Pulse electron paramagnetic resonance imaging (Pulse EPRI) is a robust method for noninvasively measuring local oxygen concentrations in vivo. For 3D tomographic EPRI, the most commonly used reconstruction algorithm is filtered back projection (FBP), in which the parabolic filtration process strongly influences image quality. In this work, we designed and compared 7 parabolic filtration methods to reconstruct both simulated and real phantoms. To evaluate these methods, we designed 3 error criteria and 1 spatial resolution criterion. It was determined that the 2 point derivative filtration method and the two-ramp-filter method have unavoidable negative effects resulting in diminished spatial resolution and increased artifacts respectively. For the noiseless phantom the rectangular-window parabolic filtration method and sinc-window parabolic filtration method were found to be optimal, providing high spatial resolution and small errors. In the presence of noise, the 3 point derivative method and Hamming-window parabolic filtration method resulted in the best compromise between low image noise and high spatial resolution. The 3 point derivative method is faster than Hamming-window parabolic filtration method, so we conclude that the 3 point derivative method is optimal for 3D FBP.
Parabolic filter; 3D FBP; EPRI; Noise; Spatial Resolution
The development of biocompatible hyperpolarized media is a crucial step towards application of hyperpolarization in vivo. This article describes the achievement of 1% hyperpolarization of 3-amino-1,2,4-triazine protons in water using the parahydrogen induced polarization technique based on signal amplification by reversible exchange (SABRE). Polarization was achieved in less than 1 min.
SABRE; Parahydrogen; Hyperpolarization
A tunable 900 MHz transmit/receive volume coil was constructed for 1H MR imaging of biological samples in a 21.1 T vertical bore magnet. To accommodate a diverse range of specimen and RF loads at such a high frequency, a sliding-ring adaptation of a low-pass birdcage was implemented through simultaneous alteration of distributed capacitance. To make efficient use of the constrained space inside the vertical bore, a modular probe design was implemented with a bottom-adjustable tuning and matching apparatus. The sliding ring coil displays good homogeneity and sufficient tuning range for different samples of various dimensions representing large span of RF loads. High resolution in vivo and ex vivo images of large rats (up to 350 g), mice and human postmortem tissues were obtained to demonstrate coil functionality and to provide examples of potential applications at 21.1 T.
High magnetic field; MRI; RF coil design; birdcage coil; vertical bore MRI; sliding-ring; 900 MHz; 21.1 Tesla; B1 homogeneity; MRI of rats; in vivo MRI
We describe the incorporation of non-uniform sampling (NUS) compressed sensing (CS) into Oriented Sample (OS) Solid-state NMR for stationary aligned samples and Magic Angle Spinning (MAS) Solid-state NMR for unoriented ‘powder’ samples Both simulated and experimental results indicate that 25% to 33% of a full linearly sampled data set is required to reconstruct two-and three-dimensional solid-state NMR spectra with high fidelity. A modest increase in signal-to-noise ratio is accompanies the reconstruction.
Inherent low sensitivity of NMR spectroscopy has been a major disadvantage, especially to study biomolecules like membrane proteins. Recent studies have successfully demonstrated the advantages of performing solid-state NMR experiments at very low and ultralow temperatures to enhance the sensitivity. However, the long spin-lattice relaxation time, T1, at very low temperatures is a major limitation. To overcome this difficulty, we demonstrate the use of a copper-chelated lipid for magic angle spinning solid-state NMR measurements on cytochrome-b5 reconstituted in multilamellar vesicles. Our results on multilamellar vesicles containing as small as 0.5 mole % of a copper-chelated lipid can significantly shorten T1 of protons, which can be used to considerably reduce the data collection time or to enhance the signal-to-noise ratio. We also monitored the effect of slow cooling on the resolution and sensitivity of 13C and 15N signals from the protein and 13C signals from lipids.
