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Singh U, Emwas AH, Jaremko M. Enhancement of weak signals by applying a suppression method to high-intense methyl and methylene signals of lipids in NMR spectroscopy. RSC Adv 2024; 14:26873-26883. [PMID: 39193283 PMCID: PMC11347981 DOI: 10.1039/d4ra03019b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/18/2024] [Indexed: 08/29/2024] Open
Abstract
Lipids play crucial roles in human biology, serving as energy stores, cell membranes, hormone production, and signaling molecules. Accordingly, their study under lipidomics has advanced the study of living organisms. 1-Dimensional (D) and 2D NMR methods, particularly 1D 1H and 2D 1H-1H Total Correlation Spectroscopy (TOCSY), are commonly used in lipidomics for quantification and structural identification. However, these NMR methods suffer from low sensitivity, especially in cases of low concentrated molecules such as protons attached to hydroxy, esters, aliphatic, or aromatic unsaturated carbons. Such molecules are common in complex mixtures such as dairy products and plant oils. On the other hand, lipids have highly populated fractions of methyl and methylene groups that result in intense peaks that overwhelm lower peaks and cause inhomogeneities in 2D TOCSY spectra. In this study, we applied a method of suppression to suppress these intense peaks of methyl and methylene groups to detect weaker peaks. The suppression method was investigated on samples of cheese, butter, a mixture of lipids, coconut oil, and olive oil. A significant improvement in peak sensitivity and visibility of cross-peaks was observed, leading to enhanced comparative quantification and structural identification of a greater number of lipids. Additionally, the enhanced sensitivity reduced the time required for the qualitative and comparative quantification of other lipid compounds and components. This, in turn, enables faster and more reliable structural identification and comparative quantification of a greater number of lipids. Additionally, it reduces the time required for the qualitative, and comparative quantification due to the enhancement of sensitivity.
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Affiliation(s)
- Upendra Singh
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal Makkah 23955-6900 Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Lab of NMR, King Abdullah University of Science and Technology (KAUST) Thuwal Makkah 23955-6900 Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI), Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal Makkah 23955-6900 Saudi Arabia
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Amina R, Habiba R, Abouddihaj B. Camel urine as a potential source of bioactive molecules showing their efficacy against pathogens: A systematic review. Saudi J Biol Sci 2024; 31:103966. [PMID: 38495380 PMCID: PMC10940778 DOI: 10.1016/j.sjbs.2024.103966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/19/2024] Open
Abstract
Camels are highly suited for severe desert conditions and able to provide most of the natural products like urine, which has been used as alternative medicine to treat diverse infections and disorders. There is, however, a shortage and paucity of scientific reviews highlighting the antifungal, antibacterial and antiviral effects of camel urine. By better understanding its antimicrobial characteristics, our overarching aim is to provide an exhaustive overview of this valuable natural product by synthesizing and summarizing data on the efficacy of this biofluid and also describing the potential substances exhibiting antimicrobial properties. We searched three databases in order to point out relevant articles (Web of Science, Scopus and Google Scholar) until December 2022. Research articles of interest evaluating the antimicrobial effects of camel urine were selected. Overall, camel urine furnished promising antibacterial activities against gram-positive bacteria, namely Staphylococcus aureus (30 mm), Bacillus cereus (22 mm), Bacillus subtilis (25 mm) and Micrococcus luteus (21 mm), as well as gram-negative bacteria, especially Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Salmonella spp., without forgetting its efficiency on Mycobacterium tuberculosis as well. The excretion also showed its potency against H1N1 virus, vesicular stomatitis virus and middle east respiratory syndrome coronavirus. Similarly, the camel urine featured strong antifungal activity against Candida albicans, Aspergillus niger, Aspergillus flavus and dermatophytes with a minimal inhibitory concentration of 0.625 μg/ml against Trichophyton violaceum, 2.5 μg/ml against Microsporum canis and 1.25 μg/ml against Trichophyton rubrum and Trichophyton mentagrophytes. This comprehensive review will be valuable for researchers interested in investigating the potential of camel urine in the development of novel broad-spectrum key molecules targeting a wide range of drug-resistant pathogenic microorganisms.
