 KiB  
Article
Identification of Novel Biomarkers in Late Preterm Neonates with Respiratory Distress Syndrome (RDS) Using Urinary Metabolomic Analysis
by Irene Christopoulou, Eirini Kostopoulou, Konstantina Matzarapi, Styliani A. Chasapi, Georgios A. Spyroulias and Anastasia Varvarigou
Metabolites 2023, 13(5), 644; https://doi.org/10.3390/metabo13050644 - 09 May 2023
Cited by 1 | Viewed by 1694
Abstract
Urine metabolomics is gaining traction as a means of identifying metabolic signatures associated with health and disease states. Thirty-one (31) late preterm (LP) neonates admitted to the neonatal intensive care unit (NICU) and 23 age-matched healthy LPs admitted to the maternity ward of [...] Read more.
Urine metabolomics is gaining traction as a means of identifying metabolic signatures associated with health and disease states. Thirty-one (31) late preterm (LP) neonates admitted to the neonatal intensive care unit (NICU) and 23 age-matched healthy LPs admitted to the maternity ward of a tertiary hospital were included in the study. Proton nuclear magnetic resonance (1H NMR) spectroscopy was employed for urine metabolomic analysis on the 1st and 3rd days of life of the neonates. The data were analyzed using univariate and multivariate statistical analysis. A unique metabolic pattern of enhanced metabolites was identified in the NICU-admitted LPs from the 1st day of life. Metabolic profiles were distinct in LPs presenting with respiratory distress syndrome (RDS). The discrepancies likely reflect differences in the gut microbiota, either due to variations in nutrient intake or as a result of medical interventions, such as the administration of antibiotics and other medications. Altered metabolites could potentially serve as biomarkers for identifying critically ill LP neonates or those at high risk for adverse outcomes later in life, including metabolic risks. The discovery of novel biomarkers may uncover potential targets for drug discovery and optimal periods for effective intervention, offering a personalized approach. Full article
(This article belongs to the Special Issue Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics)
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13 pages, 12638 KiB  
Article
1H-NMR-Based Metabonomics Study to Reveal the Progressive Metabolism Regulation of SAP Deficiency on ApoE−/− Mice
by Qian Li, Wanting Chen, Wenbin Huang, Ranran Hou, Xinping Huang, Man Xu, Limei Que, Lijing Wang and Yongxia Yang
Metabolites 2022, 12(12), 1278; https://doi.org/10.3390/metabo12121278 - 16 Dec 2022
Viewed by 1247
Abstract
Atherosclerosis is the most common disease of the vascular system and the metabolic disorder is one of its important molecular mechanisms. SAP protein is found to be highly expressed in atherosclerotic blood vessels. Our previous study found that SAP deficiency can significantly inhibit [...] Read more.
Atherosclerosis is the most common disease of the vascular system and the metabolic disorder is one of its important molecular mechanisms. SAP protein is found to be highly expressed in atherosclerotic blood vessels. Our previous study found that SAP deficiency can significantly inhibit the development of atherosclerosis. However, the regulatory effect of SAP deficiency on AS metabolism is unknown. Based on 1H-NMR metabonomics, this study investigated the serum metabolic changes in ApoE−/−;SAP−/− mice compared with ApoE−/− mice during the whole progression of atherosclerosis. The results showed that acetate, pyruvate, choline and VLDL + LDL were statistically regulated to the normal levels as in C57 mice by SAP deficiency in ApoE−/−;SAP−/− mice at 8 w (without obvious plaques). With the appearance and aggravation of atherosclerotic plaques (8 + 4 w and 8 + 8 w), the four metabolites of acetate, pyruvate, choline and VLDL + LDL were continuously regulated, which were denoted as the metabolic regulatory markers of SAP deficiency. We also found that the changes in these four metabolites had nothing to do with high-fat diet. Therefore, it was revealed that SAP deficiency regulated the metabolic disorders in ApoE−/− prior to the appearance of obvious atherosclerotic plaques, which is one of the important mechanisms leading to the inhibition of atherosclerosis, providing a new basis for the application of SAP in atherosclerosis. Full article
(This article belongs to the Special Issue Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics)
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12 pages, 1918 KiB  
Article
Solid-State NMR-Based Metabolomics Imprinting Elucidation in Tissue Metabolites, Metabolites Inhibition, and Metabolic Hub in Zebrafish by Chitosan
by Raja Ganesan, Anirban Goutam Mukherjee, Abilash Valsala Gopalakrishnan and Vasantha-Srinivasan Prabhakaran
Metabolites 2022, 12(12), 1263; https://doi.org/10.3390/metabo12121263 - 14 Dec 2022
Cited by 2 | Viewed by 1359
Abstract
In this study, we demonstrated that chitosan-applied zebrafish (Danio rerio) tissue metabolite alteration, metabolic discrimination, and metabolic phenotypic expression occurred. The spectroscopy of solid-state 1H nuclear magnetic resonance (ss 1H-NMR) has been used. Chitosan has no, or low, toxicity [...] Read more.