MRI signal-to-noise ratio (SNR) is the key factor for image quality. Conventionally, SNR is proportional to nuclear spin polarization, which scales linearly with magnetic field strength. Yet ever-stronger magnets present numerous technical and financial limitations. Low-field MRI can mitigate these constraints with equivalent SNR from non-equilibrium ‘hyperpolarization’ schemes, which increase polarization by orders of magnitude independently of the magnetic field. Here, theory and experimental validation demonstrate that combination of field independent polarization (e.g. hyperpolarization) with frequency optimized MRI detection coils (i.e. multi-turn coils using the maximum allowed conductor length) results in low-field MRI sensitivity approaching and even rivaling that of high-field MRI. Four read-out frequencies were tested using samples with identical numbers of 1H and 13C spins. Experimental SNRs at 0.0475 T were ∼40% of those obtained at 4.7 T. Conservatively, theoretical SNRs at 0.0475 T 1.13-fold higher than 4.7 T were possible despite an ∼100-fold lower detection frequency, indicating feasibility of high-sensitivity MRI without technically challenging, expensive high-field magnets. The data at 4.7 T and 0.0475 T was obtained from different spectrometers with different RF probes. The SNR comparison between the two field strengths accounted for many differences in parameters such as system noise figures and variations in the probe detection coils including Q factors and coil diameters.
hyperpolarization; MRI; NMR; low-field MRI; Litz wire; 13C
Two-dimensional 15N chemical shift/1H chemical shift and three-dimensional 1H-15N dipolar coupling/15N chemical shift/1H chemical shift MAS solid-state NMR correlation spectra of the filamentous bacteriophage Pf1 major coat protein show single-site resolution in noncrystalline, intact-phage preparations. The high sensitivity and resolution result from 1H detection at 600 MHz under 50 kHz magic angle spinning using ~ 0.5 mg of perdeuterated and uniformly 15N-labeled protein in which the exchangeable amide sites are partially or completely back-exchanged (reprotonated). Notably, the heteronuclear 1H-15N dipolar coupling frequency dimension is shown to select among 15N resonances, which will be useful in structural studies of larger proteins where the resonances exhibit a high degree of overlap in multidimensional chemical shift correlation spectra.
perdeuteration; proton detection; variable contact time cross-polarization; Pf1 bacteriophage; separated local field spectroscopy; two-dimensional NMR; three-dimensional NMR; fast MAS
Noninvasive magnetic resonance spectroscopy (MRS) with chemical shift imaging (CSI) provides valuable metabolic information for research and clinical studies, but is often limited by long scan times. Recently, spectroscopy with linear algebraic modeling (SLAM) was shown to provide compartment-averaged spectra resolved in one spatial dimension with many-fold reductions in scan-time. This was achieved using a small subset of the CSI phase-encoding steps from central image k-space that maximized the signal-to-noise ratio. Here, SLAM is extended to two- and three-dimensions (2D, 3D). In addition, SLAM is combined with sensitivity-encoded (SENSE) parallel imaging techniques, enabling the replacement of even more CSI phase-encoding steps to further accelerate scan-speed. A modified SLAM reconstruction algorithm is introduced that significantly reduces the effects of signal nonuniformity within compartments. Finally, main-field inhomogeneity corrections are provided, analogous to CSI. These methods are all tested on brain proton MRS data from a total of 24 patients with brain tumors, and in a human cardiac phosphorus 3D SLAM study at 3T. Acceleration factors of up to 120-fold versus CSI are demonstrated, including speed-up factors of 5-fold relative to already-accelerated SENSE CSI. Brain metabolites are quantified in SLAM and SENSE SLAM spectra and found to be indistinguishable from CSI measures from the same compartments. The modified reconstruction algorithm demonstrated immunity to maladjusted segmentation and errors from signal heterogeneity in brain data. In conclusion, SLAM demonstrates the potential to supplant CSI in studies requiring compartment-average spectra or large volume coverage, by dramatically reducing scan-time while providing essentially the same quantitative results.
localized spectroscopy; chemical shift imaging (CSI); SLAM; brain; cancer; heart
Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.
