51
|
Miller ADC, Chowdhury SP, Hanson HW, Linderman SK, Ghasemi HI, Miller WD, Morrissey MA, Richardson CD, Gardner BM, Mukherjee A. Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types. J Biol Eng 2024; 18:30. [PMID: 38649904 PMCID: PMC11035135 DOI: 10.1186/s13036-024-00424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
Collapse
Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hadley W Hanson
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Sarah K Linderman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Wyatt D Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Meghan A Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Arnab Mukherjee
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Bioengineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemistry, University of California, Santa Barbara, CA, 93106, USA.
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.
| |
Collapse
|
52
|
Herold D, Brauser M, Kind J, Thiele CM. Evolution of a Combined UV/Vis and NMR Setup with Fixed Pathlengths for Mass-limited Samples. Chemistry 2024; 30:e202304016. [PMID: 38360972 DOI: 10.1002/chem.202304016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/17/2024]
Abstract
The investigation of reaction mechanisms is a complex task that usually requires the use of several techniques. To obtain as much information as possible on the reaction and any intermediates - possibly invisible to one technique - the combination of techniques is a solution. In this work we present a new setup for combined UV/Vis and NMR spectroscopy and compare it to an established alternative. The presented approach allows a versatile usage of different commercially-available components like mirrors and fiber bundles as well as different fixed pathlengths according to double transmission or single transmission measurements. While a previous approach is based on a dip-probe setup for conventional NMR probes, the new one is based on a micro-Helmholtz coil array (LiquidVoxel™). This makes the use of rectangular cuvettes possible, which ensure well-defined pathlengths allowing for quantification of species. Additionally, very low quantities of compound can be analyzed due to the microfabrication and small cuvette size used. As proof-of-principle this new setup for combined UV/Vis and NMR spectroscopy is used to examine a well-studied photochromic system of the dithienylethene compound class. A thorough comparison of the pros and cons of the two setups for combined UV/Vis and NMR measurements is performed.
Collapse
Affiliation(s)
- Dominik Herold
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| | - Matthias Brauser
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| | - Jonas Kind
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| | - Christina M Thiele
- Technische Universität Darmstadt/Technical University of Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie/Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt, D-64289, Germany
| |
Collapse
|
53
|
Meyer N, Torrent J, Balme S. Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches. Small Methods 2024:e2400058. [PMID: 38644684 DOI: 10.1002/smtd.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/10/2024] [Indexed: 04/23/2024]
Abstract
Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.
Collapse
Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
| |
Collapse
|
54
|
Ma YY, Lu ZL, Xing YZ, Zheng WS, Liu CG. A fresh perspective on dissociation mechanism of cellulose in DMAc/LiCl system based on Li bond theory. Int J Biol Macromol 2024; 268:131729. [PMID: 38653429 DOI: 10.1016/j.ijbiomac.2024.131729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/06/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
In this case, various characterization technologies have been employed to probe dissociation mechanism of cellulose in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl) system. These results indicate that coordination of DMAc ligands to the Li+-Cl- ion pair results in the formation of a series of Lix(DMAc)yClz (x = 1, 2; y = 1, 2, 3, 4; z = 1, 2) complexes. Analysis of interaction between DMAc ligand and Li center indicate that Li bond plays a major role for the formation of these Lix(DMAc)yClz complexes. And the saturation and directionality of Li bond in these Lix(DMAc)yClz complexes are found to be a tetrahedral structure. The hydrogen bonds between two cellulose chains could be broken at the nonreduced end of cellulose molecule via combined effects of basicity of Cl- ion and steric hindrance of [Li (DMAc)4]+ unit. The unique feature of Li bond in Lix(DMAc)yClz complexes is a key factor in determination of the dissociation mechanism.
Collapse
Affiliation(s)
- Yi-Ying Ma
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City 132013, PR China
| | - Ze-Long Lu
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City 132013, PR China
| | - Yun-Zhu Xing
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City 132013, PR China
| | - Wei-Shi Zheng
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City 132013, PR China
| | - Chun-Guang Liu
- Department of Chemistry, Faculty of Science, Beihua University, Jilin City 132013, PR China.
| |
Collapse
|
55
|
Zhang C, Jerschow A. Range and sensitivity of 17O nuclear spin-lattice relaxation as a probe of aqueous electrolyte dynamics. J Chem Phys 2024; 160:154501. [PMID: 38624124 DOI: 10.1063/5.0196494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
The study of electrolytic solutions is of relevance in many research fields, ranging from biophysics, materials, and colloid science to catalysis and electrochemistry. The dependence of solution dynamics on the nature of electrolytes and their concentrations has been the subject of many experimental and computational studies, yet it remains challenging to obtain a full understanding of the factors that govern solution behavior. Here, we provide additional insights into the behavior of aqueous solutions of alkali chlorides by combining 17O relaxation data with diffusion and viscosity data and contrast their behavior with 1H nuclear magnetic resonance relaxation data. The main findings are that 17O relaxation correlates well with viscosity data but not with diffusion data, while 1H relaxation correlates with neither. Certain ionic trends match known ion-specific series behavior, especially at high concentrations. Notably, we also examine the ranges of the interactions and conclude that the majority of the effects are tied to local water reorientation dynamics.
Collapse
Affiliation(s)
- Chengtong Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
| | - Alexej Jerschow
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
| |
Collapse
|
56
|
Nguyen HL, Crowhurst KA. Solution NMR chemical shift assignment of apo and molybdate-bound ModA at two pHs. Biomol NMR Assign 2024:10.1007/s12104-024-10173-7. [PMID: 38642264 DOI: 10.1007/s12104-024-10173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Abstract
ModA is a soluble periplasmic molybdate-binding protein found in most gram-negative bacteria. It is part of the ABC transporter complex ModABC that moves molybdenum into the cytoplasm, to be used by enzymes that carry out various redox reactions. Since there is no clear analog for ModA in humans, this protein could be a good target for antibacterial drug design. Backbone 1H, 13C and 15N chemical shifts of apo and molybdate-bound ModA from E. coli were assigned at pHs 6.0 and 4.5. In addition, side chain atoms were assigned for apo ModA at pH 6.0. When comparing apo and molybdate-bound ModA at pH 6.0, large chemical shift perturbations are observed, not only in areas near the bound metal, but also in regions that are distant from the metal-binding site. Given the significant conformational change between apo and holo ModA, we might expect the large chemical shift changes to be more widespread; however, since they are limited to specific regions, the residues with large perturbations may reveal allosteric sites that could ultimately be important for the design of antibiotics that target ModA.
Collapse
Affiliation(s)
- Hiep Ld Nguyen
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA, 91330-8262, USA
| | - Karin A Crowhurst
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA, 91330-8262, USA.
| |
Collapse
|
57
|
Hoffmann E, Masthoff M, Kunz WG, Seidensticker M, Bobe S, Gerwing M, Berdel WE, Schliemann C, Faber C, Wildgruber M. Multiparametric MRI for characterization of the tumour microenvironment. Nat Rev Clin Oncol 2024:10.1038/s41571-024-00891-1. [PMID: 38641651 DOI: 10.1038/s41571-024-00891-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Our understanding of tumour biology has evolved over the past decades and cancer is now viewed as a complex ecosystem with interactions between various cellular and non-cellular components within the tumour microenvironment (TME) at multiple scales. However, morphological imaging remains the mainstay of tumour staging and assessment of response to therapy, and the characterization of the TME with non-invasive imaging has not yet entered routine clinical practice. By combining multiple MRI sequences, each providing different but complementary information about the TME, multiparametric MRI (mpMRI) enables non-invasive assessment of molecular and cellular features within the TME, including their spatial and temporal heterogeneity. With an increasing number of advanced MRI techniques bridging the gap between preclinical and clinical applications, mpMRI could ultimately guide the selection of treatment approaches, precisely tailored to each individual patient, tumour and therapeutic modality. In this Review, we describe the evolving role of mpMRI in the non-invasive characterization of the TME, outline its applications for cancer detection, staging and assessment of response to therapy, and discuss considerations and challenges for its use in future medical applications, including personalized integrated diagnostics.
Collapse
Affiliation(s)
- Emily Hoffmann
- Clinic of Radiology, University of Münster, Münster, Germany
| | - Max Masthoff
- Clinic of Radiology, University of Münster, Münster, Germany
| | - Wolfgang G Kunz
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Max Seidensticker
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Stefanie Bobe
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Mirjam Gerwing
- Clinic of Radiology, University of Münster, Münster, Germany
| | | | | | - Cornelius Faber
- Clinic of Radiology, University of Münster, Münster, Germany
| | - Moritz Wildgruber
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany.
| |
Collapse
|
58
|
Mukherjee K, Palchowdhury S, Maroncelli M. Do Electrostatics Control the Diffusive Dynamics of Solitary Water? NMR and MD Studies of Water Translation and Rotation in Dipolar and Ionic Solvents. J Phys Chem B 2024; 128:3689-3706. [PMID: 38588535 DOI: 10.1021/acs.jpcb.3c08300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
NMR-based measurements of the diffusion coefficients and rotation times of solitary water and benzene at 300 K are reported in a diverse collection of 13 conventional organic solvents and 10 imidazolium ionic liquids. Proton chemical shifts of water are found to be correlated to water OH-stretching frequencies, confirming the importance of electrostatic interactions in these shifts. However, the influence of magnetic interactions in aromatic solvents renders chemical shifts a less reliable indicator of electrostatics. Diffusion coefficients (DB) and rotational correlation times (τB) of benzene in the solvents examined are accurately described as functions of viscosity (η) by DB ∝ η-0.81 and τB ∝ η0.64. Literature values of DB and τB in alkane and normal alcohols, which were not included among the solvents studied here, are systematically faster than predicted by these correlations, indicating that factors beyond solvent viscosity play a role in determining the friction on benzene. In contrast to benzene, water diffusion and rotation are poorly described in terms of viscosity alone, even in the dipolar and ionic solvents measured here. The present data and the substantial literature data already available on dilute water diffusion show a systematic dependence of DW on solvent polarity among isoviscous solvents. The aspect of solvent polarity most relevant to water dynamics is the ability of a solvent to accept hydrogen bonds from water, as conveniently quantified by the frequency of water's OH stretching band, ΔνOH. The friction on translation, ζtr = kBT/DW, and rotation, ζrot = kBTτW, are both well correlated by functions of the form ζ(η, ΔνOH) = a1ηa2 exp (a3ΔνOH), where the ai are adjustable parameters. Molecular dynamics simulations reveal a strong coupling between electrostatic and nonelectrostatic water-solvent interactions, which makes it impossible to dissect the friction on water into additive dielectric and hydrodynamic components. Simulations also provide a tentative explanation for the unusual form of the correlating function ζ(η, ΔνOH), at least in the case of ζrot.
