Journal of Magnetic Resonance Open最新文献

{"title":"High resolution protein in-cell NMR in zebrafish embryos","authors":"Verónica A. Lombardo ,&nbsp;Rubina Armesto ,&nbsp;Idalia Herrera-Estrada ,&nbsp;Andrés Binolfi","doi":"10.1016/j.jmro.2023.100111","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100111","url":null,"abstract":"<div><p>In-cell NMR spectroscopy has emerged as a powerful tool to evaluate protein conformations and dynamics in the native environment of live cells. Here we extend these studies to a multicellular developing vertebrate. Zebrafish (<em>Danio rerio</em>) embryos are complex organisms with dynamic tissue organization and may be well suited for the high resolution NMR analysis of microinjected, isotopically enriched proteins. We used the intrinsically disordered protein Alpha-synuclein (aSyn) as a test model. aSyn has been thoroughly evaluated inside bacterial and mammalian cells, providing good reference points for NMR comparisons and the critical analysis of the advantages and disadvantages of the zebrafish system. High resolution 2D ¹H-¹⁵N NMR showed that aSyn in zebrafish embryos had the same conformational and biological features previously observed in mammalian cells, including conserved interactions with cellular biomolecules and the establishment of physiological protein post-translational modifications. A direct comparative analysis of gamma-synuclein (gSyn), a naturally occurring homolog of aSyn, in bacteria, mammalian cells and zebrafish embryos confirmed these observations. Our results showed that high resolution in-cell NMR is attainable in embryonic cells within the native environment of a live animal. This system provides more physiological cellular environments for high resolution, <em>in situ</em> protein biophysical studies.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100111"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"2623849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cumulant expansion framework for internal gradient distributions tensors","authors":"Leonardo A. Pedraza Pérez ,&nbsp;Gonzalo A. Álvarez","doi":"10.1016/j.jmro.2023.100136","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100136","url":null,"abstract":"<div><p>Magnetic resonance imaging is a powerful, non invasive tool for medical diagnosis. The low sensitivity for detecting the nuclear spin signals, typically limits the image resolution to several tens of micrometers in preclinical systems and millimeters in clinical scanners. Other sources of information, derived from diffusion processes of intrinsic molecules such as water in the tissues, allow getting morphological information at micrometric and submicrometric scales as potential biomarkers of several pathologies. Here we consider extracting this morphological information by probing the distribution of internal magnetic field gradients induced by the heterogeneous magnetic susceptibility of the medium. We use a cumulant expansion to derive the dephasing on the spin signal induced by the molecules that explore these internal gradients while diffusing. Based on the cumulant expansion, we define internal gradient distributions tensors (IGDT) and propose modulating gradient spin echo sequences to probe them. These IGDT contain microstructural morphological information that characterize porous media and biological tissues. We evaluate the IGDT effects on the magnetization decay with typical conditions of brain tissue and show that their effects can be experimentally observed. Our results thus provide a framework for exploiting IGDT as quantitative diagnostic tools.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100136"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666441023000444/pdfft?md5=ba2ece990376de71fb8be126e3b4c3ef&pid=1-s2.0-S2666441023000444-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92145634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Magnetic resonance imaging and velocimetry of ethane","authors":"Maria Anikeeva ,&nbsp;Maitreyi Sangal ,&nbsp;Andrey N. Pravdivtsev ,&nbsp;Maryia S. Pravdivtseva ,&nbsp;Eva Peschke ,&nbsp;Oliver Speck ,&nbsp;Jan-Bernd Hövener","doi":"10.1016/j.jmro.2023.100137","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100137","url":null,"abstract":"<div><p>This study investigates the experimental conditions required for magnetic resonance imaging (MRI) of thermally polarized hydrocarbon gas, focusing on ethane. The nuclear magnetic resonance (NMR) spectra and relaxation properties of ethane were analysed at different pressures in the range from 1.5 to 6 bar at 7 T using ¹H NMR spectroscopy. The spin-lattice relaxation time (T₁) and spin-spin relaxation time (T₂) were measured, and their dependence on the pressure was determined, showing that both relaxation times increase with pressure. Using the estimated relaxation times, we adjusted parameters for imaging of static ethane using rapid acquisition with relaxation enhancement (RARE) and fast low-angle shot (FLASH). The signal-to-noise ratio (SNR) of ethane images was evaluated and compared to the calculation for the given range of pressures. Then, we imaged flowing gas using a 2D velocity-encoded pulse sequence, which is usually used for liquid flow studies. The MRI-measured flow rates are compared to those pre-set with a pump, showing good agreement in the slow flow range. Overall, the results provide insights into the feasibility of ¹H MRI for imaging and flow measurements of thermally polarized ethane.