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PubMed1991

Simultaneous multinuclear magnetic resonance imaging and spectroscopy.

A technique has been developed to perform simultaneous multinuclear magnetic resonance imaging and spatially localized spectroscopy. It is inherently superior in terms of time efficiency over current approaches which use sequential or interleaved methods. The pulse sequence uses a parallel excitation and acquisition scheme to acquire multislice proton images concurrently with phosphorus-31 spectroscopic images. Because the phosphorus signal is necessarily collected in the presence of a gradient, an essential element of the technique is an algorithm to extract pure chemical-shift information.

Algorithms↗
PubMed1991

Regional 1H transverse magnetization studies in perfused rabbit kidney.

A Carr-Purcell-Meiboom-Gill imaging sequence consisting of 128 echoes is used to extract transverse magnetization decay curves (TDCs) at 1.9 T from 1.7 x 1.7 x 5-mm3 voxels within the cortex, outer medulla, and inner medulla of perfused rabbit kidneys. The spatially localized TDCs within each tissue type are found to be better approximated by biexponential, as opposed to monoexponential, functions. The biexponential parameters characterizing the TDCs demonstrate an improved degree of tissue specificity over that available from monoexponential analyses. The fraction of the quickly relaxing TDC component and the relaxation rate of this component are observed to decrease from cortex to inner medulla. A two-site exchange analysis is used to convert biexponential TDC parameters into water volume fractions and exchange rates. The exchange rates between the fast and slowly relaxing pools increased from cortex to inner medulla. All exchange rates were less than 1.5 Hz, indicating a relatively slow water exchange process. The imaging methods and subsequent analyses offer the potential to generate unconventional MR images with tissue contrast dependent upon water compartmentation and exchange.

Animals↗
PubMed1993

Responses of myocardial high energy phosphates and wall thickening to prolonged regional hypoperfusion induced by subtotal coronary stenosis.

The response of the myocardium to prolonged or chronic ischemia may differ from the well documented changes that occur acutely subsequent to the onset of hypoperfusion. Therefore, we have examined in an instrumented canine model and using spatially localized spectroscopy to achieve transmural differentiation, the myocardial HEP and Pi levels as well as wall thickening in situ during prolonged ischemia induced by sustained coronary artery stenosis. The results demonstrate that subtotal coronary artery occlusion causes immediate and transmurally inhomogeneous decreases in the myocardial HEP content and increase in the Pi/CP ratio; however, during prolonged mild hypoperfusion, metabolic changes occur which lead to statistically significant recovery of CP (but not ATP) and disappearance of Pi despite the persistence of reduced blood flow and oxygen supply. Upon release of the occlusion, the previously ischemic muscle recovered blood flow, and some (but not all) of its preischemic contractile function without parallel changes in the HEP levels. It is concluded that normal HEP and Pi levels cannot be equated with either the absence of underperfusion or insensitivity of NMR spectroscopy to ischemia. Rather, it is imperative that both functional and spectroscopic measurements are performed simultaneously to distinguish between ischemic myocardium which is adapted versus unadapted to the hypoperfusion.

2,3-Diphosphoglycerate↗
PubMed1993

Spatially selective RF pulses and the effects of digitization on their performance.

Spectrometers make use of D/A converters to generate RF and gradient shapes. This paper examines by exact simulations the time and amplitude digitization effects, inherent to the use of D/A converters, on the performance of amplitude modulated (AM) frequency selective RF pulses. By making use of Fourier theory and the small tip angle approximation, an approximate model of these effects on the magnetization slice profiles is derived and verified for several pulse types by computer simulations. This approximate model will be used to derive requirements for D/A converters with respect to spatial localization. The dynamics of the spin system allows pulse width modulation (PWM) as an alternative to AM for pulse envelope encoding. The effects of PWM on the slice profile are examined and compared with conventional AM pulses. It is shown by simulation and measurement that adiabatic PWM pulses can be found. In contrast to AM modulated adiabatic pulses, adiabatic PWM pulses have side bands with the same slice quality as the main slice and might therefore be useful as multislice selective pulses.

Magnetic Resonance Spectroscopy↗
PubMed1998

Hyperpolarized 3He NMR lineshape measurements in the live guinea pig lung.

Spatially localized lineshapes of hyperpolarized (HP) 3He in guinea pig lungs have been measured in vivo. Three different axial slice locations, each containing different compositions of airway sizes and orientations, were studied. Gas peaks from major bronchi (2 ppm) and alveoli (-2 ppm) were distinguished. The gas phase spectra show structural features that are a result of frequency shifts caused by bulk magnetic susceptibility. For a given slice, the spectral lineshapes reflect the airway composition within the slice location, according to theory. The peak assignments given here also agree with previous studies done by Wagshul et al. with HP 129Xe. At each of the slice locations, data were acquired during two phases of the breathing cycle, resulting in a relative frequency shift of approximately 0.3 ppm in the superior slices. Spectra obtained over a number of breaths show the dynamics of the gas buildup in the lung and provide further evidence supporting the peak assignments.

Animals↗
PubMed2006

Three-dimensional magnetic resonance microscopy of pulmonary solitary tumors in transgenic mice.

