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https://www.readbyqxmd.com/read/28822305/an-optimal-control-approach-to-design-entire-relaxation-dispersion-experiments
#1
Thoa T Nguyen, Steffen J Glaser
A general approach is introduced to optimize experiments for the analysis of spin systems in the presence of chemical exchange. Rather than optimizing individual pulse sequence elements, such as refocusing pulses, entire relaxation dispersion sequences are optimized in the form of a single shaped pulse. This is achieved by defining a performance index that is only based on the remaining signal after the relaxation dispersion sequence for a range of exchange, relaxation, offset, and rf inhomogeneity parameters...
July 31, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28771339/specific-acetylation-patterns-of-h2a-z-form-transient-interactions-with-the-bptf-bromodomain
#2
Gabriella T Perell, Neeraj K Mishra, Babu Sudhamalla, Peter D Ycas, Kabirul Islam, William C K Pomerantz
Post-translational lysine acetylation of histone tails affect both chromatin accessibility and recruitment of multi-functional bromodomain-containing proteins for modulating transcription. Bromodomain and PHD finger-containing protein (BPTF) regulates transcription, but has also been implicated with high gene expression levels in a variety of cancers. In this report, the histone variant H2A.Z, which replaces H2A in chromatin, is evaluated for affinity towards BPTF with a specific recognition pattern of acetylated lysine residues of the N-terminal tail region...
August 3, 2017: Biochemistry
https://www.readbyqxmd.com/read/28737383/alternatives-to-noesy-presat-and-cpmg-presat-for-nmr-based-metabolomics
#3
Adrien Le Guennec, Fariba Tayyari, Arthur S Edison
NMR metabolomics are primarily conducted with 1D NOESY presat for water suppression and CPMG presat as a T2 filter to remove macromolecule signals. Others pulse sequences exist for these two objectives but are not often used in metabolomics studies, because they are less robust or unknown to the NMR metabolomics community. However, recent improvements on alternative pulse sequences provide attractive alternatives to 1D NOESY presat and CPMG presat. We focus this perspective on PURGE, a water suppression technique, and PROJECT presat, a T2 filter...
July 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28647789/probing-slow-timescale-dynamics-in-proteins-using-methyl-1-h-cest
#4
Tairan Yuwen, Rui Huang, Lewis E Kay
Although (15)N- and (13)C-based chemical exchange saturation transfer (CEST) experiments have assumed an important role in studies of biomolecular conformational exchange, (1)H CEST experiments are only beginning to emerge. We present a methyl-TROSY (1)H CEST experiment that eliminates deleterious (1)H-(1)H NOE dips so that CEST profiles can be analyzed robustly to extract methyl proton chemical shifts of rare protein conformers. The utility of the experiment, along with a version that is optimized for (13)CHD2 labeled proteins, is established through studies of exchanging protein systems...
July 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28625405/metabolomic-analysis-with-1-h-nmr-for-non-invasive-diagnosis-of-hepatic-fibrosis-degree-in-patients-with-chronic-hepatitis-c
#5
Tommaso Gabbani, Maria Marsico, Patrizia Bernini, Elisabetta Lorefice, Cecilia Grappone, Maria Rosa Biagini, Stefano Milani, Vito Annese
BACKGROUND: The assessment of fibrosis degree in liver diseases is based on several non-invasive techniques, but none has been accurate. AIM: This study employed proton nuclear magnetic resonance spectroscopy to identify metabolic profiles in serum and urine, specific for different fibrosis degree in chronic hepatitis C patients. METHOD: 71 plasma, 73 serum, and 578 urine samples were collected. All samples were analyzed using (1)H-NMR spectroscopy technique and three different NMR spectra were acquired for each serum/plasma sample...
June 13, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28576318/automated-quantification-of-metabolites-in-blood-derived-samples-by-nmr
#6
Aswin Verhoeven, Eline Slagboom, Manfred Wuhrer, Martin Giera, Oleg A Mayboroda
NMR is widely applied in the field of metabolomics due to the quantitative nature of the technology and the reproducible data generated. However, because of severe spectral crowding, quantifying individual metabolites in body fluids such as serum and plasma remains a challenge. In this study, a method to automatically annotate and quantify a number of small metabolites in human serum and EDTA plasma is introduced. It combines the superior signal-to-noise ratio of the commonly applied CPMG and NOESY1D pulse sequences with the superior resolution of the 2D JRES experiment to construct a model that extracts the metabolite concentrations directly from the 1D spectra without tedious deconvolution...