Collapse
Affiliation(s)
- Kallol Mukherjee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sourav Palchowdhury
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mark Maroncelli
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
59
|
Fu R, Ramamoorthy A. 17O Solid-State NMR Spectroscopy of Lipid Membranes. J Phys Chem B 2024; 128:3527-3537. [PMID: 38568422 DOI: 10.1021/acs.jpcb.4c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Despite the limitations posed by poor sensitivity, studies have reported the unique advantages of 17O based NMR spectroscopy to study systems existing in liquid, solid, or semisolid states. 17O NMR studies have exploited the remarkable sensitivity of quadrupole coupling and chemical shift anisotropy tensors to the local environment in the characterization of a variety of intra- and intermolecular interactions and motion. Recent studies have considerably expanded the use of 17O NMR to study dynamic intermolecular interactions associated with some of the challenging biological systems under magic angle spinning (MAS) and aligned conditions. The very fast relaxing nature of 17O has been well utilized in cellular and in vivo MRS (magnetic resonance spectroscopy) and MRI (magnetic resonance imaging) applications. The main focus of this Review is to highlight the new developments in the biological solids with a detailed discussion for a few selected examples including membrane proteins and nanodiscs. In addition to the unique benefits and limitations, the remaining challenges to overcome, and the impacts of higher magnetic fields and sensitivity enhancement techniques are discussed.
Collapse
Affiliation(s)
- Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Ayyalusamy Ramamoorthy
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32310, United States
| |
Collapse
|
60
|
Dong Y, Li M, Kang L, Wang W, Li Z, Wang Y, Wu Z, Zhu C, Zhu L, Zheng X, Qian D, Dai H, Wu B, Zhao H, Wang J. A new preparation method of covalent annular nanodiscs based on MTGase. Arch Biochem Biophys 2024; 756:109997. [PMID: 38621443 DOI: 10.1016/j.abb.2024.109997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/11/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The preservation of the native conformation and functionality of membrane proteins has posed considerable challenges. While detergents and liposome reconstitution have been traditional approaches, nanodiscs (NDs) offer a promising solution by embedding membrane proteins in phospholipids encircled by an amphipathic helical protein MSP belt. Nevertheless, a drawback of commonly used NDs is their limited homogeneity and stability. In this study, we present a novel approach to construct covalent annular nanodiscs (cNDs) by leveraging microbial transglutaminase (MTGase) to catalyze isopeptide bond formation between the side chains of terminal amino acids, specifically Lysine (K) and Glutamine (Q). This methodology significantly enhances the homogeneity and stability of NDs. Characterization of cNDs and the assembly of membrane proteins within them validate the successful reconstitution of membrane proteins with improved homogeneity and stability. Our findings suggest that cNDs represent a more suitable tool for investigating interactions between membrane proteins and lipids, as well as for analyzing membrane protein structures.
Collapse
Affiliation(s)
- Yingkui Dong
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230039, China; High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Ming Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Li Kang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230039, China; High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Wanxue Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Zehua Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yizhuo Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Ziwei Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Chenchen Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Lei Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Xinwei Zheng
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Dongming Qian
- Hefei China Science Longwood Biological Technology Co., Ltd. Hefei, Anhui, 230088, China
| | - Han Dai
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; Hefei China Science Longwood Biological Technology Co., Ltd. Hefei, Anhui, 230088, China
| | - Bo Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China.
| | - Hongxin Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; Hefei China Science Longwood Biological Technology Co., Ltd. Hefei, Anhui, 230088, China.
| | - Junfeng Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230039, China; High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China.
| |
Collapse
|
61
|
Rotzinger M, Schuster N, Zangger K. Identifying Exchangeable Protons in a 1D NMR Spectrum by Spatially Selective Exchange-Editing. Chemphyschem 2024; 25:e202300713. [PMID: 38407996 DOI: 10.1002/cphc.202300713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
Signals undergoing chemical or conformational exchange in one-dimensional NMR spectra are often identified by deuterium exchange. In order to obtain quantitative information about the dynamic processes involved, one frequently used method is EXchange SpectroscopY (EXSY). To detect all exchange processes, the EXSY experiment requires the acquisition of time-consuming two-dimensional spectra. Here we report a faster alternative, an experiment which uses spatial encoding to extract similar information in a 1D exchange-edited experiment. Thereby, all protons are observed at once, but in different slices of the detection volume. The experiment can be carried out in a single scan to identify exchanging sites in a 1D spectrum by changes in signal intensity indicating exchange processes. If the exchanging partner, for example water is in molar excess the exchange-editing method easily identifies mobile protons by negative signals in the 1D 1H NMR spectrum.
Collapse
Affiliation(s)
- Markus Rotzinger
- University of Graz, Institute of Chemistry, Heinrichstraße 28, 8010, Graz, Austria
| | - Nathalie Schuster
- University of Graz, Institute of Chemistry, Heinrichstraße 28, 8010, Graz, Austria
| | - Klaus Zangger
- University of Graz, Institute of Chemistry, Heinrichstraße 28, 8010, Graz, Austria
| |
Collapse
|
62
|
Qiu Y, Dai K, Zhong S, Chen S, Wang C, Chen H, Frydman L, Zhang Z. Spatiotemporal encoding MRI in a portable low-field system. Magn Reson Med 2024. [PMID: 38623991 DOI: 10.1002/mrm.30104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
PURPOSE Demonstrate the potential of spatiotemporal encoding (SPEN) MRI to deliver largely undistorted 2D, 3D, and diffusion weighted images on a 110 mT portable system. METHODS SPEN's quadratic phase modulation was used to subsample the low-bandwidth dimension of echo planar acquisitions, delivering alias-free images with an enhanced immunity to image distortions in a laboratory-built, low-field, portable MRI system lacking multiple receivers. RESULTS Healthy brain images with different SPEN time-bandwidth products and subsampling factors were collected. These compared favorably to EPI acquisitions including topup corrections. Robust 3D and diffusion weighted SPEN images of diagnostic value were demonstrated, with 2.5 mm isotropic resolutions achieved in 3 min scans. This performance took advantage of the low specific absorption rate and relative long TEs associated with low-field MRI. CONCLUSION SPEN MRI provides a robust and advantageous fast acquisition approach to obtain faithful 3D images and DWI data in low-cost, portable, low-field systems without parallel acceleration.
Collapse
Affiliation(s)
- Yueqi Qiu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ke Dai
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Sijie Zhong
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Suen Chen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Changyue Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hao Chen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Zhiyong Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| |
Collapse
|
63
|
Sakhaii P, Bohorc B, Schliedermann U, Griesinger C. Efficient Access to Elusive 1D 13C NMR Spectra through Highly Resolved 1H, 13C-Long-Range Correlation Spectroscopy. Anal Chem 2024; 96:5843-5851. [PMID: 38452395 DOI: 10.1021/acs.analchem.3c05277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
A method for obtaining 1D 13C NMR spectra from natural products or metabolites using proton detection is described. The approach delivers singlets for every 13C signal without conducting any broadband 1H decoupling (CPD) and is based on calculating 13C projections from constant-time HMBC and conventional HSQC experiments, recorded at high digital resolution and processed to pure phases. Paramount to the proposed method is the implication of nonuniform sampling and echo processing. The echo processing produces phase-sensitive 2D CT-HMBC spectra with narrow 13C signal line shapes. Two simple HMBC pulse sequences are utilized with the suppression of homo- and heteronuclear couplings. Due to the removal of the 1H multiplet structure in F1 (no tilt at higher digital resolution), 13C singlets arise. An overall increase in 13C signal-to-noise (SINO) for all types of carbon multiplicities is observed, making the proposed technique superior compared to direct 13C excitation. For otherwise difficult-to-measure quaternary carbon atoms, a SINO enhancement of up to 6 and 12 depending on F1 resolution (3 and 6 Hz/point) is reported. Echo/anti-Echo signal detection cleans up the spectrum. Nonuniform sampling (NUS) lays the groundwork to significantly reduce the total acquisition time. Final 1D 13C projections are obtained by combining the 13C projection from CT HMBC and conventional HSQC. This orthogonal concept of combining the 13C projections from different spectra inherently minimizes the risk of missing 13C cross-peaks by inappropriate setting of long-range nJHC coupling delays and the shortcoming of T2 relaxations. The advantages and some limitations of the concept are discussed.
Collapse
Affiliation(s)
- Peyman Sakhaii
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926 Frankfurt/Main, Germany
| | - Bojan Bohorc
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926 Frankfurt/Main, Germany
| | - Uwe Schliedermann
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926 Frankfurt/Main, Germany
| | - Christian Griesinger
- NMR-Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| |
Collapse
|
64
|
Shao HC, Mengke T, Deng J, Zhang Y. 3D cine-magnetic resonance imaging using spatial and temporal implicit neural representation learning (STINR-MR). Phys Med Biol 2024; 69:095007. [PMID: 38479004 PMCID: PMC11017162 DOI: 10.1088/1361-6560/ad33b7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/27/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Objective. 3D cine-magnetic resonance imaging (cine-MRI) can capture images of the human body volume with high spatial and temporal resolutions to study anatomical dynamics. However, the reconstruction of 3D cine-MRI is challenged by highly under-sampled k-space data in each dynamic (cine) frame, due to the slow speed of MR signal acquisition. We proposed a machine learning-based framework, spatial and temporal implicit neural representation learning (STINR-MR), for accurate 3D cine-MRI reconstruction from highly under-sampled data.Approach. STINR-MR used a joint reconstruction and deformable registration approach to achieve a high acceleration factor for cine volumetric imaging. It addressed the ill-posed spatiotemporal reconstruction problem by solving a reference-frame 3D MR image and a corresponding motion model that deforms the reference frame to each cine frame. The reference-frame 3D MR image was reconstructed as a spatial implicit neural representation (INR) network, which learns the mapping from input 3D spatial coordinates to corresponding MR values. The dynamic motion model was constructed via a temporal INR, as well as basis deformation vector fields (DVFs) extracted from prior/onboard 4D-MRIs using principal component analysis. The learned temporal INR encodes input time points and outputs corresponding weighting factors to combine the basis DVFs into time-resolved motion fields that represent cine-frame-specific dynamics. STINR-MR was evaluated using MR data simulated from the 4D extended cardiac-torso (XCAT) digital phantom, as well as two MR datasets acquired clinically from human subjects. Its reconstruction accuracy was also compared with that of the model-based non-rigid motion estimation method (MR-MOTUS) and a deep learning-based method (TEMPEST).Main results. STINR-MR can reconstruct 3D cine-MR images with high temporal (<100 ms) and spatial (3 mm) resolutions. Compared with MR-MOTUS and TEMPEST, STINR-MR consistently reconstructed images with better image quality and fewer artifacts and achieved superior tumor localization accuracy via the solved dynamic DVFs. For the XCAT study, STINR reconstructed the tumors to a mean ± SD center-of-mass error of 0.9 ± 0.4 mm, compared to 3.4 ± 1.0 mm of the MR-MOTUS method. The high-frame-rate reconstruction capability of STINR-MR allows different irregular motion patterns to be accurately captured.Significance. STINR-MR provides a lightweight and efficient framework for accurate 3D cine-MRI reconstruction. It is a 'one-shot' method that does not require external data for pre-training, allowing it to avoid generalizability issues typically encountered in deep learning-based methods.
