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In situ Investigation of HdeA in Bacterial Outer Membrane Vesicles Using NMR Spectroscopy
WANG Huan, TAO Zhiqing, JIANG Guosheng, ZHANG Xu, WANG Guan, HE Lichun, LIU Maili
Chinese Journal of Magnetic Resonance, 2024, 41(1): 1-8.
DOI: 10.11938/cjmr20233069
HdeA, a molecular chaperone localized in the bacterial periplasm, plays a vital role in maintaining protein homeostasis. Previous studies of HdeA were mainly carried out in in vitro conditions, limiting our understanding of the mechanism of HdeA in its native environment. Outer membrane vesicles of bacteria are extracellular vesicles released by cells into the extracellular milieu in a controlled manner, with contents almost identical to the periplasmic environment. Thus, by enriching HdeA into the bacterial outer membrane vesicles (OMVs), we investigated the conformational changes of HdeA within OMVs via nuclear magnetic resonance (NMR) spectroscopy. The results reveal that HdeA exhibits an acid-dependent conformational change in its native environment. The high-resolution spectrum of HdeA in OMVs indicates that under low pH conditions the function of HdeA is activated through residues S15, W16, T17, S27, T32, E36, G54, T57, C66, Q71, F74 and D83. Moreover, the NMR measurement of HdeA within OMVs provides a promising way for in situ investigation of mechanisms of other periplasmic molecular chaperones via NMR spectroscopy.
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Evaluation of the Impact of b -Value Ranges on Six Body Diffusion Models in Prostate Application
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ZHOU Minxiong, QI Xuan, DU Bin, QI Dong, WANG Haijie, YANG Guang, Cai Wenmei, LIU Mengxiao, ZHANG Huiting, YAN Xu, NIE Shengdong, HE Yongsheng
Chinese Journal of Magnetic Resonance, 2024, 41(1): 9-18.
DOI: 10.11938/cjmr20233075
This paper investigated the impact of different b -value acquisition ranges (from 0 to 2 500 s/mm2 ) on the quantitative parameter calculation of six body diffusion models, including mono-exponential (Mono), diffusion kurtosis imaging (DKI), intravoxel incoherent motion (IVIM), stretch exponential model (SEM), fractional-order calculus model (FROC), and continuous time random walk model (CTRW). The influence of different b -value acquisition ranges on parameter calculation was evaluated through correlation between diffusion model parameters, t -test, and the ability to differentiate benign and malignant prostate lesions. The results showed that compared with that of the reference sampling scheme (0~2 500 s/mm2 ), the difference of the mean value of region of interest (ROI) with the same diffusion parameters gradually increases as the maximum b -value decreases, but the correlation decreases only slightly, and the ability to differentiate between benign and malignant prostate lesions remains at a similar level. Based on the experimental results, a b -value range of 0~1 500 s/mm2 is recommended for clinical practice, because this scheme takes collection efficiency into account, the correlation of more than half of its parameters with those of the reference sampling scheme is not less than 0.98, and the difference in the values of area under the curve (AUC) between benign and malignant differentiation is less than 0.01. In addition, the sensitivity of different diffusion models to the b -value scheme varies, with the parameters of SEM and CTRW models being relatively less affected by the b -value range.
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Multi-source Feature Classification Model of Pancreatic Mucinous and Serous Cystic Neoplasms Based on Deep Learning
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XU Zhenshun, YUAN Xiaohan, HUANG Ziheng, SHAO Chengwei, WU Jie, BIAN Yun
Chinese Journal of Magnetic Resonance, 2024, 41(1): 19-29.
