ORCID Profile
0000-0002-0556-8389
Current Organisations
Imperial College London
,
Murdoch University
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Publisher: American Chemical Society (ACS)
Date: 23-01-2001
DOI: 10.1021/TX000158X
Abstract: Current emphasis on efficient screening of novel therapeutic agents in toxicological studies has resulted in the evaluation of novel analytical technologies, including genomic (transcriptomic) and proteomic approaches. We have shown that high-resolution 1H NMR spectroscopy of biofluids and tissues coupled with appropriate chemometric analysis can also provide complementary data for use in in vivo toxicological screening of drugs. Metabonomics concerns the quantitative analysis of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification [Nicholson, J. K., Lindon, J. C., and Holmes, E. (1999) Xenobiotica 11, 1181-1189]. In this study, we have used 1H NMR spectroscopy to characterize the time-related changes in the urinary metabolite profiles of laboratory rats treated with 13 model toxins and drugs which predominantly target liver or kidney. These 1H NMR spectra were data-reduced and subsequently analyzed using a probabilistic neural network (PNN) approach. The methods encompassed a database of 1310 s les, of which 583 comprised a training set for the neural network, with the remaining 727 (independent cases) employed as a test set for validation. Using these techniques, the 13 classes of toxicity, together with the variations associated with strain, were distinguishable to >90%. Analysis of the 1H NMR spectral data by multilayer perceptron networks and principal components analysis gave a similar but less accurate classification than PNN analysis. This study has highlighted the value of probabilistic neural networks in developing accurate NMR-based metabonomic models for the prediction of xenobiotic-induced toxicity in experimental animals and indicates possible future uses in accelerated drug discovery programs. Furthermore, the sensitivity of this tool to strain differences may prove to be useful in investigating the genetic variation of metabolic responses and for assessing the validity of specific animal models.
Publisher: Wiley
Date: 29-12-2011
DOI: 10.1002/PCA.1268
Abstract: High salinity, caused by either natural (e.g. climatic changes) or anthropic factors (e.g. agriculture), is a widespread environmental stressor that can affect development and growth of salt-sensitive plants, leading to water deficit, the inhibition of intake of essential ions and metabolic disorders. The application of an NMR-based metabolic profiling approach to the investigation of saline-induced stress in Maize plants is presented. Zea Maize seedlings were grown in either 0, 50 or 150 mM saline solution. Plants were harvested after 2, 4 and 6 days (n = 5 per class and time point) and (1) H NMR spectroscopy was performed separately on shoot and root extracts. Spectral data were analysed and interpreted using multivariate statistical analyses. A distinct effect of time/growth was observed for the control group with relatively higher concentrations of acetoacetate at day 2 and increased levels of alanine at days 4 and 6 in root extracts, whereas concentration of alanine was positively correlated with the shoot extracts harvested at day 2 and trans-aconitic acid increased at days 4 and 6. A clear dose-dependent effect, superimposed on the growth effect, was observed for saline treated shoot and root extracts. This was correlated with increased levels of alanine, glutamate, asparagine, glycine-betaine and sucrose and decreased levels of malic acid, trans-aconitic acid and glucose in shoots. Correlation with salt-load shown in roots included elevated levels of alanine, γ-amino-N-butyric acid, malic acid, succinate and sucrose and depleted levels of acetoacetate and glucose. The metabolic effect of high salinity was predominantly consistent with osmotic stress as reported for other plant species and was found to be stronger in the shoots than the roots. Using multivariate data analysis it is possible to investigate the effects of more than one environmental stressor simultaneously.
Publisher: Elsevier BV
Date: 11-2004
DOI: 10.1016/J.JPBA.2004.08.016
Abstract: NMR spectroscopic and statistical methods have been applied to investigate the biochemical variations within and between two phenotypically normal rat strains. The 600 MHz (1)H NMR spectra of urine were acquired as part of a series of drug toxicity studies from 450 control rat urine s les from each of two strains of laboratory rat (Han Wistar and Sprague Dawley). The spectra were data-reduced to 256 intensity descriptors over a range of delta 0.2-10.0. The spectral variation was analysed both within and between strains in terms of the mean, standard deviation, skewness and kurtosis of each descriptor. It is demonstrated that spectral intensities corresponding to a number of endogenous metabolites do not show Gaussian distributions and there is evidence for bimodality for some metabolites. Additionally, despite the visual similarity of the NMR spectra from the two strains of rat, the descriptor distributions and the statistics derived from them revealed differences in the metabolite profiles, which clearly distinguished the two populations. This work is of value in the determination of biochemical normality and variability, and thus can be used to investigate, and place confidence limits on the biochemical deviations, which arise as a consequence of genetic modification or pathophysiological events.
Exploring Metabolic Consequences of CPS1 and CAD Dysregulation in Hepatocellular Carcinoma by Network Reconstruction
Publisher: Informa UK Limited
Date: 2020
DOI: 10.2147/JHC.S239039
Publisher: American Chemical Society (ACS)
Date: 03-07-2001
DOI: 10.1021/TX000231J
Abstract: The systemic biochemical effects of oral hydrazine administration (dosed at 75, 90, and 120 mg/kg) have been investigated in male Han Wistar rats using metabonomic analysis of (1)H NMR spectra of urine and plasma, conventional clinical chemistry, and liver histopathology. Plasma s les were collected both pre- and 24 h postdose, while urine was collected predose and daily over a 7 day postdose period. (1)H NMR spectra of the biofluids were analyzed visually and via pattern recognition using principal component analysis. The latter showed that there was a dose-dependent biochemical effect of hydrazine treatment on the levels of a range of low molecular weight compounds in urine and plasma, which was correlated with the severity of the hydrazine induced liver lesions. In plasma, increases in the levels of free glycine, alanine, isoleucine, valine, lysine, arginine, tyrosine, citrulline, 3-D-hydroxybutyrate, creatine, histidine, and threonine were observed. Urinary excretion of hippurate, citrate, succinate, 2-oxoglutarate, trimethylamine-N-oxide, fumarate and creatinine were decreased following hydrazine dosing, whereas taurine, creatine, threonine, N-methylnicotinic acid, tyrosine, beta-alanine, citrulline, Nalpha-acetylcitrulline and argininosuccinate excretion was increased. Moreover, the most notable effect was the appearance in urine and plasma of 2-aminoadipate, which has previously been shown to lead to neurological effects in rats. High urinary levels of 2-aminoadipate may explain the hitherto poorly understood neurological effects of hydrazine. Metabonomic analysis of high-resolution (1)H NMR spectra of biofluids has provided a means of monitoring the progression of toxicity and recovery, while also allowing the identification of novel biomarkers of development and regression of the lesion.
Publisher: Public Library of Science (PLoS)
Date: 23-12-2014
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 2015
DOI: 10.1038/AJG.2014.370
Abstract: The invasive nature of biopsy alongside issues with categorical staging and s ling error has driven research into noninvasive biomarkers for the assessment of liver fibrosis in order to stratify and personalize treatment of patients with liver disease. Here, we sought to determine whether a metabonomic approach could be used to identify signatures reflective of the dynamic, pathological metabolic perturbations associated with fibrosis in chronic hepatitis C (CHC) patients. Plasma nuclear magnetic resonance (NMR) spectral profiles were generated for two independent cohorts of CHC patients and healthy controls (n=50 original and n=63 validation). Spectral data were analyzed and significant discriminant biomarkers associated with fibrosis (as graded by enhanced liver fibrosis (ELF) and METAVIR scores) identified using orthogonal projection to latent structures (O-PLS). Increased severity of fibrosis was associated with higher tyrosine, phenylalanine, methionine, citrate and, very-low-density lipoprotein (vLDL) and lower creatine, low-density lipoprotein (LDL), phosphatidylcholine, and N-Acetyl-α1-acid-glycoprotein. Although area under the receiver operator characteristic curve analysis revealed a high predictive performance for classification based on METAVIR-derived models, <40% of identified biomarkers were validated in the second cohort. In the ELF-derived models, however, over 80% of the biomarkers were validated. Our findings suggest that modeling against a continuous ELF-derived score of fibrosis provides a more robust assessment of the metabolic changes associated with fibrosis than modeling against the categorical METAVIR score. Plasma metabolic phenotypes reflective of CHC-induced fibrosis primarily define alterations in amino-acid and lipid metabolism, and hence identify mechanistically relevant pathways for further investigation as therapeutic targets.
Publisher: American Chemical Society (ACS)
Date: 04-02-2010
DOI: 10.1021/AC902443K
Abstract: Spectroscopic profiling of biological s les is an integral part of metabolically driven top-down systems biology and can be used for identifying biomarkers of toxicity and disease. However, optimal biomarker information recovery and resonance assignment still pose significant challenges in NMR-based complex mixture analysis. The reduced signal overlap as achieved when projecting two-dimensional (2D) J-resolved (JRES) NMR spectra can be exploited to mitigate this problem and, here, full-resolution (1)H JRES projections have been evaluated as a tool for metabolic screening and biomarker identification. We show that the recoverable information content in JRES projections is intrinsically different from that in the conventional one-dimensional (1D) and Carr-Purcell-Meiboom-Gill (CPMG) spectra, because of the combined result of reduction of the over-representation of highly split multiplet peaks and relaxation editing. Principal component and correlation analyses of full-resolution JRES spectral data demonstrated that peak alignment is necessary. The application of statistical total correlation spectroscopy (STOCSY) to JRES projections improved the identification of previously overlapped small molecule resonances in JRES (1)H NMR spectra, compared to conventional 1D and CPMG spectra. These approaches are demonstrated using a galactosamine-induced hepatotoxicity study in rats and show that JRES projections have a useful and complementary role to standard one-dimensional experiments in complex mixture analysis for improved biomarker identification.
Publisher: American Chemical Society (ACS)
Date: 13-04-2009
DOI: 10.1021/PR8009885
Abstract: Covariation in the structural composition of the gut microbiome and the spectroscopically derived metabolic phenotype (metabotype) of a rodent model for obesity were investigated using a range of multivariate statistical tools. Urine and plasma s les from three strains of 10-week-old male Zucker rats (obese (fa/fa, n=8), lean (fa/-, n=8) and lean (-/-, n=8)) were characterized via high-resolution 1H NMR spectroscopy, and in parallel, the fecal microbial composition was investigated using fluorescence in situ hydridization (FISH) and denaturing gradient gel electrophoresis (DGGE) methods. All three Zucker strains had different relative abundances of the dominant members of their intestinal microbiota (FISH), with the novel observation of a Halomonas and a Sphingomonas species being present in the (fa/fa) obese strain on the basis of DGGE data. The two functionally and phenotypically normal Zucker strains (fa/- and -/-) were readily distinguished from the (fa/fa) obese rats on the basis of their metabotypes with relatively lower urinary hippurate and creatinine, relatively higher levels of urinary isoleucine, leucine and acetate and higher plasma LDL and VLDL levels typifying the (fa/fa) obese strain. Collectively, these data suggest a conditional host genetic involvement in selection of the microbial species in each host strain, and that both lean and obese animals could have specific metabolic phenotypes that are linked to their in idual microbiomes.
Publisher: Springer Science and Business Media LLC
Date: 12-06-2015
Publisher: Royal Society of Chemistry (RSC)
Date: 2001
DOI: 10.1039/B102347K
Abstract: High resolution 1H magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra have been obtained on typical C18 bonded silicas used in chromatographic solid-phase extraction separations. It has been shown for the first time that water molecules distributed in distinct physico-chemical environments within the chromatographic system can be detected directly using a simple 1H MAS NMR measurement. The resonances assigned to water protons in differing physico-chemical environments have distinct chemical shifts, line widths, relaxation times (T1 and T2) and also exhibit temperature dependent coalescence behaviour. This novel MAS approach may lead to a better understanding of the environments of other analytes in mixtures during such separations.
Publisher: Proceedings of the National Academy of Sciences
Date: 13-09-2011
Abstract: We elucidate the detailed effects of gut microbial depletion on the bile acid sub-metabolome of multiple body compartments (liver, kidney, heart, and blood plasma) in rats. We use a targeted ultra-performance liquid chromatography with time of flight mass-spectrometry assay to characterize the differential primary and secondary bile acid profiles in each tissue and show a major increase in the proportion of taurine-conjugated bile acids in germ-free (GF) and antibiotic (streptomycin enicillin)-treated rats. Although conjugated bile acids dominate the hepatic profile (97.0 ± 1.5%) of conventional animals, unconjugated bile acids comprise the largest proportion of the total measured bile acid profile in kidney (60.0 ± 10.4%) and heart (53.0 ± 18.5%) tissues. In contrast, in the GF animal, taurine-conjugated bile acids (especially taurocholic acid and tauro-β-muricholic acid) dominated the bile acid profiles (liver: 96.0 ± 14.5% kidney: 96 ± 1% heart: 93 ± 1% plasma: 93.0 ± 2.3%), with unconjugated and glycine-conjugated species representing a small proportion of the profile. Higher free taurine levels were found in GF livers compared with the conventional liver (5.1-fold P 0.001). Bile acid ersity was also lower in GF and antibiotic-treated tissues compared with conventional animals. Because bile acids perform important signaling functions, it is clear that these chemical communication networks are strongly influenced by microbial activities or modulation, as evidenced by farnesoid X receptor-regulated pathway transcripts. The presence of specific microbial bile acid co-metabolite patterns in peripheral tissues (including heart and kidney) implies a broader signaling role for these compounds and emphasizes the extent of symbiotic microbial influences in mammalian homeostasis.
Publisher: Elsevier BV
Date: 10-2011
DOI: 10.1016/J.ACA.2011.04.016
Abstract: Linear multivariate projection methods are frequently applied for predictive modeling of spectroscopic data in metabonomic studies. The OPLS method is a commonly used computational procedure for characterizing spectral metabonomic data, largely due to its favorable model interpretation properties providing separate descriptions of predictive variation and response-orthogonal structured noise. However, when the relationship between descriptor variables and the response is non-linear, conventional linear models will perform sub-optimally. In this study we have evaluated to what extent a non-linear model, kernel-based orthogonal projections to latent structures (K-OPLS), can provide enhanced predictive performance compared to the linear OPLS model. Just like its linear counterpart, K-OPLS provides separate model components for predictive variation and response-orthogonal structured noise. The improved model interpretation by this separate modeling is a property unique to K-OPLS in comparison to other kernel-based models. Simulated annealing (SA) was used for effective and automated optimization of the kernel-function parameter in K-OPLS (SA-K-OPLS). Our results reveal that the non-linear K-OPLS model provides improved prediction performance in three separate metabonomic data sets compared to the linear OPLS model. We also demonstrate how response-orthogonal K-OPLS components provide valuable biological interpretation of model and data. The metabonomic data sets were acquired using proton Nuclear Magnetic Resonance (NMR) spectroscopy, and include a study of the liver toxin galactosamine, a study of the nephrotoxin mercuric chloride and a study of Trypanosoma brucei brucei infection. Automated and user-friendly procedures for the kernel-optimization have been incorporated into version 1.1.1 of the freely available K-OPLS software package for both R and Matlab to enable easy application of K-OPLS for non-linear prediction modeling.
Publisher: Wiley
Date: 02-01-2018
DOI: 10.1111/DOM.13460
Publisher: Public Library of Science (PLoS)
Date: 18-09-2014
Publisher: American Chemical Society (ACS)
Date: 04-01-2007
DOI: 10.1021/PR060470D
Abstract: Inflammatory bowel diseases (IBD) including Crohn's disease (CD) and ulcerative colitis (UC) have a major impact on the health of in iduals and populations. Accurate diagnosis of inflammatory bowel disease (IBD) at an early stage, and correct differentiation between Crohn's disease (CD) and ulcerative colitis (UC), is important for optimum treatment and prognosis. We present here the first characterization of fecal extracts obtained from patients with CD and UC by employing a noninvasive metabonomics approach, which combines high resolution 1H NMR spectroscopy and multivariate pattern recognition techniques. The fecal extracts of both CD and UC patients were characterized by reduced levels of butyrate, acetate, methylamine, and trimethylamine in comparison with a control population, suggesting changes in the gut microbial community. Also, elevated quantities of amino acids were present in the feces from both disease groups, implying malabsorption caused by the inflammatory disease or an element of protein losing enteropathy. Metabolic differences in fecal profiles were more marked in the CD group in comparison with the control group, indicating that the inflammation caused by CD is more extensive in comparison with UC and involves the whole intestine. Furthermore, glycerol resonances were a dominant feature of fecal spectra from patients with CD but were present in much lower intensity in the control and UC groups. This work illustrates the potential of metabonomics to generate novel noninvasive diagnostics for gastrointestinal diseases and may further our understanding of disease mechanisms.
Publisher: American Chemical Society (ACS)
Date: 05-09-2018
DOI: 10.1021/ACS.JPROTEOME.8B00583
Abstract: The reduction in gut microbiota ersity is associated with a range of human diseases. Overuse of antibiotics has been associated with a diminished gut-microbial ersity in humans and may promote microbiota-associated negative effects to physical health, such as the metabolic syndrome-cluster of diseases and mental illnesses. There is a pressing need to deepen the understanding of the effects of antibiotics at the biochemical level. The current study investigated metabolic effects of two widely prescribed antibiotics-vancomycin and ciprofloxacin-on biofluids and brain tissue s les of NMRI female mice using a
Publisher: American Chemical Society (ACS)
Date: 16-09-2014
DOI: 10.1021/AC5025039
Abstract: Proton nuclear magnetic resonance (NMR)-based metabolic phenotyping of urine and blood plasma/serum s les provides important prognostic and diagnostic information and permits monitoring of disease progression in an objective manner. Much effort has been made in recent years to develop NMR instrumentation and technology to allow the acquisition of data in an effective, reproducible, and high-throughput approach that allows the study of general population s les from epidemiological collections for biomarkers of disease risk. The challenge remains to develop highly reproducible methods and standardized protocols that minimize technical or experimental bias, allowing realistic interlaboratory comparisons of subtle biomarker information. Here we present a detailed set of updated protocols that carefully consider major experimental conditions, including s le preparation, spectrometer parameters, NMR pulse sequences, throughput, reproducibility, quality control, and resolution. These results provide an experimental platform that facilitates NMR spectroscopy usage across different large cohorts of biofluid s les, enabling integration of global metabolic profiling that is a prerequisite for personalized healthcare.
Publisher: American Chemical Society (ACS)
Date: 08-06-2007
DOI: 10.1021/AC070212F
Abstract: 1H NMR spectroscopy potentially provides a robust approach for high-throughput metabolic screening of biofluids such as urine and plasma, but s le handling and preparation need careful optimization to ensure that spectra accurately report biological status or disease state. We have investigated the effects of storage temperature and time on the 1H NMR spectral profiles of human urine from two participants, collected three times a day on four different days. These were analyzed using modern chemometric methods. Analytical and preparation variation (tested between -40 degrees C and room temperature) and time of storage (to 24 h) were found to be much less influential than biological variation in s le classification. Statistical total correlation spectroscopy and discriminant function methods were used to identify the specific metabolites that were hypervariable due to preparation and biology. Significant intrain idual variation in metabolite profiles were observed even for urine collected on the same day and after at least 6 h fasting. The effect of long-term storage at different temperatures was also investigated, showing urine is stable if frozen for at least 3 months and that storage at room temperature for long periods (1-3 months) results in a metabolic profile explained by bacterial activity. Pres ling (e.g., previous day) intake of food and medicine can also strongly influence the urinary metabolic profiles indicating that collective detailed participant historical meta data are important for interpretation of metabolic phenotypes and for avoiding false biomarker discovery.
Publisher: American Chemical Society (ACS)
Date: 19-08-2008
DOI: 10.1021/PR800407J
Abstract: The time-related metabolic responses to l-arginine (ARG)-induced exocrine pancreatic toxicity were investigated using single ip doses of 1,000 and 4,000 mg/kg body weight over a 7 day experimental period in male Sprague-Dawley rats. Sequential timed urine and plasma s les were analyzed using high resolution (1)H NMR spectroscopy together with complementary clinical chemistry and histopathology analyses. Principal components analysis (PCA) and orthogonal projection on latent structures discriminant analysis (O-PLS-DA) were utilized to analyze the (1)H NMR data and to extract and identify candidate biomarkers and to construct metabolic trajectories post ARG administration. Low doses of ARG resulted in virtually no histopathological damage and distinct reversible metabolic response trajectories. High doses of ARG caused pancreatic acinar degeneration and necrosis and characteristic metabolic trajectory profiles with several distinct phases. The initial trajectory phase (0-8 h) involved changes in the urea cycle and transamination indicating a homeostatic response to detoxify excess ammonia generated from ARG catabolism. By 48 h, there was a notable enhancement of the excretion of the gut microbial metabolites, phenylacetylglycine (PAG), 4-cresol-glucuronide and 4-cresol-sulfate, suggesting that compromised pancreatic function impacts on the activity of the gut microbiota giving potential rise to a novel class of surrogate extragenomic biomarkers of pancreatic injury. The implied compromise of microbiotal function may also contribute to secondary hepatic and pancreatic toxic responses. We show here for the first time the value of metabonomic studies in investigating metabolic disruption due to experimental pancreatitis. The variety of observed systemic responses suggests that this approach may be of general value in the assessment of other animal models or human pancreatitis.
Publisher: BMJ
Date: 11-02-2019
DOI: 10.1136/GUTJNL-2018-317842
Abstract: Faecal microbiota transplant (FMT) effectively treats recurrent Clostridioides difficile infection (rCDI), but its mechanisms of action remain poorly defined. Certain bile acids affect C. difficile germination or vegetative growth. We hypothesised that loss of gut microbiota-derived bile salt hydrolases (BSHs) predisposes to CDI by perturbing gut bile metabolism, and that BSH restitution is a key mediator of FMT’s efficacy in treating the condition. Using stool collected from patients and donors pre-FMT ost-FMT for rCDI, we performed 16S rRNA gene sequencing, ultra performance liquid chromatography mass spectrometry (UPLC-MS) bile acid profiling, BSH activity measurement, and qPCR of bsh / bai CD genes involved in bile metabolism. Human data were validated in C. difficile batch cultures and a C57BL/6 mouse model of rCDI. From metataxonomics, pre-FMT stool demonstrated a reduced proportion of BSH-producing bacterial species compared with donors ost-FMT. Pre-FMT stool was enriched in taurocholic acid (TCA, a potent C. difficile germinant) TCA levels negatively correlated with key bacterial genera containing BSH-producing organisms. Post-FMT s les demonstrated recovered BSH activity and bsh / bai CD gene copy number compared with pretreatment (p .05). In batch cultures, supernatant from engineered bsh -expressing E. coli and naturally BSH-producing organisms ( Bacteroides ovatus, Collinsella aerofaciens, Bacteroides vulgatus and Blautia obeum ) reduced TCA-mediated C. difficile germination relative to culture supernatant of wild-type (BSH-negative) E. coli. C. difficile total viable counts were ~70% reduced in an rCDI mouse model after administration of E. coli expressing highly active BSH relative to mice administered BSH-negative E. coli (p .05). Restoration of gut BSH functionality contributes to the efficacy of FMT in treating rCDI.
Publisher: Proceedings of the National Academy of Sciences
Date: 22-04-2008
Abstract: Human African trypanosomiasis (HAT) is transmitted by tsetse flies and, if untreated, is fatal. Treatment depends on infection stage, and early diagnosis is crucial for effective disease management. The systemic host biochemical changes induced by HAT that enable biomarker discovery or relate to therapeutic outcome are largely unknown. We have characterized the multivariate temporal responses of mice to Trypanosoma brucei brucei infection, using 1 H nuclear magnetic resonance (NMR) spectroscopic metabolic phenotyping of urine and plasma. Marked alterations in plasma metabolic profiles were detected already 1 day postinfection. Elevated plasma concentrations of lactate, branched chain amino acids, and acetylglycoprotein fragments were noted. T. brucei brucei -infected mice also had an imbalance of plasma alanine and valine, consistent with differential gluconeogenesis (parasite)-ketogenesis (host) pathway counterflux, involving stimulated host glycolysis, ketogenesis, and enhanced lipid oxidation in the host. Histopathologic evidence of T. brucei brucei -induced extramedullary hepatic hemopoiesis, renal interstitial nephritis, and a provoked inflammatory response was also noted. Metabolic disturbance of gut microbiotal activity was associated with infection, as indicated by changes in the urinary concentrations of the microbial co-metabolites, including hippurate. Concluding, parasite infection results in multiple systemic biochemical effects in the host and disturbance of the symbiotic gut microbial metabolic interactions. Investigation of these transgenomic metabolic alterations may underpin the development of new diagnostic criteria and metrics of therapeutic efficacy.
Publisher: Elsevier
Date: 2007
Publisher: Springer Science and Business Media LLC
Date: 24-08-2016
DOI: 10.1038/NPJBIOFILMS.2016.14
Abstract: The ligand-induced transcription factor, aryl hydrocarbon receptor (AhR) is known for its capacity to tune adaptive immunity and xenobiotic metabolism—biological properties subject to regulation by the indigenous microbiome. The objective of this study was to probe the postulated microbiome-AhR crosstalk and whether such an axis could influence metabolic homeostasis of the host. Utilising a systems-biology approach combining in-depth 1 H-NMR-based metabonomics (plasma, liver and skeletal muscle) with microbiome profiling (small intestine, colon and faeces) of AhR knockout (AhR −/− ) and wild-type (AhR +/+ ) mice, we assessed AhR function in host metabolism. Microbiome metabolites such as short-chain fatty acids were found to regulate AhR and its target genes in liver and intestine. The AhR signalling pathway, in turn, was able to influence microbiome composition in the small intestine as evident from microbiota profiling of the AhR +/+ and AhR −/− mice fed with diet enriched with a specific AhR ligand or diet depleted of any known AhR ligands. The AhR −/− mice also displayed increased levels of corticosterol and alanine in serum. In addition, activation of gluconeogenic genes in the AhR −/− mice was indicative of on-going metabolic stress. Reduced levels of ketone bodies and reduced expression of genes involved in fatty acid metabolism in the liver further underscored this observation. Interestingly, exposing AhR −/− mice to a high-fat diet showed resilience to glucose intolerance. Our data suggest the existence of a bidirectional AhR-microbiome axis, which influences host metabolic pathways.
Publisher: Springer Science and Business Media LLC
Date: 07-06-2017
DOI: 10.1038/S41598-017-02529-Y
Abstract: Metabolic phenotypes reflect both the genetic and environmental factors which contribute to the development of varicose veins (VV). This study utilises analytical techniques to provide a comprehensive metabolic picture of VV disease, with the aim of identifying putative cellular pathways of disease pathogenesis. VV (n = 80) and non-VV (n = 35) aqueous and lipid metabolite extracts were analysed using 600 MHz 1 H Nuclear Magnetic Resonance spectroscopy and Ultra-Performance Liquid Chromatography Mass Spectrometry. A subset of tissue s les (8 subjects and 8 controls) were analysed for microRNA expression and the data analysed with mirBase (www.mirbase.org). Using Multivariate statistical analysis, Ingenuity pathway analysis software, DIANALAB database and published literature, the association of significant metabolites with relevant cellular pathways were understood. Higher concentrations of glutamate, taurine, myo-inositol, creatine and inosine were present in aqueous extracts and phosphatidylcholine, phosphatidylethanolamine and sphingomyelin in lipid extracts in the VV group compared with non-VV group. Out of 7 differentially expressed miRNAs, spearman correlation testing highlighted correlation of hsa-miR-642a-3p, hsa-miR-4459 and hsa-miR-135a-3p expression with inosine in the vein tissue, while miR-216a-5p, conversely, was correlated with phosphatidylcholine and phosphatidylethanolamine. Pathway analysis revealed an association of phosphatidylcholine and sphingomyelin with inflammation and myo-inositol with cellular proliferation.
Publisher: Elsevier BV
Date: 07-2001
Publisher: Elsevier BV
Date: 12-2003
Abstract: This study describes the first metabonomic approach to determining biochemical modifications following dietary intervention in humans. Significant interest in the mechanisms of action of soy isoflavones has predominantly stemmed from in vitro experiments but to date the availability of analytical tools for studying the mechanisms of action in vivo have been limited. Here a metabonomic approach based on chemometric analysis of 1H nuclear magnetic resonance spectra of blood plasma has been used to investigate metabolic changes following dietary intervention with soy isoflavones in healthy premenopausal women under controlled environmental conditions. Clear differences in the plasma lipoprotein, amino acid, and carbohydrate profiles were observed following soy intervention, suggesting a soy-induced alteration in energy metabolism.
Publisher: Informa UK Limited
Date: 21-04-2022
Publisher: American Chemical Society (ACS)
Date: 25-06-2013
DOI: 10.1021/PR301097K
Abstract: Modeling aging and age-related pathologies presents a substantial analytical challenge given the complexity of gene-environment influences and interactions operating on an in idual. A top-down systems approach is used to model the effects of lifelong caloric restriction, which is known to extend life span in several animal models. The metabolic phenotypes of caloric-restricted (CR n = 24) and pair-housed control-fed (CF n = 24) Labrador Retriever dogs were investigated by use of orthogonal projection to latent structures discriminant analysis (OPLS-DA) to model both generic and age-specific responses to caloric restriction from the ¹H NMR blood serum profiles of young and older dogs. Three aging metabolic phenotypes were resolved: (i) an aging metabolic phenotype independent of diet, characterized by high levels of glutamine, creatinine, methylamine, dimethylamine, trimethylamine N-oxide, and glycerophosphocholine and decreasing levels of glycine, aspartate, creatine and citrate indicative of metabolic changes associated largely with muscle mass (ii) an aging metabolic phenotype specific to CR dogs that consisted of relatively lower levels of glucose, acetate, choline, and tyrosine and relatively higher serum levels of phosphocholine with increased age in the CR population (iii) an aging metabolic phenotype specific to CF dogs including lower levels of liproprotein fatty acyl groups and allantoin and relatively higher levels of formate with increased age in the CF population. There was no diet metabotype that consistently differentiated the CF and CR dogs irrespective of age. Glucose consistently discriminated between feeding regimes in dogs (≥312 weeks), being relatively lower in the CR group. However, it was observed that creatine and amino acids (valine, leucine, isoleucine, lysine, and phenylalanine) were lower in the CR dogs (<312 weeks), suggestive of differences in energy source utilization. ¹H NMR spectroscopic analysis of longitudinal serum profiles enabled an unbiased evaluation of the metabolic markers modulated by a lifetime of caloric restriction and showed differences in the metabolic phenotype of aging due to caloric restriction, which contributes to longevity studies in caloric-restricted animals. Furthermore, OPLS-DA provided a framework such that significant metabolites relating to life extension could be differentiated and integrated with aging processes.
Publisher: Elsevier BV
Date: 11-2012
Publisher: Wiley
Date: 04-04-2008
Publisher: Future Science Ltd
Date: 12-2009
DOI: 10.4155/BIO.09.112
Abstract: We demonstrate the effective use of NMR spectroscopic profiles of urine and plasma from the first successful use of hepatocyte transplantation as a bridge to auxiliary partial orthotopic liver transplantation in a child antenatally diagnosed with severe ornithine transcarbamylase deficiency. In this single-patient study, NMR profiles indicated that the disrupted urea cycle could be normalized by hepatocyte cell infusion and this was confirmed using orthogonal partial least-squares-based chemometrics. However, despite dietary manipulations and adminstration of ammonia scavengers, the desired reduction in plasma ammonia was not consistently achieved between sessions of hepatocyte transplantation due to episodes of sepsis. A subsequent liver transplant corrected the metabolic abnormalities. The use of metabolic profiling has been shown to be a promising method for evaluating the efficacy of cell infusions and has demonstrated the capability for the early detection of response to therapy in real time, an approach that may be of use in wider clinical settings.
Publisher: Elsevier BV
Date: 10-2019
DOI: 10.1016/J.TIPS.2019.08.004
Abstract: Understanding metabotype (multicomponent metabolic characteristics) variation can help to generate new diagnostic and prognostic biomarkers, as well as models, with potential to impact on patient management. We present a suite of conceptual approaches for the generation, analysis, and understanding of metabotypes from body fluids and tissues. We describe and exemplify four fundamental approaches to the generation and utilization of metabotype data via multiparametric measurement of (i) metabolite levels, (ii) metabolic trajectories, (iii) metabolic entropies, and (iv) metabolic networks and correlations in space and time. This conceptual framework can underpin metabotyping in the scenario of personalized medicine, with the aim of improving clinical outcomes for patients, but the framework will have value and utility in areas of metabolic profiling well beyond this exemplar.
Publisher: American Chemical Society (ACS)
Date: 21-12-2005
DOI: 10.1021/JF0403282
Abstract: A metabonomic strategy, utilizing high-resolution 1H NMR spectroscopy in conjunction with chemometric methods (discriminant analysis with orthogonal signal correction), has been applied to the study of human biological responses to chamomile tea ingestion. Daily urine s les were collected from volunteers during a 6-week period incorporating a 2-week baseline period, 2 weeks of daily chamomile tea ingestion, and a 2-week post-treatment phase. Although strong intersubject variation in metabolite profiles was observed, clear differentiation between the s les obtained before and after chamomile ingestion was achieved on the basis of increased urinary excretion of hippurate and glycine with depleted creatinine concentration. S les obtained up to 2 weeks after daily chamomile intake formed an isolated cluster in the discriminant analysis map, from which it was inferred that the metabolic effects of chamomile ingestion were prolonged during the 2-week postdosing period. This study highlights the potential for metabonomic technology in the assessment of nutritional interventions, despite the high degree of variation from genetic and environmental sources.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 13-11-2019
DOI: 10.1126/SCITRANSLMED.AAU4760
Abstract: Transplantation of the gut microbiota of old donor mice into young germ-free mice promotes neurogenesis and prolongevity gene expression signatures.
Publisher: Elsevier BV
Date: 03-2003
DOI: 10.1016/S0031-9422(02)00719-7
Abstract: Several essential and non-essential metals (typically those from periods 4, 5 and 6 in groups 11-15 in the periodic table) are commonly detoxified in higher plants by complexation with phytochelatin. The genetic and gross metabolic basis of metal tolerance in plants is, however, poorly understood. Here, we have analyzed plant cell extracts using 1H NMR spectroscopy combined with multivariate statistical analysis of the data to investigate the biochemical consequences of Cd(2+) exposure in Silene cucubalus cell cultures. Principal components analysis of 1H NMR spectra showed clear discrimination between control and Cd(2+) dosed groups, demonstrating the metabolic effects of Cd(2+) and thus allowing the identification of increases in malic acid and acetate, and decreases in glutamine and branched chain amino acids as consequences of Cd(2+) exposure. This work shows the value of NMR-based metabolomic approaches to the determination of biochemical effects of pollutants in naturally selected populations.
Publisher: Public Library of Science (PLoS)
Date: 20-09-2017
Publisher: Georg Thieme Verlag KG
Date: 03-2004
Abstract: In order to improve the accuracy and consistency of control phytomedicine preparations worldwide, regulatory authorities are requesting research into new analytical methods for the stricter standardisation of phytomedicines. Such methods have to be both objective and robust, and should address the reproducibility of the content of the chemical profiles. NMR-based metabolomics, which combines high-resolution (1)H-NMR spectroscopy with chemometric analysis, has been employed as an innovative way to meet those demands. In this paper, chamomile flowers from three different geographical regions, namely, Egypt, Hungary and Slovakia were characterised using 1H-NMR spectroscopy followed by principal component analysis. It was found that the origin, purity and preparation methods contributed to the differences observed in prepared chamomile extracts. In addition, this method also enabled the elucidation of the molecular information embedded in the spectra responsible for the observed variability. The metabolomic strategy employed in the current study should provide an efficient tool for the quality control and authentication of phytomedicines.
Publisher: American Chemical Society (ACS)
Date: 06-05-2000
DOI: 10.1021/TX990210T
Abstract: 1H NMR spectroscopic and pattern recognition (PR)-based methods were used to investigate the biochemical variability in urine obtained from control rats and from rats treated with a hydrazine (a model hepatotoxin) or HgCl(2) (a model renal cortical toxin). The 600 MHz (1)H NMR spectra of urine s les obtained from vehicle- or toxin-treated Han-Wistar (HW) and Sprague-Dawley (SD) rats were acquired, and principal components analysis (PCA) and soft independent modeling of class analogy (SIMCA) analysis were used to investigate the (1)H NMR spectral data. Variation and strain differences in the biochemical composition of control urine s les were assessed. Control urine (1)H NMR spectra obtained from the two rat strains appeared visually similar. However, chemometric analysis of the control urine spectra indicated that HW rat urine contained relatively higher concentrations of lactate, acetate, and taurine and lower concentrations of hippurate than SD rat urine. Having established the extent of biochemical variation in the two populations of control rats, PCA was used to evaluate the metabolic effects of hydrazine and HgCl(2) toxicity. Urinary biomarkers of each class of toxicity were elucidated from the PC loadings and included organic acids, amino acids, and sugars in the case of mercury, while levels of taurine, beta-alanine, creatine, and 2-aminoadipate were elevated after hydrazine treatment. SIMCA analysis of the data was used to build predictive models (from a training set of 416 s les) for the classification of toxicity type and strain of rat, and the models were tested using an independent set of urine s les (n = 124). Using models constructed from the first three PCs, 98% of the test s les were correctly classified as originating from control, hydrazine-treated, or HgCl(2)-treated rats. Furthermore, this method was sensitive enough to predict the correct strain of the control s les for 79% of the data, based upon the class of best fit. Incorporation of these chemometric methods into automated NMR-based metabonomics analysis will enable on-line toxicological assessment of biofluids and will provide a tool for probing the mechanistic basis of organ toxicity.
Publisher: Springer Science and Business Media LLC
Date: 26-10-2020
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 06-2014
Publisher: American Chemical Society (ACS)
Date: 29-06-2011
DOI: 10.1021/PR200243T
Abstract: The interaction between the gut microbiota and their mammalian host is known to have far-reaching consequences with respect to metabolism and health. We investigated the effects of eight days of oral antibiotic exposure (penicillin and streptomycin sulfate) on gut microbial composition and host metabolic phenotype in male Han-Wistar rats (n = 6) compared to matched controls. Early recolonization was assessed in a third group exposed to antibiotics for four days followed by four days recovery (n = 6). Fluorescence in situ hybridization analysis of the intestinal contents collected at eight days showed a significant reduction in all bacterial groups measured (control, 10(10.7) cells/g feces antibiotic-treated, 10(8.4)). Bacterial suppression reduced the excretion of mammalian-microbial urinary cometabolites including hippurate, phenylpropionic acid, phenylacetylglycine and indoxyl-sulfate whereas taurine, glycine, citrate, 2-oxoglutarate, and fumarate excretion was elevated. While total bacterial counts remained notably lower in the recolonized animals (10(9.1) cells/g faeces) compared to the controls, two cage-dependent subgroups emerged with Lactobacillus/Enterococcus probe counts dominant in one subgroup. This dichotomous profile manifested in the metabolic phenotypes with subgroup differences in tricarboxylic acid cycle metabolites and indoxyl-sulfate excretion. Fecal short chain fatty acids were diminished in all treated animals. Antibiotic treatment induced a profound effect on the microbiome structure, which was reflected in the metabotype. Moreover, the recolonization process was sensitive to the microenvironment, which may impact on understanding downstream consequences of antibiotic consumption in human populations.
Publisher: Springer Science and Business Media LLC
Date: 22-12-2016
DOI: 10.1038/HR.2016.164
Publisher: Springer Science and Business Media LLC
Date: 09-01-2021
DOI: 10.1186/S13195-020-00741-Z
Abstract: Both serotonergic signalling disruption and systemic inflammation have been associated with the pathogenesis of Alzheimer’s disease (AD). The common denominator linking the two is the catabolism of the essential amino acid, tryptophan. Metabolism via tryptophan hydroxylase results in serotonin synthesis, whilst metabolism via indoleamine 2,3-dioxygenase (IDO) results in kynurenine and its downstream derivatives. IDO is reported to be activated in times of host systemic inflammation and therefore is thought to influence both pathways. To investigate metabolic alterations in AD, a large-scale metabolic phenotyping study was conducted on both urine and serum s les collected from a multi-centre clinical cohort, consisting of in iduals clinically diagnosed with AD, mild cognitive impairment (MCI) and age-matched controls. Metabolic phenotyping was applied to both urine ( n = 560) and serum ( n = 354) from the European-wide AddNeuroMed/Dementia Case Register (DCR) biobank repositories. Metabolite data were subsequently interrogated for inter-group differences influence of gender and age comparisons between two subgroups of MCI - versus those who remained cognitively stable at follow-up visits (sMCI) and those who underwent further cognitive decline (cMCI) and the impact of selective serotonin reuptake inhibitor (SSRI) medication on metabolite concentrations. Results revealed significantly lower metabolite concentrations of tryptophan pathway metabolites in the AD group: serotonin (urine, serum), 5-hydroxyindoleacetic acid (urine), kynurenine (serum), kynurenic acid (urine), tryptophan (urine, serum), xanthurenic acid (urine, serum), and kynurenine/tryptophan ratio (urine). For each listed metabolite, a decreasing trend in concentrations was observed in-line with clinical diagnosis: control MCI AD. There were no significant differences in the two MCI subgroups whilst SSRI medication status influenced observations in serum, but not urine. Urine and serum serotonin concentrations were found to be significantly lower in AD compared with controls, suggesting the bioavailability of the neurotransmitter may be altered in the disease. A significant increase in the kynurenine/tryptophan ratio suggests that this may be a result of a shift to the kynurenine metabolic route due to increased IDO activity, potentially as a result of systemic inflammation. Modulation of the pathways could help improve serotonin bioavailability and signalling in AD patients.
Publisher: American Chemical Society (ACS)
Date: 18-02-2006
DOI: 10.1021/AC0519312
Abstract: Considerable confusion appears to exist in the metabonomics literature as to the real need for, and the role of, preprocessing the acquired spectroscopic data. A number of studies have presented various data manipulation approaches, some suggesting an optimum method. In metabonomics, data are usually presented as a table where each row relates to a given s le or analytical experiment and each column corresponds to a single measurement in that experiment, typically in idual spectral peak intensities or metabolite concentrations. Here we suggest definitions for and discuss the operations usually termed normalization (a table row operation) and scaling (a table column operation) and demonstrate their need in 1H NMR spectroscopic data sets derived from urine. The problems associated with "binned" data (i.e., values integrated over discrete spectral regions) are also discussed, and the particular biological context problems of analytical data on urine are highlighted. It is shown that care must be exercised in calculation of correlation coefficients for data sets where normalization to a constant sum is used. Analogous considerations will be needed for other biofluids, other analytical approaches (e.g., HPLC-MS), and indeed for other "omics" techniques (i.e., transcriptomics or proteomics) and for integrated studies with "fused" data sets. It is concluded that data preprocessing is context dependent and there can be no single method for general use.
Publisher: American Chemical Society (ACS)
Date: 06-07-2009
DOI: 10.1021/AC900828P
Abstract: Here we present a novel method for enhanced NMR spectral information recovery, utilizing a statistical total correlation spectroscopy editing (STOCSY-E) procedure for the identification of drug metabolite peaks in biofluids and for deconvolution of drug and endogenous metabolite signals. Structurally correlated peaks from drug metabolites and those from closely related drug metabolite pathways are first identified using STOCSY. Subsequently, this correlation information is utilized to scale the biofluid (1)H NMR spectra across these identified regions, producing a modified set of spectra in which drug metabolite contributions are reduced and, thus, facilitating analysis by pattern recognition methods without drug metabolite interferences. The application of STOCSY-E is illustrated with two exemplar (1)H NMR spectroscopic data sets, posing various drug metabolic, toxicological, and analytical challenges viz. 800 MHz (1)H spectra of human urine (n = 21) collected over 10 h following dosing with the antibiotic flucloxacillin and 600 MHz (1)H NMR spectra of rat urine (n = 27) collected over 48 h following exposure to the renal papillary toxin 2-bromoethanamine (BEA). STOCSY-E efficiently identified and removed the major xenobiotic metabolite peaks in both data sets, providing enhanced visualization of endogenous changes via orthogonal to projection filtered partial least-squares discriminant analysis (OPLS-DA). OPLS-DA of the STOCSY-E spectral data from the BEA-treated rats revealed the gut bacterial-mammalian co-metabolite phenylacetylglycine as a previously unidentified surrogate biomarker of toxicity. STOCSY-E has a wide range of potential applications in clinical, epidemiology, toxicology, and nutritional studies where multiple xenobiotic metabolic interferences may confound biological interpretation. Additionally, this tool could prove useful for applications outside of metabolic analysis, for ex le, in process chemistry for following chemical reactions and equilibria and detecting impurities.
Publisher: Informa UK Limited
Date: 1999
Abstract: 1. Quantitative relationships between molecular physico-chemical properties of 22 substituted benzoic acids and the extent of excretion of their metabolites in rat urine have been investigated using computational chemistry and multivariate statistics. 2. A data set of 34 theoretically derived physico-chemical descriptors calculated was used to classify the benzoic acids according to their predominant urinary metabolic fate. 3. Quantitative structure-metabolism relationships were obtained by linear regression using combinations of physico-chemical descriptors allowing the prediction of % urinary excretion of glycine (r = 0.73) and glucuronide conjugates (r = 0.82) and % urinary excretion of the parent compound (r = 0.91).
Publisher: Elsevier BV
Date: 2023
DOI: 10.1016/J.AJPATH.2022.09.005
Abstract: Patients with cholestatic liver disease, including those with primary biliary cholangitis, can experience symptoms of impaired cognition or brain fog. This phenomenon remains unexplained and is currently untreatable. Bile duct ligation (BDL) is an established rodent model of cholestasis. In addition to liver changes, BDL animals develop cognitive symptoms early in the disease process (before development of cirrhosis and/or liver failure). The cellular mechanisms underpinning these cognitive symptoms are poorly understood. Herein, we explored the neurocognitive symptom manifestations, and tested potential therapies, in BDL mice, and used human neuronal cell cultures to explore translatability to humans. BDL animals exhibited short-term memory loss and showed reduced astrocyte coverage of the blood-brain barrier, destabilized hippoc al network activity, and neuronal senescence. Ursodeoxycholic acid (first-line therapy for most human cholestatic diseases) did not reverse symptomatic or mechanistic aspects. In contrast, obeticholic acid (OCA), a farnesoid X receptor agonist and second-line anti-cholestatic agent, normalized memory function, suppressed blood-brain barrier changes, prevented hippoc al network deficits, and reversed neuronal senescence. Co-culture of human neuronal cells with either BDL or human cholestatic patient serum induced cellular senescence and increased mitochondrial respiration, changes that were limited again by OCA. Our findings provide new insights into the mechanism of cognitive symptoms in BDL animals, suggesting that OCA therapy or farnesoid X receptor agonism could be used to limit cholestasis-induced neuronal senescence.
Publisher: Springer Science and Business Media LLC
Date: 28-07-2021
DOI: 10.1038/S41596-021-00579-1
Abstract: Metabolic phenotyping is an important tool in translational biomedical research. The advanced analytical technologies commonly used for phenotyping, including mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy, generate complex data requiring tailored statistical analysis methods. Detailed protocols have been published for data acquisition by liquid NMR, solid-state NMR, ultra-performance liquid chromatography (LC-)MS and gas chromatography (GC-)MS on biofluids or tissues and their preprocessing. Here we propose an efficient protocol (guidelines and software) for statistical analysis of metabolic data generated by these methods. Code for all steps is provided, and no prior coding skill is necessary. We offer efficient solutions for the different steps required within the complete phenotyping data analytics workflow: scaling, normalization, outlier detection, multivariate analysis to explore and model study-related effects, selection of candidate biomarkers, validation, multiple testing correction and performance evaluation of statistical models. We also provide a statistical power calculation algorithm and safeguards to ensure robust and meaningful experimental designs that deliver reliable results. We exemplify the protocol with a two-group classification study and data from an epidemiological cohort however, the protocol can be easily modified to cover a wider range of experimental designs or incorporate different modeling approaches. This protocol describes a minimal set of analyses needed to rigorously investigate typical datasets encountered in metabolic phenotyping.
Publisher: BMJ
Date: 03-06-2012
DOI: 10.1136/GUTJNL-2011-301656
Abstract: The process of weaning causes a major shift in intestinal microbiota and is a critical period for developing appropriate immune responses in young mammals. To use a new systems approach to provide an overview of host metabolism and the developing immune system in response to nutritional intervention around the weaning period. Piglets (n=14) were weaned onto either an egg-based or soya-based diet at 3 weeks until 7 weeks, when all piglets were switched onto a fish-based diet. Half the animals on each weaning diet received Bifidobacterium lactis NCC2818 supplementation from weaning onwards. Immunoglobulin production from immunologically relevant intestinal sites was quantified and the urinary (1)H NMR metabolic profile was obtained from each animal at post mortem (11 weeks). Different weaning diets induced ergent and sustained shifts in the metabolic phenotype, which resulted in the alteration of urinary gut microbial co-metabolites, even after 4 weeks of dietary standardisation. B lactis NCC2818 supplementation affected the systemic metabolism of the different weaning diet groups over and above the effects of diet. Additionally, production of gut mucosa-associated IgA and IgM was found to depend upon the weaning diet and on B lactis NCC2818 supplementation. The correlation of urinary (1)H NMR metabolic profile with mucosal immunoglobulin production was demonstrated, thus confirming the value of this multi-platform approach in uncovering non-invasive biomarkers of immunity. This has clear potential for translation into human healthcare with the development of urine testing as a means of assessing mucosal immune status. This might lead to early diagnosis of intestinal dysbiosis and with subsequent intervention, arrest disease development. This system enhances our overall understanding of pathologies under supra-organismal control.
Publisher: American Chemical Society (ACS)
Date: 21-04-2016
DOI: 10.1021/ACS.ANALCHEM.5B04159
Abstract: Fecal metabolites are being increasingly studied to unravel the host-gut microbial metabolic interactions. However, there are currently no guidelines for fecal s le collection and storage based on a systematic evaluation of the effect of time, storage temperature, storage duration, and s ling strategy. Here we derive an optimized protocol for fecal s le handling with the aim of maximizing metabolic stability and minimizing s le degradation. S les obtained from five healthy in iduals were analyzed to assess topographical homogeneity of feces and to evaluate storage duration-, temperature-, and freeze-thaw cycle-induced metabolic changes in crude stool and fecal water using a (1)H NMR spectroscopy-based metabolic profiling approach. Interin idual variation was much greater than that attributable to storage conditions. In idual stool s les were found to be heterogeneous and spot s ling resulted in a high degree of metabolic variation. Crude fecal s les were remarkably unstable over time and exhibited distinct metabolic profiles at different storage temperatures. Microbial fermentation was the dominant driver in time-related changes observed in fecal s les stored at room temperature and this fermentative process was reduced when stored at 4 °C. Crude fecal s les frozen at -20 °C manifested elevated amino acids and nicotinate and depleted short chain fatty acids compared to crude fecal control s les. The relative concentrations of branched-chain and aromatic amino acids significantly increased in the freeze-thawed crude fecal s les, suggesting a release of microbial intracellular contents. The metabolic profiles of fecal water s les were more stable compared to crude s les. Our recommendation is that intact fecal s les should be collected, kept at 4 °C or on ice during transportation, and extracted ideally within 1 h of collection, or a maximum of 24 h. Fecal water s les should be extracted from a representative amount (∼15 g) of homogenized stool s le, aliquoted, and stored at <-20 °C, avoiding further freeze-thaw cycles.
Publisher: Elsevier BV
Date: 05-2016
Publisher: SAGE Publications
Date: 02-05-2012
Abstract: Patterns of change of endogenous metabolites may closely reflect systemic and organ-specific toxic changes. The authors examined the metabolic effects of the cyanobacterial (blue-green algal) toxin microcystin-LR by 1 H-nuclear magnetic resonance (NMR) analysis of urinary endogenous metabolites. Rats were treated with a single sublethal dose, either 20 or 80 µg/kg intraperitoneally, and sacrificed at 2 or 7 days post dosing. Changes in the high-dose, 2-day sacrifice group included centrilobular hepatic necrosis and congestion, accompanied in some animals by regeneration and neovascularization. By 7 days, animals had recovered, the necrotizing process had ended, and the centrilobular areas had been replaced by regenerative, usually hypertrophic hepatocytes. There was considerable interanimal variation in the histologic process and severity, which correlated with the changes in patterns of endogenous metabolites in the urine, thus providing additional validation of the biomarker and biochemical changes. Similarity of the shape of the metabolic trajectories suggests that the mechanisms of toxic effects and recovery are similar among the in idual animals, albeit that the magnitude and timing are different for the in idual animals. Initial decreases in urinary citrate, 2-oxoglutarate, succinate, and hippurate concentrations were accompanied by a temporary increase in betaine and taurine, then creatine from 24 to 48 hours. Further changes were an increase in guanidinoacetate, dimethylglycine, urocanic acid, and bile acids. As a tool, urine can be repeatedly and noninvasively s led and metabonomics utilized to study the onset and recovery after toxicity, thus identifying time points of maximal effect. This can help to employ histopathological examination in a guided and effective fashion.
