Journal of Magnetic Resonance Open最新文献

In this work we present a 2D NMR experiment that provides insight into the full chemical exchange saturation transfer (CEST) network present in a sample. It yields all CEST profiles between any signals in a spectrum at once. The method relies on a combination of slice selective saturation during the preparation period, combined with an inverse read-out gradient applied during the evolution time. The resulting 2D spectrum yields gradient profiles in F1 with dips at the frequencies of signals that show a CEST to the corresponding signal in F2.

Aimed at fundamental understanding and design of advanced magnetic resonance experiments on basis of Hamiltonians, we describe highly convergent and exact effective Hamiltonian methods which alleviate important deficits of current less accurate methods. This involves single-spin vector effective Hamiltonian theory (SSV-EHT) to first order in the interaction frame of rf and chemical shift offsets as well as exact effective Hamiltonian theory (EEHT) being an exact approach to average Hamiltonian theory not relying on interaction frame transformations. Bringing these methods together, we present tools to analyze challenging experiments in need of considering large static components in Hamiltonian (e.g., offsets) while economizing with radiofrequency irradiation power. It is demonstrated how the two complementary tools may provide important new insight into the detailed effective Hamiltonians of advanced NMR experiments, noting that the methods are by no means restricted to NMR. This is demonstrated for isotropic mixing in liquid-state NMR and dipolar recoupling in solid-state NMR where insight into the delicate interplay between bilinear two-spin and linear single-spin terms in the effective Hamiltonian may increase understanding of determinants for broadband excitation and the formation of recoupling resonances. Furthermore, we demonstrate how simple products single-spin effective Hamiltonians may be used as generators of multiple-spin effective Hamiltonians and though this a new approach to density operator calculations for large multiple-spin systems.

In this work a rapid RNA assignment approach by combining chemical and enzymatic ¹³C and ¹⁵N stable isotope labeling is introduced. We exemplify the assignment strategy for imino N1H1 purine and N3H3 pyrimidine and aromatic C6H6 pyrimidine, C8H8 purine and C2H2 adenine resonances for a non-coding RNA comprising 66 nucleotides. The assignment strategy is based on position specific labeling by chemical solid phase synthesis and dilute stable isotope ¹³C/¹⁵N-labeling by mixing labeled and commercially available unlabeled RNA phosphoramidites. The assignment process is further facilitated by nucleotide specific labeling using T7 RNA polymerase in vitro transcription with in house produced atom specific ¹³C labeled ribonucleotide triphosphates. The approach is fast with a total NMR measurement time of only 22 h and also competitive in terms of costs as compared to the standard methodology relying on in vitro transcription using ²H, ¹⁵N and ¹³C/¹⁵N uniformly labeled ribonucleotide triphosphates. Furthermore, the assignment procedure revealed a slow exchange process on the NMR chemical shift time scale in the 66 nt non-coding RNA with possible biological implications in the regulation of bacterial competence.

Metabolomics is one of the leading approaches for understanding the toxic-mode-of-action of environmental contaminants. Nuclear Magnetic Resonance (NMR) spectroscopy has been commonly used in metabolomic studies; however, its main drawback is its relatively low sensitivity, making it challenging to study mass limited but environmentally crucial samples. In this work a 1 mm microlitre probe modified with a separate lock chamber to address this challenge, provided substantial improvements in mass sensitivity relative to conventional 5 mm NMR probes. The 1 mm probe is used to analyze various components of the model organism Daphnia magna, including hemolymph, parthenogenetic eggs, dormant eggs, and neonates. A μL volume flow system is designed for the 1 mm probe to perform an in-vivo exposure of neonates to high salt concentrations. The metabolic investigation of these samples was only achieved due to the minimum sample requirements and high salt tolerance of the probe, demonstrating that the 1 mm microlitre probe modified with a separate lock chamber holds significant potential for future metabolomic studies of mass limited samples.

A rigorous quantification of the thermodynamics, kinetic and structural changes can be approached by relaxation dispersion methods, when such motions are in the microsecond to millisecond timescale. Albeit some past efforts, it is still unclear how cosolutes modulate the fitted parameters extracted from relaxation dispersion analyses. Here, we have studied how the systematic measurement of ¹⁵N relaxation dispersion on a well-studied enzyme, undergoing two-state chemical exchange, are affected in terms of the populations of the minor state (thermodynamics) and the exchange rates (kinetics) in the presence of different cosolutes, from ions to denaturants. The cosolute-induced changes are modest but can significantly affect protein function. Specifically, exchange rates can be associated to a subtle leverage in the exchange rates. For most canonical residues, i.e. without spurious effects caused by the cosolute, the chemical shift difference ($\Delta \omega$) between both states is essentially unaffected with respect to the expected shift of water resonance. Yet, solvent exposed residues do not always follow this canonical trend. Instead, residue-cosolute interactions are large enough to induce a residue specific shift that ultimately modulates the fitted parameter $\Delta \omega$. Unfortunately, solvent accessibility analysis is not accurate enough to a priori discriminate between canonical and non-canonical residues and a full experimental analysis at varying concentrations of the cosolute is required. This observation aims to act as a word of caution for measurements of relaxation dispersion at a single-solvent condition that contains large amounts of cosolutes.

