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25 results for “NMR based metabolomics”
1H NMR based metabolomics from: <em>Citrus sinensis</em> leaves in response to Diaphorina citri infestation and Huanglongbing disease
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NMR spectroscopy-based metabolomics of organotypic retinal explants
<p>The retina consumes massive amounts of energy, yet its metabolism and substrate exploitation remain poorly understood. Here, we used a murine explant model to manipulate retinal energy metabolism under entirely controlled conditions and utilized <sup>1</sup>H-NMR spectroscopy-based metabolomics, in situenzyme detection, and cell viability readouts to uncover the pathways of retinal energy production. Our experimental manipulations resulted in varying degrees of photoreceptor degeneration, while the inner retina and retinal pigment epithelium were essentially unaffected. This selective vulnerability of photoreceptors suggested very specific adaptations in their energy metabolism. Rod photoreceptors were found to rely strongly on oxidative phosphorylation, but only mildly on glycolysis. Conversely, cone photoreceptors were dependent on glycolysis but insensitive to electron transport chain decoupling. Importantly, photoreceptors appeared to uncouple glycolytic and Krebs-cycle metabolism via three different pathways: 1) the mini-Krebs-cycle, fueled by glutamine and branched-chain amino acids, generating N-acetylaspartate; 2) the alanine-generating Cahill-cycle; 3) the lactate-releasing Cori-cycle. Moreover, the metabolomic data indicated a shuttling of taurine and hypotaurine between the retinal pigment epithelium and photoreceptors, likely resulting in an additional net transfer of reducing power to photoreceptors. These findings expand our understanding of retinal physiology and pathology and shed new light on neuronal energy homeostasis and the pathogenesis of neurodegenerative diseases.</p>
NMR spectroscopy-based metabolomics of organotypic retinal explants
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Fig. 2 in A H NMR-based metabolomic approach to study the production of antimalarial compounds from Psiadia arguta leaves (pers.) voigt
Fig. 2. (A) Aphids on leaves of P. arguta acclimatized plants, (B) Mealybugs on leaves of P. arguta acclimatized plants, (C) Aphids and (D) mealybugs.
Fig. 4. 1H in A H NMR-based metabolomic approach to study the production of antimalarial compounds from Psiadia arguta leaves (pers.) voigt
Fig. 4. 1H NMR spectra (CDCl, 600 MHz) of the ethyl acetate extracts from in vitro, healthy, attacked, and elicited acclimatized plants of P. arguta. Assignments: 3 signals a (δH 0.80, H3-19 and H3-20), b (δH 0.88, H3-18), and c (δH 1.16, H3-17) are characteristic of the labdane bicyclic ring; d (δH 0.92, H3-16), e (δH 1.71, H3-16), f (δH 2.12, H3-2′), g (δH 3.69, H2-15), and h (δH 4.13, H2-15) are assigned to labda-13(E)-en-8α-ol-15-yl acetate (1); labda-8α-ol-15-yl acetate (2); labda-13(E)-ene-8αol-15-diol (3); (8R,13S)-labda-8,15-diol (4).
Fig. 3 in A H NMR-based metabolomic approach to study the production of antimalarial compounds from Psiadia arguta leaves (pers.) voigt
Fig. 3. (A) OPLS-DA score plot, (B) permutation plot, (C) ROC plot and (D) S-plot generated from the 1H NMR spectra (600 MHz) of healthy and attacked P. arguta plantlets crude extracts. (E) Contribution plot generated from the comparison of spectral variables of attacked samples vs healthy samples. The labels 6, 7, 8 and 9 on the PCA score plot correspond to the age of the plant; AA: attacked acclimatized plants; AH: healthy acclimatized plants and VH: healthy axenic plants.
