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1.
Nat Commun ; 15(1): 3303, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38664397

ABSTRACT

The DEAD-box RNA helicase (DDX) plays a central role in many aspects of RNA metabolism by remodeling the defined structure of RNA molecules. While a number of structural studies have revealed the atomistic details of the interaction between DDX and RNA ligands, the molecular mechanism of how this molecule unwinds a structured RNA into an unstructured single-stranded RNA (ssRNA) has largely remained elusive. This is due to challenges in structurally characterizing the unwinding intermediate state and the lack of thermodynamic details underlying this process. In this study, we use solution nuclear magnetic resonance (NMR) spectroscopy to characterize the interaction of human DDX3X, a member of the DDX family, with various RNA ligands. Our results show that the inherent binding affinity of DDX3X for ssRNA is significantly higher than that for structured RNA elements. This preferential binding, accompanied by the formation of a domain-closed conformation in complex with ssRNA, effectively stabilizes the denatured ssRNA state and thus underlies the unwinding activity of DDX3X. Our results provide a thermodynamic and structural basis for the DDX function, whereby DDX can recognize and remodel a distinct set of structured RNAs to participate in a wide range of physiological processes.


Subject(s)
DEAD-box RNA Helicases , Protein Binding , RNA , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/chemistry , Humans , RNA/metabolism , RNA/chemistry , Thermodynamics , Magnetic Resonance Spectroscopy , Models, Molecular , Nucleic Acid Conformation
2.
BMC Psychiatry ; 24(1): 320, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38664663

ABSTRACT

BACKGROUND: 1H-MRS is increasingly used in basic and clinical research to explain brain function and alterations respectively. In psychosis research it is now one of the main tools to investigate imbalances in the glutamatergic system. Interestingly, however, the findings are extremely variable even within patients of similar disease states. One reason may be the variability in analysis strategies, despite suggestions for standardization. Therefore, our study aimed to investigate the extent to which the basis set configuration- which metabolites are included in the basis set used for analysis- would affect the spectral fit and estimated glutamate (Glu) concentrations in the anterior cingulate cortex (ACC), and whether any changes in levels of glutamate would be associated with psychotic-like experiences and autistic traits. METHODS: To ensure comparability, we utilized five different exemplar basis sets, used in research, and two different analysis tools, r-based spant applying the ABfit method and Osprey using the LCModel. RESULTS: Our findings revealed that the types of metabolites included in the basis set significantly affected the glutamate concentration. We observed that three basis sets led to more consistent results across different concentration types (i.e., absolute Glu in mol/kg, Glx (glutamate + glutamine), Glu/tCr), spectral fit and quality measurements. Interestingly, all three basis sets included phosphocreatine. Importantly, our findings also revealed that glutamate levels were differently associated with both schizotypal and autistic traits depending on basis set configuration and analysis tool, with the same three basis sets showing more consistent results. CONCLUSIONS: Our study highlights that scientific results may be significantly altered depending on the choices of metabolites included in the basis set, and with that emphasizes the importance of carefully selecting the configuration of the basis set to ensure accurate and consistent results, when using MR spectroscopy. Overall, our study points out the need for standardized analysis pipelines and reporting.


Subject(s)
Glutamic Acid , Gyrus Cinguli , Proton Magnetic Resonance Spectroscopy , Humans , Gyrus Cinguli/metabolism , Glutamic Acid/metabolism , Male , Adult , Female , Proton Magnetic Resonance Spectroscopy/methods , Young Adult , Personality/physiology , Psychotic Disorders/metabolism , Magnetic Resonance Spectroscopy/methods , Glutamine/metabolism
3.
PLoS One ; 19(4): e0301579, 2024.
Article in English | MEDLINE | ID: mdl-38635664