Publisher: American Chemical Society (ACS)
Date: 23-08-2016
Publisher: Springer Science and Business Media LLC
Date: 30-09-2016
Publisher: American Association for Cancer Research (AACR)
Date: 11-05-2022
DOI: 10.1158/1055-9965.EPI-21-0687
Abstract: This review aims to develop an appropriate review tool for systematically collating metabolites that are dysregulated in disease and applies the method to identify novel diagnostic biomarkers for hepatocellular carcinoma (HCC). Studies that analyzed metabolites in blood or urine s les where HCC was compared with comparison groups (healthy, precirrhotic liver disease, cirrhosis) were eligible. Tumor tissue was included to help differentiate primary and secondary biomarkers. Searches were conducted on Medline and EMBASE. A bespoke “risk of bias” tool for metabolomic studies was developed adjusting for analytic quality. Discriminant metabolites for each s le type were ranked using a weighted score accounting for the direction and extent of change and the risk of bias of the reporting publication. A total of 84 eligible studies were included in the review (54 blood, 9 urine, and 15 tissue), with six studying multiple s le types. High-ranking metabolites, based on their weighted score, comprised energy metabolites, bile acids, acylcarnitines, and lysophosphocholines. This new review tool addresses an unmet need for incorporating quality of study design and analysis to overcome the gaps in standardization of reporting of metabolomic data. Validation studies, standardized study designs, and publications meeting minimal reporting standards are crucial for advancing the field beyond exploratory studies.
Publisher: Bentham Science Publishers Ltd.
Date: 2002
Abstract: Biofluid NMR spectroscopy is a powerful tool providing a comprehensive metabolic profile of the low molecular weight components in biofluids that reflect concentrations and fluxes of endogenous metabolites involved in key intermediary cellular pathways, thereby giving an indication of an organisms physiological or pathophysiological status [1]. The interaction of pharmacological agents with cells and tissues can also be monitored using recently developed high resolution magic-angle spinning (HRMAS) NMR spectroscopic technology for biological matrices [1]. However, recent developments in both spectrometer and software technology has resulted in improved capacity for s le handling, leading to a rapid growth in the size of toxicological spectral databases, and increased the complexity of the biological spectral data generated. Thus more emphasis has been placed on the need to develop improved automated procedures for data processing and interpretation. By harnessing chemometric tools for analysis of complex spectral data, the toxicological consequences of xenobiotic exposure can be evaluated efficiently on line. Automation of spectral processing procedures and the construction of mathematically based 'expert systems' for the prediction of drug-induced toxicity founded on IH NMR spectral profiles have now been achieved. Chemometric analysis of biological NMR spectra has provided the main analytical platform for metabonomic analysis, providing a systems approach to evaluating pathophysiological or genetic influences on the metabolic status of an organism [1]. This technology is currently being given high-priority in the pharmaceutical industry with respect to development of efficient high throughput toxicity screening systems for lead candidate selection. In this article, we review the recent developments in metabonomics and consider their application in toxicological screening, disease diagnosis and functional genomics.
Publisher: Elsevier BV
Date: 03-2023
Publisher: Frontiers Media SA
Date: 21-05-2019
Publisher: American Chemical Society (ACS)
Date: 05-01-2022
DOI: 10.1021/ACS.ANALCHEM.1C04576
Abstract: Proton nuclear magnetic resonance (NMR)
Publisher: Elsevier BV
Date: 08-2001
Publisher: American Chemical Society (ACS)
Date: 21-08-2007
DOI: 10.1021/PR0702565
Abstract: In idual and topographical variation in the metabolic profiles of multiple human gastrointestinal tract (GIT) biopsies have been characterized using high-resolution magic-angle spinning (HRMAS) 1H NMR spectroscopy and pattern recognition. S les from antrum, duodenum, jejunum, ileum, and transverse colon were obtained from 8 male and 8 female participants. Each gut region generated a highly characteristic metabolic profile consistent with the varying structural and functional properties of the tissue at different longitudinal levels of the gut. The antral (stomach) mucosa contained higher levels of choline, glycogen, phosphorylethanolamine, and taurine than other gut regions. The spatially close regions of the duodenum and jejunum were equivalent in terms of their gross biochemical composition with high levels of choline, glutathione, glycerophosphocholine (GPC), and lipids relative to other gut regions. The ileal mucosa showed poor discrimination from the duodenum and jejunum tissues and generated strong amino acids signatures but had relative low GPC signals. The colon (large intestine) was high in acetate, glutamate, inositols, and lactate and low in creatine, GPC, and taurine compared to the small intestine. These longitudinal metabolic variations in the human GIT could be attributed to functional variations in energy metabolism, osmoregulation, gut microbial activity, and oxidative protection. This work indicates that 1H HRMAS NMR studies may be of value in analyzing local metabolic variation due to pathological processes in gut biopsies.
Publisher: Springer Science and Business Media LLC
Date: 16-06-2021
Publisher: Elsevier BV
Date: 08-2003
Publisher: Wiley
Date: 12-1999
DOI: 10.1002/(SICI)1522-2683(19991201)20:18<3647::AID-ELPS3647>3.0.CO;2-#
Publisher: Wiley
Date: 25-06-2015
Publisher: Elsevier BV
Date: 10-2015
DOI: 10.1016/J.IJCARD.2015.06.048
Abstract: Controversy exists concerning the beneficial or harmful effects of the presence of ectopic calcification in the coronary arteries. Additionally, further elucidation of the exact pathophysiological mechanism is needed. In this study, we sought to identify metabolic markers of vascular calcification that could assist in understanding the disease, monitoring its progress and generating hypotheses describing its pathophysiology. Untargeted lipid profiling and complementary modeling strategies were employed to compare serum s les from patients with different levels of calcific coronary artery disease (CCAD) based on their calcium score (CS). Subsequently, patients were ided into three groups: no calcification (NC CS=0 n=26), mild calcification (MC CS:1-250 n=27) and severe (SC CS>250 n=17). Phosphatidylcholine levels were found to be significantly altered in the disease states (p=0.001-0.04). Specifically, 18-carbon fatty acyl chain (FAC) phosphatidylcholines were detected in lower levels in the SC group, while 20:4 FAC lipid species were detected in higher concentrations. A statistical trend was observed with phosphatidylcholine lipids in the MC group, showing the same tendency as with the SC group. We also observed several sphingomyelin signals present at lower intensities in SC when compared with NC or MC groups (p=0.000001-0.01). This is the first lipid profiling study reported in CCAD. Our data demonstrate dysregulations of phosphatidylcholine lipid species, which suggest perturbations in fatty acid elongation/desaturation. The altered levels of the 18-carbon and 20:4 FAC lipids may be indicative of disturbed inflammation homeostasis. The marked sphingomyelin dysregulation in SC is consistent with profound apoptosis as a potential mechanism of CCAD.
Publisher: American Chemical Society (ACS)
Date: 12-2008
DOI: 10.1021/PR070340K
Abstract: The metabolic composition of fecal extracts provides a window for elucidating the complex metabolic interplay between mammals and their intestinal ecosystems, and these metabolite profiles can yield information on a range of gut diseases. Here, the metabolites present in aqueous fecal extracts of humans, mice and rats were characterized using high-resolution (1)H NMR spectroscopy coupled with multivariate pattern recognition techniques. Additionally, the effects of s le storage and preparation methods were evaluated in order to assess the stability of fecal metabolite profiles, and to optimize information recovery from fecal s les. Finally, variations in metabolite profiles were investigated in healthy mice as a function of time. Interspecies variation was found to be greater than the variation due to either time or s le preparation. Although many fecal metabolites were common to the three species, such as short chain fatty acids and branched chain amino acids, each species generated a unique profile. Relatively higher levels of uracil, hypoxanthine, phenylacetic acid, glucose, glycine, and tyrosine amino acids were present in the rat, with beta-alanine being unique to the rat, and glycerol and malonate being unique to the human. Human fecal extracts showed a greater interin idual variation than the two rodent species, reflecting the natural genetic and environmental ersity in human populations. Fecal composition in healthy mice was found to change over time, which might be explained by altered gut microbial presence or activity. The systematic characterization of fecal composition across humans, mice, and rats, together with the evaluation of inherent variation, provides a benchmark for future studies seeking to determine fecal biomarkers of disease and/or response to dietary or therapeutic interventions.
Publisher: Public Library of Science (PLoS)
Date: 18-03-2015
Publisher: Informa UK Limited
Date: 16-05-2023
Publisher: American Chemical Society (ACS)
Date: 19-05-2009
DOI: 10.1021/AC9004875
Publisher: American Chemical Society (ACS)
Date: 16-03-2021
Publisher: American Chemical Society (ACS)
Date: 26-08-2016
DOI: 10.1021/ACS.ANALCHEM.6B01481
Abstract: To better understand the molecular mechanisms underpinning physiological variation in human populations, metabolic phenotyping approaches are increasingly being applied to studies involving hundreds and thousands of biofluid s les. Hyphenated ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) has become a fundamental tool for this purpose. However, the seemingly inevitable need to analyze large studies in multiple analytical batches for UPLC-MS analysis poses a challenge to data quality which has been recognized in the field. Herein, we describe in detail a fit-for-purpose UPLC-MS platform, method set, and s le analysis workflow, capable of sustained analysis on an industrial scale and allowing batch-free operation for large studies. Using complementary reversed-phase chromatography (RPC) and hydrophilic interaction liquid chromatography (HILIC) together with high resolution orthogonal acceleration time-of-flight mass spectrometry (oaTOF-MS), exceptional measurement precision is exemplified with independent epidemiological s le sets of approximately 650 and 1000 participant s les. Evaluation of molecular reference targets in repeated injections of pooled quality control (QC) s les distributed throughout each experiment demonstrates a mean retention time relative standard deviation (RSD) of <0.3% across all assays in both studies and a mean peak area RSD of <15% in the raw data. To more globally assess the quality of the profiling data, untargeted feature extraction was performed followed by data filtration according to feature intensity response to QC s le dilution. Analysis of the remaining features within the repeated QC s le measurements demonstrated median peak area RSD values of <20% for the RPC assays and <25% for the HILIC assays. These values represent the quality of the raw data, as no normalization or feature-specific intensity correction was applied. While the data in each experiment was acquired in a single continuous batch, instances of minor time-dependent intensity drift were observed, highlighting the utility of data correction techniques despite reducing the dependency on them for generating high quality data. These results demonstrate that the platform and methodology presented herein is fit-for-use in large scale metabolic phenotyping studies, challenging the assertion that such screening is inherently limited by batch effects. Details of the pipeline used to generate high quality raw data and mitigate the need for batch correction are provided.
Publisher: Springer Science and Business Media LLC
Date: 22-09-2004
DOI: 10.1007/S00216-004-2783-Y
Abstract: This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three ex les are used as illustrations: the first ex le is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second ex le contains NMR-metabonomics data, measured on urine s les of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.
Publisher: American Chemical Society (ACS)
Date: 12-09-2022
Publisher: Elsevier BV
Date: 05-2011
Publisher: Informa UK Limited
Date: 2005
DOI: 10.1080/13547500500309259
Abstract: Metabolic fingerprints, in the form of patterns of high-concentration endogenous metabolites, of 1-nitronaphthalene (NN)-induced lung toxicity have been elucidated in bronchoalveolar lavage fluid (BALF), urine, blood plasma, and intact lung and liver tissue using NMR spectroscopy-based metabolic profiling. A single dose of NN (75 mg kg(-1)) was administered orally to Sprague-Dawley rats. BALF and lung tissue were obtained 24 h after dosing from these animals and matched control rats post-mortem. High-resolution (1)H-NMR spectroscopy of BALF s les indicated that NN caused increases in concentrations of choline, amino acids (leucine, isoleucine and alanine) and lactate together with decreased concentrations of succinate, citrate, creatine, creatinine and glucose. In addition, the intact lung weights were higher in the NN-treated group (p<0.01), consistent with pulmonary oedema. The NMR-detected perturbations indicated that NN induces a perturbation in energy metabolism in both lung and liver tissue, as well as surfactant production and osmolyte levels in the lungs. As well as reporting the first NMR spectroscopic combined examination of BALF and intact lung, this study indicates that such holistic approaches to investigating mechanisms of lung toxicity may be of value in evaluating disease progression or the effects of therapeutic intervention in pulmonary conditions such as surfactant disorders or asthma.
Publisher: American Chemical Society (ACS)
Date: 23-07-2008
DOI: 10.1021/PR800209D
Abstract: We present a metabolism-driven top-down systems biology approach to characterize metabolic changes in the mouse resulting from an infection with Plasmodium berghei, using high-resolution (1)H NMR spectroscopy and multivariate data analysis techniques. Twelve female NMRI mice were infected intravenously with approximately 20 million P. berghei-parasitized erythrocytes. Urine and plasma s les were collected 4-6 h before infection, and at days 1, 2, 3, and 4 postinfection. Multivariate analysis of spectral data showed differentiation between s les collected before and after infection, with growing metabolic distinction as the time postinfection progressed. Our analysis of plasma from P. berghei-infected mice showed marked increases in lactate and pyruvate levels, and decreased glucose, creatine, and glycerophosphoryl choline compared with preinfection, indicating glycolytic upregulation, and increased energy demand due to P. berghei infection. The dominant changes in the urinary metabolite profiles included increased levels of pipecolic acid, phenylacetylglycine, and dimethylamine, and decreased concentrations of taurine and trimethylamine- N-oxide, which may, among other factors, indicate a disturbance of the gut microbial community caused by the parasite. Although several of the observed metabolic changes are also associated with other parasitic infections, the combination of metabolic changes and, in particular, the occurrence of pipecolic acid in mouse urine postinfection are unique to a P. berghei infection. Hence, metabolic profiling may provide a sensitive diagnostic tool of Plasmodium infection and the control of malaria more generally.
Publisher: Wiley
Date: 03-2013
DOI: 10.1002/OBY.20257
Publisher: American Chemical Society (ACS)
Date: 27-08-2020
Publisher: Georg Thieme Verlag KG
Date: 07-2006
Abstract: NMR-based metabolic profiling techniques can simultaneously track changes in many plant metabolites and have found a number of applications in both systems biology and biosafety. Together with multivariate statistical analyses, NMR spectroscopy has been successfully applied to the characterisation of various herbs and plant products for quality control, authentication, determining geographical origin and for detecting adulteration of products. Additionally, the metabolic consequences of plant extracts have been demonstrated in experimental animals and in man using NMR-based metabonomics approaches to characterise the response. Here the application of NMR spectroscopy and chemometric tools for analysing plant-based products and their metabolic consequences are considered with particular emphasis on deconvolving biological complexity and minimising confounding biological variability with analytical 'noise'.
Publisher: American Chemical Society (ACS)
Date: 30-10-2007
DOI: 10.1021/PR070268Q
Abstract: The time-course of metabolic events following response to a model hepatotoxin ethionine (800 mg/kg) was investigated over a 7 day period in rats using high-resolution (1)H NMR spectroscopic analysis of urine and multivariate statistics. Complementary information was obtained by multivariate analysis of (1)H MAS NMR spectra of intact liver and by conventional histopathology and clinical chemistry of blood plasma. (1)H MAS NMR spectra of liver showed toxin-induced lipidosis 24 h postdose consistent with the steatosis observed by histopathology, while hypertaurinuria was suggestive of liver injury. Early biochemical changes in urine included elevation of guanidinoacetate, suggesting impaired methylation reactions. Urinary increases in 5-oxoproline and glycine suggested disruption of the gamma-glutamyl cycle. Signs of ATP depletion together with impairment of the energy metabolism were given from the decreased levels in tricarboxylic acid cycle intermediates, the appearance of ketone bodies in urine, the depletion of hepatic glucose and glycogen, and also hypoglycemia. The observed increase in nicotinuric acid in urine could be an indication of an increase in NAD catabolism, a possible consequence of ATP depletion. Effects on the gut microbiota were suggested by the observed urinary reductions in the microbial metabolites 3-/4-hydroxyphenyl propionic acid, dimethylamine, and tryptamine. At later stages of toxicity, there was evidence of kidney damage, as indicated by the tubular damage observed by histopathology, supported by increased urinary excretion of lactic acid, amino acids, and glucose. These studies have given new insights into mechanisms of ethionine-induced toxicity and show the value of multisystem level data integration in the understanding of experimental models of toxicity or disease.
Publisher: Elsevier BV
Date: 08-2009
Publisher: BMJ
Date: 21-06-2012
DOI: 10.1136/GUTJNL-2011-301955
Abstract: Proper interactions between the intestinal mucosa, gut microbiota and nutrient flow are required to establish homoeostasis of the host. Since the proximal part of the small intestine is the first region where these interactions occur, and since most of the nutrient absorption occurs in the jejunum, it is important to understand the dynamics of metabolic responses of the mucosa in this intestinal region. Germ-free mice aged 8-10 weeks were conventionalised with faecal microbiota, and responses of the jejunal mucosa to bacterial colonisation were followed over a 30-day time course. Combined transcriptome, histology, (1)H NMR metabonomics and microbiota phylogenetic profiling analyses were used. The jejunal mucosa showed a two-phase response to the colonising microbiota. The acute-phase response, which had already started 1 day after conventionalisation, involved repression of the cell cycle and parts of the basal metabolism. The secondary-phase response, which was consolidated during conventionalisation (days 4-30), was characterised by a metabolic shift from an oxidative energy supply to anabolic metabolism, as inferred from the tissue transcriptome and metabonome changes. Detailed transcriptome analysis identified tissue transcriptional signatures for the dynamic control of the metabolic reorientation in the jejunum. The molecular components identified in the response signatures have known roles in human metabolic disorders, including insulin sensitivity and type 2 diabetes mellitus. This study elucidates the dynamic jejunal response to the microbiota and supports a prominent role for the jejunum in metabolic control, including glucose and energy homoeostasis. The molecular signatures of this process may help to find risk markers in the declining insulin sensitivity seen in human type 2 diabetes mellitus, for instance.
Publisher: Springer Science and Business Media LLC
Date: 2012
DOI: 10.1186/GM329
Publisher: American Chemical Society (ACS)
Date: 16-12-2012
DOI: 10.1021/PR2005764
Abstract: High-resolution spectroscopic profiles of biofluids can define metabolic phenotypes, providing a window onto the impact of diet on health to reflect gene-environment interactions. (1)H NMR spectroscopic profiling was used to characterize the effect of nutritional intervention on the stability of the metabolic phenotype of 7 in iduals following a controlled 7 day dietary protocol. Inter-in idual metabolic differences influenced proportionally more of the spectrum than dietary modulation, with certain in iduals displaying a greater stability of metabolic phenotypes than others. Correlation structures between urinary metabolites were identified and used to map inter-in idual pathway differences. Choline degradation was the pathway most affected by the in idual, suggesting that the gut microbiota influence host metabolic phenotypes. This influence was further emphasized by the highly correlated excretion of the microbial-mammalian co-metabolites phenylacetylglutamine, 4-cresylsulfate (r = 0.87), and indoxylsulfate (r = 0.67) across all in iduals. Above the background of inter-in idual differences, clear biochemical effects of single type dietary interventions, animal protein, fruit and wine intake, were observed for ex le, the spectral variance introduced by fruit ingestion was attributed to the metabolites tartrate, proline betaine, hippurate, and 4-hydroxyhippurate. This differential metabolic baseline and response to selected dietary challenges highlights the importance of understanding in idual differences in metabolism and provides a rationale for evaluating dietary interventions and stratification of in iduals with respect to guiding nutrition and health programmes.
Publisher: MDPI AG
Date: 09-09-2023
Publisher: Elsevier BV
Date: 11-2000
DOI: 10.1016/S0305-0491(00)00276-5
Abstract: The metabolic profiles of three wild mammals that vary in their trophic strategies, the herbivorous bank vole (Clethrionomys glareolus), the granivorous wood mouse (Apodemus sylvaticus), and the insectivorous white-toothed shrew (Crocidura suaveolens), were compared with that of a widely used strain of laboratory rat (Sprague Dawley). In conjunction with NMR spectroscopic investigations into the urine and blood plasma composition for these mammals, high resolution magic angle spinning (HRMAS) 1H-nuclear magnetic resonance (NMR) spectroscopy was applied to investigate the composition of intact kidney s les. Adaptation to natural diet affects both renal metabolism and urinary profiles, and while these techniques have been used to study the metabolism of the laboratory rat little is known about wild small mammals. The species were readily separated by their urinary profiles using either crude metabolite ratios or statistical pattern recognition. Bank vole urine contained higher concentrations of aromatic amino acids compared with the other small mammals, while the laboratory rats produced relatively more hippurate. HRMAS 1H-NMR demonstrated striking differences in both lipid concentration and composition between the wild mammals and Sprague Dawley rats. Bank voles contained high concentrations of the aromatic amino acids phenylalanine, tyrosine and tryptophan in all tissue and biofluids studied. This study demonstrates the analytical power of combined NMR techniques for the study of inter-species metabolism and further demonstrates that metabolic data acquired on laboratory animals cannot be extended to wild species.
Publisher: Oxford University Press (OUP)
Date: 30-10-2014
DOI: 10.1093/BIOINFORMATICS/BTT612
Abstract: Summary: MetaboNetworks is a tool to create custom sub-networks in Matlab using main reaction pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes and can be used to explore transgenomic interactions, for ex le mammalian and bacterial associations. It calculates the shortest path between a set of metabolites (e.g. biomarkers from a metabonomic study) and plots the connectivity between metabolites as links in a network graph. The resulting graph can be edited and explored interactively. Furthermore, nodes and edges in the graph are linked to the Kyoto Encyclopaedia of Genes and Genomes compound and reaction pair web pages. Availability and implementation: MetaboNetworks is available from atlabcentral/fileexchange/42684. Contact: jmp111@ic.ac.uk or j.nicholson@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C8MO00190A
Abstract: When using an appropriate data analysis pipeline, protease inhibitor (PI)-containing urine s les are fit-for-purpose for metabolic phenotyping of patients with nephrotic syndrome and proteinuria.
Publisher: Wiley
Date: 11-04-2008
Publisher: American Chemical Society (ACS)
Date: 08-03-2016
Abstract: Lack of accurate dietary assessment in free-living populations requires discovery of new biomarkers reflecting food intake qualitatively and quantitatively to objectively evaluate effects of diet on health. We provide a proof-of-principle for an analytical pipeline to identify quantitative dietary biomarkers. Tartaric acid was identified by nuclear magnetic resonance spectroscopy as a dose-responsive urinary biomarker of grape intake and subsequently quantified in volunteers following a series of 4-day dietary interventions incorporating 0 g/day, 50 g/day, 100 g/day, and 150 g/day of grapes in standardized diets from a randomized controlled clinical trial. Most accurate quantitative predictions of grape intake were obtained in 24 h urine s les which have the strongest linear relationship between grape intake and tartaric acid excretion (r(2) = 0.90). This new methodological pipeline for estimating nutritional intake based on coupling dietary intake information and quantified nutritional biomarkers was developed and validated in a controlled dietary intervention study, showing that this approach can improve the accuracy of estimating nutritional intakes.
Publisher: Elsevier BV
Date: 07-2016
DOI: 10.1016/J.EJVS.2016.01.022
Abstract: Stroke is a major cause of death and disability. That three-quarters of stroke patients will never have previously manifested cerebrovascular symptoms demonstrates the unmet clinical need for new biomarkers able to stratify patient risk and elucidation of the biological dysregulations. In this study, the utility of comprehensive metabolic phenotyping is assessed to provide candidate biomarkers that relate to stroke risk in stenosing carotid plaque tissue s les. Carotid plaque tissue s les were obtained from patients with cerebrovascular symptoms of carotid origin (n = 5), and from asymptomatic patients (n = 5). Two adjacent biological replicates were obtained from each tissue. Organic and aqueous metabolite extracts were obtained separately and analysed using two ultra performance liquid chromatography coupled to mass spectrometry metabolic profiling methods. Multivariate and univariate tools were used for statistical analysis. The two study groups demonstrated distinct plaque phenotypes using multivariate data analysis. Univariate statistics also revealed metabolites that differentiated the two groups with a strong statistical significance (p = 10(-4)-10(-5)). Specifically, metabolites related to the eicosanoid pathway (arachidonic acid and arachidonic acid precursors), and three acylcarnitine species (butyrylcarnitine, hexanoylcarnitine, and palmitoylcarnitine), intermediates of the β-oxidation, were detected in higher intensities in symptomatic patients. However, metabolites implicated in the process of cell death, a process known to be upregulated in the formation of the vulnerable plaque, were unaffected. Discrimination between symptomatic and asymptomatic carotid plaque tissue is demonstrated for the first time using metabolic profiling technologies. Two biological pathways (eicosanoid and β-oxidation) were implicated in differentiating symptomatic from asymptomatic patients and will be further investigated. These results indicate that metabolic phenotyping should be further explored to investigate the chemistry of the unstable plaque, in the pursuit of candidate biomarkers for risk-stratification and targets for pharmacotherapeutic intervention.
Publisher: Springer Science and Business Media LLC
Date: 24-01-2018
Publisher: Springer Science and Business Media LLC
Date: 29-04-2020
DOI: 10.1038/S41598-020-64413-6
Abstract: We applied a metabonomic strategy to identify host biomarkers in serum to diagnose paediatric tuberculosis (TB) disease. 112 symptomatic children with presumptive TB were recruited in The Gambia and classified as bacteriologically-confirmed TB, clinically diagnosed TB, or other diseases. Sera were analysed using 1 H nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). Multivariate data analysis was used to distinguish patients with TB from other diseases. Diagnostic accuracy was evaluated using Receiver Operating Characteristic (ROC) curves. Model performance was tested in a validation cohort of 36 children from the UK. Data acquired using 1 H NMR demonstrated a sensitivity, specificity and Area Under the Curve (AUC) of 69% (95% confidence interval [CI], 56–73%), 83% (95% CI, 73–93%), and 0.78 respectively, and correctly classified 20% of the validation cohort from the UK. The most discriminatory MS data showed a sensitivity of 67% (95% CI, 60–71%), specificity of 86% (95% CI, 75–93%) and an AUC of 0.78, correctly classifying 83% of the validation cohort. Amongst children with presumptive TB, metabolic profiling of sera distinguished bacteriologically-confirmed and clinical TB from other diseases. This novel approach yielded a diagnostic performance for paediatric TB comparable to that of Xpert MTB/RIF and interferon gamma release assays.
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B811468D
Abstract: The influence of gut microbiota on the toxicity and metabolism of hydrazine has been investigated in germ-free and 'conventional' Sprague Dawley rats using 1H NMR based metabonomic analysis of urine and plasma. Toxicity was more severe in germ-free rats compared with conventional rats for equivalent exposures indicating that bacterial presence altered the nature or extent of response to hydrazine and that the toxic response can vary markedly in the absence of a functional microbiome.
Publisher: Cold Spring Harbor Laboratory
Date: 08-05-2023
DOI: 10.1101/2023.05.08.23289637
Abstract: We present compelling evidence for the existence of an extended innate viperin dependent pathway which provides crucial evidence for an adaptive response to viral agents like SARS-CoV-2. We show the in vivo biosynthesis of a family of endogenous cytosine metabolites with potential antiviral activity. Two dimensional Nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally allowed the characterization and quantification of the most abundant serum metabolites showing potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine and uracil based) analogue structures, eight of which were previously unknown in humans. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ and IL-10, suggest an association with the viperin enzyme contributing to an endogenous innate immune defence mechanism against viral infection.
Publisher: BMJ
Date: 14-05-2011
Publisher: Elsevier BV
Date: 06-2000
Publisher: Oxford University Press (OUP)
Date: 27-08-2005
DOI: 10.1093/IJE/DYH399
Publisher: American Chemical Society (ACS)
Date: 17-10-2002
DOI: 10.1021/TX0255774
Abstract: Metabonomic analysis of biofluids and tissues utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to toxicity for many xenobiotics. To assess the analytical reproducibility of metabonomic protocols, s le preparation and NMR data acquisition were performed at two sites (one using a 500 MHz and the other using a 600 MHz system) using two identical (split) sets of urine s les from an 8-day acute study of hydrazine toxicity in the rat. Despite the difference in spectrometer operating frequency, both datasets were extremely similar when analyzed using principal components analysis (PCA) and gave near-identical descriptions of the metabolic responses to hydrazine treatment. The main consistent difference between the datasets was related to the efficiency of water resonance suppression in the spectra. In a 4-PC model of both datasets combined, describing all systematic dose- and time-related variation (88% of the total variation), differences between the two datasets accounted for only 3% of the total modeled variance compared to ca. 15% for normal physiological (pre-dose) variation. Furthermore, 95% correlation (r(2)) between sites, with an analytical error comparable to normal physiological variation in concentration (4-8%). The excellent analytical reproducibility and robustness of metabonomic techniques demonstrated here are highly competitive compared to the best proteomic analyses and are in significant contrast to genomic microarray platforms, both of which are complementary techniques for predictive and mechanistic toxicology. These results have implications for the quantitative interpretation of metabonomic data, and the establishment of quality control criteria for both regulatory agencies and for integrating data obtained at different sites.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-07-2019
DOI: 10.1126/SCITRANSLMED.AAN5662
Abstract: Transplanting the gut microbiota of pathogen-free mice into germ-free mice improves skeletal muscle mass and strength.
Publisher: Elsevier BV
Date: 04-2005
DOI: 10.1016/J.JNUTBIO.2004.12.005
Abstract: A metabonomic approach to nutrition research may provide an insight into in vivo mechanisms of action following nutritional intervention. This approach was applied to investigate changes in the (1)H NMR spectral profile of urine collected from controlled dietary intervention studies conducted in premenopausal women before and following soy or miso consumption. The aim of the study was to identify the biochemical effects of a diet rich in soy isoflavones, phytochemicals which are receiving significant attention because of their potential importance to human health and wide bioactivity in vitro. By applying various chemometric techniques to the data the biochemical effects of conjugated and unconjugated isoflavones were determined. The biochemical changes observed suggest that soy isoflavone ingestion had significant effects on several metabolic pathways associated with osmolyte fluctuation and energy metabolism. These biochemical changes were more significant following ingestion of the unconjugated soy isoflavone (miso) diet suggesting that the chemical composition of the isoflavones present in soy-based foods may have an effect on their biological efficacy in vivo. This study describes a novel application for (1)H NMR analysis by determining subtle differences in biochemical profiles following dietary intervention and providing further insight into the mechanisms of action of phytochemicals in vivo.
Publisher: Wiley
Date: 10-09-2013
Abstract: Most chronic diseases have been demonstrated to have a link to nutrition. Within food and nutritional research there is a major driver to understand the relationship between diet and disease in order to improve health of in iduals. However, the lack of accurate dietary intake assessment in free-living populations, makes accurate estimation of how diet is associated with disease risk difficulty. Thus, there is a pressing need to find solutions to the inaccuracy of dietary reporting. Metabolic profiling of urine or plasma can provide an unbiased approach to characterizing dietary intake and various high-throughput analytical platforms have been used in order to implement targeted and nontargeted assays in nutritional clinical trials and nutritional epidemiology studies. This review describes first the challenges presented in interpreting the relationship between diet and health within in idual and epidemiological frameworks. Second, we aim to explore how metabonomics can benefit different types of nutritional studies and discuss the critical importance of selecting appropriate analytical techniques in these studies. Third, we propose a strategy capable of providing accurate assessment of food intake within an epidemiological framework in order establish accurate associations between diet and health.
Publisher: Public Library of Science (PLoS)
Date: 02-07-2008
Publisher: Wiley
Date: 07-2010
Abstract: Metabonomic and metabolomic studies are increasingly utilized for biomarker identification in different fields, including biology of infection. The confluence of improved analytical platforms and the availability of powerful multivariate analysis software have rendered the multiparameter profiles generated by these omics platforms a user-friendly alternative to the established analysis methods where the quality and practice of a procedure is well defined. However, unlike traditional assays, validation methods for these new multivariate profiling tools have yet to be established. We propose a validation for models obtained by CE fingerprinting of urine from mice infected with the blood fluke Schistosoma mansoni. We have analysed urine s les from two sets of mice infected in an inter-laboratory experiment where different infection methods and animal husbandry procedures were employed in order to establish the core biological response to a S. mansoni infection. CE data were analysed using principal component analysis. Validation of the scores consisted of permutation scrambling (100 repetitions) and a manual validation method, using a third of the s les (not included in the model) as a test or prediction set. The validation yielded 100% specificity and 100% sensitivity, demonstrating the robustness of these models with respect to deciphering metabolic perturbations in the mouse due to a S. mansoni infection. A total of 20 metabolites across the two experiments were identified that significantly discriminated between S. mansoni-infected and noninfected control s les. Only one of these metabolites, allantoin, was identified as manifesting different behaviour in the two experiments. This study shows the reproducibility of CE-based metabolic profiling methods for disease characterization and screening and highlights the importance of much needed validation strategies in the emerging field of metabolomics.
Publisher: American Chemical Society (ACS)
Date: 25-01-2005
DOI: 10.1021/AC048630X
Abstract: We describe here the implementation of the statistical total correlation spectroscopy (STOCSY) analysis method for aiding the identification of potential biomarker molecules in metabonomic studies based on NMR spectroscopic data. STOCSY takes advantage of the multicollinearity of the intensity variables in a set of spectra (in this case 1H NMR spectra) to generate a pseudo-two-dimensional NMR spectrum that displays the correlation among the intensities of the various peaks across the whole s le. This method is not limited to the usual connectivities that are deducible from more standard two-dimensional NMR spectroscopic methods, such as TOCSY. Moreover, two or more molecules involved in the same pathway can also present high intermolecular correlations because of biological covariance or can even be anticorrelated. This combination of STOCSY with supervised pattern recognition and particularly orthogonal projection on latent structure-discriminant analysis (O-PLS-DA) offers a new powerful framework for analysis of metabonomic data. In a first step O-PLS-DA extracts the part of NMR spectra related to discrimination. This information is then cross-combined with the STOCSY results to help identify the molecules responsible for the metabolic variation. To illustrate the applicability of the method, it has been applied to 1H NMR spectra of urine from a metabonomic study of a model of insulin resistance based on the administration of a carbohydrate diet to three different mice strains (C57BL/6Oxjr, BALB/cOxjr, and 129S6/SvEvOxjr) in which a series of metabolites of biological importance can be conclusively assigned and identified by use of the STOCSY approach.
Publisher: American Chemical Society (ACS)
Date: 12-1995
DOI: 10.1021/TX00050A008
Abstract: 1H NMR spectroscopic methods have been applied to compare the in vitro reactivity of the renal papillary nephrotoxin 2-bromoethanamine (BEA) with those of selected halide-substituted nephrotoxic analogues, 2-chloroethanamine (CEA), 2-fluoroethanamine (FEA), and 1-phenyl-2-iodoethanamine (PIEA). The primary 1H NMR-detectable transformation during a 24 h incubation of confluent Madin Darby canine kidney (MDCK) cells with BEA, CEA, and FEA (at concentrations up to the IC50 determined by neutral red uptake) was the appearance in cell culture media of 2-oxazolidone (OX). Additional novel signals assigned as FEA carbamate (N-carbamoyl-2-fluoroethanamine) were observed in media collected following incubation of cells with FEA. We propose that N-carbamate intermediates are formed from the spontaneous reaction of these haloalkylamines with HCO(3-)-buffered growth media and that OX is formed from the carbamate via elimination of the hydrogen halide. Further 1H NMR experiments, conducted for up to 8 h at 25 degrees C on 5 mM solutions of BEA, CEA, and FEA in 2H2O containing a 20-fold excess of HCO3- at pH 7.6, demonstrated a time-dependent decrease in the concentration of the free haloalkylamines accompanied by the production of N-carbamate intermediates and OX. Under these pseudo-first-order reaction conditions, the formation of OX from BEA was complete within approximately 6 h. In similar reaction conditions OX formation from CEA (24 h after initiation) had reached 54% of its final equilibrium concentration. Equivalent experiments demonstrated that PIEA was almost completely converted to 4-phenyl-2-oxazolidinone (PHOX) within 2 h. These observations reveal the strong disposition of this series of haloalkylamines toward reaction with HCO3- and indicate that the compounds in this family may exist only transiently as free amines in vivo, where there will virtually always be excess HCO3-. The physiological relevance of the in vitro findings is further indicated by the NMR-detectable conversion of BEA to OX and also an alkylating aziridine (AZ) moiety in rat plasma containing BEA. The ability to form carbamoylated species and OX (or PHOX) may mediate the toxicity of this series of haloalkylamines and hence is potentially of considerable significance.
Publisher: EMBO
Date: 2008
DOI: 10.1038/MSB4100190
Publisher: Elsevier BV
Date: 12-1998
Publisher: Wiley
Date: 27-01-2005
Publisher: American Chemical Society (ACS)
Date: 11-01-2021
Publisher: American Chemical Society (ACS)
Date: 24-06-2013
DOI: 10.1021/PR4000152
Publisher: Springer Science and Business Media LLC
Date: 2008
Publisher: Springer Science and Business Media LLC
Date: 14-11-2012
DOI: 10.1038/NATURE11708
Abstract: Metabolic phenotyping involves the comprehensive analysis of biological fluids or tissue s les. This analysis allows biochemical classification of a person's physiological or pathological states that relate to disease diagnosis or prognosis at the in idual level and to disease risk factors at the population level. These approaches are currently being implemented in hospital environments and in regional phenotyping centres worldwide. The ultimate aim of such work is to generate information on patient biology using techniques such as patient stratification to better inform clinicians on factors that will enhance diagnosis or the choice of therapy. There have been many reports of direct applications of metabolic phenotyping in a clinical setting.
Publisher: Elsevier
Date: 2016
Publisher: American Chemical Society (ACS)
Date: 04-12-2012
DOI: 10.1021/AC302360V
Abstract: We describe a new multivariate statistical approach to recover metabolite structure information from multiple (1)H NMR spectra in population s le sets. Subset optimization by reference matching (STORM) was developed to select subsets of (1)H NMR spectra that contain specific spectroscopic signatures of biomarkers differentiating between different human populations. STORM aims to improve the visualization of structural correlations in spectroscopic data by using these reduced spectral subsets containing smaller numbers of s les than the number of variables (n ≪ p). We have used statistical shrinkage to limit the number of false positive associations and to simplify the overall interpretation of the autocorrelation matrix. The STORM approach has been applied to findings from an ongoing human metabolome-wide association study on body mass index to identify a biomarker metabolite present in a subset of the population. Moreover, we have shown how STORM improves the visualization of more abundant NMR peaks compared to a previously published method (statistical total correlation spectroscopy, STOCSY). STORM is a useful new tool for biomarker discovery in the "omic" sciences that has widespread applicability. It can be applied to any type of data, provided that there is interpretable correlation among variables, and can also be applied to data with more than one dimension (e.g., 2D NMR spectra).
Publisher: Springer Science and Business Media LLC
Date: 05-02-2008
Abstract: Bipolar affective disorder is a severe and debilitating psychiatric condition characterized by the alternating mood states of mania and depression. Both the molecular pathophysiology of the disorder and the mechanism of action of the mainstays of its treatment remain largely unknown. Here, (1)H NMR spectroscopy-based metabonomic analysis was performed to identify molecular changes in post-mortem brain tissue (dorsolateral prefrontal cortex) of patients with a history of bipolar disorder. The observed changes were then compared to metabolic alterations identified in rat brain following chronic oral treatment with either lithium or valproate. This is the first study to use (1)H NMR spectroscopy to study post-mortem bipolar human brain tissue, and it is the first to compare changes in disease brain with changes induced in rat brain following mood stabilizer treatment. Several metabolites were found to be concordantly altered in both the animal and human tissues. Glutamate levels were increased in post-mortem bipolar brain, while the glutamate/glutamine ratio was decreased following valproate treatment, and gamma-aminobutyric acid levels were increased after lithium treatment, suggesting that the balance of excitatory/inhibitory neurotransmission is central to the disorder. Both creatine and myo-inositol were increased in the post-mortem brain but depleted with the medications. Lastly, the level of N-acetyl aspartate, a clinically important metabolic marker of neuronal viability, was found to be unchanged following chronic mood stabilizer treatment. These findings promise to provide new insight into the pathophysiology of bipolar disorder and may be used to direct research into novel therapeutic strategies.
Publisher: Informa UK Limited
Date: 2004
Publisher: Wiley
Date: 04-2000
DOI: 10.1002/(SICI)1099-1492(200004)13:2<64::AID-NBM612>3.0.CO;2-X
Abstract: The technique of magic angle spinning (MAS) high resolution (1)H NMR spectroscopy applied to intact tissues provides excellent peak resolution and thus much biochemical information. The use of computer-based pattern recognition techniques to classify human renal cortex tissue s les as normal or tumour based on their (1)H MAS NMR spectra has been investigated. In this preliminary study of 22 paired control and tumour s les, exploratory data analysis using principal components based on NMR spectral intensities showed clear separation of the two classes. Furthermore, using the supervised method of linear discriminant analysis, based on in idual data point intensities or on integrated spectral regions, it was possible to distinguish between the normal and tumour kidney cortex tissue with 100% accuracy, including a single ex le of a metastatic tumour from a primary lung carcinoma. A tumour s le from the collecting duct of the kidney showed a different NMR spectral profile, and pattern recognition indicated that this s le did not classify with the cortical tumours.
Publisher: American Chemical Society (ACS)
Date: 14-03-2017
Publisher: Oxford University Press (OUP)
Date: 12-2008
DOI: 10.1373/CLINCHEM.2008.112219
Abstract: Background: Compromised sexual health is a major rehabilitative barrier for men with lower–spinal cord injury (SCI). Although studies have revealed decreased sperm motility, the quantitative biochemical changes that underlie the infertility mechanism remain poorly understood. Methods: We employed a nontargeted approach combining 800 MHz hydrogen nuclear magnetic resonance (1H NMR) spectroscopy and ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) with pattern recognition methods to analyze seminal fluid metabolite profiles in 10 men with and 8 without SCI above thoracic vertebra 10 (T10). Results: The metabolic phenotype for SCI could be predicted from the 1H NMR data. The median concentration of uridine in fertile controls was 1.55 mmol/L (range 1.0–5.0 mmol/L), but was undetectable by both NMR and MS in all but 2 in iduals from the SCI group, one who later fathered a child without assisted fertility techniques. Conclusions: We hypothesize that uridine is likely to be an essential precursor to metabolites required for capacitation and is a potential marker for the prognosis of post-SCI functional fertility recovery. We derived the term “seminal oligouridinosis” to describe this newly identified condition.
Publisher: American Chemical Society (ACS)
Date: 17-08-2020
Publisher: American Chemical Society (ACS)
Date: 11-01-2017
DOI: 10.1021/ACS.ANALCHEM.6B03405
Abstract: Medical swabs are routinely used worldwide to s le human mucosa for microbiological screening with culture methods. These are usually time-consuming and have a narrow focus on screening for particular microorganism species. As an alternative, direct mass spectrometric profiling of the mucosal metabolome provides a broader window into the mucosal ecosystem. We present for the first time a minimal effort/minimal-disruption technique for augmenting the information obtained from clinical swab analysis with mucosal metabolome profiling using desorption electrospray ionization mass spectrometry (DESI-MS) analysis. Ionization of mucosal biomass occurs directly from a standard rayon swab mounted on a rotating device and analyzed by DESI MS using an optimized protocol considering swab-inlet geometry, tip-s le angles and distances, rotation speeds, and reproducibility. Multivariate modeling of mass spectral fingerprints obtained in this way readily discriminate between different mucosal surfaces and display the ability to characterize biochemical alterations induced by pregnancy and bacterial vaginosis (BV). The method was also applied directly to bacterial biomass to confirm the ability to detect intact bacterial species from a swab. These results highlight the potential of direct swab analysis by DESI-MS for a wide range of clinical applications including rapid mucosal diagnostics for microbiology, immune responses, and biochemistry.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 29-04-2015
DOI: 10.1126/SCITRANSLMED.AAA5680
Abstract: In a large-scale population-based metabolic phenotyping study, erse sets of urinary metabolites, including gut microbial co-metabolites, were reproducibly associated with human adiposity.
Publisher: American Chemical Society (ACS)
Date: 13-09-2018
DOI: 10.1021/ACS.ANALCHEM.8B02412
Abstract: We report an extensive 600 MHz NMR trial of quantitative lipoprotein and small-molecule measurements in human blood serum and plasma. Five centers with eleven 600 MHz NMR spectrometers were used to analyze 98 s les including 20 quality controls (QCs), 37 commercially sourced, paired serum and plasma s les, and two National Institute of Science and Technology (NIST) reference material 1951c replicates. S les were analyzed using rigorous protocols for s le preparation and experimental acquisition. A commercial lipoprotein subclass analysis was used to quantify 105 lipoprotein subclasses and 24 low molecular weight metabolites from the NMR spectra. For all spectrometers, the instrument specific variance in measuring internal QCs was lower than the percentage described by the National Cholesterol Education Program (NCEP) criteria for lipid testing [triglycerides <2.7% cholesterol <2.8% low-density lipoprotein (LDL) cholesterol <2.8% high-density lipoprotein (HDL) cholesterol <2.3%], showing exceptional reproducibility for direct quantitation of lipoproteins in both matrixes. The average relative standard deviations (RSDs) for the 105 lipoprotein parameters in the 11 instruments were 4.6% and 3.9% for the two NIST s les, whereas they were 38% and 40% for the 37 commercially sourced plasmas and sera, respectively, showing negligible analytical compared to biological variation. The coefficient of variance (CV) obtained for the quantification of the small molecules across the 11 spectrometers was below 15% for 20 out of the 24 metabolites analyzed. This study provides further evidence of the suitability of NMR for high-throughput lipoprotein subcomponent analysis and small-molecule quantitation with the exceptional required reproducibility for clinical and other regulatory settings.
Publisher: MDPI AG
Date: 20-07-2022
DOI: 10.3390/MICROORGANISMS10071464
Abstract: Industrial production of synthetic nitrogen fertilizers and their crop application have caused considerable environmental impacts. Some eco-friendly alternatives try to solve them but raise some restrictions. We tested a novel method to produce a nitrogen bioinoculant by enriching a soil microbial community in bioreactors supplying N2 by air pumping. The biomass enriched with diazotrophic bacteria was diluted and applied to N-depleted and sterilized soil of tomato plants. We estimated microbial composition and ersity by 16S rRNA metabarcoding from soil and bioreactors at different run times and during plant uprooting. Bioreactors promoted the N-fixing microbial community and revealed a hided ersity. One hundred twenty-four (124) operational taxonomic units (OTUs) were assigned to bacteria with a greater Shannon ersity during the reactor’s steady state. A total of 753 OTUs were found in the rhizospheres with higher bio ersity when the lowest concentration of bacteria was applied. The apparent bacterial abundance in the batch and continuous bioreactors suggested a more specific functional ecological organization. We demonstrate the usefulness of bioreactors to evidence hidden ersity in the soil when it passes through bioreactors. By obtaining the same growth of inoculated plants and the control with chemical synthesis fertilizers, we evidence the potential of the methodology that we have called directed bioprospecting to grow a complex nitrogen-fixing microbial community. The simplicity of the reactor’s operation makes its application promising for developing countries with low technological progress.
Publisher: American Chemical Society (ACS)
Date: 31-08-2011
DOI: 10.1021/PR200326K
Abstract: Consumption of cruciferous vegetables (CVs) is inversely correlated to many human diseases including cancer (breast, lung, and bladder), diabetes, and cardiovascular and neurological disease. Presently, there are no readily measurable biomarkers of CV consumption and intake of CVs has relied on dietary recall. Here, biomarkers of CV intake were identified in the urine of 20 healthy Caucasian adult males using (1)H NMR spectroscopy with multivariate statistical modeling. The study was separated into three phases of 14 days: a run-in period with restricted CV consumption (phase I) a high CV phase where participants consumed 250 g/day of both broccoli and Brussels sprouts (phase II) a wash-out phase with a return to restricted CV consumption (phase III). Each study participant provided a complete cumulative urine collection over 48 h at the end of each phase a spot urine (U0), 0-10 h (U0-10), 10-24 h (U10-24), and 24-48 h (U24-48) urine s les. Urine s les obtained after consumption of CVs were differentiated from low CV diet s les by four singlet (1)H NMR spectroscopic peaks, one of which was identified as S-methyl-l-cysteine sulfoxide (SMCSO) and the three other peaks were tentatively identified as other metabolites structurally related to SMCSO. These stable urinary biomarkers of CV consumption will facilitate future assessment of CVs in nutritional population screening and dietary intervention studies and may correlate to population health outcomes.
Publisher: Wiley
Date: 25-01-2008
DOI: 10.1111/J.1462-2920.2007.01503.X
Abstract: A role for the intestinal microbiota is routinely cited as a potential aetiological factor in colorectal cancer initiation and progression. As the majority of bacteria in the gut are refractory to culture we investigated this ecosystem in subjects with colorectal cancer and with adenomatous polyposis who are at high risk of developing colorectal cancer, using culture-independent methods. Twenty colorectal cancer and 20 polypectomized volunteers were chosen for this analysis. An exploration of the ersity and temporal stability of the dominant bacteria and several bacterial subgroups was undertaken using 16S rRNA gene denaturing gradient gel electrophoresis and ribosomal intergenic spacer analysis (RISA). Metabonomic analysis of the distal gut microbiota's environment was also undertaken. A significantly reduced temporal stability and increased ersity for the microbiota of subjects with colorectal cancer and polyposis was evident. A significantly increased ersity of the Clostridium leptum and C. coccoides subgroups was also noted for both disease groups. A clear ision in the metabonome was observed for the colorectal cancer and polypectomized subjects compared with control volunteers. The intestinal microbiota and their metabolites are significantly altered in both colorectal cancer and polypectomized subjects compared with controls.
Publisher: Springer Science and Business Media LLC
Date: 19-02-2008
Abstract: Modelling the time-related behaviour of biological systems is essential for understanding their dynamic responses to perturbations. In metabolic profiling studies, the s ling rate and number of s ling points are often restricted due to experimental and biological constraints. A supervised multivariate modelling approach with the objective to model the time-related variation in the data for short and sparsely s led time-series is described. A set of piecewise Orthogonal Projections to Latent Structures (OPLS) models are estimated, describing changes between successive time points. The in idual OPLS models are linear, but the piecewise combination of several models accommodates modelling and prediction of changes which are non-linear with respect to the time course. We demonstrate the method on both simulated and metabolic profiling data, illustrating how time related changes are successfully modelled and predicted. The proposed method is effective for modelling and prediction of short and multivariate time series data. A key advantage of the method is model transparency, allowing easy interpretation of time-related variation in the data. The method provides a competitive complement to commonly applied multivariate methods such as OPLS and Principal Component Analysis (PCA) for modelling and analysis of short time-series data.
Publisher: Royal Society of Chemistry (RSC)
Date: 2004
DOI: 10.1039/B314316N
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1AY05427A
Publisher: BMJ
Date: 11-2017
Publisher: Bentham Science Publishers Ltd.
Date: 05-2009
DOI: 10.2174/138161209788168119
Abstract: The 'gut origin of sepsis' concept describes the role of the intestine in the development of sepsis and the post-operative Multi Organ Dysfunction Syndrome (MODS). Translocation of the microbiota from the gut into the systemic milieu is thought to be integral to this process. However, advances in molecular biology have demonstrated numerous mechanisms of interkingdom signalling within the gut and evidence suggests that the gut microbiota may directly influence the mammalian phenotype. The gut ecosystem fluctuates significantly in response to exogenous and surgical trauma yet until recently it has not been possible to study this non invasively and thus it is not known how current perioperative infection control strategies influence the microbiome and the consequences of this intervention for the host. However, novel analytical techniques such as metabonomics and metagenomics are permitting the in vivo analysis of the gut microbiome and are creating new avenues of research that have significant surgical applications. Furthermore, the protective mechanisms of commensal biota are increasingly being recognised, suggesting that perioperative modulation of the gut microbiome with pre, pro and synbiotics may beneficially influence surgical outcome. This paper reviews the role of the gut microbiome in determining surgical outcome, and highlights research into the mammalian microbial symbiotic axis which is leading to novel therapeutic interventions in surgery.
Publisher: Springer Science and Business Media LLC
Date: 21-07-2022
Publisher: Elsevier BV
Date: 03-2023
DOI: 10.1016/J.JHEP.2022.10.031
Abstract: Acute liver failure (ALF) is a life-threatening disease characterised by high-grade inflammation and immunoparesis with a high incidence of death from sepsis. Here, we aimed to describe the metabolic dysregulation in ALF and determine whether systemic immune responses are modulated via the lysophosphatidylcholine(LPC)-autotaxin(ATX)-lysophosphatidylcholinic acid (LPA) pathway. 96 ALF patients, 71 healthy controls (HC), 104 patients with cirrhosis and 31 septic patients were recruited. The pathways of interest were identified based on multivariate statistical analysis of proton nuclear magnetic resonance ( LPC 16:0 was found highly discriminant between ALF and HC. There was an increase in ATX and LPA in ALF compared to HC and sepsis. LPCs 16:0, 18:0 and 18:1 were reduced in ALF patients with poor prognosis. Treatment of monocytes with LPA 16:0 increased their PD-L1 expression and reduced CD155, CD163, MerTK levels, without effect on T and NK/CD56+T cells immune checkpoints. LPAR1 and 3 antagonism in culture reversed the LPA effect on monocyte expression of MerTK and CD163. MerTK and CD163, but not LPARs genes, were differently expressed and upregulated in monocytes from ALF patients compared to controls. Reduced amounts of LPCs are biomarkers of poor prognosis in patients with ALF. The LPC-ATX-LPA axis appears to modulate innate immune response in ALF via LPAR1 and LPAR3. Further investigations are required to identify novel therapeutic agents targeting these receptors. Liver disease is the 5
Publisher: MDPI AG
Date: 16-04-2016
DOI: 10.3390/NU11040861
Abstract: Supplementation with inulin-propionate ester (IPE), which delivers propionate to the colon, suppresses ad libitum energy intake and stimulates the release of satiety hormones acutely in humans, and prevents weight gain. In order to determine whether IPE remains effective when incorporated into food products (FP), IPE needs to be added to a widely accepted food system. A bread roll and fruit smoothie were produced. Twenty-one healthy overweight and obese humans participated. Participants attended an acclimatisation visit and a control visit where they consumed un-supplemented food products (FP). Participants then consumed supplemented-FP, containing 10 g/d inulin or IPE for six days followed by a post-supplementation visit in a randomised crossover design. On study visits, supplemented-FP were consumed for the seventh time and ad libitum energy intake was assessed 420 min later. Blood s les were collected to assess hormones and metabolites. Resting energy expenditure (REE) was measured using indirect calorimetry. Taste and appearance ratings were similar between FP. Ad libitum energy intake was significantly different between treatments, due to a decreased intake following IPE-FP. These observations were not related to changes in blood hormones and metabolites. There was an increase in REE following IPE-FP. However, this effect was lost after correcting for changes in fat free mass. Our results suggest that IPE suppresses appetite and may alter REE following its incorporation into palatable food products.
