Ultrafast diffusion exchange nuclear magnetic resonance.
Ontology highlight
ABSTRACT:
SUBMITTER: Mankinen O
PROVIDER: S-EPMC7319991 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In this work, the second-order kinetics of molecules exchanging between chemically distinct microenvironments, such as those found in nanoemulsions, is studied using nuclear magnetic resonance (NMR). A unique aspect of NMR exchange studies in nanoemulsions is that the difference in molecular resonance frequencies between the two phases, which determines whether the exchange is fast, intermediate, or slow on the NMR timescale, can depend upon the emulsion droplet composition, which is also determined by the kinetic exchange constants themselves. Within the fast-exchange regime, changes in resonance frequencies and line widths with dilution were used to extract the exchange rate constants from the NMR spectra in a manner analogous to determining the kinetic parameters in NMR ligand binding experiments. As a demonstration, the kinetic exchange parameters of isoflurane release from an emulsification of isoflurane and perflurotributylamine (FC43) were determined using NMR dilution and diffusion studies.
| S-EPMC8442839 | biostudies-literature
Project description:Hydrogen exchange between solute and water molecules occurs across a wide range of timescales. Rapid hydrogen-exchange processes can effectively diminish 1H-15N scalar couplings. We demonstrate that the self-decoupling of 15N nuclear magnetic resonance can allow quantitative investigations of hydrogen exchange on a micro- to millisecond timescale, which is relatively difficult to analyze with other methods. Using a Liouvillian matrix incorporating hydrogen exchange as a mechanism for scalar relaxation, the hydrogen exchange rate can be determined from 15N NMR line shapes recorded with and without 1H decoupling. Self-decoupling offers a simple approach to analyze the kinetics of hydrogen exchange in a wide range of timescale.
| S-EPMC7067644 | biostudies-literature
Project description:Structure determination of secondary DNA structural elements, such as G-quadruplexes, gains an increasing importance as fundamental physiological roles are being associated with the formation of such structures in vivo. A truncated native DNA sequence generally requires further optimization to obtain a candidate with desired nuclear magnetic resonance (NMR) properties for structural analysis in solution. The optimum sequence is expected to form one dominant, stable molecular entity in solution with well-resolved NMR peaks. However, DNA sequences are prone to form structures composed of one, two, three, or four strands depending on sequence and solution conditions. The thorough characterization of the molecularity (stoichiometry and molecular weight) and appropriate solution conditions for sequences with different modifications traditionally applies analytical techniques that generally do not represent the solution conditions for NMR structure determination. Here we present the application of diffusion-ordered NMR spectroscopy as a useful analytical tool for the optimization and analysis of DNA secondary structural elements, specifically, the DNA G-quadruplex structures, including those formed in the human telomeric sequence and in the promoter regions of bcl-2 and c-myc genes.
| S-EPMC1993845 | biostudies-literature
Project description:PurposeAn emerging topic in diffusion magnetic resonance is imaging blood microcirculation alongside water diffusion using the intravoxel incoherent motion (IVIM) model. Recently, a combined IVIM diffusion tensor imaging (IVIM-DTI) model was proposed, which accounts for both anisotropic pseudo-diffusion due to blood microcirculation and anisotropic diffusion due to tissue microstructures. In this article, we propose a robust IVIM-DTI approach for simultaneous diffusion and pseudo-diffusion tensor imaging.MethodsConventional IVIM estimation methods can be broadly divided into two-step (diffusion and pseudo-diffusion estimated separately) and one-step (diffusion and pseudo-diffusion estimated simultaneously) methods. Here, both methods were applied on the IVIM-DTI model. An improved one-step method based on damped Gauss-Newton algorithm and a Gaussian prior for the model parameters was also introduced. The sensitivities of these methods to different parameter initializations were tested with realistic in silico simulations and experimental in vivo data.ResultsThe one-step damped Gauss-Newton method with a Gaussian prior was less sensitive to noise and the choice of initial parameters and delivered more accurate estimates of IVIM-DTI parameters compared to the other methods.ConclusionOne-step estimation using damped Gauss-Newton and a Gaussian prior is a robust method for simultaneous diffusion and pseudo-diffusion tensor imaging using IVIM-DTI model. Magn Reson Med 79:2367-2378, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
| S-EPMC5836966 | biostudies-literature
Project description:Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface-averaging methods are used, position-dependent measurements of the effective diffusion coefficient are currently: (1) invasive to the biofilm, (2) performed under unnatural conditions, (3) lethal to cells, and/or (4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate results and prohibit further (time-dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: (1) measure the effective diffusion coefficient for water in live biofilms, (2) monitor how the effective diffusion coefficient changes over time under growth conditions, and (3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two-dimensional effective diffusion coefficient maps within Shewanella oneidensis MR-1 biofilms using pulsed-field gradient nuclear magnetic resonance methods, and used them to calculate surface-averaged relative effective diffusion coefficient (D(rs)) profiles. We found that (1) D(rs) decreased from the top of the biofilm to the bottom, (2) D(rs) profiles differed for biofilms of different ages, (3) D(rs) profiles changed over time and generally decreased with time, (4) all the biofilms showed very similar D(rs) profiles near the top of the biofilm, and (5) the D(rs) profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm.