RDC; Spin relaxation; Relaxation dispersion; Hoogsteen; Excited states
Techniques that accelerate data acquisition without sacrificing the advantages of fast Fourier transform (FFT) reconstruction could benefit a wide variety of magnetic resonance experiments. Here we discuss an approach for reconstructing multidimensional nuclear magnetic resonance (NMR) spectra and MR images from sparsely-sampled time domain data, by way of iterated maps. This method exploits the computational speed of the FFT algorithm and is done in a deterministic way, by reformulating any a priori knowledge or constraints into projections, and then iterating. In this paper we explain the motivation behind this approach, the formulation of the specific projections, the benefits of using a ‘QUasi-Even Sampling, plus jiTter’ (QUEST) sampling schedule, and various methods for handling noise. Applying the iterated maps method to real 2D NMR and 3D MRI of solids data, we show that it is flexible and robust enough to handle large data sets with significant noise and artifacts.
sparse sampling; iterative maps; multi-dimensional nuclear magnetic resonance; magnetic resonance imaging
Lorentz Effect Imaging (LEI) is an MRI technique that has been proposed for direct imaging of neuronal activity. While promising results have been obtained in phantoms and in the human median nerve in vivo, its contrast mechanism is still not fully understood. In this paper, computational model simulations were used to investigate how electromagnetohydrodynamics (EMHD) may explain the LEI contrast.
Three computational models of an electrolyte-filled phantom subject to an applied current dipole, synchronized to oscillating magnetic field gradients of an LEI protocol, were developed to determine the velocity and displacement of water molecules as well as the resulting signal loss in an MR image. The simulated images were compared to images from previous LEI phantom experiments with identical properties for different stimulus current amplitudes and polarities.
The first model, which evaluated ion trajectories based on Stokes flow using different mobility values, did not generate an appreciable signal loss due to an insufficient number of water molecules associated with the ion hydration shells. The second model, which computed particle drift based on the Lorentz force of charged particles in free space, was able to approximate the magnitude, but not the distribution of signal loss observed in the experimental images. The third model, which computed EMHD based on the Lorentz force and Navier-Stokes equations for flow of a conducting fluid, provided results consistent with both the magnitude and distribution of signal loss seen in the LEI experiments. Our EMHD model further yields information on electrical potential, velocity, displacement, and pressure, which are not readily available in an experiment, thereby providing a robust means to study and optimize LEI for imaging neuronal activity in the human cortex.
functional magnetic resonance imaging; neuronal current MRI; Lorentz effect imaging; electromagnetohydrodynamics; oscillating magnetic field gradients; computational modeling
We propose a new approach to stabilizing the inverse Laplace transform of a multiexponential decay signal, a classically ill-posed problem, in the context of nuclear magnetic resonance relaxometry. The method is based on extension to a second, indirectly detected, dimension, that is, use of the established framework of two-dimensional relaxometry, followed by projection onto the desired axis. Numerical results for signals comprised of discrete T1 and T2 relaxation components and experiments performed on agarose gel phantoms are presented. We find markedly improved accuracy, and stability with respect to noise, as well as insensitivity to regularization in quantifying underlying relaxation components through use of the two-dimensional as compared to the one-dimensional inverse Laplace transform. This improvement is demonstrated separately for two different inversion algorithms, nonnegative least squares and non-linear least squares, to indicate the generalizability of this approach. These results may have wide applicability in approaches to the Fredholm integral equation of the first kind.
Inverse problems; NMR relaxometry; Fredholm integral
ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [Bahrami, A., Tonelli, M., Sahu, S.C., Singarapu, K.K., Eghbalnia, H.R., Markley, J.L., 2012. PLoS ONE 7, e33173.]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 hours). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 hours. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.
ADAPT-NMR; Bruker; Reduced Dimensionality; Fast NMR data collection; Computational Biology; Structural Biology
Sensitivity and resolution are the two fundamental obstacles to extending solid-state nuclear magnetic resonance to even larger protein systems. Here, a novel long-observation-window band-selective homonuclear decoupling (LOW BASHD) scheme is introduced that increases resolution up to a factor of 3 and sensitivity up to 1.8 by decoupling backbone alpha-carbon (Cα) and carbonyl (C′) nuclei in U-13C-labeled proteins during direct 13C acquisition. This approach introduces short (<200 μs) pulse breaks into much longer (~8 ms) sampling windows to efficiently refocus the J-coupling interaction during detection while avoiding the deleterious effects on sensitivity inherent in rapid stroboscopic band-selective homonuclear decoupling techniques. A significant advantage of LOW BASHD detection is that it can be directly incorporated into existing correlation methods, as illustrated here for 2D CACO, NCO, and NCA correlation spectroscopy applied to the β1 immunoglobulin binding domain of protein G and 3D CBCACO correlation spectroscopy applied to the α-subunit of tryptophan synthase.