Publisher: Springer Science and Business Media LLC
Date: 19-02-2008
Abstract: Kernel-based classification and regression methods have been successfully applied to modelling a wide variety of biological data. The Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method offers unique properties facilitating separate modelling of predictive variation and structured noise in the feature space. While providing prediction results similar to other kernel-based methods, K-OPLS features enhanced interpretational capabilities allowing detection of unanticipated systematic variation in the data such as instrumental drift, batch variability or unexpected biological variation. We demonstrate an implementation of the K-OPLS algorithm for MATLAB and R, licensed under the GNU GPL and available at rojects/kopls/ . The package includes essential functionality and documentation for model evaluation (using cross-validation), training and prediction of future s les. Incorporated is also a set of diagnostic tools and plot functions to simplify the visualisation of data, e.g. for detecting trends or for identification of outlying s les. The utility of the software package is demonstrated by means of a metabolic profiling data set from a biological study of hybrid aspen. The properties of the K-OPLS method are well suited for analysis of biological data, which in conjunction with the availability of the outlined open-source package provides a comprehensive solution for kernel-based analysis in bioinformatics applications.
Publisher: Informa UK Limited
Date: 11-2011
DOI: 10.4161/GMIC.18754
Publisher: Elsevier
Date: 2007
Publisher: BMJ
Date: 30-03-2018
DOI: 10.1136/GUTJNL-2016-313627
Abstract: It is evident that the gut microbiota and factors that influence its composition and activity effect human metabolic, immunological and developmental processes. We previously reported that extreme physical activity with associated dietary adaptations, such as that pursued by professional athletes, is associated with changes in faecal microbial ersity and composition relative to that of in iduals with a more sedentary lifestyle. Here we address the impact of these factors on the functionality/metabolic activity of the microbiota which reveals even greater separation between exercise and a more sedentary state. Metabolic phenotyping and functional metagenomic analysis of the gut microbiome of professional international rugby union players (n=40) and controls (n=46) was carried out and results were correlated with lifestyle parameters and clinical measurements (eg, dietary habit and serum creatine kinase, respectively). Athletes had relative increases in pathways (eg, amino acid and antibiotic biosynthesis and carbohydrate metabolism) and faecal metabolites (eg, microbial produced short-chain fatty acids (SCFAs) acetate, propionate and butyrate) associated with enhanced muscle turnover (fitness) and overall health when compared with control groups. Differences in faecal microbiota between athletes and sedentary controls show even greater separation at the metagenomic and metabolomic than at compositional levels and provide added insight into the diet-exercise-gut microbiota paradigm.
Publisher: American Chemical Society (ACS)
Date: 24-03-2005
DOI: 10.1021/TX049869B
Abstract: We present here the potential of an integrated metabonomic strategy to deconvolute the biofluid metabolic signatures in experimental animals following multiple organ toxicities, using the well-known hepato- and nephrotoxin, thioacetamide. Male Han-Wistar rats were dosed with thioacetamide (150 mg/kg, n = 25), and urine, plasma, liver, and kidney s les were collected postdose for conventional NMR and magic angle spinning (MAS) NMR spectroscopy. These data were correlated with histopathology and plasma clinical chemistry collected at all time points. 1H MAS NMR data from liver and kidney were related to sequential 1H NMR measurements in urine and plasma using pattern recognition methods. One-dimensional 1H NMR spectra were data-reduced and analyzed using principal components analysis (PCA) to show the time-dependent biochemical variations induced by thioacetamide toxicity. From the eigenvector loadings of the PCA, those regions of the 1H NMR spectra, and hence the combinations of endogenous metabolites marking the main phase of the toxic episode, were identified. The thioacetamide-induced biochemical manifestations included a renal and hepatic lipidosis accompanied by hypolipidaemia increased urinary excretion of taurine and creatine concomitant with elevated creatine in liver, kidney, and plasma a shift in energy metabolism characterized by depleted liver glucose and glycogen reduced urinary excretion of tricarboxylic acid cycle intermediates and raised plasma ketone bodies increased levels of tissue and plasma amino acids leading to amino aciduria verifying necrosis-enhanced protein degradation and renal dysfunction and elevated hepatic and urinary bile acids indicating secondary damage to the biliary system. This integrated metabonomic approach has been able to identify the tissue of origin for biomarkers present in the metabolic profiles of biofluids, following the onset and progression of a multiorgan pathology, and as such highlights its potential in the evaluation of embedded toxicity in novel drug candidates.
Publisher: Proceedings of the National Academy of Sciences
Date: 15-08-2006
Abstract: Here, we study the intricate relationship between gut microbiota and host cometabolic phenotypes associated with dietary-induced impaired glucose homeostasis and nonalcoholic fatty liver disease (NAFLD) in a mouse strain (129S6) known to be susceptible to these disease traits, using plasma and urine metabotyping, achieved by 1 H NMR spectroscopy. Multivariate statistical modeling of the spectra shows that the genetic predisposition of the 129S6 mouse to impaired glucose homeostasis and NAFLD is associated with disruptions of choline metabolism, i.e., low circulating levels of plasma phosphatidylcholine and high urinary excretion of methylamines (dimethylamine, trimethylamine, and trimethylamine- N -oxide), coprocessed by symbiotic gut microbiota and mammalian enzyme systems. Conversion of choline into methylamines by microbiota in strain 129S6 on a high-fat diet reduces the bioavailability of choline and mimics the effect of choline-deficient diets, causing NAFLD. These data also indicate that gut microbiota may play an active role in the development of insulin resistance.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 02-2013
Abstract: Malnutrition is well known in Malawi, including a severe form—kwashiorkor—in which children do not simply waste away, they also suffer edema, liver damage, skin ulceration, and anorexia. Smith et al. (p. 548 see the Perspective by Relman ) investigated the microbiota of pairs of twins in Malawian villages and found notable differences in the composition of the gut microbiota in children with kwashiorkor. In these children, a bacterial species related to Desulfovibrio , which has been associated with bowel disease and inflammation, was noticeable. When the fecal flora from either the healthy or the sick twin was transplanted into groups of germ-free mice, the mice that received the kwashiorkor s le started to lose weight, like their human counterpart.
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1093/AJCN/NQX072
Abstract: Interin idual variation in the response to diet is common, but the underlying mechanism for such variation is unclear. The objective of this study was to use a metabolic profiling approach to identify a panel of urinary metabolites representing in iduals demonstrating typical (homogeneous) metabolic responses to healthy diets, and subsequently to define the association of these metabolites with improvement of risk factors for cardiovascular diseases (CVDs). 24-h urine s les from 158 participants with pre-hypertension and stage 1 hypertension, collected at baseline and following the consumption of a carbohydrate-rich, a protein-rich, and a monounsaturated fat-rich healthy diet (6 wk/diet) in a randomized, crossover study, were analyzed by proton (1H) nuclear magnetic resonance (NMR) spectroscopy. Urinary metabolite profiles were interrogated to identify typical and variable responses to each diet. We quantified the differences in absolute excretion of metabolites, distinguishing between dietary comparisons within the typical response groups, and established their associations with CVD risk factors using linear regression. Globally all 3 diets induced a similar pattern of change in the urinary metabolic profiles for the majority of participants (60.1%). Diet-dependent metabolic variation was not significantly associated with total cholesterol or low-density lipoprotein (LDL) cholesterol concentration. However, blood pressure (BP) was found to be significantly associated with 6 urinary metabolites reflecting dietary intake [proline-betaine (inverse), carnitine (direct)], gut microbial co-metabolites [hippurate (direct), 4-cresyl sulfate (inverse), phenylacetylglutamine (inverse)], and tryptophan metabolism [N-methyl-2-pyridone-5-carboxamide (inverse)]. A d ened clinical response was observed in some in iduals with variable metabolic responses, which could be attributed to nonadherence to diet (≤25.3%), variation in gut microbiome activity (7.6%), or a combination of both (7.0%). These data indicate interin idual variations in BP in response to dietary change and highlight the potential influence of the gut microbiome in mediating this relation. This approach provides a framework for stratification of in iduals undergoing dietary management. The original OmniHeart intervention study and the metabolomics study were registered at www.clinicaltrials.gov as NCT00051350 and NCT03369535, respectively.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 18-12-2021
Publisher: Springer Science and Business Media LLC
Date: 03-2015
DOI: 10.1038/BJC.2015.38
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C6SC03738K
Abstract: Imaging using 3-D DESI mass spectral data combined with deep learning reveals the topology and heterogeneity of colorectal cancer.
Publisher: EMBO
Date: 2011
DOI: 10.1038/MSB.2011.57
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-06-2012
Abstract: The composition and activity of the gut microbiota codevelop with the host from birth and is subject to a complex interplay that depends on the host genome, nutrition, and life-style. The gut microbiota is involved in the regulation of multiple host metabolic pathways, giving rise to interactive host-microbiota metabolic, signaling, and immune-inflammatory axes that physiologically connect the gut, liver, muscle, and brain. A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to manipulate the gut microbiota to combat disease and improve health.
Publisher: American Physiological Society
Date: 08-2007
DOI: 10.1152/AJPRENAL.00095.2007
Abstract: The renal Fanconi syndrome is a defect of proximal tubular function causing aminoaciduria and low-molecular-weight proteinuria. Dent's disease and Lowe syndrome are defined X-linked forms of Fanconi syndrome there is also an autosomal dominant idiopathic form (ADIF), phenotypically similar to Dent's disease though its gene defect is still unknown. To assess whether their respective gene products are ultimately involved in a common reabsorptive pathway for proteins and low-molecular-mass endogenous metabolites, we compared renal Fanconi urinary proteomes and metabonomes with normal (control) urine using mass spectrometry and 1 H-NMR spectroscopy, respectively. Urine from patients with low-molecular-weight proteinuria secondary to ifosfamide treatment (tubular proteinuria TP) was also analyzed for comparison. All four of the disorders studied had characteristic proteomic and metabonomic profiles. Uromodulin was the most abundant protein in normal urine, whereas Fanconi urine was dominated by albumin. 1 H-NMR spectroscopic data showed differences in the metabolic profiles of Fanconi urine vs. normal urine, due mainly to aminoaciduria. There were differences in the urinary metabolite and protein compositions between the three genetic forms of Fanconi syndrome: cluster analysis grouped the Lowe and Dent's urinary proteomes and metabonomes together, whereas ADIF and TP clustered together separately. Our findings demonstrate a distinctive “polypeptide and metabolite fingerprint” that can characterize the renal Fanconi syndrome they also suggest that more subtle and cause-specific differences may exist between the different forms of Fanconi syndrome that might provide novel insights into the underlying mechanisms and cellular pathways affected.
Publisher: Springer New York
Date: 14-10-2009
Publisher: Springer Science and Business Media LLC
Date: 17-11-2015
DOI: 10.1038/SREP16865
Abstract: Persistent infection with oncogenic Human Papillomavirus (HPV) is necessary for cervical carcinogenesis. Although evidence suggests that the vaginal microbiome plays a functional role in the persistence or regression of HPV infections, this has yet to be described in women with cervical intra-epithelial neoplasia (CIN). We hypothesised that increasing microbiome ersity is associated with increasing CIN severity. llumina MiSeq sequencing of 16S rRNA gene licons was used to characterise the vaginal microbiota of women with low-grade squamous intra-epithelial lesions (LSIL n = 52), high-grade (HSIL n = 92), invasive cervical cancer (ICC n = 5) and healthy controls (n = 20). Hierarchical clustering analysis revealed an increased prevalence of microbiomes characterised by high- ersity and low levels of Lactobacillus spp. (community state type-CST IV) with increasing disease severity, irrespective of HPV status (Normal = 2/20,10% LSIL = 11/52,21% HSIL = 25/92,27% ICC = 2/5,40%). Increasing disease severity was associated with decreasing relative abundance of Lactobacillus spp. The vaginal microbiome in HSIL was characterised by higher levels of Sneathia sanguinegens (P 0.01), Anaerococcus tetradius (P 0.05) and Peptostreptococcus anaerobius (P 0.05) and lower levels of Lactobacillus jensenii (P 0.01) compared to LSIL. Our results suggest advancing CIN disease severity is associated with increasing vaginal microbiota ersity and may be involved in regulating viral persistence and disease progression.
Publisher: American Chemical Society (ACS)
Date: 16-02-2009
DOI: 10.1021/AC801982H
Abstract: Structural assignment of resonances is an important problem in NMR spectroscopy, and statistical total correlation spectroscopy (STOCSY) is a useful tool aiding this process for small molecules in complex mixture analysis and metabolic profiling studies. STOCSY delivers intramolecular information (delineating structural connectivity) and in metabolism studies can generate information on pathway-related correlations. To understand further the behavior of STOCSY for structural assignment, we analyze the statistical distribution of structural and nonstructural correlations from 1050 (1)H NMR spectra of normal rat urine s les. We find that the distributions of structural/nonstructural correlations are significantly different (p 0.89 is required to assign two peaks to the same metabolite with high probability (positive predictive value, PPV = 0.9), whereas sensitivity and specificity are equal at 93% for r = 0.22. To assess the wider applicability of our results, we analyze (1)H NMR spectra of urine from rats treated with 115 model toxins or physiological stressors. Across the data sets, we find that the thresholds required to obtain PPV = 0.9 are not significantly different and the degree of overlap between the structural and nonstructural distributions is always small (median AUC = 0.97). The STOCSY method is effective for structural characterization under erse biological conditions and s le sizes provided the degree of correlation resulting from nonstructural associations (e.g., from nonstationary processes) is small. This study validates the use of the STOCSY approach in the routine assignment of signals in NMR metabolic profiling studies and provides practical benchmarks against which researchers can interpret the results of a STOCSY analysis.
Publisher: American Chemical Society (ACS)
Date: 09-08-2002
DOI: 10.1021/TX020020+
Abstract: The biochemical effects of a series of commonly used drug carrier vehicles were investigated using (1)H NMR spectroscopic and pattern recognition based metabonomic analysis. Animals were treated by oral gavage with six dosage vehicles: 0.5% (w/v) sodium carboxymethylcellulose/0.2% (v/v)tween microemulsion (consisting of propylene glycol, ethanol, cremophor, and corn oil glycerides) labrafil [consisting of poly(ethylene glycol) 300 esterified with oleic acid] (30%)/corn oil (70%) 0.1 M sodium phosphate buffered water poly(ethylene glycol) 300 and 0.5% methocel. Urine s les (n = 7) collected over a 96 h period post administration were analyzed using 600 MHz (1)H NMR spectroscopy, and principal components analysis of the spectral data was used to analyze these data. Of the six vehicles studied, three (labrafil/corn oil, PEG 300 and microemulsion) gave rise to strong vehicle-related signals in the (1)H NMR spectra of urine and were, therefore, deemed to be less suitable for NMR-based toxicity studies. To investigate any biochemical consequences of vehicle dosing, PCA was used to analyze spectral regions that did not contain vehicle-related signals, i.e., the NMR-detectable endogenous metabolite profile. PEG 300 and labrafil/corn oil induced changes in the biochemical composition of urine including increased concentrations of dicarboxylic acids, creatinine, taurine, and sugars, indicating that these vehicles were bioactive in their own right and that this might confound interpretation of biochemical effects of weakly toxic drugs dosed in these carriers. This study shows the importance of selecting appropriate vehicles for NMR-based metabonomic studies with a view to minimizing the possibility of vehicle resonances obscuring endogenous compound peaks. Furthermore, we have shown that at least two of the commonly used drug carrier vehicles caused metabolic perturbations in the urine profile. These alterations in the biochemical profile reflect vehicle-induced changes in the physiological status of the organism that may obscure the pharmacologic or toxicologic effects of drugs.
Publisher: Elsevier BV
Date: 12-2010
Publisher: American Chemical Society (ACS)
Date: 22-06-2010
DOI: 10.1021/PR900200V
Abstract: Tissue injury and repair are often overlapping consequences of disease or toxic exposure, but are not often considered as distinct processes in molecular studies. To establish the systemic metabolic response to liver regeneration, the partial hepatectomy (PH) model has been studied in the rat by an integrated metabonomics strategy, utilizing (1)H NMR spectroscopy of urine, liver and serum. Male Sprague-Dawley rats were subjected to either surgical removal of approximately two-thirds of the liver, sham operated (SO) surgery, or no treatment (n = 10/group) and s les collected over a 7 day period. A number of urinary metabolic perturbations were observed in PH rats compared with SO and control animals, including elevated levels of taurine, hypotaurine, creatine, guanidinoacetic acid, betaine, dimethylglycine and bile acids. Serum betaine and creatine were also elevated after PH, while levels of triglyceride were reduced. In the liver, triglycerides, cholesterol, alanine and betaine were elevated after PH, while choline and its derivatives were reduced. Upon examining the dynamic pattern of urinary response (the 'metabolic trajectory'), several metabolites could be categorized into groups likely to reflect perturbations to different processes such as dietary intake or hepatic 1-carbon metabolism. Several of the urinary perturbations observed during the regenerative phase of the PH model have also been observed after exposure to liver toxins, indicating that hepatic regeneration may make a contribution to the systemic alterations in metabolism associated with hepatotoxicity. The observed changes in 1-carbon and lipid metabolism are consistent with the proposed role of these pathways in the activation of a regenerative response and provide further evidence regarding the utility of urinary NMR profiles in the detection of liver-specific pathology. Biofluid (1)H NMR-based metabolic profiling provides new insight into the role of metabolism of liver regeneration, and suggests putative biomarkers for the noninvasive monitoring of the regeneration process.
Publisher: American Chemical Society (ACS)
Date: 03-05-2016
DOI: 10.1021/ACS.JPROTEOME.6B00090
Abstract: The Zucker (fa/fa) rat is a valuable and extensively utilized model for obesity research. However, the metabolic networks underlying the systemic response in the obese Zucker rats remain to be elucidated. This information is important to further our understanding of the circulation of the microbial or host-microbial metabolites and their impact on host metabolism. (1)H nuclear magnetic resonance spectroscopy-based metabolic profiling was used to probe global metabolic differences in portal vein and peripheral blood plasma, urine and fecal water between obese (fa/fa, n = 12) and lean (fa/+, n = 12) Zucker rats. Urinary concentrations of host-microbial co-metabolites were found to be significantly higher in lean Zucker rats. Higher concentrations of fecal lactate, short chain fatty acids (SCFAs), 3-hydroxyphenyl propionic acid and glycerol, and lower levels of valine and glycine were observed in obese rats compared with lean animals. Regardless of phenotype, concentrations of SCFAs, tricarboxylic acid cycle intermediates, and choline metabolites were higher in portal vein blood compared to peripheral blood. However, higher levels of succinate, phenylalanine and tyrosine were observed in portal vein blood compared with peripheral blood from lean rats but not in obese rats. Our findings indicate that the absorption of propionate, acetate, choline, and trimethylamine is independent of the Zucker rat phenotypes. However, urinary host-microbial co-metabolites were highly associated with phenotypes, suggesting distinct gut microbial metabolic activities in lean and obese Zucker rats. This work advances our understanding of metabolic processes associated with obesity, particularly the metabolic functionality of the gut microbiota in the context of obesity.
Publisher: Springer Science and Business Media LLC
Date: 09-10-2020
DOI: 10.1038/S41598-020-73762-1
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher: Springer Science and Business Media LLC
Date: 28-10-2021
DOI: 10.1038/S41598-021-00530-0
Abstract: Phenotypic ersity in urinary metabolomes of different geographical populations has been recognized recently. In this study, urinary metabolic signatures from Western (United Kingdom) and South-East Asian (Thai) cholangiocarcinoma patients were characterized to understand spectral variability due to host carcinogenic processes and/or exogenous differences (nutritional, environmental and pharmaceutical). Urinary liquid chromatography mass spectroscopy (LC–MS) spectral profiles from Thai (healthy = 20 and cholangiocarcinoma = 14) and UK cohorts (healthy = 22 and cholangiocarcinoma = 10) were obtained and modelled using chemometric data analysis. Healthy metabolome disparities between the two distinct populations were primarily related to differences in dietary practices and body composition. Metabolites excreted due to drug treatment were dominant in urine specimens from cholangiocarcinoma patients, particularly in Western in iduals. Urine from participants with sporadic (UK) cholangiocarcinoma contained greater levels of a nucleotide metabolite (uridine seudouridine). Higher relative concentrations of 7-methylguanine were observed in urine specimens from Thai cholangiocarcinoma patients. The urinary excretion of hippurate and methyladenine (gut microbial-host co-metabolites) showed a similar pattern of lower levels in patients with malignant biliary tumours from both countries. Intrinsic (body weight and body composition) and extrinsic (xenobiotic metabolism) factors were the main causes of disparities between the two populations. Regardless of the underlying aetiology, biological perturbations associated with cholangiocarcinoma urine metabolome signatures appeared to be influenced by gut microbial community metabolism. Dysregulation in nucleotide metabolism was associated with sporadic cholangiocarcinoma, possibly indicating differences in mitochondrial energy production pathways between cholangiocarcinoma tumour subtypes. Mapping population-specific metabolic disparities may aid in interpretation of disease processes and identification of candidate biomarkers.
Publisher: Elsevier BV
Date: 09-2008
DOI: 10.1016/J.CELL.2008.08.026
Abstract: Analyzing metabolites (small molecules <1 kDa) in body fluids such as urine and plasma using various spectroscopic methods provides information on the metabotype (metabolic phenotype) of in iduals or populations, information that can be applied to personalized medicine or public healthcare.
Publisher: Elsevier BV
Date: 06-2023
Publisher: Public Library of Science (PLoS)
Date: 08-09-2011
Publisher: American Chemical Society (ACS)
Date: 23-02-2007
DOI: 10.1021/PR060596A
Abstract: We have used a simplified gnotobiotic mouse model to evaluate the effects of single bacterial species, Lactobacillus paracasei NCC2461, on the metabolic profiles of intact intestinal tissues using high-resolution magic-angle-spinning 1H NMR spectroscopy (HRMAS). A total of 24 female gnotobiotic mice were ided into three groups: a control group supplemented with water and two groups supplemented with either live L. paracasei or a gamma-irradiated equivalent. HRMAS was used to characterize the biochemical components of intact epithelial tissues from the duodenum, jejunum, ileum, proximal, and distal colons in all animals and data were analyzed using chemometrics. Variations in relative concentrations of amino acids, anti-oxidant, and creatine were observed relating to different physiological properties in each intestinal tissue. Metabolic characteristics of lipogenesis and fat storage were observed in the jejunum and colon. Colonization with live L. paracasei induced region-dependent changes in the metabolic profiles of all intestinal tissues, except for the colon, consistent with modulation of intestinal digestion, absorption of nutrients, energy metabolism, lipid synthesis and protective functions. Ingestion of gamma-irradiated bacteria produced no effects on the observed metabolic profiles. 1H MAS NMR spectroscopy was able to generate characteristic metabolic signatures reflecting the structure and function of intestinal tissues. These signals acted as reference profiles with which to compare changes in response to gut microbiota manipulation at the tissue level as demonstrated by ingestion of a bacterial probiotic.
Publisher: American Chemical Society (ACS)
Date: 19-01-2008
DOI: 10.1021/AC701988A
Abstract: Previously we have demonstrated the use of 1H magic angle spinning (MAS) NMR spectroscopy for the topographical variations in functional metabolic signatures of intact human intestinal biopsy s les. Here we have analyzed a series of MAS 1H NMR spectra (spin-echo, one-dimensional, and diffusion-edited) and 31P-{1H} spectra and focused on analyzing the enhancement of information recovery by use of the statistical total correlation spectroscopy (STOCSY) method. We have applied a heterospectroscopic cross-examination performed on the same s les and between 1H and 31P-{1H} spectra (heteronuclear STOCSY) to recover latent metabolic information. We show that heterospectroscopic correlation can give new information on the molecular compartmentation of metabolites in intact tissues, including the statistical "isolation" of a phospholipid/triglyceride vesicle pool in intact tissue. The application of 31P-1H HET-STOCSY allowed the cross-assignment of major 31P signals to their equivalent 1H NMR spectra, e.g., for phosphorylcholine and phosphorylethanolamine. We also show pathway correlations, e.g., the ascorbate-glutathione pathway, in the STOCSY analysis of intact tissue spectra. These 31P-1H HET-STOCSY spectra also showed different topographical regions, particular for minor signals in different tissue microenvironments. This approach could be extended to allow the detection of altered distributions within metabolic subcompartments as well as conventional metabonomics concentration-based diagnostics.
Publisher: American Chemical Society (ACS)
Date: 04-1998
DOI: 10.1021/TX9700679
Publisher: American Chemical Society (ACS)
Date: 10-03-2017
Publisher: American Chemical Society (ACS)
Date: 02-04-2019
DOI: 10.1021/ACS.JPROTEOME.9B00040
Abstract: Obesity and its comorbidities are increasing worldwide imposing a heavy socioeconomic burden. The effects of obesity on the metabolic profiles of tissues (liver, kidney, pancreas), urine, and the systemic circulation were investigated in the Zucker rat model using
Publisher: Springer Science and Business Media LLC
Date: 19-01-2017
Publisher: Elsevier BV
Date: 2022
DOI: 10.1016/J.NUMECD.2021.09.031
Abstract: Substantial scientific evidence supports the effectiveness of a Mediterranean diet (MedDiet) in managing type 2 diabetes mellitus (T2DM). Potential benefits of time restricted feeding (TRF) in T2DM are unknown. The MedDietFast trial aims to investigate the efficacy of a MedDiet with or without TRF compared to standard care diet in managing T2DM. 120 adults aged 20-75 with a body mass index (BMI) of 20-35 kg/m The MedDietFast trial will examine the feasibility and effectiveness of a MedDiet with/without TRF in T2DM patients. Potential synergistic effects of a MedDiet with TRF will be evaluated. Future studies will generate microbiomic and metabolomic data for translation of findings into simple and effective management plans for T2DM patients. Australia and New Zealand Clinical Trials Register, ACTRN12619000246189.
Publisher: Oxford University Press (OUP)
Date: 16-12-2014
DOI: 10.1093/JNCI/DJU353
Publisher: Springer Science and Business Media LLC
Date: 21-07-2022
Publisher: Springer Science and Business Media LLC
Date: 14-05-2015
DOI: 10.1038/SREP10198
Abstract: Advanced glycation endproducts (AGEs) are believed to play a significant role in the pathophysiology of a variety of diseases including diabetes and cardiovascular diseases. Non-invasive skin autofluorescence (SAF) measurement serves as a proxy for tissue accumulation of AGEs. We assessed reference SAF and skin reflectance (SR) values in a Saudi population (n = 1,999) and evaluated the existing risk stratification scale. The mean SAF of the study cohort was 2.06 (SD = 0.57) arbitrary units (AU), which is considerably higher than the values reported for other populations. We show a previously unreported and significant difference in SAF values between men and women, with median (range) values of 1.77 AU (0.79–4.84 AU) and 2.20 AU (0.75–4.59 AU) respectively ( p -value « 0.01). Age, presence of diabetes and BMI were the most influential variables in determining SAF values in men, whilst in female participants, SR was also highly correlated with SAF. Diabetes, hypertension and obesity all showed strong association with SAF, particularly when gender differences were taken into account. We propose an adjusted, gender-specific disease risk stratification scheme for Middle Eastern populations. SAF is a potentially valuable clinical screening tool for cardiovascular risk assessment but risk scores should take gender and ethnicity into consideration for accurate diagnosis.
Publisher: BMJ
Date: 06-07-2018
DOI: 10.1136/THORAXJNL-2017-211073
Abstract: To characterise the sketetal muscle metabolic phenotype during early critical illness. Vastus lateralis muscle biopsies and serum s les (days 1 and 7) were obtained from 63 intensive care patients (59% male, 54.7±18.0 years, Acute Physiology and Chronic Health Evaluation II score 23.5±6.5). From day 1 to 7, there was a reduction in mitochondrial beta-oxidation enzyme concentrations, mitochondrial biogenesis markers (PGC1α messenger mRNA expression (−27.4CN (95% CI −123.9 to 14.3) n=23 p=0.025) and mitochondrial DNA copy number (−1859CN (IQR −5557–1325) n=35 p=0.032). Intramuscular ATP content was reduced compared tocompared with controls on day 1 (17.7mmol/kg /dry weight (dw) (95% CI 15.3 to 20.0) vs. 21.7 mmol/kg /dw (95% CI 20.4 to 22.9) p .001) and decreased over 7 days (−4.8 mmol/kg dw (IQR −8.0–1.2) n=33 p=0.001). In addition, the ratio of phosphorylated:total AMP-K (the bioenergetic sensor) increased (0.52 (IQR −0.09–2.6) n=31 p .001). There was an increase in intramuscular phosphocholine (847.2AU (IQR 232.5–1672) n=15 p=0.022), intramuscular tumour necrosis factor receptor 1 (0.66 µg (IQR −0.44–3.33) n=29 p=0.041) and IL-10 (13.6 ng (IQR 3.4–39.0) n=29 p=0.004). Serum adiponectin (10.3 µg (95% CI 6.8 to 13.7) p .001) and ghrelin (16.0 ng/mL (IQR −7–100) p=0.028) increased. Network analysis revealed a close and direct relationship between bioenergetic impairment and reduction in muscle mass and between intramuscular inflammation and impaired anabolic signaling. ATP content and muscle mass were unrelated to lipids delivered. Decreased mitochondrial biogenesis and dysregulated lipid oxidation contribute to compromised skeletal muscle bioenergetic status. In addition, intramuscular inflammation was associated with impaired anabolic recovery with lipid delivery observed as bioenergetically inert. Future clinical work will focus on these key areas to ameliorate acute skeletal muscle wasting. NCT01106300 .
Publisher: American Chemical Society (ACS)
Date: 05-05-2021
Publisher: American Chemical Society (ACS)
Date: 28-11-2011
DOI: 10.1021/PR200566T
Abstract: With successes of genome-wide association studies, molecular phenotyping systems are developed to identify genetically determined disease-associated biomarkers. Genetic studies of the human metabolome are emerging but exclusively apply targeted approaches, which restricts the analysis to a limited number of well-known metabolites. We have developed novel technical and statistical methods for systematic and automated quantification of untargeted NMR spectral data designed to perform robust and accurate quantitative trait locus (QTL) mapping of known and previously unreported molecular compounds of the metabolome. For each spectral peak, six summary statistics were calculated and independently tested for evidence of genetic linkage in a cohort of F2 (129S6xBALB/c) mice. The most significant evidence of linkages were obtained with NMR signals characterizing the glycerate (LOD10-42) at the mutant glycerate kinase locus, which demonstrate the power of metabolomics in quantitative genetics to identify the biological function of genetic variants. These results provide new insights into the resolution of the complex nature of metabolic regulations and novel analytical techniques that maximize the full utilization of metabolomic spectra in human genetics to discover mappable disease-associated biomarkers.
Publisher: Hindawi Limited
Date: 13-12-2021
DOI: 10.1002/TSM2.215
Publisher: Wiley
Date: 31-12-2005
DOI: 10.1002/NBM.935
Abstract: Strategies such as genomics, proteomics and metabonomics are being applied with increasing frequency in the pharmaceutical industry. For each of these approaches, toxicological response can be measured by terms of deviation from control or baseline status. However, in order to accurately define drug-induced response, it is necessary to characterize the normal degree of physiological variation in the absence of stimuli. Here, 1H NMR spectroscopic-based analyses of the metabolic composition of urine in experimental animals under various normal physiological conditions are reviewed. In particular, the effects of inter-animal and diurnal variation, gender, age, diet, species, strain, hormonal status and stress on the biochemical composition of urine are explored. Pattern recognition methods facilitate the comparison of urine NMR spectra over a given time-course, enabling the establishment of changes in profile and highlighting the dynamic metabolic status of an organism. Thus metabonomic approaches based on information-rich spectroscopic data sets can be used to evaluate normal physiological variation and for investigation of drug safety issues.
Publisher: Elsevier
Date: 2018
Publisher: American Chemical Society (ACS)
Date: 11-03-2009
DOI: 10.1021/PR800892U
Abstract: The mechanism of action of standard drug treatments for psychiatric disorders remains fundamentally unknown, despite intensive investigation in academia and the pharmaceutical industry. So far, little is known about the effects of psychotropic medications on brain metabolism in either humans or animals. In this study, we investigated the effects of a range of psychotropic drugs on rat brain metabolites. The drugs investigated were haloperidol, clozapine, olanzapine, risperidone, aripiprazole (antipsychotics) valproate, carbamazapine (mood stabilizers) and phenytoin (antiepileptic drug). The relative concentrations of endogenous metabolites were determined using high-resolution proton nuclear magnetic resonance (1H NMR) spectroscopy. The results revealed that different classes of psychotropic drugs modulated a range of metabolites, where each drug induced a distinct neurometabolic profile. Some common responses across several drugs or within a class of drug were also observed. Antipsychotic drugs and mood stabilizers, with the exception of olanzapine, consistently increased N-acetylaspartate (NAA) levels in at least one brain area, suggesting a common therapeutic response on increased neuronal viability. Most drugs also altered the levels of several metabolites associated with glucose metabolism, neurotransmission (including glutamate and aspartate) and inositols. The heterogenic pharmacological response reflects the functional and physiological ersity of the therapeutic interventions, including side effects. Further study of these metabolites in preclinical models should facilitate the development of novel drug treatments for psychiatric disorders with improved efficacy and side effect profiles.
Publisher: Elsevier BV
Date: 07-1997
DOI: 10.1016/S0731-7085(97)00066-6
Abstract: 750 MHz 1H NMR spectroscopy has been used to characterise in detail the abnormal low molecular weight metabolites of urine from two patients with inborn errors of metabolism. One case of the rare condition 2-hydroxyglutaric aciduria has been examined. There is at present no rapid routine method to detect this genetic defect, although NMR spectroscopy of urine is shown to provide a distinctive pattern of resonances. Assignment of a number of prominent urinary metabolites not normally seen in control urine could be made on the basis of their known NMR spectral parameters including the diagnostic marker 2-hydroxyglutaric acid, which served to confirm the condition. In addition, 750 MHz 1H NMR spectroscopy has been used to characterise further the abnormal metabolic profile of urine from a patient with maple syrup urine disease. This abnormality arises from a defect in branched chain keto-acid decarboxylase activity and results in a build up in the urine of high levels of branched chain oxo- and hydroxy-acids resulting from altered metabolism of the branched chain amino acids, valine, leucine and isoleucine. A number of previously undetected abnormal metabolites have been identified through the use of one-dimensional and two-dimensional J-resolved and COSY 750 MHz 1H NMR spectroscopy, including ethanol, 2-hydroxy-isovalerate, 2,3-dihydroxy-valerate, 2-oxo-3-methyl-n-valerate and 2-oxo-isocaproate. NMR spectroscopy of urine, particularly when combined with automatic data reduction and computer pattern recognition using a combination of biochemical markers, promises to provide an efficient alternative to other techniques for the diagnosis of inborn errors of metabolism.
Publisher: American Chemical Society (ACS)
Date: 02-11-2010
DOI: 10.1021/PR100798R
Publisher: American Chemical Society (ACS)
Date: 09-08-2012
DOI: 10.1021/PR300430U
Abstract: An NMR-based pharmacometabonomic approach was applied to investigate inter-animal variation in response to isoniazid (INH 200 and 400 mg/kg) in male Sprague-Dawley rats, alongside complementary clinical chemistry and histopathological analysis. Marked inter-animal variability in central nervous system (CNS) toxicity was identified following administration of a high dose of INH, which enabled characterization of CNS responders and CNS non-responders. High-resolution post-dose urinary ¹H NMR spectra were modeled both by their xenobiotic and endogenous metabolic information sets, enabling simultaneous identification of the differential metabolic fate of INH and its associated endogenous metabolic consequences in CNS responders and CNS non-responders. A characteristic xenobiotic metabolic profile was observed for CNS responders, which revealed higher urinary levels of pyruvate isonicotinylhydrazone and β-glucosyl isonicotinylhydrazide and lower levels of acetylisoniazid compared to CNS non-responders. This suggested that the capacity for acetylation of INH was lower in CNS responders, leading to increased metabolism via conjugation with pyruvate and glucose. In addition, the endogenous metabolic profile of CNS responders revealed higher urinary levels of lactate and glucose, in comparison to CNS non-responders. Pharmacometabonomic analysis of the pre-dose ¹H NMR urinary spectra identified a metabolic signature that correlated with the development of INH-induced adverse CNS effects and may represent a means of predicting adverse events and acetylation capacity when challenged with high dose INH. Given the widespread use of INH for the treatment of tuberculosis, this pharmacometabonomic screening approach may have translational potential for patient stratification to minimize adverse events.
Publisher: Informa UK Limited
Date: 03-2004
Abstract: This article describes the new approach known as metabonomics, a combination of data-rich analytical chemistry and chemometrics for profiling metabolism in complex systems. Two main analytical approaches have been used, namely nuclear magnetic resonance spectroscopy and mass spectrometry, however, most literature on mammalian systems pertains to nuclear magnetic resonance spectroscopy. The technologies are reviewed in relation to other -omics, and how these methods can be applied to drug safety assessment, characterization of genetically modified animal models of disease, diagnosis of human disease and drug therapy monitoring is demonstrated.
Publisher: Elsevier
Date: 2017
DOI: 10.1016/BS.AFNR.2016.12.002
Abstract: Nutrition provides the building blocks for growth, repair, and maintenance of the body and is key to maintaining health. Exposure to fast foods, mass production of dietary components, and wider importation of goods have challenged the balance between diet and health in recent decades, and both scientists and clinicians struggle to characterize the relationship between this changing dietary landscape and human metabolism with its consequent impact on health. Metabolic phenotyping of foods, using high-density data-generating technologies to profile the biochemical composition of foods, meals, and human s les (pre- and postfood intake), can be used to map the complex interaction between the diet and human metabolism and also to assess food quality and safety. Here, we outline some of the techniques currently used for metabolic phenotyping and describe key applications in the food sciences, ending with a broad outlook at some of the newer technologies in the field with a view to exploring their potential to address some of the critical challenges in nutritional science.
Publisher: Informa UK Limited
Date: 12-2022
DOI: 10.2147/CEG.S371965
Publisher: American Chemical Society (ACS)
Date: 10-01-2012
DOI: 10.1021/AC201767G
Abstract: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) provides localized information about the molecular content of a tissue s le. To derive reliable conclusions from MSI data, it is necessary to implement appropriate processing steps in order to compare peak intensities across the different pixels comprising the image. Here, we review commonly used normalization methods, and propose a rational data processing strategy, for robust evaluation and modeling of MSI data. The approach includes newly developed heuristic methods for selecting biologically relevant peaks and pixels to reduce the size of a data set and remove the influence of the applied MALDI matrix. The methods are demonstrated on a MALDI MSI data set of a sagittal section of rat brain (4750 bins, m/z = 50-1000, 111 × 185 pixels) and the proposed preferred normalization method uses the median intensity of selected peaks, which were determined to be independent of the MALDI matrix. This was found to effectively compensate for a range of known limitations associated with the MALDI process and irregularities in MS image s ling routines. This new approach is relevant for processing of all MALDI MSI data sets, and thus likely to have impact in biomarker profiling, preclinical drug distribution studies, and studies addressing underlying molecular mechanisms of tissue pathology.
Publisher: Springer Science and Business Media LLC
Date: 06-12-2013
Abstract: Obtaining comprehensive, untargeted metabolic profiles for complex solid s les, e.g., animal tissues, requires s le preparation and access to information-rich analytical methodologies such as mass spectrometry (MS). Here we describe a practical two-step process for tissue s les that is based on extraction into 'aqueous' and 'organic' phases for polar and nonpolar metabolites. Separation methods such as ultraperformance liquid chromatography (UPLC) in combination with MS are needed to obtain sufficient resolution to create diagnostic metabolic profiles and identify candidate biomarkers. We provide detailed protocols for s le preparation, chromatographic procedures, multivariate analysis and metabolite identification via tandem MS (MS/MS) techniques and high-resolution MS. By using these optimized approaches, analysis of a set of s les using a 96-well plate format would take ~48 h: 1 h for system setup, 8-10 h for s le preparation, 34 h for UPLC-MS analysis and 2-3 h for preliminary/exploratory data processing, representing a robust method for untargeted metabolic screening of tissue s les.
Publisher: Elsevier BV
Date: 11-2022
DOI: 10.1016/J.BURNS.2022.08.021
Abstract: Surgical wound excision is a necessary procedure for burn patients that require the removal of eschar. The extent of excision is currently guided by clinical judgement, with excessinto healthy tissue potentially leading to excessive scar, or inadequate debridement increasing risk of infection. Thus, an objective real-time measure to facilitate accurate excision could support clinical judgement and improve this surgical procedure. This study was designed to investigate the potential use of Rapid evaporative ionisation mass spectrometry (REIMS) as a tool to support data-driven objective tissue excision. Data were acquired using a multi-platform approach that consisted of both Rapid Evaporative Ionisation Mass Spectrometry (REIMS) performed on intact skin, and comprehensive liquid chromatography-mass spectrometry (LC-MS/MS) lipidomics performed on homogenised skin tissue extracts. Data were analysed using principal components analysis (PCA) and multivariate orthogonal projections to latent squares discriminant analysis (OPLS-DA) and logistic regression to determine the predictability of the models. PCA and OPLS-DA models of the REIMS and LC-MS/MS lipidomics data reported separation of excised and healthy tissue. Molecular fingerprints generated from REIMS analysis of healthy skin tissue revealed a high degree of heterogeneity, however, intra-in idual variance was smaller than inter-in idual variance. Both platforms indicated high levels of skin classification accuracy. In addition, OPLS-DA of the LC-MS/MS lipidomic data revealed significant differences in specific lipid classes between healthy control and excised skin s les including lower free fatty acids (FFA), monoacylglycerols (MAG), lysophosphatidylglycerol (LPG) and lysophosphatidylethanolamines (LPE) in excised tissue and higher lactosylceramides (LCER) and cholesterol esters (CE) compared to healthy control tissue. Having established the heterogeneity in the biochemical composition of healthy skin using REIMS and LC-MS/MS, our data show that REIMS has the potential to distinguish between excied and healthy skin tissue s les. This pilot study suggests that REIMS may be an effective tool to support accurate tissue excision during burn surgery.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2012
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B814426E
Abstract: The first application of high field NMR spectroscopy (800 MHz for (1)H observation) to human hepatic bile (as opposed to gall bladder bile) is reported. The bile s le used for detailed investigation was from a donor liver with mild fat infiltration, collected during organ retrieval prior to transplantation. In addition, to focus on the detection of bile acids in particular, a bile extract was analysed by 800 MHz (1)H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS. In the whole bile s le, 40 compounds have been assigned with the aid of two-dimensional (1)H-(1)H TOCSY and (1)H-(13)C HSQC spectra. These include phosphatidylcholine, 14 amino acids, 10 organic acids, 4 carbohydrates and polyols (glucose, glucuronate, glycerol and myo-inositol), choline, phosphocholine, betaine, trimethylamine-N-oxide and other small molecules. An initial NMR-based assessment of the concentration range of some key metabolites has been made. Some observed chemical shifts differ from expected database values, probably due to a difference in bulk diamagnetic susceptibility. The NMR spectra of the whole extract gave identification of the major bile acids (cholic, deoxycholic and chenodeoxycholic), but the glycine and taurine conjugates of a given bile acid could not be distinguished. However, this was achieved by HPLC-NMR/MS, which enabled the separation and identification of ten conjugated bile acids with relative abundances varying from approximately 0.1% (taurolithocholic acid) to 34.0% (glycocholic acid), of which, only the five most abundant acids could be detected by NMR, including the isomers glycodeoxycholic acid and glycochenodeoxycholic acid, which are difficult to distinguish by conventional LC-MS analysis. In a separate experiment, the use of UPLC-MS allowed the detection and identification of 13 bile acids. This work has shown the complementary potential of NMR spectroscopy, MS and hyphenated NMR/MS for elucidating the complex metabolic profile of human hepatic bile. This will be useful baseline information in ongoing studies of liver excretory function and organ transplantation.
Publisher: American Chemical Society (ACS)
Date: 27-02-2007
DOI: 10.1021/AC062305N
Publisher: Wiley
Date: 29-11-2010
DOI: 10.1002/CNCR.25738
Abstract: The worldwide epidemic of obesity and the global incidence of cancer are both increasing. There is now epidemiological evidence to support a correlation between obesity, weight gain, and some cancers. Metabolic or bariatric surgery can provide sustained weight loss and reduced obesity-related mortality. These procedures can also improve the metabolic profile to decrease cardiovascular risk and resolve diabetes in morbidly obese patients. The operations offer several physiological steps, the so-called BRAVE effects: 1) bile flow alteration, 2) reduction of gastric size, 3) anatomical gut rearrangement and altered flow of nutrients, 4) vagal manipulation and 5) enteric gut hormone modulation. Metabolic operations are also associated with a significant reduction of cancer incidence and mortality. The cancer-protective role of metabolic surgery is strongest for female obesity-related tumors however, the underlying mechanisms may involve both weight-dependent and weight-independent effects. These include the improvement of insulin resistance with attenuation of the metabolic syndrome as well as decreased oxidative stress and inflammation in addition to the beneficial modulation of sex steroids, gut hormones, cellular energetics, immune system, and adipokines. Elucidating the precise metabolic mechanisms of cancer prevention by metabolic surgery can increase our understanding of how obesity, diabetes, and metabolic syndrome are associated with cancer. It may also offer novel treatment strategies in the management of tumor generation and growth.
Publisher: Springer Science and Business Media LLC
Date: 09-01-2016
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5AY00850F
Abstract: An automated nESI-HRMS method for targeted quantitative analysis and global metabolic profiling of urine s les.
Publisher: Oxford University Press (OUP)
Date: 10-09-2013
DOI: 10.1093/IJE/DYH241
Publisher: American Chemical Society (ACS)
Date: 28-11-2011
DOI: 10.1021/AC202516E
Publisher: Wiley
Date: 09-02-2007
DOI: 10.1111/J.1742-4658.2007.05673.X
Abstract: This minireview is based on a lecture given at the First Maga Circe Conference on metabolomics held at Sabaudia, Italy, in March 2006 in which the analytical and statistical techniques used in metabonomics, efforts at standardization and some of the major applications to pharmaceutical research and development are reviewed. Metabonomics involves the determination of multiple metabolites simultaneously in biofluids, tissues and tissue extracts. Applications to preclinical drug safety studies are illustrated by the Consortium for Metabonomic Toxicology, a collaboration involving several major pharmaceutical companies. This consortium was able, through the measurement of a dataset of NMR spectra of rodent urine and serum s les, to build a predictive expert system for liver and kidney toxicity. A secondary benefit was the elucidation of the endogenous biochemicals responsible for the classification. The use of metabonomics in disease diagnosis and therapy monitoring is discussed with an exemplification from coronary artery disease, and the concept of pharmaco-metabonomics as a way of predicting an in idual's response to treatment is exemplified. Finally, some advantages and perceived difficulties of the metabonomics approach are summarized.
Publisher: Elsevier BV
Date: 03-2017
Publisher: SAGE Publications
Date: 07-2007
Publisher: American Chemical Society (ACS)
Date: 16-09-2006
DOI: 10.1021/PR060124W
Abstract: A novel statistically integrated proteometabonomic method has been developed and applied to a human tumor xenograft mouse model of prostate cancer. Parallel 2D-DIGE proteomic and 1H NMR metabolic profile data were collected on blood plasma from mice implanted with a prostate cancer (PC-3) xenograft and from matched control animals. To interpret the xenograft-induced differences in plasma profiles, multivariate statistical algorithms including orthogonal projection to latent structure (OPLS) were applied to generate models characterizing the disease profile. Two approaches to integrating metabonomic data matrices are presented based on OPLS algorithms to provide a framework for generating models relating to the specific and common sources of variation in the metabolite concentrations and protein abundances that can be directly related to the disease model. Multiple correlations between metabolites and proteins were found, including associations between serotransferrin precursor and both tyrosine and 3-D-hydroxybutyrate. Additionally, a correlation between decreased concentration of tyrosine and increased presence of gelsolin was also observed. This approach can provide enhanced recovery of combination candidate biomarkers across multi-omic platforms, thus, enhancing understanding of in vivo model systems studied by multiple omic technologies.
Publisher: Informa UK Limited
Date: 1999
Publisher: American Chemical Society (ACS)
Date: 13-05-2016
DOI: 10.1021/ACS.ANALCHEM.5B04020
Abstract: We propose a novel data-driven approach aiming to reliably distinguish discriminatory metabolites from nondiscriminatory metabolites for a given spectroscopic data set containing two biological phenotypic subclasses. The automatic spectroscopic data categorization by clustering analysis (ASCLAN) algorithm aims to categorize spectral variables within a data set into three clusters corresponding to noise, nondiscriminatory and discriminatory metabolites regions. This is achieved by clustering each spectral variable based on the r(2) value representing the loading weight of each spectral variable as extracted from a orthogonal partial least-squares discriminant (OPLS-DA) model of the data set. The variables are ranked according to r(2) values and a series of principal component analysis (PCA) models are then built for subsets of these spectral data corresponding to ranges of r(2) values. The Q(2)X value for each PCA model is extracted. K-means clustering is then applied to the Q(2)X values to generate two clusters based on minimum Euclidean distance criterion. The cluster consisting of lower Q(2)X values is deemed devoid of metabolic information (noise), while the cluster consists of higher Q(2)X values is then further subclustered into two groups based on the r(2) values. We considered the cluster with high Q(2)X but low r(2) values as nondiscriminatory, while the cluster with high Q(2)X and r(2) values as discriminatory variables. The boundaries between these three clusters of spectral variables, on the basis of the r(2) values were considered as the cut off values for defining the noise, nondiscriminatory and discriminatory variables. We evaluated the ASCLAN algorithm using six simulated (1)H NMR spectroscopic data sets representing small, medium and large data sets (N = 50, 500, and 1000 s les per group, respectively), each with a reduced and full resolution set of variables (0.005 and 0.0005 ppm, respectively). ASCLAN correctly identified all discriminatory metabolites and showed zero false positive (100% specificity and positive predictive value) irrespective of the spectral resolution or the s le size in all six simulated data sets. This error rate was found to be superior to existing methods for ascertaining feature significance: univariate t test by Bonferroni correction (up to 10% false positive rate), Benjamini-Hochberg correction (up to 35% false positive rate) and metabolome wide significance level (MWSL, up to 0.4% false positive rate), as well as by various OPLS-DA parameters: variable importance to projection, (up to 15% false positive rate), loading coefficients (up to 35% false positive rate), and regression coefficients (up to 39% false positive rate). The application of ASCLAN was further exemplified using a widely investigated renal toxin, mercury II chloride (HgCl2) in rat model. ASCLAN successfully identified many of the known metabolites related to renal toxicity such as increased excretion of urinary creatinine, and different amino acids. The ASCLAN algorithm provides a framework for reliably differentiating discriminatory metabolites from nondiscriminatory metabolites in a biological data set without the need to set an arbitrary cut off value as applied to some of the conventional methods. This offers significant advantages over existing methods and the possibility for automation of high-throughput screening in "omics" data.
Publisher: Springer Science and Business Media LLC
Date: 13-07-2017
DOI: 10.1038/S41598-017-05689-Z
Abstract: Inflammatory and metabolic diseases can originate during early-life and have been correlated with shifts in intestinal microbial ecology. Here we demonstrate that minor environmental fluctuations during the early neonatal period had sustained effects on the developing porcine microbiota and host-microbe interface. These inter-replicate effects appear to originate during the first day of life, and are likely to reflect very early microbiota acquisition from the environment. We statistically link early systemic inflammation with later local increases in inflammatory cytokine (IL-17) production, which could have important enteric health implications. Immunity, intestinal barrier function, host metabolism and host-microbiota co-metabolism were further modified by Bifidobacterium lactis NCC2818 supplementation, although composition of the in situ microbiota remained unchanged. Finally, our robust model identified novel, strong correlations between urinary metabolites (eg malonate, phenylacetylglycine, alanine) and mucosal immunoglobulin (IgM) and cytokine (IL-10, IL-4) production, thus providing the possibility of the development of urinary ‘dipstick’ tests to assess non-accessible mucosal immune development and identify early precursors (biomarkers) of disease. These results have important implications for infants exposed to neonatal factors including caesarean delivery, antibiotic therapy and delayed discharge from hospital environments, which may predispose to the development of inflammatory and metabolic diseases in later life.