Collapse
Affiliation(s)
- Hua-Chieh Shao
- The Medical Artificial Intelligence and Automation (MAIA) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States of America
| | - Tielige Mengke
- The Medical Artificial Intelligence and Automation (MAIA) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States of America
| | - Jie Deng
- The Medical Artificial Intelligence and Automation (MAIA) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States of America
| | - You Zhang
- The Medical Artificial Intelligence and Automation (MAIA) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States of America
| |
Collapse
|
65
|
Dal Poggetto G, DiCaprio A, Reibarkh M, Cohen RD. Ultra-clean pure shift NMR with optimal water suppression for analysis of aqueous pharmaceutical samples. Analyst 2024; 149:2227-2231. [PMID: 38517550 DOI: 10.1039/d3an02150e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Pure shift NMR experiments greatly enhance spectral resolution by collapsing multiplet structures into singlets and, with water suppression, can be used for aqueous samples. Here, we combine ultra-clean pure-shift NMR (SAPPHIRE) with two different internally encoded water suppression schemes to achieve optimal performance for small molecule and macrocyclic peptide pharmaceuticals in water and acetonitrile-water mixtures.
Collapse
Affiliation(s)
| | - Adam DiCaprio
- Merck & Co., Inc., 770 Sumneytown Pike, 19846, West Point, PA, USA
| | - Mikhail Reibarkh
- Merck & Co., Inc., 126 East Lincoln Avenue, 07065, Rahway, NJ, USA.
| | - Ryan D Cohen
- Merck & Co., Inc., 126 East Lincoln Avenue, 07065, Rahway, NJ, USA.
| |
Collapse
|
66
|
Yousf S, Batra HS, Jha RM, Sardesai DM, Ananthamohan K, Chugh J, Sharma S. Identification of potential serum biomarkers associated with HbA1c levels in Indian type 2 diabetic subjects using NMR-based metabolomics. Clin Chim Acta 2024; 557:117857. [PMID: 38484908 DOI: 10.1016/j.cca.2024.117857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND The prevalence of type 2 diabetes mellitus (T2DM), a progressive metabolic disorder characterized by chronic hyperglycemia and the development of insulin resistance, has increased globally, with worrying statistics coming from children, adolescents, and young adults from developing countries like India. Here, we investigated unique circulating metabolic signatures associated with prediabetes and T2DM in an Indian cohort using NMR-based metabolomics. MATERIALS AND METHODS The study subjects included healthy volunteers (N = 101), prediabetic subjects (N = 75), and T2DM patients (N = 108). Serum metabolic profiling was performed using 1H NMR spectroscopy and major perturbed metabolites were identified by multivariate analysis and receiver operating characteristic (ROC) modules. RESULTS Of the 36 aqueous abundant metabolites, 24 showed a statistically significant difference between healthy volunteers, prediabetics, and established T2DM subjects. On performing multivariate ROC curve analysis with 5 commonly dysregulated metabolites (namely, glucose, pyroglutamate, o-phosphocholine, serine, and methionine) in prediabetes and T2DM, AUC values obtained were 0.96 (95 % confidence interval (CI) = 0.93, 0.98) for T2DM; and 0.88 (95 % CI = 0.81, 0.93) for prediabetic subjects, respectively. CONCLUSION We propose that the identified metabolite panel can be used in the future as a biomarker for clinical diagnosis, patient surveillance, and for predicting individuals at risk for developing diabetes.
Collapse
Affiliation(s)
- Saleem Yousf
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India; Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hitender S Batra
- Department of Biochemistry, Armed Forces Medical College (AFMC), Wanowrie, Pune 411040, India; Department of Biochemistry, Symbiosis Medical College for Women, Pune 412115, India.
| | - Rakesh M Jha
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Devika M Sardesai
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Kalyani Ananthamohan
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
| | - Shilpy Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India.
| |
Collapse
|
67
|
Sheberstov KF, Sonnefeld A, Bodenhausen G. Collective long-lived zero-quantum coherences in aliphatic chains. J Chem Phys 2024; 160:144308. [PMID: 38602293 DOI: 10.1063/5.0196808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
In nuclear magnetic resonance, long-lived coherences constitute a class of zero-quantum (ZQ) coherences that have lifetimes that can be longer than the relaxation lifetimes T2 of transverse magnetization. So far, such coherences have been observed in systems with two coupled spins with spin quantum numbers I = 1/2, where a term S0T0+T0S0 in the density operator corresponds to a coherent superposition between the singlet S0 and the central triplet T0 state. Here, we report on the excitation and detection of collective long-lived coherences in AA'MM'XX' spin systems in molecules containing a chain of at least three methylene (-CH2-) groups. Several variants of excitation by polychromatic spin-lock induced crossing (poly-SLIC) are introduced that can excite a non-uniform distribution of the amplitudes of terms such as S0S0T0S0S0T0, S0T0S0S0T0S0, and T0S0S0T0S0S0. Once the radio frequency fields are switched off, these are not eigenstates, leading to ZQ precession involving all six protons, a process that can be understood as a propagation of spin order along the chain of CH2 groups before the reconversion into observable magnetization by a second poly-SLIC pulse that can be applied to any one or several of the CH2 groups. In the resulting 2D spectra, the ω2 domain shows SQ spectra with the chemical shifts of the CH2 groups irradiated during the reconversion, while the ω1 dimension shows ZQ signals in absorption mode with linewidths on the order of 0.1 Hz that are not affected by the inhomogeneity of the static magnetic field but can be broadened by chemical exchange as occurs in drug screening. The ZQ frequencies are primarily determined by differences ΔJ between vicinal J-couplings.
Collapse
Affiliation(s)
- Kirill F Sheberstov
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Anna Sonnefeld
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Geoffrey Bodenhausen
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| |
Collapse
|
68
|
Leal Auccaise AC, Masiewicz E, Kolodziejski K, Kruk D. Dynamic of binary molecular systems-Advantages and limitations of NMR relaxometry. J Chem Phys 2024; 160:144116. [PMID: 38606737 DOI: 10.1063/5.0188257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
1H spin-lattice relaxation studies have been performed for binary systems, including glycerol as the first component and alanine, glycine, and aspartic acid (with different levels of deuteration) as the second one. The relaxation studies have been performed in the frequency range from 10 kHz to 10 MHz vs temperature. A theoretical framework, including all relevant 1H-1H and 1H-2H relaxation pathways, has been formulated. The theory has been exploited for a thorough interpretation of a large set of the experimental data. The importance of the 1H-2H relaxation contributions has been discussed, and the possibility of revealing dynamical properties of individual liquid components in binary liquids has been carefully investigated. As far as the dynamical properties of the specific binary liquids, chosen as an example, are considered, it has been shown that in the presence of the second component (alanine, glycine, and aspartic acid), both molecular fractions undergo dynamics similar to that of glycerol in bulk.
Collapse
Affiliation(s)
- Adriane Consuelo Leal Auccaise
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Elzbieta Masiewicz
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Karol Kolodziejski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Danuta Kruk
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
| |
Collapse
|
69
|
Berto RP, Bugler H, Dias G, Oliveira M, Ueda L, Dertkigil S, Costa PDP, Rittner L, Merkofer JP, van de Sande DMJ, Amirrajab S, Drenthen GS, Veta M, Jansen JFA, Breeuwer M, van Sloun RJG, Qayyum A, Rodero C, Niederer S, Souza R, Harris AD. Results of the 2023 ISBI challenge to reduce GABA-edited MRS acquisition time. MAGMA 2024:10.1007/s10334-024-01156-9. [PMID: 38613715 DOI: 10.1007/s10334-024-01156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
PURPOSE Use a conference challenge format to compare machine learning-based gamma-aminobutyric acid (GABA)-edited magnetic resonance spectroscopy (MRS) reconstruction models using one-quarter of the transients typically acquired during a complete scan. METHODS There were three tracks: Track 1: simulated data, Track 2: identical acquisition parameters with in vivo data, and Track 3: different acquisition parameters with in vivo data. The mean squared error, signal-to-noise ratio, linewidth, and a proposed shape score metric were used to quantify model performance. Challenge organizers provided open access to a baseline model, simulated noise-free data, guides for adding synthetic noise, and in vivo data. RESULTS Three submissions were compared. A covariance matrix convolutional neural network model was most successful for Track 1. A vision transformer model operating on a spectrogram data representation was most successful for Tracks 2 and 3. Deep learning (DL) reconstructions with 80 transients achieved equivalent or better SNR, linewidth and fit error compared to conventional 320 transient reconstructions. However, some DL models optimized linewidth and SNR without actually improving overall spectral quality, indicating a need for more robust metrics. CONCLUSION DL-based reconstruction pipelines have the promise to reduce the number of transients required for GABA-edited MRS.
Collapse
Affiliation(s)
- Rodrigo Pommot Berto
- Department of Biomedical Engineering, University of Calgary, Calgary, Canada
- Department of Radiology, University of Calgary, Calgary, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Hanna Bugler
- Department of Biomedical Engineering, University of Calgary, Calgary, Canada.
- Department of Radiology, University of Calgary, Calgary, Canada.
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Gabriel Dias
- School of Electrical and Computer Engineering, University of Campinas, Campinas, Brazil
| | - Mateus Oliveira
- School of Electrical and Computer Engineering, University of Campinas, Campinas, Brazil
| | - Lucas Ueda
- School of Electrical and Computer Engineering, University of Campinas, Campinas, Brazil
- Research and Development Center in Telecommunications, CPQD, Campinas, Brazil
| | - Sergio Dertkigil
- School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Paula D P Costa
- School of Electrical and Computer Engineering, University of Campinas, Campinas, Brazil
- Artificial Intelligence Lab., Recod.Ai, University of Campinas, Campinas, Brazil
| | - Leticia Rittner
- School of Electrical and Computer Engineering, University of Campinas, Campinas, Brazil
| | - Julian P Merkofer
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dennis M J van de Sande
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Sina Amirrajab
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Gerhard S Drenthen
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, Netherlands
| | - Mitko Veta
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jacobus F A Jansen
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, Netherlands
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Marcel Breeuwer
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- MR R&D-Clinical Science, Philips Healthcare, Best, Netherlands
| | - Ruud J G van Sloun
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Abdul Qayyum
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Cristobal Rodero
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Steven Niederer
- National Heart & Lung Institute, Imperial College London, London, UK
- The Alan Turing Institute, London, UK
| | - Roberto Souza
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Department of Electrical and Software Engineering, University of Calgary, Calgary, Canada
| | - Ashley D Harris
- Department of Radiology, University of Calgary, Calgary, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
70
|
Korzeczek MC, Dagys L, Müller C, Tratzmiller B, Salhov A, Eichhorn T, Scheuer J, Knecht S, Plenio MB, Schwartz I. Towards a unified picture of polarization transfer - pulsed DNP and chemically equivalent PHIP. J Magn Reson 2024; 362:107671. [PMID: 38614057 DOI: 10.1016/j.jmr.2024.107671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/15/2024]
Abstract
Nuclear spin hyperpolarization techniques, such as dynamic nuclear polarization (DNP) and parahydrogen-induced polarization (PHIP), have revolutionized nuclear magnetic resonance and magnetic resonance imaging. In these methods, a readily available source of high spin order, either electron spins in DNP or singlet states in hydrogen for PHIP, is brought into close proximity with nuclear spin targets, enabling efficient transfer of spin order under external quantum control. Despite vast disparities in energy scales and interaction mechanisms between electron spins in DNP and nuclear singlet states in PHIP, a pseudo-spin formalism allows us to establish an intriguing equivalence. As a result, the important low-field polarization transfer regime of PHIP can be mapped onto an analogous system equivalent to pulsed-DNP. This establishes a correspondence between key polarization transfer sequences in PHIP and DNP, facilitating the transfer of sequence development concepts. This promises fresh insights and significant cross-pollination between DNP and PHIP polarization sequence developers.