ABSTRACT

We present here the solution structures of the protein thioredoxin-1 from Plasmodium falciparum (PfTrx-1), in its reduced and oxidized forms. They were determined by high-resolution NMR spectroscopy at 293 K on uniformly 13C-, 15N-enriched, matched samples allowing to identification of even small structural differences. PfTrx-1 shows an α/ß-fold with a mixed five-stranded ß-sheet that is sandwiched between 4 helices in a ß1 α1 ß2 α2 ß3 α3 ß4 ß5 α4 topology. The redox process of the CGPC motif leads to significant structural changes accompanied by larger chemical shift changes from residue Phe25 to Ile36, Thr70 to Thr74, and Leu88 to Asn91. By high-field high-pressure NMR spectroscopy, rare conformational states can be identified that potentially are functionally important and can be used for targeted drug development. We performed these experiments in the pressure range from 0.1 MPa to 200 MPa. The mean combined, random-coil corrected B1* values of reduced and oxidized thioredoxin are quite similar with -0.145 and -0.114 ppm GPa-1, respectively. The mean combined, random-coil corrected B2* values in the reduced and oxidized form are 0.179 and 0.119 ppm GPa-2, respectively. The mean ratios of the pressure coefficients B2/B1 are -0.484 and -0.831 GPa-1 in the reduced and oxidized form respectively. They differ at some points in the structure after the formation of the disulfide bond between C30 and C33. The thermodynamical description of the pressure dependence of chemical shifts requires the assumption of at least three coexisting conformational states of PfTrx-1. These three conformational states were identified in the reduced as well as in the oxidized form of the protein, therefore, they represent sub-states of the two main oxidation states of PfTrx-1.


Subject(s)
Plasmodium falciparum , Thioredoxins , Amino Acid Sequence , Plasmodium falciparum/metabolism , Thioredoxins/metabolism , Magnetic Resonance Spectroscopy , Protein Structure, Secondary , Oxidation-Reduction
4.
Cells ; 13(8)2024 Apr 09.
Article in English | MEDLINE | ID: mdl-38667276

ABSTRACT

Cancer cell lines are frequently used in metabolomics, such as in vitro tumor models. In particular, A2780 cells are commonly used as a model for ovarian cancer to evaluate the effects of drug treatment. Here, we compare the NMR metabolomics profiles of A2780 and cisplatin-resistant A2780 cells with those of cells derived from 10 patients with high-grade serous ovarian carcinoma (collected during primary cytoreduction before any chemotherapeutic treatment). Our analysis reveals a substantial similarity among all primary cells but significant differences between them and both A2780 and cisplatin-resistant A2780 cells. Notably, the patient-derived cells are closer to the resistant A2780 cells when considering the exo-metabolome, whereas they are essentially equidistant from A2780 and A2780-resistant cells in terms of the endo-metabolome. This behavior results from dissimilarities in the levels of several metabolites attributable to the differential modulation of underlying biochemical pathways. The patient-derived cells are those with the most pronounced glycolytic phenotype, whereas A2780-resistant cells mainly diverge from the others due to alterations in a few specific metabolites already known as markers of resistance.


Subject(s)
Cisplatin , Drug Resistance, Neoplasm , Magnetic Resonance Spectroscopy , Metabolomics , Ovarian Neoplasms , Humans , Female , Cisplatin/pharmacology , Ovarian Neoplasms/metabolism , Ovarian Neoplasms/pathology , Ovarian Neoplasms/drug therapy , Metabolomics/methods , Cell Line, Tumor , Magnetic Resonance Spectroscopy/methods , Metabolome/drug effects , Antineoplastic Agents/pharmacology
5.
Mar Drugs ; 22(4)2024 Apr 20.
Article in English | MEDLINE | ID: mdl-38667803

ABSTRACT

Three novel meroterpenoids, taladrimanins B-D (1-3), were isolated from the marine-derived fungus Talaromyces sp. M27416, alongside three biogenetically related compounds (4-6). We delineated taladrimanin B's (1) structure using HRESIMS and NMR, confirmed its configuration via quantum chemical NMR analysis and DP4+ methodology, and verified it through X-ray crystallography. ECD calculations determined the absolute configuration of compound 1, while comparative NMR and ECD analyses elucidated the absolute configurations of 2 and 3. These compounds are drimane-type meroterpenoids with a C10 polyketide unit (8R-configuration). We proposed a biosynthetic pathway and noted that compound 1 showed cytotoxic activity against MKN-45 and 5637 cell lines and selective antibacterial effects against Staphylococcus aureus CICC 10384.