In this study, we demonstrated that chitosan-applied zebrafish (Danio rerio) tissue metabolite alteration, metabolic discrimination, and metabolic phenotypic expression occurred. The spectroscopy of solid-state 1H nuclear magnetic resonance (ss 1H-NMR) has been used. Chitosan has no, or low, toxicity and is a biocompatible biomaterial; however, the metabolite mechanisms underlying the biological effect of chitosan are poorly understood. The zebrafish is now one of the most popular ecotoxicology models. Zebrafish were exposed to chitosan concentrations of 0, 50, 100, 200, and 500 mg/L, and the body tissue was subjected to metabolites-targeted profiling. The zebrafish samples were measured via solvent-suppressed and T2-filtered methods with in vivo zebrafish metabolites. The metabolism of glutamate, glutamine, glutathione (GSH), taurine, trimethylamine (TMA), and its N-oxide (TMAO) is also significantly altered. Here, we report the quantification of metabolites and the biological application of chitosan. The metabolomics profile of chitosan in zebrafish has been detected, and the results indicated disturbed amino acid metabolism, the TCA cycle, and glycolysis. Our results demonstrate the potential of comparative metabolite profiling for discovering bioactive metabolites and they highlight the power of chitosan-applied chemical metabolomics to uncover new biological insights. Full article
(This article belongs to the Special Issue Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics)
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16 pages, 3220 KiB  
Article
NMR-Based Metabolomic Analysis of Plasma in Patients with Adult Congenital Heart Disease and Associated Pulmonary Arterial Hypertension: A Pilot Study
by Beizhu Xu, Caihua Huang, Caojin Zhang, Donghai Lin and Weifeng Wu
Metabolites 2022, 12(9), 845; https://doi.org/10.3390/metabo12090845 - 08 Sep 2022
Cited by 5 | Viewed by 2094
Abstract
Patients with unrepaired congenital heart disease (CHD) are prone to pulmonary arterial hypertension (PAH). The ovine pulmonary arterial smooth muscle cells exposed to increased pulmonary blood flow (PBF) exhibited hyperproliferation and metabolic alterations, but the metabolic disorders of patients with CHD and associated [...] Read more.
Patients with unrepaired congenital heart disease (CHD) are prone to pulmonary arterial hypertension (PAH). The ovine pulmonary arterial smooth muscle cells exposed to increased pulmonary blood flow (PBF) exhibited hyperproliferation and metabolic alterations, but the metabolic disorders of patients with CHD and associated PAH (PAH-CHD) have not yet been fully understood. Adult CHD patients were prospectively included and divided into the PAH-CHD group (n = 24) and CHD group (n = 38), while healthy adults were included as healthy control (HC) group (n = 29). Plasma from each subject was prepared for nuclear magnetic resonance (NMR) detection. 1H-NMR spectra were acquired using 850 MHz NMR spectrometer. A total of 28 metabolites were identified from the NMR spectra and their relative concentrations were calculated and analyzed by multivariate and univariate statistical analyses and metabolic pathway analysis. Receiver operating characteristic (ROC) curve analysis and correlation analysis were performed to identify potential biomarkers and assess their roles in clinical assessment. Multivariate statistical analysis showed that the metabolic profile of PAH-CHD was altered relative to CHD or HC, while that of CHD was altered relative to HC. The identified characteristic metabolites were alanine, glucose, glycine, threonine and lactate, and the areas under the ROC curves (AUCs) were 0.769, 0.808, 0.711, 0.842 and 0.817, respectively. Multivariate ROC curve analysis showed AUCs ranging from 0.895 to 0.955 for the combination of these characteristic metabolites. The correlation analysis indicated that lactate and threonine were significantly correlated with mean pulmonary arterial pressure, pulmonary vascular resistance and N-terminal pro-B-type natriuretic peptide. The increased PBF could trigger global metabolic alterations in patients with CHD, which were more severe in patients with PAH-CHD. The characteristic metabolites have the potential to be biomarkers of PAH-CHD, which could be used for its noninvasive diagnosis, severity and prognosis assessment, thereby improving the management of PAH-CHD. Full article
(This article belongs to the Special Issue Determination and Analysis of Known and Unknown Metabolites in NMR-Based Metabolomics)
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