Membrane proteins participate in a diverse range of cellular functions. Because of their therapeutic and biological importance, membrane proteins have been the focus of intense research efforts aiming at characterizing their three-dimensional structures, dynamics, and interactions. Despite recent progress in X-ray crystallography, electron microscopy, and solution NMR, membrane protein structures remain underrepresented in the protein data bank. One of the key challenges is related to the fact that membrane proteins reside in a heterogeneous environment of cell membranes, and the physical and chemical properties of the membrane have, in many cases, direct effects on membrane protein structure and function. Solid-state NMR is an emerging structural method that is uniquely positioned to characterize membrane proteins in lipid bilayers that closely mimic native membranes. We discuss here modern magic angle spinning solid-state NMR methodologies for a complete structure determination, beginning from sample preparation requirements, to structure determination methods, to modern ultrafast magic angle spinning NMR methods that allow for improved sensitivity of NMR detection.
Nuclear magnetic resonance (NMR)-based metabolomics has led to several pathbreaking developments in the characterization of the plant metabolome. New techniques for data processing and analysis of NMR spectra have improved the identification and quantitation of primary and secondary plant metabolites. The exciting possibility of using machine learning algorithms and artificial-intelligence tools such as deep learning and neural networks for multivariate statistical analysis of NMR data has opened up new avenues of research in integrating 'Big Data' methods with plant metabolomics. Quantitative metabolite fingerprinting using two-dimensional (2D) ultrafast and high-resolution magic angle spinning (HR-MAS) NMR experiments has provided unique perspectives on the interactions of plant metabolic networks and their responses to external environment stresses. Plant NMR metabolomic studies have contributed significantly to the understanding of plant classification and taxonomy, the interaction of plant metabolic networks, bioactivity and mechanism of action of significant metabolites in medicinally important plants, genetically modified plants and their ecological implications, plant-organism interactions, plant defense against herbivore and pathogen attacks, and plant metabolome response to abiotic stress.
Regulation of gene expression, DNA replication, and repair, all converge on chromatin and its repeating unit, the nucleosome. Nucleosomes are inherently dynamic macromolecular assemblies that are bound and manipulated by a wide array of proteins. Structural biology of nucleosomes is a large and exciting field that is in need of a range of complementary techniques. With the introduction of advanced, high-resolution solution and, since recently, solid-state NMR techniques to the nucleosome, NMR offers an attractive alternative to crystallographic and microscopic methods to uncover the molecular mechanisms in chromatin biology. In this article, we review the practical aspects of nucleosome studies by NMR. After a brief description of nucleosome structure and functions, and outlining some of the main questions in the field, we highlight the key aspects in the preparation of nucleosome samples. We then review the application of backbone-based and methyl-TROSY solution-state NMR and C-13- and H-1-detected solid-state NMR. Finally, we detail the advantages and limitations of these approaches.
Selective 2D J-resolved spectroscopy delivers 2D spectra where exclusively homonuclear couplings to a selected spin feature as doublets along the indirect dimension, facilitating their measurement. The original experiment, SERF, uses frequency-selective pulses in order to manipulate the evolution of particular couplings. This basic principle has been improved and expanded upon in many follow-up experiments over the years. Experiments using the Zangger-Sterk or PSYCHE pulse sequence elements have resulted in variants called G-SERF and PSYCHEDELIC, respectively, and allow observation of a wider spectral bandwidth and decoupling of spins with close chemical shifts. Also, strategies to achieve high-resolution full absorption mode line shapes have been proposed. Finally, homonuclear decoupling methods have been introduced to suppress couplings to nonselected spins in the spectrum and thus avoid spectral overlap. Rather than providing a historic and comprehensive overview of the many different variations of SERF, this article presents the selective 2D J-resolved spectroscopy as a modular experiment, where these various features can be introduced to fit a particular situation. Advantages and drawbacks of each variation are discussed.