Human blood is the most widely used biospecimen in the clinic and the metabolomics field. While both mass spectrometry and NMR spectroscopy are the two premier analytical platforms in the metabolomics field, NMR exhibits several unsurpassed characteristics for blood metabolite analysis, the most important of which are its ability to identify unknown metabolites and its quantitative nature. However, the relatively small number of metabolites accessible by NMR has restricted the scope of its applications. Enhancing the limit of identified metabolites in blood will therefore greatly impact NMR-based metabolomics. Continuing our efforts to address this major issue, our current study describes the identification of 12 metabolites, which expands the number of quantifiable blood metabolites by ∼15%. These results, in combination with our earlier efforts, now provide access to nearly 90 metabolites, which is the highest to date for a simple 1D ¹H NMR experiment that is widely used in the metabolomics field. Metabolites were identified based on the comprehensive investigation of human blood and plasma using 1D/2D NMR techniques. The newly identified metabolites were validated based on chemical shift databases, spectra of authentic compounds obtained under conditions identical to blood/plasma, and, finally, spiking experiments using authentic compounds. Considering the high reproducibility of NMR and the sensitivity of chemical shifts to altered sample conditions, experimental protocols and peak annotations are provided for the newly identified metabolites, which serve as a template for identification of blood metabolites for routine applications. Separately, the identified metabolites were evaluated for their sensitivity to preanalytical conditions. The results reveal that among the newly identified metabolites, inosine monophosphate (IMP) and nicotinamide are associated with labile coenzymes and their levels are sensitive to preanalytical conditions. The study demonstrates the expansion of quantifiable blood metabolites using NMR to a new height and is expected to greatly impact blood metabolomics.

Nuclear Magnetic Resonance (NMR) has been widely used in Petroleum Science and Engineering to study geological formations (porous media) in laboratories or under well-logging conditions. In both cases, NMR is still evolving to provide more accurate data on well productivity. In well-logging, NMR is one of the main tools used in determining the economic viability of an oil well due to the reliability of measurements of fluid types, porosity, pore size, and permeability of the reservoir under analysis. There are two kinds of NMR well-logging techniques: Wireline and Logging While Drilling (LWD). In the latter, due to the drilling process, measurements are made with the NMR tool translating, vibrating and, in some cases, rotating relatively to the geological formation. To understand the behavior of NMR signals measured under LWD conditions, not yet including displacement and drill vibration, we have recently developed a single-sided magnet, probes, and a mechanical system that emulates a relative sinusoidal motion between the sample and the applied magnetic field. This equipment was used to emulate a LWD tool operating under normal pressure and temperature conditions.

Intrinsically disordered regions (IDRs) lack stable tertiary structure and instead rapidly interconvert between different conformations. This structural plasticity enables IDRs to act as key players in cellular signaling pathways. Transcription factors are enriched in IDRs, many of which are stabilized by or acquire tertiary structure in the presence of DNA or other binding partners. Using the T-cell factor/lymphoid enhancer binding factor 1 (TCF/LEF-1) transcription factor as a model system, we characterized the structure and dynamics of the high-mobility group (HMG) domain in the absence of DNA. Inclusion of the IDRs that flank the HMG domain led to enhanced solubility of the protein. Secondary ¹³Cα chemical shifts, ¹H nuclear Overhauser effects, ¹⁵N spin relaxation, and ¹H^N solvent paramagnetic relaxation enhancements indicate that the three helices in the HMG domain are oriented similarly to the DNA-bound form of the protein. By contrast, the flanking IDRs do not show evidence of structure. Helix 1 and helix 3 appear to be less stable in the DNA-free conformation, indicating some form of conformational exchange or local motion in the absence of DNA. Given the high degree of sequence conservation in the TCF/LEF family of transcription factors, our results should apply to other members of the family.

This primer covers de-bugging NMR hardware, at the level of major components (not the circuit board level). It is intended for users of NMR who are unlikely to build their own spectrometer, but will need to localize the malfunction to individual small sub-systems. Brand names and some part numbers of appropriate test equipment and lab-gadgets are given. But many users will find themselves in need of special purpose NMR probes, so construction of a dedicated probe is not beyond consideration. Thus, simple single-resonance probe circuits are discussed at greater length. The need for tuning and coupling of the probe tuned circuit is treated as an exercise in impedance matching.

A transceiver volume coil for High Field Magnetic Resonance Imaging was developed based on Temnikov’s NMR probe coil. The critical advantage of this design is that requires only one trimmer capacitor for both tuning and matching. Electromagnetic simulations of our coil were compared to a four-rung birdcage coil to evaluate their performances. A transceiver coil prototype, called the double-cross coil and a birdcage coil were built to compare and contrast their feasibility. Both coil prototypes were operated in the linear mode. Experimental quality factors were $Q_u/Q_l=101/45$ for the double-cross coil and $Q_u/Q_l=105/43$ for the birdcage coil. Phantom images were acquired to test the viability of each coil for high field magnetic resonance imaging applications. The signal-to-noise ratios, noise factors and uniformity values were also calculated: $85.26/0.74/44.48$ for the double-cross coil and $76.54/1.9/65.65$ for the birdcage coil. These volume coils showed similar performance, but the double-cross coil has better uniformity and a slightly lower noise figure than the birdcage coil. A remarkable agreement of experimental and simulated $B_1$ was obtained for the double-cross coil. These experimental and numerical results demonstrate the feasibility of the double-cross volume coil with better uniformity for rodent magnetic resonance imaging at 7 T.