DOI: 10.11938/cjmr20233064
This study aims to classify and differentiate mucinous and serous cystic neoplasms of the pancreas using a multi-source feature classification model based on deep learning for preoperative auxiliary diagnosis. Deep learning features and radiomics features were extracted from segmented images using deep learning and radiomics technology, respectively. Clinical features were also evaluated and quantified. LASSO (least absolute shrinkage and selection operator) and cross-validation methods were applied to screen the features, and two multi-source feature models were constructed: the radiomics combined with deep learning (RAD_DL) model and the clinical feature combined with RAD_DL (Clinical_RAD_DL) model. Traditional radiomics (RAD) and deep learning (DL) models were used as controls. SVM (support vector machine), ADAboost (adaptive boosting), Random Forest, and Logistic were selected for classification. The Clinical_RAD_DL feature model shows the best classification performance, with the accuracy of 0.923 1, recall rate of 0.882 4, precision of 0.882 0, F 1-score of 0.882 2, and AUC value of 0.912 6. The experimental results indicate that the multi-source feature classification model based on deep learning has good performance in classifying pancreatic serous cystic neoplasms and pancreatic mucinous cystic neoplasms, and can assist clinical accurate diagnosis and treatment.
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Quantitative Refocused INEPT Method Based on Simulated Annealing Optimization
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CHEN Lei, LIU Hongbing, LIU Huili, WANG Liying
Chinese Journal of Magnetic Resonance, 2024, 41(1): 30-42.
DOI: 10.11938/cjmr20233071
In this paper, we presented a quantitative refocused INEPT (Refocused Insensitive Nuclei Enhanced by Polarization Transfer) method based on simulated annealing optimization, which utilizes the optimized polarization transfer and refocus delay set to yield nearly uniform enhancement for CH, CH2 and CH3 groups. The 180° composite pulses are applied in 13 C channel to overcome the inhomogeneity of B 1 field and the offset effect to improve the measurement reliability. Simulated annealing optimization is further applied to achieve quantitative spectral editing of refocused INEPT. The above methods were validated using model compounds such as artemisinin and simvastatin, and the relative standard deviations of the quantitative integrals with Case I delay set were 1.6% and 3.3%, respectively. As an application of the proposed method, major fatty acid compositions in soybean oils were determined using quantitative refocused INEPT, and the results were consistent with those determined by conventional quantitative 13 C NMR, while the measurement time was significantly reduced. The quantitative refocused INEPT method is particularly attractive for rapid, accurate detection of complex systems such as petroleum and polymers.
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Structural Elucidation of Hybutimibe
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XU Xiaojie, CHEN Yan’an, LI Xufei, ZHANG Yuncai, ZHANG Yong, ZHAN Dongkai, PAN Ting
Chinese Journal of Magnetic Resonance, 2024, 41(1): 43-55.
DOI: 10.11938/cjmr20233065
The structure of hybutimibe was analyzed by ultraviolet absorption spectroscopy, infrared absorption spectroscopy, mass spectrometry, nuclear magnetic resonance (1 H NMR, 13 C NMR, DEPT, 1 H-1 H COSY, 1 H-1 H NOESY, 1 H-13 C HSQC and 1 H-13 C HMBC) spectroscopy and single crystal diffraction. The 1 H and 13 C NMR signals of hybutimibe were assigned. The crystal structure of hybutimibe was studied by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and powder X-ray diffraction (PXRD).
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Discovery and Structural Characterization of Impurities in the Synthesis of Darolutamide Intermediate
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MA Huifang, TONG Yue, WANG Rongfan, XIE Jianwei
Chinese Journal of Magnetic Resonance, 2024, 41(1): 56-66.
DOI: 10.11938/cjmr20233078
Darolutamide is an important drug for the treatment of prostate cancer. When studying its synthesis process, three impurities A , B , and C were discovered and purified in the first step of Suzuki coupling and the second step of hydrolysis deprotection reactions. Impurities A and B came from the first-step reaction, and impurity C came from the second-step reaction. The structures of impurities A and B were further determined through high-resolution mass spectrometry (HRMS), 1 H nuclear magnetic resonance (NMR), and 13 C NMR methods. It was discovered that impurities A and B were the deborated pinacol ester product of compound 2 and the double coupling product of compound 1 , respectively. The accurate structures of compound 3 and impurity C were determined using HRMS, 1 H NMR, 13 C NMR, 1 H-1 H COSY (correlation spectroscopy), 1 H-13 C HSQC (heteronuclear singular quantum correlation), 1 H-13 C HMBC (heteronuclear multiple bond correlation) and 1 H-1 H NOESY (nuclear overhauser effect spectroscopy). The formation mechanisms and avoidance methods of these impurities were also discussed.