Subject(s)
Anti-Bacterial Agents , Staphylococcus aureus , Talaromyces , Terpenes , Talaromyces/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/isolation & purification , Humans , Cell Line, Tumor , Staphylococcus aureus/drug effects , Terpenes/pharmacology , Terpenes/chemistry , Terpenes/isolation & purification , Crystallography, X-Ray , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/isolation & purification , Microbial Sensitivity Tests , Aquatic Organisms , Molecular Structure , Magnetic Resonance Spectroscopy
6.
Tomography ; 10(4): 493-503, 2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38668396

ABSTRACT

Quantifying an imaging modality's ability to reproduce results is important for establishing its utility. In magnetic resonance spectroscopic imaging (MRSI), new acquisition protocols are regularly introduced which improve upon their precursors with respect to signal-to-noise ratio (SNR), total acquisition duration, and nominal voxel resolution. This study has quantified the within-subject and between-subject reproducibility of one such new protocol (reduced-field-of-view density-weighted concentric ring trajectory (rFOV-DW-CRT) MRSI) by calculating the coefficient of variance of data acquired from a test-retest experiment. The posterior cingulate cortex (PCC) and the right superior corona radiata (SCR) were selected as the regions of interest (ROIs) for grey matter (GM) and white matter (WM), respectively. CVs for between-subject and within-subject were consistently around or below 15% for Glx, tCho, and Myo-Ins, and below 5% for tNAA and tCr.


Subject(s)
Magnetic Resonance Imaging , Humans , Reproducibility of Results , Male , Female , Adult , Magnetic Resonance Imaging/methods , Gray Matter/diagnostic imaging , Signal-To-Noise Ratio , Magnetic Resonance Spectroscopy/methods , Brain/diagnostic imaging , White Matter/diagnostic imaging , Young Adult
7.
Zhongguo Zhong Yao Za Zhi ; 49(3): 728-734, 2024 Feb.
Article in Chinese | MEDLINE | ID: mdl-38621876

ABSTRACT

Mesona chinensis is a common medicinal and edible plant in the Lingnan region of China, which has extensive pharmacological activity. However, the study of its chemical constituents is not sufficient. In this study, a variety of modern chromatographic separation techniques were used to isolate two compounds from 95% ethanol extract of the grass parts of M. chinensis. Their absolute configurations were determined by ultraviolet spectroscopy(UV), infrared spectroscopy(IR), high resolution mass spectrometry(HR-ESI-MS), 1D and 2D nuclear magnetic resonance(1D NMR and 2D NMR), and single-crystal X-ray diffraction(SC-XRD). Specifically, they were two new benzoyl-sesquiterpenes and named mesonanol A and mesonanol B, respectively. The results of the pharmacological activity evaluation showed that neither of the two new compounds showed obvious antiviral and anti-inflammatory activities.


Subject(s)
Lamiaceae , Sesquiterpenes , Magnetic Resonance Spectroscopy , Mass Spectrometry , Spectrophotometry, Infrared , Molecular Structure
8.
Zhongguo Zhong Yao Za Zhi ; 49(6): 1549-1557, 2024 Mar.
Article in Chinese | MEDLINE | ID: mdl-38621938