July 11, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28546889/tuning-the-spin-coherence-time-of-cu-ii-bis-oxamato-and-cu-ii-bis-oxamidato-complexes-by-advanced-esr-pulse-protocols
#7
Ruslan Zaripov, Evgeniya Vavilova, Iskander Khairuzhdinov, Kev Salikhov, Violeta Voronkova, Mohammad A Abdulmalic, Francois E Meva, Saddam Weheabby, Tobias Rüffer, Bernd Büchner, Vladislav Kataev
We have investigated with the pulsed ESR technique at X- and Q-band frequencies the coherence and relaxation of Cu spins S = 1/2 in single crystals of diamagnetically diluted mononuclear [n-Bu4N]2[Cu(opba)] (1%) in the host lattice of [n-Bu4N]2[Ni(opba)] (99%, opba = o-phenylenebis(oxamato)) and of diamagnetically diluted mononuclear [n-Bu4N]2[Cu(opbon-Pr2)] (1%) in the host lattice of [n-Bu4N]2[Ni(opbon-Pr2)] (99%, opbon-Pr2 = o-phenylenebis(N(propyl)oxamidato)). For that we have measured the electron spin dephasing time Tm at different temperatures with the two-pulse primary echo and with the special Carr-Purcell-Meiboom-Gill (CPMG) multiple microwave pulse sequence...
2017: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/28495594/elevated-%C3%AE-s-ms-timescale-backbone-dynamics-in-the-transition-state-analog-form-of-arginine-kinase
#8
Omar Davulcu, Yu Peng, Rafael Brüschweiler, Jack J Skalicky, Michael S Chapman
Arginine kinase catalyzes reversible phosphoryl transfer between arginine and ATP. Crystal structures of arginine kinase in an open, substrate-free form and closed, transition state analog (TSA) complex indicate that the enzyme undergoes substantial domain and loop rearrangements required for substrate binding, catalysis, and product release. Nuclear magnetic resonance (NMR) has shown that substrate-free arginine kinase is rigid on the ps-ns timescale (average S(2)=0.84±0.08) yet quite dynamic on the µs-ms timescale (35 residues with Rex, 12%), and that movements of the N-terminal domain and the loop comprising residues I182-G209 are rate-limiting on catalysis...
May 8, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28480603/a-single-shot-t2-mapping-protocol-based-on-echo-split-gradient-spin-echo-acquisition-and-parametric-multiplexed-sensitivity-encoding-based-on-projection-onto-convex-sets-reconstruction
#9
Mei-Lan Chu, Hing-Chiu Chang, Koichi Oshio, Nan-Kuei Chen
PURPOSE: To develop a high-speed T2 mapping protocol that is capable of accurately measuring T2 relaxation time constants from a single-shot acquisition. THEORY: A new echo-split single-shot gradient-spin-echo (GRASE) pulse sequence is developed to acquire multicontrast data while suppressing signals from most nonprimary echo pathways in Carr-Purcell-Meiboom-Gill (CPMG) echoes. Residual nonprimary pathway signals are taken into consideration when performing T2 mapping using a parametric multiplexed sensitivity encoding based on projection onto convex sets (parametric-POCSMUSE) reconstruction method that incorporates extended phase graph modeling of GRASE signals...