Publisher: American Chemical Society (ACS)
Date: 07-04-2010
DOI: 10.1021/PR901019Z
Publisher: Springer Science and Business Media LLC
Date: 20-04-2008
DOI: 10.1038/NATURE06882
Publisher: American Chemical Society (ACS)
Date: 12-07-2021
Publisher: American Chemical Society (ACS)
Date: 08-03-2006
DOI: 10.1021/AC0517085
Publisher: Springer Science and Business Media LLC
Date: 25-06-2018
Publisher: Springer Science and Business Media LLC
Date: 07-10-2022
DOI: 10.1038/S43856-022-00185-6
Abstract: Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated. To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D ( n = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery n = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level. Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control. We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.IJPARA.2008.10.010
Abstract: In order to enhance our understanding of physiological and pathological consequences of a patent Schistosoma mansoni infection in the mouse, we examined the metabolic responses of different tissue s les recovered from the host animal using a metabolic profiling strategy. Ten female NMRI mice were infected with approximately 80 S. mansoni cercariae each, and 10 uninfected age- and sex-matched animals served as controls. At day 74 post infection (p.i.), mice were killed and jejunum, ileum, colon, liver, spleen and kidney s les were removed. We employed (1)H magic angle spinning-nuclear magnetic resonance spectroscopy to generate tissue-specific metabolic profiles. The spectral data were analyzed using multivariate modelling methods including an orthogonal signal corrected-projection to latent structure analysis and hierarchical principal component analysis to assess the differences and/or similarities in metabolic responses between infected and non-infected control mice. Most tissues obtained from S. mansoni-infected mice were characterized by high levels of amino acids, such as leucine, isoleucine, lysine, glutamine and asparagine. High levels of membrane phospholipid metabolites, including glycerophosphoryl choline and phosphoryl choline were found in the ileum, colon, liver and spleen of infected mice. Additionally, low levels of energy-related metabolites, including lipids, glucose and glycogen were observed in ileum, spleen and liver s les of infected mice. Energy-related metabolites in the jejunum, liver and renal medulla were found to be positively correlated with S. mansoni worm burden upon dissection. These findings show that a patent S. mansoni infection causes clear disruption of metabolism in a range of tissues at a molecular level, which can be interpreted in relation to the previously reported signature in a biofluid (i.e. urine), giving further evidence of the global effect of the infection.
Publisher: Springer Science and Business Media LLC
Date: 07-01-2022
DOI: 10.1038/S41598-021-03833-4
Abstract: This study aims to explore the immediate effects of bariatric surgery on serum tryptophan–kynurenine pathway metabolites in in iduals with type 2 diabetes and BMI 30. With the goal of providing insight into the link between tryptophan pathway metabolites, type 2 diabetes, and chronic obesity-induced inflammation. This longitudinal study included 20 participants. Half were diagnosed with type 2 diabetes. 11 and 9 underwent RYGB and SG respectively. Blood s les were obtained at pre-operative and 3 months post-operative timepoints. Tryptophan and downstream metabolites of the kynurenine pathway were quantified with an ultrahigh-performance liquid chromatography tandem mass spectrometry with electrospray ionisation method. At 3 months post-operation, RYGB led to significant reductions in tryptophan, kynurenic acid and xanthurenic acid levels when compared to baseline. Significant reductions of the same metabolites after surgery were also observed in in iduals with T2D irrespective of surgical procedure. These metabolites were significantly correlated with serum HbA1c levels and BMI. Bariatric surgery, in particular RYGB reduces serum levels of tryptophan and its downstream kynurenine metabolites. These metabolites are associated with T2D and thought to be potentially mechanistic in the systemic processes of obesity induced inflammation leading to insulin resistance. Its reduction after surgery is associated with an improvement in glycaemic control (HbA1c).
Publisher: Springer Science and Business Media LLC
Date: 11-03-2021
DOI: 10.1038/S41586-021-03412-7
Abstract: Transmission of SARS-CoV-2 is uncontrolled in many parts of the world control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant
Publisher: Springer Science and Business Media LLC
Date: 29-07-2022
DOI: 10.1038/S41598-022-16886-W
Abstract: A growing body of evidence supports the concept of a systemic response to non-severe thermal trauma. This provokes an immunosuppressed state that predisposes paediatric patients to poor recovery and increased risk of secondary morbidity. In this study, to understand the long-term systemic effects of non-severe burns in children, targeted mass spectrometry assays for biogenic amines and tryptophan metabolites were performed on plasma collected from child burn patients at least three years post injury and compared to age and sex matched non-burn (healthy) controls. A panel of 12 metabolites, including urea cycle intermediates, aromatic amino acids and quinolinic acid were present in significantly higher concentrations in children with previous burn injury. Correlation analysis of metabolite levels to previously measured cytokine levels indicated the presence of multiple cytokine-metabolite associations in the burn injury participants that were absent from the healthy controls. These data suggest that there is a sustained immunometabolic imprint of non-severe burn trauma, potentially linked to long-term immune changes that may contribute to the poor long-term health outcomes observed in children after burn injury.
Publisher: American Chemical Society (ACS)
Date: 11-05-2006
DOI: 10.1021/PR060024Q
Abstract: We present here a definitive metabonomic analysis in order to detect novel biomarker and metabolite information, implicating specific putative protein targets in the toxicological mechanism of bromobenzene-induced centrilobular hepatic necrosis. Male Han-Wistar rats were dosed with bromobenzene (1.5 g/kg, n = 25) and blood plasma, urine and liver s les were collected for NMR and magic angle spinning (MAS) NMR spectroscopy at various time-points postdose, with histopathology and clinical pathology performed in parallel. Liver s les were analyzed by 600 MHz 1H MAS NMR techniques and the resultant spectra were correlated to sequential 1H NMR measurements in urine and blood plasma using pattern recognition methods. 1D 1H NMR spectra were data-reduced and analyzed using principal components analysis (PCA) to show the time-dependent biochemical variations induced by bromobenzene toxicity. In addition to a holistic view of the effect of hepatic toxicity on the metabolome, a number of putative protein targets of bromobenzene and its metabolites were identified including those enzymes of the glutathione cycle, exemplified by the presence of a novel biomarker, 5-oxoproline, in liver tissue, blood plasma, and urine. As such, this work establishes the importance of metabonomics technology in resolving the mechanistic complexity of drug toxicity as well as the benefits of frontloading this approach in drug safety evaluation and biomarker discovery.
Publisher: Elsevier
Date: 2014
Publisher: American Chemical Society (ACS)
Date: 13-05-2006
DOI: 10.1021/AC060168O
Abstract: A new analytical strategy for biomarker recovery from directly coupled ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC Tof MS) data on biofluids is presented and exemplified using a study on hydrazine-induced liver toxicity. A key step in the strategy involves a novel procedure for reducing the spectroscopic search space by differential analysis of cohorts of normal and pathological s les using an orthogonal projection to latent structures discriminant analysis (O-PLS-DA). This efficiently sorts principal discriminators of toxicity from the background of thousands of metabolic features commonly observed in data sets generated by UPLC-MS analysis of biological fluids and is thus a powerful tool for biomarker discovery.
Publisher: Elsevier BV
Date: 02-2020
DOI: 10.1093/AJCN/NQZ293
Publisher: Elsevier BV
Date: 09-2016
Publisher: Elsevier BV
Date: 07-2011
DOI: 10.1016/J.TIM.2011.05.006
Abstract: There is growing awareness of the importance of the gut microbiome in health and disease, and recognition that the microbe to host metabolic signalling is crucial to understanding the mechanistic basis of their interaction. This opens new avenues of research for advancing knowledge on the aetiopathologic consequences of dysbiosis with potential for identifying novel microbially-related drug targets. Advances in both sequencing technologies and metabolic profiling platforms, coupled with mathematical integration approaches, herald a new era in characterizing the role of the microbiome in metabolic signalling within the host and have far reaching implications in promoting health in both the developed and developing world.
Publisher: American Chemical Society (ACS)
Date: 02-06-2009
DOI: 10.1021/AC900567E
Publisher: Informa UK Limited
Date: 1996
DOI: 10.3109/00498259609046706
Abstract: 1. 1H and 19F-nmr spectroscopy was used to investigate quantitatively the urinary excretion of the metabolites of 15 substituted phenols in the rat. The compounds studied were: 2-, 3-, and 4-fluorophenols 2-, 3-, and 4-trifluoromethylphenol 2,4-, 2,6- and 3,4-difluorophenol 2-fluoro-5-trifluoromethylphenol, 3-fluoro-5-trifluoromethylphenol, 2-trifluoromethyl-4-fluorophenol 3-chloro-4-fluorophenol, 3-fluoro-4-chlorophenol, and 3-methyl-4-fluorophenol. All compounds were dosed to the Sprague-Dawley rat (10 mg/kg i.p.) and urine was collected over the periods 0-8, 8-24 and 24-48 h post-dosing and analyzed using nmr spectroscopy. 2. The compounds were excreted in the urine mainly as glucuronide or sulphate conjugates or as the unchanged parent compound. There was considerable variation in the urinary excretion of the compounds over 48 h ranging from 22.1 to 93.6% of the dose. There was no apparent relationship between the molecular weight of compounds or their metabolites and the percentage molar recovery of each in the urine. 3. Ortho-substituted phenols in general showed a greater propensity for glucuronidation than did either meta- or para-substituted compounds, irrespective of the substituent group. The molar glucuronide-to-sulphate ratio for ortho-substituted compounds was found to be 2.2 +/- 0.9 whereas the ratio for both meta- and para-substituted compounds was 0.8 +/- 0.2 (p < 0.0001). 4. There were characteristic substituent effects of phenolic glucuronidation or sulphation on the 19F-nmr chemical shifts for both F- and CF3-substituted phemols and these substituent effects were a useful aid to metabolite signal assignment. 5. These studies show that nmr spectroscopy provides a rapid and convenient approach to the construction of metabolic databases of simple xenobiotics for the investigation of structure-metabolism relationships.
Publisher: American Chemical Society (ACS)
Date: 27-06-2006
DOI: 10.1021/PR0504182
Abstract: Stress in the form of moderate periods of maternal separation of newborn rats has been postulated to cause permanent changes in the central nervous system and diseases in later life. It is also considered that dietary supplementation with long chain polyunsaturated fatty acids (LC-PUFAs) can potentially ameliorate the effects of stress. The metabolic consequences of early life maternal separation stress were investigated in rats (2-14 days after birth), either alone or in combination with secondary acute water avoidance stress at 3-4 months of age. The effect of a LC-PUFA-enriched dietary intervention in stressed animals was also assessed. Systematic changes in metabolic biochemistry were evaluated using 1H nuclear magnetic resonance spectroscopy of blood plasma and multivariate pattern recognition techniques. The biochemical response to stress was characterized by decreased levels of total lipoproteins and increased levels of amino acids, glucose, lactate, creatine, and citrate. Secondary acute water avoidance stress also caused elevated levels of O-acetyl glycoproteins in blood plasma. LC-PUFAs dietary enrichment did not alter the metabolic response to stress, but did result in a modified lipoprotein profile. This work indicates that the different stressor types resulted in some common systemic metabolic responses that involve changes in energy and muscle metabolism, but that they are not reversible by dietary intervention.
Publisher: Cold Spring Harbor Laboratory
Date: 19-06-2022
DOI: 10.1101/2022.06.18.22276437
Abstract: The biology driving in idual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct “systemic recovery” profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app , designed to test our findings prospectively.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-08-2016
DOI: 10.1126/SCITRANSLMED.AAG1026
Abstract: Cervical cerclage using braided suture material disrupts vaginal microbial stability and increases inflammation.
Publisher: American Chemical Society (ACS)
Date: 04-10-2007
DOI: 10.1021/PR0703021
Abstract: Detection and classification of in vivo drug toxicity is an expensive and time-consuming process. Metabolic profiling is becoming a key enabling tool in this area as it provides a unique perspective on the characterization and mechanisms of response to toxic insult. As part of the Consortium on Metabonomic Toxicology (COMET) project, a substantial metabolic and pathological database was constructed. We chose a set of 80 treatments to build a modeling system for toxicity prediction using NMR spectroscopy of urine s les (n=12935) from laboratory rats (n=1652). The compound structures and activities were erse but there was an emphasis on the selection of hepato and nephrotoxins. We developed a two-stage strategy based on the assumptions that (a) adverse effects would produce metabolic profiles deviating from those of normal animals and (b) such deviations would be similar for treatments having similar physiological effects. To address the first stage, we developed a multivariate model of normal urine, using principal components analysis of specially preprocessed 1H NMR spectra. The model demonstrated a high correspondence between the occurrence of toxicity and abnormal metabolic profiles. In the second stage, we extended a density estimation method, "CLOUDS", to compute multidimensional similarities between treatments. Crucially, the technique allowed a distribution-free estimate of similarity across multiple animals and time points for each treatment and the resulting matrix of similarities showed segregation between liver toxins and other treatments. Using the similarity matrix, we were able to correctly identify the target organ of two "blind" treatments, even at sub-toxic levels. To further validate the approach, we then applied a leave-one-out approach to predict the main organ of toxicity (liver or kidney) showing significant responses using the three most similar matches in the matrix. Where predictions could be made, there was an error rate of 8%. The sensitivities to liver and kidney toxicity were 67 and 41%, respectively, whereas the corresponding specificities were 77 and 100%. In some cases, it was not possible to make predictions because of interference by drug-related metabolite signals (18%), an inconsistent histopathological or urinary response (11%), genuine class overlap (8%), or lack of similarity to any other treatment (2%). This study constitutes the largest validation to date of the metabonomic approach to preclinical toxicology assessment, confirming that the methodology offers practical utility for rapid in vivo drug toxicity screening.
Publisher: Royal Society of Chemistry (RSC)
Date: 21-08-2002
DOI: 10.1039/B205128C
Abstract: 1H nuclear magnetic resonance (NMR)-based metabonomics is a well-established technique used to analyse and interpret complex multiparametric metabolic data, and has a wide number of applications in the development of pharmaceuticals. However, interpretation of biological data can be confounded by extraneous variation in the data such as fluctuations in either experimental conditions or in physiological status. Here we have shown the novel application of a data filtering method, orthogonal signal correction (OSC), to biofluid NMR data to minimise the influence of inter- and intra-spectrometer variation during data acquisition, and also to minimise innate physiological variation. The removal of orthogonal variation exposed features of interest in the NMR data and facilitated interpretation of the derived multivariate models. Furthermore, analysis of the orthogonal variation provided an explanation of the systematic analytical/biological changes responsible for confounding the original NMR data.
Publisher: Oxford University Press (OUP)
Date: 18-05-2019
Abstract: To characterize serum metabolic signatures associated with atherosclerosis in the coronary or carotid arteries and subsequently their association with incident cardiovascular disease (CVD). We used untargeted one-dimensional (1D) serum metabolic profiling by proton nuclear magnetic resonance spectroscopy (1H NMR) among 3867 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), with replication among 3569 participants from the Rotterdam and LOLIPOP studies. Atherosclerosis was assessed by coronary artery calcium (CAC) and carotid intima-media thickness (IMT). We used multivariable linear regression to evaluate associations between NMR features and atherosclerosis accounting for multiplicity of comparisons. We then examined associations between metabolites associated with atherosclerosis and incident CVD available in MESA and Rotterdam and explored molecular networks through bioinformatics analyses. Overall, 30 1H NMR measured metabolites were associated with CAC and/or IMT, P = 1.3 × 10−14 to 1.0 × 10−6 (discovery) and P = 5.6 × 10−10 to 1.1 × 10−2 (replication). These associations were substantially attenuated after adjustment for conventional cardiovascular risk factors. Metabolites associated with atherosclerosis revealed disturbances in lipid and carbohydrate metabolism, branched chain, and aromatic amino acid metabolism, as well as oxidative stress and inflammatory pathways. Analyses of incident CVD events showed inverse associations with creatine, creatinine, and phenylalanine, and direct associations with mannose, acetaminophen-glucuronide, and lactate as well as apolipoprotein B (P & 0.05). Metabolites associated with atherosclerosis were largely consistent between the two vascular beds (coronary and carotid arteries) and predominantly tag pathways that overlap with the known cardiovascular risk factors. We present an integrated systems network that highlights a series of inter-connected pathways underlying atherosclerosis.
Publisher: Massachusetts Medical Society
Date: 09-01-2014
Publisher: American Chemical Society (ACS)
Date: 06-08-2014
DOI: 10.1021/AC501853D
Abstract: Breast milk (BM) is a biofluid that has a fundamental role in early life nutrition and has direct impact on growth, neurodevelopment, and health. Global metabolic profiling is increasingly being utilized to characterize complex metabolic changes in biological s les. However, in order to achieve broad metabolite coverage, it is necessary to employ more than one analytical platform, typically requiring multiple s le preparation protocols. In an effort to improve analytical efficiency and retain comprehensive coverage of the metabolome, a new extraction methodology was developed that successfully retains metabolites from BM in a single-phase using an optimized methyl-tert-butyl ether solvent system. We conducted this single-phase extraction procedure on a representative pool of BM, and characterized the metabolic composition using LC-QTOF-MS and GC-Q-MS for polar and lipidic metabolites. To ensure that the extraction method was reproducible and fit-for-purpose, the analytical procedure was evaluated on both platforms using 18 metabolites selected to cover a range of chromatographic retention times and biochemical classes. Having validated the method, the metabolic signature of BM composition was mapped as a metabolic reaction network highlighting interconnected biological pathways and showing that the LC-MS and GC-MS platforms targeted largely different domains of the network. Subsequently, the same protocol was applied to ascertain compositional differences between BM at week 1 (n = 10) and 4 weeks (n = 9) post-partum. This single-phase approach is more efficient in terms of time, simplicity, cost, and s le volume than the existing two-phase methods and will be suited to high-throughput metabolic profiling studies of BM.
Publisher: Wiley
Date: 06-07-2011
Abstract: Bile flow restoration is a crucial step in the recovery process post transplantation of the liver. Here, metabolic trajectories based on changes in bile secretion - a known marker of functionality - have been utilised as an approach for discovering bile fluxes during transplantation. A total of ten liver transplants were monitored and from these 68 bile s les from both donors and recipients were collected and analysed using ultra-performance LC-MS in combination with multivariate statistical analysis. Based on the principal component scores constructed from the total bile fingerprint, differentiation of the bile acid concentrations before and after transplantation was detected. A trend was also observed, by constructing metabolic trajectories, whereby the post-transplant profiles approached the position of pre-transplant profiles within 30-60 min of the restoration of bile secretion function. The ten major conjugated bile acid salts were measured and a significant increase in concentrations of taurocholic acid and taurochenodeoxycholic acid were seen after transplantation. In addition, the ratios of secondary bile acids detected in gall bladder and hepatic bile were measured before and after transplantation. This study suggests that bile acid ratios in the donor liver at the pre-transplant and post-transplant stage may be important and that profiling of secreted bile after transplantation may aid clinical assessment and progress post-transplantation.
Publisher: Informa UK Limited
Date: 06-09-2020
Publisher: American Chemical Society (ACS)
Date: 22-12-2007
DOI: 10.1021/PR060594Q
Abstract: We provide an overview of how the underlying philosophy of chemometrics is integrated throughout metabonomic studies. Four steps are demonstrated: (1) definition of the aim, (2) selection of objects, (3) s le preparation and characterization, and (4) evaluation of the collected data. This includes the tools applied for linear modeling, for ex le, Statistical Experimental Design (SED), Principal Component Analysis (PCA), Partial least-squares (PLS), Orthogonal-PLS (OPLS), and dynamic extensions thereof. This is illustrated by ex les from the literature.
Publisher: Springer Science and Business Media LLC
Date: 21-07-2015
DOI: 10.1038/NRGASTRO.2015.114
Abstract: Disease risk and treatment response are determined, at the in idual level, by a complex history of genetic and environmental interactions, including those with our endogenous microbiomes. Personalized health care requires a deep understanding of patient biology that can now be measured using a range of '-omics' technologies. Patient stratification involves the identification of genetic and/or phenotypic disease subclasses that require different therapeutic strategies. Stratified medicine approaches to disease diagnosis, prognosis and therapeutic response monitoring herald a new dimension in patient care. Here, we explore the potential value of metabolic profiling as applied to unmet clinical needs in gastroenterology and hepatology. We describe potential applications in a number of diseases, with emphasis on large-scale population studies as well as metabolic profiling on the in idual level, using spectrometric and imaging technologies that will leverage the discovery of mechanistic information and deliver novel health care solutions to improve clinical pathway management.
Publisher: Springer Science and Business Media LLC
Date: 10-2004
DOI: 10.1038/NBT1015
Abstract: Understanding the relationships between human genetic factors, the risks of developing major diseases and the molecular basis of drug efficacy and toxicity is a fundamental problem in modern biology. Predicting biological outcomes on the basis of genomic data is a major challenge because of the interactions of specific genetic profiles with numerous environmental factors that may conditionally influence disease risks in a nonlinear fashion. 'Global' systems biology attempts to integrate multivariate biological information to better understand the interaction of genes with the environment. The measurement and modeling of such erse information sets is difficult at the analytical and bioinformatic modeling levels. Highly complex animals such as humans can be considered 'superorganisms' with an internal ecosystem of erse symbiotic microbiota and parasites that have interactive metabolic processes. We now need novel approaches to measure and model metabolic compartments in interacting cell types and genomes that are connected by cometabolic processes in symbiotic mammalian systems.
Publisher: Cold Spring Harbor Laboratory
Date: 28-04-2023
DOI: 10.1101/2023.04.24.537960
Abstract: Globally, burns are a significant cause of injury that can cause substantial acute trauma as well as lead to increased incidence of chronic co-morbidity and disease. To date, research has primarily focused on the systemic response to severe injury, with little in the literature reported on impact of non-severe injuries ( % total burn surface area TBSA). To elucidate the metabolic consequences of non-severe burn injury, longitudinal plasma was collected from adults (n=35) who presented at hospital with a non-severe burn injury at admission, and at 6 week follow up. A cross-sectional baseline s le was also collected from non-burn control participants (n=14). S les underwent multiplatform metabolic phenotyping using 1 H nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry to quantify 112 lipoprotein and glycoproteins signatures and 852 lipid species from across 20 subclasses. Multivariate data modelling (Orthogonal projection to latent structures-discriminate analysis) revealed alterations in lipoprotein and lipid metabolism when comparing baseline control to hospital admission s les, with the phenotypic signature found to be sustained at follow up. Univariate (Mann-Whitney U) testing and OPLS-DA indicated specific increases in GlycB (p-value .0e -4 ), low density lipoprotein-2 subfractions (Variable importance in projection score VIP .83e -1 ) and monoacyglyceride (20:4)(p-value .0e -4 ) and decreases in circulating anti-inflammatory high-density lipoprotein-4 subfractions (VIP .75e -1 ), phosphatidylcholines, phosphatidylglycerols, phosphatidylinositols and phosphatidylserines. The results indicate a persistent systemic metabolic phenotype that occurs even in cases of non-severe burn injury. The phenotype is indicative of an acute inflammatory profile which continues to be sustained post-injury, suggesting an impact on systems health beyond the site of injury. The phenotypes contained metabolic signatures consistent with chronic inflammatory states reported to have elevated incidence post-burn injury. Such phenotypic signatures may provide patient stratification opportunities, to identify in idual responses to injury, personalise intervention strategies and improve acute care, reducing risk of chronic co-morbidity.
Publisher: Proceedings of the National Academy of Sciences
Date: 16-08-2004
Abstract: Schistosomiasis, a chronic and debilitating parasitic disease, affects ≈200 million people in the developing world and imposes a substantial public health and economic impact. Accurately diagnosing at the in idual level, monitoring disease progression, and assessing the impact of pharmacological interventions at the population level are of prime importance for controlling schistosomiasis. Using a Schistosoma mansoni -mouse model, we present a characterization of a parasitic infection by metabolic profiling, employing 1 H NMR spectroscopy and multivariate pattern recognition techniques. We infected 10 mice with 80 S. mansoni cercariae each and collected urine s les 49 and 56 days postinfection. Urine s les were also obtained from 10 uninfected control mice at the same time. The metabolic signature of an S. mansoni infection consists of reduced levels of the tricarboxylic acid cycle intermediates, including citrate, succinate, and 2-oxoglutarate, and increased levels of pyruvate, suggesting stimulated glycolysis. A disturbance of amino acid metabolism was also associated with an S. mansoni infection, as indicated by depletion of taurine, 2-oxoisocaproate, and 2-oxoisovalerate and elevation of tryptophan in the urine. A range of microbial-related metabolites, i.e., trimethylamine, phenylacetylglycine, acetate, p -cresol glucuronide, butyrate, propionate, and hippurate, were also coupled with an S. mansoni infection, indicating disturbances in the gut microbiota. Our work highlights the potential of metabolic profiling to enhance our understanding of biological responses to parasitic infections. It also holds promise as a basis for novel diagnostic tests with high sensitivity and specificity and for improved disease surveillance and control.
Publisher: BMJ
Date: 21-10-2010
Abstract: Atrial tachyarrhythmias are a common complication of atrial septal defects. The objective was to determine the effect of atrial septal defect closure on pre-existing atrial tachyarrhythmias and to investigate if such an effect is present after either surgical or percutaneous closure. Medline, EMBASE, Cochrane Library, and Google Scholar databases were searched between 1967 and 2009. The search was expanded using the 'related articles' function and reference lists of key studies. All studies reporting pre- and post- closure incidence (or prevalence) of atrial tachyarrhythmias in the same patient groups were included. Data were independently extracted by two authors according to a pre-defined protocol. Incongruities were settled by consensus decision. Twenty six studies were identified including 1841 patients who underwent surgical closure and 945 who underwent percutaneous closure. Meta-analysis using a random effects model demonstrated a reduction in the prevalence of atrial tachyarrhythmias following atrial septal defect closure [OR = 0.66 (95% CI 0.57-0.77)]. This effect was demonstrated after both percutaneous [OR = 0.49 (95% CI 0.32-0.76)] and surgical closure [OR = 0.72 (95% CI 0.60-0.87)]. Immediate (<30 days) and mid-term (30 days - 5 years) follow-up also demonstrated a reduction in AT prevalence [ORs of 0.80 (95% CI 0.66-0.97) and 0.47 (95% CI 0.36-0.62) respectively]. Atrial septal defect closure, whether surgical or percutaneous, is associated with a reduction in the post-closure prevalence of pre-existing atrial tachyarrhythmias and atrial fibrillation in the short to medium term.
Publisher: American Chemical Society (ACS)
Date: 02-06-0007
DOI: 10.1021/AC500317C
Abstract: Exploratory or untargeted ultra performance liquid chromatography-mass spectrometry (UPLC-MS) profiling offers an overview of the complex lipid species ersity present in blood plasma. Here, we evaluate and compare eight s le preparation protocols for optimized blood plasma lipid extraction and measurement by UPLC-MS lipid profiling, including four protein precipitation methods (i.e., methanol, acetonitrile, isopropanol, and isopropanol-acetonitrile) and four liquid-liquid extractions (i.e., methanol combined with chloroform, dichloromethane, and methyl-tert butyl ether and isopropanol with hexane). The eight methods were then benchmarked using a set of qualitative and quantitative criteria selected to warrant compliance with high-throughput analytical workflows: protein removal efficiency, selectivity, repeatability, and recovery efficiency of the s le preparation. We found that protein removal was more efficient by precipitation (99%) than extraction (95%). Additionally, isopropanol appeared to be the most straightforward and robust solvent (61.1% of features with coefficient of variation (CV) < 20%) while enabling a broad coverage and recovery of plasma lipid species. These results demonstrate that isopropanol precipitation is an excellent s le preparation procedure for high-throughput untargeted lipid profiling using UPLC-MS. Isopropanol precipitation is not limited to untargeted profiling and could also be of interest for targeted UPLC-MS/MS lipid analysis. Collectively, these data show that lipid profiling greatly benefits from an isopropanol precipitation in terms of simplicity, protein removal efficiency, repeatability, lipid recovery, and coverage.
Publisher: Elsevier BV
Date: 12-2003
Abstract: Principal component analysis (PCA) has been applied to three nuclear magnetic resonance (NMR) spectral editing methods, namely, the Carr-Purcell-Meiboom-Gill spin-echo, diffusion editing, and skyline projection of a two-dimensional J-resolved spectrum, obtained from high-resolution magic-angle spinning NMR spectroscopy of liver tissues, to distinguish between control and hydrazine-treated rats. The effects of the toxin on rat liver biochemistry were directly observed and characterized by depleted levels of liver glycogen, choline, taurine, trimethylamine N-oxide, and glucose and by elevated levels of lipids and alanine. The highly unsaturated omega-3-type fatty acid was observed for the first time in hydrazine-treated rat liver. The contributions of the metabolites to the separation of control from dosed liver tissues varied depending on the type of spectral editing method used. We have shown that subtle changes in the metabolic profiles can be selectively lified using a metabonomics approach based on the different NMR spectral editing techniques in conjunction with PCA.
Publisher: Springer Science and Business Media LLC
Date: 26-09-2013
DOI: 10.1038/SREP02769
Abstract: Despite immense efforts to combat malaria in tropical and sub-tropical regions, the potency of this vector-borne disease and its status as a major driver of morbidity and mortality remain undisputed. We develop an analytical pipeline for characterizing Plasmodium infection in a mouse model and identify candidate urinary biomarkers that may present alternatives to immune-based diagnostic tools. We employ 1 H nuclear magnetic resonance (NMR) profiling followed by multivariate modeling to discover diagnostic spectral regions. Identification of chemical structures is then made on the basis of statistical spectroscopy, multinuclear NMR and entrapment of candidates by iterative liquid chromatography (LC) and mass spectrometry (MS). We identify two urinary metabolites (i) 4-amino-1-[3-hydroxy-5-(hydroxymethyl)-2,3-dihydrofuran-2-yl]pyrimidin-2(1H)-one, (ii) 2-amino-4-({[5-(4-amino-2-oxopyrimidin-1(2H)-yl)-4-hydroxy-4,5-dihydrofuran-2-yl]methyl}sulfanyl)butanoic acid that were detected only in Plasmodium berghei -infected mice. These metabolites have not been described in the mammalian or parasite metabolism to date. This analytical pipeline could be employed in prospecting for infection biomarkers in human populations.
Publisher: Elsevier BV
Date: 09-2004
Publisher: Royal Society of Chemistry (RSC)
Date: 2003
DOI: 10.1039/B302360P
Abstract: It has been shown extensively, that chemometric investigations of 1H NMR spectra of rat urine taken from animals dosed with model toxins produce characteristic patterns of metabolic responses and that this permits the identification of biomarkers of toxic response and regeneration. To date, metabonomic methods have been mainly optimised for urine which contains mainly low molecular weight moieties, and thus a conventional 1-dimensional 1H NMR pulse sequence is an efficient means of obtaining information-rich data. In the case of biofluids such as blood plasma or serum, which contain a wide range of macromolecules the resonances of which can overlap with peaks from small molecule metabolites, the information giving rise to s le classification can be concealed in a conventional NMR spectrum andthis presents a different analytical challenge in terms of chemometric analysis of spectral profiles. Here, the use of other types of NMR data have been investigated and it is shown that by using spectra where the peak intensities are edited according to their molecular diffusion coefficients, it is possible to improve differentiation of control animals and those treated with the model hepatotoxin, alpha-naphthylisothiocyanate (ANIT). By using diffusion-edited spectroscopy, plasma lipid moieties are less attenuated than those from small endogenous metabolites and thus the toxin-induced changes to the lipoprotein profiles are more easily detectable.
Publisher: Springer Science and Business Media LLC
Date: 18-03-2015
DOI: 10.1038/IJO.2015.33
Publisher: Springer Science and Business Media LLC
Date: 25-05-2006
DOI: 10.1007/S11095-006-0025-Z
Abstract: In this review, the background to the approach known as metabonomics is provided, giving a brief historical perspective and summarizing the analytical and statistical techniques used. Some of the major applications of metabonomics relevant to pharmaceutical Research & Development are then reviewed including the study of various influences on metabolism, such as diet, lifestyle, and other environmental factors. The applications of metabonomics in drug safety studies are explained with special reference to the aims and achievements of the Consortium for Metabonomic Toxicology. Next, the role that metabonomics might have in disease diagnosis and therapy monitoring is provided with some ex les, and the concept of pharmacometabonomics as a way of predicting an in idual's response to treatment is highlighted. Some discussion is given on the strengths and weaknesses, opportunities of, and threats to metabonomics.
Publisher: Oxford University Press (OUP)
Date: 16-01-2029
Abstract: The inflammatory bowel diseases [IBD], Crohn’s disease and ulcerative colitis, are chronic, idiopathic gastrointestinal diseases. Although their precise aetiology is unknown, it is thought to involve a complex interaction between genetic predisposition and an abnormal host immune response to environmental exposures, probably microbial. Microbial dysbiosis has frequently been documented in IBD. Metabolomics [the study of small molecular intermediates and end products of metabolism in biological s les] provides a unique opportunity to characterize disease-associated metabolic changes and may be of particular use in quantifying gut microbial metabolism. Numerous metabolomic studies have been undertaken in IBD populations, identifying consistent alterations in a range of molecules across several biological matrices. This systematic review aims to summarize these findings. A comprehensive, systematic search was carried out using Medline and Embase. All studies were reviewed by two authors independently using predefined exclusion criteria. Sixty-four relevant papers were assessed for quality and included in the review. Consistent metabolic perturbations were identified, including increases in levels of branched chain amino acids and lipid classes across stool, serum, plasma and tissue biopsy s les, and reduced levels of microbially modified metabolites in both urine [such as hippurate] and stool [such as secondary bile acids] s les. This review provides a summary of metabolomic research in IBD to date, highlighting underlying themes of perturbed gut microbial metabolism and mammalian–microbial co-metabolism associated with disease status.
Publisher: American Chemical Society (ACS)
Date: 26-11-2009
DOI: 10.1021/AC801993M
Abstract: Human seminal fluid (HSF) is a complex mixture of reacting glandular metabolite and protein secretions that provides critical support functions in fertilization. We have employed 600-MHz (1)H NMR spectroscopy to compare and contrast the temporal biochemical and biophysical changes in HSF from infertile men with spinal cord injury compared to age-matched controls. We have developed new approaches to data analysis and visualization to facilitate the interpretation of the results, including the first application of the recently published K-STOCSY concept to a biofluid, enhancing the extraction of information on biochemically related metabolites and assignment of resonances from the major seminal protein, semenogelin. Principal components analysis was also applied to evaluate the extent to which macromolecules influence the overall variation in the metabolic data set. The K-STOCSY concept was utilized further to determine the relationships between reaction rates and metabolite levels, revealing that choline, N-acetylglucosamine, and uridine are associated with higher peptidase activity. The novel approach adopted here has the potential to capture dynamic information in any complex mixture of reacting chemicals including other biofluids or cell extracts.
Publisher: Elsevier BV
Date: 09-2017
Publisher: Springer Science and Business Media LLC
Date: 08-2020
Abstract: The combination of measurements of the W boson polarization in top quark decays performed by the ATLAS and CMS collaborations is presented. The measurements are based on proton-proton collision data produced at the LHC at a centre-of-mass energy of 8 TeV, and corresponding to an integrated luminosity of about 20 fb − 1 for each experiment. The measurements used events containing one lepton and having different jet multiplicities in the final state. The results are quoted as fractions of W bosons with longitudinal ( F 0 ), left-handed ( F L ), or right-handed ( F R ) polarizations. The resulting combined measurements of the polarization fractions are F 0 = 0 . 693 ± 0 . 014 and F L = 0 . 315 ± 0 . 011. The fraction F R is calculated from the unitarity constraint to be F R = − 0 . 008 ± 0 . 007. These results are in agreement with the standard model predictions at next-to-next-to-leading order in perturbative quantum chromodynamics and represent an improvement in precision of 25 (29)% for F 0 ( F L ) with respect to the most precise single measurement. A limit on anomalous right-handed vector ( V R ), and left- and right-handed tensor ( g L , g R ) tWb couplings is set while fixing all others to their standard model values. The allowed regions are [ − 0 . 11 , 0 . 16] for V R , [ − 0 . 08 , 0 . 05] for g L , and [ − 0 . 04 , 0 . 02] for g R , at 95% confidence level. Limits on the corresponding Wilson coefficients are also derived.
Publisher: American Chemical Society (ACS)
Date: 24-02-2023
Publisher: Elsevier
Date: 2014
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1MB05023K
Abstract: The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional (1)H and (13)C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major inter-species differences observed were in the phase II conjugation of extra-genomic metabolites the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.
Publisher: Elsevier BV
Date: 10-2016
Publisher: American Chemical Society (ACS)
Date: 12-02-2021
Publisher: Elsevier BV
Date: 08-1994
Abstract: Multivariate data analysis techniques have been used to compare 600-MHz 1H nuclear magnetic resonance (NMR) spectra of urine obtained from patients with inborn errors of metabolism (IEM) and urine obtained from healthy subjects. These spectra are very complex each contains many thousands of resonances with a high dynamic range. A consistent method of reducing this wealth of data to manageable proportions is presented as a two-stage process. Computer-based spectral descriptors are automatically generated and then reduced to two-dimensional maps for visualization of clustering. Data-scaling methodology has been developed to achieve complete separation between spectra from control adults and those from adult patients with independently diagnosed IEM. The methods were refined by relating IEM s les to the mean of the control s les and applying supervised learning techniques to identify descriptors contributing to class separation. This approach allowed separation of the various classes of IEM and achieved optimal separation of patients with cystinuria from those with oxalic aciduria the principal metabolites responsible for this separation were determined as lysine and glyoxalate. The methods developed were then extended by application to the more subtle problem of classifying urine collected from healthy subjects under different physiological conditions (i.e., pre- and post-exercise and in different stages of hydration) where, unlike the IEM case, any underlying biochemical differences were not known at the outset. Fluid-loaded and fluid-deprived s les could be partially separated as well as fluid-deprived and fluid-restored s les. Partial classification of s les on the basis of subject was also observed. Therefore, intersubject differences were liable to obscure the separation by physiological state. However, by relating each s le to a mean of the normal daily urine s les for the same person and applying a form of "range scaling" to exclude data which contributed least to class separation, improved classification of the hydration states resulted, from which it was possible to deduce those biochemical substances which were altered. These novel techniques for the data reduction and classification of NMR spectra make comprehensive use of all of the NMR spectral information and have clear potential to assist in clinical diagnosis.
Publisher: American Chemical Society (ACS)
Date: 19-05-2021
Publisher: American Chemical Society (ACS)
Date: 29-07-2006
DOI: 10.1021/PR060157B
Abstract: Irritable Bowel Syndrome (IBS) is a common multifactorial intestinal disorder for which the aetiology remains largely undefined. Here, we have used a Trichinella spiralis (T. spiralis)-induced model of post-infective IBS, and the effects of probiotic bacteria on gut dysfunction have been investigated using a metabonomic strategy. A total of 44 mice were ided into four groups: an uninfected control group and three T. spiralis-infected groups, one as infected control and the two other groups subsequently treated with either Lactobacillus paracasei (L. paracasei) NCC2461 in spent culture medium (SCM) or with L. paracasei-free SCM. Plasma, jejunal wall and longitudinal myenteric muscle s les were collected at day 21 post-infection. An NMR-based metabonomic approach characterized that the plasma metabolic profile of T. spiralis-infected mice showed an increased energy metabolism (lactate, citrate, alanine), fat mobilization (acetoacetate, 3-D-hydroxybutyrate, lipoproteins) and a disruption of amino acid metabolism due to increased protein breakdown, which were related to the intestinal hypercontractility. Increased levels of taurine, creatine and glycerophosphorylcholine in the jejunal muscles were associated with the muscular hypertrophy and disrupted jejunal functions. L. paracasei treatment normalized the muscular activity and the disturbed energy metabolism as evidenced by decreased glycogenesis and elevated lipid breakdown in comparison with untreated T. spiralis-infected mice. Changes in the levels of plasma metabolites (glutamine, lysine, methionine) that might relate to a modulation of immunological responses were also observed in the presence of the probiotic treatment. The work presented here suggests that probiotics may be beneficial in patients with IBS.
Publisher: Springer Science and Business Media LLC
Date: 17-07-2020
Publisher: Elsevier BV
Date: 04-2001
Publisher: American Society for Microbiology
Date: 22-12-2020
DOI: 10.1128/MSYSTEMS.00677-20
Abstract: Improved control of dietary confounders, through the use of an objective dietary assessment score, has uncovered further insights into the complex, multifactorial relationship between diet, exercise, the gut microbiome, and metabolism. Each of the models pertaining to diet healthiness, physical exercise, or a combination of both, displayed a distinct metabolic and functional microbial signature.
Publisher: Springer Science and Business Media LLC
Date: 28-10-2019
DOI: 10.1038/S41598-019-51901-7
Abstract: A number of bifidobacterial species are found at a particularly high prevalence and abundance in faecal s les of healthy breastfed infants, a phenomenon that is believed to be, at least partially, due to the ability of bifidobacteria to metabolize H uman M ilk O ligosaccharides (HMOs). In the current study, we isolated a novel strain of Bifidobacterium kashiwanohense , named APCKJ1, from the faeces of a four-week old breastfed infant, based on the ability of the strain to utilise the HMO component fucosyllactose. We then determined the full genome sequence of this strain, and employed the generated data to analyze fucosyllactose metabolism in B. kashiwanohense APCKJ1. Transcriptomic and growth analyses, combined with metabolite analysis, in vitro hydrolysis assays and heterologous expression, allowed us to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense APCKJ1. Homologs of the key genes for this metabolic pathway were identified in particular in infant-derived members of the Bifdobacterium genus, revealing the apparent niche-specific nature of this pathway, and allowing a broad perspective on bifidobacterial fucosyllactose and L-fucose metabolism.
Publisher: Elsevier BV
Date: 11-2010
Publisher: Proceedings of the National Academy of Sciences
Date: 21-10-2022
Abstract: Genome-wide association studies (GWASs) have identified genetic loci associated with the risk of Alzheimer’s disease (AD), but the molecular mechanisms by which they confer risk are largely unknown. We conducted a metabolome-wide association study (MWAS) of AD-associated loci from GWASs using untargeted metabolic profiling (metabolomics) by ultraperformance liquid chromatography–mass spectrometry (UPLC-MS). We identified an association of lactosylceramides (LacCer) with AD-related single-nucleotide polymorphisms (SNPs) in ABCA7 ( P = 5.0 × 10 −5 to 1.3 × 10 −44 ). We showed that plasma LacCer concentrations are associated with cognitive performance and genetically modified levels of LacCer are associated with AD risk. We then showed that concentrations of sphingomyelins, ceramides, and hexosylceramides were altered in brain tissue from Abca7 knockout mice, compared with wild type (WT) ( P = 0.049–1.4 × 10 −5 ), but not in a mouse model of amyloidosis. Furthermore, activation of microglia increases intracellular concentrations of hexosylceramides in part through induction in the expression of sphingosine kinase, an enzyme with a high control coefficient for sphingolipid and ceramide synthesis. Our work suggests that the risk for AD arising from functional variations in ABCA7 is mediated at least in part through ceramides. Modulation of their metabolism or downstream signaling may offer new therapeutic opportunities for AD.
Publisher: Elsevier BV
Date: 05-1995
DOI: 10.1016/0006-2952(95)93773-2
Abstract: Male Fischer 344 rats were dosed with 2-bromoethanamine hydrobromide (BEA, N = 6) or [1,2,2,-2H4]-bromoethanamine hydrobromide (BEA-d4, N = 6) at 150 mg/kg i.p. and urine was collected -24 to 0 hr pre-dose and at 0-2 hr, 2-4 hr, 4-8 hr and 8-12 hr post-dose (p.d.). Urine s les were analysed directly using 500 and 600 MHz 1H NMR and 92.1 MHz 2H NMR spectroscopy. The major observed effect of BEA treatment was the induction of transient elevations in urinary glutaric acid (GTA) and adipic acid (ADA) excretion lasting up to 24 hr p.d. Most of the GTA was excreted in the 0-8 hr p.d. with maximal rates of 100-120 microM/hr for each rat occurring between 4 and 8 hr p.d. in animals treated with BEA or BEA-d4. GTA and ADA were shown to be of endogenous origin as there was no detectable incorporation of the 2H label into either compound following treatment of rats with BEA-d4. Following BEA-treatment there was an initial decrease in the levels of urinary citrate, succinate, 2-oxoglutarate and trimethylamine-N-oxide. A subsequent recovery of citrate and succinate was noted following the onset of medullary nephropathy. The abnormal urinary metabolite profiles were similar to that observed in the urine of humans with glutaric aciduria type II (an inborn error of metabolism) caused by a lack of mitochondrial fatty acyl coenzyme A dehydrogenases indicating that BEA or its metabolites have similar metabolic consequences. The BEA metabolite aziridine was detected by 1H and 2H NMR spectroscopy of the urine 8 hr p.d. together with BEA itself and two novel metabolites 2-oxazolidone (OX) and 5-hydroxy-2-oxazolidone (HOX). The formation of OX requires the reaction of BEA with endogenous bicarbonate followed by a cyclisation reaction eliminating HBr. Dosing rats with authentic OX resulted in the excretion of HOX but did not cause glutaric or adipic aciduria indicating that either aziridine or BEA itself was responsible for the presumed defect in mitochondrial metabolism.
Publisher: Elsevier BV
Date: 10-2007
DOI: 10.1016/J.JPBA.2007.06.017
Abstract: The amount of active ingredient in 20 commercially sourced batches of praziquantel (PZQ) tablets was determined using a high-performance liquid chromatography-ultraviolet (HPLC-UV) assay in conjunction with an anthentic, lot of PZQ powder. The general composition of each batch of tablets was also examined by means of (1)H nuclear magnetic resonance (NMR) spectroscopy and the NMR data were subjected to pattern recognition analysis by means of principal component analysis. The HPLC-UV results showed that each batch of PZQ tablets contained approximately the required amount of PZQ (600 mg per tablet). The NMR analysis showed a high degree of compositional variation between manufacturers, which caused by variation in excipients, along with some batch-to-batch variation in the tablets from a single manufacturer. Additionally, the PZQ tablets from one manufacturer were found to have an extra component (methyl-4-hydroxybenzoate) that was not detected in the other preparations.
Publisher: Elsevier BV
Date: 1998
Publisher: Elsevier BV
Date: 11-1997
Publisher: American Chemical Society (ACS)
Date: 08-03-2019
Publisher: American Chemical Society (ACS)
Date: 13-09-2006
DOI: 10.1021/PR060265Y
Abstract: Dietary composition has been shown to influence metabolism and to impact on the prevalence and risk for certain diseases, but hitherto, there have been no systematic studies on the effects of dietary modulation of human metabolic phenotype (metabotype). Here, we have applied 1H NMR spectroscopy in combination with multivariate statistical analysis to characterize the effects of three diets: "vegetarian", "low meat", and "high meat" on the metabotype signature of human participants. Twelve healthy male participants (age range of 25-74 years) consumed each of these diets, in a randomized order, for continuous 15-day-periods with an intervening washout period between each diet of 7 days duration. Each participant provided three consecutive 24-hour urine collections on days 13, 14, and 15 of each dietary period, and 1H NMR spectra were acquired on all s les. Pattern recognition analysis allowed differentiation of the characteristic metabolic signatures of the diets with creatine, carnitine, acetylcarnitine, and trimethylamine-N-oxide (TMAO) being elevated in the high-meat consumption period. Application of orthogonal projection to latent structure discriminant analysis (O-PLS-DA) allowed the low-meat diet and vegetarian diet signatures to be characterized, and p-hydroxyphenylacetate (a microbial mammalian cometabolite) was higher in the vegetarian than meat diet s les, signaling an alteration of the bacterial composition or metabolism in response to diet. This work shows the potential for the routine use of metabonomics in nutritional and epidemiological studies, in characterizing and predicting the metabolic effects and the influence of diet on human metabotypes.
Publisher: Elsevier BV
Date: 07-2016
Publisher: Elsevier BV
Date: 08-2015
Publisher: Wiley
Date: 20-04-2005
DOI: 10.1002/MRM.20447
Abstract: High-resolution magic angle spinning (HRMAS) (1)H NMR spectroscopy has been applied to the biochemical characterization of specific brain regions in rats in order to establish baseline levels of tissue metabolite profiles with which to compare models of neuropathology or toxic lesion. Cores of tissue (20 mg) from the brain stem, cerebellum, frontal cortex, and hippoc us were obtained from histologically defined coronal slices of brain from 18 male Sprague-Dawley rats. HRMAS (1)H NMR spectra were acquired for each of the regions s led and the degree of inters le variability, as assessed by principal components analysis and discriminant analysis by projection to latent structure was found to be low. Clear region-specific differences in the biochemical profiles were observed using both comparison of metabolite ratios and/or pattern recognition methods. Relatively low concentrations of GABA in the cerebellum, high concentrations of taurine and N-acetylaspartate in the cortex, and high levels of choline, glycerophosphocholine, and phosphocholine in the hippoc us predominantly influenced the classification of the different brain regions. Additionally, N-acetylaspartylglutamate was detected in the brain stem, but was largely absent from the other regions examined. Such analyses provide a baseline reference for further HRMAS NMR spectroscopic studies to monitor disease and pharmacological insults in specific regions of the brain.
Publisher: MDPI AG
Date: 04-12-2020
Abstract: Background: Overweight and obesity amongst women of reproductive age are increasingly common in developed economies and are shown to adversely affect birth outcomes and both childhood and adulthood health risks in the offspring. Metabolic profiling in conditions of overweight and obesity in pregnancy could potentially be applied to elucidate the molecular basis of the adverse effects of gestational weight gain (GWG) and postpartum weight loss (WL) on future risks for cardiovascular disease (CVD) and other chronic diseases. Methods: Biofluid s les were collected from 114 ethnically erse pregnant women with body mass index (BMI) between 25 and 40 kg/m2 from Chicago (US), as part of a randomized lifestyle intervention trial (Maternal Offspring Metabolics: Family Intervention Trial NCT01631747). At 15 weeks, 35 weeks of gestation, and at 1 year postpartum, the blood plasma lipidome and metabolic profile of urine s les were analyzed by liquid chromatography mass spectrometry (LC-MS) and 1H nuclear magnetic resonance spectroscopy (1H NMR) respectively. Results: Urinary 4-deoxyerythronic acid and 4-deoxythreonic acid were found to be positively correlated to BMI. Seventeen plasma lipids were found to be associated with GWG and 16 lipids were found to be associated with WL, which included phosphatidylinositols (PI), phosphatidylcholines (PC), lysophospholipids (lyso-), sphingomyelins (SM) and ether phosphatidylcholine (PC-O). Three phospholipids found to be positively associated with GWG all contained palmitate side-chains, and amongst the 14 lipids that were negatively associated with GWG, seven were PC-O. Six of eight lipids found to be negatively associated with WL contained an 18:2 fatty acid side-chain. Conclusions: Maternal obesity was associated with characteristic urine and plasma metabolic phenotypes, and phospholipid profile was found to be associated with both GWG and postpartum WL in metabolically healthy pregnant women with overweight/obesity. Postpartum WL may be linked to the reduction in the intake of linoleic acid/conjugated linoleic acid food sources in our study population.
Publisher: Elsevier BV
Date: 10-1994
DOI: 10.1016/0731-7085(94)00073-5
Abstract: A general method of automatically reducing NMR spectra to provide numerical descriptors of s les has been developed and investigated. These descriptors can be used as input to pattern recognition or multivariate algorithms for s le classification. The methods have been tested using 600 MHz one-dimensional 1H NMR spectra of biofluids which are complex mixtures. The approach is, in principle, applicable to multidimensional and heteronuclear NMR spectra and to other types of liquid s les such as oils and foodstuffs as well as to situations such as 1H or 31P NMR in vivo and solid state NMR in drug formulation analysis. The method relies upon apportioning the information in the spectra to in idual contiguous segments and allowing specified regions of the spectra to be omitted. Three approaches, based on the number of peaks, the summed peak heights and the summed peak areas respectively in each segment, have been tested. The effect of segment width and overlap and the effects of manipulation of the NMR spectra have been evaluated in terms of the classification of the s les using principal components analysis. A simple method of generating NMR based spectral descriptors for object classification is thus proposed.
Publisher: Oxford University Press (OUP)
Date: 12-09-2017
Publisher: EMBO
Date: 2008
DOI: 10.1038/MSB.2008.56
Publisher: American Chemical Society (ACS)
Date: 13-12-2011
DOI: 10.1021/AC102523Q
Abstract: Hydrophilic interaction ultra performance liquid chromatography (HILIC-UPLC) permits the analysis of highly polar metabolites, providing complementary information to reversed-phase (RP) chromatography. HILIC-UPLC-TOF-MS was investigated for the global metabolic profiling of rat urine s les generated in an experimental hepatotoxicity study of galactosamine (galN) and the concomitant investigation of the protective effect of glycine. Within-run repeatability and stability over a large s le batch (>200 s les, 60 h run-time) was assessed through the repeat analysis of a quality control s le. Following system equilibration, excellent repeatability was observed in terms of retention time (CV < 1.7%), signal intensity (CV < 14%), and mass variability (<0.005 amu), providing a good measure of reproducibility. Classification of urinary metabolic profiles according to treatment was observed, with significant changes in specific metabolites after galN exposure, including increased urocanic acid, N-acetylglucosamine, and decreased 2-oxoglutarate. A novel finding from this HILIC-UPLC-MS approach was elevated urinary tyramine in galN-treated rats, reflecting disturbed amino acid metabolism. These results show HILIC-UPLC-MS to be a promising method for global metabolic profiling, demonstrating high within-run repeatability, even over an extended run time. Retention of polar endogenous analytes and xenobiotic metabolites was improved compared with RP studies, including galN, N-acetylglucosamine, oxoglutarate, and urocanic acid, enhancing metabolome coverage and potentially improving biomarker discovery.