ABSTRACT

The dichloromethane fraction of Kadsura heteroclita roots was separated and purified by chromatographic techniques(e.g., silica gel, Sephadex LH-20, ODS, MCI column chromatography) and semi-preparative HPLC. Twenty compounds were isolated from K. heteroclita, and their structures were identified by NMR, MS, UV, and X-ray single crystal diffraction techniques. Twenty compounds were isolated from K. heteroclita, which were identified as xuetongdilactone G(1), mallomacrostin C(2), 3,4-seco(24Z)-cychmrt-4(28),24-diene-3,26-dioic acid 3-methyl ester(3), nigranoic acid(4), methyl ester schizanlactone E(5), schisandronic acid(6), heteroclic acid(7), wogonin(8),(2R,3R)-4'-O-methyldihydroquercetin(9), 15,16-bisnor-13-oxo-8(17),11E-labdadien-19-oic acid(10), stigmast-4-ene-6ß-ol-3-one(11), psoralen(12),(1R,2R,4R)-trihydroxy-p-menthane(13), homovanillyl alcohol(14), 2-(4-hydroxyphenyl)-ethanol(15), coniferaldehyde(16),(E)-7-(4-hydroxy-3-methoxyphenyl)-7-methylbut-8-en-9-one(17), acetovanillone(18), vanillic acid(19) and vanillin(20). Compound 1 is a new compound named xuetongdilactone G. Compounds 2-3 and 8-20 are isolated from K. heteroclita for the first time.


Subject(s)
Kadsura , Kadsura/chemistry , Magnetic Resonance Spectroscopy , Plant Roots/chemistry , Esters/analysis
9.
J Phys Chem B ; 128(15): 3527-3537, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38568422

ABSTRACT

Despite the limitations posed by poor sensitivity, studies have reported the unique advantages of 17O based NMR spectroscopy to study systems existing in liquid, solid, or semisolid states. 17O NMR studies have exploited the remarkable sensitivity of quadrupole coupling and chemical shift anisotropy tensors to the local environment in the characterization of a variety of intra- and intermolecular interactions and motion. Recent studies have considerably expanded the use of 17O NMR to study dynamic intermolecular interactions associated with some of the challenging biological systems under magic angle spinning (MAS) and aligned conditions. The very fast relaxing nature of 17O has been well utilized in cellular and in vivo MRS (magnetic resonance spectroscopy) and MRI (magnetic resonance imaging) applications. The main focus of this Review is to highlight the new developments in the biological solids with a detailed discussion for a few selected examples including membrane proteins and nanodiscs. In addition to the unique benefits and limitations, the remaining challenges to overcome, and the impacts of higher magnetic fields and sensitivity enhancement techniques are discussed.


Subject(s)
Magnetic Fields , Membrane Proteins , Magnetic Resonance Spectroscopy , Membrane Proteins/chemistry , Anisotropy , Lipids
10.
Clin Res Cardiol ; 113(5): 781-789, 2024 May.
Article in English | MEDLINE | ID: mdl-38619578

ABSTRACT

BACKGROUND: Cardiac magnetic resonance (CMR) provides information on morpho-functional abnormalities and myocardial tissue characterisation. Appropriate indications for CMR in athletes are uncertain. OBJECTIVE: To analyse the CMR performed at our Institute to evaluate variables associated with pathologic findings in a large cohort of athletes presenting with different clinical conditions. METHODS: All the CMR performed at our Institute in athletes aged > 14 years were recruited. CMR indications were investigated. CMR was categorised as "positive" or "negative" based on the presence of morphological and/or functional abnormalities and/or the presence of late gadolinium enhancement (excluding the right ventricular insertion point), fat infiltration, or oedema. Variables associated with "positive" CMR were explored. RESULTS: A total of 503 CMR were included in the analysis. "Negative" and "positive" CMR were 61% and 39%, respectively. Uncommon ventricular arrhythmias (VAs) were the most frequent indications for CMR, but the proportion of positive results was low (37%), and only polymorphic ventricular patterns were associated with positive CMR (p = 0.006). T-wave inversion at 12-lead ECG, particularly on lateral and inferolateral leads, was associated with positive CMR in 34% of athletes (p = 0.05). Echocardiography abnormalities resulted in a large proportion (58%) of positive CMR, mostly cardiomyopathies. CONCLUSION: CMR is more efficient in identifying a pathologic cardiac substrate in athletes in case of VAs (i.e., polymorphic beats), abnormal ECG repolarisation (negative T-waves in inferolateral leads), and borderline echocardiographic findings (LV hypertrophy, mildly depressed LV function). On the other hand, CMR is associated with a large proportion of negative results. Therefore, a careful clinical selection is needed to indicate CMR in athletes appropriately.


