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Biomedical subjects

S W Provencher

Publications and source records attributed to S W Provencher.

At least 19 recordsLinked to original sources
PubMed2003

Detection of elevated glutathione in meningiomas by quantitative in vivo 1H MRS.

Glutathione has major roles in removing free radicals and toxins from normal tissues, but its presence in tumor cells hinders the effectiveness of many anticancer therapies. Analysis of short echo time brain tumor (1)H spectra at 1.5 T using a linear combination of metabolite spectra (LCModel) suggested a significant contribution of glutathione to meningioma spectra. By in vivo MRS (TE = 30 ms, TR = 2020 ms), reduced glutathione was found to be significantly elevated in meningiomas (3.3 +/- 1.5 mM, Mann Whitney, P < 0.005) compared to normal white matter (1.2 +/- 0.15 mM) and low-grade gliomas (1.0 +/- 0.26 mM), in agreement with published histofluorescence studies of tumor biopsies. Glx concentrations were also found to be elevated in meningiomas compared to astrocytomas or normal white matter, indicative of metabolic differences. The ability to noninvasively quantify reduced glutathione in vivo may aid selection of treatment therapies and also provide an indication of tumor aggressiveness.

Astrocytoma↗
PubMed2001

Automatic quantitation of localized in vivo 1H spectra with LCModel.

The LCModel method analyzes an in vivo spectrum as a Linear Combination of Model in vitro spectra from individual metabolite solutions. Complete model spectra, rather than individual resonances, are used in order to incorporate maximum prior information into the analysis. A nearly model-free constrained regularization method automatically accounts for the baseline and lineshape in vivo without imposing a restrictive parameterized form on them. LCModel is automatic (non-interactive) with no subjective input. Approximately maximum-likelihood estimates of the metabolite concentrations and their uncertainties (Cramér-Rao lower bounds) are obtained. LCModel analyses of spectra from users with fields from 1.5 to 9.4 T and a wide range of sequences, particularly with short TE, are used here to illustrate the capabilities and limitations of LCModel and proton MRS.

Algorithms↗
PubMed1999

Toward an in vivo neurochemical profile: quantification of 18 metabolites in short-echo-time (1)H NMR spectra of the rat brain.

Localized in vivo (1)H NMR spectroscopy was performed with 2-ms echo time in the rat brain at 9.4 T. Frequency domain analysis with LCModel showed that the in vivo spectra can be explained by 18 metabolite model solution spectra and a highly structured background, which was attributed to resonances with fivefold shorter in vivo T(1) than metabolites. The high spectral resolution (full width at half maximum approximately 0.025 ppm) and sensitivity (signal-to-noise ratio approximately 45 from a 63-microL volume, 512 scans) was used for the simultaneous measurement of the concentrations of metabolites previously difficult to quantify in (1)H spectra. The strongly represented signals of N-acetylaspartate, glutamate, taurine, myo-inositol, creatine, phosphocreatine, glutamine, and lactate were quantified with Cramér-Rao lower bounds below 4%. Choline groups, phosphorylethanolamine, glucose, glutathione, gamma-aminobutyric acid, N-acetylaspartylglutamate, and alanine were below 13%, whereas aspartate and scyllo-inositol were below 22%. Intra-assay variation was assessed from a time series of 3-min spectra, and the coefficient of variation was similar to the calculated Cramér-Rao lower bounds. Interassay variation was determined from 31 pooled spectra, and the coefficient of variation for total creatine was 7%. Tissue concentrations were found to be in very good agreement with neurochemical data from the literature.

Amino Acids↗
PubMed1999

Water diffusion in rat brain in vivo as detected at very large b values is multicompartmental.

The diffusion-weighted signal attenuation of water in rat brain was measured with pulsed-field gradient nuclear magnetic resonance methods in a single voxel under in vivo and global ischemic conditions. The diffusion-attenuated water signal was observed in vivo at b values of 300 ms/microm2 (strength of diffusion weighting) and diffusion times up to 400 ms. A series of constant diffusion time (CT) experiments with varied gradient directions and diffusion times revealed a multiexponential decay with apparent diffusion coefficients (ADC) covering two orders of magnitude from 1 to 0.01 microm2/ms. In a four-exponential fit, the observed changes during global ischemia could be fully explained by changes in the relative volume fractions only with unchanged ADCs. An anisotropy of the ADC, detected at small b values, was not observed for the ADC at large b values, but for the concomitant volume fractions. An inverse Laplace Transform of the CT curves, performed with CONTIN, resulted in continuously distributed diffusion coefficients, for which the term 'diffusogram' is proposed. This approach was more appropriate than a discrete exponential model with four to six components, being related to the morphology of brain tissue and its cell size distribution. On the basis of an analytical, quantitative model, it is suggested that the measured ADC at small b values reflects mainly properties of the restricting boundaries, i.e. the relative volume fractions and the extracellular tortuosity, while the intrinsic intracellular diffusion constant and the exchange time are predicted to have minor influence.