Publisher: Elsevier BV
Date: 05-2021
Publisher: No publisher found
Date: 1999
DOI: 10.1002/(SICI)1522-2683(19991201)20:18<3647::AID-ELPS3647>3.0.CO;2-%23
Publisher: Elsevier
Date: 2007
Publisher: American Chemical Society (ACS)
Date: 03-05-2007
DOI: 10.1021/PR060412S
Abstract: The biochemical effects of acute and chronic psychological stress have been investigated in male Sprague-Dawley rats using a combination of 1H NMR spectral analysis of plasma and conventional hematological analyses. Animals were subjected to 35 consecutive days of 6-h sessions of stress, and following a 9 day break, were stressed for a further 6-h period. Plasma s les were collected at 0, 1, 3, and 6 h on days 1, 9, 21, 35, and 44, measured using 600 MHz 1H NMR spectroscopy, and analyzed by Principal Components Analysis. Time-dependent biochemical effects of psychological stress on a range of endogenous metabolites were evident and were correlated with the intensity of the stress response as defined by corticosterone and hematological parameters. Following acute stress, increases in the levels of glucose and ketone bodies, and decreases in the levels of acetate, alanine, isoleucine, lactate, leucine, valine, and lipoproteins, were observed. Chronic stress-induced increases in plasma levels of alanine, lactate (day 9), and leucine, valine, and choline (day 44) and decreases in acetate (day 9) and lipoprotein concentrations were observed. Positive correlations between plasma corticosterone level and glucose and glycerol, and between plasma lipoprotein concentrations and hemoglobin levels, were established using Projection to Latent Structures (PLS) analysis. This study indicates the potential of using NMR-based metabonomic strategies for the characterization of endogenous metabolic perturbations induced by psychological stressors and lifestyle choices.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 12-2013
DOI: 10.1161/HYPERTENSIONAHA.113.01810
Abstract: Black compared with non-Hispanic white Americans have higher systolic and diastolic blood pressure and rates of prehypertension/hypertension. Reasons for these adverse findings remain obscure. Analyses here focused on relations of foods/nutrients/urinary metabolites and higher black blood pressure for 369 black compared with 1190 non-Hispanic white Americans aged 40 to 59 years from 8 population s les. Multiple linear regression, standardized data from four 24-hour dietary recalls per person, two 24-hour urine collections, and 8 blood pressure measurements were used to quantitate the role of foods, nutrients, and metabolites in higher black blood pressure. Compared with non-Hispanic white Americans, blacks’ average systolic/diastolic pressure was higher by 4.7/3.4 mm Hg (men) and 9.0/4.8 mm Hg (women). Control for higher body mass index of black women reduced excess black systolic/diastolic pressure to 6.8/3.8 mm Hg. Lesser intake of vegetables, fruits, grains, vegetable protein, glutamic acid, starch, fiber, minerals, and potassium, and higher intake of processed meats, pork, eggs, and sugar-sweetened beverages, along with higher cholesterol and higher Na/K ratio, related to in higher black blood pressure. Control for 11 nutrient and 10 non-nutrient correlates reduced higher black systolic/diastolic pressure to 2.3/2.3 mm Hg (52% and 33% reduction in men) and to 5.3/2.8 mm Hg (21% and 27% reduction in women). Control for foods/urinary metabolites had little further influence on higher black blood pressure. Less favorable multiple nutrient intake by blacks than non-Hispanic white Americans accounted, at least in part, for higher black blood pressure. Improved dietary patterns can contribute to prevention/control of more adverse black blood pressure levels.
Publisher: Elsevier BV
Date: 08-2003
Publisher: American Chemical Society (ACS)
Date: 10-2001
DOI: 10.1021/TX010067F
Abstract: We present here a novel integrative metabonomic approach to probe toxic effects of drugs in experimental animals using alpha-naphthylisothiocyanate (ANIT) as a model hepatotoxicant. Male Han-Wistar rats were dosed with ANIT (150 mg/kg, n = 25), and plasma and liver s les were collected for NMR and magic-angle spinning (MAS) NMR spectroscopy at 3, 7, 24, 31, and 168 h postdosing. Urine was collected continuously for 3 days prior to dosing and up to 168 h postdose. Histopathology and plasma clinical chemistry was also performed at all time points. Liver s les were analyzed either intact by 600 MHz 1H MAS NMR techniques or using high resolution (liquid state) 1H NMR of water-acetonitrile extracts. These data were related to sequential 1H NMR measurements in urine and plasma using pattern recognition methods. 1D 1H NMR spectra were data-reduced and analyzed using principal components analysis (PCA) to show the time-dependent biochemical variations induced by ANIT toxicity. From the eigenvector loadings of the PCA, those regions of the 1H NMR spectra and hence the combinations of endogenous metabolites marking the main phase of the toxic episode were identified. The ANIT-induced biochemical manifestations included a hepatic lipidosis associated with hyperlipidaemia hyperglycaemia and glycosuria increased urinary excretion of taurine and creatine a shift in energy metabolism characterized by increased plasma ketone bodies with reduced urinary excretion of tricarboxylic acid cycle intermediates and raised hepatic bile acids leading to bile aciduria. The integration of metabolic data derived from several sources gives a holistic approach to the study of time-related toxic effects in the intact system and enables the characterization of key metabolic effects during the development and recovery from a toxic lesion.
Publisher: Springer Science and Business Media LLC
Date: 11-07-2014
Publisher: Elsevier BV
Date: 05-1996
DOI: 10.1016/0742-8413(95)02105-1
Abstract: The biochemical effects and comparative nephroxicity of mercury II chloride (HgCl2) dosed at 0.75 mg/kg i.p. was investigated in the Fisher 344 rat (F344) and Mastomys natalensis using high resolution 1H nuclear magnetic resonance (NMR) spectroscopy of urine, histopathology and clinical chemical techniques. The effects of HgCl2 treatment were followed for up to 4 days post-dosing (p.d.). In F344 rats there was extensive proximal tubular damage and renal cortical necrosis together with elevated levels of urinary gamma-glutamyl transpeptidase (gamma GT), alkaline phosphatase (ALP) and lactate dehydrogenase (LDH). The 1H NMR spectra of urine obtained from Hg-treated F344 rats also showed increased levels of glucose, alanine, lactate, valine and hippurate (0-48h p.d.) with decreased levels of citrate, succinate and 2-oxoglutarate (24-48h p.d.). Mastomys were found to be highly resistant to HgCl2 toxicity at 0.75 mg/kg and the histological appearance of the renal cortex of treated animals was virtually identical to controls. There were no elevations in urinary ALP, gamma GT and LDH activities in HgCl2-treated Mastomys and there were no biochemical abnormalities in low MW components of Mastomys urine following HgCl2-treatment, as shown by 1H NMR spectroscopy. Urinary gamma GT activity was found to be much higher in F344 rats than Mastomys. Since gamma GT activity is involved in the tubular reabsorption of Hg2+, the lower levels of gamma GT in Mastomys might partially account for the lower toxicity of Hg2+ in this species.
Publisher: Springer Science and Business Media LLC
Date: 05-02-2021
Publisher: Cold Spring Harbor Laboratory
Date: 05-06-2020
DOI: 10.1101/2020.06.04.20046292
Abstract: The composition and metabolic function of the gut microbiome in the elite athlete differs from that of non-athletes. However, short-term fitness improvement in the sedentary adult does not replicate the microbiome characteristics seen in the athlete. Whether sustained fitness improvement over a prolonged period can lead to pronounced and beneficial alteration in the gut microbiome is unknown. The objective was to explore this possibility. This study used a repeated-measures, case-study approach to explore changes in the gut microbiome of two unfit volunteers undertaking progressive exercise training over a 6-month period. Training was to culminate in the completion of a marathon or Olympic-distance triathlon. The volunteers were s led every two weeks for six months and microbiome, metabolome, diet, body composition, and cardiorespiratory fitness data were recorded. Both participants completed their respective goals with improved body composition and fitness parameters over the training period. Increases in α- ersity of the gut microbiota occurred with sustained training and fluctuations occurred in response to training events (e.g., injury, illness and training peaks). Participants’ fat mass and BMI reduced during the study and was significantly associated with increased urinary measurements of N-methyl nicotinate (P value 0.001) and hippurate (P value 0.05), and decreased phenylacetylglutamine (P value 0.05). These results suggest that sustained fitness improvements result in alterations to gut microbiota and physiologically-relevant metabolites. This study provides longitudinal analysis of the response of the gut microbiome to real-world events during progressive fitness training, including intercurrent illness and injury.
Publisher: American Chemical Society (ACS)
Date: 18-11-2015
DOI: 10.1021/ACS.ANALCHEM.5B02794
Abstract: Lipid mediators, highly bioactive compounds synthesized from polyunsaturated fatty acids (PUFAs), have a fundamental role in the initiation and signaling of the inflammatory response. Although extensively studied in isolation, only a limited number of analytical methods offer a comprehensive coverage of the oxylipin synthetic cascade applicable to a wide range of human biofluids. We report the development of an ultrahigh-performance liquid chromatography-electrospray ionization triple quadrupole mass spectrometry (UHPLC-MS) assay to quantify oxylipins and their PUFA precursors in 100 μL of human serum, plasma, urine, and cell culture supernatant. A single 15 min UHPLC run enables the quantification of 43 oxylipins and 5 PUFAs, covering pro and anti-inflammatory lipid mediators synthesized across the cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP450) pathways. The method was validated in multiple biofluid matrixes (serum, plasma, urine, and cell supernatant) and suppliers, ensuring its suitability for large scale metabonomic studies. The approach is accurate, precise, and reproducible (RSD < 15%) over multiple days and concentrations. Very high sensitivity is achieved with limits of quantification inferior to picograms for the majority of analytes (0.05-125 pg) and linear range spanning up to 5 orders of magnitude. This enabled the quantification of the great majority of these analytes at their low endogenous level in human biofluids. We successfully applied the procedure to in iduals undergoing a fasting intervention oxylipin profiles highlighted significantly altered PUFA and inflammatory profiles in accordance with previously published studies as well as offered new insight on the modulation of the biosynthetic cascade responsible for the regulation of oxylipins.
Publisher: Wiley
Date: 27-04-2011
Publisher: American Chemical Society (ACS)
Date: 11-08-2010
DOI: 10.1021/PR1003449
Publisher: Public Library of Science (PLoS)
Date: 22-08-2007
Publisher: Royal Society of Chemistry (RSC)
Date: 15-11-2002
DOI: 10.1039/B208254N
Abstract: The pharmaceutical industry has embraced emerging technologies such as genomics, proteomics and metabonomics over the past decade with a view to minimizing attrition and expanding drug development pipelines. Metabonomic technology, based on the multivariate analysis of complex biological profiles generated from spectroscopic instruments, has enabled the construction of successful expert systems for toxicity screening and disease diagnosis. Here we describe the evolution of chemometric and bioinformatic methodologies to accommodate the multi- and megavariate data generated by high resolution NMR spectroscopy of biofluids, tissues and cell cultures and explore their potential role in mining, modeling and predicting metabolic data.
Publisher: Oxford University Press (OUP)
Date: 05-01-2012
DOI: 10.1093/AJE/KWR292
Publisher: Oxford University Press (OUP)
Date: 08-08-2017
Abstract: Infertility is a complex disorder with significant medical, psychological and financial consequences for patients. With live-birth rates per cycle below 30% and a drive from the Human Fertilisation and Embryology Authority (HFEA) to encourage single embryo transfer, there is significant research in different areas aiming to improve success rates of fertility treatments. One such area is investigating the causes of infertility at a molecular level, and metabolomics techniques provide a platform for studying relevant biofluids in the reproductive tract. The aim of this systematic review is to examine the recent findings for the potential application of metabolomics to female reproduction, specifically to the metabolomics of follicular fluid (FF), embryo culture medium (ECM) and endometrial fluid. To our knowledge no other systematic review has investigated this topic. English peer-reviewed journals on PubMed, Science Direct, SciFinder, were systematically searched for studies investigating metabolomics and the female reproductive tract with no time restriction set for publications. Studies were assessed for quality using the risk of bias assessment and ROBIN-I. There were 21 studies that met the inclusion criteria and were included in the systematic review. Metabolomic studies have been employed for the compositional analysis of various biofluids in the female reproductive tract, including FF, ECM, blastocoele fluid and endometrial fluid. There is some weak evidence that metabolomics technologies studying ECM might be able to predict the viability of in idual embryos and implantation rate better than standard embryo morphology, However these data were not supported by randomized the controlled trials (RCTs) which showed no evidence that using metabolomics is able to improve the most important reproductive outcomes, such as clinical pregnancy and live-birth rates. This systematic review provides guidance for future metabolomic studies on biofluids of the female reproductive tract, with a summary of the current findings, promise and pitfalls in metabolomic techniques. The approaches discussed can be adapted by other metabolomic studies. A range of sophisticated modern metabolomic techniques are now more widely available and have been applied to the analysis of the female reproductive tract. However, this review has revealed the paucity of metabolomic studies in the field of fertility and the inconsistencies of findings between different studies, as well as a lack of research examining the metabolic effects of various gynecological diseases. By incorporating metabolomic technology into an increased number of well designed studies, a much greater understanding of infertility at a molecular level could be achieved. However, there is currently no evidence for the use of metabolomics in clinical practice to improve fertility outcomes.
Publisher: Elsevier BV
Date: 08-1993
DOI: 10.1016/0731-7085(93)80171-V
Abstract: Extensive assignments of resonances in the 600 MHz 1H-NMR spectra of cerebrospinal fluid are reported. These have been achieved by the measurement of a combination of two-dimensional experiments comprising homonuclear J-resolved, COSY45, and double-quantum filtered COSY (DQCOSY) spectra. By these means the previous total of 18 endogenous metabolites, of which in general only selected resonances have been assigned, has been augmented to 46 molecules including all of the resonances of both alpha- and beta-anomers of glucose. With only a few exceptions all resonances have been assigned for all of the metabolites. In addition, the effect of freeze-drying on the 600 MHz 1H-NMR spectrum of human cerebrospinal fluid (CSF) is presented using both lyophilization with reconstitution into either H2O or D2O. Freeze-drying and reconstitution into H2O causes a significant sharpening of many small molecule resonances, including notably those of glutamate and glutamine as well as other amino acids and in addition causes the loss of volatile components, principally acetone. Further exchange of the H2O solvent by D2O causes no additional changes in the spectra.
Publisher: Wiley
Date: 28-01-2015
DOI: 10.1111/EVJ.12333
Abstract: Metabonomics is emerging as a powerful tool for disease screening and investigating mammalian metabolism. This study aims to create a metabolic framework by producing a preliminary reference guide for the normal equine metabolic milieu. To metabolically profile plasma, urine and faecal water from healthy racehorses using high resolution (1) H-nuclear magnetic resonance (NMR) spectroscopy and to provide a list of dominant metabolites present in each biofluid for the benefit of future research in this area. This study was performed using 7 Thoroughbreds in race training at a single time point. Urine and faecal s les were collected noninvasively and plasma was obtained from s les taken for routine clinical chemistry purposes. Biofluids were analysed using (1) H-NMR spectroscopy. Metabolite assignment was achieved via a range of one- and 2-dimensional experiments. A total of 102 metabolites were assigned across the 3 biological matrices. A core metabonome of 14 metabolites was ubiquitous across all biofluids. All biological matrices provided a unique window on different aspects of systematic metabolism. Urine was the most populated metabolite matrix with 65 identified metabolites, 39 of which were unique to this biological compartment. A number of these were related to gut microbial host cometabolism. Faecal s les were the most metabolically variable between animals acetate was responsible for the majority (28%) of this variation. Short-chain fatty acids were the predominant features identified within this biofluid by (1) H-NMR spectroscopy. Metabonomics provides a platform for investigating complex and dynamic interactions between the host and its consortium of gut microbes and has the potential to uncover markers for health and disease in a variety of biofluids. Inherent variation in faecal extracts along with the relative abundance of microbial-mammalian metabolites in urine and invasive nature of plasma s ling, infers that urine is the most appropriate biofluid for the purposes of metabonomic analysis.
Publisher: Elsevier BV
Date: 08-2020
Publisher: Springer Science and Business Media LLC
Date: 16-01-2009
DOI: 10.1007/S11064-008-9904-5
Abstract: 3-Nitropropionic acid (3-NP)-induced neurotoxicity can be used as a model for the genetic neurodegenerative disorder Huntington's disease (HD). A metabolic profiling strategy was adopted to explore the biochemical consequences of 3-NP administered to rats in specific brain regions. (1)H NMR spectroscopy was used to characterize the metabolite composition of several brain regions following 3-NP-intoxication. Dose-dependent increases in succinate levels were observed in all neuroanatomical regions, resulting from the 3-NP-induced inhibition of succinate dehydrogenase. Global decreases in taurine and GABA were observed in the majority of brain regions, whereas altered lipid profiles were observed only in the globus pallidus and dorsal striatum. Depleted phosphatidylcholine and elevated glycerol levels, which are indicative of apoptosis, were also observed in the frontal cortex of the 3-NP model. Many of the metabolic anomalies are consistent with those reported in HD. The 3-NP-induced model of HD provides a means of monitoring potential mechanisms of pathology and therapeutic response for drug interventions, which can be efficiently assessed using metabolic profiling strategies.
Publisher: Elsevier BV
Date: 05-2018
DOI: 10.1016/J.EJVS.2018.01.027
Abstract: Deep vein thrombosis (DVT) is a major health problem, responsible for significant morbidity and mortality. The identification of a simple and effective diagnostic biomarker of DVT remains a challenge. Metabolomics have recently emerged as a new powerful scientific tool to characterise metabolic phenotypes of complex diseases and investigate small molecules in biofluids. The aim of the study was to identify the blood and vein wall metabolomic signature of DVT in a murine experimental model. An established inferior vena cava ligation mouse model of DVT (n=10) was used and compared with sham surgery controls (n=10). Comprehensive untargeted metabolic profiling of serum and vein wall extracts was undertaken using liquid chromatography coupled mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy. Multivariate and univariate statistical analysis demonstrated a differential metabolic profile when comparing DVT mice and control animals. Serum from DVT mice was characterised by differential concentrations of adenosine (decreased in DVT mice 9.6 fold), adenine (decreased 10.6 fold), and tricyclic acid cycle (TCA) intermediates, including citrate, succinate, and fumarate (1.5, 2.3, and 2.8 fold decreases, respectively). l-carnitine was found to be of greater abundance in the serum of DVT animals (67.0 fold change). A number of lipid moiety classes, including sphingomyelins, phosphatidylcholines, and triglycerides, were differentially abundant. Several metabolites were found in vein wall, including acetylcarnitine (increased in DVT mice 1.9 fold), adenosine (increased 2.2 fold), and ceramide (increased 2.7 fold). Correlation analysis illustrated the biochemical relationships between assigned metabolites, with the discriminatory molecules being highly correlated with each other, in both serum and vein wall. The present findings demonstrate that metabolic dysregulations in DVT centre on energy metabolism, sphingolipid, and adenosine metabolism, representing a DVT specific metabolite signature in a murine experimental model.
Publisher: Springer Science and Business Media LLC
Date: 30-01-2023
DOI: 10.1038/S41590-022-01380-2
Abstract: The biology driving in idual patient responses to severe acute respiratory syndrome coronavirus 2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data and covering a year after disease onset, from 215 infected in iduals with differing disease severities. Our analyses revealed distinct ‘systemic recovery’ profiles, with specific progression and resolution of the inflammatory, immune cell, metabolic and clinical responses. In particular, we found a strong inter-patient and intra-patient temporal covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites, which highlighted candidate immunologic and metabolic pathways influencing the restoration of homeostasis, the risk of death and that of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool shiny.mrc-bsu.cam.ac.uk/apps/covid-19-systemic-recovery-prediction-app , designed to test our findings prospectively.
Publisher: BMJ
Date: 10-04-2019
DOI: 10.1136/GUTJNL-2019-318424
Abstract: To investigate the underlying mechanisms behind changes in glucose homeostasis with delivery of propionate to the human colon by comprehensive and coordinated analysis of gut bacterial composition, plasma metabolome and immune responses. Twelve non-diabetic adults with overweight and obesity received 20 g/day of inulin-propionate ester (IPE), designed to selectively deliver propionate to the colon, a high-fermentable fibre control (inulin) and a low-fermentable fibre control (cellulose) in a randomised, double-blind, placebo-controlled, cross-over design. Outcome measurements of metabolic responses, inflammatory markers and gut bacterial composition were analysed at the end of each 42-day supplementation period. Both IPE and inulin supplementation improved insulin resistance compared with cellulose supplementation, measured by homeostatic model assessment 2 (mean±SEM 1.23±0.17 IPE vs 1.59±0.17 cellulose, p=0.001 1.17±0.15 inulin vs 1.59±0.17 cellulose, p=0.009), with no differences between IPE and inulin (p=0.272). Fasting insulin was only associated positively with plasma tyrosine and negatively with plasma glycine following inulin supplementation. IPE supplementation decreased proinflammatory interleukin-8 levels compared with cellulose, while inulin had no impact on the systemic inflammatory markers studied. Inulin promoted changes in gut bacterial populations at the class level (increased Actinobacteria and decreased Clostridia) and order level (decreased Clostridiales) compared with cellulose, with small differences at the species level observed between IPE and cellulose. These data demonstrate a distinctive physiological impact of raising colonic propionate delivery in humans, as improvements in insulin sensitivity promoted by IPE and inulin were accompanied with different effects on the plasma metabolome, gut bacterial populations and markers of systemic inflammation.
Publisher: Wiley
Date: 06-11-2009
DOI: 10.1002/MRC.2485
Abstract: The time-related metabolic effects of 1-cyano-2-hydroxy-3-butene (CHB, crambene), a naturally occurring nitrile and experimental model toxin causing exocrine pancreatitis, have been investigated in rats using high-resolution NMR spectroscopy of urine and serum in combination with pattern recognition analysis. Rats were administered CHB subcutaneously in two doses, 15 mg/kg dose (n = 10) and 150 mg/kg (n = 10), and conventional histopathology and clinical chemistry assessments were performed. Urine s les were collected at - 16 and 0, 8, 24, 48, 72, 96, 120, 144 and 168 h postdosing and serum s les were collected at 48 and 168 h postdosing these were analyzed using a range of 1D and 2D NMR spectroscopic methods. The metabolic profile perturbations seen throughout the time-course of the study are described, and the application of the spectral correlation technique Statistical TOtal Correlation SpectroscopY (STOCSY) to detect both structural and novel toxicological connectivities between xenobiotic and endogenous metabolite signals is illustrated for the first time. As a result, it is suggested that the STOCSY approach may be of wider application in the identification of toxic versus nontoxic metabolites in drug metabolism studies.
Publisher: Elsevier
Date: 2016
Publisher: American Society for Microbiology
Date: 29-04-2011
Abstract: The gut microbiota enhances the host’s metabolic capacity for processing nutrients and drugs and modulate the activities of multiple pathways in a variety of organ systems. We have probed the systemic metabolic adaptation to gut colonization for 20 days following exposure of axenic mice ( n = 35) to a typical environmental microbial background using high-resolution 1 H nuclear magnetic resonance (NMR) spectroscopy to analyze urine, plasma, liver, kidney, and colon (5 time points) metabolic profiles. Acquisition of the gut microbiota was associated with rapid increase in body weight (4%) over the first 5 days of colonization with parallel changes in multiple pathways in all compartments analyzed. The colonization process stimulated glycogenesis in the liver prior to triggering increases in hepatic triglyceride synthesis. These changes were associated with modifications of hepatic Cyp8b1 expression and the subsequent alteration of bile acid metabolites, including taurocholate and tauromuricholate, which are essential regulators of lipid absorption. Expression and activity of major drug-metabolizing enzymes (Cyp3a11 and Cyp2c29) were also significantly stimulated. Remarkably, statistical modeling of the interactions between hepatic metabolic profiles and microbial composition analyzed by 16S rRNA gene pyrosequencing revealed strong associations of the Coriobacteriaceae family with both the hepatic triglyceride, glucose, and glycogen levels and the metabolism of xenobiotics. These data demonstrate the importance of microbial activity in metabolic phenotype development, indicating that microbiota manipulation is a useful tool for beneficially modulating xenobiotic metabolism and pharmacokinetics in personalized health care. IMPORTANCE Gut bacteria have been associated with various essential biological functions in humans such as energy harvest and regulation of blood pressure. Furthermore, gut microbial colonization occurs after birth in parallel with other critical processes such as immune and cognitive development. Thus, it is essential to understand the bidirectional interaction between the host metabolism and its symbionts. Here, we describe the first evidence of an in vivo association between a family of bacteria and hepatic lipid metabolism. These results provide new insights into the fundamental mechanisms that regulate host-gut microbiota interactions and are thus of wide interest to microbiological, nutrition, metabolic, systems biology, and pharmaceutical research communities. This work will also contribute to developing novel strategies in the alteration of host-gut microbiota relationships which can in turn beneficially modulate the host metabolism.
Publisher: MDPI AG
Date: 20-01-2021
Abstract: The incidence of neuroendocrine neoplasms (NEN) is increasing, but established biomarkers have poor diagnostic and prognostic accuracy. Here, we aim to define the systemic metabolic consequences of NEN and to establish the diagnostic utility of proton nuclear magnetic resonance spectroscopy (1H-NMR) for NEN in a prospective cohort of patients through a single-centre, prospective controlled observational study. Urine s les of 34 treatment-naïve NEN patients (median age: 59.3 years, range: 36–85): 18 had pancreatic (Pan) NEN, of which seven were functioning 16 had small bowel (SB) NEN 20 age- and sex-matched healthy control in iduals were analysed using a 600 MHz Bruker 1H-NMR spectrometer. Orthogonal partial-least-squares-discriminant analysis models were able to discriminate both PanNEN and SBNEN patients from healthy control (Healthy vs. PanNEN: AUC = 0.90, Healthy vs. SBNEN: AUC = 0.90). Secondary metabolites of tryptophan, such as trigonelline and a niacin-related metabolite were also identified to be universally decreased in NEN patients, while upstream metabolites, such as kynurenine, were elevated in SBNEN. Hippurate, a gut-derived metabolite, was reduced in all patients, whereas other gut microbial co-metabolites, trimethylamine-N-oxide, 4-hydroxyphenylacetate and phenylacetylglutamine, were elevated in those with SBNEN. These findings suggest the existence of a new systems-based neuroendocrine circuit, regulated in part by cancer metabolism, neuroendocrine signalling molecules and gut microbial co-metabolism. Metabonomic profiling of NEN has diagnostic potential and could be used for discovering biomarkers for these tumours. These preliminary data require confirmation in a larger cohort.
Publisher: American Chemical Society (ACS)
Date: 13-05-2014
DOI: 10.1021/AC500161K
Publisher: Wiley
Date: 03-11-2017
DOI: 10.1002/MRC.4669
Abstract: NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: Raw data are not made available instead, the information is slimed down into a string of characters (the list of peaks). Although historical limitations of technology explain this practice, it is not acceptable in the era of Internet. The idea of modernizing the strategy for sharing NMR data is not new, and some repositories exist, but sharing raw data is still not an established practice. Here, we present a powerful toolbox built on recent technologies that runs inside the browser and provides a means to store, share, analyse, and interact with original NMR data. Stored spectra can be streamlined into the publication pipeline, to improve the revision process for instance. The set of tools is still basic but is intended to be extended. The project is open source under the Massachusetts Institute of Technology (MIT) licence.
Publisher: Elsevier
Date: 2018
Publisher: Oxford University Press (OUP)
Date: 14-11-2009
DOI: 10.1093/BIOINFORMATICS/BTN586
Abstract: Motivation: Metabolic profiles derived from high resolution 1H-NMR data are complex, therefore statistical and machine learning approaches are vital for extracting useful information and biological insights. Focused modelling on targeted subsets of metabolites and s les can improve the predictive ability of models, and techniques such as genetic algorithms (GAs) have a proven utility in feature selection problems. The Consortium for Metabonomic Toxicology (COMET) obtained temporal NMR spectra of urine from rats treated with model toxins and stressors. Here, we develop a GA approach which simultaneously selects sets of s les and spectral regions from the COMET database to build robust, predictive classifiers of liver and kidney toxicity. Results: The results indicate that using simultaneous s le and variable selection improved performance by over 9% compared with either method alone. Simultaneous selection also halved computation time. Successful classifiers repeatedly selected particular variables indicating that this approach can aid defining biomarkers of toxicity. Novel visualizations of the results from multiple computations were developed to aid the interpretability of which s les and variables were frequently selected. This method provides an efficient way to determine the most discriminatory variables and s les for any post-genomic dataset. Availability: GA code available from www1.imperial.ac.uk/medicine eople/r.cavill/ Contact: r.cavill@imperial.ac.uk t.ebbels@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Elsevier BV
Date: 08-2005
Abstract: Gender-dependent metabolic variation in Han Wistar rats (n=25 male and n=25 female) was investigated using (1)H nuclear magnetic resonance (NMR) spectroscopy of urine coupled with chemometric methods. Statistically discriminatory regions of the spectra for male and female rats were identified and biomarker characterization was achieved by the further application of solid-phase extraction chromatography with NMR detection and high-performance liquid chromatography mass spectrometry. A novel discriminating molecule was identified as the sulfate conjugate of m-hydroxyphenylpropionic acid, which was excreted in higher concentrations by male rats. Other gender-related metabolite differences in the urine profiles included higher levels of trimethylamine-N-oxide, N,N'-dimethylglycine, m-hydroxyphenylpropionic acid, N-acetylglycoprotein, and cholate in s les from female animals. These studies emphasize the utility of multicomponent metabolic profiling for investigating physiological and genetic variation in experimental animals that may be of relevance to their use as models of toxicity and disease.
Publisher: Proceedings of the National Academy of Sciences
Date: 07-01-2014
Abstract: Mass spectrometry imaging (MSI) technology represents a highly promising approach in cancer research. Here, we outline current roadblocks in translational MSI and introduce a comprehensive workflow designed to address current methodological limitations. An integrated bioinformatics platform is presented that allows intuitive histology-directed interrogation of MSI datasets. We show that this strategy permits the analysis of multivariate molecular signatures with direct correlation to morphological regions of interest, which can offer new insights into how different tumor microenvironmental populations interact with one another and generate novel region-of-interest specific biomarkers and therapeutic targets.
Publisher: Oxford University Press (OUP)
Date: 03-1997
DOI: 10.1093/NDT/12.3.404
Abstract: From the experiments described, it can be seen that there are different research approaches that can be taken and these are summarized in Table 1. Whereas much scientific research is principally hypothesis led, there remains, nevertheless, an important place for exploratory research. High resolution NMR can measure, directly and simultaneously, a wide range of endogenous metabolites in biological fluids and has the unique capability of providing structural information on the metabolites detected. It has proved to be a powerful research tool with which to study inherited metabolic diseases, renal disease, drug metabolism, and toxicity, and can be used to monitor the effects of drug therapy. For instance, by using a library of experimental toxins one can map the metabolic profile of site-specific nephron injury. With this approach in man one could eventually take an unknown disease such as Balkan nephropathy and predict the initial site of tubular injury, the mode of injury and therefore the kind of toxin capable of producing that injury. NMR spectroscopic techniques are still advancing rapidly, with ever increasing sensitivity and sophistication of NMR pulse sequences to enhance structural elucidation in complex mixtures. Given the advances in directly coupled HPLC-NMR and even HPLC-NMR-mass spectroscopy it is likely that these technologies in conjunction with pattern recognition will make major contribution to our understanding of renal processes and provide new diagnostic insights in the 21st century.
Publisher: Cold Spring Harbor Laboratory
Date: 30-07-2023
DOI: 10.1101/2023.07.28.550938
Abstract: Impaired wound healing in burn injuries can lead to complications such as skin graft loss, infection, and increased risk of scarring, which impacts long-term patient outcomes and quality of life. While wound repair in severe burns has received substantial research attention, poor wound outcomes in cases of non- severe burns (classified as % of the total body surface area (TBSA)) remain relatively understudied despite also having considerable physiological impact and constituting the majority of hospital admissions for burns. Predicting outcomes in the early stages of healing would decrease financial and patient burden, and aid in preventing long-term complications from poor wound healing. Lipids have been implicated in inflammation and tissue repair processes and may play essential roles in burn wound healing. Longitudinal plasma s les were collected from patients (n=20) with non-severe ( % TBSA) flame or scald burns over a 6-week period including timepoints pre- and post-surgical intervention. S les were analysed using liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy to detect 850 lipid species and 112 lipoproteins. Statistical analyses, including orthogonal projection to latent structures-discriminant analysis was performed to identify changes associated with either re-epithelialisation or delayed wound re-epithelisation. The results demonstrated that the plasma lipid and lipoprotein profiles at admission could predict wound re-epithelisation outcomes at two weeks post-surgery, and that these discriminatory profiles were maintained over a 6-week period. Triacylglycerides, diacylglycerides (DAG) and low density lipoprotein (LDL) subfractions were associated with delayed wound closure, with DAG(18:2_18:3) and LDL/High density lipoprotein (HDL) ratio having the most influence (p-value 0.02, Cliff’s delta 0.7), while HDL subfractions, phosphatidylinositols, phosphatidylcholines (PC), and phosphatidylserines were associated with re-epithelisation at two weeks post-surgery, with PC(16:0_18:1) and HDL-2 apolipoprotein-A1 showing the greatest influence on the model (p-value 0.01, Cliff’s delta -0.7). We demonstrate clinical prediction of wound re-epithelisation in non-severe burn patients using lipid and lipoprotein profiling. Further validation of the models will potentially lead to personalised intervention strategies to enhance injury outcomes, reducing the risk of chronic complications post-burn injury. Demonstration of wound healing prediction from time of hospital admission for non-severe burns. Plasma lipid and lipoprotein profiles within 48 hours of admission to hospital with non-severe burn injury are distinctly different between patients whose wounds re-epithelialized within two weeks and those with delayed re-epithelisation. Patients with delayed wound re-epithelisation have a persistent lipid and lipoprotein signature from burns admission up to six weeks post-injury.
Publisher: Elsevier BV
Date: 05-2010
DOI: 10.1016/J.IJPARA.2009.11.003
Abstract: Co-infection with hookworm and schistosomes is a common phenomenon in sub-Saharan Africa, as well as in parts of South America and southeast Asia. As a first step towards understanding the metabolic response of a hookworm-schistosome co-infection in humans, we investigated the metabolic consequences of co-infection in an animal model, using a nuclear magnetic resonance (NMR)-based metabolic profiling technique, combined with multivariate statistical analysis. Urine and serum s les were obtained from hamsters experimentally infected with 250 Necator americanus infective L(3) and 100 Schistosoma japonicum cercariae simultaneously. In the co-infection model, similar worm burdens were observed as reported for single infection models, whereas metabolic profiles of co-infection represented a combination of the altered metabolite profiles induced by single infections with these two parasites. Consistent differences in metabolic profiles between the co-infected and non-infected control hamsters were observed from 4 weeks p.i. onwards. The predominant metabolic alterations in co-infected hamsters consisted of depletion of amino acids, tricarboxylic acid cycle intermediates (e.g. citrate and succinate) and glucose. Moreover, alterations of a series of gut microbial-related metabolites, such as decreased levels of hippurate, 3-hydroxyphenylpropionic acid, 4-hydroxyphenylpropionic acid and trimethylamine-N-oxide, and increased concentrations of 4-cresol glucuronide and phenylacetylglycine were associated with co-infection. Our results provide a first step towards understanding the metabolic response of an animal host to multiple parasitic infections.
Publisher: Oxford University Press (OUP)
Date: 2015
DOI: 10.1039/C5TX00113G
Abstract: The cytotoxicity of mitragynine, the dominant alkaloid of the narcotic-like herb, Mitragyna speciosa Korth (Kratom) involves cell cycle arrest, apoptosis and opiate receptors.
Publisher: Springer Science and Business Media LLC
Date: 12-1995
DOI: 10.1007/BF02733668
Abstract: Aggressive behavior has negative effects on animal welfare and growth performance in pigs. The dopamine receptor D2 (DRD2) has a critical neuromodulator role in the dopamine signal pathway within the brain to control behavior. A functional single-nucleotide polymorphism (SNP), rs1110730503, in the promoter region of the porcine DRD2 gene was identified, which affects aggressive behavior in pigs. A chromatin immunoprecipitation (ChIP) assay was used to identify the interactions between interferon regulatory factor 1 (IRF1) and IRF2 with the DRD2 gene. The overexpression or knockdown of these two transcription factors in porcine kidney-15 (PK15) and porcine neuronal cells (PNCs) indicate that the binding of IRF1 to DRD2 promotes the transcription of the DRD2 gene, but the binding of IRF2 to the DRD2 gene inhibits its transcription. Furthermore, IRF1 and IRF2 are functionally antagonistic to each other. The downregulation of DRD2 or upregulation of IRF2 increased the apoptosis rate of porcine neuroglial cells. Taken together, we found that transcriptional factors IRF1 and IRF2 have vital roles in regulating the transcription of the DRD2 gene, and rs1110730503 (-915A/T) is a functional SNP that influences IRF2 binding to the promoter of the DRD2 gene. These findings will provide further insight towards controlling aggressive behavior in pigs.
Publisher: EMBO
Date: 2008
DOI: 10.1038/MSB.2008.40
Publisher: BMJ
Date: 21-01-2020
DOI: 10.1136/GUTJNL-2019-319620
Abstract: Due to the global increase in obesity rates and success of bariatric surgery in weight reduction, an increasing number of women now present pregnant with a previous bariatric procedure. This study investigates the extent of bariatric-associated metabolic and gut microbial alterations during pregnancy and their impact on fetal development. A parallel metabonomic (molecular phenotyping based on proton nuclear magnetic resonance spectroscopy) and gut bacterial (16S ribosomal RNA gene licon sequencing) profiling approach was used to determine maternal longitudinal phenotypes associated with malabsorptive/mixed (n=25) or restrictive (n=16) procedures, compared with women with similar early pregnancy body mass index but without bariatric surgery (n=70). Metabolic profiles of offspring at birth were also analysed. Previous malabsorptive, but not restrictive, procedures induced significant changes in maternal metabolic pathways involving branched-chain and aromatic amino acids with decreased circulation of leucine, isoleucine and isobutyrate, increased excretion of microbial-associated metabolites of protein putrefaction (phenylacetlyglutamine, p- cresol sulfate, indoxyl sulfate and p- hydroxyphenylacetate), and a shift in the gut microbiota. The urinary concentration of phenylacetylglutamine was significantly elevated in malabsorptive patients relative to controls (p=0.001) and was also elevated in urine of neonates born from these mothers (p=0.021). Furthermore, the maternal metabolic changes induced by malabsorptive surgery were associated with reduced maternal insulin resistance and fetal/birth weight. Metabolism is altered in pregnant women with a previous malabsorptive bariatric surgery. These alterations may be beneficial for maternal outcomes, but the effect of elevated levels of phenolic and indolic compounds on fetal and infant health should be investigated further.
Publisher: Springer Science and Business Media LLC
Date: 11-2011
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 07-2015
Publisher: Springer Science and Business Media LLC
Date: 04-2022
DOI: 10.1038/S41598-022-09588-W
Abstract: Lipids play essential roles in the hepatitis C virus (HCV) life cycle and patients with chronic HCV infection display disordered lipid metabolism which resolves following successful anti-viral therapy. It has been proposed that HCV genotype 3 (HCV-G3) infection is an independent risk factor for hepatocellular carcinoma and evidence suggests lipogenic proteins are involved in hepatocarcinogenesis. We aimed to characterise variation in host lipid metabolism between participants chronically infected with HCV genotype 1 (HCV-G1) and HCV-G3 to identify likely genotype-specific differences in lipid metabolism. We combined several lipidomic approaches: analysis was performed between participants infected with HCV-G1 and HCV-G3, both in the fasting and non-fasting states, and after sustained virological response (SVR) to treatment. Sera were obtained from 112 fasting patients (25% with cirrhosis). Serum lipids were measured using standard enzymatic methods. Lathosterol and desmosterol were measured by gas-chromatography mass spectrometry (MS). For further metabolic insight on lipid metabolism, ultra-performance liquid chromatography MS was performed on all s les. A subgroup of 13 participants had whole body fat distribution determined using in vivo magnetic resonance imaging and spectroscopy. A second cohort of (non-fasting) sera were obtained from HCV Research UK for comparative analyses: 150 treatment naïve patients and 100 non-viraemic patients post-SVR. HCV-G3 patients had significantly decreased serum apoB, non-HDL cholesterol concentrations, and more hepatic steatosis than those with HCV-G1. HCV-G3 patients also had significantly decreased serum levels of lathosterol, without significant reductions in desmosterol. Lipidomic analysis showed lipid species associated with reverse cholesterol transport pathway in HCV-G3. We demonstrated that compared to HCV-G1, HCV-G3 infection is characterised by low LDL cholesterol levels, with preferential suppression of cholesterol synthesis via lathosterol, associated with increasing hepatic steatosis. The genotype-specific lipid disturbances may shed light on genotypic variations in liver disease progression and promotion of hepatocellular cancer in HCV-G3.
Publisher: Springer Science and Business Media LLC
Date: 02-2002
DOI: 10.1038/NRD728
Abstract: The later that a molecule or molecular class is lost from the drug development pipeline, the higher the financial cost. Minimizing attrition is therefore one of the most important aims of a pharmaceutical discovery programme. Novel technologies that increase the probability of making the right choice early save resources, and promote safety, efficacy and profitability. Metabonomics is a systems approach for studying in vivo metabolic profiles, which promises to provide information on drug toxicity, disease processes and gene function at several stages in the discovery-and-development process.
Publisher: Elsevier BV
Date: 08-2003
Publisher: American Chemical Society (ACS)
Date: 12-10-2009
DOI: 10.1021/PR9005266
Abstract: The amino sugar galactosamine (galN) induces alterations in the hepatic uridine nucleotide pool and has been widely used as a model of human viral hepatitis. Histopathological and clinical chemistry analyses of a cohort of rats following administration of galN revealed extreme interin idual variability in the extent of the toxic response which enabled classification of 'responder' and 'non-responder' phenotypes. An integrative metabolic profiling approach was applied to characterize biomarkers of exposure to galN in urine, serum, feces and liver from responders and non-responders. The presence of N-acetylglucosamine and galN in the urine correlated with the occurrence and extent of toxic response. Conversely, the novel identification of galN-pyrazines in the feces of non-responders and their virtual absence in the feces of responders suggests an alternative means of distribution and metabolism of galN in non-responders. The absence of the UDP-hexosamines in the liver of non-responders further supports differential metabolism of galN and suggests an ability of non-responders to avoid UDP-glucose depletion. An observed disturbance of gut microbial derived metabolites in the urine and feces of non-responders may suggest a role of the microflora in reducing the effective dose of galN. This systems level metabonomic approach has provided new mechanistic insights into differential response to galN and is widely applicable to the study of interin idual variation in metabolism for any xenobiotic intervention.
Publisher: Springer Science and Business Media LLC
Date: 06-05-2010
Abstract: The production of 'global' metabolite profiles involves measuring low molecular-weight metabolites (<1 kDa) in complex biofluids/tissues to study perturbations in response to physiological challenges, toxic insults or disease processes. Information-rich analytical platforms, such as mass spectrometry (MS), are needed. Here we describe the application of ultra-performance liquid chromatography-MS (UPLC-MS) to urinary metabolite profiling, including s le preparation, stability/storage and the selection of chromatographic conditions that balance metabolome coverage, chromatographic resolution and throughput. We discuss quality control and metabolite identification, as well as provide details of multivariate data analysis approaches for analyzing such MS data. Using this protocol, the analysis of a s le set in 96-well plate format, would take ca. 30 h, including 1 h for system setup, 1-2 h for s le preparation, 24 h for UPLC-MS analysis and 1-2 h for initial data processing. The use of UPLC-MS for metabolic profiling in this way is not faster than the conventional HPLC-based methods but, because of improved chromatographic performance, provides superior metabolome coverage.
Publisher: American Chemical Society (ACS)
Date: 16-10-2019
DOI: 10.1021/ACS.JPROTEOME.9B00460
Abstract: Venous thromboembolism (VTE), chronic venous disease (CVD), and venous leg ulceration (VLU) are clinical manifestations of a poorly functioning venous system. Though common, much is unknown of the pathophysiology and progression of these conditions. Metabolic phenotyping has been employed to explore mechanistic pathways involved in venous disease. A systematic literature review was performed: full text, primary research articles on the applications of nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) in human participants and animals were included for qualitative synthesis. Seventeen studies applying metabolic phenotyping to venous disease were identified: six on CVD, two on VLU, and nine on VTE both animal (
Publisher: American Chemical Society (ACS)
Date: 10-02-2022
DOI: 10.1021/ACS.JPROTEOME.1C00851
Abstract: Trimethylamine (TMA) and its
Publisher: American Chemical Society (ACS)
Date: 11-02-2013
DOI: 10.1021/PR300909V
Abstract: Patients with a body mass index (BMI) above 35 kg/m(2) with metabolic diseases benefit from Roux-en-Y gastric bypass (RYGB) independently of their final BMI and the amount of body weight lost. However, the weight loss independent metabolic effects induced by RYGB remain less well understood. To elucidate metabolic changes after RYGB, (1)H NMR spectroscopy-based urine metabolic profiles from RYGB (n = 7), ad libitum-fed sham (AL, n = 5), and body-weight-matched sham (BWM, n = 5) operated mice were obtained. Gut morphometry and fecal energy content were analyzed. Food intake and body weight of RYGB mice were significantly reduced (p = 0.001) compared to sham-AL. There was a strong tendency that BWM-shams required less food to maintain the same body weight as RYGB mice (p = 0.05). No differences were found in fecal energy content between the groups, excluding malabsorption in RYGB animals. Unlike RYGB-operated rats, gut hypertrophy was not observed in RYGB-operated mice. Urinary tricarboxylic acid cycle intermediates were higher in the sham groups, suggesting altered mitochondrial metabolism after RYGB surgery. Higher urinary levels of trimethylamine, hippurate and trigonelline in RYGB mice indicate that the RYGB operation caused microbial disturbance. Taken together, we demonstrate for the first time that there are RYGB specific metabolic effects, which are independent of food intake and body weight loss. Increased utilization of TCA cycle intermediates and altered gut microbial-host co-metabolites might indicate increased energy expenditure and microbial changes in the gut, respectively.
Publisher: Elsevier BV
Date: 04-2017
Publisher: Springer Science and Business Media LLC
Date: 16-10-2023
Publisher: S. Karger AG
Date: 2016
DOI: 10.1159/000441820
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 07-2015
Publisher: Wiley
Date: 11-2010
DOI: 10.1002/CEM.1359
Abstract: Metabonomics is a key element in systems biology, and with current analytical methods, generates vast amounts of quantitative or qualitative metabolic data. Understanding of the global function of the living organism can be achieved by integration of ‘omics’ approaches including metabonomics, genomics, transcriptomics and proteomics, increasing the complexity of the full data sets. Multivariate statistical approaches are well suited to extract the characterizing metabolic information associated with each level of dynamic process. In this review, we discuss techniques that have evolved from principal component analysis and partial least squares (PLS) methods with a focus on improved interpretation and modeling with respect to biomarker recovery and data visualization in the context of metabonomic applications. Visualization is of paramount importance to investigate complex metabolic signatures, the power and potential of which is illustrated with key papers. Recent improvements based on the removal of orthogonal variation are discussed in terms of interpretation enhancement, and are supported by relevant applications. Flexibility of PLS methods in general and of O‐PLS in particular allows implementation of derivative methods such as O2‐PLS, O‐PLS‐variance components, nonlinear methods, and batch modeling to improve analysis of complex data sets, which facilitates extraction of information related to subtle biological processes. These approaches can be used to address issues present in complex multi‐factorial data sets. Thus, we highlight the key advantages and limitations of the different latent variable applications for top‐down systems biology and assess the differences between the methods available. Copyright © 2010 John Wiley & Sons, Ltd.
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C4MB00097H
Abstract: The purpose of this study was to give a comprehensive insight into the systemic metabolic phenotype of mice with a single or dual infection with Plasmodium berghei and Heligmosomoides bakeri .
Publisher: American Chemical Society (ACS)
Date: 13-12-2004
DOI: 10.1021/AC048803I
Abstract: In general, applications of metabonomics using biofluid NMR spectroscopic analysis for probing abnormal biochemical profiles in disease or due to toxicity have all relied on the use of chemometric techniques for s le classification. However, the well-known variability of some chemical shifts in 1H NMR spectra of biofluids due to environmental differences such as pH variation, when coupled with the large number of variables in such spectra, has led to the situation where it is necessary to reduce the size of the spectra or to attempt to align the shifting peaks, to get more robust and interpretable chemometric models. Here, a new approach that avoids this problem is demonstrated and shows that, moreover, inclusion of variable peak position data can be beneficial and can lead to useful biochemical information. The interpretation of chemometric models using combined back-scaled loading plots and variable weights demonstrates that this peak position variation can be handled successfully and also often provides additional information on the physicochemical variations in metabonomic data sets.
Publisher: EMBO
Date: 2010
DOI: 10.1038/MSB.2010.49
Abstract: We characterize the integrated response of a rat host to the liver fluke Fasciola hepatica using a combination of 1 H nuclear magnetic resonance spectroscopic profiles (liver, kidney, intestine, brain, spleen, plasma, urine, feces) and multiplex cytokine markers of systemic inflammation. Multivariate mathematical models were built to describe the main features of the infection at the systems level. In addition to the expected modulation of hepatic choline and energy metabolism, we found significant perturbations of the nucleotide balance in the brain, together with increased plasma IL‐13, suggesting a shift toward modulation of immune reactions to minimize inflammatory damage, which may favor the co‐existence of the parasite in the host. Subsequent analysis of brain extracts from other trematode infection models (i.e. Schistosoma mansoni , and Echinostoma caproni ) did not elicit a change in neural nucleotide levels, indicating that the neural effects of F. hepatica infection are specific. We propose that the topographically extended response to invasion of the host as characterized by the modulated global metabolic phenotype is stratified across several bio‐organizational levels and reflects the direct manipulation of host–nucleotide balance.
Publisher: Elsevier BV
Date: 06-2017
Publisher: Wiley
Date: 10-10-2008
Publisher: Elsevier BV
Date: 1990
Publisher: Georg Thieme Verlag KG
Date: 08-2002
DOI: 10.1055/S-2002-33793
Abstract: There is increasing interest in evaluating the clinical efficacy of herbal medicines. However, there are significant analytical problems associated with quality control and the measurement of the overall composition of such complex, multi-component mixtures as normally required in the pharmaceutical industry. Here we describe a novel NMR spectroscopic and pattern recognition analytical approach to investigate composition and variability of a commonly used herbal medicine. 600 MHz (1)H-NMR spectroscopy and principal components analysis (PCA) was used to discriminate between batches of 14 commercially available feverfew s les based on multi-component metabolite profiles. Two of the batches were significantly different from the other twelve. The twelve remaining classes could be classified into discrete groups by PCA on the basis of minor differences in overall chemical composition. NMR based pattern recognition (PR) analysis of extracts proved to be superior to PR analysis of HPLC traces of the same mixtures. This work indicates the potential value of NMR combined with PCA for the characterisation of complex natural product mixtures, and the discrimination of s les containing allegedly identical ingredients.
Publisher: American Chemical Society (ACS)
Date: 08-04-2015
DOI: 10.1021/AC503775M
Publisher: American Chemical Society (ACS)
Date: 11-2007
DOI: 10.1021/AC0713961
Abstract: As part of our ongoing development of methods for enhanced biomarker information recovery from spectroscopic data we present the first ex le of a new hetero-nuclear statistical total correlation spectroscopy (HET-STOCSY) approach applied to intact tissue s les collected as part of a toxicological study. One-dimensional 1H and 31P-{1H} magic angle spinning (MAS) NMR spectra of intact liver s les after galactosamine (galN) treatment to rats and after cotreatment of galN plus uridine were collected at 275 K. In idual s les were also followed by 1H and 31P-{1H} MAS NMR through time generating time dependent modulations in metabolite signatures relating to toxicity. High-resolution 1H NMR spectra of urine and plasma and clinical chemical data were also collected to establish a biological framework in which to place these novel statistical heterospectroscopic data. In HET-STOCSY, calculation of the covariance between the 31P-{1H} and 1H NMR signals of phosphorus containing metabolites allows their molecular connectivities to be established and the construction of virtual two-dimensional heteronuclear correlation spectra that connect all protons on the molecule to the heteroatom. We show how HET-STOCSY applied to MAS NMR spectra of liver s les can be used to augment biomarker detection. This approach is generic and can be applied to correlate the covarying signals for any spin-active nuclei where there is parallel or serial collection of data.