Electron spin relaxation times at 295 K were measured at frequencies between 250 MHz and 34 GHz for perdeuterated 2,2,6,6-tetramethyl-4-piperidone-1-oxyl (PDT) in five solvents with viscosities that result in tumbling correlation times, τR, between 4 and 50 ps and for three 14N/15N pairs of nitroxides in water with τR between 9 and 19 ps. To test the impact of structure on relaxation three additional nitroxides with τR between 10 and 26 ps were studied. In this fast tumbling regime T2−1 ∼ T1−1 at frequencies up to about 9 GHz. At 34 GHz T2−1 > T1−1 due to increased contributions to T2−1 from incomplete motional averaging of g-anisotropy, and T2−1 − T1−1 is proportional to τR. The contribution to T1−1 from spin rotation is independent of frequency and decreases as τR increases. Spin rotation dominates T1−1 at 34 GHz for all τR studied, and at all frequencies studied for τR = 4 ps. The contribution to T1−1 from modulation of nitrogen hyperfine anisotropy increases as frequency decreases and as τR increases; it dominates at low frequencies for τR > ∼ 15 ps. The contribution from modulation of g anisotropy is significant only at 34 GHz. Inclusion of a thermally-activated process was required to account for the observation that for most of the radicals, T1−1 was smaller at 250 MHz than at 1 to 2 GHz. The significant 15N/14N isotope effect, the small H/D isotope effect, and the viscosity dependence of the magnitude of the contribution from the thermally-activated process suggest that it arises from intramolecular motions of the nitroxide ring that modulate the isotropic A values.
The performance of multi-coil (MC) magnetic field modeling is compared to dedicated wire patterns for the generation of spherical harmonic (SH) shapes as these are the workhorse for spatial encoding and magnetic field homogenization in MR imaging and spectroscopy. To this end, an example 48 channel MC setup is analyzed and shown to be capable of generating all first through fourth order SH shapes over small and large regions-of-interest relevant for MR investigations. The MC efficiency for the generation of linear gradient fields shares the same order of magnitude with classic and state-of-the-art SH gradient coils. MC field modeling becomes progressively more efficient with the synthesis of more complex field shapes that require the combination of multiple SH terms. The possibility of a region-specific optimization of both magnetic field shapes and generation performance with the MC approach are discussed with emphasis on the possible trade-off between the field accuracy and generation efficiency.
MC shimming has been shown previously to outperform current SH shimming. Along with the efficiency gains of MC shimming shown here, the MC concept has the potential to 1) replace conventional shim systems that are based on sets of dedicated SH coils and 2) allow optimal object-specific shim solutions similar to object-specific RF coils.
magnetic fields; modeling; efficiency; accuracy; spherical harmonic functions
Non Adiabatic Rapid Sweep (NARS) EPR spectroscopy has been introduced for application to nitroxide-labeled biological samples (AW Kittell et al, (2011)). Displays are pure absorption, and are built up by acquiring data in spectral segments that are concatenated. In this paper we extend the method to frozen solutions of copper-imidazole, a square planar copper complex with four in-plane nitrogen ligands. Pure absorption spectra are created from concatenation of 170 5-gauss segments spanning 850 G at 1.9 GHz. These spectra, however, are not directly useful since nitrogen superhyperfine couplings are barely visible. Application of the moving difference (MDIFF) algorithm to the digitized NARS pure absorption spectrum is used to produce spectra that are analogous to the first harmonic EPR. The signal intensity is about 4 times higher than when using conventional 100 kHz field modulation, depending on line shape. MDIFF not only filters the spectrum, but also the noise, resulting in further improvement of the SNR for the same signal acquisition time. The MDIFF amplitude can be optimized retrospectively, different spectral regions can be examined at different amplitudes, and an amplitude can be used that is substantially greater than the upper limit of the field modulation amplitude of a conventional EPR spectrometer, which improves the signal-to-noise ratio of broad lines.