Collapse
Affiliation(s)
- Martin C Korzeczek
- Institute of Theoretical Physics and IQST, Albert-Einstein Allee 11, Ulm University, 89081, Ulm, Germany
| | | | | | - Benedikt Tratzmiller
- Institute of Theoretical Physics and IQST, Albert-Einstein Allee 11, Ulm University, 89081, Ulm, Germany; Carl Zeiss MultiSEM GmbH, 73447, Oberkochen, Germany
| | - Alon Salhov
- NVision Imaging Technologies GmbH, 89081, Ulm, Germany; Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, 91904, Givat Ram, Israel
| | - Tim Eichhorn
- NVision Imaging Technologies GmbH, 89081, Ulm, Germany
| | | | | | - Martin B Plenio
- Institute of Theoretical Physics and IQST, Albert-Einstein Allee 11, Ulm University, 89081, Ulm, Germany.
| | - Ilai Schwartz
- NVision Imaging Technologies GmbH, 89081, Ulm, Germany.
| |
Collapse
|
71
|
Paudel HP, Lander GR, Crawford SE, Duan Y. Sensing at the Nanoscale Using Nitrogen-Vacancy Centers in Diamond: A Model for a Quantum Pressure Sensor. Nanomaterials (Basel) 2024; 14:675. [PMID: 38668169 PMCID: PMC11054777 DOI: 10.3390/nano14080675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The sensing of stress under harsh environmental conditions with high resolution has critical importance for a range of applications including earth's subsurface scanning, geological CO2 storage monitoring, and mineral and resource recovery. Using a first-principles density functional theory (DFT) approach combined with the theoretical modelling of the low-energy Hamiltonian, here, we investigate a novel approach to detect unprecedented levels of pressure by taking advantage of the solid-state electronic spin of nitrogen-vacancy (NV) centers in diamond. We computationally explore the effect of strain on the defect band edges and band gaps by varying the lattice parameters of a diamond supercell hosting a single NV center. A low-energy Hamiltonian is developed that includes the effect of stress on the energy level of a ±1 spin manifold at the ground state. By quantifying the energy level shift and split, we predict pressure sensing of up to 0.3 MPa/Hz using the experimentally measured spin dephasing time. We show the superiority of the quantum sensing approach over traditional optical sensing techniques by discussing our results from DFT and theoretical modelling for the frequency shift per unit pressure. Importantly, we propose a quantum manometer that could be useful to measure earth's subsurface vibrations as well as for pressure detection and monitoring in high-temperature superconductivity studies and in material sciences. Our results open avenues for the development of a sensing technology with high sensitivity and resolution under extreme pressure limits that potentially has a wider applicability than the existing pressure sensing technologies.
Collapse
Affiliation(s)
- Hari P. Paudel
- National Energy Technology Laboratory, United States Department of Energy, Pittsburgh, PA 15236, USA; (G.R.L.); (S.E.C.)
- NETL Support Contractor, 626 Cochrans Mill Road, Pittsburgh, PA 15236, USA
| | - Gary R. Lander
- National Energy Technology Laboratory, United States Department of Energy, Pittsburgh, PA 15236, USA; (G.R.L.); (S.E.C.)
- NETL Support Contractor, 3610 Collins Ferry Road, Morgantown, WV 26505, USA
| | - Scott E. Crawford
- National Energy Technology Laboratory, United States Department of Energy, Pittsburgh, PA 15236, USA; (G.R.L.); (S.E.C.)
| | - Yuhua Duan
- National Energy Technology Laboratory, United States Department of Energy, Pittsburgh, PA 15236, USA; (G.R.L.); (S.E.C.)
| |
Collapse
|
72
|
Mikolajewicz N, Yee PP, Bhanja D, Trifoi M, Miller AM, Metellus P, Bagley SJ, Balaj L, de Macedo Filho LJM, Zacharia BE, Aregawi D, Glantz M, Weller M, Ahluwalia MS, Kislinger T, Mansouri A. Systematic Review of Cerebrospinal Fluid Biomarker Discovery in Neuro-Oncology: A Roadmap to Standardization and Clinical Application. J Clin Oncol 2024:JCO2301621. [PMID: 38608213 DOI: 10.1200/jco.23.01621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/17/2024] [Accepted: 02/26/2024] [Indexed: 04/14/2024] Open
Abstract
Effective diagnosis, prognostication, and management of CNS malignancies traditionally involves invasive brain biopsies that pose significant risk to the patient. Sampling and molecular profiling of cerebrospinal fluid (CSF) is a safer, rapid, and noninvasive alternative that offers a snapshot of the intracranial milieu while overcoming the challenge of sampling error that plagues conventional brain biopsy. Although numerous biomarkers have been identified, translational challenges remain, and standardization of protocols is necessary. Here, we systematically reviewed 141 studies (Medline, SCOPUS, and Biosis databases; between January 2000 and September 29, 2022) that molecularly profiled CSF from adults with brain malignancies including glioma, brain metastasis, and primary and secondary CNS lymphomas. We provide an overview of promising CSF biomarkers, propose CSF reporting guidelines, and discuss the various considerations that go into biomarker discovery, including the influence of blood-brain barrier disruption, cell of origin, and site of CSF acquisition (eg, lumbar and ventricular). We also performed a meta-analysis of proteomic data sets, identifying biomarkers in CNS malignancies and establishing a resource for the research community.
Collapse
Affiliation(s)
- Nicholas Mikolajewicz
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Patricia P Yee
- Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA
| | - Debarati Bhanja
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Mara Trifoi
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Alexandra M Miller
- Departments of Neurology and Pediatrics, Memorial Sloan Kettering Cancer Center, Manhattan, NY
| | - Philippe Metellus
- Department of Neurosurgery, Ramsay Santé, Hôpital Privé Clairval, Marseille, France
| | - Stephen J Bagley
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | - Brad E Zacharia
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Dawit Aregawi
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Michael Glantz
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
| | - Manmeet S Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Alireza Mansouri
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, PA
| |
Collapse
|
73
|
González-Delgado JM, Thompson PM, Andrałojć W, Gdaniec Z, Ghiladi RA, Franzen S. Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes. J Phys Chem B 2024; 128:3383-3397. [PMID: 38563384 DOI: 10.1021/acs.jpcb.3c07176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.
Collapse
Affiliation(s)
| | - Peter M Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
74
|
Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
Collapse
Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
| |
Collapse
|
75
|
Kubicki DJ, Prochowicz D, Hofstetter A, Ummadisingu A, Emsley L. Speciation of Lanthanide Metal Ion Dopants in Microcrystalline All-Inorganic Halide Perovskite CsPbCl 3. J Am Chem Soc 2024; 146:9554-9563. [PMID: 38548624 PMCID: PMC11009948 DOI: 10.1021/jacs.3c11427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Lanthanides are versatile modulators of optoelectronic properties owing to their narrow optical emission spectra across the visible and near-infrared range. Their use in metal halide perovskites (MHPs) has recently gained prominence, although their fate in these materials has not yet been established at the atomic level. We use cesium-133 solid-state NMR to establish the speciation of all nonradioactive lanthanide ions (La3+, Ce3+, Pr3+, Nd3+, Sm3+, Sm2+, Eu3+, Eu2+, Gd3+, Tb3+, Dy3+, Ho3+, Er3+, Tm3+, Yb3+, Lu3+) in microcrystalline CsPbCl3. Our results show that all lanthanides incorporate into the perovskite structure of CsPbCl3 regardless of their oxidation state (+2, +3).
Collapse
Affiliation(s)
| | - Daniel Prochowicz
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Albert Hofstetter
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Amita Ummadisingu
- Manufacturing
Futures Laboratory, Department of Chemical Engineering, University College London, Torrington Place, WC1E 7JE London, United Kingdom
| | - Lyndon Emsley
- Laboratory
of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
76
|
Wesołek-Leszczyńska A, Pastusiak K, Bogdański P, Szulińska M. Can Adipokine FAM19A5 Be a Biomarker of Metabolic Disorders? Diabetes Metab Syndr Obes 2024; 17:1651-1666. [PMID: 38616989 PMCID: PMC11016272 DOI: 10.2147/dmso.s460226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024] Open
Abstract
Aim One of the most critical functions of adipose tissue is the production of adipokines, ie, numerous active substances that regulate metabolism. One is the newly discovered FAM19A5, whose older name is TAFA-5. Purpose The study aimed to review the literature on the FAM19A5 protein. Methods The review was conducted in December 2023 using the PubMed (Medline) search engine. Sixty-four papers were included in the review. Results This protein exhibits the characteristics of an adipokine with positive features for maintaining homeostasis. The results showed that FAM19A5 was highly expressed in adipose tissue, with mild to moderate expression in the brain and ovary. FAM19A5 may also inhibit vascular smooth muscle cell proliferation and migration through the perivascular adipose tissue paracrine pathway. Serum levels of FAM19A5 were decreased in obese children compared with healthy controls. There are negative correlations between FAM19A5, body mass index, and fasting insulin. Serum FAM19A5 level is correlated with type 2 diabetes, waist circumference, waist-to-hip ratio, glutamic pyruvic transferase, fasting plasma glucose, HbA1c, and mean shoulder pulse wave velocity. FAM19A5 expression was reduced in mice with obesity. However, the data available needs to be clarified or contradictory. Conclusion Considering today's knowledge about FAM19A5, we cannot consider this protein as a biomarker of the metabolic syndrome. According to current knowledge, FAM19A5 cannot be considered a marker of metabolic disorders because the results of studies conducted in this area are unclear.