Publisher: Springer Science and Business Media LLC
Date: 13-05-2010
Abstract: Metabolic profiling, metabolomic and metabonomic studies require robust study protocols for any large-scale comparisons and evaluations. Detailed methods for solution-state NMR spectroscopy have been summarized in an earlier protocol. This protocol details the analysis of intact tissue s les by means of high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy and we provide a detailed description of s le collection, preparation and analysis. Described here are (1)H NMR spectroscopic techniques such as the standard one-dimensional, relaxation-edited, diffusion-edited and two-dimensional J-resolved pulse experiments, as well as one-dimensional (31)P NMR spectroscopy. These are used to monitor different groups of metabolites, e.g., sugars, amino acids and osmolytes as well as larger molecules such as lipids, non-invasively. Through the use of NMR-based diffusion coefficient and relaxation times measurements, information on molecular compartmentation and mobility can be gleaned. The NMR methods are often combined with statistical analysis for further metabonomics analysis and biomarker identification. The standard acquisition time per s le is 8-10 min for a simple one-dimensional (1)H NMR spectrum, giving access to metabolite information while retaining tissue integrity and hence allowing direct comparison with histopathology and MRI/MRS findings or the evaluation together with biofluid metabolic-profiling data.
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/B907021D
Abstract: The widely-used blood anticoagulants citrate and EDTA give rise to prominent peaks in (1)H NMR spectra of plasma s les collected in epidemiological and clinical studies, and these cause varying levels of interference in recovering biochemical information on endogenous metabolites. To investigate both the potential metabolic information loss caused by these substances and any possible inter-molecular interactions between the anticoagulants and endogenous components, the (1)H NMR spectra of 40 split human plasma s les collected from 20 in iduals into either citrate or EDTA have been analysed. Endogenous metabolite peaks were selectively obscured by large citrate peaks or those from free EDTA and its calcium and magnesium complexes. It is shown that the endogenous metabolites that give rise to peaks obscured by those from EDTA or citrate almost invariably also have other resonances that allow their identification and potential quantitation. Also, metabolic information recovery could be maximised by use of spectral editing techniques such as spin-echo, diffusion-editing and J-resolved experiments. The NMR spectral effects of any interactions between the added citrate or EDTA and endogenous components were found to be negligible. Finally, identification of split s les was feasible using simple multivariate statistical approaches such as principal components analysis. Thus even when legacy epidemiological plasma s les have been collected using the NMR-inappropriate citrate or EDTA anticoagulants, useful biochemical information can still be recovered effectively.
Publisher: Wiley
Date: 08-2006
DOI: 10.1002/CEM.1006
Abstract: The characteristics of the OPLS method have been investigated for the purpose of discriminant analysis (OPLS‐DA). We demonstrate how class‐orthogonal variation can be exploited to augment classification performance in cases where the in idual classes exhibit ergence in within‐class variation, in analogy with soft independent modelling of class analogy (SIMCA) classification. The prediction results will be largely equivalent to traditional supervised classification using PLS‐DA if no such variation is present in the classes. A discriminatory strategy is thus outlined, combining the strengths of PLS‐DA and SIMCA classification within the framework of the OPLS‐DA method. Furthermore, res ling methods have been employed to generate distributions of predicted classification results and subsequently assess classification belief. This enables utilisation of the class‐orthogonal variation in a proper statistical context. The proposed decision rule is compared to common decision rules and is shown to produce comparable or less class‐biased classification results. Copyright © 2007 John Wiley & Sons, Ltd.
Publisher: American Chemical Society (ACS)
Date: 05-07-2011
DOI: 10.1021/AC201065J
Abstract: Ultra-performance liquid chromatography coupled to mass spectrometry (UPLC/MS) has been used increasingly for measuring changes of low molecular weight metabolites in biofluids/tissues in response to biological challenges such as drug toxicity and disease processes. Typically s les show high variability in concentration, and the derived metabolic profiles have a heteroscedastic noise structure characterized by increasing variance as a function of increased signal intensity. These sources of experimental and instrumental noise substantially complicate information recovery when statistical tools are used. We apply and compare several preprocessing procedures and introduce a statistical error model to account for these bioanalytical complexities. In particular, the use of total intensity, median fold change, locally weighted scatter plot smoothing, and quantile normalizations to reduce extraneous variance induced by s le dilution were compared. We demonstrate that the UPLC/MS peak intensities of urine s les should respond linearly to variable s le dilution across the intensity range. While all four studied normalization methods performed reasonably well in reducing dilution-induced variation of urine s les in the absence of biological variation, the median fold change normalization is least compromised by the biologically relevant changes in mixture components and is thus preferable. Additionally, the application of a subsequent log-based transformation was successful in stabilizing the variance with respect to peak intensity, confirming the predominant influence of multiplicative noise in peak intensities from UPLC/MS-derived metabolic profile data sets. We demonstrate that variance-stabilizing transformation and normalization are critical preprocessing steps that can benefit greatly metabolic information recovery from such data sets when widely applied chemometric methods are used.
Publisher: American Chemical Society (ACS)
Date: 13-08-2008
DOI: 10.1021/PR700864X
Abstract: The effects of the antibiotic vancomycin (2 x 100 mg/kg/day) on the gut microbiota of female mice (outbred NMRI strain) were studied, in order to assess the relative contribution of the gut microbiome to host metabolism. The host's metabolic phenotype was characterized using (1)H NMR spectroscopy of urine and fecal extract s les. Time-course changes in the gut microbiotal community after administration of vancomycin were monitored using 16S rRNA gene PCR and denaturing gradient gel electrophoresis (PCR-DGGE) analysis and showed a strong effect on several species, mostly within the Firmicutes. Vancomycin treatment was associated with fecal excretion of uracil, amino acids and short chain fatty acids (SCFAs), highlighting the contribution of the gut microbiota to the production and metabolism of these dietary compounds. Clear differences in gut microbial communities between control and antibiotic-treated mice were observed in the current study. Reduced urinary excretion of gut microbial co-metabolites phenylacetylglycine and hippurate was also observed. Regression of urinary hippurate and phenylacetylglycine concentrations against the fecal metabolite profile showed a strong association between these urinary metabolites and a wide range of fecal metabolites, including amino acids and SCFAs. Fecal choline was inversely correlated with urinary hippurate. Metabolic profiling, coupled with the metagenomic study of this antibiotic model, illustrates the close inter-relationship between the host and microbial "metabotypes", and will provide a basis for further experiments probing the understanding of the microbial-mammalian metabolic axis.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5AN01041A
Abstract: Tissue extraction optimization for untargeted metabolic profiling.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 10-01-2023
Publisher: MDPI AG
Date: 20-07-2021
Abstract: Improved methods are required for investigating the systemic metabolic effects of SARS-CoV-2 infection and patient stratification for precision treatment. We aimed to develop an effective method using lipid profiles for discriminating between SARS-CoV-2 infection, healthy controls, and non-SARS-CoV-2 respiratory infections. Targeted liquid chromatography–mass spectrometry lipid profiling was performed on discovery (20 SARS-CoV-2-positive 37 healthy controls 22 COVID-19 symptoms but SARS-CoV-2negative) and validation (312 SARS-CoV-2-positive 100 healthy controls) cohorts. Orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and Kruskal–Wallis tests were applied to establish discriminant lipids, significance, and effect size, followed by logistic regression to evaluate classification performance. OPLS-DA reported separation of SARS-CoV-2 infection from healthy controls in the discovery cohort, with an area under the curve (AUC) of 1.000. A refined panel of discriminant features consisted of six lipids from different subclasses (PE, PC, LPC, HCER, CER, and DCER). Logistic regression in the discovery cohort returned a training ROC AUC of 1.000 (sensitivity = 1.000, specificity = 1.000) and a test ROC AUC of 1.000. The validation cohort produced a training ROC AUC of 0.977 (sensitivity = 0.855, specificity = 0.948) and a test ROC AUC of 0.978 (sensitivity = 0.948, specificity = 0.922). The lipid panel was also able to differentiate SARS-CoV-2-positive in iduals from SARS-CoV-2-negative in iduals with COVID-19-like symptoms (specificity = 0.818). Lipid profiling and multivariate modelling revealed a signature offering mechanistic insights into SARS-CoV-2, with strong predictive power, and the potential to facilitate effective diagnosis and clinical management.
Publisher: Elsevier BV
Date: 2020
Publisher: Wiley
Date: 15-11-2016
DOI: 10.1111/NBU.12240
Publisher: Elsevier BV
Date: 04-2004
Publisher: Hindawi Limited
Date: 2004
DOI: 10.1155/2004/862164
Abstract: High field 1 H NMR spectroscopy has been employed to obtain, in conjunction with chemometric analysis, information regarding fluctuations in endogenous metabolic profiles for Crotalaria cobalticola plant cells following exposure to cobalt chloride. Such ‘metabolomic’ type data analysis is often confounded by experimental, environmental or genetic factors that are not correlated to the classifications of interest and serve only to complicate the extraction of meaningful answers from a dataset. This work demonstrates the application of data filtering to remove extraneous data that result from spectrometer variation rather than being correlated with the classes of interest. S les were analysed from Crotalaria cobalticola suspension cell culture following exposure to cobalt chloride using 2 spectrometers. Removal of confounding data due to spectrometer variation resulted in clear separation between control and dosed classes. It was then possible to use the model to determine key changes in biochemical status caused as a result of exposure to cobalt. Branched chain amino acids, succinate and secondary metabolite precursors phenylalanine and tyrosine were all higher in the control s les, whilst choline, glutamate, alanine and lactate were higher in the dosed s les.
Publisher: Elsevier
Date: 2010
Publisher: Proceedings of the National Academy of Sciences
Date: 07-2021
Abstract: While the effects of gut microbes on brain development and function have been described, the mechanisms remain largely unknown. Here, we report that tryptophan-metabolizing gut microbes secrete indoles that regulate neurogenesis in the adult hippoc us. This stimulatory effect on adult neurogenesis is mediated by the metabolic- and immune-linked aryl hydrocarbon receptor (AhR). Another AhR ligand, the tryptophan metabolite kynurenine, failed to induce neurogenesis, suggesting ligand specificity of AhR-mediated regulation of adult neurogenesis. The indole-AhR signaling pathway elevates transcription factors and signaling proteins that promote adult neurogenesis, as well as key markers of synaptic maturation. Our data demonstrate a symbiotic gut–brain coregulatory axis that connects the metabolic status of gut microbes to the control of neurogenesis in the adult hippoc us.
Publisher: Informa UK Limited
Date: 2021
Publisher: Elsevier
Date: 2016
Publisher: Elsevier BV
Date: 11-2019
Publisher: Oxford University Press (OUP)
Date: 06-09-2022
Abstract: COVID-19 is associated with neurological complications including stroke, delirium and encephalitis. Furthermore, a post-viral syndrome dominated by neuropsychiatric symptoms is common, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of COVID-19 severity. We investigated the dynamics of, and relationship between, serum markers of brain injury [neurofilament light (NfL), glial fibrillary acidic protein (GFAP) and total tau] and markers of dysregulated host response (autoantibody production and cytokine profiles) in 175 patients admitted with COVID-19 and 45 patients with influenza. During hospitalization, sera from patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependent manner, with evidence of ongoing active brain injury at follow-up 4 months later. These biomarkers were associated with elevations of pro-inflammatory cytokines and the presence of autoantibodies to a large number of different antigens. Autoantibodies were commonly seen against lung surfactant proteins but also brain proteins such as myelin associated glycoprotein. Commensurate findings were seen in the influenza cohort. A distinct process characterized by elevation of serum total tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses unlike NfL and GFAP. These results demonstrate that brain injury is a common consequence of both COVID-19 and influenza, and is therefore likely to be a feature of severe viral infection more broadly. The brain injury occurs in the context of dysregulation of both innate and adaptive immune responses, with no single pathogenic mechanism clearly responsible.
Publisher: American Society for Pharmacology & Experimental Therapeutics (ASPET)
Date: 12-2002
Abstract: The urinary excretion of metabolites of 2,3-benzofuran was studied in Sprague-Dawley rats (n = 5) given a single dose of 150 mg/kg i.p. Urine s les were collected at defined intervals up to 7 days postdose and analyzed using (1). H NMR and directly coupled high performance liquid chromatography (HPLC)-NMR, HPLC-(mass spectrometry) MS and HPLC-MS-NMR methods. The principal metabolites were determined to be 2-hydroxyphenylacetic acid and 2-(2-hydroxyethyl)phenyl hydrogen sulfate, representing 24.3 +/- 6.0% and 19.6 +/- 6.4% of the dose, respectively. This indicates that metabolism of benzofuran to the polar species excreted in urine involves cleavage of the furan ring.
Publisher: American Chemical Society (ACS)
Date: 07-08-2015
DOI: 10.1021/ACS.JPROTEOME.5B00277
Abstract: Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its etiopathogenesis and earlier diagnosis. Here, we investigated the fecal metabolic phenotype of patients with advanced colorectal neoplasia and controls using (1)H-nuclear magnetic resonance (NMR) spectroscopy and multivariate modeling. The fecal microbiota composition was assessed by quantitative real-time PCR as well as Wif-1 methylation levels in stools, serum, and urine and correlated to the metabolic profile of each patient. The predictivity of the model was 0.507 (Q(2)Y), and the explained variance was 0.755 (R(2)Y). Patients with advanced colorectal neoplasia demonstrated increased fecal concentrations of four short-chain fatty acids (valerate, acetate, propionate, and butyrate) and decreased signals relating to β-glucose, glutamine, and glutamate. The predictive accuracy of the multivariate (1)H NMR model was higher than that of the guaiac-fecal occult blood test and the Wif-1 methylation test for predicting advanced colorectal neoplasia. Correlation analysis between fecal metabolites and bacterial profiles revealed strong associations between Faecalibacterium prausnitzii and Clostridium leptum species with short-chain fatty acids concentration and inverse correlation between Faecalibacterium prausnitzii and glucose. These preliminary results suggest that fecal metabonomics may potentially have a future role in a noninvasive colorectal screening program and may contribute to our understanding of the role of these dysregulated molecules in the cross-talk between the host and its bacterial microbiota.
Publisher: American Chemical Society (ACS)
Date: 15-06-2006
DOI: 10.1021/PR0503376
Abstract: Administration of high doses of the histamine antagonist methapyrilene to rats causes periportal liver necrosis. The mechanism of toxicity is ill-defined and here we have utilized an integrated systems approach to understanding the toxic mechanisms by combining proteomics, metabonomics by 1H NMR spectroscopy and genomics by microarray gene expression profiling. Male rats were dosed with methapyrilene for 3 days at 150 mg/kg/day, which was sufficient to induce liver necrosis, or a subtoxic dose of 50 mg/kg/day. Urine was collected over 24 h each day, while blood and liver tissues were obtained at 2 h after the final dose. The resulting data further define the changes that occur in signal transduction and metabolic pathways during methapyrilene hepatotoxicity, revealing modification of expression levels of genes and proteins associated with oxidative stress and a change in energy usage that is reflected in both gene rotein expression patterns and metabolites. The difficulties of combining and interpreting multiomic data are considered.
Publisher: Elsevier BV
Date: 12-2015
Publisher: Wiley
Date: 22-10-2021
Abstract: Prior investigation has suggested a positive association between increased colonic propionate production and circulating odd‐chain fatty acids (OCFAs pentadecanoic acid [C15:0], heptadecanoic acid [C17:0]). As the major source of propionate in humans is the microbial fermentation of dietary fiber, OCFAs have been proposed as candidate biomarkers of dietary fiber. The objective of this study is to critically assess the plausibility, robustness, reliability, dose‐response, time‐response aspects of OCFAs as potential biomarkers of fermentable fibers in two independent studies using a validated analytical method. OCFAs are first assessed in a fiber supplementation study, where 21 participants received 10 g dietary fiber supplementation for 7 days. OCFAs are then assessed in a highly controlled inpatient setting, which 19 participants consumed a high fiber (45.1 g per day) and a low fiber diet (13.6 g per day) for 4 days. Collectively in both studies, dietary intakes of fiber as fiber supplementations or having consumed a high fiber diet do not increase circulating levels of OCFAs. The dose and temporal relations are not observed. Current study has generated new insight on the utility of OCFAs as fiber biomarkers and highlighted the importance of critical assessment of candidate biomarkers before application.
Publisher: American Chemical Society (ACS)
Date: 20-08-2020
Publisher: American Chemical Society (ACS)
Date: 10-08-2012
DOI: 10.1021/AC300586M
Publisher: Springer Science and Business Media LLC
Date: 31-05-2017
DOI: 10.1038/SREP46832
Abstract: Scientific Reports 5: Article number: 10198 published online: 14 May 2015 updated: 31 May 2017. The Acknowledgements section in this Article is incomplete. “We would like to express our gratitude to all the participants of the study, management of both King Fahad Medical Research Center (KFMRC) and Arabian centers, and all the students who volunteered to help us in recruiting the subjects.
Publisher: Royal Society of Chemistry (RSC)
Date: 17-12-2003
DOI: 10.1039/B209155K
Abstract: The application of chemometric methods to 1H NMR spectroscopic data has been documented for pathophysiological processes. In this study we show the application of 1H NMR-based metabonomics to investigate a relationship between serum metabolic profiles and hypertension. Although hypertension can be defined using blood pressure measurements, the underlying aetiology and metabolic effects are not so readily identified. Serum profiles for patients with low/normal systolic blood pressure (SBP or = 150 mm Hg n = 17) were acquired using 1H NMR spectroscopy. Orthogonal signal correction followed by principal components analysis were applied to these NMR data in order to facilitate interpretation, and the resulting chemometric models were validated using Soft Independent Modelling of Class Analogy. Using 1H NMR-based metabonomics, it was possible to distinguish low/ normal SBP serum s les from borderline and high SBP s les. Borderline and high SBP s les, however, were indiscriminate from each other. Our preliminary results showed that there was a relationship between serum metabolic profiles and blood pressure which, in part, was due to lipoprotein particle composition differences between the s les. Furthermore, our results indicated that serum pathology associated with blood pressure is apparent at SBP values > 130 mm Hg, which the WHO and ISH currently define as the limit between normal and high-normal.
Publisher: Informa UK Limited
Date: 29-11-2010
Publisher: Springer Science and Business Media LLC
Date: 30-09-2016
DOI: 10.1007/S11011-016-9906-Y
Abstract: Hepatic encephalopathy (HE) is a neuropsychiatric syndrome which frequently accompanies acute or chronic liver disease. It is characterized by a variety of symptoms of different severity such as cognitive deficits and impaired motor functions. Currently, HE is seen as a consequence of a low grade cerebral oedema associated with the formation of cerebral oxidative stress and deranged cerebral oscillatory networks. However, the pathogenesis of HE is still incompletely understood as liver dysfunction triggers exceptionally complex metabolic derangements in the body which need to be investigated by appropriate technologies. This review summarizes technological approaches presented at the ISHEN conference 2014 in London which may help to gain new insights into the pathogenesis of HE. Dynamic in vivo
Publisher: American Chemical Society (ACS)
Date: 23-01-2008
DOI: 10.1021/AC702040D
Abstract: We present a novel application of the heteronuclear statistical total correlation spectroscopy (HET-STOCSY) approach utilizing statistical correlation between one-dimensional 19F/1H NMR spectroscopic data sets collected in parallel to study drug metabolism. Parallel one-dimensional (1D) 800 MHz 1H and 753 MHz 19F{1H} spectra (n = 21) were obtained on urine s les collected from volunteers (n = 6) at various intervals up to 24 h after oral dosing with 500 mg of flucloxacillin. A variety of statistical relationships between and within the spectroscopic datasets were explored without significant loss of the typically high 1D spectral resolution, generating 1H-1H STOCSY plots, and novel 19F-1H HET-STOCSY, 19F-19F STOCSY, and 19F-edited 1H-1H STOCSY (X-STOCSY) spectroscopic maps, with a resolution of approximately 0.8 Hz t for both nuclei. The efficient statistical editing provided by these methods readily allowed the collection of drug metabolic data and assisted structure elucidation. This approach is of general applicability for studying the metabolism of other fluorine-containing drugs, including important anticancer agents such as 5-fluorouracil and flutamide, and is extendable to any drug metabolism study where there is a spin-active X-nucleus (e.g., 13C, 15N, 31P) label present.
Publisher: Elsevier BV
Date: 11-2019
Publisher: Oxford University Press (OUP)
Date: 08-02-2008
DOI: 10.1093/IJE/DYM284
Abstract: Metabolic profiling of biofluid specimens is an established method for investigating disease states in clinical studies but is only recently being applied to large-scale human population studies. As part of protocol development for the UK Biobank study, a (1)H nuclear magnetic resonance (NMR)-based metabonomic analysis of specimen storage effects and analytical reproducibility was carried out using urine and serum specimens from 40 volunteers. Aliquots of each specimen were stored for t = 0 and t = 24 h at 4 degrees C prior to freezing, and in the case of serum s les for a further 12 h (t = 36), to determine whether the storage times affected specimen composition and quality. A blinded split-specimen matching exercise was implemented to assign candidate spectral pairs stored for different times using multivariate statistical analysis of the NMR data. Using a chemometric strategy, split specimens at time t = 0 and t = 24 or 36 h after storage at 4 degrees C were easily paired and the split-specimen matching task was reduced to a workable size. (1)H NMR profiling established that the t = 24 h urine and serum groups showed no systematic metabolite changes, indicating biochemical stability. Some small differences in serum specimens stored for t = 36 h at 4 degrees C were detectable only by multivariate analysis, and were attributed to generalized alterations in proteins and protein fragments, and possibly trimethylamine-N-oxide. No other specific metabolite was implicated. For the purposes of NMR-based analysis, storage of urine and serum for up to t = 24 h at 4 degrees C does not detectably affect the metabolic profile and the methodology is robust. Future application of multivariate methods to data-rich studies should substantially enhance information recovery from epidemiological studies.
Publisher: Springer Science and Business Media LLC
Date: 07-2006
Publisher: American Chemical Society (ACS)
Date: 20-01-2017
DOI: 10.1021/ACS.JPROTEOME.6B00710
Abstract: Metabolic phenotyping of obese populations can shed light on understanding environmental interactions underpinning obesogenesis. Obesity and its comorbidities are a major health and socioeconomic concern globally and are highly prevalent in the Middle East. We employed nuclear magnetic resonance spectroscopy to characterize the metabolic signature of urine and blood plasma for a cohort of obese (n = 50) compared to non-obese (n = 48) Saudi participants. The urinary metabolic phenotype of obesity was characterized by higher concentrations of N-acetyl glycoprotein fragments, bile acids, lysine, and methylamines and lower concentrations of tricarboxylic acid cycle intermediates, glycine, and gut microbial metabolites. The plasma metabolic phenotype of obesity was dominated by sugars, branched chain amino acids, and lipids, particularly unsaturated lipids, with lower levels of plasma phosphorylcholine and HDL. Serum hepatic enzymes, triglycerides, and cholesterol mapped to specific metabolic phenotypes, potentially indicating the dysregulation of multiple distinct obesity-related pathways. Differences between urine and plasma phenotypes of obesity for this Saudi population and that reported for Caucasian in iduals indicate population disparities in pathways relating to ketogenesis (more apparent in the Saudi obese population), dysregulated liver function, and the gut microbiome. Mapping population-specific metabolic perturbations may hold promise in establishing population differences relevant to disease risk and stratification of in iduals with respect to discovery of new therapeutic targets.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-06-2012
DOI: 10.1126/SCITRANSLMED.3004244
Abstract: Abnormal microbial-host metabolic interactions underlying disease provide new targets for therapeutic intervention.
Publisher: Springer Science and Business Media LLC
Date: 28-09-2011
DOI: 10.1038/NPP.2011.219
Publisher: Public Library of Science (PLoS)
Date: 27-02-2008
Publisher: Elsevier
Date: 2007
Publisher: Springer Science and Business Media LLC
Date: 25-10-1107
Abstract: Metabolic profiling, metabolomic and metabonomic studies mainly involve the multicomponent analysis of biological fluids, tissue and cell extracts using NMR spectroscopy and/or mass spectrometry (MS). We summarize the main NMR spectroscopic applications in modern metabolic research, and provide detailed protocols for biofluid (urine, serum lasma) and tissue s le collection and preparation, including the extraction of polar and lipophilic metabolites from tissues. 1H NMR spectroscopic techniques such as standard 1D spectroscopy, relaxation-edited, diffusion-edited and 2D J-resolved pulse sequences are widely used at the analysis stage to monitor different groups of metabolites and are described here. They are often followed by more detailed statistical analysis or additional 2D NMR analysis for biomarker discovery. The standard acquisition time per s le is 4-5 min for a simple 1D spectrum, and both preparation and analysis can be automated to allow application to high-throughput screening for clinical diagnostic and toxicological studies, as well as molecular phenotyping and functional genomics.
Publisher: American Chemical Society (ACS)
Date: 06-04-2007
DOI: 10.1021/PR060685N
Abstract: Long-term restriction of energy intake without malnutrition is a robust intervention that has been shown to prolong life and delay age-related morbidity. A 1H NMR-based metabonomic strategy was used to monitor urinary metabolic profiles throughout the lifetimes of control-fed and diet-restricted dogs. Urinary metabolic trajectories were constructed for each dog, and metabolic variation was found to be predominantly influenced by age. Urinary excretion of creatinine increased with age, reaching a maximum between ages 5 and 9 years and declining thereafter. Excretion of mixed glycoproteins was noted at earlier ages, which may be a reflection of growth patterns. In addition, consistent metabolic variation related to diet was also characterized, and energy-associated metabolites, such as creatine, 1-methylnicotinamide, lactate, acetate, and succinate, were depleted in urine from diet-restricted dogs. Both aging and diet restriction altered activities of the gut microbiotia, manifested by variation of aromatic metabolites and aliphatic amine compounds. This analysis allowed the metabolic response to two different physiological processes to be monitored throughout the lifetime of the canine population and may form part of a strategy to monitor and reduce the impact of age related diseases in the dog, as well as providing more general insights into extension of longevity in higher mammals.
Publisher: MDPI AG
Date: 31-08-2022
Abstract: One of the most recognisable features of ageing is a decline in brain health and cognitive dysfunction, which is associated with perturbations to regular lipid homeostasis. Although ageing is the largest risk factor for several neurodegenerative diseases such as dementia, a loss in cognitive function is commonly observed in adults over the age of 65. Despite the prevalence of normal age-related cognitive decline, there is a lack of effective methods to improve the health of the ageing brain. In light of this, exercise has shown promise for positively influencing neurocognitive health and associated lipid profiles. This review summarises age-related changes in several lipid classes that are found in the brain, including fatty acyls, glycerolipids, phospholipids, sphingolipids and sterols, and explores the consequences of age-associated pathological cognitive decline on these lipid classes. Evidence of the positive effects of exercise on the affected lipid profiles are also discussed to highlight the potential for exercise to be used therapeutically to mitigate age-related changes to lipid metabolism and prevent cognitive decline in later life.
Publisher: American Chemical Society (ACS)
Date: 02-03-2012
DOI: 10.1021/PR201161F
Abstract: Galactosamine (galN) is widely used as an in vivo model of acute liver injury. We have applied an integrative approach, combining histopathology, clinical chemistry, cytokine analysis, and nuclear magnetic resonance (NMR) spectroscopic metabolic profiling of biofluids and tissues, to study variability in response to galactosamine following successive dosing. On re-challenge with galN, primary non-responders displayed galN-induced hepatotoxicity (induced response), whereas primary responders exhibited a less marked response (adaptive response). A systems-level metabonomic approach enabled simultaneous characterization of the xenobiotic and endogenous metabolic perturbations associated with the different response phenotypes. Elevated serum cytokines were identified and correlated with hepatic metabolic profiles to further investigate the inflammatory response to galN. The presence of urinary N-acetylglucosamine (glcNAc) correlated with toxicological outcome and reflected the dynamic shift from a resistant to a sensitive phenotype (induced response). In addition, the urinary level of glcNAc and hepatic level of UDP-N-acetylhexosamines reflected an adaptive response to galN. The unique observation of galN-pyrazines and altered gut microbial metabolites in fecal profiles of non-responders suggested that gut microfloral metabolism was associated with toxic outcome. Pharmacometabonomic modeling of predose urinary and fecal NMR spectroscopic profiles revealed a erse panel of metabolites that classified the dynamic shift between a resistant and sensitive phenotype. This integrative pharmacometabonomic approach has been demonstrated for a model toxin however, it is equally applicable to xenobiotic interventions that are associated with wide variation in efficacy or toxicity and, in particular, for prediction of susceptibility to toxicity.
Publisher: Public Library of Science (PLoS)
Date: 29-08-2012
Publisher: Wiley
Date: 08-08-2008
Publisher: Elsevier BV
Date: 03-2015
DOI: 10.1038/KI.2014.297
Abstract: We studied the extent and nature of renal involvement in a cohort of 117 adult patients with mitochondrial disease, by measuring urinary retinol-binding protein (RBP) and albumin established markers of tubular and glomerular dysfunction, respectively. Seventy-five patients had the m.3243A>G mutation and the most frequent phenotypes within the entire cohort were 14 with MELAS, 33 with MIDD, and 17 with MERRF. Urinary RBP was increased in 29 of 75 of m.3243A>G patients, whereas albumin was increased in 23 of the 75. The corresponding numbers were 16 and 14, respectively, in the 42 non-m.3243A>G patients. RBP and albumin were higher in diabetic m.3243A>G patients than in nondiabetics, but there were no significant differences across the three major clinical phenotypes. The urine proteome (mass spectrometry) and metabonome (nuclear magnetic resonance) in a subset of the m.3243A>G patients were markedly different from controls, with the most significant alterations occurring in lysosomal proteins, calcium-binding proteins, and antioxidant defenses. Differences were also found between asymptomatic m.3243A>G carriers and controls. No patients had an elevated serum creatinine level, but 14% had hyponatremia, 10% had hypophosphatemia, and 14% had hypomagnesemia. Thus, abnormalities in kidney function are common in adults with mitochondrial disease, exist in the absence of elevated serum creatinine, and are not solely explained by diabetes.
Publisher: American Chemical Society (ACS)
Date: 28-08-2012
DOI: 10.1021/PR2012544
Publisher: Springer Science and Business Media LLC
Date: 09-08-2018
DOI: 10.1038/S41591-018-0169-5
Abstract: In the version of this article originally published, the received date was missing. It should have been listed as 2 January 2018. The error has been corrected in the HTML and PDF versions of this article.
Publisher: Elsevier
Date: 2016
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 14-01-2021
Publisher: American Chemical Society (ACS)
Date: 06-2012
DOI: 10.1021/PR300197D
Abstract: Administration of the noncompetitive N-methyl-D-aspartate (NMDA) receptor antagonist phencyclidine (PCP) to rodents is widely used as preclinical model for schizophrenia. Most studies on this model employ methods investigating behavior and brain abnormalities. However, little is known about the corresponding peripheral effects. In this study, we analyzed changes in brain and serum molecular profiles, together with alterations in behavior after acute PCP treatment of rats. Furthermore, abnormalities in peripheral protein expression of first and recent onset antipsychotic free schizophrenia patients were assessed for comparison with the preclinical model. PCP treatment induced hyperlocomotion and stereotypic behavior, which have been related to positive symptoms of schizophrenia. Multiplex immunoassay profiling of serum revealed molecular abnormalities similar to those seen in first and recent onset, antipsychotic free schizophrenia patients. Also, increased insulin levels were detected after administration of a glucose tolerance test (GTT), consistent with previous studies showing changes in insulin signaling in patients with schizophrenia. Finally, schizophrenia-relevant alterations in brain molecules were found in the hippoc us and to a lesser extent in the frontal cortex using liquid-chromatography mass spectrometry and (1)H nuclear magnetic resonance spectroscopy. In conclusion, this study identified behavioral and molecular alterations in the acute PCP rat model, which are also observed in human schizophrenia. We propose that the corresponding changes in serum in both animals and patients may have utility as surrogate markers in this model to facilitate discovery and development of novel drugs for treatment of certain pathological features of schizophrenia.
Publisher: American Chemical Society (ACS)
Date: 03-06-2009
DOI: 10.1021/PR900099X
Abstract: Symbiotic gut microbes can have a significant influence on host health and disease etiology. Here, we assessed the effects of inoculating germfree mice with human baby microbiota (HBM, n=17) on the biochemical composition of intact intestinal tissues (duodenum, jejunum, ileum, proximal and distal colon) using magic-angle-spinning 1H NMR spectroscopy. We compared the HBM tissue metabolite profiles with those from conventional (n=9) and conventionalized (n=10) mice. Each topographical intestinal region showed a specific metabolic profile that was altered differentially by the various microbiomes, especially for osmolytes. In each animal model, duodenum had higher ethanolamine and myo-inositol, and ileum higher taurine and betaine than other gut regions. HBM mice showed lower taurine and myo-inositol in the colon, and all ex-germfree animals had higher taurine, choline and ethanolamine in the jejunum. Interestingly, the jejunum of HBM mice was marked by a higher glutathione level and lower concentrations of its precursor methionine when compared to other groups. Proximal and distal colon tissues were differentiated in the different microbiome models by the concentrations of bacterial products (higher in conventional animals). These studies show the depth of gut microbiome modulations of the intestinal biochemistry.
Publisher: American Chemical Society (ACS)
Date: 13-05-2010
DOI: 10.1021/PR901188E
Abstract: Autism is an early onset developmental disorder with a severe life-long impact on behavior and social functioning that has associated metabolic abnormalities. The urinary metabolic phenotypes of in iduals (age range=3-9 years old) diagnosed with autism using the DSM-IV-TR criteria (n = 39 male = 35 female = 4), together with their nonautistic siblings (n = 28 male = 14 female = 14) and age-matched healthy volunteers (n = 34, male = 17 female = 17) have been characterized for the first time using (1)H NMR spectroscopy and pattern recognition methods. Novel findings associated with alterations in nicotinic acid metabolism within autistic in iduals showing increased urinary excretion of N-methyl-2-pyridone-5-carboxamide, N-methyl nicotinic acid, and N-methyl nicotinamide indicate a perturbation in the tryptophan-nicotinic acid metabolic pathway. Multivariate statistical analysis indicated urinary patterns of the free amino acids, glutamate and taurine were significantly different between groups with the autistic children showing higher levels of urinary taurine and a lower level of urinary glutamate, indicating perturbation in sulfur and amino acid metabolism in these children. Additionally, metabolic phenotype (metabotype) differences were observed between autistic and control children, which were associated with perturbations in the relative patterns of urinary mammalian-microbial cometabolites including dimethylamine, hippurate, and phenyacetylglutamine. These biochemical changes are consistent with some of the known abnormalities of gut microbiota found in autistic in iduals and the associated gastrointestinal dysfunction and may be of value in monitoring the success of therapeutic interventions.
Publisher: American Chemical Society (ACS)
Date: 05-06-2012
DOI: 10.1021/PR3001628
Abstract: Most chronic diseases impairing current human public health involve not only the human genome but also gene-environment interactions, and in the latter case the gut microbiome is an important factor. This makes the classical single drug-receptor target drug discovery paradigm much less applicable. There is widespread and increasing international interest in understanding the properties of traditional Chinese medicines (TCMs) for their potential utilization as a source of new drugs for Western markets as emerging evidence indicates that most TCM drugs are actually targeting both the host and its symbiotic microbes. In this review, we explore the challenges of and opportunities for harmonizing Eastern-Western drug discovery paradigms by focusing on emergent functions at the whole body level of humans as superorganisms. This could lead to new drug candidate compounds for chronic diseases targeting receptors outside the currently accepted "druggable genome" and shed light on current high interest issues in Western medicine such as drug-drug and drug-diet-gut microbial interactions that will be crucial in the development and delivery of future therapeutic regimes optimized for the in idual patient.
Publisher: Future Medicine Ltd
Date: 10-2005
Abstract: The utility of metabonomics in the evaluation of xenobiotic toxicity has been comprehensively assessed by the Consortium for Metabonomic Toxicology (COMET), formed between five major pharmaceutical companies and Imperial College London, UK. The main objectives were to assess methodologies, to generate a metabonomic database using 1 H nuclear magnetic resonance (NMR) spectroscopy of rodent urine and blood serum and to build a predictive expert system for target organ toxicity. The analytic and biologic variation that might arise through the use of metabonomics was evaluated and a high degree of robustness demonstrated. With the completion of 147 studies, the chief deliverables of a curated database of rodent biofluid NMR spectra and computer-based expert systems for the prediction of kidney or liver toxicity in rat and mouse based on the spectral data have been generated, and delivered to the sponsoring companies. The project, with its relatively modest resources, has met and exceeded all of its targets and was judged a resounding success by the sponsoring companies who are, in many cases, already enhancing and making use of the data in their in-house studies.
Publisher: American Chemical Society (ACS)
Date: 17-05-2006
DOI: 10.1021/AC051972Y
Abstract: Concurrent with the explosion in the number of publications reporting biomarker discovery by profiling technologies, such as proteomics and pattern recognition, has been the increase in evidence highlighting the susceptibility of these approaches to analytical and experimental bias. The work presented here addresses these timely issues by delivering a detailed characterization of the effect of common sources of bias in clinical studies on serum and plasma profiles generated by a key technology in metabonomics, NMR spectroscopy. Specifically, differences in composition when blood s les were collected onto and in the absence of ice, over a series of serum-clot contact times, the stability of NMR-prepared s les over time and the effect on the metabolic profile of freeze-thawing were examined. While differences between in iduals were far greater than variation from any other experimental factor, each of the conditions examined did cause slight alterations to the NMR profile that could produce a systematic bias. Variation due to clotting time caused changes in energy metabolites, which were delayed by ice with no other spectral effects. Room-temperature stability and hence NMR spectral repeatability were high (<1% intras le variation). Higher molecular weight species such as lipoproteins were more susceptible to the variations present in the examined factors. These observations have implications for profiling study design, and hence, our results form a new and valuable resource for those attempting clinical metabolic profiling, for regulatory agencies involved in the licensing of clinical tests and in the generation of international reporting standards for metabonomics.
Publisher: Springer Science and Business Media LLC
Date: 07-05-2021
DOI: 10.1186/S40168-021-01052-7
Abstract: The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear. Here, we applied an integrative systems medicine approach (faecal metagenomics, plasma and urine metabolomics, hepatic transcriptomics) in 2 well-characterised human cohorts of subjects with obesity (discovery n = 49 and validation n = 628) and an independent cohort formed by both in iduals with and without obesity ( n = 130), combined with in vitro and animal models. Serum ferritin levels, as a markers of liver iron stores, were positively associated with liver fat accumulation in parallel with lower gut microbial gene richness, composition and functionality. Specifically, ferritin had strong negative associations with the Pasteurellaceae , Leuconostocaceae and Micrococcaea families. It also had consistent negative associations with several Veillonella , Bifidobacterium and Lactobacillus species, but positive associations with Bacteroides and Prevotella spp. Notably, the ferritin-associated bacterial families had a strong correlation with iron-related liver genes. In addition, several bacterial functions related to iron metabolism (transport, chelation, heme and siderophore biosynthesis) and NAFLD (fatty acid and glutathione biosynthesis) were also associated with the host serum ferritin levels. This iron-related microbiome signature was linked to a transcriptomic and metabolomic signature associated to the degree of liver fat accumulation through hepatic glucose metabolism. In particular, we found a consistent association among serum ferritin, Pasteurellaceae and Micrococcacea families, bacterial functions involved in histidine transport, the host circulating histidine levels and the liver expression of GYS2 and SEC24B. Serum ferritin was also related to bacterial glycine transporters, the host glycine serum levels and the liver expression of glycine transporters. The transcriptomic findings were replicated in human primary hepatocytes, where iron supplementation also led to triglycerides accumulation and induced the expression of lipid and iron metabolism genes in synergy with palmitic acid. We further explored the direct impact of the microbiome on iron metabolism and liver fact accumulation through transplantation of faecal microbiota into recipient’s mice. In line with the results in humans, transplantation from ‘high ferritin donors’ resulted in alterations in several genes related to iron metabolism and fatty acid accumulation in recipient’s mice. Altogether, a significant interplay among the gut microbiome, iron status and liver fat accumulation is revealed, with potential significance for target therapies.
Publisher: Cambridge University Press (CUP)
Date: 05-05-2010
DOI: 10.1017/S0031182010000260
Abstract: The uses of metabolic profiling technologies such as mass spectrometry and nuclear magnetic resonance spectroscopy in parasitology have been multi-faceted. Traditional uses of spectroscopic platforms focused on determining the chemical composition of drugs or natural products used for treatment of parasitic infection. A natural progression of the use of these tools led to the generation of chemical profiles of the parasite in in vitro systems, monitoring the response of the parasite to chemotherapeutics, profiling metabolic consequences in the host organism and to deriving host-parasite interactions. With the dawn of the post-genomic era the paradigm in many research areas shifted towards Systems Biology and the integration of biomolecular interactions at the level of the gene, protein and metabolite. Although these technologies have yet to deliver their full potential, metabolic profiling has a key role to play in defining diagnostic or even prognostic metabolic signatures of parasitic infection and in deciphering the molecular mechanisms underpinning the development of parasite-induced pathologies. The strengths and weaknesses of the various spectroscopic technologies and analytical strategies are summarized here with respect to achieving these goals.
Publisher: Wiley
Date: 06-1999
DOI: 10.1002/(SICI)1522-2594(199906)41:6<1108::AID-MRM6>3.0.CO;2-M
Abstract: High-resolution magic angle spinning 1H NMR (MAS-NMR) spectroscopy was used to investigate the biochemical composition of normal renal cortex and renal papilla s les from rats, and results were compared with those from conventional 1H NMR analysis of protein-free tissue extracts. 1H MAS NMR spectra of s les obtained from inner and outer cortex were found to be broadly similar in terms of metabolite profile, and intra- and inter-animal variability was small. However, the MAS NMR spectra from renal papilla s les were qualitatively and quantitatively different from those obtained from cortex. High levels of free amino acids and several organic acids were detected in the cortex, together with choline, glucose, and trimethylamine-N-oxide. The dominant metabolite resonances observed in papillary tissue were from glycerophosphocholine (GPC), betaine, myo-inositol, and sorbitol. On increasing the magic angle spinning rate from 4,200 to 12,000 Hz, the lipid MAS 1H NMR signal profile remained largely unchanged in papillary tissue, whereas "new" resonances from triglycerides appeared in the spectra of cortical tissue, this effect being reversible on returning the spinning rate to 4,200 Hz. Further investigation into the behavior of the lipid components under different spinning rates suggested that the lipids in the cortex were present in more motionally constrained environments than those in the papilla. 1H MAS NMR spectra of tissues are of value both in interrogation of the biochemical composition of whole tissue, and in obtaining information on the mobility and compartmentalization of certain metabolites.
Publisher: Frontiers Media SA
Date: 2011
Publisher: American Chemical Society (ACS)
Date: 16-01-2013
DOI: 10.1021/PR3010106
Abstract: Colorectal cancer (CRC) is a major cause of morbidity and mortality in developed countries. Despite operative advances and the widespread adoption of combined-modality treatment, the 5-year survival rarely exceeds 60%. Improving our understanding of the biological processes involved in CRC development and progression will help generate new diagnostic and prognostic approaches. Previous studies have identified altered metabolism as a common feature in carcinogenesis, and quantitative measurement of this altered activity (metabonomics/metabolomics) has the potential to generate novel metabolite-based biomarkers for CRC diagnosis, staging and prognostication. In the present study we applied high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy to analyze metabolites in intact tumor s les (n = 83) and s les of adjacent mucosa (n = 87) obtained from 26 patients undergoing surgical resection for CRC. Orthogonal partial least-squares discriminant analysis (OPLS-DA) of metabolic profiles identified marked biochemical differences between cancer tissue and adjacent mucosa (R(2) = 0.72 Q(2) = 0.45 AUC = 0.91). Taurine, isoglutamine, choline, lactate, phenylalanine, tyrosine (increased concentrations in tumor tissue) together with lipids and triglycerides (decreased concentrations in tumor tissue) were the most discriminant metabolites between the two groups in the model. In addition, tumor tissue metabolic profiles were able to distinguish between tumors of different T- and N-stages according to TNM classification. Moreover, we found that tumor-adjacent mucosa (10 cm from the tumor margin) harbors unique metabolic field changes that distinguish tumors according to T- and N-stage with higher predictive capability than tumor tissue itself and are accurately predictive of 5-year survival (AUC = 0.88), offering a highly novel means of tumor classification and prognostication in CRC.
Publisher: Elsevier BV
Date: 02-2021
Publisher: Proceedings of the National Academy of Sciences
Date: 12-02-2008
Abstract: Humans have evolved intimate symbiotic relationships with a consortium of gut microbes (microbiome) and in idual variations in the microbiome influence host health, may be implicated in disease etiology, and affect drug metabolism, toxicity, and efficacy. However, the molecular basis of these microbe–host interactions and the roles of in idual bacterial species are obscure. We now demonstrate a“transgenomic” approach to link gut microbiome and metabolic phenotype (metabotype) variation. We have used a combination of spectroscopic, microbiomic, and multivariate statistical tools to analyze fecal and urinary s les from seven Chinese in iduals (s led twice) and to model the microbial–host metabolic connectivities. At the species level, we found structural differences in the Chinese family gut microbiomes and those reported for American volunteers, which is consistent with population microbial cometabolic differences reported in epidemiological studies. We also introduce the concept of functional metagenomics, defined as “the characterization of key functional members of the microbiome that most influence host metabolism and hence health.” For ex le, Faecalibacterium prausnitzii population variation is associated with modulation of eight urinary metabolites of erse structure, indicating that this species is a highly functionally active member of the microbiome, influencing numerous host pathways. Other species were identified showing different and varied metabolic interactions. Our approach for understanding the dynamic basis of host–microbiome symbiosis provides a foundation for the development of functional metagenomics as a probe of systemic effects of drugs and diet that are of relevance to personal and public health care solutions.
Publisher: American Chemical Society (ACS)
Date: 15-04-2004
DOI: 10.1021/TX034212W
Abstract: Metabonomics can be viewed as the process of defining multivariate metabolic trajectories that describe the systemic response of organisms to physiological perturbations through time. We have explored the hypothesis that the homothetic geometry of a metabolic trajectory, i.e., the metabolic response irrespective of baseline values and overall magnitude, defines the mode of response of the organism to treatment and is hence the key property when considering the similarity between two sets of measurements. A modeling strategy to test for homothetic geometry, called scaled-to-maximum, aligned, and reduced trajectories (SMART) analysis, is presented that together with principal components analysis (PCA) facilitates the visualization of multivariate response similarity and hence the interpretation of metabonomic data. Several ex les of the utility of this approach from toxicological studies are presented as follows: interlaboratory variation in hydrazine response, CCl(4) dose-response relationships, and interspecies comparison of bromobenzene toxicity. In each case, the homothetic trajectories hypothesis is shown to be an important concept for the successful multivariate modeling and interpretation of systemic metabolic change. Overall, geometric trajectory analysis based on a homothetic modeling strategy like SMART facilitates the amalgamation and comparison of metabonomic data sets and can improve the accuracy and precision of classification models based on metabolic profile data. Because interlaboratory variation, normal physiological variation, dose-response relationships, and interspecies differences are also key areas of concern in genomic and proteomic as well as metabonomic studies, the methods presented here may also have an impact on many other multilaboratory efforts to produce screenable "-omics" databases useful for gauging toxicity in safety assessment and drug discovery.
Publisher: American Chemical Society (ACS)
Date: 26-11-2014
DOI: 10.1021/PR400748F
Abstract: Bariatric procedures such as the Roux-en-Y gastric bypass (RYGB) operation offer profound metabolic enhancement in addition to their well-recognized weight loss effects. They are associated with significant reduction in cardiovascular disease risk and mortality, which suggests a surgical modification on cardiac metabolism. Metabolic phenotyping of the cardiac tissue and plasma postsurgery may give insight into cardioprotective mechanisms. The aim of the study was to compare the metabolic profiles of plasma and heart tissue extracts from RYGB- and sham-operated Wistar rats to identify the systemic and cardiac signature of metabolic surgery. A total of 27 male Wistar rats were housed in idually for a week and subsequently underwent RYGB (n = 13) or sham (n = 14) operation. At week 8 postoperation, a total of 27 plasma s les and 16 heart tissue s les (8 RYGB 8 Sham) were collected from animals and analyzed using (1)H nuclear magnetic resonance (NMR) spectroscopy and ultra performance liquid chromatography (UPLC-MS) to characterize the global metabolite perturbation induced by RYGB operation. Plasma bile acids, phosphocholines, amino acids, energy-related metabolites, nucleosides and amine metabolites, and cardiac glycogen and amino acids were found to be altered in the RYGB operated group. Correlation networks were used to identify metabolite association. The metabolic phenotype of this bariatric surgical model inferred systematic change in both myocardial and systemic activity post surgery. The altered metabolic profile following bariatric surgery reflects an enhancement of cardiac energy metabolism through TCA cycle intermediates, cardiorenal protective activity, and biochemical caloric restriction. These surgically induced metabolic shifts identify some of the potential mechanisms that contribute toward bariatric cardioprotection through gut microbiota ecological fluxes and an enterocardiac axis to shield against metabolic syndrome of cardiac dysfunction.
Publisher: BMJ
Date: 08-06-2021
DOI: 10.1136/GUTJNL-2020-323609
Abstract: Gut function remains largely underinvestigated in undernutrition, despite its critical role in essential nutrient digestion, absorption and assimilation. In areas of high enteropathogen burden, alterations in gut barrier function and subsequent inflammatory effects are observable but remain poorly characterised. Environmental enteropathy (EE)—a condition that affects both gut morphology and function and is characterised by blunted villi, inflammation and increased permeability—is thought to play a role in impaired linear growth (stunting) and severe acute malnutrition. However, the lack of tools to quantitatively characterise gut functional capacity has h ered both our understanding of gut pathogenesis in undernutrition and evaluation of gut-targeted therapies to accelerate nutritional recovery. Here we survey the technology landscape for potential solutions to improve assessment of gut function, focussing on devices that could be deployed at point-of-care in low-income and middle-income countries (LMICs). We assess the potential for technological innovation to assess gut morphology, function, barrier integrity and immune response in undernutrition, and highlight the approaches that are currently most suitable for deployment and development. This article focuses on EE and undernutrition in LMICs, but many of these technologies may also become useful in monitoring of other gut pathologies.
Publisher: American Society for Microbiology
Date: 26-06-2018
DOI: 10.1128/MSYSTEMS.00044-18
Abstract: The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and erse gut microbiome characteristics. These characteristics are associated with levels of protein consumption and levels of physical activity. The results of this study show that increasing the fitness levels of physically inactive humans leads to modest but detectable changes in gut microbiota characteristics. For the first time, we show that regular whey protein intake leads to significant alterations to the composition of the gut virome.
Publisher: American Chemical Society (ACS)
Date: 19-06-2017
DOI: 10.1021/ACS.JPROTEOME.6B00894
Abstract: Abdominal aortic aneurysm (AAA) is a complex disease posing diagnostic and therapeutic challenges. Metabonomics may aid in the diagnosis of AAA, determination of in idualized risk, discovery of therapeutic targets, and improve understanding of pathogenesis. A systematic review of the ersity and outcomes of existing AAA metabonomic research has been performed. Original research studies applying metabonomics to human aneurysmal disease are included. Seven relevant articles were identified: four studies were based on plasma/serum metabolite profiling, and three studies examined aneurysmal tissue. Aminomalonic acid, guanidinosuccinic acid, and glycerol emerge as potential plasma biomarkers of large aneurysm. Lipid profiling improves predictive models of aneurysm presence. Patterns of metabolite variation associated with AAA relate to carbohydrate and lipid metabolism. Perioperative perturbations in metabolites suggest differential systemic inflammatory responses to surgery, generating hypotheses for adjunctive perioperative therapy. Significant limitations include small study sizes, lack of correction for multiple testing false discovery rates, and single time-point s ling. Metabolic profiling carries the potential to identify biomarkers of AAA and elucidate pathways underlying aneurysmal disease. Statistically and methodologically robust studies are required for validation, addressing the hiatus in understanding mechanisms of aneurysm growth and developing effective treatment strategies.
Publisher: American Chemical Society (ACS)
Date: 19-02-2018
Publisher: American Chemical Society (ACS)
Date: 16-06-2005
DOI: 10.1021/PR050032R
Abstract: We report details of metabolic profiles for small intestinal s les obtained using high-resolution magic-angle-spinning (HRMAS) (1)H NMR spectroscopy. Intact s les of jejunum and ileum from male Long Evans rats were analyzed on a 600 MHz spectrometer using standard one and two-dimensional (1)H NMR spectroscopic pulse sequences. The metabolic profiles of ileum and jejunum predominantly comprised a number of amino acids, lipids, glycerophosphocholine (GPC), choline, creatine, and ethanol, a number of carboxylic acids including acetate and lactate, and nucleoside bases including cytosine, isocytosine, and uracil. Principal component analysis (PCA) was applied to these NMR data to characterize the biochemical differences between jejunum and ileum tissues. Compared with ileum, jejunum contained higher levels of lipids, GPC, choline, lactate and creatinine, but lower levels of amino acids and acetate. In addition, the age dependence of the biochemical composition of intestinal tissues from young rats (15, 36 days and 3-4 months old) was studied. In general, levels of lipids, lactate, taurine and creatinine were positively correlated with age while amino acids and GPC decreased in the older age group. This study will provide a metabolic reference for further studies assessing the metabolic consequences of nutrition, stress and gut microbiota on intestinal composition.