EPR; ESR; NARS; MDIFF; moving average; non-adiabatic rapid sweep; direct detection; biological copper
•Echo decay curves were measured on segmentally deuterated, octameric proteins.•The echo dephasing time (Tm) was extracted from each data set.•Spin relaxation was correlated to the spatial distribution of protons.•Temperature and concentration dependence of Tm and T1 was measured.•The effect of deuteration on relaxation and dipolar coupling were discussed.
Pulsed electron–electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems.
EPR; Relaxation; Tm; Spin-label; PELDOR; DEER; Deuteration
A number of experimental issues in the measurement of multi-component T2 and T1ρ relaxations in native and enzymatically digested articular cartilage were investigated by microscopic MRI (μMRI). The issues included the bath solutions (physiological saline and phosphate buffered saline (PBS)), the imaging resolution (35 to 140 μm), the specimen orientations (0° and 55°), and the strength of spin-lock frequencies (0.5 to 2 kHz) in the T1ρ experiments. In addition to cartilage, the samples of agar gel and doped water solution were also used in the investigation. Two imaging sequences were used: CPMG-SE and MSME. All raw data were analyzed by the non-negative least square (NNLS) method. The MSME sequence was shown to result in the observation of multi-component T2, even in the gel and liquid samples, demonstrating the artificial uncleanness of this sequence in the multi-component measurements. The soaking of cartilage in PBS reduced the observable T2 components to one at both 0° and 55°, suggesting the effect of phosphate ions on proton exchange between different pools of water molecules. The cartilage orientation with respect to the external magnetic field and the spin-lock strengths in the T1ρ experiment both affected the quantification of the multi-component relaxation. The transitions between a mono-component and multi-components in cartilage under various experimental conditions call for the extra caution in interpreting the relaxation results.
cartilage; T2 relaxation; T1ρ relaxation; multi-component; MRI; PBS; chemical exchange
Earlier dynamic nuclear polarization (DNP) experiments with frozen xenon/1-propanol/trityl mixtures have demonstrated spontaneous formation of pure xenon clusters above 120 K, enabling spectrally-resolved real-time measurements of 129Xe nuclear magnetization in the clusters and in the surrounding radical-rich matrix. A spin-diffusion bottleneck was postulated to explain the peculiar time evolution of 129Xe signals in the clusters as well as the apparent discontinuity of 129Xe polarization across the cluster boundaries. A self-contained ab initio model of nuclear spin diffusion in heterogeneous systems is developed here, incorporating the intrinsic T1 relaxation towards the temperature-dependent equilibrium along with the spin-diffusion coefficients based on the measured NMR line widths and the known atomic densities in each compartment. This simple model provides the physical basis for the observed spin-diffusion bottleneck and is in a good quantitative agreement with the earlier measurements. A simultaneous fit of the model to the time-dependent NMR data at two different DNP frequencies provides excellent estimates of the cluster size, the intrinsic sample temperature, and 129Xe T1 constants. The model was also applied to the NMR data acquired during relaxation towards thermal equilibrium after microwaves were turned off to estimate T1 relaxation time constants inside and outside the clusters. Fitting the model to data during and after DNP provides estimates of cluster size that are in complete agreement.
Hyperpolarization; MRI; chemical shift; dipolar broadening; nuclear spin diffusion; solid-state diffusion; partial differential equations
We report a 1.5-mm NMR probe based on high temperature superconductors operating at 14.1 T optimized for 13C detection. The probe has a total sample volume of about 35 microliters (μL) with an active volume of 20 μL and provides exceptional mass sensitivity for 13C detection. The probe also has excellent 1H sensitivity and employs a 2H channel lock; 15N irradiation capability can be added in the future. The coils are cooled to about 20 K using a standard Agilent cryogenic refrigeration system, and the sample temperature is regulated near room temperature. The coil design considerations are discussed in detail. This probe is ideal for directly detected 13C NMR experiments for natural products chemistry and metabolomics applications, for which 35 μL is an optimal sample volume. The outstanding 13C sensitivity of this probe allowed us to directly determine the 13C connectivity on 1.1 mg of natural abundance histidine using an INADEQUATE experiment. We demonstrated the utility of this probe for 13C-based metabolomics using a synthetic mixture of common natural abundance metabolites whose concentrations ranged from 1 to 5 mM (40 to 200 nmol).