Subject(s)
Cardiology , Cardiomyopathies , Humans , Contrast Media , Gadolinium , Arrhythmias, Cardiac , Athletes , Magnetic Resonance Spectroscopy , Magnetic Resonance Imaging, Cine/methods , Predictive Value of Tests
11.
Spectrochim Acta A Mol Biomol Spectrosc ; 314: 124224, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38574611

ABSTRACT

Overuse of doxycycline (DOXY) can cause serious problems to human health, environment and food quality. So, it is essential to develop a new sensing methodology that is both sensitive and selective for the quantitative detection of DOXY. In our current research, we synthesized a simple fluorescent probe 4,4'-bis(benzyloxy)-1,1'-biphenyl (BBP) for the highly selective detection of doxycycline by through fluorescence spectroscopy. The probe BBP displayed ultra-sensitivity towards doxycycline due to Forster resonance energy transfer (FRET). Fluorescence spectroscopy, density functional theory (DFT), 1H NMR titration, UV-Vis, and Job's plot were used to confirm the sensing mechanism. The charge transfer between the probe and analyte was further examined qualitatively by electron density differences (EDD) and quantitively by natural bond orbital (NBO) analyses. Whereas the non-covalent nature of probe BBP towards DOXY was verified by theoretical non-covalent interaction (NCI) analysis as along with Bader's quantum theory of atoms in molecules (QTAIM) analysis. Furthermore, probe BBP was also practically employed for the detection of doxycycline in fish samples, pharmaceutical wastewater and blood samples.


Subject(s)
Doxycycline , Fluorescent Dyes , Animals , Humans , Fluorescent Dyes/chemistry , Spectrometry, Fluorescence/methods , Fluorescence Resonance Energy Transfer , Magnetic Resonance Spectroscopy
12.
BMJ Open ; 14(4): e077390, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38637128

ABSTRACT

INTRODUCTION: Radical chemoradiotherapy represents the gold standard for locally advanced cervical cancer. However, despite significant progress in improving local tumour control, distant relapse continues to impact overall survival. The development of predictive and prognostic biomarkers is consequently important to risk-stratify patients and identify populations at higher risk of poorer treatment response and survival outcomes. Exploratory study of using Magnetic resonance Prognostic Imaging markers for Radiotherapy In Cervix cancer (EMPIRIC) is a prospective exploratory cohort study, which aims to investigate the role of multiparametric functional MRI (fMRI) using diffusion-weighed imaging (DWI), dynamic contrast-enhanced (DCE) and blood oxygen level-dependent imaging (BOLD) MRI to assess treatment response and predict outcomes in patients undergoing radical chemoradiotherapy for cervical cancer. METHODS AND ANALYSIS: The study aims to recruit 40 patients across a single-centre over 2 years. Patients undergo multiparametric fMRI (DWI, DCE and BOLD-MRI) at three time points: before, during and at the completion of external beam radiotherapy. Tissue and liquid biopsies are collected at diagnosis and post-treatment to identify potential biomarker correlates against fMRI. The primary outcome is to evaluate sensitivity and specificity of quantitative parameters derived from fMRI as predictors of progression-free survival at 2 years following radical chemoradiotherapy for cervical cancer. The secondary outcome is to investigate the roles of fMRI as predictors of overall survival at 2 years and tumour volume reduction across treatment. Statistical analyses using regression models and survival analyses are employed to evaluate the relationships between the derived parameters, treatment response and clinical outcomes. ETHICS AND DISSEMINATION: The EMPIRIC study received ethical approval from the NHS Health Research Authority (HRA) on 14 February 2022 (protocol number RD2021-29). Confidentiality and data protection measures are strictly adhered to throughout the study. The findings of this study will be disseminated through peer-reviewed publications and scientific conferences, aiming to contribute to the growing body of evidence on the use of multiparametric MRI in cervical cancer management. TRIAL REGISTRATION NUMBER: NCT05532930.