Collapse
Affiliation(s)
- Agnieszka Wesołek-Leszczyńska
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznań, Poland
- Doctoral School, Poznan University Of Medical Sciences, Poznań, Poland
| | - Katarzyna Pastusiak
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Paweł Bogdański
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Monika Szulińska
- Department of Treatment of Obesity, Metabolic Disorders and Clinical Dietetics, Poznan University of Medical Sciences, Poznań, Poland
| |
Collapse
|
77
|
Rua AJ, Alexandrescu AT. Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure. bioRxiv 2024:2024.04.06.588434. [PMID: 38645208 PMCID: PMC11030341 DOI: 10.1101/2024.04.06.588434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Domain Z7 of nuclear transcription factor ZNF711 has the consensus last metal-ligand H23 found in odd-numbered zinc-fingers of this protein replaced by a phenylalanine. Ever since the discovery of ZNF711 it has been thought that Z7 is probably non-functional because of the H23F substitution. The presence of H26 three positions downstream prompted us to examine if this histidine could substitute as the last metal ligand. The Z7 domain adopts a stable tertiary structure upon metal binding. The NMR structure of Zn2+-bound Z7 shows the classical ββα-fold of CCHH zinc fingers. Mutagenesis and pH titration experiments indicate that H26 is not involved in metal binding and that Z7 has a tridentate metal-binding site comprised of only residues C3, C6, and H19. By contrast, an F23H mutation that introduces a histidine in the consensus position forms a tetradentate ligand. The structure of the WT Z7 is stable causing restricted ring-flipping of phenyalanines 10 and 23. Dynamics are increased with either the H26A or F23H substitutions and aromatic ring rotation is no longer hindered in the two mutants. The mutations have only small effects on the Kd values for Zn2+ and Co2+ and retain the high thermal stability of the WT domain above 80 °C. Like two previously reported designed zinc fingers with the last ligand replaced by water, the WT Z7 domain is catalytically active, hydrolyzing 4-nitophenyl acetate. We discuss the implications of naturally occurring tridentate zinc fingers for cancer mutations and drug targeting of notoriously undruggable transcription factors. Our findings that Z7 can fold with only a subset of three metal ligands suggests the recent view that most everything about protein structure can be predicted through homology modeling might be premature for at least the resilient and versatile zinc-finger motif.
Collapse
Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
| | | |
Collapse
|
78
|
Wu P, Zehnder J, Schröder N, Blümmel PEW, Salmon L, Damberger FF, Lipps G, Allain FHT, Wiegand T. Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy. J Am Chem Soc 2024; 146:9583-9596. [PMID: 38538061 PMCID: PMC11009956 DOI: 10.1021/jacs.3c11836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein-DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.
Collapse
Affiliation(s)
- Pengzhi Wu
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Johannes Zehnder
- Laboratory
of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
| | - Nina Schröder
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Pascal E. W. Blümmel
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Loïc Salmon
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Fred. F. Damberger
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Georg Lipps
- Institute
of Chemistry and Bioanalytics, University
of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland
| | - Frédéric H.-T. Allain
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Thomas Wiegand
- Laboratory
of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- Max-Planck-Institute
for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
79
|
Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
Collapse
Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| |
Collapse
|
80
|
Lyu D, Märker K, Zhou Y, Zhao EW, Gunnarsdóttir AB, Niblett SP, Forse AC, Grey CP. Understanding Sorption of Aqueous Electrolytes in Porous Carbon by NMR Spectroscopy. J Am Chem Soc 2024; 146:9897-9910. [PMID: 38560816 PMCID: PMC11009947 DOI: 10.1021/jacs.3c14807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Ion adsorption at solid-water interfaces is crucial for many electrochemical processes involving aqueous electrolytes including energy storage, electrochemical separations, and electrocatalysis. However, the impact of the hydronium (H3O+) and hydroxide (OH-) ions on the ion adsorption and surface charge distributions remains poorly understood. Many fundamental studies of supercapacitors focus on non-aqueous electrolytes to avoid addressing the role of functional groups and electrolyte pH in altering ion uptake. Achieving microscopic level characterization of interfacial mixed ion adsorption is particularly challenging due to the complex ion dynamics, disordered structures, and hierarchical porosity of the carbon electrodes. This work addresses these challenges starting with pH measurements to quantify the adsorbed H3O+ concentrations, which reveal the basic nature of the activated carbon YP-50F commonly used in supercapacitors. Solid-state NMR spectroscopy is used to study the uptake of lithium bis(trifluoromethanesulfonyl)-imide (LiTFSI) aqueous electrolyte in the YP-50F carbon across the full pH range. The NMR data analysis highlights the importance of including the fast ion-exchange processes for accurate quantification of the adsorbed ions. Under acidic conditions, more TFSI- ions are adsorbed in the carbon pores than Li+ ions, with charge compensation also occurring via H3O+ adsorption. Under neutral and basic conditions, when the carbon's surface charge is close to zero, the Li+ and TFSI- ions exhibit similar but lower affinities toward the carbon pores. Our experimental approach and evidence of H3O+ uptake in pores provide a methodology to relate the local structure to the function and performance in a wide range of materials for energy applications and beyond.
Collapse
Affiliation(s)
- Dongxun Lyu
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | | | - Yuning Zhou
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | | | | | - Samuel P. Niblett
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Alexander C. Forse
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Clare P. Grey
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
81
|
Sardo M, Morais T, Soares M, Vieira R, Ilkaeva M, Lourenço MAO, Marín-Montesinos I, Mafra L. Unravelling the structure of CO 2 in silica adsorbents: an NMR and computational perspective. Chem Commun (Camb) 2024; 60:4015-4035. [PMID: 38525497 PMCID: PMC11003455 DOI: 10.1039/d3cc05942a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
This comprehensive review describes recent advancements in the use of solid-state NMR-assisted methods and computational modeling strategies to unravel gas adsorption mechanisms and CO2 speciation in porous CO2-adsorbent silica materials at the atomic scale. This work provides new perspectives for the innovative modifications of these materials rendering them more amenable to the use of advanced NMR methods.
Collapse
Affiliation(s)
- Mariana Sardo
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Tiago Morais
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Chemistry, University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
| | - Márcio Soares
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Ricardo Vieira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Marina Ilkaeva
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Chemical and Environmental Engineering, University of Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain
| | - Mirtha A O Lourenço
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Ildefonso Marín-Montesinos
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Luís Mafra
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| |
Collapse
|
82
|
Woods JG, Achten E, Asllani I, Bolar DS, Dai W, Detre JA, Fan AP, Fernández-Seara MA, Golay X, Günther M, Guo J, Hernandez-Garcia L, Ho ML, Juttukonda MR, Lu H, MacIntosh BJ, Madhuranthakam AJ, Mutsaerts HJ, Okell TW, Parkes LM, Pinter N, Pinto J, Qin Q, Smits M, Suzuki Y, Thomas DL, Van Osch MJP, Wang DJJ, Warnert EAH, Zaharchuk G, Zelaya F, Zhao M, Chappell MA. Recommendations for quantitative cerebral perfusion MRI using multi-timepoint arterial spin labeling: Acquisition, quantification, and clinical applications. Magn Reson Med 2024. [PMID: 38594906 DOI: 10.1002/mrm.30091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/09/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Accurate assessment of cerebral perfusion is vital for understanding the hemodynamic processes involved in various neurological disorders and guiding clinical decision-making. This guidelines article provides a comprehensive overview of quantitative perfusion imaging of the brain using multi-timepoint arterial spin labeling (ASL), along with recommendations for its acquisition and quantification. A major benefit of acquiring ASL data with multiple label durations and/or post-labeling delays (PLDs) is being able to account for the effect of variable arterial transit time (ATT) on quantitative perfusion values and additionally visualize the spatial pattern of ATT itself, providing valuable clinical insights. Although multi-timepoint data can be acquired in the same scan time as single-PLD data with comparable perfusion measurement precision, its acquisition and postprocessing presents challenges beyond single-PLD ASL, impeding widespread adoption. Building upon the 2015 ASL consensus article, this work highlights the protocol distinctions specific to multi-timepoint ASL and provides robust recommendations for acquiring high-quality data. Additionally, we propose an extended quantification model based on the 2015 consensus model and discuss relevant postprocessing options to enhance the analysis of multi-timepoint ASL data. Furthermore, we review the potential clinical applications where multi-timepoint ASL is expected to offer significant benefits. This article is part of a series published by the International Society for Magnetic Resonance in Medicine (ISMRM) Perfusion Study Group, aiming to guide and inspire the advancement and utilization of ASL beyond the scope of the 2015 consensus article.
Collapse
Affiliation(s)
- Joseph G Woods
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Center for Functional Magnetic Resonance Imaging, Department of Radiology, University of California San Diego, La Jolla, California, USA
| | - Eric Achten
- Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
| | - Iris Asllani
- Department of Neuroscience, University of Sussex, Brighton, UK
- Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, New York, USA
| | - Divya S Bolar
- Center for Functional Magnetic Resonance Imaging, Department of Radiology, University of California San Diego, La Jolla, California, USA
| | - Weiying Dai
- Department of Computer Science, State University of New York at Binghamton, Binghamton, New York, USA
| | - John A Detre
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Audrey P Fan
- Department of Biomedical Engineering, University of California Davis, Davis, California, USA
- Department of Neurology, University of California Davis, Davis, California, USA
| | - María A Fernández-Seara
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Xavier Golay
- UCL Queen Square Institute of Neurology, University College London, London, UK
- Gold Standard Phantoms, Sheffield, UK
| | - Matthias Günther
- Imaging Physics, Fraunhofer Institute for Digital Medicine MEVIS, Bremen, Germany
- Department of Physics and Electrical Engineering, University of Bremen, Bremen, Germany
| | - Jia Guo
- Department of Bioengineering, University of California Riverside, Riverside, California, USA
| | | | - Mai-Lan Ho
- Department of Radiology, University of Missouri, Columbia, Missouri, USA
| | - Meher R Juttukonda
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanzhang Lu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bradley J MacIntosh
- Hurvitz Brain Sciences Program, Centre for Brain Resilience & Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Computational Radiology & Artificial Intelligence unit, Oslo University Hospital, Oslo, Norway
| | - Ananth J Madhuranthakam
- Department of Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Henk-Jan Mutsaerts
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Thomas W Okell
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Laura M Parkes
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Nandor Pinter
- Dent Neurologic Institute, Buffalo, New York, USA
- University at Buffalo Neurosurgery, Buffalo, New York, USA
| | - Joana Pinto
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Qin Qin
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marion Smits
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Medical Delta, Delft, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Yuriko Suzuki
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - David L Thomas
- Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Matthias J P Van Osch
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danny J J Wang
- Laboratory of FMRI Technology (LOFT), Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, California, USA
| | - Esther A H Warnert
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Greg Zaharchuk
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Fernando Zelaya
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Moss Zhao
- Department of Radiology, Stanford University, Stanford, California, USA
- Maternal & Child Health Research Institute, Stanford University, Stanford, California, USA
| | - Michael A Chappell
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK
| |
Collapse
|
83
|
Lin H, Zou J, Wang K, Feng Y, Xu C, Lyu J, Qin J. Dual-space high-frequency learning for transformer-based MRI super-resolution. Comput Methods Programs Biomed 2024; 250:108165. [PMID: 38631131 DOI: 10.1016/j.cmpb.2024.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND AND OBJECTIVE Magnetic resonance imaging (MRI) can provide rich and detailed high-contrast information of soft tissues, while the scanning of MRI is time-consuming. To accelerate MR imaging, a variety of Transformer-based single image super-resolution methods are proposed in recent years, achieving promising results thanks to their superior capability of capturing long-range dependencies. Nevertheless, most existing works prioritize the design of transformer attention blocks to capture global information. The local high-frequency details, which are pivotal to faithful MRI restoration, are unfortunately neglected. METHODS In this work, we propose a high-frequency enhanced learning scheme to effectively improve the awareness of high frequency information in current Transformer-based MRI single image super-resolution methods. Specifically, we present two entirely plug-and-play modules designed to equip Transformer-based networks with the ability to recover high-frequency details from dual spaces: 1) in the feature space, we design a high-frequency block (Hi-Fe block) paralleled with Transformer-based attention layers to extract rich high-frequency features; while 2) in the image intensity space, we tailor a high-frequency amplification module (HFA) to further refine the high-frequency details. By fully exploiting the merits of the two modules, our framework can recover abundant and diverse high-frequency information, rendering faithful MRI super-resolved results with fine details. RESULTS We integrated our modules with six Transformer-based models and conducted experiments across three datasets. The results indicate that our plug-and-play modules can enhance the super-resolution performance of all foundational models to varying degrees, surpassing the capabilities of existing state-of-the-art single image super-resolution networks. CONCLUSION Comprehensive comparison of super-resolution images and high-frequency maps from various methods, clearly demonstrating that our module possesses the capability to restore high-frequency information, showing huge potential in clinical practice for accelerated MRI reconstruction.