Animals↗
PubMed1997

Conformational analysis of galanin using end to end distance distribution observed by Förster resonance energy transfer.

The structural dynamics of the flexible neuropeptide galanin in solution were studied by Förster resonance energy transfer measurements at different temperatures by time-resolved fluorescence spectroscopy to determine its conformational heterogeneity. Endogenous tryptophan at position 2 acted as the fluorescent donor and the non fluorescent acceptor dinitrophenyl or the fluorescent acceptor dansyl were selectively attached to lysine 25 in porcine galanin. The coexistence of different structures of the neuropeptide galanin in trifluoroethanol solution was revealed by the model independent analysis of the distribution of relaxation times from the time-resolved resonance energy transfer data. Multiple conformational states are reflected by distinct end-to-end distance populations. The conformations differ in mean donor-acceptor distance by about 15, and are consistent with the extended and folded backbone conformations of two alpha-helical regions separated by a flexible hinge. The effect that the labelling of galanin has on binding to the receptor was also evaluated. DNP-galanin showed the same high affinity to galanin receptors as unlabelled galanin, whereas DNS-galanin had significantly reduced affinity.

Chemical Phenomena↗
PubMed1993

Estimation of metabolite concentrations from localized in vivo proton NMR spectra.

The LCModel method analyzes an in vivo spectrum as a Linear Combination of Model spectra of metabolite solutions in vitro. By using complete model spectra, rather than just individual resonances, maximum information and uniqueness are incorporated into the analysis. A constrained regularization method accounts for differences in phase, baseline, and lineshapes between the in vitro and in vivo spectra, and estimates the metabolite concentrations and their uncertainties. LCModel is fully automatic in that the only input is the time-domain in vivo data. The lack of subjective interaction should help the exchange and comparison of results. More than 3000 human brain STEAM spectra from patients and healthy volunteers have been analyzed with LCModel. N-acetylaspartate, cholines, creatines, myo-inositol, and glutamate can be reliably determined, and abnormal levels of these or elevated levels of lactate, alanine, scyllo-inositol, glutamine, or glucose clearly indicate numerous pathologies. A computer program will be available.

Brain Chemistry↗
PubMed1988

Three-dimensional reconstruction from electron micrographs of disordered specimens. I. Method.

A method is presented for three-dimensional reconstruction from electron micrographs of a specimen containing a disordered collection of identical objects with unknown orientations. All the data from all the images are simultaneously used to obtain an approximately maximum likelihood estimate of the three-dimensional electron density, which is represented as a truncated expansion in a complete orthonormal set of basis functions. Anomalous objects can nevertheless be detected and eliminated. The method remains under statistical control, and a hypothesis test is used to choose the lowest resolution reconstruction that is consistent with the data. Error propagation is quantitatively traced from the micrograph to the reconstructed electron density. Random orientation is not necessary, and prior knowledge of preferred orientation can be used to advantage. Similarly, symmetry in the object is not necessary, but it can be imposed and exploited, if appropriate. Evidence is presented that useful reconstructions can be obtained with only one or two extra tilts from highly disordered specimens, even if the objects are asymmetric. The companion paper discusses in detail the implementation and verification of the method.

Mathematics↗
PubMed1988

Three-dimensional reconstruction from electron micrographs of disordered specimens. II. Implementation and results.

The computational procedures to implement the method described in the companion paper for three-dimensional reconstruction from projections of a disordered collection of single particles are presented. Computer simulations are used to demonstrate the way the method functions, and practical aspects are discussed in detail. Examples are given of how different symmetries can be exploited by imposing selection rules on the model equations. Applications to negatively stained 50S ribosomes and to cryo-electron micrographs of thin vitrified layers of unstained and unsupported tomato bushy stunt and Semliki Forest viruses are described, and the resulting reconstructions are presented.

Geobacillus stearothermophilus↗
PubMed1986

The secondary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by circular dichroic spectroscopy.

Ribosomal proteins from Escherichia coli MRE600 have been obtained by a new, mild purification procedure. This involves extraction of the subunits with salt followed by chromatographic fractionation in the presence of salt. The use of urea or other denaturing agents and conditions is avoided. A survey of the secondary structure of the 30 S and 50 S proteins, as observed by circular dichroic spectroscopy, is presented. The spectra have been analysed by a new procedure which uses a library of 16 circular dichroic spectra of proteins with a known three-dimensional structure. This method provides a more reliable analysis, especially of the contribution from beta-sheet. The results show that most of the 30 S proteins have a high alpha-helix content, whereas the 50 S proteins are more diverse. The latter group shows a larger contribution from beta-sheet. The data presented here are compared with those already published for a number of proteins which were, with one exception, prepared in the presence of urea. In most cases we find higher alpha-helix and beta-sheet values for the salt-extracted proteins than for the corresponding urea-treated proteins. In those cases, however, where special care was taken to renature the urea-treated proteins agreement is found to within the expected experimental error. The results show that salt-extracted ribosomal proteins have a well-defined secondary structure with a relatively small contribution from unordered structure.