Subject(s)
Uterine Cervical Neoplasms , Female , Humans , Prognosis , Uterine Cervical Neoplasms/diagnostic imaging , Uterine Cervical Neoplasms/radiotherapy , Prospective Studies , Cohort Studies , Neoplasm Recurrence, Local/diagnostic imaging , Neoplasm Recurrence, Local/pathology , Magnetic Resonance Imaging/methods , Chemoradiotherapy/methods , Magnetic Resonance Spectroscopy
14.
Circ Cardiovasc Imaging ; 17(4): e016042, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38563190

ABSTRACT

BACKGROUND: Assessing myocardial strain by cardiac magnetic resonance feature tracking (FT) has been found to be useful in patients with overt hypertrophic cardiomyopathy (HCM). Little is known, however, of its role in sarcomere gene mutation carriers without overt left ventricular hypertrophy (subclinical HCM). METHODS: Thirty-eight subclinical HCM subjects and 42 healthy volunteers were enrolled in this multicenter case-control study. They underwent a comprehensive cardiac magnetic resonance study. Two-dimensional global radial, circumferential, and longitudinal strain of the left ventricle (LV) were evaluated by FT analysis. RESULTS: The subclinical HCM sample was 41 (22-51) years old and 32% were men. FT analysis revealed a reduction in global radial strain (29±7.2 versus 47.9±7.4; P<0.0001), global circumferential strain (-17.3±2.6 -versus -20.8±7.4; P<0.0001) and global longitudinal strain (-16.9±2.4 versus -20.5±2.6; P<0.0001) in subclinical HCM compared with control subjects. The significant differences persisted when considering the 23 individuals free of all the structural and functional ECG and cardiac magnetic resonance abnormalities previously described. Receiver operating characteristic curve analyses showed that the differential diagnostic performances of FT in discriminating subclinical HCM from normal subjects were good to excellent (global radial strain with optimal cut-off value of 40.43%: AUC, 0.946 [95% CI, 0.93-1.00]; sensitivity 90.48%, specificity 94.44%; global circumferential strain with cut-off, -18.54%: AUC, 0.849 [95% CI, 0.76-0.94]; sensitivity, 88.10%; specificity, 72.22%; global longitudinal strain with cut-off, -19.06%: AUC, 0.843 [95% CI, 0.76-0.93]; sensitivity, 78.57%; specificity, 78.95%). Similar values were found for discriminating those subclinical HCM subjects without other phenotypic abnormalities from healthy volunteers (global radial strain with optimal cut-off 40.43%: AUC, 0.966 [95% CI, 0.92-1.00]; sensitivity, 90.48%; specificity, 95.45%; global circumferential strain with cut-off, -18.44%: AUC, 0.866 [95% CI, 0.76-0.96]; sensitivity, 92.86%; specificity, 77.27%; global longitudinal strain with cut-off, -17.32%: AUC, 0.838 [95% CI, 0.73-0.94]; sensitivity, 90.48%; specificity, 65.22%). CONCLUSIONS: Cardiac magnetic resonance FT-derived parameters are consistently lower in subclinical patients with HCM, and they could emerge as a good tool for discovering the disease during a preclinical phase.


Subject(s)
Cardiomyopathy, Hypertrophic , Sarcomeres , Male , Humans , Young Adult , Adult , Middle Aged , Female , Case-Control Studies , Sarcomeres/genetics , Sarcomeres/pathology , Magnetic Resonance Imaging, Cine/methods , Cardiomyopathy, Hypertrophic/diagnostic imaging , Cardiomyopathy, Hypertrophic/genetics , Cardiomyopathy, Hypertrophic/pathology , Magnetic Resonance Spectroscopy , Mutation
15.
Physiol Plant ; 176(2): e14270, 2024.
Article in English | MEDLINE | ID: mdl-38566280

ABSTRACT

The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.