Collapse
Affiliation(s)
- Haoneng Lin
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong
| | - Jing Zou
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong.
| | - Kang Wang
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong
| | - Yidan Feng
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong
| | - Cheng Xu
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong
| | - Jun Lyu
- Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Jing Qin
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong
| |
Collapse
|
84
|
Ghini V, Sorbi F, Fambrini M, Magherini F. NMR Metabolomics of Primary Ovarian Cancer Cells in Comparison to Established Cisplatin-Resistant and -Sensitive Cell Lines. Cells 2024; 13:661. [PMID: 38667276 PMCID: PMC11049548 DOI: 10.3390/cells13080661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer cell lines are frequently used in metabolomics, such as in vitro tumor models. In particular, A2780 cells are commonly used as a model for ovarian cancer to evaluate the effects of drug treatment. Here, we compare the NMR metabolomics profiles of A2780 and cisplatin-resistant A2780 cells with those of cells derived from 10 patients with high-grade serous ovarian carcinoma (collected during primary cytoreduction before any chemotherapeutic treatment). Our analysis reveals a substantial similarity among all primary cells but significant differences between them and both A2780 and cisplatin-resistant A2780 cells. Notably, the patient-derived cells are closer to the resistant A2780 cells when considering the exo-metabolome, whereas they are essentially equidistant from A2780 and A2780-resistant cells in terms of the endo-metabolome. This behavior results from dissimilarities in the levels of several metabolites attributable to the differential modulation of underlying biochemical pathways. The patient-derived cells are those with the most pronounced glycolytic phenotype, whereas A2780-resistant cells mainly diverge from the others due to alterations in a few specific metabolites already known as markers of resistance.
Collapse
Affiliation(s)
- Veronica Ghini
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
| | - Flavia Sorbi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy; (F.S.); (M.F.)
| | - Massimiliano Fambrini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy; (F.S.); (M.F.)
| | - Francesca Magherini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy; (F.S.); (M.F.)
| |
Collapse
|
85
|
Haro Mares NB, Döller SC, Wissel T, Hoffmann M, Vogel M, Buntkowsky G. Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry. Molecules 2024; 29:1669. [PMID: 38611950 PMCID: PMC11013127 DOI: 10.3390/molecules29071669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.
Collapse
Affiliation(s)
- Nadia B. Haro Mares
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Sonja C. Döller
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Markus Hoffmann
- Department of Chemistry and Biochemistry, State University of New York at Brockport, Brockport, NY 14420, USA
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, D-64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| |
Collapse
|
86
|
Leclaire J, Heldebrant DJ, Grubel K, Septavaux J, Hennebelle M, Walter E, Chen Y, Bañuelos JL, Zhang D, Nguyen MT, Ray D, Allec SI, Malhotra D, Joo W, King J. Tetrameric self-assembling of water-lean solvents enables carbamate anhydride-based CO 2 capture chemistry. Nat Chem 2024:10.1038/s41557-024-01495-z. [PMID: 38589626 DOI: 10.1038/s41557-024-01495-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
Carbon capture, utilization and storage is a key yet cost-intensive technology for the fight against climate change. Single-component water-lean solvents have emerged as promising materials for post-combustion CO2 capture, but little is known regarding their mechanism of action. Here we present a combined experimental and modelling study of single-component water-lean solvents, and we find that CO2 capture is accompanied by the self-assembly of reverse-micelle-like tetrameric clusters in solution. This spontaneous aggregation leads to stepwise cooperative capture phenomena with highly contrasting mechanistic and thermodynamic features. The emergence of well-defined supramolecular architectures displaying a hydrogen-bonded internal core, reminiscent of enzymatic active sites, enables the formation of CO2-containing molecular species such as carbamic acid, carbamic anhydride and alkoxy carbamic anhydrides. This system extends the scope of adducts and mechanisms observed during carbon capture. It opens the way to materials with a higher CO2 storage capacity and provides a means for carbamates to potentially act as initiators for future oligomerization or polymerization of CO2.
Collapse
Affiliation(s)
- Julien Leclaire
- CNRS ICBMS UMR 5246, Universite Claude Bernard Lyon 1, Villeurbanne, France.
| | - David J Heldebrant
- Pacific Northwest National Laboratory, Richland, WA, USA.
- Washington State University Pullman, Pullman, WA, USA.
| | | | - Jean Septavaux
- CNRS ICBMS UMR 5246, Universite Claude Bernard Lyon 1, Villeurbanne, France
- Secoya Technologies, Ottignies-Louvain-la-Neuve, Belgium
| | - Marc Hennebelle
- CNRS ICBMS UMR 5246, Universite Claude Bernard Lyon 1, Villeurbanne, France
| | - Eric Walter
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Chen
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Difan Zhang
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Debmalya Ray
- Pacific Northwest National Laboratory, Richland, WA, USA
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sarah I Allec
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Wontae Joo
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jaelynne King
- Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
87
|
Marinova P, Tamahkyarova K. Synthesis and Biological Activities of Some Metal Complexes of Peptides: A Review. BioTech (Basel) 2024; 13:9. [PMID: 38651489 PMCID: PMC11036290 DOI: 10.3390/biotech13020009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted using various database platforms such as MetalPDB. The rising prominence of therapeutic peptides encompasses anticancer, antiviral, antimicrobial, and anti-neurodegenerative properties. The metals Na, K, Mg, Ca, Fe, Mn, Co, Cu, Zn, and Mo are ten of the twenty elements that are considered essential for life. Crucial for understanding the biological role of metals is the exploration of metal-bound proteins and peptides. Aside from essential metals, there are other non-essential metals that also interact biologically, exhibiting either therapeutic or toxic effects. Irregularities in metal binding contribute to diseases like Alzheimer's, neurodegenerative disorders, Wilson's, and Menkes disease. Certain metal complexes have potential applications as radiopharmaceuticals. The examination of these complexes was achieved by preforming UV-Vis, IR, EPR, NMR spectroscopy, and X-ray analysis. This summary, although unable to cover all of the studies in the field, offers a review of the ongoing experimentation and is a basis for new ideas, as well as strategies to explore and gain knowledge from the extensive realm of peptide-chelated metals and biotechnologies.
Collapse
Affiliation(s)
- Petja Marinova
- Department of General and Inorganic Chemistry with Methodology of Chemistry Education, Faculty of Chemistry, University of Plovdiv, “Tzar Assen” Str. 24, 4000 Plovdiv, Bulgaria;
| | | |
Collapse
|
88
|
Perras FA, Paterson AL. Automatic fitting of multiple-field solid-state NMR spectra. Solid State Nucl Magn Reson 2024; 131:101935. [PMID: 38603990 DOI: 10.1016/j.ssnmr.2024.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
The NMR lineshapes produced by half-integer quadrupolar nuclei are sensitive to 11 distinct fit parameters per inequivalent site. To date, automatic fitting routines have failed to replace manual parameter insertion and evaluation due to the importance of local minima and the need for fitting multiple-field magic-angle spinning (MAS) and static spectra simultaneously. Herein we introduce a new tool, AMES-Fit (Automatic Multiple Experiment Simulation and Fitting), to automatically find the global best-fit simulation parameters for a series of multiple-field NMR lineshapes. AMES-Fit uses an adaptive step size random search algorithm to dynamically probe parameter space and requires minimal human input. The best fits are obtained in a few minutes of computation time that would otherwise have required several person-hours of work. The program is freely available and open-source.
Collapse
Affiliation(s)
- Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA, 50011, United States; Department of Chemistry, Iowa State University, Ames, IA, 50011, United States.
| | - Alexander L Paterson
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, United States
| |
Collapse
|
89
|
Lin X, Chen Y, Huang C, Feng X, Chen B, Huang Y, Chen Z. CTCOSY-JRES: A high-resolution three-dimensional NMR method for unveiling J-couplings. J Magn Reson 2024; 362:107675. [PMID: 38631172 DOI: 10.1016/j.jmr.2024.107675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
Two-dimensional (2D) J-resolved spectroscopy provides valuable information on J-coupling constants for molecular structure analysis by resolving one-dimensional (1D) spectra. However, it is challenging to decipher the J-coupling connectivity in 2D J-resolved spectra because the J-coupling connectivity cannot be directly provided. In addition, 2D homonuclear correlation spectroscopy (COSY) can directly elucidate molecular structures by tracking the J-coupling connectivity between protons. However, this method is limited by the problem of spectral peak crowding and is only suitable for simple sample systems. To fully understand the intuitive coupling relationship and coupling constant information, we propose a three-dimensional (3D) COSY method called CTCOSY-JRES (Constant-Time COrrelation SpectroscopY and J-REsolved Spectroscopy) in this paper. By combining the J-resolved spectrum with the constant-time COSY technique, a doubly decoupled COSY spectrum can be provided while preserving the J-coupling constant along an additional dimension, ensuring high-resolution analysis of J-coupling connectivity and J-coupling information. Moreover, compression sensing and fold-over correction techniques are introduced to accelerate experimental acquisition. The CTCOSY-JRES method has been successfully validated in a variety of sample systems, including industrial, agricultural, and biopharmaceutical samples, revealing complex coupling interactions and providing deeper insights into the resolution of molecular structures.
Collapse
Affiliation(s)
- Xiaoqing Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Yulei Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Chengda Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiaozhen Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Bo Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China.