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100137"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666441023000456/pdfft?md5=ee9e2d935852d4ca5b924b20bb456221&pid=1-s2.0-S2666441023000456-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92087350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inductively coupled, transmit-receive coils for proton MRI and X-nucleus MRI/MRS in small animals","authors":"Atsushi M. Takahashi ,&nbsp;Jitendra Sharma ,&nbsp;David O. Guarin ,&nbsp;Julie Miller ,&nbsp;Hiroaki Wakimoto ,&nbsp;Daniel P. Cahill ,&nbsp;Yi-Fen Yen","doi":"10.1016/j.jmro.2023.100123","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100123","url":null,"abstract":"<div><p>We report several inductively coupled RF coil designs that are very easy to construct, produce high signal-to-noise ratio (SNR) and high spatial resolution while accommodating life support, anesthesia and monitoring in small animals. Inductively coupled surface coils were designed for hyperpolarized ¹³ C MR spectroscopic imaging (MRSI) of mouse brain, with emphases on the simplicity of the circuit design, ease of use, whole-brain coverage, and high SNR. The simplest form was a resonant loop designed to crown the mouse head for a snug fit to achieve full coverage of the brain with high sensitivity when inductively coupled to a broadband pick-up coil. Here, we demonstrated the coil's performance in hyperpolarized ¹³ C MRSI of a normal mouse and a glioblastoma mouse model at 4.7 T. High SNR exceeding 70:1 was obtained in the brain with good spatial resolution (1.53 mm x 1.53 mm). Similar inductively coupled loop for other X-nuclei can be made very easily in a few minutes and achieve high performance, as demonstrated in ³¹ P spectroscopy. Similar design concept was expanded to splitable, inductively coupled volume coils for high-resolution proton MRI of marmoset at 3T and 9.4T, to easily accommodate head restraint, vital-sign monitoring, and anesthesia delivery.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100123"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3135445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Solid state nuclear magnetic resonance of polymers","authors":"Gustavo Alberto Monti ,&nbsp;Rodolfo Héctor Acosta ,&nbsp;Ana Karina Chattah ,&nbsp;Yamila Garro Linck","doi":"10.1016/j.jmro.2023.100119","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100119","url":null,"abstract":"<div><p>The development of Solid-State Nuclear Magnetic Resonance (SSNMR) in Argentina took a great buster at the beginning of the 1990s along with the acquisition of many “state-of-the-art” high-field NMR spectrometers, two of them multipurpose solid-liquid spectrometers. From then to nowadays, the study of solid samples, including polymers, has been a current topic at the NMR group of the Facultad de Matemática, Astronomía, Física y Computación of Universidad Nacional de Córdoba, in Argentina. In this work, we propose a review approach of several research works on solid polymers performed in our group, covering low-field relaxation studies and high-resolution SSNMR.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100119"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introducing NMR strategies to define water molecules that drive metal binding in a transcriptional regulator","authors":"M. Villarruel Dujovne ,&nbsp;M. Bringas ,&nbsp;I.C. Felli ,&nbsp;E. Ravera ,&nbsp;S. Di Lella ,&nbsp;D.A. Capdevila","doi":"10.1016/j.jmro.2023.100114","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100114","url":null,"abstract":"<div><p><em>Staphylococcus aureus</em> CzrA is a paradigmatic member of the ArsR family of transcriptional metalloregulators, which are critical for the bacterial response to stress. Zinc binding to CzrA, which induces DNA derepression, is entropically driven, as shown by calorimetry. A detailed equilibrium dynamics study of different allosteric states of CzrA revealed that zinc induces an entropy redistribution that controls for DNA binding regulation; however, this change in conformational entropy only accounts for a small net contribution to the total entropy. This difference between the change in conformational entropy vs. total entropy of zinc binding implies a significant contribution of solvent molecule rearrangements to this equilibrium. However, the absence of major structural changes suggests that solvent rearrangements occur mainly on the protein surface and/or from zinc desolvation, concomitant with a dynamical redistribution of conformational entropy. Previous results also suggest that zinc binding not only leads to a redistribution of protein internal dynamics, but also release of water molecules from the protein surface. In turn, these water molecules may make a significant contribution to the allosteric response that results in dissociation from the DNA.</p><p>Quantifying the differential hydration of two conformational states that share very similar crystal structures and then correlating this with the protein's solvent entropy change constitutes an unresolved problem, even when thermodynamics suggest a significant contribution of solvent entropy. Here, we present different avenues to dissect hydration dynamics in a metal-binding transcriptional regulator that provide different insights into this complex problem. We explore primary solution NMR tools for probing protein–water interactions: the laboratory frame nuclear Overhauser effect (NOE) and its rotating frame counterpart (ROE) between long-lived water molecules and the protein residues. The wNOE/wROE ratio is a promising tool for the detection of hydration dynamics near the surface of a protein in a site-specific manner, minimizing contamination from bulk solvent. Molecular dynamics simulations and computational methods designed to provide a spatially resolved picture of solvent thermodynamics were also employed to provide a more complete panorama of solvent redistribution.