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1.
Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii.
Zahn, S, Kubatova, N, Pyper, DJ, Cassidy, L, Saxena, K, Tholey, A, Schwalbe, H, Soppa, J
The FEBS journal. 2021;(6):2042-2062
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Abstract
The genome of the halophilic archaeon Haloferax volcanii encodes more than 40 one-domain zinc finger µ-proteins. Only one of these, HVO_2753, contains four C(P)XCG motifs, suggesting the presence of two zinc binding pockets (ZBPs). Homologs of HVO_2753 are widespread in many euryarchaeota. An in frame deletion mutant of HVO_2753 grew indistinguishably from the wild-type in several media, but had a severe defect in swarming and in biofilm formation. For further analyses, the protein was produced homologously as well as heterologously in Escherichia coli. HVO_2753 was stable and folded in low salt, in contrast to many other haloarchaeal proteins. Only haloarchaeal HVO_2753 homologs carry a very hydrophilic N terminus, and NMR analysis showed that this region is very flexible and not part of the core structure. Surprisingly, both NMR analysis and a fluorimetric assay revealed that HVO_2753 binds only one zinc ion, despite the presence of two ZBPs. Notably, the analysis of cysteine to alanine mutant proteins by NMR as well by in vivo complementation revealed that all four C(P)XCG motifs are essential for folding and function. The NMR solution structure of the major conformation of HVO_2753 was solved. Unexpectedly, it was revealed that ZBP1 was comprised of C(P)XCG motifs 1 and 3, and ZBP2 was comprised of C(P)XCG motifs 2 and 4. There are several indications that ZBP2 is occupied by zinc, in contrast to ZBP1. To our knowledge, this study represents the first in-depth analysis of a zinc finger µ-protein in all three domains of life.
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Deuterium metabolic imaging - Back to the future.
De Feyter, HM, de Graaf, RA
Journal of magnetic resonance (San Diego, Calif. : 1997). 2021;:106932
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Abstract
Deuterium metabolic spectroscopy (DMS) and imaging (DMI) have recently been described as simple and robust MR-based methods to map metabolism with high temporal and/or spatial resolution. The metabolic fate of a wide range of suitable deuterated substrates, including glucose and acetate, can be monitored with deuterium MR methods in which the favorable MR characteristics of deuterium prevent many of the complications that hamper other techniques. The short T1 relaxation times lead to good MR sensitivity, while the low natural abundance prevents the need for water or lipid suppression. The sparsity of the deuterium spectra in combination with the low resonance frequency provides relative immunity to magnetic field inhomogeneity. Taken together, these features combine into a highly robust metabolic imaging method that has strong potential to become a dominant MR research tool and a viable clinical imaging modality. This perspective reviews the history of deuterium as a metabolic tracer, the use of NMR as a detection method for deuterium in vitro and in vivo and the recent development of DMS and DMI. Following a review of the NMR characteristics and the biological effects of deuterium, the promising future of DMI is outlined.
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The nuclear magnetic resonance metabolic profile: Impact of fasting status.
Smy, L, De Biase, I, Genzen, JR, Yuzyuk, T
Clinical biochemistry. 2021;:85-92
Abstract
INTRODUCTION Measurement of lipoprotein subclass concentration (-c), particle number (-p), and size (-s) by nuclear magnetic resonance (NMR) has gained traction in the clinical laboratory due to associations between smaller lipid particle sizes and atherogenic risk, especially for LDL-p. The standard protocols for lipoprotein measurements by NMR require fasting blood samples; however, patients may not fast properly before sample collection. The study objective was to evaluate the impact of fasting status on the NMR-based lipid profile and to identify key parameters differentiating between fasting and post-meal specimens. METHODS Forty-eight self-reported healthy male and female participants were recruited. Blood was collected after a 12 h fast and 4 h after a high fat meal. Samples were analyzed using the AXINON LipoFIT by NMR assay. The measurements included triglyceride, total cholesterol, IDL-c, and LDL, HDL, VLDL concentration, particle number, and size, as well as glucose, and four amino acids (alanine, valine, leucine and isoleucine). RESULTS As expected, triglycerides increased after the meal (58%, p < 0.0001). Significant changes were also observed for VLDL, LDL, and HDL parameters, and the branched chain amino acids. The ratio of Valine*VLDL-c/LDL-c or Isoleucine*VLDL-c/LDL-c provided equally effective differentiation of fasting and post-meal samples. The ratio cutoffs (79.1 and 23.6 when calculated using valine and isoleucine, respectively) had sensitivities of 86% and specificities of 93-95%. CONCLUSIONS The clinical impact on NMR results from post-meal samples warrants further evaluation. Algorithms to differentiate fasting and post-meal specimens may be useful in identifying suboptimal specimens.
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Nuclear Magnetic Resonance Derived Biomarkers for Evaluating Cardiometabolic Risk in Youth and Young Adults Across the Spectrum of Glucose Tolerance.