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Preparation Efficiency of Singlet States in Multi-spin Systems with Different Coupling Configurations
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WANG Ziwen, XIN Jiaxiang, WEI Daxiu, YAO Yefeng
Chinese Journal of Magnetic Resonance, 2024, 41(1): 67-76.
DOI: 10.11938/cjmr20233063
Nuclear spin singlet is a special quantum state that lasts longer than T 1 and can be used to study slow diffusion and motion between molecules. The preparation of singlet states is the key to their successful application. Currently, various methods for preparing singlet states have been reported in the literature, which are mainly applicable to isolated two-spin systems. When the nuclear spin involved in the singlet state is coupled to other spins, the preparation efficiency of the singlet state often decreases. In this paper, taking a three-spin system as an example, we studied the effect of non-singlet spin coupling on the preparation efficiency of singlet states under different coupling configurations. The simulation results show that as the singlet spin changes from weak coupling to strong coupling, the preparation efficiency of the singlet state will maintain a certain stability when the coupling between the singlet spin and the non-singlet spin is symmetrical. This characteristic can provide a reference for selecting appropriate spins to prepare singlet states in complex systems. We experimentally verified this conclusion using a three-spin system in the N-acetyl-L-aspartic acid (NAA) molecule. By adjusting the pH of the NAA molecule, the three-spin system can transfer from weak coupling to strong coupling. The experimental results show that the preparation efficiency of the singlet state is significantly higher when the three spins are in strong coupling than that when the spins are in weak coupling.
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Independent Development of Sample Preparation Tools for Solid-state NMR
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CHEN Yang, ZHOU Meng, LI Yong, YANG Haijun
Chinese Journal of Magnetic Resonance, 2024, 41(1): 77-86.
DOI: 10.11938/cjmr20233074
In recent years, several research units have introduced solid-state nuclear magnetic resonance (NMR) spectrometers. So far, solid-state NMR spectrometers have not been domestically manufactured and the equipment is completely dependent on imports. Therefore, both the instruments and sample preparation systems are expensive. The sample loading rotor is the crucial consumable in the magic angle spinning (MAS) NMR experiment. However, the extremely tough requirement on dimensional precision poses a great challenge in the machining of rotors. By analyzing the characteristics and practical applications of the imported 3.2 mm rotor and its sample preparation tools, we optimized the connection between the rotor parts, improved the sealing of rotor, and developed the MAS rotor and its sample preparation tools independently. The test results show that the self-made MAS rotor can run normally at 12 kHz, which meets the requirements of conventional solid-state NMR experiments. The sample preparation toolbox has advantages of simplicity and safety.
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Development and Validation of Zero-field NMR Spectrometer Based on Compact Atomic Magnetometer
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FU Fangyue, GUO Qingqian, FENG Xiaoyu, XU Jiayu, YAO Zekun, HU Tao, YANG Xiaodong, CHANG Yan
Chinese Journal of Magnetic Resonance, 2024, 41(1): 87-98.
DOI: 10.11938/cjmr20233060
Conventional high-field nuclear magnetic resonance (NMR) spectrometer necessitates advanced superconducting technology, which usually involves a magnet of large volume and high maintenance cost. Moreover, strong magnet often has severe magnetic field inhomogeneity, leading to NMR line broadening. Zero- to ultralow-field (ZULF) NMR emerged as a complementary approach to traditional high-field NMR techniques. In this paper, a portable zero-field NMR spectrometer based on a compact atomic magnetometer was developed, which adopted an integrated control system based on a multi-function data acquisition card (National Instruments PCIe-6353). The spectrometer is of a main magnetic field strength less than 1 nT and enables achieving high-resolution J -spectrum under zero-field environment. Specifically, a series of single pulse excitation experiments for the initial adiabatic state was carried out to calibrate the triaxial magnetic field coils. Then a modified composite pulse sequence was developed to further validate the performance of zero-field NMR spectrometer by single-spin control experiments for the 13 C-1 H spin system.