1H-NMR-based urine metabolomics of prostate cancer and benign prostatic hyperplasia
<p>This dataset was collected from patients diagnosed with prostate cancer (R-sample_number) and benign prostatic hyperplasia (T-sample_number) using 1H-NMR spectroscopy.</p> <p>For more details check our paper: https://doi.org/10.1016/j.heliyon.2024.e28949</p>
[Dataset] 1H‑NMR based‑metabolomics reveals alterations in the metabolite profiles of chickens infected with ascarids and concurrent histomonosis infection
<p>The dataset associated with the publication "1H‑NMR based‑metabolomics reveals alterations in the metabolite profiles of chickens infected with ascarids and concurrent histomonosis infection" in <i>Gut Pathogens</i> (DOI: 10.1186/s13099-023-00584-7) comprises NMR measurements of plasma and liver samples. This dataset stems from a controlled study involving laying hens subject to mixed infections of <i>Ascaridia galli</i> and<i> Heterakis gallinarum</i>. Monitoring 108 individual hens over weeks 2 to 18 post-infection, samples of plasma and liver were collected at specific intervals. The dataset encompasses measurements of antibodies against histomonas, alpha 1 acid glycoprotein, and worm burdens, providing essential information for understanding the metabolic alterations induced by these infections in chickens.</p>
Fig. 5 in A H NMR-based metabolomic approach to study the production of antimalarial compounds from Psiadia arguta leaves (pers.) voigt
Fig. 5. Compounds identified in P. arguta attacked plants.
Fig. 1 in A H NMR-based metabolomic approach to study the production of antimalarial compounds from Psiadia arguta leaves (pers.) voigt
Fig. 1. Process for obtaining all experimental plants in the present study.
NMR Based Metabolomics Kinetics in ARDS Patients
ClinicalTrials.gov study NCT06036056. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Using Preprocedural Urine NMR(Nuclear Magnetic Resonance) -Based Metabolomics Analysis
ClinicalTrials.gov study NCT03731962. IPD Sharing: NO. Countries: 1. Publications: 0.
Metabolomic Profile of Vitreoretinal Diseases: an NMR-Based Approach Using Vitreous.
ClinicalTrials.gov study NCT06429969. IPD Sharing: NO. Countries: 1. Publications: 0.
NMR Based Metabolomic Study of Serum Biomarkers in Patients With Parkinson's Disease and Atypical Parkinsonian Syndrome
ClinicalTrials.gov study NCT06490926. IPD Sharing: NO. Countries: 1. Publications: 0.
The Diagnostic Pattern and Prognosis of Multiple Myeloma Patients With Myocardial Amyloidosis Were Evaluated by NMR Based Metabolomics
ClinicalTrials.gov study NCT05718401. IPD Sharing: Not stated. Countries: 1. Publications: 0.
NMR based clinical metabolomics study revealed disturbed glucose-alanine metabolism in Gestational Diabetes
<p><strong>Background and Aim:</strong> Altered gluconeogenesis from alanine (i.e. glucose-alanine cycle) that increases the levels of<br> serum alanine aminotransferase (ALT) are linked to the development of type II diabetes (T2DM) [1,2]. A recent study also revealed that elevated serum ALT levels in early pregnancy are associated with the risk of subsequent development of gestational<br> diabetes mellitus (GDM) and preeclampsia in late pregnancy [3]. So based on this, we hypothesized that the circulatory<br> alanine and alanine to glucose ratio (AGR) would be altered in GDM and may serve as an indicative biomarker to improve<br> the clinical diagnosis of GDM. <strong>Methods:</strong> The circulatory levels of alanine and glucose were estimated for 50 GDM patients and 49 age matched healthy female subjects using 800 MHz NMR spectroscopy. The NMR spectra were analyzed using NMR suite of commercial software (CHENOMX). The estimated circulatory levels of alanine and glucose were used to determine the circulatory<br> AGR levels as [Alanine in µM]/[Glucose in mM] and the values are reported as Mean ± SEM (SEM is standard error in mean).<br> <strong>Results:</strong> The present study aims to compare the serum metabolic profiles of alanine (Ala) and alanine to glucose ratio (AGR)<br> between age and sex matched GDM patients (N=50; pre term =32, post term=18) and healthy normal control (NC) female<br> subjects (N=49). The comparison revealed that the circulatory levels of alanine and AGR are significantly decreased in GDM<br> patients (Ala=397.5 ± 28.12| AGR=94.65 ± 9.06) compared to NC subjects (Ala =515.1 ± 24.03 | AGR=166.3 ± 7.577) <strong>(Figure 1A and 1B)</strong>. The respective p-values for comparison of alanine and AGR found to be 0.002 (**) and <0.0001, ****). The disturbed glucose-alanine metabolic cycle in GDM patients was further corroborated through performing metabolic Pearson r correlation analysis between alanine and glucose <strong>(Figure 1C and 1D)</strong>. For NC subjects, the circulatory metabolites alanine and glucose found to be strongly correlated (r=0.61, 95% CI=0.40 to 0.76; R square =0.37) with two-tailed p-value <0.0001 (see Table depicted in <strong>Figure 1E)</strong>. Whereas for GDM subjects, the circulatory metabolites alanine and glucose found to be moderately correlated (r=0.45, 95% CI=0.19 to 0.64; R square =0.20, <strong>Fig. 1E</strong>) with two tailed p-value =0.002 suggesting that the glucose-alanine metabolic cycle is altered in GDM. Overall, the observed changes in circulatory metabolites and metabolic ratios clearly suggested that the gluconeogenesis from alanine is disturbed in GDM and this abnormal glucose-alanine metabolism is possibly associated with the development of disease and its progression.</p> <p><strong>References:</strong><br> [1] N. Sattar, O. Scherbakova, I. Ford, D.S. O'Reilly, A. Stanley, E. Forrest, P.W. MacFarlane, C.J. Packard, S.M. Cobbe, J.<br> Shepherd, Elevated alanine aminotransferase predicts new-onset type 2 diabetes independently of classical risk<br> factors, metabolic syndrome, and C-reactive protein in the west of Scotland coronary prevention study, Diabetes 53<br> (2004) 2855-2860.<br> [2] N.H. Cho, H.C. Jang, S.H. Choi, H.R. Kim, H.K. Lee, J.C. Chan, S. Lim, Abnormal liver function test predicts type 2<br> diabetes: a community-based prospective study, Diabetes care 30 (2007) 2566-2568.<br> [3] S.M. Lee, J.S. Park, Y.J. Han, W. Kim, S.H. Bang, B.J. Kim, C.W. Park, M.Y. Kim, Elevated alanine aminotransferase in<br> early pregnancy and subsequent development of gestational diabetes and preeclampsia, Journal of Korean Medical<br> Science 35 (2020)</p>
Significantly decreased hypoxanthine levels in bone marrow plasma of aplastic anemia patients revealed by 800 MHz NMR based metabolomics analysis
<p><strong>Background:</strong> Compared to plasma, the hypoxanthine (HX) concentration is three times higher in the human bone marrow <strong>[R1]</strong> and its availability is crucial to regulate the de novo purine synthesis in human bone marrow <em>in vivo</em> <strong>[R1]</strong>. Studies have shown that circulatory HX levels in the plasma increase in patients with solid tumors and leukemia <strong>[R2]</strong>. Aplastic anemia (AA) is rare disorder of bone marrow failure characterized by hypocellularity and peripheral cytopenias. As purine biosynthesis is essential for normal cell growth and proliferation, we hypothesized that bone marrow HX levels will be decreased in aplastic anemia (AA) patients and may reset back partially in AA patients showing clinical improvement. </p> <p><strong>Aim:</strong> To compare the HX levels in bone marrow plasma samples of AA patients and control subjects and further to check its metabolic reprogramming in AA patients showing clinical improvement. </p> <p><strong>Methods:</strong> The HX levels of bone marrow plasma metabolites were estimated for 56 AA patients and 20 control subjects using 800 MHz NMR spectroscopy. The NMR spectra were analyzed using NMR suite of commercial software (CHENOMX). The levels of altered metabolites in AA patients w.r.t control were estimated and the values are reported as Mean ± SD (SD is standard deviation). The diagnostic potential is evaluated employing standard receiver operating characteristic (ROC) curve analysis.</p> <p><strong>Results:</strong> The present study aims to compare the bone marrow plasma metabolic profiles of hypoxanthine between age and sex matched AA patients (N=40; mean age 32.31±16.03, male/female ratio of 22/18) and follow-up AA patients (N=16) with respect to age matched control subjects (N=20, mean age=39.5±18.48 years, male/female ratio of 11/9). The comparison revealed that the HX levels are significantly decreased in AA patients (HX=3.62 ± 3.17) compared to NC subjects (HX = 20.89 ± 12.73) and improved slightly in follow-up patients (HX=6.21 ±4.77, however no statistically significant change compared to AA patients). Further, the circulatory HX levels exhibit significant diagnostic potential with area under ROC (AUROC) curve values equal to 0.96 [95%CI = 0.92–1.00].</p> <p><strong>Concluding remarks:</strong> The depleted HX levels in the bone marrow plasma suggested altered/compromised purine biosynthesis/metabolism in AA patients and future studies are warranted to underscore its role in the disease pathobiology.</p> <p> </p> <p><strong>Reference:</strong></p> <p>[R1] King, M.E., Honeysett, J.M. and Howell, S.B., 1983. Regulation of de novo purine synthesis in human bone marrow mononuclear cells by hypoxanthine. <em>The Journal of clinical investigation</em>, <em>72</em>(3), pp.965-970.</p> <p>[R2] Wung WE, Howell SB. Hypoxanthine concentrations in normal subjects and patients with solid tumors and leukemia. Cancer research. 1984 Jul;44(7):3144-8.</p>