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Affiliation(s)
- Ressmi Amina
- Laboratory of Biotechnology and Sustainable Development of Natural Resources, Life Sciences Department, Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni Mellal 23023, Morocco
| | - Raqraq Habiba
- Laboratory of Biotechnology and Sustainable Development of Natural Resources, Life Sciences Department, Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni Mellal 23023, Morocco
| | - Barguigua Abouddihaj
- Laboratory of Biotechnology and Sustainable Development of Natural Resources, Life Sciences Department, Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni Mellal 23023, Morocco
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Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics. Metabolites 2023; 13:metabo13020155. [PMID: 36837774 PMCID: PMC9964739 DOI: 10.3390/metabo13020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.
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Emwas AH, Szczepski K, Al-Younis I, Lachowicz JI, Jaremko M. Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways. Front Pharmacol 2022; 13:805782. [PMID: 35387341 PMCID: PMC8977530 DOI: 10.3389/fphar.2022.805782] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
Fluxomics is an innovative -omics research field that measures the rates of all intracellular fluxes in the central metabolism of biological systems. Fluxomics gathers data from multiple different -omics fields, portraying the whole picture of molecular interactions. Recently, fluxomics has become one of the most relevant approaches to investigate metabolic phenotypes. Metabolic flux using 13C-labeled molecules is increasingly used to monitor metabolic pathways, to probe the corresponding gene-RNA and protein-metabolite interaction networks in actual time. Thus, fluxomics reveals the functioning of multi-molecular metabolic pathways and is increasingly applied in biotechnology and pharmacology. Here, we describe the main fluxomics approaches and experimental platforms. Moreover, we summarize recent fluxomic results in different biological systems.
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Affiliation(s)
- Abdul-Hamid Emwas
- King Abdullah University of Science and Technology, Core Labs, Thuwal, Saudi Arabia
| | - Kacper Szczepski
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Inas Al-Younis
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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LeVatte M, Keshteli AH, Zarei P, Wishart DS. Applications of Metabolomics to Precision Nutrition. Lifestyle Genom 2021; 15:1-9. [PMID: 34518463 DOI: 10.1159/000518489] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/07/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND For thousands of years, disabilities due to nutrient deficiencies have plagued humanity. Rickets, scurvy, anemia, stunted growth, blindness, and mental handicaps due to nutrient deficiencies affected up to 1/10 of the world's population prior to 1900. The discovery of essential amino acids, vitamins, and minerals, in the early 1900s, led to a fundamental change in our understanding of food and a revolution in human health. Widespread vitamin and mineral supplementation, the development of recommended dietary allowances, and the implementation of food labeling and testing along with significant improvements in food production and food quality have meant that nutrient-related disorders have almost vanished in the developed world. The success of nutritional science in preventing disease at a population-wide level is one of the great scientific triumphs of the 20th century. The challenge for nutritional science in the 21st century is to understand how to use nutrients and other food constituents to enhance human health or prevent disease at a more personal level. This is the primary goal of precision nutrition. SUMMARY Precision nutrition is an emerging branch of nutrition science that aims to use modern omics technologies (genomics, proteomics, and metabolomics) to assess an individual's response to specific foods or dietary patterns and thereby determine the most effective diet or lifestyle interventions to prevent or treat specific diseases in that individual. Metabolomics is vital to nearly every aspect of precision nutrition. It can be used to comprehensively characterize the thousands of chemicals in foods, to identify food byproducts in human biofluids or tissues, to characterize nutrient deficiencies or excesses, to monitor biochemical responses to dietary interventions, to track long-term or short-term dietary habits, and to guide the development of nutritional therapies. In this review, we will describe how metabolomics has been used to advance the field of precision nutrition by providing some notable examples or use cases. First, we will describe how metabolomics helped launch the field of precision nutrition through the diagnosis and dietary therapy of individuals with inborn errors of metabolism. Next, we will describe how metabolomics is being used to comprehensively characterize the full chemical complexity of many key foods, and how this is revealing much more about nutrients than ever imagined. Third, we will describe how metabolomics is being used to identify food consumption biomarkers and how this opens the door to a more objective and quantitative assessments of an individual's diet and their response to certain foods. Finally, we will describe how metabolomics is being coupled with other omics technologies to develop custom diets and lifestyle interventions that are leading to positive health benefits. Key Message: Metabolomics is vital to the advancement of nutritional science and in making the dream of precision nutrition a reality.
