Biomedical subjects

E Holmes

Publications and source records attributed to E Holmes.

At least 19 recordsLinked to original sources

PubMed2006

Probing latent biomarker signatures and in vivo pathway activity in experimental disease states via statistical total correlation spectroscopy (STOCSY) of biofluids: application to HgCl2 toxicity.

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.

Acute Kidney Injury↗

PubMed2005

Curve-fitting method for direct quantitation of compounds in complex biological mixtures using 1H NMR: application in metabonomic toxicology studies.

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 samples 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 samples 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.

Animals↗

PubMed2005

Sexual dimorphism in urinary metabolite profiles of Han Wistar rats revealed by nuclear-magnetic-resonance-based metabonomics.

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 samples 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.

Animals↗

PubMed2005

Metabolic characterization of distinct neuroanatomical regions in rats by magic angle spinning 1H nuclear magnetic resonance spectroscopy.

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 hippocampus 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 sampled and the degree of intersample 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 hippocampus 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.

Animals↗

PubMed2005

Chemometric analysis of biofluids following toxicant induced hepatotoxicity: a metabonomic approach to distinguish the effects of 1-naphthylisothiocyanate from its products.

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.

1-Naphthylamine↗

PubMed2002

Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological NMR spectra.

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.

Animals↗

PubMed2002

Structure-metabolism relationships of substituted anilines: prediction of N-acetylation and N-oxanilic acid formation using computational chemistry.

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.

Acetylation↗

PubMed2002

A capture-recapture model to estimate prevalence of children born in Scotland with developmental eye defects.

BACKGROUND: Microphthalmia, anophthalmia and coloboma (MAC) are closely related structural developmental eye defects that have caused public concern in the UK following media reports of apparent clusters of cases. An extensive search was carried out to identify potential cases, and diagnoses were confirmed by ophthalmological review. Despite this effort, it was recognised that some cases would remain unidentified. Capture-recapture methods could improve the accuracy of the study's birth prevalence estimate. METHODS: A register of all children born with the developmental eye defects of MAC in Scotland (1981-96) was compiled. This identified 188 cases from eight national ascertainment sources. The methods described by Hook and Regal were used to determine possible estimates for each source. A log-linear method of capture-recapture was used to fit a model to the number of children identified by the different combinations of the eight national sources, and the individual sources were included in the model as main effects. RESULTS: Maximum-likelihood estimates were calculated for tables of captured/not captured by one source versus any other source. The estimated number of unobserved cases for the most complete source, the register of congenital anomalies for Scotland, and the seven others combined is 78 (95% CI 53-115). Estimates calculated from two different log-linear models of the numbers of cases unobserved by all sources were 61 (95% CI 43-86) and 175 (95% CI 106-287). An external check with an independent congenital-anomalies register in one region, which is known to have high completeness, gave an estimate of 120. The study found a birth prevalence of MAC in Scotland of 1.9/10000, based on total live births during the study period. The capture-recapture analysis suggests that the true birth prevalence lies between 2.4/10 000 and 3.5/10000. DISCUSSION: Our experience shows that, even with multiple sources of ascertainment and considerable resources directed at case identification, a considerable level of under-ascertainment of congenital eye-anomalies still results, and suggests that the use of capture-recapture analysis would be a useful addition to congenital anomalies registers for needs assessment, disease-burden estimates and health-service planning.

Eye Abnormalities↗

PubMed2002

Real-time modelling of influenza outbreaks--a linear regression analysis.

Seasonal outbreaks of influenza exert a considerable burden on health services, and are notorious for their variability from year to year. Making use of historical data from the Scottish sentinelle surveillance since 1972, a potential candidate model has been derived based on simple linear regression. It was applied with a measure of success in the 1999-2000 winter season.

Disease Outbreaks↗

PubMed2001

P-glycoprotein in the catfish intestine: inducibility by xenobiotics and functional properties.

The p-glycoprotein (pgp)-mediated multixenobiotic resistance (MXR) mechanism of aquatic animals has been associated with protection against pollution. Recent studies in mammals suggest that intestinal pgp may modulate intestinal bioavailability of dietary xenobiotics. In order to further delineate this mechanism in the catfish, these studies: (1) examined the pgp-related distribution in the intestine and liver of catfish, (2) evaluated the MXR response following exposure to various dietary xenobiotics and a prototypic pgp inducer and (3) evaluated pgp functional activity in membrane vesicles, using prototypic substrates and inhibitors. For this purpose, catfish were exposed in vivo to the pgp inducer vincristine (VIN), and the xenobiotics beta-naphthoflavone (BNF), benzo[a]pyrene (BaP), and 3,4,3',4'-tetrachlorobiphenyl (TCB). Membrane vesicles, prepared from liver and intestine (proximal and distal sections) of control and exposed catfish, were subjected to SDS PAGE, Western Blot, and detection with the pgp C219 monoclonal antibody. Transport activity was evaluated in vitro using the pgp substrate [3H]vinblastine (VBL), and the pgp inhibitor verapamil (VP). Immunoblot studies demonstrated a pgp-related protein of approximately 170 kDa in the intestine and liver of catfish. This protein appears to be very susceptible to degradation, and was present in higher levels in the liver, in comparison to the intestine, where regional differences were not observed. Dietary exposure to the pgp substrate VIN, or the xenobiotics BNF, BaP, and TCB, did not appear to affect pgp-related reactivity. Transport studies with VBL indicate that the pgp-related protein of the catfish intestine displays classic pgp-mediated multidrug resistance (MDR) characteristics, such as energy-dependency, and sensitivity to VP. These studies suggest that the pgp-related protein in the catfish intestine and liver is not only immunochemically, but also functionally related to the mammalian MDR. Moreover, the results presented indicate that pgp-related reactivity and transport in intestinal vesicles of catfish may be influenced by factors including method sensitivity, sample collection, sample preparation, and immunoblot conditions.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2001