Publisher: American Chemical Society (ACS)
Date: 23-02-2015
DOI: 10.1021/PR5009898
Abstract: Current optimum medical treatments have had limited success in the primary prevention of cardiovascular events, underscoring the need for new pharmaceutical targets and enhanced understanding of mechanistic metabolic dysregulation. Here, we use a combination of novel metabolic profiling methodologies, based on ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS) followed by chemometric modeling, data integration, and pathway mapping, to create a systems-level metabolic atlas of atherogenesis. We apply this workflow to compare arterial tissue incorporating plaque lesions to intimal thickening tissue (immediate preplaque stage). We find changes in several metabolite species consistent with well-established pathways in atherosclerosis, such as the cholesterol, purine, pyrimidine, and ceramide pathways. We then illustrate differential levels of previously unassociated lipids to atherogenesis, namely, phosphatidylethanolamine-ceramides (t-test p-values: 3.8 × 10(-6) to 9.8 × 10(-12)). Most importantly, these molecules appear to be interfacing two pathways recognized for their involvement in atherosclerosis: ceramide and cholesterol. Furthermore, we show that β-oxidation intermediates (i.e., acylcarnitines) manifest a pattern indicating truncation of the process and overall dysregulation of fatty acid metabolism and mitochondrial dysfunction. We develop a metabolic framework that offers the ability to map significant statistical associations between detected biomarkers. These dysregulated molecules and consequent pathway modulations may provide novel targets for pharmacotherapeutic intervention.
Publisher: Elsevier BV
Date: 09-2010
Publisher: American Chemical Society (ACS)
Date: 24-11-2014
DOI: 10.1021/PR5008202
Abstract: Parasitic infections such as leishmaniasis induce a cascade of host physiological responses, including metabolic and immunological changes. Infection with Leishmania major parasites causes cutaneous leishmaniasis in humans, a neglected tropical disease that is difficult to manage. To understand the determinants of pathology, we studied L. major infection in two mouse models: the self-healing C57BL/6 strain and the nonhealing BALB/c strain. Metabolic profiling of urine, plasma, and feces via proton NMR spectroscopy was performed to discover parasite-specific imprints on global host metabolism. Plasma cytokine status and fecal microbiome were also characterized as additional metrics of the host response to infection. Results demonstrated differences in glucose and lipid metabolism, distinctive immunological phenotypes, and shifts in microbial composition between the two models. We present a novel approach to integrate such metrics using correlation network analyses, whereby self-healing mice demonstrated an orchestrated interaction between the biological measures shortly after infection. In contrast, the response observed in nonhealing mice was delayed and fragmented. Our study suggests that trans-system communication across host metabolism, the innate immune system, and gut microbiome is key for a successful host response to L. major and provides a new concept, potentially translatable to other diseases.
Publisher: Elsevier BV
Date: 1990
Publisher: American Chemical Society (ACS)
Date: 28-05-2003
DOI: 10.1021/JF025677F
Abstract: Flavonoid consumption via tea drinking has been attributed a number of potential health benefits including cancer prevention, anti-inflammatory action, and cardioprotectant activity. Although the predominant flavonoids in fresh leaf and green tea are known to be flavan-3-ols and flavan-3-O-gallates ("the catechins"), the biochemical effects of tea polyphenol consumption on living systems are generally poorly understood. Metabonomic methods utilizing (1)H NMR spectroscopy of biofluids and principal component analysis (PCA) have been applied to investigate the bioavailability and metabolic responses of rats to a single dose of 22 mg of epicatechin (EC) dissolved in water. Urine s les were collected twice daily (0-8 and 8-24 h) from male Sprague-Dawley rats (n = 10) prior to dosing and for 2 days after dosing. A series of subtle urinary biochemical effects were evident from the (1)H NMR spectra showing that EC was both bioavailable and biochemically active. The identifiable biochemical effects associated with EC dosing included decreased urinary concentrations of taurine, citrate, dimethylamine, and 2-oxoglutarate. These effects were predominately seen within the first 8 h after dosing. EC metabolites were also observed in the urine during this time period. PCA of later time points after dosing (24-32 and 32-48 h) showed that the effects of EC were reversible. This is the first in vivo study demonstrating the overall endogenous metabolic effects of EC consumption and shows the bioavailability of EC via metabolic effects and excretion of EC metabolites.
Publisher: American Chemical Society (ACS)
Date: 30-06-2015
DOI: 10.1021/ACS.JPROTEOME.5B00105
Abstract: Schizophrenia is a neuropsychiatric disorder affecting 1% of the world's population. Due to both a broad range of symptoms and disease heterogeneity, current therapeutic approaches to treat schizophrenia fail to address all symptomatic manifestations of the disease. Therefore, disease models that reproduce core pathological features of schizophrenia are needed for the elucidation of pathological disease mechanisms. Here, we employ a comprehensive global label-free liquid chromatography-mass spectrometry proteomic (LC-MS(E)) and metabonomic (LC-MS) profiling analysis combined with the targeted proteomics (selected reaction monitoring and multiplex immunoassay) of serum and brain tissues to investigate a chronic phencyclidine (PCP) rat model in which glutamatergic hypofunction is induced through noncompetitive NMDAR-receptor antagonism. Using a multiplex immunoassay, we identified alterations in the levels of several cytokines (IL-5, IL-2, and IL-1β) and fibroblast growth factor-2. Extensive proteomic and metabonomic brain tissue profiling revealed a more prominent effect of chronic PCP treatment on both the hippoc al proteome and metabonome compared to the effect on the frontal cortex. Bioinformatic pathway analysis confirmed prominent abnormalities in NMDA-receptor-associated pathways in both brain regions, as well as alterations in other neurotransmitter systems such as kainate, AMPA, and GABAergic signaling in the hippoc us and in proteins associated with neurodegeneration. We further identified abundance changes in the level of the superoxide dismutase enzyme (SODC) in both the frontal cortex and hippoc us, which indicates alterations in oxidative stress and substantiates the apoptotic pathway alterations. The present study could lead to an increased understanding of how perturbed glutamate receptor signaling affects other relevant biological pathways in schizophrenia and, therefore, support drug discovery efforts for the improved treatment of patients suffering from this debilitating psychiatric disorder.
Publisher: Wiley
Date: 11-1992
Abstract: Bacteroides species are promising indicators for differentiating livestock and human fecal contamination in water because of their high concentration in feces and potential host specificity. In this study, a real-time PCR assay was designed to target Bacteroides species (AllBac) present in human, cattle, and equine feces. Direct PCR lification (without DNA extraction) using the AllBac assay was tested on feces diluted in water. Fecal concentrations and threshold cycle were linearly correlated, indicating that the AllBac assay can be used to estimate the total amount of fecal contamination in water. Real-time PCR assays were also designed for bovine-associated (BoBac) and human-associated (HuBac) Bacteroides 16S rRNA genes. Assay specificities were tested using human, bovine, swine, canine, and equine fecal s les. The BoBac assay was specific for bovine fecal s les (100% true-positive identification 0% false-positive identification). The HuBac assay had a 100% true-positive identification, but it also had a 32% false-positive rate with potential for cross- lification with swine feces. The assays were tested using creek water s les from three different watersheds. Creek water did not inhibit PCR, and results from the AllBac assay were correlated with those from Escherichia coli concentrations (r2= 0.85). The percentage of feces attributable to bovine and human sources was determined for each s le by comparing the values obtained from the BoBac and HuBac assays with that from the AllBac assay. These results suggest that real-time PCR assays without DNA extraction can be used to quantify fecal concentrations and provide preliminary fecal source identification in watersheds.
Publisher: Wiley
Date: 06-1998
DOI: 10.1002/(SICI)1099-1492(199806/08)11:4/5<235::AID-NBM507>3.0.CO;2-V
Abstract: Pattern recognition approaches were developed and applied to the classification of 600 MHz 1H NMR spectra of urine from rats dosed with compounds that induced organ-specific damage in either the liver or kidney. Male rats were separated into groups (n = 5) and each treated with one of the following compounds adriamycin, allyl alcohol, 2-bromoethanamine hydrobromide, hexachlorobutadiene, hydrazine, lead acetate, mercury II chloride, puromycin aminonucleoside, sodium chromate, thioacetamide, 1,1,2-trichloro-3,3,3-trifluoro-1-propene or dose vehicle. Urine s les were collected over a 7 day time-course and analysed using 600 MHz 1H NMR spectroscopy. Each NMR spectrum was data-reduced to provide 256 intensity-related descriptors of the spectra. Data corresponding to the periods 8-24 h, 24-32 h and 32-56 h post-dose were first analysed using principal components analysis (PCA). In addition, s les obtained 120-144 h following the administration of adriamycin and puromycin were included in the analysis in order to compensate for the late onset of glomerular toxicity. Having established that toxin-related clustering behaviour could be detected in the first three principal components (PCs), three-quarters of the data were used to construct a soft independent modelling of class analogy (SIMCA) model. The remainder of the data were used as a test set of the model. Only three out of 61 s les in the test set were misclassified. Finally as a further test of the model, data from the 1H NMR spectra of urine from rats that had been treated with uranyl nitrate were used. Successful prediction of the toxicity type of the compound was achieved based on NMR urinalysis data confirming the robust nature of the derived model.
Publisher: Springer Science and Business Media LLC
Date: 21-06-2022
DOI: 10.1038/S41598-022-13640-0
Abstract: Broad-spectrum antimicrobial use during the treatment of critical illness influences gastrointestinal fermentation endpoints, host immune response and metabolic activity including the conversion of primary to secondary bile acids. We previously observed reduced fermentation capacity in the faecal microbiota of critically ill children upon hospital admission. Here, we further explore the timecourse of the relationship between the microbiome and bile acid profile in faecal s les collected from critically ill children. The microbiome was assayed by sequencing of the 16S rRNA gene, and faecal water bile acids were measured by liquid chromatography mass spectrometry. In comparison to admission faecal s les, members of the Lachnospiraceae recovered during the late-acute phase (days 8–10) of hospitalisation. Patients with infections had a lower proportion of Lachnospiraceae in their gut microbiota than controls and patients with primary admitting diagnoses. Keystone species linked to ecological recovery were observed to decline with the length of PICU admission. These species were further suppressed in patients with systemic infection, respiratory failure, and undergoing surgery. Bile acid composition recovers quickly after intervention for critical illness which may be aided by the compositional shift in Lachnospiraceae . Our findings suggest gut microbiota recovery can be readily assessed via measurement of faecal bile acids.
Publisher: American Chemical Society (ACS)
Date: 30-05-2008
DOI: 10.1021/AC702584G
Abstract: A novel model-free statistical approach (self modeling curve resolution, SMCR) has been applied to recover biochemical information from complex overlapping signals in (1)H NMR spectra of blood serum in a long-term study of caloric restriction (CR) in the dog (n = 24 control fed (CF) and n = 24 CR animals). A new statistical spectroscopic construct, the spectrotype, is proposed which is a spectroscopic subset description or component of a metabolic phenotype. Characterization of the (1)H NMR profiles according to their evolutionary contribution of each spectrotype gives clues to the kinetics of the macro-biochemical response profiles and the identity of the underlying biochemical constituents, governing the evolutionary global response to an intervention. This information can be used to monitor and predict the end point of the biological process and to identify the mechanisms responsible for those changes. Here a SMCR strategy together with a pattern recognition method, principal component analysis (PCA) was used to resolve sets of spectrotypes, without a priori information. From the (1)H NMR evolutionary response profiles, two spectrotypes were identified and resolved spectrotype 1 dominated by lipids featuring contributions from phosphatidylcholine, lipoprotein lipid fatty acyl groups from triglycerides, phospholipids, and cholesteryl esters plus total cholesterol (i.e., both esterified and unesterified) spectrotype 2 comprising glucose signals and a poorly resolved envelope of albumin and N-acetylated glycoprotein resonances. The relative contributions of these spectrotypes in each s le were calculated. For both caloric restricted (CR) and control fed (CF) dogs between ages 1 and 9 years, the contribution of spectrotype 2 > spectrotype 1, whereas for dogs aged between 9 and 12 years spectrotype 1 > spectrotype 2. Therefore, SMCR analysis pinpointed ages where nutrition and aging metabolic changes became significant within serum s les as well as providing the in idual longitudinal contribution profiles associated with each spectrotype, which could potentially be used as part of a strategy to monitor and predict longevity and morbidity in populations. Hence SMCR is a useful addition to the chemometric "toolbox" for metabolic analysis and should have erse applications within other biomedical conditions characterized by subtle time-dependent changes.
Publisher: Elsevier
Date: 2007
Publisher: EMBO
Date: 2007
DOI: 10.1038/MSB4100153
Publisher: Informa UK Limited
Date: 2002
DOI: 10.1080/00498250110100739
Abstract: 1. The relationship between the in vivo metabolism of substituted anilines, in particular N-acetylation and subsequent formation of oxanilic acids, and their molecular physico-chemical properties has been investigated using computational chemistry and pattern-recognition methods. The methods revealed that the physico-chemical properties most important for N-acetylation and subsequent oxanilic acid formation were electronic descriptors based on partial atomic charges and the susceptibility of the molecules to nucleophilic attack at certain ring positions. 2. The calculated partial atom charge on the amine nitrogen was the parameter most important for predicting that an aniline would be N-acetylated. The calculated nucleophilic susceptibility of the aromatic carbon para to the amino group (NS4) was the most significant parameter for determining oxanilic acid formation following N-acetylation. Thus, highly electron-withdrawing groups substituted at this position gave higher nucleophilic susceptibilities that were related to the presence of an oxanilic acid metabolite. 3. If the parameters relating to N-acetylation were modified by other electron-withdrawing groups in the ring (particularly at the position ortho to the amino group), then acetylation and subsequent oxanilic acid formation did not occur. The introduction of groups that allow the possibility of competing oxidative metabolic pathways elsewhere in the molecule (e.g. CH(3)) also affected the production of oxanilic acids. 4. Using chemometric analysis of the computed physico-chemical properties, the result has been the generation of a model that classifies the metabolism of a number of anilines. This could be used to predict the acetylation and oxanilic formation propensity of a number of substituted anilines whose metabolism was unknown to the system, demonstrating that such techniques may be of use for predicting metabolism and hence could provide support for rational drug design.
Publisher: American Chemical Society (ACS)
Date: 08-01-2008
DOI: 10.1021/PR070350L
Abstract: Multivariate metabolic profiles from biofluids such as urine and plasma are highly indicative of the biological fitness of complex organisms and can be captured analytically in order to derive top-down systems biology models. The application of currently available modeling approaches to human and animal metabolic pathway modeling is problematic because of multicompartmental cellular and tissue exchange of metabolites operating on many time scales. Hence, novel approaches are needed to analyze metabolic data obtained using minimally invasive s ling methods in order to reconstruct the patho-physiological modulations of metabolic interactions that are representative of whole system dynamics. Here, we show that spectroscopically derived metabolic data in experimental liver injury studies (induced by hydrazine and alpha-napthylisothiocyanate treatment) can be used to derive insightful probabilistic graphical models of metabolite dependencies, which we refer to as metabolic interactome maps. Using these, system level mechanistic information on homeostasis can be inferred, and the degree of reversibility of induced lesions can be related to variations in the metabolic network patterns. This approach has wider application in assessment of system level dysfunction in animal or human studies from noninvasive measurements.
Publisher: Informa UK Limited
Date: 05-2019
DOI: 10.2147/HMER.S193996
Publisher: American Chemical Society (ACS)
Date: 14-05-2010
DOI: 10.1021/AC1007078
Abstract: We have developed an ultra performance liquid chromatography-mass spectrometry (UPLC-MS(E)) method to measure bile acids (BAs) reproducibly and reliably in biological fluids and have applied this approach for indications of hepatic damage in experimental toxicity studies. BAs were extracted from serum using methanol, and an Acquity HSS column coupled to a Q-ToF mass spectrometer was used to separate and identify 25 in idual BAs within 5 min. Employing a gradient elution of water and acetonitrile over 21 min enabled the detection of a wide range of endogenous metabolites, including the BAs. The utilization of MS(E) allowed for characteristic fragmentation information to be obtained in a single analytical run, easily distinguishing glycine and taurine BA conjugates. The proportions of these conjugates were altered markedly in an experimental toxic state induced by galactosamine exposure in rats. Principally, taurine-conjugated BAs were greatly elevated ( approximately 50-fold from control levels), and were highly correlated to liver damage severity as assessed by histopathological scoring (r = 0.83), indicating their potential as a sensitive measure of hepatic damage. The UPLC-MS approach to BA analysis offers a sensitive and reproducible tool that will be of great value in exploring both markers and mechanisms of hepatotoxicity and can readily be extended to clinical studies of liver damage.
Publisher: American Chemical Society (ACS)
Date: 13-03-2009
DOI: 10.1021/PR801068X
Abstract: Coevolution shapes interorganismal crosstalk leading to profound and erse cellular and metabolic changes as observed in gut dysbiosis in human diseases. Here, we modulated a simplified gut microbiota using pro-, pre-, and synbiotics to assess the depth of systemic metabolic exchanges in mice, using a multicompartmental modeling approach with metabolic signatures from 10 tissue/fluid compartments. The nutritionally induced microbial changes modulated host lipid, carbohydrate, and amino acid metabolism at a panorganismal scale. Galactosyl-oligosaccharides reduced lipogenesis, triacylglycerol incorporation into lipoproteins and triglyceride concentration in the liver and the kidney. Those changes were not correlated with decreased plasma lipoproteins that were specifically induced by L. rhamnosus supplementation. Additional alteration of transmethylation metabolic pathways (homocysteine-betaine) was observed in the liver and the pancreas following pre- and synbiotic microbial modulation, which may be of interest for control of glucose metabolism and insulin sensitivity. Probiotics also reduced hepatic glycogen and glutamine and adrenal ascorbate with inferred effects on energy homeostasis, antioxidation, and steroidogenesis. These studies show the breadth and the depth of gut microbiome modulations of host biochemistry and reveal that major mammalian metabolic processes are under symbiotic homeostatic control.
Publisher: Future Science Ltd
Date: 04-2015
DOI: 10.4155/BIO.14.300
Abstract: Background: Tenofovir disoproxil fumarate (TDF) is an antiretroviral drug used for the treatment of Human Immunodeficiency Virus and Hepatitis B infections. Results: A metabolite that has previously not been observed in the circulation of humans was detected by LC–MS/MS in early time point plasma s les following administration of TDF to healthy volunteers. The metabolite was identified using a range of LC–MS/MS-based techniques as a monoester of TDF, derived from the partially hydrolyzed bis-ester prodrug. TDF, when spiked into plasma, was observed to degrade first to the putative monoester and subsequently to tenofovir. Conclusion: The presence of this unstable metabolite in some s les has implications for s le collection, handling and storage in studies of tenofovir where serum concentrations are determined.
Publisher: Springer Science and Business Media LLC
Date: 10-12-2020
DOI: 10.1038/S41598-020-78031-9
Abstract: Finding early disease markers using non-invasive and widely available methods is essential to develop a successful therapy for Alzheimer’s Disease. Few studies to date have examined urine, the most readily available biofluid. Here we report the largest study to date using comprehensive metabolic phenotyping platforms (NMR spectroscopy and UHPLC-MS) to probe the urinary metabolome in-depth in people with Alzheimer’s Disease and Mild Cognitive Impairment. Feature reduction was performed using metabolomic Quantitative Trait Loci, resulting in the list of metabolites associated with the genetic variants. This approach helps accuracy in identification of disease states and provides a route to a plausible mechanistic link to pathological processes. Using these mQTLs we built a Random Forests model, which not only correctly discriminates between people with Alzheimer’s Disease and age-matched controls, but also between in iduals with Mild Cognitive Impairment who were later diagnosed with Alzheimer’s Disease and those who were not. Further annotation of top-ranking metabolic features nominated by the trained model revealed the involvement of cholesterol-derived metabolites and small-molecules that were linked to Alzheimer’s pathology in previous studies.
Publisher: Wiley
Date: 06-11-2009
DOI: 10.1002/MRC.2521
Abstract: High-resolution (1)H magic angle spinning (MAS) NMR spectroscopy is a useful tool for analysing intact tissues as a component of metabonomic studies. The effect of referencing MAS NMR spectra to the chemical shifts of glucose or to that or trimethylsilylpropionic acid on the resultant multivariate statistical models have been investigated. It is shown that referencing to known chemical shifts of either alpha-glucose or beta-glucose in (1)H MAS NMR-based metabolic data of intact liver tissues is preferred. This has been exemplified in studies of galactosamine toxicity in the rat where co-administration of glycine ameliorates the toxic response. This approach leads to better aligned sets of spectra and reduces the inter-s le variability in multivariate statistical models. If glucose is not present in the tissue under study, then a number of alternative internal reference chemical shifts are presented. Finally, the chemical shift difference between that of the anomeric H1 proton of alpha-glucose and residual water is confirmed as a suitable internal temperature calibration method.
Publisher: American Chemical Society (ACS)
Date: 08-03-2013
DOI: 10.1021/PR400051S
Abstract: We investigated the short-term (7 days) and long-term (60 days) metabolic effect of high fat diet induced obesity (DIO) and weight gain in isogenic C57BL/6 mice and examined the specific metabolic differentiation between mice that were either strong-responders (SR), or non-responders (NR) to weight gain. Mice (n = 80) were fed a standard chow diet for 7 days prior to randomization into a high-fat (HF) (n = 56) or a low-fat (LF) (n = 24) diet group. The (1)H NMR urinary metabolic profiles of LF and HF mice were recorded 7 and 60 days after the diet switch. On the basis of the body weight gain (BWG) distribution of HF group, we identified NR mice (n = 10) and SR mice (n = 14) to DIO. Compared with LF, HF feeding increased urinary excretion of glycine conjugates of β-oxidation intermediate (hexanoylglycine), branched chain amino acid (BCAA) catabolism intermediates (isovalerylglycine, α-keto-β-methylvalerate and α-ketoisovalerate) and end-products of nicotinamide adenine dinucleotide (NAD) metabolism (N1-methyl-2-pyridone-5-carboxamide, N1-methyl-4-pyridone-3-carboxamide) suggesting up-regulation of mitochondrial oxidative pathways. In the HF group, NR mice excreted relatively more hexanoylglycine, isovalerylglycine, and fewer tricarboxylic acid (TCA) cycle intermediate (succinate) in comparison to SR mice. Thus, subtle regulation of ketogenic pathways in DIO may alleviate the saturation of the TCA cycle and mitochondrial oxidative metabolism.
Publisher: Springer Science and Business Media LLC
Date: 30-06-2021
DOI: 10.1038/S41586-021-03739-1
Abstract: Although two-dose mRNA vaccination provides excellent protection against SARS-CoV-2, there is little information about vaccine efficacy against variants of concern (VOC) in in iduals above eighty years of age 1 . Here we analysed immune responses following vaccination with the BNT162b2 mRNA vaccine 2 in elderly participants and younger healthcare workers. Serum neutralization and levels of binding IgG or IgA after the first vaccine dose were lower in older in iduals, with a marked drop in participants over eighty years old. Sera from participants above eighty showed lower neutralization potency against the B.1.1.7 (Alpha), B.1.351 (Beta) and P.1. (Gamma) VOC than against the wild-type virus and were more likely to lack any neutralization against VOC following the first dose. However, following the second dose, neutralization against VOC was detectable regardless of age. The frequency of SARS-CoV-2 spike-specific memory B cells was higher in elderly responders (whose serum showed neutralization activity) than in non-responders after the first dose. Elderly participants showed a clear reduction in somatic hypermutation of class-switched cells. The production of interferon-γ and interleukin-2 by SARS-CoV-2 spike-specific T cells was lower in older participants, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high-risk population and that specific measures to boost vaccine responses in this population are warranted, particularly where variants of concern are circulating.
Publisher: Springer Science and Business Media LLC
Date: 14-06-2021
DOI: 10.1186/S40168-021-01086-X
Abstract: Bariatric surgery, used to achieve effective weight loss in in iduals with severe obesity, modifies the gut microbiota and systemic metabolism in both humans and animal models. The aim of the current study was to understand better the metabolic functions of the altered gut microbiome by conducting deep phenotyping of bariatric surgery patients and bacterial culturing to investigate causality of the metabolic observations. Three bariatric cohorts ( n = 84, n = 14 and n = 9) with patients who had undergone Roux-en-Y gastric bypass (RYGB), sleeve gastrectomy (SG) or laparoscopic gastric banding (LGB), respectively, were enrolled. Metabolic and 16S rRNA bacterial profiles were compared between pre- and post-surgery. Faeces from RYGB patients and bacterial isolates were cultured to experimentally associate the observed metabolic changes in biofluids with the altered gut microbiome. Compared to SG and LGB, RYGB induced the greatest weight loss and most profound metabolic and bacterial changes. RYGB patients showed increased aromatic amino acids-based host-bacterial co-metabolism, resulting in increased urinary excretion of 4-hydroxyphenylacetate, phenylacetylglutamine, 4-cresyl sulphate and indoxyl sulphate, and increased faecal excretion of tyramine and phenylacetate. Bacterial degradation of choline was increased as evidenced by altered urinary trimethylamine- N -oxide and dimethylamine excretion and faecal concentrations of dimethylamine. RYGB patients’ bacteria had a greater capacity to produce tyramine from tyrosine, phenylalanine to phenylacetate and tryptophan to indole and tryptamine, compared to the microbiota from non-surgery, normal weight in iduals. 3-Hydroxydicarboxylic acid metabolism and urinary excretion of primary bile acids, serum BCAAs and dimethyl sulfone were also perturbed following bariatric surgery. Altered bacterial composition and metabolism contribute to metabolic observations in biofluids of patients following RYGB surgery. The impact of these changes on the functional clinical outcomes requires further investigation.
Publisher: Springer Science and Business Media LLC
Date: 22-03-2017
DOI: 10.1038/MP.2016.27
Publisher: Public Library of Science (PLoS)
Date: 22-08-2006
Publisher: American Chemical Society (ACS)
Date: 19-10-2002
DOI: 10.1021/TX025571E
Abstract: We report here the combined application of (1)H magic angle spinning (MAS) and high-resolution NMR spectroscopy and pattern recognition methods to study the effects of a model toxin (D-galactosamine) in liver spheroid cultures. (1)H NMR spectra of metabolic profiles of spheroids showed closer similarities to intact liver spectra than those of isolated hepatocytes, suggesting their superiority as an in vitro model system. Batches of spheroids were prepared from male Sprague Dawley rat livers and incubated in control hepatocyte medium or medium containing D-galactosamine (4 or 20 mM) for 4 or 24 h. Intact spheroids were packed into rotors and analyzed using MAS-NMR spectroscopy or homogenized and analyzed using conventional (1)H NMR spectroscopy. Principal components analysis, (PCA), of the NMR data revealed separation of control and D-galactosamine-treated spheroids based on changes in the concentrations of the triglycerides and elevations in cholesterol and esters. The absence of cholesterol in hepatocytes and the relative under-representation of the lipid resonances offer an important advantage of spheroids over hepatocytes for the (1)H NMR studies of fatty liver. Orthogonal signal correction (OSC) was used as a data filter to remove non-dose-dependent variation from the NMR spectra, improving the classification of treated spheroids and controls. This work shows that useful metabolic information can be obtained on drug toxicity by the use of combined MAS-NMR and high-resolution NMR of liver spheroids and that such studies may enhance the validation of in vitro techniques against in vivo models for metabolic profiling.
Publisher: Springer Science and Business Media LLC
Date: 22-11-2012
Publisher: Springer Science and Business Media LLC
Date: 19-09-2011
Abstract: The urinary metabolic fingerprint of a patent Schistosoma mansoni infection in the mouse has been characterized using spectroscopic methods. However, the temporal dynamics of metabolic alterations have not been studied at the systems level. Here, we investigated the systems metabolic changes in the mouse upon S. mansoni infection by modeling the sequence of metabolic events in urine, plasma and faecal water. Ten female NMRI mice, aged 5 weeks, were infected with 80 S. mansoni cercariae each. Ten age- and sex-matched mice remained uninfected and served as a control group. Urine, plasma and faecal s les were collected 1 day before, and on eight time points until day 73 post-infection. Biofluid s les were subjected to 1 H nuclear magnetic resonance (NMR) spectroscopy and multivariate statistical analyses. Differences between S. mansoni -infected and uninfected control mice were found from day 41 onwards. One of the key metabolic signatures in urine and faecal extracts was an alteration in several gut bacteria-related metabolites, whereas the plasma reflected S. mansoni infection by changes in metabolites related to energy homeostasis, such as relatively higher levels of lipids and decreased levels of glucose. We identified 12 urinary biomarkers of S. mansoni infection, among which hippurate, phenylacetylglycine (PAG) and 2-oxoadipate were particularly robust with regard to disease progression. Thirteen plasma metabolites were found to differentiate infected from control mice, with the lipid components, D-3-hydroxybutyrate and glycerophosphorylcholine showing greatest consistency. Faecal extracts were highly variable in chemical composition and therefore only five metabolites were found discriminatory of infected mice, of which 5-aminovalerate was the most stable and showed a positive correlation with urinary PAG. The composite metabolic signature of S. mansoni in the mouse derived from perturbations in urinary, faecal and plasma composition showed a coherent response in altered energy metabolism and in gut microbial activity. Our findings provide new mechanistic insight into host-parasite interactions across different compartments and identified a set of temporally robust biomarkers of S. mansoni infection, which might assist in derivation of diagnostic assays or metrics for monitoring therapeutic response.
Publisher: American Chemical Society (ACS)
Date: 18-04-2023
Publisher: Wiley
Date: 07-2007
DOI: 10.1002/CEM.1071
Abstract: The orthogonal projections to latent structures (OPLS) method has been successfully applied in various chemical and biological systems for modeling and interpretation of linear relationships between a descriptor matrix and response matrix. A kernel‐based reformulation of the original OPLS algorithm is presented where the kernel Gram matrix is utilized as a replacement for the descriptor matrix. This enables usage of the ‘kernel trick’ to efficiently transform the data into a higher‐dimensional feature space where predictive and response‐orthogonal components are calculated. This strategy has the capacity to improve predictive performance considerably in situations where strong non‐linear relationships exist between descriptor and response variables while retaining the OPLS model framework. We put particular focus on describing properties of the rearranged algorithm in relation to the original OPLS algorithm. Four separate problems, two simulated and two real spectroscopic data sets, are employed to illustrate how the algorithm enables separate modeling of predictive and response‐orthogonal variation in the feature space. This separation can be highly beneficial for model interpretation purposes while providing a flexible framework for supervised regression. Copyright © 2007 John Wiley & Sons, Ltd.
Publisher: Informa UK Limited
Date: 08-2005
DOI: 10.1080/00498250500297940
Abstract: Metabonomics using high-resolution 1H-NMR spectroscopy of biofluids and pattern recognition is highly successful at distinguishing both organ- and sub-organ-specific toxicity. In the current study, this technique was investigated to distinguish the different biological effects caused by 1-naphthylisothiocyanate (ANIT)-induced hepatotoxicity in the rat from that induced by exposure to 1-naphthylisocyanate (NI) and 1-naphthylamine (NA), two products of the metabolism of ANIT. While all three toxicants produced perturbations in similar urinary metabolites, principal components analysis of the temporal progression identified that the rapid initial glycosuria associated with ANIT toxicity was also present with NI but not NA dosing. However, longer-term perturbations in the urinary excretion of succinate, lactate and acetate were common to all three toxicants. The metabolic effects of the three compounds were also followed in blood plasma and liver tissue. Of the three toxicants, the most marked perturbations were induced by ANIT exposure, then NI, thereby indicating the effects of ANIT, NI and NA toxicity were distinct, with ANIT being the most, and NA the least, toxic of the three compounds. This indicates that metabonomics may be useful for following severity and mechanisms of toxicity in a series of related compounds during drug development.
Publisher: American Chemical Society (ACS)
Date: 13-02-2012
DOI: 10.1021/AC203200X
Abstract: Liquid chromatography coupled to mass spectrometry (LC-MS) is a major platform in metabolic profiling but has not yet been comprehensively assessed as to its repeatability and reproducibility across multiple spectrometers and laboratories. Here we report results of a large interlaboratory reproducibility study of ultra performance (UP) LC-MS of human urine. A total of 14 stable isotope labeled standard compounds were spiked into a pooled human urine s le, which was subject to a 2- to 16-fold dilution series and run by UPLC coupled to time-of-flight MS at three different laboratories all using the same platform. In each lab, identical s les were run in two phases, separated by at least 1 week, to assess between-day reproducibility. Overall, platform reproducibility was good with median mass accuracies below 12 ppm, median retention time drifts of less than 0.73 s and coefficients of variation of intensity of less than 18% across laboratories and ionization modes. We found that the intensity response was highly linear within each run, with a median R(2) of 0.95 and 0.93 in positive and negative ionization modes. Between-day reproducibility was also high with a mean R(2) of 0.93 for a linear relationship between the intensities of ions recorded in the two phases across the laboratories and modes. Most importantly, between-lab reproducibility was excellent with median R(2) values of 0.96 and 0.98 for positive and negative ionization modes, respectively, across all pairs of laboratories. Interestingly, the three laboratories observed different amounts of adduct formation, but this did not appear to be related to reproducibility observed in each laboratory. These studies show that UPLC-MS is fit for the purpose of targeted urinary metabolite analysis but that care must be taken to optimize laboratory systems for quantitative detection due to variable adduct formation over many compound classes.
Publisher: Wiley
Date: 2000
DOI: 10.1002/1522-2594(200008)44:2<201::AID-MRM6>3.0.CO;2-5
Abstract: High-resolution magic angle spinning (MAS) (1)H NMR spectra of small s les (ca. 8 mg) of intact rat liver are reported for the first time. One dimensional spectra reveal a number of large well-resolved NMR signals mainly from low to medium molecular weight compounds (generally 4) linked glucose units with either alpha(1-->4) units adjacent or alpha(1-->6) linked branches could be resolved in a high-resolution (1)H NMR experiment giving direct in situ information on the ratio of alpha(1-->4) to alpha(1-->6) units. This indicates that despite the relatively high MW (>1,000,000 Daltons) there is considerable segmental motion in the glycogen molecules giving long (1)H T(2) relaxation times. Magn Reson Med 44:201-207, 2000.
Publisher: Elsevier
Date: 2018
Publisher: Future Medicine Ltd
Date: 04-2009
DOI: 10.2217/BMM.09.11
Abstract: Intestinal ischemia/reperfusion (I/R) injury initiates a systemic inflammatory response syndrome with a high associated mortality rate. Early diagnosis is essential for reducing surgical mortality, yet current clinical biomarkers are insufficient. Metabonomics is a novel strategy for studying intestinal I/R, which may be used as part of a systems approach for quantitatively analyzing the intestinal microbiome during gut injury. By deconvolving the mammalian–microbial symbiotic relationship systems biology thus has the potential for personalized risk stratification in patients exposed to intestinal I/R. This review describes the mechanism of intestinal I/R and explores the essential role of the intestinal microbiota in the initiation of systemic inflammatory response syndrome. Furthermore, it analyzes current and future approaches for elucidating the mechanism of this condition.
Publisher: Oxford University Press (OUP)
Date: 21-08-2014
Publisher: Springer Science and Business Media LLC
Date: 27-04-2012
Publisher: American Chemical Society (ACS)
Date: 22-06-2009
DOI: 10.1021/PR900185S
Publisher: Springer Science and Business Media LLC
Date: 07-2005
DOI: 10.1038/NBT0705-833
Publisher: American Chemical Society (ACS)
Date: 22-07-2009
DOI: 10.1021/AC901240J
Abstract: We present a new approach for analysis, information recovery, and display of biological (1)H nuclear magnetic resonance (NMR) spectral data, cluster analysis statistical spectroscopy (CLASSY), which profiles qualitative and quantitative changes in biofluid metabolic composition by utilizing a novel local-global correlation clustering scheme to identify structurally related spectral peaks and arrange metabolites by similarity of temporal dynamic variation. Underlying spectral data sets are presented in a novel graphical format to represent high-dimensionality biochemical information conveying both statistical metabolite relationships and their responses to experimental perturbation simultaneously in a high-throughput and intuitive manner. The method is exemplified using multiple 600 MHz (1)H NMR spectra of rat (n = 40) urine s les collected over 160 h following the development of experimental pancreatitis induced by L-arginine (ARG) and a wider range of model toxins including acetaminophen, galactosamine, and 2-bromoethanamine. The CLASSY approach deconvolutes complex biofluid mixture spectra into quantitative fold-change metabolic trajectories and clusters metabolites by commonalities of coexpression patterns. We demonstrate that the developing pathological processes cause coordinated changes in the levels of many compounds which share similar pathway connectivities. Variability in in idual responses to toxin exposure is also readily detected and visualized allowing the assessment of interanimal variability. As an untargeted, unsupervised approach, CLASSY provides significant advantages in biological information recovery in terms of increased throughput, interpretability, and robustness and has wide potential metabonomic/metabolomic applications in clinical, toxicological, and nutritional studies of biofluids as well as in studies of cellular biochemistry, microbial fermentation monitoring, and functional genomics.
Publisher: Elsevier BV
Date: 04-2005
DOI: 10.1016/J.TAAP.2004.06.031
Abstract: Interspecies variation between rats and mice has been studied for hydrazine toxicity using a novel metabonomics approach. Hydrazine hydrochloride was administered to male Sprague-Dawley rats (30 mg/kg, n = 10 and 90 mg/kg, n = 10) and male B6C3F mice (100 mg/kg, n = 8 and 250 mg/kg, n = 8) by oral gavage. In each species, the high dose was selected to produce the major histopathologic effect, hepatocellular lipid accumulation. Urine s les were collected at sequential time points up to 168 h post dose and analyzed by 1H NMR spectroscopy. The metabolites of hydrazine, namely diacetyl hydrazine and 1,4,5,6-tetrahydro-6-oxo-3-pyridazine carboxylic acid (THOPC), were detected in both the rat and mouse urine s les. Monoacetyl hydrazine was detected only in urine s les from the rat and its absence in the urine of the mouse was attributed to a higher activity of N-acetyl transferases in the mouse compared with the rat. Differential metabolic effects observed between the two species included elevated urinary beta-alanine, 3-D-hydroxybutyrate, citrulline, N-acetylcitrulline, and reduced trimethylamine-N-oxide excretion unique to the rat. Metabolic principal component (PC) trajectories highlighted the greater degree of toxic response in the rat. A data scaling method, scaled to maximum aligned and reduced trajectories (SMART) analysis, was used to remove the differences between the metabolic starting positions of the rat and mouse and varying magnitudes of effect, to facilitate comparison of the response geometries between the rat and mouse. Mice followed "biphasic" open PC trajectories, with incomplete recovery 7 days after dosing, whereas rats followed closed "hairpin" time profiles, indicating functional reversibility. The greater magnitude of metabolic effects observed in the rat was supported by the more pronounced effect on liver pathology in the rat when compared with the mouse.
Publisher: American Chemical Society (ACS)
Date: 03-2022
DOI: 10.1021/ACS.ANALCHEM.1C05389
Abstract: SARS-CoV-2 infection causes a significant reduction in lipoprotein-bound serum phospholipids give rise to supramolecular phospholipid composite (SPC) signals observed in diffusion and relaxation edited
Publisher: Wiley
Date: 10-08-2001
DOI: 10.1002/MRC.907
Publisher: Elsevier BV
Date: 03-2006
DOI: 10.1016/J.MOLBIOPARA.2005.10.010
Abstract: A metabolic profiling strategy was used to investigate the metabolic responses of Syrian hamsters (SLAC) to a Schistosoma japonicum infection using high resolution 1H nuclear magnetic resonance (NMR) spectroscopy and pattern recognition. In two independent experiments, male hamsters were each infected with 100 S. japonicum cercariae. At days 34-36 post-infection, urine was obtained from hamsters housed in idually in metabolism cages. At the same time, urine was collected from age- and sex-matched infection-free control hamsters. The main biochemical effects of a S. japonicum infection in the hamster consisted of reduced levels of urinary tricarboxylic acid cycle intermediates, including citrate and succinate and increased levels of pyruvate. In addition, a range of microbial-related metabolites, such as hippurate, p-cresol glucuronide, phenylacetylglycine and trimethylamine were also associated with a S. japonicum infection. Most of the observed biochemical effects were in common with those previously characterized for a S. mansoni infection in a mouse host. The major distinguishing consequence of a S. japonicum infection in the hamster was the inhibition of manufacture or utilization of short-chain fatty acids, when compared to a S. mansoni infection in the mouse.
Publisher: Springer Science and Business Media LLC
Date: 07-12-2019
DOI: 10.1038/S41390-019-0709-9
Abstract: The mechanisms responsible for the associations between very preterm birth and a higher risk of poor cardiovascular and metabolic health in adult life are unknown. Here, we compare the clinical and molecular phenotypes of healthy, normal-weight young adults (18-27 years), born very preterm (<33 weeks gestational age (GA)) and at full-term (37-42 weeks GA). Outcomes included whole-body MRI, hepatic and muscle We recruited 156 volunteers, 69 preterm (45 women 24 men) and 87 born at full-term (45 women 42 men). Preterm in iduals had a significantly altered blood pressure profile, including higher systolic blood pressure (SBP mmHg: preterm men 133.4 ± 10.1, term men 23.0 ± 6.9 preterm women 124.3 ± 7.1, term women 118.4 ± 8.0, p < 0.01 for all). Furthermore, preterm men had fewer long telomeres (145-48.5 kb: preterm men 14.1 ± 0.9%, term men 17.8 ± 1.1%, p < 0.05 48.5-8.6 kb: preterm men 28.2 ± 2.6, term men 37.0 ± 2.4%, p < 0.001) and a higher proportion of shorter telomeres (4.2-1.3 kb: preterm men 40.4 ± 3.5%, term men 29.9 ± 3.2%, p < 0.01). Our data indicate that healthy young adults born very preterm manifest clinical and molecular evidence of accelerated ageing.
Publisher: American Chemical Society (ACS)
Date: 12-12-2002
DOI: 10.1021/AC010643C
Abstract: Drug-plasma protein binding may greatly influence the bioavailability and metabolism of a plasma-borne drug, the bound form being partially protected from the metabolic fate of the unbound drug. Traditionally, equilibrium values (e.g., percentage binding) for drug-protein binding have been measured to rationalize in vivo phenomena. However, such studies overlook the influence of kinetics. A rapid method of simultaneously determining kinetic rate constants and equilibrium constants from chromatographic profiles has been developed, based on the use of immobilized protein columns and HPLC. By measuring the chromatographic profiles (the position and width) of a retained and an unretained compound one can directly determine both the rate and equilibrium constants. Results are presented for the binding of L-tryptophan to human serum albumin to exemplify the method. The association equilibrium constant (Ka) and the association and dissociation rate constants (k(a) and k(d), respectively) were thereby measured in an aqueous pH 7.4 environment at 37 degrees C as 0.84 10(4) M(-1), 5.8 10(4) M(-1) s(-1), and 6.9 s(-1), respectively. These compare favorably with previously published results. The described method may be used in quantitative structure-property relationship-based rational drug discovery or for the rationalization of drug pharmacokinetics.
Publisher: Elsevier BV
Date: 10-09-2004
Publisher: Informa UK Limited
Date: 22-02-2019
DOI: 10.1080/00498254.2018.1559376
Abstract: 1. The metabolic fate and urinary excretion of 2-bromophenol, a phenolic metabolite of bromobenzene, was investigated in male Sprague-Dawley rats following single intraperitoneal doses at either 0, 100, or 200 mg/kg.2. Urine was collected for seven days and s les analysed using
Publisher: American Chemical Society (ACS)
Date: 22-09-2015
DOI: 10.1021/ACS.ANALCHEM.5B01556
Abstract: Bile acids are important end products of cholesterol metabolism. While they have been identified as key factors in lipid emulsification and absorption due to their detergent properties, bile acids have also been shown to act as signaling molecules and intermediates between the host and the gut microbiota. To further the investigation of bile acid functions in humans, an advanced platform for high throughput analysis is essential. Herein, we describe the development and application of a 15 min UPLC procedure for the separation of bile acid species from human biofluid s les requiring minimal s le preparation. High resolution time-of-flight mass spectrometry was applied for profiling applications, elucidating rich bile acid profiles in both normal and disease state plasma. In parallel, a second mode of detection was developed utilizing tandem mass spectrometry for sensitive and quantitative targeted analysis of 145 bile acid (BA) species including primary, secondary, and tertiary bile acids. The latter system was validated by testing the linearity (lower limit of quantification, LLOQ, 0.25-10 nM and upper limit of quantification, ULOQ, 2.5-5 μM), precision (≈6.5%), and accuracy (81.2-118.9%) on inter- and intraday analysis achieving good recovery of bile acids (serum lasma 88% and urine 93%). The ultra performance liquid chromatography-mass spectrometry (UPLC-MS)/MS targeted method was successfully applied to plasma, serum, and urine s les in order to compare the bile acid pool compositional difference between preprandial and postprandial states, demonstrating the utility of such analysis on human biofluids.
Publisher: Elsevier BV
Date: 07-2002
DOI: 10.1016/S0006-2952(02)01016-X
Abstract: The metabolite profiles from livers of toxin-treated rats were investigated using high resolution 1H NMR spectroscopy of aqueous (acetonitrile/water), lipidic (chloroform/methanol) extracts and magic angle spinning (MAS)-NMR spectroscopy of intact tissue. Rats were treated with the model cholestatic hepatotoxin, alpha-naphthylisothiocyanate (ANIT, 150 mg/kg) and NMR spectra of liver were analysed using principal components analysis (PCA) to extract novel toxicity biomarker information. 1H NMR spectra of control aqueous extracts showed signals from a range of organic acids and bases, amino acids, sugars, and glycogen. Chloroform/methanol extracts showed signals from a range of saturated and unsaturated triglycerides, phospholipids and cholesterol. The MAS 1H NMR spectra of livers showed a composite of signals found in both aqueous and lipophilic extracts. Following ANIT treatment, 1H NMR-PCA of aqueous extracts indicated a progressive reduction in glucose and glycogen, together with increases in bile acid, choline, and phosphocholine signals. 1H NMR-PCA of chloroform/methanol extracts showed elevated triglyceride levels. The 1H MAS-NMR-PCA analysis allowed direct detection of all of the ANIT-induced tissue perturbations revealed by 1H NMR of extracts, enabling metabolic characterisation of the lesion, which included steatosis, bile duct obstruction and altered glucose/glycogen metabolism. MAS-NMR spectroscopy requires minimal s le preparation and, unlike 1H NMR spectroscopy of tissue extracts, does not discriminate metabolites based on their solubility in a particular solvent and so this is a particularly useful exploratory tool in biochemical toxicology.
Publisher: Springer Science and Business Media LLC
Date: 22-06-2020
Publisher: American Chemical Society (ACS)
Date: 05-09-2018
Publisher: American Chemical Society (ACS)
Date: 16-02-2011
DOI: 10.1021/AC102870U
Abstract: Statistical total correlation spectroscopy (STOCSY) is a well-established and valuable method in the elucidation of both inter- and intrametabolite correlations in NMR metabonomic data sets. Here, the STOCSY approach is extended in a novel Iterative-STOCSY (I-STOCSY) tool in which correlations are calculated initially from a driver peak of interest and subsequently for all peaks identified as correlating with a correlation coefficient greater than a set threshold. Consequently, in a single automated run, the majority of information contained in multiple STOCSY calculations from all peaks recursively correlated to the original user defined driver peak of interest are recovered. In addition, highly correlating peaks are clustered into putative structurally related sets, and the results are presented in a fully interactive plot where each set is represented by a node node-to-node connections are plotted alongside corresponding spectral data colored by the strength of connection, thus allowing the intuitive exploration of both inter- and intrametabolite connections. The I-STOCSY approach has been here applied to a (1)H NMR data set of 24 h postdose aqueous liver extracts from rats treated with the model hepatotoxin galactosamine and has been shown both to recover the previously deduced major metabolic effects of treatment and to generate new hypotheses even on this well-studied model system. I-STOCSY, thus, represents a significant advance in correlation based analysis and visualization, providing insight into inter- and intrametabolite relationships following metabolic perturbations.
Publisher: American Chemical Society (ACS)
Date: 15-02-2008
DOI: 10.1021/PR800098N
Publisher: Springer Science and Business Media LLC
Date: 21-11-2013
DOI: 10.1038/JHH.2013.115
Publisher: Elsevier BV
Date: 02-2006
DOI: 10.1016/J.JPBA.2005.07.019
Abstract: Mercury II chloride (HgCl2) toxicity was investigated in Sprague-Dawley rats using high-resolution magic angle spinning (HRMAS) 1H NMR spectroscopy in conjunction with principal component analysis (PCA). Intact renal cortex and papilla s les from Sprague-Dawley rats treated with HgCl2 at two dose levels (0.5 and 2 mg/kg) and from matched controls (n=5 per group) were assessed at 48 h p.d. HgCl2) caused depletion of renal osmolytes such as glycerophosphocholine (GPC), betaine, trimethylamine N-oxide (TMAO), myo-inositol and taurine in both the renal cortex and the papilla. In addition, relatively higher concentrations of valine, isobutyrate, threonine and glutamate were observed in HgCl2-treated rats, particularly in the renal cortex, which may reflect a counterbalance response to the observed loss of other classes of renal osmolytes. Increased levels of glutamate were present in the cortex of treated rats, which may be associated with HgCl2-induced renal acidosis and disruption of the tricarboxylic acid cycle. A dose response was observed in both cortical and papillary tissue with increasing severity of metabolic disruption in the high dose group. 1H HRMAS NMR profiles of in idual animals correlated well with conventional clinical chemistry and histology confirming the reproducibility of the technology and generating complementary molecular pathway information.
Publisher: Wiley
Date: 08-2002
DOI: 10.1002/CEM.733
Abstract: Multivariate statistical batch processing (BP) analysis of 1 H nuclear magnetic resonance (NMR) urine spectra was employed to establish time‐dependent metabolic variations in animals treated with the model hepatotoxin hydrazine. Hydrazine was administered orally to rats (at 90 mg kg −1 ), and urine s les were collected from dosed rats and matched control animals (n = 5 per group) at time points up to 168 h post‐dose. Urine s les were analysed via 1 H NMR spectroscopy and partial least squares‐based batch processing analysis, treating each rat as an in idual batch comprising a series of timed urine s les. A model defining the mean urine profile was established for the control group, and s les obtained from hydrazine‐treated animals were assessed using this model. Time‐dependent deviations from the control model were evident in all hydrazine‐treated animals, and hepatotoxicity was manifested by increased urinary excretion of taurine, creatine, 2‐aminoadipate, citrulline and β‐alanine together with depletion of urinary levels of citrate, succinate and hippurate. The experiment was repeated at six different pharmaceutical centres in order to assess the robustness of the technology and to establish the natural variability in the data. Results were consistent across the data for all centres. BP plots showed a characteristic pattern for each toxin, allowing the time points at which there were maximum metabolic differences to be determined and providing a means of visualizing the net toxin‐induced metabolic movement of urinary metabolism. BP may prove to be a powerful metabonomic tool in defining time‐dependent metabolic consequences of toxicity and is an efficient means of visualizing inter‐animal variations in response as well as defining multivariate statistical limits of normality in terms of biofluid composition. Copyright © 2002 John Wiley & Sons, Ltd.
Publisher: American Chemical Society (ACS)
Date: 02-2007
DOI: 10.1021/PR070717M
Publisher: American Medical Association (AMA)
Date: 20-09-2019
Publisher: American Chemical Society (ACS)
Date: 27-02-2012
DOI: 10.1021/PR2010154
Publisher: BMJ
Date: 07-2016
Publisher: American Chemical Society (ACS)
Date: 23-01-2021
Publisher: American Chemical Society (ACS)
Date: 16-08-2008
DOI: 10.1021/PR8005099
Publisher: American Chemical Society (ACS)
Date: 04-10-2017
DOI: 10.1021/ACS.JPROTEOME.7B00568
Abstract: Lower urinary tract symptoms (LUTS), including urinary incontinence, urgency and nocturia, affect approximately half of women worldwide. Current diagnostic methods for LUTS are invasive and costly, while available treatments are limited by side effects leading to poor patient compliance. In this study, we aimed to identify urine metabolic signatures associated with LUTS using proton nuclear magnetic resonance (
Publisher: Wiley
Date: 31-05-2018
DOI: 10.1111/HEPR.12904
Abstract: Gut microbial dysbiosis is implicated in the pathogenesis of non-alcoholic steatohepatitis (NASH). We investigated downstream effects of gut microbiota modulation on markers of hepatic inflammation, steatosis, and hepatic and peripheral insulin sensitivity in patients with NASH using rifaximin therapy. Patients with biopsy-proven NASH and elevated aminotransferase values were included in this open-label pilot study, all receiving 6 weeks rifaximin 400 mg twice daily, followed by a 6-week observation period. The primary endpoint was change in alanine aminotransferase (ALT) after 6 weeks of rifaximin. Secondary endpoints were change in hepatic lipid content and insulin sensitivity measured with a hyperinsulinemic-euglycemic cl . Fifteen patients (13 men and 2 women) with a median (range) age of 46 (32-63) years were included. Seven had diabetes on oral hypoglycemic medications and 8 had no diabetes. After 6 weeks of therapy, no differences were seen in ALT (55 [33-191] vs. 63 [41-218] IU/L, P = 0.41), peripheral glucose uptake (28.9 [19.4-48.3] to 25.5 [17.7-47.9] μmol/kg/min, P = 0.30), hepatic insulin sensitivity (35.2 [15.3-51.7]% vs. 30.0 [10.8-50.5]%, P = 0.47), or hepatic lipid content (21.6 [2.2-46.2]% vs. 24.8 [1.7-59.3]%, P = 0.59) before and after rifaximin treatment. After 12 weeks from baseline, serum ALT increased to 83 (30-217) IU/L, P = 0.02. There was a significant increase in the homeostasis model assessment-estimated insulin resistance index (P = 0.05). The urinary metabolic profile indicated a significant reduction in urinary hippurate with treatment, which reverted to baseline after cessation of rifaximin, although there was no consistent difference in relative abundance of fecal microbiota with treatment. These data do not indicate a beneficial effect of rifaximin in patients with NASH.