NMR based clinical metabolomics study revealed aberrant proline biosynthesis and mitochondrial dysfunction in patients of mild cognitive impairment
<p>The prevalence of type-2 diabetes mellitus (T2DM) is tremendously increasing in older population because of several reasons and studies have shown that such old-age T2DM patients have 50-65% higher risk of developing cognitive impairment and its progression towards mild cognitive impairment (MCI). The studies claim that in the majority of MCI patients, the diabetes selectively involves the brain and the condition is now considered as a neuroendocrine disorder, even referred to as type 3 diabetes (T3D). Impaired glucose metabolism and mitochondrial dysfunction in neurodegenerative diseases, particularly in MCI, is compelling. Therefore, clinical interest is emerging to understand the role of mitochondria in T2DM and T3D which may provide important insights into pathogenesis of such chronic diseases and may indeed provide a target for improved patient care. The present study, therefore, aims to compare the serum metabolic profiles of MCI patients with age and sex matched T2DM patients with respect to normal control (NC) subjects. The results revealed that abnormal glutamate-to-glutamine cycling and proline metabolism in MCI patients. Compared to T2DM patients, the elevated circulatory proline levels in MCI patients hinted towards abnormal mitochondrial functioning underlying cognitive impairment.</p>
NMR based serum metabolomics analysis revealed similar serum metabolic alterations in Ischemic and Hemorrhagic Stroke patients
<p><strong>Background and Objective: </strong>Brain stroke (caused by interrupted blood supply to the brain) is one of the most common causes of disability and is the second highest cause of death in the world. Early diagnosis and treatment raises the chance of surviving a stroke, and can result in little or no disability. Treatment is based on the type of stroke and its primary cause; for ischaemic stroke (IS), medication or surgery or both can be recommended, whereas, for haemorrhagic stroke (HS, also known as intracerebral hemorrhage), surgery is recommended. However, there are scarcity of clinical markers which can differentiate IS from HS and further can provide information about severity of cerebral ischemia, endothelial injury, blood–brain barrier disruption, atherosclerosis, thrombus formation, inflammation, and oxidative stress. Metabolomics is a promising approach for identification of metabolic biomarkers and alterations associated with the diseased biology The present study is an effort to identify the diagnostic panel of serum metabolic profiles to differentiate between IS and HS patients and further could help predicting the severity of the cerebral ischemia. <strong>Methods:</strong> Blood serum samples were collected from suspected brain stroke patients at hospital admission within 6 hours after onset. The serum samples of patients clinically confirmed for IS and HS were only analysed using 800 MHz NMR spectroscopy. For comparative evaluation, the serum samples from 60 age and sex matched normal control (NC) subjects were also obtained for NMR analysis. The partial least square-discriminant analysis (PLS-DA) was performed to confirm the serum metabolic disparity between the study groups and metabolic features of discriminatory relevance were identified making composite use of mean decrease accuracy (MDA) score values estimated for metabolic features employing machine learning random forest (RF) classification analysis. The diagnostic potential of discriminatory metabolites were finally evaluated using receiver operating characteristic (ROC) curve analysis. <strong>Results</strong>: The serum metabolic profiles of total 107 brain stroke patients (48 IS and 60 HS) were measured and compared with those of 60 age and sex matched normal control (NC) subjects. Compared to NC, the serum levels of various amino acids (histidine, glutamine, threonine, alanine, glycine, dimethylglycine, pyruvate, etc.) were found to be decreased in both HS and IS patients, whereas those of creatine, mannitol, mannose, malonate and organic acids (such as acetate, 3-hydroxybutyrate and 3-hydroxy-isobutyrate) were found to be increased in the sera of brain stroke patients. However, the area under ROC (AUROC) curve values for majority of metabolic features found to be less than 0.8 for the discrimination between IS and HS suggesting that circulatory metabolic features lack sufficient sensitivity and specificity. <strong>Conclusions:</strong> The study provided primary evidence that various circulatory metabolites (including histidine, glutamine, and alanine) exhibited strong diagnostic potential for distinguishing brain stroke condition from NC subject, however, poor diagnostic accuracy in distinguishing IS from HS. Nevertheless, these metabolic changes can be used to assess the severity of brain stroke condition and monitoring patient response to treatment in emergency settings.</p>