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Affiliation(s)
- Marcia LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Parvin Zarei
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Department of Computing Sciences, University of Alberta, Edmonton, Alberta, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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Noreldeen HAA, Liu X, Xu G. Metabolomics of lung cancer: Analytical platforms and their applications. J Sep Sci 2019; 43:120-133. [DOI: 10.1002/jssc.201900736] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Hamada A. A. Noreldeen
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian P. R. China
- University of Chinese Academy of Sciences Beijing P. R. China
- Marine Chemistry LabMarine Environment DivisionNational Institute of Oceanography and Fisheries Hurghada Egypt
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian P. R. China
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Research and Application Progress of Paper-based Microfluidic Sample Preconcentration. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61203-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR Spectroscopy for Metabolomics Research. Metabolites 2019; 9:E123. [PMID: 31252628 PMCID: PMC6680826 DOI: 10.3390/metabo9070123] [Citation(s) in RCA: 519] [Impact Index Per Article: 103.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Uttar Pradesh 226014, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Fatimah Alahmari
- Department of NanoMedicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Lukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
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Emwas AH, Saccenti E, Gao X, McKay RT, dos Santos VAPM, Roy R, Wishart DS. Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine. Metabolomics 2018; 14:31. [PMID: 29479299 PMCID: PMC5809546 DOI: 10.1007/s11306-018-1321-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 01/09/2018] [Indexed: 12/11/2022]
Abstract
1H NMR spectra from urine can yield information-rich data sets that offer important insights into many biological and biochemical phenomena. However, the quality and utility of these insights can be profoundly affected by how the NMR spectra are processed and interpreted. For instance, if the NMR spectra are incorrectly referenced or inconsistently aligned, the identification of many compounds will be incorrect. If the NMR spectra are mis-phased or if the baseline correction is flawed, the estimated concentrations of many compounds will be systematically biased. Furthermore, because NMR permits the measurement of concentrations spanning up to five orders of magnitude, several problems can arise with data analysis. For instance, signals originating from the most abundant metabolites may prove to be the least biologically relevant while signals arising from the least abundant metabolites may prove to be the most important but hardest to accurately and precisely measure. As a result, a number of data processing techniques such as scaling, transformation and normalization are often required to address these issues. Therefore, proper processing of NMR data is a critical step to correctly extract useful information in any NMR-based metabolomic study. In this review we highlight the significance, advantages and disadvantages of different NMR spectral processing steps that are common to most NMR-based metabolomic studies of urine. These include: chemical shift referencing, phase and baseline correction, spectral alignment, spectral binning, scaling and normalization. We also provide a set of recommendations for best practices regarding spectral and data processing for NMR-based metabolomic studies of biofluids, with a particular focus on urine.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, KAUST, Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Kingdom of Saudi Arabia
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, India
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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Hajjar D, Kremb S, Sioud S, Emwas AH, Voolstra CR, Ravasi T. Anti-cancer agents in Saudi Arabian herbals revealed by automated high-content imaging. PLoS One 2017; 12:e0177316. [PMID: 28609451 PMCID: PMC5469452 DOI: 10.1371/journal.pone.0177316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 04/25/2017] [Indexed: 12/14/2022] Open
Abstract