Chung, ST, Matta, ST, Meyers, AG, Cravalho, CK, Villalobos-Perez, A, Dawson, JM, Sharma, VR, Sampson, ML, Otvos, JD, Magge, SN
Frontiers in endocrinology. 2021;:665292
Abstract
UNLABELLED Youth with obesity have an increased risk for cardiometabolic disease, but identifying those at highest risk remains a challenge. Four biomarkers that might serve this purpose are "by products" of clinical NMR LipoProfile® lipid testing: LPIR (Lipoprotein Insulin Resistance Index), GlycA (inflammation marker), BCAA (total branched-chain amino acids), and glycine. All are strongly related to insulin resistance and type 2 diabetes (T2DM) in adults (glycine inversely) and are independent of biological and methodological variations in insulin assays. However, their clinical utility in youth is unclear. We compared fasting levels of these biomarkers in 186 youth (42 lean normal glucose tolerant (NGT), 88 obese NGT, 23 with prediabetes (PreDM), and 33 with T2DM. All four biomarkers were associated with obesity and glycemia in youth. LPIR and GlycA were highest in youth with PreDM and T2DM, whereas glycine was lowest in youth with T2DM. While all four were correlated with HOMA-IR (Homeostatic Model Assessment for Insulin Resistance), LPIR had the strongest correlation (LPIR: r = 0.6; GlycA: r = 0.4, glycine: r = -0.4, BCAA r = 0.2, all P < 0.01). All four markers correlated with HbA1c (LPIR, GlycA, BCAA r ≥ 0.3 and glycine: r = -0.3, all P < 0.001). In multi-variable regression models, LPIR, GlycA, and glycine were independently associated with HOMA-IR (Adjusted R2 = 0.473, P < 0.001) and LPIR, glycine, and BCAA were independently associated with HbA1c (Adjusted R2 = 0.33, P < 0.001). An LPIR index of >44 was associated with elevated blood pressure, BMI, and dyslipidemia. Plasma NMR-derived markers were related to adverse markers of cardiometabolic risk in youth. LPIR, either alone or in combination with GlycA, should be explored as a non-insulin dependent predictive tool for development of insulin resistance and diabetes in youth. CLINICAL TRIAL REGISTRATION Clinicaltrials.gov, identifier NCT:02960659.
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Compartmental diffusion and microstructural properties of human brain gray and white matter studied with double diffusion encoding magnetic resonance spectroscopy of metabolites and water.
Lundell, H, Najac, C, Bulk, M, Kan, HE, Webb, AG, Ronen, I
NeuroImage. 2021;:117981
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Abstract
Double diffusion encoding (DDE) of the water signal offers a unique ability to separate the effect of microscopic anisotropic diffusion in structural units of tissue from the overall macroscopic orientational distribution of cells. However, the specificity in detected microscopic anisotropy is limited as the signal is averaged over different cell types and across tissue compartments. Performing side-by-side water and metabolite DDE spectroscopic (DDES) experiments provides complementary measures from which intracellular and extracellular microscopic fractional anisotropies (μFA) and diffusivities can be estimated. Metabolites are largely confined to the intracellular space and therefore provide a benchmark for intracellular μFA and diffusivities of specific cell types. By contrast, water DDES measurements allow examination of the separate contributions to water μFA and diffusivity from the intra- and extracellular spaces, by using a wide range of b values to gradually eliminate the extracellular contribution. Here, we aimed to estimate tissue and compartment specific human brain microstructure by combining water and metabolites DDES experiments. We performed our DDES measurements in two brain regions that contain widely different amounts of white matter (WM) and gray matter (GM): parietal white matter (PWM) and occipital gray matter (OGM) in a total of 20 healthy volunteers at 7 Tesla. Metabolite DDES measurements were performed at b = 7199 s/mm2, while water DDES measurements were performed with a range of b values from 918 to 7199 s/mm2. The experimental framework we employed here resulted in a set of insights pertaining to the morphology of the intracellular and extracellular spaces in both gray and white matter. Results of the metabolite DDES experiments in both PWM and OGM suggest a highly anisotropic intracellular space within neurons and glia, with the possible exception of gray matter glia. The water μFA obtained from the DDES results at high b values in both regions converged with that of the metabolite DDES, suggesting that the signal from the extracellular space is indeed effectively suppressed at the highest b value. The μFA measured in the OGM significantly decreased at lower b values, suggesting a considerably lower anisotropy of the extracellular space in GM compared to WM. In PWM, the water μFA remained high even at the lowest b value, indicating a high degree of organization in the interstitial space in WM. Tortuosity values in the cytoplasm for water and tNAA, obtained with correlation analysis of microscopic parallel diffusivity with respect to GM/WM tissue fraction in the volume of interest, are remarkably similar for both molecules, while exhibiting a clear difference between gray and white matter, suggesting a more crowded cytoplasm and more complex cytomorphology of neuronal cell bodies and dendrites in GM than those found in long-range axons in WM.
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Myocardial inflammation and energetics by cardiac MRI: a review of emerging techniques.