Subject(s)
Metabolome , Metabolomics , Metabolomics/methods , Metabolome/physiology , Mass Spectrometry , Magnetic Resonance Spectroscopy , Plants/metabolism
16.
AAPS J ; 26(3): 40, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38570383

ABSTRACT

In a lyophilized protein/disaccharide system, the ability of the disaccharide to form a homogeneous mixture with the protein and to slow the protein mobility dictates the stabilization potential of the formulation. Human serum albumin was lyophilized with sucrose or trehalose in histidine, phosphate, or citrate buffer. 1H T1 relaxation times were measured by solid-state NMR spectroscopy and were used to assess the homogeneity and mobility of the samples after zero, six, and twelve months at different temperatures. The mobility of the samples decreased after 6 and 12 months storage at elevated temperatures, consistent with structural relaxation of the amorphous disaccharide matrix. Formulations with sucrose had lower mobility and greater stability than formulations with trehalose.


Subject(s)
Sucrose , Trehalose , Humans , Trehalose/chemistry , Temperature , Serum Albumin, Human , Drug Stability , Disaccharides , Magnetic Resonance Spectroscopy , Freeze Drying
17.
Methods Mol Biol ; 2797: 115-124, 2024.
Article in English | MEDLINE | ID: mdl-38570456

ABSTRACT

Fragment-based screening by ligand-observed 1D NMR and binding interface mapping by protein-observed 2D NMR are popular methods used in drug discovery. These methods allow researchers to detect compound binding over a wide range of affinities and offer a simultaneous assessment of solubility, purity, and chemical formula accuracy of the target compounds and the 15N-labeled protein when examined by 1D and 2D NMR, respectively. These methods can be applied for screening fragment binding to the active (GMPPNP-bound) and inactive (GDP-bound) states of oncogenic KRAS mutants.


Subject(s)
Drug Discovery , Proto-Oncogene Proteins p21(ras) , Proto-Oncogene Proteins p21(ras)/genetics , Ligands , Magnetic Resonance Spectroscopy , Proteins , Protein Binding , Binding Sites
18.
Methods Mol Biol ; 2797: 237-252, 2024.
Article in English | MEDLINE | ID: mdl-38570464

ABSTRACT

The activation level of RAS can be determined by GTP hydrolysis rate (khy) and GDP-GTP exchange rates (kex). Either impaired GTP hydrolysis or enhanced GDP-GTP exchange causes the aberrant activation of RAS in oncogenic mutants. Therefore, it is important to quantify the khy and kex for understanding the mechanisms of RAS oncogenesis and drug development. Conventional methods have individually measured the kex and khy of RAS. However, within the intracellular environment, GTP hydrolysis and GDP-GTP exchange reactions occur simultaneously under conditions where GTP concentration is kept constant. In addition, the intracellular activity of RAS is influenced by endogenous regulatory proteins, such as RAS GTPase activating proteins (GAPs) and the guanine-nucleotide exchange factors (GEFs). Here, we describe the in vitro and in-cell NMR methods to estimate the khy and kex simultaneously by measuring the time-dependent changes of the fraction of GTP-bound ratio under the condition of constant GTP concentration.


Subject(s)
Guanine Nucleotide Exchange Factors , ras GTPase-Activating Proteins , Guanosine Triphosphate/metabolism , ras GTPase-Activating Proteins/metabolism , Hydrolysis , Guanine Nucleotide Exchange Factors/metabolism , Magnetic Resonance Spectroscopy , Guanosine Diphosphate/metabolism
19.
Methods Mol Biol ; 2797: 195-209, 2024.
Article in English | MEDLINE | ID: mdl-38570461

ABSTRACT

Knowledge of how effectors interact with RAS GTPases is key to understanding how these switch-like proteins function in cells. Effectors bind specifically to GTP-loaded RAS using RAS association (RA) or RAS binding domains (RBDs) that show wide-ranging affinities and thermodynamic characteristics. Both normal development and RAS-induced tumorigenesis depend on multiple distinct effector proteins that are frequently co-expressed and co-localized, suggesting an antagonistic nature to signaling whereby multiple proteins compete for a limited pool of activated GTPase. NMR spectroscopy offers a powerful approach to multiplex effectors and/or regulatory enzymes and quantifies their interaction with RAS, expanding our biophysical and systems-level understanding of RAS signaling in a more integrated and physiologically relevant setting. Here we describe a method to directly quantitate GTPase binding to competing effectors, using wild-type KRAS complex with ARAF and PLCε1 as a model. Unlabeled RBD/RA domains are added simultaneously to isotopically labeled RAS, and peak intensities at chemical shifts characteristic of individually bound domains provide quantitation. Similar competition-based assays can be run with small molecule interactors, GEF/GAP domains, or regulatory enzymes that drive posttranslational modifications. Such efforts bring in vitro interaction experiments in line with more complex cellular environments.