Natural products have been used for medical applications since ancient times. Commonly, natural products are structurally complex chemical compounds that efficiently interact with their biological targets, making them useful drug candidates in cancer therapy. Here, we used cell-based phenotypic profiling and image-based high-content screening to study the mode of action and potential cellular targets of plants historically used in Saudi Arabia’s traditional medicine. We compared the cytological profiles of fractions taken from Juniperus phoenicea (Arar), Anastatica hierochuntica (Kaff Maryam), and Citrullus colocynthis (Hanzal) with a set of reference compounds with established modes of action. Cluster analyses of the cytological profiles of the tested compounds suggested that these plants contain possible topoisomerase inhibitors that could be effective in cancer treatment. Using histone H2AX phosphorylation as a marker for DNA damage, we discovered that some of the compounds induced double-strand DNA breaks. Furthermore, chemical analysis of the active fraction isolated from Juniperus phoenicea revealed possible anti-cancer compounds. Our results demonstrate the usefulness of cell-based phenotypic screening of natural products to reveal their biological activities.
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Affiliation(s)
- Dina Hajjar
- KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stephan Kremb
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Salim Sioud
- Analytical Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul-Hamid Emwas
- NMR Core Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- * E-mail: (TR); (CRV)
| | - Timothy Ravasi
- KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- * E-mail: (TR); (CRV)
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Guo J, Shi Y, Xu C, Zhong R, Zhang F, Niu B, Wang J, Zhang T. Data on the optimization of a GC-MS procedure for the determination of total plasma myo-inositol. Data Brief 2016; 8:1040-3. [PMID: 27508261 PMCID: PMC4969248 DOI: 10.1016/j.dib.2016.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/07/2016] [Accepted: 07/13/2016] [Indexed: 11/18/2022] Open
Abstract
Myo-inositol (MI) is one of the stereoisomers of hexahydroxycyclohexane, which plays an important role in intracellular signal pathway. Derivatization is an indispensable step in both external and internal standard method during the chromatography-mass spectrometer (GC-MS) detection, as MI can't be ionized directly. It is valuable to optimize the derivative process and the detection volume for clinical detection. This article contains optimization data related to research publication "Quantification of plasma myo-inositol using gas chromatography-mass spectrometry" [1]. Here we introduce the data on the optimized derivatization volume, temperature, duration and the detection volume.
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Affiliation(s)
- Jin Guo
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yingfei Shi
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Chengbao Xu
- Chinese Academy of Inspection & Quarantine, Beijing 100023, China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Feng Zhang
- Chinese Academy of Inspection & Quarantine, Beijing 100023, China
| | - Bo Niu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
- Corresponding authors at: Capital Institute of Pediatrics, Beijing 100020, China. Fax: +86 010 85631504.Capital Institute of PediatricsBeijing100020China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
- Corresponding authors at: Capital Institute of Pediatrics, Beijing 100020, China. Fax: +86 010 85631504.Capital Institute of PediatricsBeijing100020China
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Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GAN, Raftery D, Steinbeck C, Salek RM, Wishart DS. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res 2016; 15:360-73. [PMID: 26745651 PMCID: PMC4865177 DOI: 10.1021/acs.jproteome.5b00885] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, KAUST , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus , Lucknow, Uttar Pradesh, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University , Bathurst, New South Wales, Australia
| | - Lorraine Brennan
- UCD Insitute of Food and Health, UCD , Belfield, Dublin, Ireland
| | - Leonardo Tenori
- FiorGen Foundation , 50019 Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Centro Risonanze Magnetiche - CERM, University of Florence , Florence, Italy
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio , Campinas, São Paulo, Brazil
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue, Seattle, Washington 98109, United States
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David S Wishart
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta, Canada
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