May 7, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28396388/altering-the-allosteric-pathway-in-igps-suppresses-millisecond-motions-and-catalytic-activity
#10
George P Lisi, Kyle W East, Victor S Batista, J Patrick Loria
Imidazole glycerol phosphate synthase (IGPS) is a V-type allosteric enzyme, meaning that its catalytic rate is critically dependent on activation by its allosteric ligand, N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR). The allosteric mechanism of IGPS is reliant on millisecond conformational motions for efficient catalysis. We engineered four mutants of IGPS designed to disrupt millisecond motions and allosteric coupling to identify regions that are critical to IGPS function...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28388495/local-diffusion-and-diffusion-t2-distribution-measurements-in-porous-media
#11
S Vashaee, B Newling, B MacMillan, F Marica, M Li, B J Balcom
Slice-selective pulsed field gradient (PFG) and PFG-T2 measurements are developed to measure spatially-resolved molecular diffusion and diffusion-T2 distributions. A spatially selective adiabatic inversion pulse was employed for slice-selection. The slice-selective pulse is able to select a coarse slice, on the order of 1cm, at an arbitrary position in the sample. The new method can be employed to characterize oil-water mixtures in porous media. The new technique has an inherent sensitivity advantage over phase encoding imaging based methods due to signal being localized from a thick slice...
May 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28379688/effects-of-doxorubicin-cisplatin-and-tamoxifen-on-the-metabolic-profile-of-human-breast-cancer-mcf-7-cells-as-determined-by-1-h-high-resolution-magic-angle-spinning-nuclear-magnetic-resonance
#12
Roberta M Maria, Wanessa F Altei, Heloisa S Selistre-de-Araujo, Luiz A Colnago
Doxorubicin (Doxo), cisplatin (Cis), and tamoxifen (Tamo) are part of many chemotherapeutic regimens. However, there have been limited studies of the way metabolism in breast cancer is affected by chemotherapy. We studied, through (1)H high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy, the metabolic profile of human breast cancer MCF-7 control (Con) cells as well as MCF-7 cells treated with Tamo, Cis, and Doxo. (1)H HR-MAS NMR single-pulse spectra evidenced signals from the cell compounds, including fatty acids (membranes), water-soluble proteins, and metabolites...
April 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28351813/1d-and-2d-diffusion-pore-imaging-on-a-preclinical-mr-system-using-adaptive-rephasing-feasibility-and-pulse-sequence-comparison
#13
Marco Bertleff, Sebastian Domsch, Frederik B Laun, Tristan A Kuder, Lothar R Schad
Diffusion pore imaging (DPI) has recently been proposed as a means to acquire images of the average pore shape in an image voxel or region of interest. The highly asymmetric gradient scheme of its sequence makes it substantially demanding in terms of the hardware of the NMR system. The aim of this work is to show the feasibility of DPI on a preclinical 9.4T animal scanner. Using water-filled capillaries with an inner radius of 10μm, four different variants of the DPI sequence were compared in 1D and 2D measurements...
May 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28345344/unravelling-and-quantifying-the-nmr-invisible-metabolites-interacting-with-human-serum-albumin-by-binding-competition-and-t2-relaxation-based-decomposition-analysis
#14
Ruben Barrilero, Noelia Ramírez, Joan Carles Vallvé, Delia Taverner, Rocío Fuertes, Núria Amigó, Xavier Correig
Quantitative profiling of low-molecular-weight metabolites (LMWMs) by (1)H NMR is routinely used in high-throughput serum metabolomics. First, the protein background is attenuated using a T2 filter; then, the LMWM signals are resolved by line-shape fitting. However, protein-binding modifies the motional properties of LMWM, and their signal partially attenuates with the T2 filter, along with the protein background. Consequently, the quantified LMWM signals do not reflect the total concentration in serum but the nonbinding part...
May 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28306342/nmr-based-plasma-metabolomic-discrimination-for-male-fertility-assessment-of-rats-treated-with-eurycoma-longifolia-extracts
#15
Forough Ebrahimi, Baharudin Ibrahim, Chin-Hoe Teh, Vikneswaran Murugaiyah, Kit-Lam Chan
Male infertility is one of the leading causes of infertility which affects many couples worldwide. Semen analysis is a routine examination of male fertility status which is usually performed on semen samples obtained through masturbation that may be inconvenient to patients. Eurycoma longifolia (Tongkat Ali, TA), native to Malaysia, has been traditionally used as a remedy to boost male fertility. In our recent studies in rats, upon the administration of high-quassinoid content extracts of TA including TA water (TAW), quassinoid-rich TA (TAQR) extracts, and a low-quassinoid content extract including quassinoid-poor TA (TAQP) extract, sperm count (SC) increased in TAW- and TAQR-treated rats when compared to the TAQP-treated and control groups...