Dynamic nuclear polarization (DNP) is a method of enhancing the nuclear magnetic resonance (NMR) signal, usually in the solid state, and has gained huge popularity in the past 15 years or so, with the ability to perform DNP at high fields (>3T). In DNP, the large electron spin polarization is transferred to nuclear spins, using on-resonance (or nearly on-resonance) microwave (MW) irradiation on the electrons, creating what is known as nuclear hyperpolarization. In most cases, monochromatic continuous-wave (CW) MW irradiation is used (i.e., MW irradiation at a single frequency), and the frequency of the MW irradiation is chosen such that the highest DNP enhancement is achieved. One method of further increasing the nuclear enhancement is frequency/field modulation. Frequency/field modulation and pulsed DNP techniques were first introduced for low-field DNP (<3 T), where they proved to be very effective methods for increasing the DNP enhancement compared to CW irradiation. Later, researchers creating polarized proton and deuteron targets used frequency modulation to enhance polarization of their targets at magnetic fields of similar to 2.5T. Since 2010, several groups have demonstrated that frequency modulation or trains of chirp pulses can enhance the DNP performance severalfold in static (nonspinning) DNP experiments for NMR at high fields (>3T). In this article, we review the theory behind frequency modulation in DNP at high fields and discuss the practical aspects of the frequency-modulated DNP experiment under static conditions.
A major advantage of Magnetic Resonance Imaging (MRI) is its ability to generate soft tissue contrast. Flexibility in designing custom or open source pulse sequences has a direct impact on the ability to rapidly prototype MR techniques and strategies. However, it is important to be cognizant of the MR safety risks that are associated with such custom sequences. In this article, we discuss methods to compute SAR using Q-matrices followed by a compression algorithm to speed up SAR computation. We demonstrate the integration of these computations with open source pulse sequence programming tools such as Pulseq to predict RF power deposition. Examples of numerical simulation and experimental results as well as the code used to generate these results are provided.
The electromagnetic fields of a magnetic resonance (MR) system incur risks for researchers, participants, and building staff. These risks include the missile effects, burns, acoustic damage, peripheral nerve stimulation, and damage to medical implants. MR safety can be managed through a combination of training, zone signage, device labeling, and careful participant screening. Restricting access to MR areas and requiring all research projects to obtain prior institutional approval are crucial for safety.
RF fields from transmit body coils and transmit arrays can induce large voltages and currents in receive arrays. These voltages and currents can in turn cause excessive heating of the coils and parts of an array and can lead to excessive heating of the surfaces of a coil former. Heating of coil parts can compromise the reliability of a coil and can also adversely affect image quality of a patient examination. Insertion of RF blocking circuits into a coil are essential in preventing excessive heating, and they are essential, as well, in preventing excessive currents from being induced in the tissues situated beneath the coil. Here, the heating of coil parts from the transmit fields of standard body coils is reviewed, including heating from DC control and power supply lines, with steps that can be taken to mitigate this heating. The goal for coil design is to improve reliability and meet the regulatory standards (IEC and FDA) for medical equipment.
Magnetic resonance imaging (MRI) heavily relies on using gradient coils to encode the spatial origin of the recorded nuclear induction signals. In this article, the properties of the magnetic fields generated by the gradient coil are discussed, and the approaches to control the interactions of these fields with the environment are reviewed. Thereafter, current gradient design methods based on discretized stream function formalism are introduced, along with selected engineering, manufacturing, and safety considerations.
This article introduces the basic electromagnetic theory, different solvers principles, and also more practical matters such as a practical workflow, the need and means of validating a simulation, and a nonexhaustive list of simulation software (open source and commercial).
To understand the biofluid mechanics of blood in the circulatory system, in this article, we have used mathematics as a tool to comprehend the flow phenomenon of blood in human arteries under magnetic field effect having arterial diseases and develop methods to cure them. We have considered a two-dimensional flow model, in which blood is considered to be laminar, unsteady, and incompressible, through an arterial segment having atherosclerosis or aneurysm under magnetic field effect. Numerical investigation of flow of blood and heat transfer has been performed for better understanding of blood flow through arteries with a diseased condition. The heat transfer characteristic has been analyzed by taking into consideration the dissipation of energy due to applied magnetic field and the viscosity of blood. The Crank-Nicolson method and vorticity-stream function formulation have been adopted to solve the problem using implicit finite difference. The streamline and temperature contours have been plotted to understand the flow pattern in the diseased artery, which alters significantly in the diseased part in the presence of magnetic field. The area of low WSS region inside the diseased part reduces when exposed to magnetic field strength and makes the arterial state less pathological, which gave us the way to use drug delivery system with magnetic nanoparticles in the diseased artery. The study shows that the WSS has a reducing effect on increasing particle concentration at the downstream of the stenosis, which depicts the vigorous flow circulation zone.