Circular Dichroism↗
PubMed1985

Secondary structure of the pore-forming colicin A and its C-terminal fragment. Experimental fact and structure prediction.

Conformational investigations, using circular dichroism, on the pore-forming protein, colicin A (Mr 60 000), and a C-terminal bromelain fragment (Mr 20 000) were undertaken to estimate their secondary structure and to search for pH-dependent conformational changes. Colicin A and the bromelain peptide are mainly alpha-helical with an enrichment of the alpha-helical content in the C-terminal domain carrying the ionophoric activity. The non-negligible beta-sheet structure in the C-terminal domain is unstable and is easily transformed into alpha-helix upon decreasing the polarity of the solvent. No evidence of pH-dependent conformational modification, correlated with modification of colicin A activity, could be obtained. The secondary structure estimated on the basis of experimental data favoured a model in which the pore is built of a minimal number of six transmembrane alpha-helical segments. Search for such segments in the amino acid sequence of the C-terminal domain of colicin A was carried out by combining secondary structure prediction methods with hydrophobicity and hydrophobic movement calculations. Similar calculations on the C-terminal domains of colicin E1 and IB indicate a common structure of the pores formed by colicin A, E1 and IB. Only two or three putative transmembrane segments could be selected in the sequences of colicin A, IB or E1. As a result, it is concluded that the channel is probably not built by a single colicin molecule but more likely by an oligomer.

Chemical Phenomena↗
PubMed1983

Stopped-flow solution scattering using synchrotron radiation: apparatus, data collection and data analysis.

We have constructed an experimental system, under remote control, for stopped-flow X-ray scattering using synchrotron radiation. It has been used, in conjunction with an annular detector and its associated electronics, to obtain good scattering curves, with time-slices as short as 200 ms, in a new study of the dissociation of the enzyme complex aspartate transcarbamylase. The data have been analysed by new statistical methods, and they agree well with the results from parallel chemical quench experiments. For studying dissociation reactions, stopped-flow X-ray scattering is a quite practical method, which need not use very much more material than conventional stopped-flow experiments.

Aspartate Carbamoyltransferase↗
PubMed1981

Estimation of globular protein secondary structure from circular dichroism.

A new method is developed in which a circular dichroism (CD) spectrum is analyzed directly as a linear combination of the CD spectra (from 190 to 240 nm) of 16 proteins whose secondary structures are known from X-ray crystallography. This avoids the dilemma encountered in previous methods of trying to define single reference CD spectra that were supposed to characterize such broad and variable classes as helix, beta sheet, beta turn, and "remainder". It also permits a more accurate and flexible analysis. The usual instability in using so many parameters is automatically controlled by a simple constrained statistical regularization procedure (similar to ridge regression). Sixteen tests were made by removing 1 spectrum at a time from the set of 16 and analyzing it in terms of the other 15. The product moment correlation coefficients between the computed fractions of helix, beta sheet, beta turn, and remainder and the fractions from the X-ray data were 0.96, 0.94, 0.31,, and 0.49, respectively. Thus, the helix and beta-sheet accuracy is very good. (The corresponding values calculated by a previous method with four reference spectra were 0.85, 0.25, --0.31, and 0.46.).

Circular Dichroism↗
PubMed1979

Direct analysis of continuous relaxation spectra.

The dynamic response of a complex biological or chemical system to a perturbation must often be described by an integral over an effectively continuous relaxation spectrum. Because of its well known instability to experimental error, the direct estimation of the spectrum is generally considered unfeasible. However, we show that good estimates can be obtained by constraining the spectrum to be the smoothest one that is consistent with the data. Also constraining the spectrum to be non-negative, if there is a priori knowledge of this, can further increase its accuracy. The method is completely automatic in that no initial estimates or assumptions about the functional form of the spectrum are necessary. Therefore models can be tested more rigorously and objectively since the functional form that they predict for the spectrum need not be assumed at the outset of the analysis as with parameter-fitting procedures. The method is illustrated on simulated data on the photodissociation of CO from heme proteins at low temperatures. The nonuniqueness of the solutions is discussed.

Carbon Monoxide↗
PubMed1976

A Fourier method for the analysis of exponential decay curves.

A method based on the Fourier convolution theorem is developed for the analysis of data composed of random noise, plus an unknown constant "base line," plus a sum of (or an integral over a continuous spectrum of) exponential decay functions. The Fourier method's usual serious practical limitation of needing high accuracy data over a very wide range is eliminated by the introduction of convergence parameters and a Gaussian taper window. A computer program is described for the analysis of discrete spectra, where the data involves only a sum of exponentials. The program is completely automatic in that the only necessary inputs are the raw data (not necessarily in equal intervals of time); no potentially biased initial guesses concerning either the number or the values of the components are needed. The outputs include the number of components, the amplitudes and time constants together with their estimated errors, and a spectral plot of the solution. The limiting resolving power of the method is studied by analyzing a wide range of simulated two-, three-, and four-component data. The results seem to indicate that the method is applicable over a considerably wider range of conditions than nonlinear least squares or the method of moments.

Computers↗