June 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28294621/quantification-of-metabolites-by-nmr-spectroscopy-in-the-presence-of-protein
#16
Jens Wallmeier, Claudia Samol, Lisa Ellmann, Helena U Zacharias, Franziska C Vogl, Muriel Garcia, Katja Dettmer, Peter J Oefner, Wolfram Gronwald
The high reliability of NMR spectroscopy makes it an ideal tool for large-scale metabolomic studies. However, the complexity of biofluids and, in particular, the presence of macromolecules poses a significant challenge. Ultrafiltration and protein precipitation are established means of deproteinization and recovery of free or total metabolite content, but neither is ever complete. In addition, aside from cost and labor, all deproteinization methods constitute an additional source of experimental variation. The Carr-Purcell-Meiboom-Gill (CPMG) echo-train acquisition of NMR spectra obviates the need for prior deproteinization by attenuating signals from macromolecules, but concentration values of metabolites measured in blood plasma will not necessarily reflect total or free metabolite content...
March 24, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28216958/-1-h-nmr-based-serum-metabolomics-reveals-erythromycin-induced-liver-toxicity-in-albino-wistar-rats
#17
Atul Rawat, Durgesh Dubey, Anupam Guleria, Umesh Kumar, Amit K Keshari, Swati Chaturvedi, Anand Prakash, Sudipta Saha, Dinesh Kumar
INTRODUCTION: Erythromycin (ERY) is known to induce hepatic toxicity which mimics other liver diseases. Thus, ERY is often used to produce experimental models of drug-induced liver-toxicity. The serum metabolic profiles can be used to evaluate the liver-toxicity and to further improve the understanding of underlying mechanism. OBJECTIVE: To establish the serum metabolic patterns of Erythromycin induced hepatotoxicity in albino wistar rats using (1)H NMR based serum metabolomics...
October 2016: Journal of Pharmacy & Bioallied Sciences
https://www.readbyqxmd.com/read/28161394/magic-angle-effect-plays-a-major-role-in-both-t1rho-and-t2-relaxation-in-articular-cartilage
#18
H Shao, C Pauli, S Li, Y Ma, A S Tadros, A Kavanaugh, E Y Chang, G Tang, J Du
PURPOSE: To investigate the effect of sample orientation on T1rho and T2 values of articular cartilage in histologically confirmed normal and abnormal regions using a whole-body 3T scanner. MATERIALS AND METHODS: Eight human cadaveric patellae were evaluated using a 2D CPMG sequence for T2 measurement as well as a 2D spin-locking prepared spiral sequence and a 3D magnetization-prepared angle-modulated partitioned-k-space spoiled gradient echo snapshots (3D MAPSS) sequence for T1rho measurement...
February 1, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28130009/practical-considerations-for-the-acquisition-of-ultra-wideline-14-n-nmr-spectra
#19
Stanislav L Veinberg, Austin W Lindquist, Michael J Jaroszewicz, Robert W Schurko
Several considerations for the acquisition, processing, and analysis of high quality ultra-wideline (UW) (14)N solid-state NMR (SSNMR) powder patterns under static conditions are discussed. It is shown that the (14)N quadrupolar parameters may be determined accurately using the frequencies of only two discontinuities in (14)N NMR powder patterns that are dominated by the first-order quadrupolar interaction, thereby eliminating the need for the acquisition of the entire pattern and concomitantly reducing experimental time...
December 21, 2016: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/28110117/an-adaptive-method-for-determining-an-acquisition-parameter-t0-in-a-modified-cpmg-sequence
#20
Donghui Xing, Yiren Fan, Jianfei Hao, Xinmin Ge, Chaoliu Li, Yufeng Xiao, Fei Wu
The modified CPMG (Carr-Purcell-Meiboom-Gill) pulse sequence is a common sequence used for measuring the internal magnetic field gradient distribution of formation rocks, for which t0 (the duration of the first window) is a key acquisition parameter. In order to obtain the optimal t0, an adaptive method is proposed in this paper. By studying the factors influencing discriminant factor σ and its variation trend using T2-G forward numerical simulation, it is found that the optimal t0 corresponds to the maximum value of σ...
January 9, 2017: Journal of Magnetic Resonance
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