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Tritrakarn T, Takahashi M, Okamura T. Optimization of RF coil geometry for NMR/MRI applications using a genetic algorithm. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 362:107685. [PMID: 38636265 DOI: 10.1016/j.jmr.2024.107685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
A simulation method that employs a genetic algorithm (GA) for optimizing radio frequency (RF) coil geometry is developed to maximize signal intensity in nuclear magnetic resonance (NMR)/magnetic resonance imaging (MRI) applications. NMR/MRI has a wide range of applications, including medical imaging, and chemical and biological analysis to investigate the structure, dynamics, and interactions of molecules. However, NMR suffers from inherently low signal intensity, which depends on factors related to RF coil geometry. The investigation of coil geometry is crucial for improving signal intensity, leading to a reduction in the number of scans and a shorter total scan time. We have explored a better optimization method by modifying RF coil geometry to maximize signal intensity. The RF coil geometry comprises wire elements, each of which is a small vector representing the current flow, and GA chooses some of the prepared wire elements for optimization. The optimization of a substrate coil with a surface perpendicular to a static field was demonstrated for single-sided NMR system applications while considering various cylindrical sample diameters. A non-optimized and a GA-optimized substrate coil were compared through simulation and experiment to confirm the performance of the GA simulation. The maximum error between simulation and experiment was below 5%, with an average of less than 3%, confirming simulation reliability. The results indicated that the GA improved signal intensity by approximately 10% and reduced the necessary total scan time by around 20%. Finally, we explain the limitations and explore other potential applications of this GA-based simulation method.
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Affiliation(s)
- Techit Tritrakarn
- School of Engineering, Department of Mechanical Engineering, Tokyo Institute of Technology, 4259 Nagatusta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan.
| | - Masato Takahashi
- Laboratory for Advanced NMR Application and Development, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuji Okamura
- School of Engineering, Department of Mechanical Engineering, Tokyo Institute of Technology, 4259 Nagatusta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
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Uchimiya M, Olofsson M, Powers MA, Hopkinson BM, Moran MA, Edison AS. 13C NMR metabolomics: J-resolved STOCSY meets INADEQUATE. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 347:107365. [PMID: 36634594 DOI: 10.1016/j.jmr.2022.107365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Robust annotation of metabolites is a challenging task in metabolomics. Among available applications, 13C NMR experiment INADEQUATE determines direct 13C-13C connectivity unambiguously, offering indispensable information on molecular structure. Despite its great utility, it is not always practical to collect INADEQUATE data on every sample in a large metabolomics study because of its relatively long experiment time. Here, we propose an alternative approach that maintains the quality of information but saves experiment time. In this approach, individual samples in a study are first screened by 13C homonuclear J-resolved experiment (JRES). Next, JRES data are processed by statistical total correlation spectroscopy (STOCSY) to extract peaks that behave similarly among samples. Finally, INADEQUATE is collected on one internal pooled sample to select STOCSY peaks that originate from the same compound. We tested this concept using the 13C-labeled endometabolome of a model marine diatom strain incubated under various settings, intending to cover a range of metabolites produced under different external conditions. This scheme was able to extract known diatom metabolites proline, 2,3-dihydroxypropane-1-sulfonate (DHPS), β-1,3-glucan, choline, and glutamate. This pipeline also detected unknown compounds with structural information, which is valuable in metabolomics where a priori knowledge of metabolites is not always available. The ability of this scheme was seen even in sugar regions, which are usually challenging in 1H NMR due to severe peak overlap. JRES and INADEQUATE were highly complementary; INADEQUATE provided directly-bonded 13C networks, whereas JRES linked INADEQUATE networks within the same compound but broken by nitrogen or sulfur atoms, highlighting the advantage of this integrated approach.
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Affiliation(s)
- Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Malin Olofsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Sweden; Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - McKenzie A Powers
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Arthur S Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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Wishart DS, Cheng LL, Copié V, Edison AS, Eghbalnia HR, Hoch JC, Gouveia GJ, Pathmasiri W, Powers R, Schock TB, Sumner LW, Uchimiya M. NMR and Metabolomics-A Roadmap for the Future. Metabolites 2022; 12:678. [PMID: 35893244 PMCID: PMC9394421 DOI: 10.3390/metabo12080678] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
Metabolomics investigates global metabolic alterations associated with chemical, biological, physiological, or pathological processes. These metabolic changes are measured with various analytical platforms including liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). While LC-MS methods are becoming increasingly popular in the field of metabolomics (accounting for more than 70% of published metabolomics studies to date), there are considerable benefits and advantages to NMR-based methods for metabolomic studies. In fact, according to PubMed, more than 926 papers on NMR-based metabolomics were published in 2021-the most ever published in a given year. This suggests that NMR-based metabolomics continues to grow and has plenty to offer to the scientific community. This perspective outlines the growing applications of NMR in metabolomics, highlights several recent advances in NMR technologies for metabolomics, and provides a roadmap for future advancements.
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Affiliation(s)
- David S. Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Leo L. Cheng
- Department of Pathology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715, USA;
| | - Arthur S. Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (A.S.E.); (G.J.G.); (M.U.)
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602-0001, USA
| | - Hamid R. Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA; (H.R.E.); (J.C.H.)
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA; (H.R.E.); (J.C.H.)
| | - Goncalo J. Gouveia
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (A.S.E.); (G.J.G.); (M.U.)
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602-0001, USA
| | - Wimal Pathmasiri
- Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Tracey B. Schock
- National Institute of Standards and Technology (NIST), Chemical Sciences Division, Charleston, SC 29412, USA;
| | - Lloyd W. Sumner
- Interdisciplinary Plant Group, MU Metabolomics Center, Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (A.S.E.); (G.J.G.); (M.U.)
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Johnston TL, Edison AS, Ramaswamy V, Freytag N, Merritt ME, Thomas JN, Hooker JW, Litvak IM, Brey WW. Application of Counter-wound Multi-arm Spirals in HTS Resonator Design. IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY : A PUBLICATION OF THE IEEE SUPERCONDUCTIVITY COMMITTEE 2022; 32:1500304. [PMID: 35449718 PMCID: PMC9017787 DOI: 10.1109/tasc.2022.3146109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Significant sensitivity improvements have been achieved by utilizing high temperature superconducting (HTS) resonators in nuclear magnetic resonance (NMR) probes. Many nuclei such as 13C benefit from strong excitation fields which cannot be produced by traditional HTS resonator designs. We investigate the use of double-sided, counter-wound multi-arm spiral HTS resonators with the aim of increasing the excitation field at the required nuclear Larmor frequency for 13C. When compared to double-sided, counter-wound spiral resonators with similar geometry, simulations indicate that the multi-arm spiral version develops a more uniform current distribution. Preliminary tests of a two-arm resonator indicate that it may produce a stronger excitation field.
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Affiliation(s)
- Taylor L Johnston
- National High Magnetic Laboratory, Tallahassee, FL 32310, USA and also with the Department of Chemistry and Biochemistry, Florida State University
| | | | | | | | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32601, USA
| | - Jeremy N Thomas
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA and also with the Department of Physics, Florida State University
| | - Jerris W Hooker
- Department of Electrical and Computer Engineering, FAMU-FSU College of Engineering, Tallahassee, FL 32310, USA
| | - Ilya M Litvak
- National High Magnetic Laboratory, Tallahassee, FL 32310, USA and also with Florida State University
| | - William W Brey
- National High Magnetic Laboratory, Tallahassee, FL 32310, USA and also with Florida State University
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