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China.
| |
Collapse
|
90
|
Shimshoni E, Solomonov I, Sagi I, Ghini V. Integrated Metabolomics and Proteomics of Symptomatic and Early Presymptomatic States of Colitis. J Proteome Res 2024; 23:1420-1432. [PMID: 38497760 DOI: 10.1021/acs.jproteome.3c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Colitis has a multifactorial pathogenesis with a strong cross-talk among microbiota, hypoxia, and tissue metabolism. Here, we aimed to characterize the molecular signature of the disease in symptomatic and presymptomatic stages of the inflammatory process at the tissue and fecal level. The study is based on two different murine models for colitis, and HR-MAS NMR on "intact" colon tissues and LC-MS/MS on colon tissue extracts were used to derive untargeted metabolomics and proteomics information, respectively. Solution NMR was used to derive metabolomic profiles of the fecal extracts. By combining metabolomic and proteomic analyses of the tissues, we found increased anaerobic glycolysis, accompanied by an altered citric acid cycle and oxidative phosphorylation in inflamed colons; these changes associate with inflammation-induced hypoxia taking place in colon tissues. Different colitis states were also characterized by significantly different metabolomic profiles of fecal extracts, attributable to both the dysbiosis characteristic of colitis as well as the dysregulated tissue metabolism. Strong and distinctive tissue and fecal metabolomic signatures can be detected before the onset of symptoms. Therefore, untargeted metabolomics of tissues and fecal extracts provides a comprehensive picture of the changes accompanying the disease onset already at preclinical stages, highlighting the diagnostic potential of global metabolomics for inflammatory diseases.
Collapse
Affiliation(s)
- Elee Shimshoni
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Veronica Ghini
- Department of Chemistry, University of Florence, Sesto Fiorentino, Florence 50019, Italy
- Center of Magnetic Resonance (CERM), University of Florence, Sesto Fiorentino, Florence 50019, Italy
| |
Collapse
|
91
|
Tang H, Huang Y, Yuan D, Liu J. Atherosclerosis, gut microbiome, and exercise in a meta-omics perspective: a literature review. PeerJ 2024; 12:e17185. [PMID: 38584937 PMCID: PMC10999153 DOI: 10.7717/peerj.17185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Background Cardiovascular diseases are the leading cause of death worldwide, significantly impacting public health. Atherosclerotic cardiovascular diseases account for the majority of these deaths, with atherosclerosis marking the initial and most critical phase of their pathophysiological progression. There is a complex relationship between atherosclerosis, the gut microbiome's composition and function, and the potential mediating role of exercise. The adaptability of the gut microbiome and the feasibility of exercise interventions present novel opportunities for therapeutic and preventative approaches. Methodology We conducted a comprehensive literature review using professional databases such as PubMed and Web of Science. This review focuses on the application of meta-omics techniques, particularly metagenomics and metabolomics, in studying the effects of exercise interventions on the gut microbiome and atherosclerosis. Results Meta-omics technologies offer unparalleled capabilities to explore the intricate connections between exercise, the microbiome, the metabolome, and cardiometabolic health. This review highlights the advancements in metagenomics and metabolomics, their applications in research, and examines how exercise influences the gut microbiome. We delve into the mechanisms connecting these elements from a metabolic perspective. Metagenomics provides insight into changes in microbial strains post-exercise, while metabolomics sheds light on the shifts in metabolites. Together, these approaches offer a comprehensive understanding of how exercise impacts atherosclerosis through specific mechanisms. Conclusions Exercise significantly influences atherosclerosis, with the gut microbiome serving as a critical intermediary. Meta-omics technology holds substantial promise for investigating the gut microbiome; however, its methodologies require further refinement. Additionally, there is a pressing need for more extensive cohort studies to enhance our comprehension of the connection among these element.
Collapse
Affiliation(s)
- Haotian Tang
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yanqing Huang
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Didi Yuan
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Junwen Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| |
Collapse
|
92
|
Meyer NMT, Pohrt A, Wernicke C, Pletsch-Borba L, Apostolopoulou K, Haberbosch L, Machann J, Pfeiffer AFH, Spranger J, Mai K. Improvement in Visceral Adipose Tissue and LDL Cholesterol by High PUFA Intake: 1-Year Results of the NutriAct Trial. Nutrients 2024; 16:1057. [PMID: 38613089 PMCID: PMC11013849 DOI: 10.3390/nu16071057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
We assessed the effect of a dietary pattern rich in unsaturated fatty acids (UFA), protein and fibers, without emphasizing energy restriction, on visceral adipose tissue (VAT) and cardiometabolic risk profile. Within the 36-months randomized controlled NutriAct trial, we randomly assigned 502 participants (50-80 years) to an intervention or control group (IG, CG). The dietary pattern of the IG includes high intake of mono-/polyunsaturated fatty acids (MUFA/PUFA 15-20% E/10-15% E), predominantly plant protein (15-25% E) and fiber (≥30 g/day). The CG followed usual care with intake of 30% E fat, 55% E carbohydrates and 15% E protein. Here, we analyzed VAT in a subgroup of 300 participants via MRI at baseline and after 12 months, and performed further metabolic phenotyping. A small but comparable BMI reduction was seen in both groups (mean difference IG vs. CG: -0.216 kg/m2 [-0.477; 0.045], partial η2 = 0.009, p = 0.105). VAT significantly decreased in the IG but remained unchanged in the CG (mean difference IG vs. CG: -0.162 L [-0.314; -0.011], partial η2 = 0.015, p = 0.036). Change in VAT was mediated by an increase in PUFA intake (ß = -0.03, p = 0.005) and induced a decline in LDL cholesterol (ß = 0.11, p = 0.038). The NutriAct dietary pattern, particularly due to high PUFA content, effectively reduces VAT and cardiometabolic risk markers, independent of body weight loss.
Collapse
Affiliation(s)
- Nina Marie Tosca Meyer
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Anne Pohrt
- Institute of Biometry and Clinical Epidemiology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Charlotte Wernicke
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Laura Pletsch-Borba
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- BIH Charité Junior Clinician Scientist Program, BIH Biomedical Innovation Academy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Konstantina Apostolopoulou
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Linus Haberbosch
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- BIH Charité Junior Digital Clinician Scientist Program, BIH Biomedical Innovation Academy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jürgen Machann
- Institute for Diabetes Research and Metabolic Diseases (IDM), Helmholtz Center Munich, University of Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany;
- Section on Experimental Radiology, Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Otfried-Müller-Straße 12/1, 72076 Tübingen, Germany
- German Center for Diabetes Research, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Andreas F. H. Pfeiffer
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- German Center for Diabetes Research, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Joachim Spranger
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- German Center for Diabetes Research, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
- Department of Human Nutrition, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Potsdamer Str. 58, 10785 Berlin, Germany
- Max Rubner Center for Cardiovascular Metabolic Renal Research, Hessische Str. 3-4, 10115 Berlin, Germany
| | - Knut Mai
- Department of Endocrinology and Metabolism, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (N.M.T.M.)
- NutriAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- German Center for Diabetes Research, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
- Department of Human Nutrition, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Potsdamer Str. 58, 10785 Berlin, Germany
- Max Rubner Center for Cardiovascular Metabolic Renal Research, Hessische Str. 3-4, 10115 Berlin, Germany
| |
Collapse
|
93
|
Razew A, Herail Q, Miyachiro M, Anoyatis-Pelé C, Bougault C, Dessen A, Arthur M, Simorre JP. Monitoring Drug-Protein Interactions in the Bacterial Periplasm by Solution Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2024; 146:9252-9260. [PMID: 38500259 DOI: 10.1021/jacs.4c00604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The rapid spread of antimicrobial resistance across bacterial pathogens poses a serious risk to the efficacy and sustainability of available treatments. This puts pressure on research concerning the development of new drugs. Here, we present an in-cell NMR-based research strategy to monitor the activity of the enzymes located in the periplasmic space delineated by the inner and outer membranes of Gram-negative bacteria. We demonstrate its unprecedented analytical power in monitoring in situ and in real time (i) the hydrolysis of β-lactams by β-lactamases, (ii) the interaction of drugs belonging to the β-lactam family with their essential targets, and (iii) the binding of inhibitors to these enzymes. We show that in-cell NMR provides a powerful analytical tool for investigating new drugs targeting the molecular components of the bacterial periplasm.
Collapse
Affiliation(s)
- Alicja Razew
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Quentin Herail
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Mayara Miyachiro
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | | | - Catherine Bougault
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Andrea Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| |
Collapse
|
94
|
Bizet M, Byrne D, Biaso F, Gerbaud G, Etienne E, Briola G, Guigliarelli B, Urban P, Dorlet P, Kalai T, Truan G, Martinho M. Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid. Chemistry 2024; 30:e202304307. [PMID: 38277424 DOI: 10.1002/chem.202304307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
Collapse
Affiliation(s)
- Maxime Bizet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix Marseille Univ, CNRS, IMM, 13402, Marseille, France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Giuseppina Briola
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Philippe Urban
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Pierre Dorlet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Tamas Kalai
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, PO Box 99 Szigeti st. 12, H-7602 7624, Pécs, Hungary
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Marlène Martinho
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| |
Collapse
|
95
|
Wang Y, Zhao H, Yang C, Fang L, Zheng L, Lv H, Stavropoulos P, Ai L, Zhang J. Chiral Recognition of Chiral (Hetero)Cyclic Derivatives Probed by Tetraaza Macrocyclic Chiral Solvating Agents via 1H NMR Spectroscopy. Anal Chem 2024; 96:5188-5194. [PMID: 38506628 DOI: 10.1021/acs.analchem.3c05395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In the field of chiral recognition, chiral cyclic organic compounds, especially heterocyclic organic compounds, have attracted little attention and have been rarely studied as chiral substrates by means of 1H NMR spectroscopy. In this paper, enantiomers of thiohydantoin derivatives, representing typical five-membered N,N-heterocycles, have been synthesized and utilized for assignment of absolute configuration and analysis of enantiomeric excess. All enantiomers have been successfully differentiated with the assistance of novel tetraaza macrocyclic chiral solvating agents (TAMCSAs) by 1H NMR spectroscopy. Surprisingly, unprecedented nonequivalent chemical shift values (up to 2.052 ppm) of the NH proton of substrates have been observed, a new milestone in the evaluation of enantiomers. To better understand the intermolecular interactions between host and guest, Job plots and theoretical calculations of (S)-G1 and (R)-G1 with TAMCSA 1a were investigated and revealed significant geometric differentiation between the diastereomers. In order to evaluate practical applications of the present systems in analyzing optical purity of chiral substrates, enantiomeric excesses of a typical substrate (G1) with different optical compositions in the presence of a representative TAMCSA (1a) can be accurately calculated based on the integration of the NH proton's signal peaks. Importantly, this work provides a significant breakthrough in exploring and developing the chiral recognition of chiral heterocyclic organic compounds by 1H NMR spectroscopy.