Tsampasian, V, Swift, AJ, Assadi, H, Chowdhary, A, Swoboda, P, Sammut, E, Dastidar, A, Cabrero, JB, Del Val, JR, Nair, S, et al
BMC medical imaging. 2021;(1):164
Abstract
The role of inflammation in cardiovascular pathophysiology has gained a lot of research interest in recent years. Cardiovascular Magnetic Resonance has been a powerful tool in the non-invasive assessment of inflammation in several conditions. More recently, Ultrasmall superparamagnetic particles of iron oxide have been successfully used to evaluate macrophage activity and subsequently inflammation on a cellular level. Current evidence from research studies provides encouraging data and confirms that this evolving method can potentially have a huge impact on clinical practice as it can be used in the diagnosis and management of very common conditions such as coronary artery disease, ischaemic and non-ischaemic cardiomyopathy, myocarditis and atherosclerosis. Another important emerging concept is that of myocardial energetics. With the use of phosphorus magnetic resonance spectroscopy, myocardial energetic compromise has been proved to be an important feature in the pathophysiological process of several conditions including diabetic cardiomyopathy, inherited cardiomyopathies, valvular heart disease and cardiac transplant rejection. This unique tool is therefore being utilized to assess metabolic alterations in a wide range of cardiovascular diseases. This review systematically examines these state-of-the-art methods in detail and provides an insight into the mechanisms of action and the clinical implications of their use.
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Magnetic Resonance Spectroscopy as a Non-invasive Method to Quantify Muscle Carnosine in Humans: a Comprehensive Validity Assessment.
da Eira Silva, V, Painelli, VS, Shinjo, SK, Ribeiro Pereira, W, Cilli, EM, Sale, C, Gualano, B, Otaduy, MC, Artioli, GG
Scientific reports. 2020;(1):4908
Abstract
Carnosine is a dipeptide abundantly found in human skeletal muscle, cardiac muscle and neuronal cells having numerous properties that confers performance enhancing effects, as well as a wide-range of potential therapeutic applications. A reliable and valid method for tissue carnosine quantification is crucial for advancing the knowledge on biological processes involved with carnosine metabolism. In this regard, proton magnetic resonance spectroscopy (1H-MRS) has been used as a non-invasive alternative to quantify carnosine in human skeletal muscle. However, carnosine quantification by 1H-MRS has some potential limitations that warrant a thorough experimental examination of its validity. The present investigation examined the reliability, accuracy and sensitivity for the determination of muscle carnosine in humans using in vitro and in vivo experiments and comparing it to reference method for carnosine quantification (high-performance liquid chromatography - HPLC). We used in vitro 1H-MRS to verify signal linearity and possible noise sources. Carnosine was determined in the m. gastrocnemius by 1H-MRS and HPLC to compare signal quality and convergent validity. 1H-MRS showed adequate discriminant validity, but limited reliability and poor agreement with a reference method. Low signal amplitude, low signal-to-noise ratio, and voxel repositioning are major sources of error.
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Magnetic Resonance Spectroscopy of the Head and Neck: Principles, Applications, and Challenges.
Fujima, N, Carlota Andreu-Arasa, V, Barest, GD, Srinivasan, A, Sakai, O
Neuroimaging clinics of North America. 2020;(3):283-293
Abstract
Several investigations have revealed the utility of magnetic resonance spectroscopy (MRS) as an adjunct in the evaluation of lesions of the head and neck. This technique remains a challenge in the head and neck because of its low signal-to-noise ratio and long acquisition times. In this review article, the basics of image acquisition technique and reported clinical utilities of head and neck MRS are presented.
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Recent directions in the solid-state NMR study of synthetic and natural calcium phosphates.
Gervais, C, Bonhomme, C, Laurencin, D
Solid state nuclear magnetic resonance. 2020;:101663
Abstract
Materials containing a calcium phosphate component have been the subject of much interest to NMR spectroscopists, especially in view of understanding the structure and properties of mineralized tissues like bone and teeth, and of developing synthetic biomaterials for bone regeneration. Here, we present a selection of recent developments in their structural characterization using advanced solid state NMR experiments, highlighting the level of insight which can now be accessed.
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NMR spectroscopy: a powerful tool for the analysis of polyphenols in extra virgin olive oil.
Olmo-Cunillera, A, López-Yerena, A, Lozano-Castellón, J, Tresserra-Rimbau, A, Vallverdú-Queralt, A, Pérez, M
Journal of the science of food and agriculture. 2020;(5):1842-1851
Abstract
Extra virgin olive oil (EVOO), a key component of the Mediterranean diet, has aroused interest in recent years due to its health properties. Nuclear magnetic resonance (NMR) spectroscopy is an appropriate tool for the accurate quantification of minor compounds in complex food matrices, such as polyphenols in olive oil. Flavonoids, lignans, secoiridoids and phenolic acids and alcohols in EVOO have been identified and quantified by NMR. This review provides an overview of the major developments in the structural elucidation of polyphenol compounds in EVOO. © 2019 Society of Chemical Industry.