Temperature, specific absorption rate (SAR), or a temperature-time integral (otherwise known as thermal dose) - all three seem appropriate as a choice for a radiofrequency (RF) safety metric in magnetic resonance imaging (MRI). The article discusses the challenges associated with implementing these metrices. Next, the potential of a validated bioheat transfer model, such as the generic bioheat transfer model (GBHTM) framework, in improving RF safety is discussed along with the additional considerations and data that would be needed to appropriately implement a thermal dose threshold-based metric to make MRI more flexible, powerful, yet safer.
Thermometry response of a fluoroptic probe is modeled. It is shown that fluoroptic temperature probes may take several seconds to reach the true temperature. Next, the modeled response is used to develop a generic relationship between the measured and true temperatures, and the relationship is used to investigate the difference between the true and measured temperatures for step, ramp, and exponentially varying true temperatures. The results show that fluoroptic probes may introduce time-varying error in measuring steady or time-varying temperatures. Additional analysis may be needed to estimate the true temperature and develop correlations between thermogenic hazards and true temperature-time history.
Aquatic organisms are challenged by multiple environmental stressors related to global warming, ocean acidification, or exposure to pollutants. Organisms are able to respond to these stressors by activating adaptive and defensive mechanisms, which could result in stress-induced physiological alterations that are ultimately reflected in their metabolite composition. Therefore, the necessity of determining the biological effects of environmental disturbances on organisms and gaining in-depth insights into the metabolism of living organisms has enabled the progress of metabolomics in the fields of environmental research and ecotoxicology. Metabolomics is a powerful approach with a huge potential to assess and reveal in a complex biological system altered metabolism produced in response to environmental stressors, exposure to toxicants or diseases. The high applicability of this approach is due to its ability to qualitatively and quantitatively characterize the chemical profile of low molecular weight metabolites (metabolome) present in cells, tissues, organs, and biofluids as end products of the cellular regulatory pathways. Thus, providing a snapshot of the phenotype of a biological system, metabolomics offers useful contributions to the understanding of the functional status of aquatic organisms and comprehensive insights into important metabolic processes. Over the last two decades, the number of scientific publications that adopted nuclear magnetic resonance (NMR)-based metabolomics to elucidate the interactions between aquatic organisms and their environment has increased consistently. Studies that applied NMR metabolomics on aquatic organisms, both invertebrates and fish, are reviewed herein to demonstrate its potential to unveil the modes of actions of environmental stressors and identify metabolite biomarkers.
Purpose: To investigate the induced heating in vivo due to the radiofrequency (RF) power deposition from a 3 T birdcage, whole-body transmit coil. Method: Seven anesthetized and fleeced sheep were used in the study. The heating was induced by depositing the scanner-reported whole-body average specific absorption rate (SAR) between 1.6 and 4.0 W kg(-1) in sheep continuously for an hour. Two cases were studied, one, when the sheep head was placed in the isocenter (N = 3) and the other, when the sheep body was placed in the isocenter (N = 3). One sheep was used to evaluate the effect of anesthesia on the body temperature in the absence of any RF power deposition. The temperatures were measured using magnetic resonance (MR)-compatible fluoroptic probes. Results: The rate of brain temperature rise was measured as similar to 0.6-1.0 degrees C W-1 kg(-1) h(-1) when the sheep head was placed in the isocenter. In comparison, the rate of rectal temperature rise was measured as similar to 0.6-1.3 degrees C W-1 kg(-1) h(-1) when the sheep trunk was placed in the isocenter. Conclusions: The results suggest that the temperature change may exceed the maximum permissible safe temperature change limit in the body (i.e., 1 degrees C) with allowable RF power deposition.