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100114"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1693969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple electron spin resonance echoes observed for paramagnetic defects in diamond at room temperature","authors":"Aharon Blank,&nbsp;Boaz Koren,&nbsp;Alexander Sherman","doi":"10.1016/j.jmro.2023.100133","DOIUrl":"10.1016/j.jmro.2023.100133","url":null,"abstract":"<div><p>Magnetic resonance offers an invaluable testbed for observing and studying the fundamental concepts of quantum cavity interactions with two-level systems in the microwave regime. Typically, these experiments are conducted at low cryogenic temperatures, utilizing spin systems embedded within a high-quality (Q-factor) superconducting cavity. Recent studies indicate that under these conditions, especially in a high-cooperativity regime with strong collective coupling between an electron spin system and a microwave cavity, multiple spin echoes can be detected. These echoes are interpreted as manifestations of coherent quantum effects. To put it simply, photons within the cavity can excite the spin system, which subsequently can stimulate the cavity, creating a feedback loop. In our research, we demonstrate that a specially designed moderate-Q cavity, paired with diamond crystals rich in nitrogen vacancy (NV) centers, allows us to observe such nonlinear quantum phenomena, even at ambient temperatures. Crucially, our experimental design necessitates amplifying the net number of spins for a specific, limited spin concentration. This is achieved by lowering the spins' thermodynamic temperature (as opposed to their physical temperature) to a few kelvins. Notably, we find that maintaining high cooperativity or strong coupling is not essential for these observations. The potential to observe significant microwave cavity quantum effects at room temperature could be useful for future applications, such as quantum memories and quantum sensing.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100133"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666441023000419/pdfft?md5=de70c9a0e7b49643a6f7c5503ac0bcc2&pid=1-s2.0-S2666441023000419-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78958023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Essential tools of linear algebra for calculating nuclear spin dynamics of chemically exchanging systems","authors":"Jingyan Xu,&nbsp;Danila A. Barskiy","doi":"10.1016/j.jmro.2023.100132","DOIUrl":"10.1016/j.jmro.2023.100132","url":null,"abstract":"<div><p>In this work, we describe essential tools of linear algebra necessary for calculating the effect of chemical exchange on spin dynamics and polarization transfer in various nuclear magnetic resonance (NMR) experiments. We show how to construct matrix representations of Hamiltonian, relaxation, and chemical exchange superoperators in both Hilbert and Liouville space, as well as demonstrate corresponding codes in Python. Examples of applying the code are given for problems involving chemical exchange between NH<span><math><msub><mrow></mrow><mrow><mn>3</mn></mrow></msub></math></span> and NH<span><math><msubsup><mrow></mrow><mrow><mn>4</mn></mrow><mrow><mo>+</mo></mrow></msubsup></math></span> at zero and high magnetic field and polarization transfer from parahydrogen relevant in SABRE (signal amplification by reversible exchange) at low magnetic field (0-20<!--> <!-->mT). The presented methodology finds utility for describing the effect of chemical exchange on NMR spectra and can be extended further by taking into account non-linearities in the master equation.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100132"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666441023000407/pdfft?md5=48d5ddc0968c74dfc974a98139168acd&pid=1-s2.0-S2666441023000407-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91472861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring quantum thermodynamics with NMR","authors":"C.H.S. Vieira ,&nbsp;J.L.D. de Oliveira ,&nbsp;J.F.G. Santos ,&nbsp;P.R. Dieguez ,&nbsp;R.M. Serra","doi":"10.1016/j.jmro.2023.100105","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100105","url":null,"abstract":"<div><p>Quantum thermodynamics seeks to extend non-equilibrium stochastic thermodynamics to small quantum systems where non-classical features are essential to its description. Such a research area has recently provided meaningful theoretical and experimental advances by exploring the wealth and the power of quantum features along with informational aspects of a system’s thermodynamics. The relevance of such investigations is related to the fact that quantum technological devices are currently at the forefront of science and engineering applications. This short review article provides an overview of some concepts in quantum thermodynamics highlighting test-of-principles experiments using nuclear magnetic resonance techniques.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100105"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1693968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved linker length in double dsRBD proteins from plants restricts interdomain motion","authors":"Florencia C. Mascali ,&nbsp;Roberta Crespo ,&nbsp;Leandro C. Tabares ,&nbsp;Rodolfo M. Rasia","doi":"10.1016/j.jmro.2023.100109","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100109","url":null,"abstract":"<div><p>Double stranded RNA binding domains (dsRBDs) are ubiquitous in all kingdoms of life. They can participate both in RNA and protein recognition and are usually present in multiple copies in multidomain proteins. We analyzed the linkers between dsRBDs in different proteins and found that sequences corresponding to plant proteins have a highly conserved linker length. In order to assess the importance of linker length in the conformational freedom of double dsRBD plant proteins, we introduced lanthanide binding tags (LBTs) in different positions of the dsRBD containing protein HYL1 from <em>Arabidopsis thaliana</em>. These constructs were used to obtain conformational restraints from Double electron–electron resonance (DEER) measurements on doubly labeled proteins and from paramagnetic relaxation enhancement (PRE) in single labeled samples. Fitting the experimental datasets to a computational model of the ensemble created by allowing freedom to the linker region we found that the domains tend to explore a particular region of the allowed conformational space. The high conservation in linker length suggests that this restricted conformational sampling is functional, possibly hindering HYL1-dsRBD2 from contacting the substrate dsRNA and allowing it to participate in protein-protein interactions.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100109"},"PeriodicalIF":2.624,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}