Collapse
Affiliation(s)
- Yu Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hongmei Zhao
- State Key Laboratory of Information Photonics and Communications, School of Science, Beijing University of Posts and Telecommunications, Beijing 100876, P. R. China
| | - Chunxia Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Lixia Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Li Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hehua Lv
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Pericles Stavropoulos
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Lin Ai
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Jiaxin Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| |
Collapse
|
96
|
Stenström O, Diehl C, Modig K, Akke M. Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit. Proc Natl Acad Sci U S A 2024; 121:e2317747121. [PMID: 38527204 PMCID: PMC10998626 DOI: 10.1073/pnas.2317747121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-ligand complex formation is fundamental to biological function. A central question is whether proteins spontaneously adopt binding-competent conformations to which ligands bind conformational selection (CS) or whether ligands induce the binding-competent conformation induced fit (IF). Here, we resolve the CS and IF binding pathways by characterizing protein conformational dynamics over a wide range of ligand concentrations using NMR relaxation dispersion. We determined the relative flux through the two pathways using a four-state binding model that includes both CS and IF. Experiments conducted without ligand show that galectin-3 exchanges between the ground-state conformation and a high-energy conformation similar to the ligand-bound conformation, demonstrating that CS is a plausible pathway. Near-identical crystal structures of the apo and ligand-bound states suggest that the high-energy conformation in solution corresponds to the apo crystal structure. Stepwise additions of the ligand lactose induce progressive changes in the relaxation dispersions that we fit collectively to the four-state model, yielding all microscopic rate constants and binding affinities. The ligand affinity is higher for the bound-like conformation than for the ground state, as expected for CS. Nonetheless, the IF pathway contributes greater than 70% of the total flux even at low ligand concentrations. The higher flux through the IF pathway is explained by considerably higher rates of exchange between the two protein conformations in the ligand-associated state. Thus, the ligand acts to decrease the activation barrier between protein conformations in a manner reciprocal to enzymatic transition-state stabilization of reactions involving ligand transformation.
Collapse
Affiliation(s)
- Olof Stenström
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Carl Diehl
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Kristofer Modig
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| |
Collapse
|
97
|
Mailhiot S, Mankinen O, Li J, Kharbanda Y, Telkki VV, Urbańczyk M. CAT on MOUSE: Control and automation of temperature for single-sided NMR instruments such as NMR-MOUSE. Magn Reson Chem 2024; 62:252-258. [PMID: 37344254 DOI: 10.1002/mrc.5376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
Temperature-dependent experiments are a rapidly growing area of interest for low-field NMR. In this work, we present a new device for wide-range temperature control for single-sided NMR instruments. The presented device, called CAT, is simple to build, inexpensive, and easy to modify to accommodate different samples. We present the capabilities of the device using a freezing temperature study of acetic acid/water mixtures. Additionally, we present the stability of the device over long measurement times. We believe that by introducing such a device with an open-source design, we allow researchers to use it in a wide range of applications and to fully incorporate variable-temperature studies in the world of single-sided instruments.
Collapse
Affiliation(s)
| | - Otto Mankinen
- NMR Research Unit, University of Oulu, Oulu, Finland
| | - Jing Li
- NMR Research Unit, University of Oulu, Oulu, Finland
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
| | - Yashu Kharbanda
- NMR Research Unit, University of Oulu, Oulu, Finland
- Laboratoire Navier (Ecole des Ponts ParisTech-Université Gustave Eiffel), Champs-sur-Marne, France
| | | | - Mateusz Urbańczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
98
|
Jacobs PS, Brink W, Reddy R. A review of recent developments and applications of high-permittivity dielectric shimming in magnetic resonance. NMR Biomed 2024; 37:e5094. [PMID: 38214202 DOI: 10.1002/nbm.5094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/20/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
We present a review outlining the basic mechanism, background, recent technical developments, and clinical applications of aqueous dielectric padding in the field of MRI. Originally meant to be a temporary solution, it has gained traction as an effective method for correcting B1 + inhomogeneities due to the unique properties of the calcium titanate and barium titanate perovskites used. Aqueous dielectric pads have used a variety of high-permittivity materials over the years to improve the quality of MRI acquisitions at 1.5 and 3 T and more recently for 7 T neuroimaging applications. The technical development and assessment of these pads have been advanced by an increased use of mathematical modeling and electromagnetic simulations. These tools have allowed for a more complete understanding of the physical interactions between dielectric pads and the RF coil, making testing and safety assessments more accurate. The ease of use and effectiveness that dielectric pads offer have allowed them to become more commonplace in tackling imaging challenges in more clinically focused environments. More recently, they have seen usage not only in anatomical imaging methods but also in specialized metabolic imaging sequences such as GluCEST and NOEMTR . New colossally high-permittivity materials have been proposed; however, practical utilization has been a continued challenge due to unfavorable frequency dependences as well as safety limitations. A new class of metasurfaces has been under development to address the shortcomings of conventional dielectric padding while also providing increased performance in enhancing MRI images.
Collapse
Affiliation(s)
- Paul S Jacobs
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wyger Brink
- Magnetic Detection and Imaging group, TechMed Centre, University of Twente, Enschede, The Netherlands
| | - Ravinder Reddy
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
99
|
Wild JM, Gleeson FV, Svenningsen S, Grist JT, Saunders LC, Collier GJ, Sharma M, Tcherner S, Mozaffaripour A, Matheson AM, Parraga G. Review of Hyperpolarized Pulmonary Functional 129 Xe MR for Long-COVID. J Magn Reson Imaging 2024; 59:1120-1134. [PMID: 37548112 DOI: 10.1002/jmri.28940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023] Open
Abstract
The respiratory consequences of acute COVID-19 infection and related symptoms tend to resolve 4 weeks post-infection. However, for some patients, new, recurrent, or persisting symptoms remain beyond the acute phase and persist for months, post-infection. The symptoms that remain have been referred to as long-COVID. A number of research sites employed 129 Xe magnetic resonance imaging (MRI) during the pandemic and evaluated patients post-infection, months after hospitalization or home-based care as a way to better understand the consequences of infection on 129 Xe MR gas-exchange and ventilation imaging. A systematic review and comprehensive search were employed using MEDLINE via PubMed (April 2023) using the National Library of Medicine's Medical Subject Headings and key words: post-COVID-19, MRI, 129 Xe, long-COVID, COVID pneumonia, and post-acute COVID-19 syndrome. Fifteen peer-reviewed manuscripts were identified including four editorials, a single letter to the editor, one review article, and nine original research manuscripts (2020-2023). MRI and MR spectroscopy results are summarized from these prospective, controlled studies, which involved small sample sizes ranging from 9 to 76 participants. Key findings included: 1) 129 Xe MRI gas-exchange and ventilation abnormalities, 3 months post-COVID-19 infection, and 2) a combination of MRI gas-exchange and ventilation abnormalities alongside persistent symptoms in patients hospitalized and not hospitalized for COVID-19, 1-year post-infection. The persistence of respiratory symptoms and 129 Xe MRI abnormalities in the context of normal or nearly normal pulmonary function test results and chest computed tomography (CT) was consistent. Longitudinal improvements were observed in long-term follow-up of long-COVID patients but mean 129 Xe gas-exchange, ventilation heterogeneity values and symptoms remained abnormal, 1-year post-infection. Pulmonary functional MRI using inhaled hyperpolarized 129 Xe gas has played a role in detecting gas-exchange and ventilation abnormalities providing complementary information that may help develop our understanding of the root causes of long-COVID. LEVEL OF EVIDENCE: 1 TECHNICAL EFFICACY: Stage 5.
Collapse
Affiliation(s)
- Jim M Wild
- POLARIS, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Fergus V Gleeson
- Department of Radiology, Oxford University Hospitals, Oxford, UK
| | - Sarah Svenningsen
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - James T Grist
- Department of Radiology, Oxford University Hospitals, Oxford, UK
| | - Laura C Saunders
- POLARIS, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Guilhem J Collier
- POLARIS, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Maksym Sharma
- Robarts Research Institute, Western University, London, Ontario, Canada
- Department of Medical Biophysics, Western University, London, Ontario, Canada
| | - Sam Tcherner
- Robarts Research Institute, Western University, London, Ontario, Canada
- Department of Medical Biophysics, Western University, London, Ontario, Canada
| | - Ali Mozaffaripour
- Robarts Research Institute, Western University, London, Ontario, Canada
- Department of Medical Biophysics, Western University, London, Ontario, Canada
| | - Alexander M Matheson
- Robarts Research Institute, Western University, London, Ontario, Canada
- Department of Medical Biophysics, Western University, London, Ontario, Canada
| | - Grace Parraga
- Robarts Research Institute, Western University, London, Ontario, Canada
- Department of Medical Biophysics, Western University, London, Ontario, Canada
- Division of Respirology, Department of Medicine, Western University, London, Ontario, Canada
| |
Collapse
|
100
|
Steiner K, Bermel W, Soong R, Lysak DH, Jenne A, Downey K, Wolff WW, Costa PM, Ronda K, Moxley-Paquette V, Pellizzari J, Simpson AJ. A simple 1H ( 12C/ 13C) filtered experiment to quantify and trace isotope enrichment in complex environmental and biological samples. J Magn Reson 2024; 361:107653. [PMID: 38471414 DOI: 10.1016/j.jmr.2024.107653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Nuclear magnetic resonance (NMR) based 13C tracing has broad applications across medical and environmental research. As many biological and environmental samples are heterogeneous, they experience considerable spectral overlap and relatively low signal. Here a 1D 1H-12C/13C is introduced that uses "in-phase/opposite-phase" encoding to simultaneously detect and discriminate both protons attached to 12C and 13C at full 1H sensitivity in every scan. Unlike traditional approaches that focus on the 12C/13C satellite ratios in a 1H spectrum, this approach creates separate sub-spectra for the 12C and 13C bound protons. These spectra can be used for both quantitative and qualitative analysis of complex samples with significant spectral overlap. Due to the presence of the 13C dipole, faster relaxation of the 1H-13C pairs results in slight underestimation compared to the 1H-12C pairs. However, this is easily compensated for, by collecting an additional reference spectrum, from which the absolute percentage of 13C can be calculated by difference. When combined with the result, 12C and 13C percent enrichment in both 1H-12C and 1H-13C fractions are obtained. As the approach uses isotope filtered 1H NMR for detection, it retains nearly the same sensitivity as a standard 1H spectrum. Here, a proof-of-concept is performed using simple mixtures of 12C and 13C glucose, followed by suspended algal cells with varying 12C /13C ratios representing a complex mixture. The results consistently return 12C/13C ratios that deviate less than 1 % on average from the expected. Finally, the sequence was used to monitor and quantify 13C% enrichment in Daphnia magna neonates which were fed a 13C diet over 1 week. The approach helped reveal how the organisms utilized the 12C lipids they are born with vs. the 13C lipids they assimilate from their diet during growth. Given the experiments simplicity, versatility, and sensitivity, we anticipate it should find broad application in a wide range of tracer studies, such as fluxomics, with applications spanning various disciplines.
Collapse
Affiliation(s)
- Katrina Steiner
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Rudolf-Plank-Str. 23, Ettlingen 76275, Germany
| | - Ronald Soong
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - William W Wolff
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Peter M Costa
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Kiera Ronda
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Vincent Moxley-Paquette
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Jacob Pellizzari
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto, 1265 Military Trail, Toronto, ON M1C 1A4, Canada.
| |
Collapse
|