Acoustic noise is a frequently overlooked hazard of MRI. A sufficiently high dose of noise will temporarily reduce hearing acuity and potentially contribute toward a permanent hearing deficit that accrues over time. At a higher noise dose, permanent hearing damage may occur nearly immediately, with the potential for instantaneous hearing loss at even higher noise levels. Other potentially deleterious short-term and long-term health effects due to noise have been reported. In general, MRI scanners are capable of producing a damaging dose of acoustic noise and are forbidden, by regulation, from producing noise levels (140 dB) capable of immediate hearing loss. Therefore, hearing protection is essential and appropriate solutions are widely available. MRI noise exposure limits (99 dBA) are derived from occupational guidelines; however, there is an ongoing debate on appropriate occupational noise exposure thresholds as a function of exposure profile for hearing acuity conservation, as evidenced by the different regulations across the world. The purpose of this article is as follows: an overview of pertinent regulations, hearing protection options and the critical need for proper usage training, summarize the health concerns associated with high noise dose, focus specifically on MRI exposure findings, summarize MRI incident reports, and propose improved operational safety practices for patients receiving an MRI scan. In conclusion, properly applied hearing protection, appropriately sized for the patient, for all scanning conditions is strongly recommended, eliminating the likelihood of any contribution to long-term hearing loss and reducing the likelihood of distress for acoustically sensitive patients.
This article discusses the MR modeling of electromagnetic fields generated by the RF coil within a phantom or the human head or body, termed the scatterer, using integral equations. There are two variations in MRI modeling, which are discussed in broad outline. In the first, the scatterer is assumed to be homogeneous, and the known electric and magnetic surface currents generated by the incident RF coil fields are calculated. From these currents, it would be possible to calculate the fields in the interior even if the scatterer is inhomogeneous and average complex permittivity was used. In the second volumetric approach, the inhomogeneous dielectric scatterer is replaced by a polarizable current density, and the scattering fields are calculated in terms of the electric flux density from which the electric and magnetic fields are calculated. The weak formulation is used, and fast Fourier transform is applied to speed up the calculations. The volumetric results obtained in 7 min of a head excited by a plane wave compare very well with the finite difference time domain results which take typically a couple of hours.
The cell walls in plants and microbes serve as a central source for biorenewable energy and biomaterials, as well as the target for novel antibiotics and antifungals. They are biocomposites abundant in complex carbohydrates, a class of biologically important but underinvestigated molecules. Solid-state nuclear magnetic resonance (ssNMR) of carbohydrate materials and cell walls has made significant progress over the past 10 years. This article summarizes the recent ssNMR studies that have elucidated the polymorphic structure and heterogeneous dynamics of polysaccharides and other biomolecules, such as proteins, lignin, and pigment, in the intact cell walls or biofilms of 11 species across plants, fungi, bacteria, and algae. We also highlight the assistance of magic-angle spinning dynamic nuclear polarization (MAS-DNP) in the enhanced detection of the interaction interface involving lowly populated biopolymers and summarize the recent applications of natural-abundance MAS-DNP in cell-wall research, which could substantially broaden the scope of biomolecular NMR by skipping isotope labeling.
Magic-angle spinning (MAS) NMR coupled with dynamic nuclear polarization (DNP) has the possibility to increase the sensitivity of MAS NMR by several orders of magnitude. While DNP enables many experiments that are sensitivity limited, such as those on dilute samples or those that measure long-range distances, interpretation of DNP NMR spectra is often limited by broad lines and chemical shift degeneracy. Segmental isotopic labeling using split intein technology can provide an opportunity to overcome this issue. Isotopic labeling of only a segment of a protein that is otherwise unlabeled reduces the chemical shift degeneracy. In this article, we describe the current state of the art for producing segmentally isotopically labeled proteins using split inteins. We discuss some of the potential applications of segmental isotopic labeling, particularly those that exploit the increased experimental sensitivity of DNP-enhanced MAS NMR spectroscopy.
In this article, factors that influence magnetic resonance imaging (MRI) radio-frequency (RF)-induced heating and voltage for patients with active implantable medical devices (AIMDs) are analyzed based on the transfer function method and the transmission line model. The influence of each factor is analyzed in the form of transmission line coefficients and impedances. These factors include factors of the media environment and factors of AIMDs. The analysis of the media environment factors provides insights into the tissue-simulating medium selection, and the analysis of AIMD factors can help the design of MRI conditionally safe AIMDs.