We attempted to accurately detect pulmonary solitary tumors and other complicated pulmonary disorders in aging inbred transgenic mice by cardiac- and respiratory-gated MR microscopy at 4.7 Tesla. A comparison of in vivo MR images with histological results demonstrated that submillimeter lung tumors and most of the nontumor lesions could be detected by screening with two-dimensional (2D) gradient echo (GRE) imaging. Subsequently performed 2D spin-echo (SE) imaging provided higher image contrast, which distinguished the tumors from the surrounding complications. On the 3D GRE images and the generated maximum intensity projection (MIP) and volume-rendered (VR) images, proper spatial localization of solitary tumors relative to the orientation of the pulmonary vessels was exhibited, and the tumor volume could also be measured. This promising method is noninvasive and has the potential to eventually replace invasive histopathology because it obviates the need to kill groups of animals at multiple time points.

Algorithms↗
PubMed2006

Age and gender dependence of human cardiac phosphorus metabolites determined by SLOOP 31P MR spectroscopy.

The aim of this study was to apply (31)P magnetic resonance spectroscopy (MRS) using spatial localization with optimal point spread function (SLOOP) to investigate possible age and gender dependencies of the energy metabolite concentrations in the human heart. Thirty healthy volunteers (18 males and 12 females, 21-67 years old, mean = 40.7 years) were examined with the use of (31)P-MRS on a 1.5 T scanner. Intra- and interobserver variability measures (determined in eight of the volunteers) were both 3.8% for phosphocreatine (PCr), and 4.7% and 8.3%, respectively, for adenosine triphosphate (ATP). High-energy phosphate (HEP) concentrations in mmol/kg wet weight were 9.7 +/- 2.4 (age < 40 years, N = 16) and 7.7 +/- 2.5 (age >or= 40 years, N = 14) for PCr, and 5.1 +/- 1.0 (age < 40 years) and 4.1 +/- 0.8 (age >or= 40 years) for ATP, respectively. Separated by gender, PCr concentrations of 9.2 +/- 2.4 (men, N = 18) and 8.0 +/- 2.8 (women, N = 12) and ATP concentrations of 4.9 +/- 1.0 (men) and 4.2 +/- 0.9 (women) were measured. A significant decrease of PCr and ATP was found for volunteers older than 40 years (P < 0.05), but the differences in metabolic concentrations between both sexes were not significant. In conclusion, age has a minor but still significant impact on cardiac energy metabolism, and no significant gender differences were detected.

Adenosine Triphosphate↗
PubMed2006

Sources of functional apparent diffusion coefficient changes investigated by diffusion-weighted spin-echo fMRI.

The mechanism behind previously observed changes in the apparent diffusion coefficient (ADC) during brain activation is not well understood. Therefore, we investigated the signal source and spatial specificity of functional magnetic resonance imaging (fMRI) ADC changes systematically in the visual cortex of cats using diffusion-weighted (DW) spin-echo (SE) fMRI with b-values of 2, 200, and 800 s/mm(2), and echo times (TE) of 16, 28, and 60 ms at 9.4 T. For b > or = 200 s/mm(2), no ADC changes were detected in brain parenchyma, suggesting a minimal tissue contribution to the ADC change. For b < or = 200 s/mm(2), TE-dependent ADC increases were observed. When the venous blood contribution was minimized, the ADC change was higher at the middle cortical layer than at the cortical surface, which is mainly attributed to a functional elevation in arterial blood volume. At TE = 16 ms, the highest ADC changes occurred at the cortical surface with its large draining veins, which can mainly be explained by an additional contribution from the venous blood oxygenation changes. Our TE-dependent ADC results agree with computer simulations based on a three-compartment model. The contribution of arterial blood volume changes in ADC fMRI offers an improvement in spatial localization for SE-BOLD fMRI studies.

Animals↗
PubMed2006

Dependence of gradient-echo and spin-echo BOLD fMRI at 4 T on diffusion weighting.

Diffusion weighting and spin-echo (SE) acquisitions can be used to help improve the spatial localization of BOLD fMRI at the cost of reduced acquisition rates and lower signal-to-noise ratio (SNR). To evaluate these costs, SE and gradient-echo (GE) data were acquired at 4 T at five diffusion weightings ranging from b = 0 to 1110 s/mm(2) using a robust visual stimulus. The data showed reduced functional contrast when diffusion weighting was applied. As the amount of diffusion weighting increased, the functional contrast initially dropped sharply, and then remained relatively constant for diffusion weightings above 15 s/mm(2) for SE and 30 s/mm(2) for GE data. GE functional BOLD contrast was attenuated to 94.0 +/- 10.1, 87.6 +/- 12.2, 86.4 +/- 8.8 and 83.3 +/- 20.6% of the non-diffusion-weighted GE contrast for diffusion weightings of 15, 30, 200 and 1,110 s/mm(2). The non-diffusion-weighted SE contrast greatly reduced to 19.3 +/- 3.3% of the non-diffusion-weighted GE contrast, demonstrating the large activation attenuation of a SE acquisition. The SE contrast was further reduced to 10.0 +/- 3.6, 9.0 +/- 2.5 and 8.6 +/- 2.0% of the non-diffusion-weighted GE contrast for the 15, 30 and 200 s/mm(2) diffusion-weighted data. These results suggest that only a small amount of diffusion weighting is necessary to suppress the vascular contribution and spin-echo imaging should only be used if there is adequate statistical power available or accurate localization is critical.