Subject(s)
Signal Transduction , ras Proteins , ras Proteins/metabolism , Proteins/metabolism , Magnetic Resonance Spectroscopy , Protein Binding
20.
Cardiovasc Diabetol ; 23(1): 120, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38566090

ABSTRACT

BACKGROUND: Obesity is often associated with multiple comorbidities. However, whether obese subjects with hyperlipidemia in the absence of other complications have worse cardiac indices than metabolically healthy obese subjects is unclear. Therefore, we aimed to determine the effect of hyperlipidemia on subclinical left ventricular (LV) function in obesity and to evaluate the association of cardiac parameters with body fat distribution. MATERIALS AND METHODS: Ninety-two adults were recruited and divided into 3 groups: obesity with hyperlipidemia (n = 24, 14 males), obesity without hyperlipidemia (n = 25, 13 males), and c ntrols (n = 43, 25 males). LV strain parameters (peak strain (PS), peak diastolic strain rate (PDSR), peak systolic strain rate) derived from cardiovascular magnetic resonance tissue tracking were measured and compared. Dual-energy X-ray absorptiometer was used to measure body fat distribution. Correlations of hyperlipidemia and body fat distribution with LV strain were assessed by multivariable linear regression. RESULTS: Obese individuals with preserved LV ejection fraction showed lower global LV longitudinal, circumferential, and radial PS and longitudinal and circumferential PDSR than controls (all P < 0.05). Among obese patients, those with hyperlipidemia had lower longitudinal PS and PDSR and circumferential PDSR than those without hyperlipidemia (- 12.8 ± 2.9% vs. - 14.2 ± 2.7%, 0.8 ± 0.1 s-1 vs. 0.9 ± 0.3 s-1, 1.2 ± 0.2 s-1 vs. 1.4 ± 0.2 s-1; all P < 0.05). Multivariable linear regression demonstrated that hyperlipidemia was independently associated with circumferential PDSR (ß = - 0.477, P < 0.05) in obesity after controlling for growth differences, other cardiovascular risk factors, and central fat distribution. In addition, android fat had an independently negative relationship with longitudinal and radial PS (ß = - 0.486 and ß = - 0.408, respectively; all P < 0.05); and visceral fat was negatively associated with longitudinal PDSR (ß = - 0.563, P < 0.05). Differently, gynoid fat was positively correlated with circumferential PS and PDSR and radial PDSR (ß = 0.490, ß = 0.481, and ß = 0.413, respectively; all P < 0.05). CONCLUSION: Hyperlipidemia is independently associated with subclinical LV diastolic dysfunction in obesity. Central fat distribution (android and visceral fat) has a negative association, while peripheral fat distribution (gynoid fat) has a positive association on subclinical LV function. These results suggest that appropriate management of hyperlipidemia may be beneficial for obese patients, and that the differentiation of fat distribution in different regions may facilitate the precise management of obese patients. Clinical trials registration Effect of lifestyle intervention on metabolism of obese patients based on smart phone software (ChiCTR1900026476).


Subject(s)
Hyperlipidemias , Ventricular Dysfunction, Left , Male , Adult , Humans , Ventricular Function, Left , Hyperlipidemias/diagnosis , Hyperlipidemias/epidemiology , Obesity/complications , Obesity/diagnosis , Obesity/epidemiology , Ventricular Dysfunction, Left/diagnostic imaging , Ventricular Dysfunction, Left/etiology , Stroke Volume , Body Fat Distribution , Magnetic Resonance Spectroscopy/adverse effects
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