Investigations into biochemical changes due to diurnal variation and estrus cycle in female rats using high-resolution (1)H NMR spectroscopy of urine and pattern recognition.

Metabonomic methods utilizing (1)H NMR spectroscopy and pattern recognition analysis (NMR-PR) have been applied to investigate biochemical variation in a control population of female rats over time in relation to diurnal and estrus cycle fluctuations. Urine samples were collected twice daily (6 AM-6 PM and 6 PM-6 AM) from female rats (n = 10) for a period of 10 days. (1)H NMR spectroscopic analysis and PR were performed on each sample. Subtle differences in the endogenous metabolite excretion profiles of urine samples at the various stages of the estrus cycle were observed. The main inherent metabolic clustering in the principal components analysis (PCA) maps was related to interrat variation and was observed in the first two principal components (PCs), accounting for 66% of the variance in these data. Separation of urinary data according to time of sampling (day and night) was achieved in the lower PCs. Some of the differences in the urinary profiles of day and night samples causing this separation were attributed to the increase in metabolic activity of the rat during the night. Individual rat data were also mapped as a function of time, using PCA, to produce a metabolic trajectory, which in a number of cases facilitated separation of one or more stages of the estrus cycle. Several of the fluctuations observed between urine samples collected during the different stages of the estrus cycle may be related to hormone levels. Although variation in metabolite profiles relating to both diurnal and hormonal variation could be detected these perturbations were minor compared with the effects observed due to interrat variation. This is the first time that a hormonal cycle has been described for individuals based on NMR spectroscopic and multivariate analysis of metabolic data and shows the value of metabonomic methods in the investigation of physiological variation and rhythms.

Animals↗

PubMed2001

Directly coupled high-performance liquid chromatography and nuclear magnetic resonance spectroscopic with chemometric studies on metabolic variation in Sprague--Dawley rats.

We report here the first combined use of NMR-PR (pattern recognition) analysis and directly coupled HPLC--NMR analysis to identify metabolic subpopulations in normal laboratory animals and their discriminating endogenous urinary biomarkers. Urine samples obtained from control Sprague-Dawley rats (n = 68) were analyzed using (1)H NMR spectroscopy and principal components (PC) analysis to investigate physiological variability. Two distinct subpopulations of animals were classified based on metabolite excretion profiles. Analysis of the PC loadings established the spectral regions that were responsible for classification of the subpopulations and was used to direct the identification of biomarkers using a directly coupled HPLC--NMR analysis. One population had low urinary hippurate levels together with an increased concentration of 3-(3-hydroxyphenyl)propionic acid (3-HPPA)and 3-hydroxycinnamic acid (3-HCA). The other subpopulation excreted high levels of hippurate. Thus, we report the bimodal occurrence of hippuric acid and chlorogenic acid metabolites in a genetically homogeneous population of rats maintained under identical conditions, which may have significance in relation to the understanding of the consequences of biochemical variation in animals used for drug toxicity testing.

Animals↗

PubMed2001

High-resolution (1)H NMR and magic angle spinning NMR spectroscopic investigation of the biochemical effects of 2-bromoethanamine in intact renal and hepatic tissue.

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 samples were obtained from liver, renal cortex, and renal medulla. Tissue samples were also removed at 2 and 24 h from matched controls (n = 6). (1)H MAS NMR spectroscopic techniques were used to analyze samples 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.

Animals↗

PubMed2001

Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks.

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 samples, 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.

Animals↗

PubMed2001

Metabonomic investigations into hydrazine toxicity in the rat.

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 samples 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.

Administration, Oral↗

PubMed2001

NMR and pattern recognition studies on the time-related metabolic effects of alpha-naphthylisothiocyanate on liver, urine, and plasma in the rat: an integrative metabonomic approach.

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 samples 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 samples 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.

1-Naphthylisothiocyanate↗

PubMed2001

Investigation of water environments in a C18 bonded silica phase using 1H magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy.

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.

Journal Article↗

PubMed2000

An NMR-based metabonomic approach to investigate the biochemical consequences of genetic strain differences: application to the C57BL10J and Alpk:ApfCD mouse.

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.

Amino Acids↗