Publisher: American Chemical Society (ACS)
Date: 30-08-2008
DOI: 10.1021/AC801053G
Abstract: Optimizing NMR experimental parameters for high-throughput metabolic phenotyping requires careful examination of the total biochemical information obtainable from (1)H NMR data, which includes concentration and molecular dynamics information. Here we have applied two different types of mathematical transformation (calculation of the first derivative of the NMR spectrum and Gaussian shaping of the free-induction decay) to attenuate broad spectral features from macromolecules and enhance the signals of small molecules. By application of chemometric methods such as principal component analysis (PCA), orthogonal projections to latent structures discriminant analysis (O-PLS-DA) and statistical spectroscopic tools such as statistical total correlation spectroscopy (STOCSY), we show that these methods successfully identify the same potential biomarkers as spin-echo (1)H NMR spectra in which broad lines are suppressed via T2 relaxation editing. Finally, we applied these methods for identification of the metabolic phenotype of patients with type 2 diabetes. This "virtual" relaxation-edited spectroscopy (RESY) approach can be particularly useful for high-throughput screening of complex mixtures such as human plasma and may be useful for extraction of latent biochemical information from legacy or archived NMR data sets for which only standard 1D data sets exist.
Publisher: Oxford University Press (OUP)
Date: 09-2005
Publisher: SAGE Publications
Date: 24-10-2017
Abstract: The application of metabonomic science to interrogate stroke permits the study of metabolite entities, small enough to cross the blood-brain barrier, that provide insight into neuronal dysfunction, and may serve as reservoirs of biomarker discovery. This systematic review examines the applicability of metabolic profiling in ischemic stroke research. Six human studies utilizing metabolic profiling to analyze biofluids from ischemic stroke patients have been included, employing 1 H-NMR and/or mass spectrometry to analyze plasma, serum, and/or urine in a targeted or untargeted fashion. Three are diagnostic studies, and one investigates prognostic biomarkers of stroke recurrence following transient ischemic attack. Two studies focus on metabolic distinguishers of depression or cognitive impairment following stroke. Identified biomarkers from blood and urine predominantly relate to homocysteine and folate, branched chain amino acid, and lipid metabolism. Statistical models are well fitted and reproducible, with excellent validation outcomes, demonstrating the feasibility of metabolic profiling to study a complex disorder with multicausal pathology, such as stroke.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 21-05-2019
DOI: 10.1002/HEP.30661
Abstract: Pregnancy is associated with progressive hypercholanemia, hypercholesterolemia, and hypertriglyceridemia, which can result in metabolic disease in susceptible women. Gut signals modify hepatic homeostatic pathways, linking intestinal content to metabolic activity. We sought to identify whether enteric endocrine signals contribute to raised serum bile acids observed in human and murine pregnancies, by measuring fibroblast growth factor (FGF) 19/15 protein and mRNA levels, and 7α‐hydroxy‐4‐cholesten‐3‐one. Terminal ileal farnesoid X receptor (FXR)‐mediated gene expression and apical sodium bile acid transporter (ASBT) protein concentration were measured by qPCR and western blotting. Shotgun whole‐genome sequencing and ultra‐performance liquid chromatography tandem mass spectrometry were used to determine the cecal microbiome and metabonome. Targeted and untargeted pathway analyses were performed to predict the systemic effects of the altered metagenome and metabolite profiles. Dietary CA supplementation was used to determine whether the observed alterations could be overcome by intestinal bile acids functioning as FXR agonists. Human and murine pregnancy were associated with reduced intestinal FXR signaling, with lower FGF19/15 and resultant increased hepatic bile acid synthesis. Terminal ileal ASBT protein was reduced in murine pregnancy. Cecal bile acid conjugation was reduced in pregnancy because of elevated bile salt hydrolase‐producing Bacteroidetes . CA supplementation induced intestinal FXR signaling, which was not abrogated by pregnancy, with strikingly similar changes to the microbiota and metabonome as identified in pregnancy. Conclusion : The altered intestinal microbiota of pregnancy enhance bile acid deconjugation, reducing ileal bile acid uptake and lowering FXR induction in enterocytes. This exacerbates the effects mediated by reduced bile acid uptake transporters in pregnancy. Thus, in pregnant women and mice, there is reduced FGF19/15‐mediated hepatic repression of hepatic bile acid synthesis, resulting in hypercholanemia.
Publisher: American Chemical Society (ACS)
Date: 15-01-2013
DOI: 10.1021/AC302330A
Abstract: The acquisition of localized molecular spectra with mass spectrometry imaging (MSI) has a great, but as yet not fully realized, potential for biomedical diagnostics and research. The methodology generates a series of mass spectra from discrete s le locations, which is often analyzed by visually interpreting specifically selected images of in idual masses. We developed an intuitive color-coding scheme based on hyperspectral imaging methods to generate a single overview image of this complex data set. The image color-coding is based on spectral characteristics, such that pixels with similar molecular profiles are displayed with similar colors. This visualization strategy was applied to results of principal component analysis, self-organizing maps and t-distributed stochastic neighbor embedding. Our approach for MSI data analysis, combining automated data processing, modeling and display, is user-friendly and allows both the spatial and molecular information to be visualized intuitively and effectively.
Publisher: American Chemical Society (ACS)
Date: 11-05-2006
DOI: 10.1021/PR050399W
Abstract: A new multivariate statistical approach, based on the novel combination of projection on latent structure analysis with an inbuilt orthogonal filter (OPLS-DA) coupled with a spectroscopic correlation method statistical total correlation spectroscopy (STOCSY), was used to characterize the in vivo metabolic pathway perturbations of a model renal cortical toxin HgCl2, in the rat, using urine as an indicator of metabolic homeostasis disruption. This method provided an unbiased, sensitive approach to biomarker extraction and identification, and showed potential for generating potential novel pathway connectivities.
Publisher: Springer Science and Business Media LLC
Date: 08-2008
DOI: 10.1007/S11894-008-0075-Y
Abstract: In their intestine, humans possess an "extended genome" of millions of microbial genes-the microbiome. Because this complex symbiosis influences host metabolism, physiology, and gene expression, it has been proposed that humans are complex biologic "superorganisms." Advances in microbiologic analysis and systems biology are now beginning to implicate the gut microbiome in the etiology of localized intestinal diseases such as the irritable bowel syndrome, inflammatory bowel disease, and colon cancer. These approaches also suggest possible links between the gut and previously unassociated systemic conditions such as type 2 diabetes and obesity. The elucidation of the intestinal microbiome is therefore likely to underpin future disease prevention strategies, personalized health care regimens, and the development of novel therapeutic interventions. This review summarizes the research that is defining our understanding of the intestinal microbiome and highlights future areas of research in gastroenterology and human health in which the intestinal microbiome will play a significant role.
Publisher: American Society of Tropical Medicine and Hygiene
Date: 05-01-2011
Publisher: Elsevier BV
Date: 09-2019
Publisher: Elsevier
Date: 2017
Publisher: Wiley
Date: 2000
Publisher: Elsevier BV
Date: 03-2003
DOI: 10.1016/S0041-008X(02)00079-0
Abstract: The role that metabonomics has in the evaluation of xenobiotic toxicity studies is presented here together with a brief summary of published studies. To provide a comprehensive assessment of this approach, the Consortium for Metabonomic Toxicology (COMET) has been formed between six pharmaceutical companies and Imperial College of Science, Technology and Medicine (IC), London, UK. The objective of this group is to define methodologies and to apply metabonomic data generated using (1)H NMR spectroscopy of urine and blood serum for preclinical toxicological screening of candidate drugs. This is being achieved by generating databases of results for a wide range of model toxins which serve as the raw material for computer-based expert systems for toxicity prediction. The project progress on the generation of comprehensive metabonomic databases and multivariate statistical models for prediction of toxicity, initially for liver and kidney toxicity in the rat and mouse, is reported. Additionally, both the analytical and biological variation which might arise through the use of metabonomics has been evaluated. An evaluation of intersite NMR analytical reproducibility has revealed a high degree of robustness. Second, a detailed comparison has been made of the ability of the six companies to provide consistent urine and serum s les using a study of the toxicity of hydrazine at two doses in the male rat, this study showing a high degree of consistency between s les from the various companies in terms of spectral patterns and biochemical composition. Differences between s les from the various companies were small compared to the biochemical effects of the toxin. A metabonomic model has been constructed for urine from control rats, enabling identification of outlier s les and the metabolic reasons for the deviation. Building on this success, and with the completion of studies on approximately 80 model toxins, first expert systems for prediction of liver and kidney toxicity have been generated.
Publisher: American Chemical Society (ACS)
Date: 2008
DOI: 10.1021/TX700335D
Abstract: We have reviewed the main contributions to the development of NMR-based metabonomic and metabolic profiling approaches for toxicological assessment, biomarker discovery, and studies on toxic mechanisms. The metabonomic approach, (defined as the quantitative measurement of the multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification) was originally developed to assist interpretation in NMR-based toxicological studies. However, in recent years there has been extensive fusion with metabolomic and other metabolic profiling approaches developed in plant biology, and there is much wider coverage of the biomedical and environmental fields. Specifically, metabonomics involves the use of spectroscopic techniques with statistical and mathematical tools to elucidate dominant patterns and trends directly correlated with time-related metabolic fluctuations within spectral data sets usually derived from biofluids or tissue s les. Temporal multivariate metabolic signatures can be used to discover biomarkers of toxic effect, as general toxicity screening aids, or to provide novel mechanistic information. This approach is complementary to proteomics and genomics and is applicable to a wide range of problems, including disease diagnosis, evaluation of xenobiotic toxicity, functional genomics, and nutritional studies. The use of biological fluids as a source of whole organism metabolic information enhances the use of this approach in minimally invasive longitudinal studies.
Publisher: American Chemical Society (ACS)
Date: 20-06-2007
DOI: 10.1021/PR070164F
Abstract: 1H NMR spectroscopy was used to investigate the metabolic effects of the hepatotoxin galactosamine (galN) and the mechanism by which glycine protects against such toxicity. Rats were acclimatized to a 0 or 5% glycine diet for 6 days and subsequently administered vehicle, galN (500 mg/kg), glycine (5% via the diet), or both galN and glycine. Urine was collected over 12 days prior to administration of galN and for 24 hours thereafter. Serum and liver tissue were s led on termination, 24 hours post-dosing. The metabolic profiles of biofluids and tissues were determined using high-field 1H NMR spectroscopy. Orthogonal-projection to latent structures discriminant analysis (O-PLS-DA) was applied to model the spectral data and enabled the hepatic, urinary, and serum metabolites that discriminated between control and treated animals to be determined. Histopathological data and clinical chemistry measurements confirmed the protective effect of glycine. The level of N-acetylglucosamine (glcNAc) in the post-dose urine was found to correlate strongly with the degree of galN-induced liver damage, and the urinary level of glcNAc was not significantly elevated in rats treated with both galN and glycine. Treatment with glycine alone was found to significantly increase hepatic levels of uridine, UDP-glucose, and UDP-galactose, and in view of the known effects of galactosamine, this suggests that the protective role of glycine against galN toxicity might be mediated by changes in the uridine nucleotide pool rather than by preventing Kupffer cell activation. Thus, we present a novel hypothesis: that administration of glycine increases the hepatic uridine nucleotide pool which counteracts the galN-induced depletion of these pools and facilitates complete metabolism of galN. These novel data highlight the applicability of NMR-based metabonomics in elucidating multicompartmental metabolic consequences of toxicity and toxic salvage.
Publisher: American Chemical Society (ACS)
Date: 26-07-2005
DOI: 10.1021/AC050455C
Abstract: This work presents the first application of high-resolution magic angle spinning (HR-MAS) 1H NMR spectroscopy to human liver biopsy s les, allowing a determination of their metabolic profiles before removal from donors, during cold perfusion, and after implantation into recipients. The assignment of peaks observed in the 1H HR-MAS NMR spectra was aided by the use of two-dimensional J-resolved, TOCSY and 1H-13C HMQC spectra. The spectra were dominated by resonances from triglycerides, phospholipids, and glycogen and from a variety of small molecules including glycerophosphocholine (GPC), glucose, lactate, creatine, acetate, amino acids, and nucleoside-related compounds such as uridine and adenosine. In agreement with histological data obtained on the same biopsies, two of the six livers were found to contain high amounts of triglycerides by NMR spectroscopy, which also indicated that these tissues contained a higher degree of unsaturated lipids and a lower proportion of phospholipids and low molecular weight compounds. Additionally, proton T2 relaxation times indicated two populations of lipids, a higher mobility triglyceride fraction and a lower mobility phospholipid fraction, the proportions of which changed according to the degree of fat content. GPC was found to decrease from the pretransplant to the posttransplant biopsy of all livers except for one with a histologically confirmed high lipid content, and this might represent a biomarker of liver function posttransplantation. NMR signals produced by the liver preservation solution were clearly detected in the cold perfusion stage biopsies of all livers but remained in the posttransplant spectra of only the two livers with a high lipid content and were prominent mainly in the graft that later developed primary graft dysfunction. This study has shown biochemical differences between livers used for transplants that can be related to the degree and type of lipid composition. This technology might therefore provide a novel screening approach for donor organ quality and a means to assess function in the recipient after transplantation.
Publisher: Elsevier BV
Date: 10-2012
DOI: 10.1016/J.EJVS.2012.05.020
Abstract: Nuclear magnetic resonance (NMR) spectroscopy is an established tool for metabolic profiling of tissues or biofluids with utility in identifying disease biomarkers and changes in enzymatic or gene expression. This pilot study aims to compare the metabolic profiles of intact varicose and non-varicose vein tissue via magic angle spinning (MAS) NMR spectroscopy with a view to promoting the understanding of the pathogenesis of varicose vein formation. Varicose vein tissue (n = 8) was collected from patients undergoing varicose veins surgery. Control non-varicose great saphenous vein s les were collected from patients undergoing lower limb utation (n = 3) and peripheral arterial bypass surgery (n = 5). Intact tissue s les (average weight 10.33 ± 0.8 mg) from each vein segment were analysed using 1D MAS (1)H NMR (600 MHz) spectroscopy. For selected vein s les, two-dimensional (2D) NMR experiments were performed. Differences between spectra from varicose and non-varicose tissues were elucidated using a variety of multivariate statistical analyses. The metabolic profiles of varicose veins s les were clearly differentiated from non-varicose veins s les. Lipid metabolites were present at a higher concentration in the non-varicose veins group whilst creatine, lactate and myo-inositol metabolites were more characteristic of the varicose veins group. We demonstrate differential metabolic profiles between varicose veins and non-varicose veins. Elucidating the metabolic signature underlying varicose veins can further improve our understanding of the biological mechanisms of disease initiation, progression, and aid in identifying putative therapeutic targets.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 09-2019
DOI: 10.1097/CCM.0000000000003841
Abstract: Adverse physiology and antibiotic exposure devastate the intestinal microbiome in critical illness. Time and cost implications limit the immediate clinical potential of microbial sequencing to identify or treat intestinal dysbiosis. Here, we examined whether metabolic profiling is a feasible method of monitoring intestinal dysbiosis in critically ill children. Prospective multicenter cohort study. Three U.K.-based PICUs. Mechanically ventilated critically ill ( n = 60) and age-matched healthy children ( n = 55). Collection of urine and fecal s les in children admitted to the PICU. A single fecal and urine s le was collected in healthy controls. Untargeted and targeted metabolic profiling using 1H-nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry or urine and fecal s les. This was integrated with analysis of fecal bacterial 16S ribosomal RNA profiles and clinical disease severity indicators. We observed separation of global urinary and fecal metabolic profiles in critically ill compared with healthy children. Urinary excretion of mammalian-microbial co-metabolites hippurate, 4-cresol sulphate, and formate were reduced in critical illness compared with healthy children. Reduced fecal excretion of short-chain fatty acids (including butyrate, propionate, and acetate) were observed in the patient cohort, demonstrating that these metabolites also distinguished between critical illness and health. Dysregulation of intestinal bile metabolism was evidenced by increased primary and reduced secondary fecal bile acid excretion. Fecal butyrate correlated with days free of intensive care at 30 days ( r = 0.38 p = 0.03), while urinary formate correlated inversely with vasopressor requirement ( r = –0.2 p = 0.037). Disruption to the functional activity of the intestinal microbiome may result in worsening organ failure in the critically ill child. Profiling of bacterial metabolites in fecal and urine s les may support identification and treatment of intestinal dysbiosis in critical illness.
Publisher: American Chemical Society (ACS)
Date: 05-04-2012
DOI: 10.1021/AC300153K
Abstract: High-resolution magic-angle s le spinning (HR-MAS) (1)H NMR spectroscopy of tissue biopsies combined with chemometric techniques has emerged as a valuable methodology for disease diagnosis and environmental assessments. However, the tissue mass required for such experiments is of the order of 10 mg, and this can compromise the metabolic evaluation because of tissue heterogeneity. Tissue availability is often a limitation for clinical studies due to histopathological requirements, which are currently the gold standard for diagnosis, for ex le, in the case of tumors. Here, we introduce the use of a rotating micro-NMR detector that optimizes the coil filling factor such that mass-limited s les can be measured. We show the results for measuring nanoliter volume tissue biopsies using a commercial HR-MAS probe for the first time. The method has been tested with bovine muscle and human gastric mucosal tumor tissue s les. The gain in mass sensitivity is approximate up to 17-fold, and the adequate spectral resolution (3 Hz) allows the measurement of the metabolite profiles in nanoliter volume s les, thereby limiting the ambiguity resulting from heterogeneous tissues thus, the approach presents diagnostic potential for studies by metabonomics of mass-limited biopsies.
Publisher: IOP Publishing
Date: 06-08-2018
Abstract: The appetite-regulating effects of non-digestible carbohydrates (NDC) have in part previously been attributed to their effects on intestinal transit rates as well as microbial production of short chain fatty acids (SCFA). Increased colonic production of the SCFA propionate has been shown to reduce energy intake and stimulate gut hormone secretion acutely in humans. We investigated the effect of the propiogenic NDC, L-rhamnose, on gastrointestinal transit times using a combined We used a dual L-rhamnose significantly slowed GE rates (by 19.5 min) but there was no difference in OCTT between treatments. However, breath H The NDCs tested had a minimal effect on intestinal transit time. Our data suggest that L-rhamnose is partially fermented in the small intestine and that breath H
Publisher: Oxford University Press (OUP)
Date: 2013
DOI: 10.1039/C2TX20030A
Publisher: Wiley
Date: 08-11-2000
DOI: 10.1016/S0014-5793(00)02147-5
Abstract: As the human genome sequencing projects near completion, there is an active search for technologies that can provide insights into the genetic basis for physiological variation and interpreting gene expression in terms of phenotype at the whole organism level in order to understand the pathophysiology of disease. We present a novel metabonomic approach to the investigation of genetic influences on metabolic balance and metabolite excretion patterns in two phenotypically normal mouse models (C57BL10J and Alpk:ApfCD). Chemometric techniques were applied to optimise recovery of biochemical information from complex (1)H NMR urine spectra and to determine metabolic biomarker differences between the two strains. Differences were observed in tricarboxylic acid cycle intermediates and methylamine pathway activity. We suggest here a new 'metabotype' concept, which will be of value in relating quantitative physiological and biochemical data to both phenotypic and genetic variation in animals and man.
Publisher: Oxford University Press (OUP)
Date: 03-02-2010
DOI: 10.1093/NDT/GFQ025
Publisher: American Chemical Society (ACS)
Date: 15-06-2005
DOI: 10.1021/AC0503456
Abstract: A new software tool has been developed that provides automated measurement of signal intensities in NMR spectra of complex mixtures without using data reduction procedures. The algorithm finds best-fit transformations between signals in reference compound spectra and the corresponding signals in analyte spectra. Unlike other algorithms, it is insensitive to variation in chemical shift and can even be used for relative quantitation of compounds whose identities have not yet been established. Additionally, the parameters of the transformation provide information and error metrics that may assist in the streamlining of quality control. The approach presented is general in scope but has been tested by application to peak quantitation in NMR spectra of biofluids. Replicate NMR measurements of solutions of biologically important compounds at various concentrations were made. Further NMR data were collected on urine s les from human, rat, and mouse, which were "spiked" with reference compound solutions at known concentrations. Finally, existing data from an independent toxicology project involving several hundred s les were analyzed, and the consistency of the measurements for metabolites that give multiple NMR signals was assessed. The results of all these tests give confidence that the technique can be used in automated quantitation of compounds in large NMR data sets with minimal operator intervention.
Publisher: American Chemical Society (ACS)
Date: 21-11-2011
DOI: 10.1021/PR200938V
Abstract: A two by two experimental study has been designed to determine the effect of gut microbiota on energy metabolism in mouse models. The metabolic phenotype of germ-free (GF, n = 20) and conventional (n = 20) mice was characterized using a NMR spectroscopy-based metabolic profiling approach, with a focus on sexual dimorphism (20 males, 20 females) and energy metabolism in urine, plasma, liver, and brown adipose tissue (BAT). Physiological data of age-matched GF and conventional mice showed that male animals had a higher weight than females in both groups. In addition, conventional males had a significantly higher total body fat content (TBFC) compared to conventional females, whereas this sexual dimorphism disappeared in GF animals (i.e., male GF mice had a TBFC similar to those of conventional and GF females). Profiling of BAT hydrophilic extracts revealed that sexual dimorphism in normal mice was absent in GF animals, which also displayed lower BAT lactate levels and higher levels of (D)-3-hydroxybutyrate in liver, plasma, and BAT, together with lower circulating levels of VLDL. These data indicate that the gut microbiota modulate the lipid metabolism in BAT, as the absence of gut microbiota stimulated both hepatic and BAT lipolysis while inhibiting lipogenesis. We also demonstrated that (1)H NMR metabolic profiles of BAT were excellent predictors of BW and TBFC, indicating the potential of BAT to fight against obesity.
Publisher: American Chemical Society (ACS)
Date: 27-06-2008
DOI: 10.1021/AC800859X
Publisher: Royal Society of Chemistry (RSC)
Date: 21-01-2002
DOI: 10.1039/B109430K
Abstract: Multivariate statistical batch processing (BP) analysis of 1H NMR urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin, alpha-naphthylisothiocyanate (ANIT). ANIT (100 mg kg(-1)) was administered orally to rats (n = 5) and urine s les were collected from dosed and matching control rats at time-points up to 168 h post-dose. Urine s les were measured via 1H NMR spectroscopy and partial least squares (PLS) based batch processing analysis was used to interpret the spectral data, treating each rat as an in idual batch comprising a series of timed urine s les. A model defining the mean urine profile over the 7 day study period was established, together with model confidence limits (+/-3 standard deviation), for the control group. S les obtained from ANIT treated animals were evaluated using the control model. Time-dependent deviations from the control model were evident in all ANIT treated animals consisting of glycosuria, bile aciduria, an initial decrease in taurine levels followed by taurinuria and a reduction of tricarboxylic acid cycle intermediate excretion. BP provided an efficient means of visualising the biochemical response to ANIT in terms of both inter-animal variation and net variation in metabolite excretion profiles. BP also allowed multivariate statistical limits for normality to be established and provided a template for defining the sequence of time-dependent metabolic consequences of toxicity in NMR based metabonomic studies.
Publisher: American Chemical Society (ACS)
Date: 08-10-2014
DOI: 10.1021/PR500161W
Abstract: We have investigated the urinary and plasma metabolic phenotype of acute pancreatitis (AP) patients presenting to the emergency room at a single center London teaching hospital with acute abdominal pain using (1)H NMR spectroscopy and multivariate modeling. Patients were allocated to either the AP (n = 15) or non-AP patients group (all other causes of abdominal pain, n = 21) on the basis of the national guidelines. Patients were assessed for three clinical outcomes: (1) diagnosis of AP, (2) etiology of AP caused by alcohol consumption and cholelithiasis, and (3) AP severity based on the Glasgow score. S les from AP patients were characterized by high levels of urinary ketone bodies, glucose, plasma choline and lipid, and relatively low levels of urinary hippurate, creatine and plasma-branched chain amino acids. AP could be reliably identified with a high degree of sensitivity and specificity (OPLS-DA model R(2) = 0.76 and Q(2)Y = 0.59) using panel of discriminatory biomarkers consisting of guanine, hippurate and creatine (urine), and valine, alanine and lipoproteins (plasma). Metabolic phenotyping was also able to distinguish between cholelithiasis and colonic inflammation among the heterogeneous non-AP group. This work has demonstrated that combinatorial biomarkers have a strong diagnostic and prognostic potential in AP with relevance to clinical decision making in the emergency unit.
Publisher: Wiley
Date: 14-09-2013
Publisher: Elsevier BV
Date: 08-2010
Publisher: Springer Science and Business Media LLC
Date: 26-04-2017
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 25-08-2014
DOI: 10.1002/HEP.27264
Abstract: There is no clinically applicable biomarker for surveillance of hepatocellular carcinoma (HCC), because the sensitivity of serum alpha-fetoprotein (AFP) is too low for this purpose. Here, we determined the diagnostic performance of a panel of urinary metabolites of HCC patients from West Africa. Urine s les were collected from Nigerian and Gambian patients recruited on the case-control platform of the Prevention of Liver Fibrosis and Cancer in Africa (PROLIFICA) program. Urinary proton nuclear magnetic resonance ((1) H-NMR) spectroscopy was used to metabolically phenotype 290 subjects: 63 with HCC 32 with cirrhosis (Cir) 107 with noncirrhotic liver disease (DC) and 88 normal control (NC) healthy volunteers. Urine s les from a further cohort of 463 subjects (141 HCC, 56 Cir, 178 DC, and 88 NC) were analyzed, the results of which validated the initial cohort. The urinary metabotype of patients with HCC was distinct from those with Cir, DC, and NC with areas under the receiver operating characteristic (AUROC) curves of 0.86 (0.78-0.94), 0.93 (0.89-0.97), and 0.89 (0.80-0.98) in the training set and 0.81 (0.73-0.89), 0.96 (0.94-0.99), and 0.90 (0.85-0.96), respectively, in the validation cohort. A urinary metabolite panel, comprising inosine, indole-3-acetate, galactose, and an N-acetylated amino acid (NAA), showed a high sensitivity (86.9% [75.8-94.2]) and specificity (90.3% [74.2-98.0]) in the discrimination of HCC from cirrhosis, a finding that was corroborated in a validation cohort (AUROC: urinary panel = 0.72 AFP = 0.58). Metabolites that were significantly increased in urine of HCC patients, and which correlated with clinical stage of HCC, were NAA, dimethylglycine, 1-methylnicotinamide, methionine, acetylcarnitine, 2-oxoglutarate, choline, and creatine. The urinary metabotyping of this West African cohort identified and validated a metabolite panel that diagnostically outperforms serum AFP.
Publisher: Elsevier BV
Date: 02-1997
DOI: 10.1016/S0742-8413(96)00146-6
Abstract: The renal papillary toxin, propyleneimine (PI), was administered at 20 or 30 microliters/kg i.p. to male Sprague Dawley (SD) rats (n = 5), Fischer 344 (F344) rats (n = 4), and to multimammate desert mice (Mastomys natalensis, n = 4). Urine was collected at time points up to 4 days p.d. and the toxicological response of the different animal models to PI compared using 1H NMR spectroscopy of urine, renal histopathology, and urinary assays for alkaline phosphatase (ALP), lactate dehydrogenase (LDH), and gamma-glutamyl transpeptidase (gamma GT). The renal papillae of both F344 and SD rats showed extensive necrotic lesions 4 days post-dosing and in some cases sloughing of the papilla. However, only slight renal papillary necrosis (RPN) was observed in Mastomys treated with 20 microliters/kg PI and, although slight to moderate damage was observed at 30 microliters/kg, PI-treated Mastomys showed substantially less RPN than either group of PI-treated rats. 1H NMR urinalysis showed that PI treatment caused a decrease in the urinary concentrations of succinate (0-24 hr p.d.) and citrate (24-48 hr p.d.) and an increase in creatine (0-48 hr p.d.) in all animal models. Trimethylamine-N-oxide (24-48 hr) and 2-oxoglutarate concentrations decreased initially following the administration of PI and then rose above control levels. The 1H NMR-detected urinary biochemical effects of PI in all three models were similar. However, taurine concentrations were elevated in the urine of Mastomys following PI treatment, perhaps indicating a degree of liver damage, whereas taurinuria was not seen in either SD or F344 rats. These observations are discussed in relation to the potential mechanism of PI-toxicity.
Publisher: American Chemical Society (ACS)
Date: 22-09-2015
Abstract: Specific and sensitive food biomarkers are necessary to support dietary intake assessment and link nutritional habits to potential impact on human health. A multistep nutritional intervention study was conducted to suggest novel biomarkers for coffee consumption. (1)H NMR metabolic profiling combined with multivariate data analysis resolved 2-furoylglycine (2-FG) as a novel putative biomarker for coffee consumption. We relatively quantified 2-FG in the urine of coffee drinkers and investigated its origin, metabolism, and excretion kinetics. When searching for its potential precursors, we found different furan derivatives in coffee products, which are known to get metabolized to 2-FG. Maximal urinary excretion of 2-FG occurred 2 h after consumption (p = 0.0002) and returned to baseline after 24 h (p = 0.74). The biomarker was not excreted after consumption of coffee substitutes such as tea and chicory coffee and might therefore be a promising acute biomarker for the detection of coffee consumption in human urine.
Publisher: American Chemical Society (ACS)
Date: 06-03-2013
DOI: 10.1021/PR300900B
Abstract: Hippurate, the glycine conjugate of benzoic acid, is a normal constituent of the endogenous urinary metabolite profile and has long been associated with the microbial degradation of certain dietary components, hepatic function and toluene exposure, and is also commonly used as a measure of renal clearance. Here we discuss the potential relevance of hippurate excretion with regard to normal endogenous metabolism and trends in excretion relating to gender, age, and the intestinal microbiota. Additionally, the significance of hippurate excretion with respect to disease states including obesity, diabetes, gastrointestinal diseases, impaired renal function, psychological disorders and autism, as well as toxicity and parasitic infection, are considered.
Publisher: Informa UK Limited
Date: 1995
DOI: 10.3109/00498259509061916
Abstract: 1. The quantitative urinary excretion of the sulphate and glucuronide metabolites of 15 substituted phenols dosed to rat has been determined using high resolution 19F-nmr spectroscopy. 2. The urinary metabolic fate of each of the compounds was related to a series of calculated physicochemical properties for each compound to produce quantitative structure-metabolism relationships (QSMRs). Using these calculated molecular properties it was possible to predict the urinary recovery of xenobiotic material as a percentage of the administered dose, to classify the compounds according to their 'dominant' metabolite pattern and to predict quantitatively the proportions of glucuronide and sulphate conjugates in the urine by the use of multiple linear regression. 3. The quantitative predictions were tested by cross-validation and good prediction of total xenobiotic urinary recovery as a percentage of the administered dose was achieved based on an equation involving the electrophilic superdelocalizability at C4 (para to the hydroxyl function), the smallest principal ellipsoid axis dimension and the heat of formation. The largest moment of inertia and the electrophilic superdelocalizability at C3 were found to be the most significant factors for the prediction of the percentage glucuronide in the urine, and the urinary excretion of sulphate conjugates as a percentage of total urinary recovery was negatively correlated with the glucuronide excretion as little parent compound was excreted.
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D2AN01097F
Abstract: A JEDI NMR pulse experiment incorporating relaxation, diffusion and J-modulation peak editing was implemented at a low field (80 MHz) spectrometer system to quantify two recently discovered plasma markers of SARS-CoV-2 infection and general inflammation.
Publisher: American Chemical Society (ACS)
Date: 25-01-2005
DOI: 10.1021/TX0498915
Abstract: Hydrazine is a model toxin that induces both hepatotoxic and neurotoxic effects in experimental animals. The direct biochemical effects of hydrazine in kidney, liver, and brain tissue were assessed in male Sprague-Dawley rats using magic angle spinning nuclear magnetic resonance (NMR) spectroscopy. A single dose of hydrazine (90 mg/kg) resulted in changes to the biochemical composition of the liver after 24 h including an increase in triglycerides and beta-alanine, together with a decrease in hepatic glycogen, glucose, choline, taurine, and trimethylamine-N-oxide (TMAO). From histopathology measurements of liver tissue, minimal to mild hepatocyte alteration was observed in all animals at 24 h. The NMR spectra of the renal cortex at 24 h after dosing were dominated by a marked increase in the tissue concentration of 2-aminoadipate (2-AA) and beta-alanine, concomitant with depletions in TMAO, myo-inositol, choline, taurine, glutamate, and lysine. No alteration to the NMR spectral profile of the substantia nigra was observed after hydrazine administration, but perturbations to the relative concentrations of creatine, aspartate, myo-inositol, and N-acetyl aspartate were apparent in the hippoc us of hydrazine-treated animals at 24 h postdose. No overt signs of histopathological toxicity were observed in either the kidney or the brain regions examined. Elevated alanine levels were observed in all tissues indicative of a general inhibition of alanine transaminase activity. By 168 h postdose, NMR spectral profiles of treated rats appeared similar to those of matched controls for all tissue types indicative of recovery from toxic insult.
Publisher: Springer Science and Business Media LLC
Date: 03-10-2018
DOI: 10.1038/S41598-018-32938-6
Abstract: Clinical investigations lack predictive value when diagnosing pneumonia, especially when patients are ventilated and develop ventilator associated pneumonia (VAP). New tools to aid diagnosis are important to improve outcomes. This pilot study examines the potential for a panel of inflammatory mediators to aid in the diagnosis. Forty-four ventilated patients, 17 with pneumonia and 27 with brain injuries, eight of whom developed VAP, were recruited. 51 inflammatory mediators, including cytokines and oxylipins, were measured in patients’ serum using flow cytometry and mass spectrometry. The mediators could separate patients admitted to ICU with pneumonia compared to brain injury with an area under the receiver operating characteristic curve (AUROC) 0.75 (0.61–0.90). Changes in inflammatory mediators were similar in both groups over the course of ICU stay with 5,6-dihydroxyeicosatrienoic and 8,9-dihydroxyeicosatrienoic acids increasing over time and interleukin-6 decreasing. However, brain injured patients who developed VAP maintained inflammatory profiles similar to those at admission. A multivariate model containing 5,6-dihydroxyeicosatrienoic acid, 8,9-dihydroxyeicosatrienoic acid, intercellular adhesion molecule-1, interleukin-6, and interleukin-8, could differentiate patients with VAP from brain injured patients without infection (AUROC 0.94 (0.80–1.00)). The use of a selected group of markers showed promise to aid the diagnosis of VAP especially when combined with clinical data.
Publisher: American Chemical Society (ACS)
Date: 04-12-2010
DOI: 10.1021/AC901728W
Abstract: We demonstrate the statistical integration of nuclear magnetic resonance (NMR) spectroscopy and capillary electrophoresis (CE) data in order to describe a pathological state caused by Schistosoma mansoni infection in a mouse model based on urinary metabolite profiles. Urine s les from mice 53 days post infection with S. mansoni and matched controls were analyzed via NMR spectroscopy and CE. The two sets of metabolic profiles were first processed and analyzed independently and were subsequently integrated using statistical correlation methods in order to facilitate cross assignment of metabolites. Using this approach, metabolites such as 3-ureidopropionate, p-cresol glucuronide, phenylacetylglycine, indoxyl sulfate, isocitrate, and trimethylamine were identified as differentiating between infected and control animals. These correlation analyses facilitated structural elucidation using the identification power of one technique to enhance and validate the other, but also highlighted the enhanced ability to detect functional correlations between metabolites, thereby providing potential for achieving deeper mechanistic insight into the biological process.
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3MB70215D
Abstract: The NMRI outbred mouse model is widely used for studying metabolic disease, toxicity, and infection, yet information regarding baseline metabolism of this murine strain is relatively sparse. Using different batches of female NMRI mice, we assessed the stability of the metabolic phenotype with increasing age and weight, and determined the influence of acclimatization on the metabolic profile of biofluids (urine, plasma, and faecal water). Differences in urinary concentrations of 3-ureidopropionate, 2-oxoisocaproate, trimethylamine, and glycine were detected between three batches of 9-week-old female NMRI mice using proton nuclear magnetic resonance ((1)H NMR) spectroscopy coupled with multivariate statistical analysis. An acclimatization period of 2 weeks was imposed after the mice entered the laboratory environment. Strong differences in the faecal metabolome pre- and post-acclimatization were found (reduction in amino acid concentrations), whilst the urine metabolome showed increased levels of trimethylamine-N-oxide, phenylacetyl glycine, and hippurate with decreased excretion of formate and betaine post-acclimatization. Temporal variation in the metabolite profiles over a 16-week study stabilized around 7-week-old animals. The results from this study strongly argue for inclusion of an acclimatization period prior to starting an investigative procedure, and suggest that the metabolic phenotypes of female NMRI mice are more stable at around 7 weeks of age. We have also identified a set of metabolites that are more susceptible to variation in concentration. This information can serve as a benchmark in order to establish confidence in systematic variation attributable to pathology or therapeutic intervention above the background metabolic variation in the NMRI mouse.
Publisher: Springer Science and Business Media LLC
Date: 11-03-2015
DOI: 10.1038/SREP08988
Abstract: The composition and structure of the pregnancy vaginal microbiome may influence susceptibility to adverse pregnancy outcomes. Studies on the pregnant vaginal microbiome have largely been limited to Northern American populations. Using MiSeq sequencing of 16S rRNA gene licons, we characterised the vaginal microbiota of a mixed British cohort of women (n = 42) who experienced uncomplicated term delivery and who were s led longitudinally throughout pregnancy (8–12, 20–22, 28–30 and 34–36 weeks gestation) and 6 weeks postpartum. We show that vaginal microbiome composition dramatically changes postpartum to become less Lactobacillus spp. dominant with increased alpha- ersity irrespective of the community structure during pregnancy and independent of ethnicity. While the pregnancy vaginal microbiome was characteristically dominated by Lactobacillus spp. and low alpha- ersity, unlike Northern American populations, a significant number of pregnant women this British population had a L. jensenii -dominated microbiome characterised by low alpha- ersity. L. jensenii was predominantly observed in women of Asian and Caucasian ethnicity whereas L. gasseri was absent in s les from Black women. This study reveals new insights into biogeographical and ethnic effects upon the pregnancy and postpartum vaginal microbiome and has important implications for future studies exploring relationships between the vaginal microbiome, host health and pregnancy outcomes.
Publisher: Springer Science and Business Media LLC
Date: 08-04-2005
DOI: 10.1038/NRMICRO1152
Abstract: The mammalian gut microbiota interact extensively with the host through metabolic exchange and co-metabolism of substrates. Such metabolome-metabolome interactions are poorly understood, but might be implicated in the aetiology of many human diseases. In this paper, we assess the importance of the gut microbiota in influencing the disposition, fate and toxicity of drugs in the host, and conclude that appropriate consideration of in idual human gut microbial activities will be a necessary part of future personalized health-care paradigms.
Publisher: Elsevier BV
Date: 11-2018
Publisher: Springer Science and Business Media LLC
Date: 31-05-2018
Publisher: Elsevier BV
Date: 10-2019
DOI: 10.1093/JN/NXZ138
Abstract: Measurement of multiple food intake exposure biomarkers in urine may offer an objective method for monitoring diet. The potential of spot and cumulative urine s les that have reduced burden on participants as replacements for 24-h urine collections has not been evaluated. The aim of this study was to determine the utility of spot and cumulative urine s les for classifying the metabolic profiles of people according to dietary intake when compared with 24-h urine collections in a controlled dietary intervention study. Nineteen healthy in iduals (10 male, 9 female, aged 21-65 y, BMI 20-35 kg/m2) each consumed 4 distinctly different diets, each for 1 wk. Spot urine s les were collected ∼2 h post meals on 3 intervention days/wk. Cumulative urine s les were collected daily over 3 separate temporal periods. A 24-h urine collection was created by combining the 3 cumulative urine s les. Urine s les were analyzed with metabolite fingerprinting by both high-resolution flow infusion electrospray mass spectrometry (FIE-HRMS) and proton nuclear magnetic resonance spectroscopy (1H-NMR). Concentrations of dietary intake biomarkers were measured with liquid chromatography triple quadrupole mass spectrometry and by integration of 1H-NMR data. Cross-validation modeling with 1H-NMR and FIE-HRMS data demonstrated the power of spot and cumulative urine s les in predicting dietary patterns in 24-h urine collections. Particularly, there was no significant loss of information when post-dinner (PD) spot or overnight cumulative s les were substituted for 24-h urine collections (classification accuracies of 0.891 and 0.938, respectively). Quantitative analysis of urine s les also demonstrated the relation between PD spot s les and 24-h urines for dietary exposure biomarkers. We conclude that PD spot urine s les are suitable replacements for 24-h urine collections. Alternatively, cumulative s les collected overnight predict similarly to 24-h urine s les and have a lower collection burden for participants.
Publisher: Baishideng Publishing Group Inc.
Date: 2016
Publisher: Wiley
Date: 09-2008
Abstract: Increasing rates of success in liver transplantation have increased the number of cases considered. However, liver post‐transplant graft dysfunction of liver transplants (TXs) is not fully understood and by applying holistic approaches we can investigate metabolic change deriving from confounding factors such as liver fat content, ischaemia time, donor age, recipient's health, etc. Twenty‐six hepatic bile s les taken from liver donors and recipients were retrieved from a total of six TXs, from these one recipient underwent post‐graft dysfunction. CE was employed to fingerprint bile collected at 10 min increments in the donors and in the recipients. The electropherograms of these s les were aligned and normalised using correlation optimised warping algorithms and modelled with multivariate techniques. The resulting metabolic signatures were compared in general donors and recipients showed distinct fingerprints and clustered separately. When a partial least square discriminant analysis (PLS‐DA) model was constructed between donor and recipient's s les, a recipient of a 32 year old liver with normal steatosis, and shortest cold ischaemia time showed as the observation nearest to its donor observation, denoting minimal metabolic change. This study proposes CE fingerprinting of human bile as a promising technique to help unravel the complex metabolic pathways involved during transplantation.
Publisher: Public Library of Science (PLoS)
Date: 27-10-2015
Publisher: Wiley
Date: 16-09-2011
Publisher: F1000 Research Ltd
Date: 02-08-2018
DOI: 10.12688/WELLCOMEOPENRES.14706.1
Abstract: Background: Changes in intestinal mucosal integrity and gut microbial balance occur in severe acute malnutrition (SAM), resulting in treatment failure and adverse clinical outcomes (gram-negative sepsis, diarrhoea and high case-fatality). Transient lactose intolerance, due to loss of intestinal brush border lactase, also complicates SAM, thus milk based feeds may not be optimal for nutritional rehabilitation. Since the gut epithelial barrier can be supported by short chain fatty acids, derived from microbiota fermentation by particular fermentable carbohydrates, we postulated that an energy-dense nutritional feed comprising of legume-based fermentable carbohydrates, incorporated with lactose-free versions of standard World Health Organization (WHO) F75/F100 nutritional feeds will enhance epithelial barrier function in malnourished children, reduce and promote resolution of diarrhoea and improve overall outcome. Methods: We will investigate in an open-label trial in 160 Ugandan children with SAM, defined by mid-upper arm circumference .5cm and/or presence of kwashiorkor. Children will be randomised to a lactose-free, chickpea-enriched feed containing 2 kcal/ml, provided in quantities to match usual energy provision (experimental) or WHO standard treatment F75 (0.75 kcal/ml) and F100 (1 kcal/ml) feeds on a 1:1 basis, conducted at Mbale Regional Referral Hospital nutritional rehabilitation unit. The primary outcomes are change in MUAC at day 90 and survival to day 90. Secondary outcomes include: i) moderate to good weight gain ( g/kg/day), ii) de novo development of diarrhoea ( loose stools/day), iii) time to diarrhoea resolution (if loose stools/day), and iv) time to oedema resolution (if kwashiorkor) and change in intestinal biomarkers (faecal calprotectin). Discussion: We hypothesize that, if introduced early in the management of malnutrition, such lactose-free, fermentable carbohydrate-based feeds, could safely and cheaply improve global outcome by reducing lactose intolerance-related diarrhoea, improving mucosal integrity and enhancing immunity, and limiting the risk of systemic infection and associated broad-spectrum antibiotic resistance. Registration: ISRCTN 10309022 .
Publisher: Elsevier BV
Date: 11-2022
DOI: 10.1093/AJCN/NQAB211
Publisher: American Chemical Society (ACS)
Date: 28-10-2009
DOI: 10.1021/PR900711J
Abstract: Hookworms (Ancylostoma duodenale and Necator americanus) are blood-feeding intestinal nematodes that infect approximately 700 million people worldwide. To further our understanding of the systems metabolic response of the mammalian host to hookworm infection, we employed a metabolic profiling strategy involving the combination of (1)H NMR spectroscopic analysis of urine and serum and multivariate data analysis techniques to investigate the biochemical consequences of a N. americanus infection in the hamster. The infection was characterized by altered energy metabolism, consistent with hookworm-induced anemia. Additionally, disturbance of gut microbiotal activity was associated with a N. americanus infection, manifested in the alterations of microbial-mammalian cometabolites, including phenylacetylglycine, p-cresol glucuronide, 4-hydroxy-3-methyl-phenylpropionic acid, hippurate, 4-hydroxyphenylactate, and dimethylamine. The correlation between worm burden and metabolite concentrations also reflected a changed energy metabolism and gut microbial state. Furthermore, elevated levels of urinary 2-aminoadipate was a characteristic feature of the infection, which may be associated with the documented neurological consequences of hookworm infection.
Publisher: American Chemical Society (ACS)
Date: 08-12-2006
DOI: 10.1021/AC051444M
Abstract: Statistical heterospectroscopy (SHY) is a new statistical paradigm for the coanalysis of multispectroscopic data sets acquired on multiple s les. This method operates through the analysis of the intrinsic covariance between signal intensities in the same and related molecules measured by different techniques across cohorts of s les. The potential of SHY is illustrated using both 600-MHz 1H NMR and UPLC-TOFMS data obtained from control rat urine s les (n = 54) and from a corresponding hydrazine-treated group (n = 58). We show that direct cross-correlation of spectral parameters, viz. chemical shifts from NMR and m/z data from MS, is readily achievable for a variety of metabolites, which leads to improved efficiency of molecular biomarker identification. In addition to structure, higher level biological information can be obtained on metabolic pathway activity and connectivities by examination of different levels of the NMR to MS correlation and anticorrelation matrixes. The SHY approach is of general applicability to complex mixture analysis, if two or more independent spectroscopic data sets are available for any s le cohort. Biological applications of SHY as demonstrated here show promise as a new systems biology tool for biomarker recovery.
Publisher: Springer Science and Business Media LLC
Date: 06-07-2007
DOI: 10.1007/S00125-007-0738-5
Abstract: Complex changes in gene expression are associated with insulin resistance and non-alcoholic fatty liver disease (NAFLD) promoted by feeding a high-fat diet (HFD). We used functional genomic technologies to document molecular mechanisms associated with diet-induced NAFLD. Male 129S6 mice were fed a diet containing 40% fat (high-fat diet, HFD) for 15 weeks. Glucose tolerance, in vivo insulin secretion, plasma lipid profile and adiposity were determined. Plasma metabonomics and liver transcriptomics were used to identify changes in gene expression associated with HFD-induced NAFLD. In HFD-fed mice, NAFLD and impaired glucose and lipid homeostasis were associated with increased hepatic transcription of genes involved in fatty acid uptake, intracellular transport, modification and elongation, whilst genes involved in beta-oxidation and lipoprotein secretion were, paradoxically, also upregulated. NAFLD developed despite strong and sustained downregulation of transcription of the gene encoding stearoyl-coenzyme A desaturase 1 (Scd1) and uncoordinated regulation of transcription of Scd1 and the gene encoding sterol regulatory element binding factor 1c (Srebf1c) transcription. Inflammatory mechanisms appeared to be stimulated by HFD. Our results provide an accurate representation of subtle changes in metabolic and gene expression regulation underlying disease-promoting and compensatory mechanisms, collectively contributing to diet-induced insulin resistance and NAFLD. They suggest that proposed models of NAFLD pathogenesis can be enriched with novel diet-reactive genes and disease mechanisms.
Publisher: American Chemical Society (ACS)
Date: 21-01-2006
DOI: 10.1021/PR050244O
Abstract: The metabolic consequences of Huntington's disease in the R6/2 mouse model were investigated using NMR spectroscopy and pattern recognition to characterize selected brain regions, muscle, blood, and urine. Global increases in relative brain concentrations of osmolytes, creatine, glutamine, and lactate, and decreases in acetate and N-acetylaspartate were found together with striatal-specific lower concentrations of GABA and choline. Clear differentiation of R6/2 and wild-type mice was also obtained for urine and blood metabolite profiles that may have applicability for monitoring HD in human populations.
Publisher: American Chemical Society (ACS)
Date: 11-03-2006
DOI: 10.1021/PR0503782
Abstract: (1)H NMR spectroscopy-based metabonomic analysis was employed to investigate plasma s les from 21 pairs of monozygotic twins discordant for schizophrenia and 8 pairs of age-matched healthy twins in an effort to disentangle genetic and epigenetic components of schizophrenia. We identified alterations in the lipid profile of both affected and unaffected schizophrenia twins. Additionally, there is a close association of VLDL/LDL signals and Global Functioning Scores in female twins suffering from schizophrenia. Our results further support a link between metabolic disturbances and the etiopathology of schizophrenia.
Publisher: American Chemical Society (ACS)
Date: 23-06-2007
DOI: 10.1021/AC0703754
Abstract: Although NMR spectroscopic techniques coupled with multivariate statistics can yield much useful information for classifying biological s les based on metabolic profiles, biomarker identification remains a time-consuming and complex procedure involving separation methods, two-dimensional NMR, and other spectroscopic tools. We present a new approach to aid complex biomixture analysis that combines diffusion ordered (DO) NMR spectroscopy with statistical total correlation spectroscopy (STOCSY) and demonstrate its application in the characterization of urinary biomarkers and enhanced information recovery from plasma NMR spectra. This method relies on calculation and display of the covariance of signal intensities from the various nuclei on the same molecule across a series of spectra collected under different pulsed field gradient conditions that differentially attenuate the signal intensities according to translational molecular diffusion rates. We term this statistical diffusion-ordered spectroscopy (S-DOSY). We also have developed a new visualization tool in which the apparent diffusion coefficients from DO spectra are projected onto a 1D NMR spectrum (diffusion-ordered projection spectroscopy, DOPY). Both methods either alone or in combination have the potential for general applications to any complex mixture analysis where the s le contains compounds with a range of diffusion coefficients.
Publisher: Royal Society of Chemistry (RSC)
Date: 2005
DOI: 10.1039/B501890K
Publisher: Wiley
Date: 16-04-2001
DOI: 10.1002/MRM.1106
Abstract: The metabolic consequences of xenobiotic-induced toxicity were investigated using high-resolution magic angle spinning (MAS) NMR spectroscopy of intact tissue. Renal papillary necrosis (RPN) was induced in Sprague-Dawley rats (n = 12) via a single i.p. dose of 250 mg/kg 2-bromoethanamine (BEA) hydrobromide. At 2, 4, 6, and 24 h after treatment with BEA, three animals were killed and tissue s les were obtained from liver, renal cortex, and renal medulla. Tissue s les were also removed at 2 and 24 h from matched controls (n = 6). (1)H MAS NMR spectroscopic techniques were used to analyze s les of intact tissue ( approximately 10 mg). Decreased levels of nonperturbing renal osmolytes (glycerophosphocholine, betaine, and myo-inositol) were observed in the renal papilla of BEA-treated animals at 6 and 24 h postdose (p.d.), concomitant with a relative increase in the tissue concentration of creatine. Increased levels of glutaric acid were found in all tissues studied in BEA-treated animals at 4 and 6 h p.d., indicating the inhibition of mitochondrial fatty acyl CoA dehydrogenases and mitochondrial dysfunction. Increased levels of trimethylamine-N-oxide occurred in the renal cortex at 6 h p.d. Changes in the metabolite profile of liver included an increase in the relative concentrations of triglycerides, lysine, and leucine. The novel application of (1)H MAS NMR to the biochemical analysis of intact tissues following a toxic insult highlights the potential of this technique as a toxicological probe in providing a direct link between urinary biomarkers of toxicity and histopathological evaluation of toxicological lesions.
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Elaine Holmes.