| S-EPMC2898744 | biostudies-literature
Project description:Diffusion-attenuated MR signal for heterogeneous media has been represented as a sum of signals from anisotropic Gaussian sub-domains to the extent that this approximation is permissible. Any effect of macroscopic (global or ensemble) anisotropy in the signal can be removed by averaging the signal values obtained by differently oriented experimental schemes. The resulting average signal is identical to what one would get if the micro-domains are isotropically (e.g., randomly) distributed with respect to orientation, which is the case for "powdered" specimens. We provide exact expressions for the orientationally-averaged signal obtained via general gradient waveforms when the microdomains are characterized by a general diffusion tensor possibly featuring three distinct eigenvalues. This extends earlier results which covered only axisymmetric diffusion as well as measurement tensors. Our results are expected to be useful in not only multidimensional diffusion MR but also solid-state NMR spectroscopy due to the mathematical similarities in the two fields.
| S-EPMC6426978 | biostudies-literature
Project description:PurposeTo develop a subspace learning method for the recently proposed subspace-based MRSI approach known as SPICE, and achieve ultrafast 1 H-MRSI of the brain.Theory and methodsA novel strategy is formulated to learn a low-dimensional subspace representation of MR spectra from specially acquired training data and use the learned subspace for general MRSI experiments. Specifically, the subspace learning problem is formulated as learning "empirical" distributions of molecule-specific spectral parameters (e.g., concentrations, lineshapes, and frequency shifts) by integrating physics-based model and the training data. The learned spectral parameters and quantum mechanical simulation basis can then be combined to construct acquisition-specific subspace for spatiospectral encoding and processing. High-resolution MRSI acquisitions combining ultrashort-TE/short-TR excitation, sparse sampling, and the elimination of water suppression have been performed to evaluate the feasibility of the proposed method.ResultsThe accuracy of the learned subspace and the capability of the proposed method in producing high-resolution 3D 1 H metabolite maps and high-quality spatially resolved spectra (with a nominal resolution of ?2.4 × 2.4 × 3 mm3 in 5 minutes) were demonstrated using phantom and in vivo studies. By eliminating water suppression, we are also able to extract valuable information from the water signals for data processing ( B0 map, frequency drift, and coil sensitivity) as well as for mapping tissue susceptibility and relaxation parameters.ConclusionsThe proposed method enables ultrafast 1 H-MRSI of the brain using a learned subspace, eliminating the need of acquiring subject-dependent navigator data (known as D1 ) in the original SPICE technique. It represents a new way to perform MRSI experiments and an important step toward practical applications of high-resolution MRSI.
| S-EPMC6824949 | biostudies-literature
Project description:BackgroundConventional MRI sequences are often affected in neuropediatric imaging by unavoidable movements. Therefore, children younger than 6 years usually have to be examined under sedation/anesthesia. A new real-time MRI technique with automatic slice advancement allows for motion-robust T2-weighted volume coverage of the whole brain within a few seconds in adults.ObjectiveTo evaluate to which extent the new volume coverage method can be used to visualize cerebrospinal fluid and reduce the need for anesthesia in children.Materials and methodsWe assessed 30 children ages 6 years and younger with suspected or proven hydrocephalus, hygroma or macrocephalus using volume coverage sequences with 20 slices per second in three planes. If necessary, a parent was placed in the bore together with the child for calming and gentle immobilization. We compared visualization of cerebrospinal fluid spaces and course of the shunt catheter in volume coverage sequences vs. fast spin-echo sequences.ResultsThe clinical issue could be sufficiently assessed in all children with use of volume coverage sequences, whereas conventional fast spin-echo sequences performed moderately to poorly. Visualization of the tip of a shunt failed in 16% of volume coverage scans and 27% of turbo spin-echo scans. A subsequent examination under anesthesia was never necessary. None of the examinations had to be stopped prematurely.ConclusionThe motion-robust volume coverage sequences with T2-type contrast can be used to avoid sedation of children in the evaluation of cerebrospinal fluid spaces, even in the presence of vigorous motion. For other indications and contrasts, the technique must still be evaluated.
| S-EPMC7604272 | biostudies-literature
Project description:Base pairs are fundamental building blocks of RNA. The base pairs of low stability are often critical in RNA functions. Here, we develop a solid-state NMR-based water-RNA exchange spectroscopy (WaterREXSY) to characterize RNA in solid. The approach uses different chemical exchange rates between iminos and water to evaluate base pair stability; the less stable ones would exchange more frequently, leading to stronger cross-peaks on WaterREXSY. Applied to the riboA71-adenine complex (the 71nt-aptamer domain of add adenine riboswitch from Vibrio vulnificus), the U47⋅U51 base pair, which is critical in ligand binding, was found to be less stable than other base pairs. The imino-water exchange rates of U47 at different temperatures are about 500-800 s-1, indeed indicative of low stability. This implies a highly complex and plastic triad involving U47⋅U51 and that the opening of the U47⋅U51 base pair may be the early stage of ligand release.
| S-EPMC9619310 | biostudies-literature
Project description:Mesoporous materials are promising catalysts for production of biofuels. Herein, H-MCM-41 catalysts with different concentrations of the silica Bindzil binder (10-50 wt%) were prepared and characterized using pulsed-field gradient (PFG) NMR in the powder form and as extrudates. Effective diffusion coefficients (De) are measured in all cases. Diffusivities of n-hexadecane were found smaller for extrudates as compared to the powder catalysts. The estimates of diffusive tortuosity were also determined. PFG NMR data showed one major component that reveals diffusion in interconnected meso- and micropores and one other minor component (1-2%) that may correspond to more isolated pores or may represent complex effects of restricted diffusion. Therefore, several approaches including initial slope analysis of spin-echo attenuation curves, two-component fitting and Laplace inversion were used to discuss different aspects of diffusional transport in the studied H-MCM-41 materials. Correlations between De and the amount of Bindzil, the specific surface area, the micropore volume, the particle size, the total acid sites and the Lewis acid sites are discussed.
| S-EPMC8985658 | biostudies-literature