Serum based clinical metabolomics analysis by NMR revealed abnormalities in mannose and myo-inositol metabolism in Scleroderma
<p><strong>Background and hypothesis</strong></p> <p>Systemic sclerosis (SSc) is a chronic autoimmune disorder characterized by fibrosis of the skin and internal organs, as well as vascular damage. Recent research has suggested that abnormal metabolism of certain sugars, such as mannose and myo-inositol, may contribute to the development and progression of SSc. Clinical studies have found that SSc patients have increased mannose and decreased myoinositol levels in their blood plasma/serum samples compared to those of healthy controls, suggesting that abnormal mannose and myoinositol metabolism may contribute to SSc pathogenesis. However, further research on patient cohorts of different ethnicity is imperative to validate these findings and understanding the mechanisms underlying these metabolic abnormalities and to develop new therapies that target these pathways. The present hypothesis-free NMR based clinical metabolomics study is an effort in this direction to compare the circulatory levels of mannose, myo-inositol and other endogenous metabolites in the sera of scleroderma patients and control subjects so that to validate the proposed abnormalities in mannose and myo-inositol metabolic pathways and association between them. The selected metabolic features and the metabolic ratio i.e. myo-inositol to mannose ratio (MMR) were further evaluated for their clinical potential in diagnostic and prognostic screening. <strong>Methods: </strong>The serum sample from 83 SSc patients meeting ACR 1980 criteria for Systemic Sclerosis, and 43 age and sex matched normal controls, were analyzed using one dimensional (1D) <sup>1</sup>H NMR spectroscopy coupled with multivariate statistical analysis such as Partial Least Square-Discriminate Analysis (PLS-DA). The NMR spectra were analysed using NMR suite of commercial software CHENOMX (www.chenomx.com/) and the metabolic concentrations were measured with respect to endogenous metabolite formate (as an internal calibration standard and concentration was set to 30 µM). For evaluating serum metabolic disparity between the study groups, the machine learning model was generated using random forest (RF) classification method and the Mean decrease accuracy (MDA) scores were used to identify the distinctive metabolic abnormalities in SSc. Univariate receiver operator characteristic (ROC) curve analysis was used to evaluate the diagnostic potential of the selected metabolic features. <strong>Results: </strong>There was clear distinction between SSc and healthy controls on the PLS-DA score plots and aberrant metabolic changes were evident in the sera of SSc patients. The sera of SSc patients were characterized by decreased serum levels of alanine, valine, <strong>myoinositol</strong>, creatinine, pyruvate, and lactate; whereas the serum levels of, acetate, 3-hydroxybutyrate and <strong>mannose</strong> were found to be significantly elevated. The majority of these metabolic alterations found to be well consistence with those reported previously in other clinical metabolomics studies [1,2]. Further, the circulatory MMR levels were estimated as [Myo-inositol/ Mannose] and compared between the study groups. Like myo-inositol, the MMR levels were also found to be significantly decreased in SSc patients. <strong>Conclusion: </strong>The altered levels of myo-inositol and other endogenous metabolites in the sera of SSc patients suggested abnormalities in myo-inositol metabolism in SSc patients and future studies are warranted to underscore its role in the pathobiology of scleroderma.</p> <p><strong>References:</strong></p> <p><strong>[1] </strong>Federica Murgia, Silvia Svegliati, Simone Poddighe, Milena Lussu, Aldo Manzin, Tatiana Spadoni, Colomba Fischetti, Armando Gabrielli, and Luigi Atzori. "Metabolomic profile of systemic sclerosis patients." Scientific Reports 8, no. 1 (2018): 7626.</p> <p><strong>[2].</strong> Thomas Bögl, Franz Mlynek, Markus Himmelsbach, Norbert Sepp, Wolfgang Buchberger, and Marija Geroldinger-Simić. "Plasma metabolomic profiling reveals four possibly disrupted mechanisms in systemic sclerosis." Biomedicines 10, no. 3 (2022): 607.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.