Adult↗
PubMedDate not supplied

Quantitation of proton NMR spectra of the human brain using tissue water as an internal concentration reference.

The use of cerebral water as an internal intensity standard for the quantitation of spatially localized proton spectra of the human brain is investigated. The method is validated on standard samples of N-acetyl aspartate (NAA) and lactate, and possible sources of error are discussed. Using the STEAM pulse sequence, concentrations of choline, creatine and NAA in frontal lobe white matter are found to be 1.9 +/- 0.5, 10.6 +/- 1.3 and 16.6 +/- 2.3 mumol/g wet wt, respectively, in 10 normal volunteers. In the thalamus, the concentrations are 2.0 +/- 0.4, 11.6 +/- 2.0 and 17.2 +/- 1.3 mumol/g wet wt, respectively. Choline and creatine concentrations are in good agreement with conventional biochemical values: NAA concentrations are found to be three-fold higher, suggesting overlap of the NAA signal with other compounds. Quantitation relative to tissue water is a convenient and rapid means of quantitating proton spectra of the human brain.

Adult↗
PubMed2004

Wiskott-Aldrich syndrome protein and the cytoskeletal dynamics of dendritic cells.

The regulated migration and spatial localization of dendritic cells in response to environmental signals are critical events during the initiation of physiological immune responses and maintenance of tolerance. Cells deficient in the Wiskott-Aldrich syndrome protein (WASP) have been used to demonstrate the importance of the dynamic remodelling of the actin-based cytoskeleton during the selective adhesion and migration of these cells. Unlike most cell types, macrophages, dendritic cells, and osteoclasts utilize a specialized adhesive array termed the podosome in order to migrate. Podosomes are composed of many of the same structural and regulatory proteins as seen in the more commonly found focal adhesion, but are unique in their requirement for WASP. Without WASP, podosomes cannot form and the affected cells are obliged to use focal adhesions for their migratory activities. Once activated by a series of upstream regulatory proteins, WASP acts as a scaffold for the binding of the potent actin nucleating protein complex known as Arp2/3. This article reviews the available evidence that suggests that failures in the regulation of the actin cytoskeleton may contribute significantly to the immunopathology of the Wiskott-Aldrich syndrome.

Actins↗
PubMed2003

A new bioinformatic approach to detect common 3D sites in protein structures.

An innovative bioinformatic method has been designed and implemented to detect similar three-dimensional (3D) sites in proteins. This approach allows the comparison of protein structures or substructures and detects local spatial similarities: this method is completely independent from the amino acid sequence and from the backbone structure. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereochemical groups that are defined independently from the notion of amino acid. An efficient heuristic for finding similarities that uses graphs of triangles of chemical groups to represent the protein structures has been developed. The implementation of this heuristic constitutes a software named SuMo (Surfing the Molecules), which allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases. To show the relevance of this approach, we focused on two extreme examples illustrating convergent and divergent evolution. In two unrelated serine proteases, SuMo detects one common site, which corresponds to the catalytic triad. In the legume lectins family composed of >100 structures that share similar sequences and folds but may have lost their ability to bind a carbohydrate molecule, SuMo discriminates between functional and non-functional lectins with a selectivity of 96%. The time needed for searching a given site in a protein structure is typically 0.1 s on a PIII 800MHz/Linux computer; thus, in further studies, SuMo will be used to screen the PDB.

Algorithms↗
PubMed2006

Matrix-assisted laser desorption/ionization imaging mass spectrometry for direct measurement of clozapine in rat brain tissue.

Matrix-assisted laser desorption/ionization hyphenated with quadrupole time-of-flight (QTOF) mass spectrometry (MS) has been used to directly determine the distribution of pharmaceuticals in rat brain tissue slices which might unravel their disposition for new drug development. Clozapine, an antipsychotic drug, and norclozapine were used as model compounds to investigate fundamental parameters such as matrix and solvent effects and irradiance dependence on MALDI intensity but also to address the issues with direct tissue imaging MS technique such as (1) uniform coating by the matrix, (2) linearity of MALDI signals, and (3) redistribution of surface analytes. The tissue sections were coated with various matrices on MALDI plates by airspray deposition prior to MS detection. MALDI signals of analytes were detected by monitoring the dissociation of the individual protonated molecules to their predominant MS/MS product ions. The matrices were chosen for tissue applications based on their ability to form a homogeneous coating of dense crystals and to yield greater sensitivity. Images revealing the spatial localization in tissue sections using MALDI-QTOF following a direct infusion of (3)H-clozapine into rat brain were found to be in good correlation with those using a radioautographic approach. The density of clozapine and its major metabolites from whole brain homogenates was further confirmed using fast high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) procedures.

Animals↗
PubMed1994

Network analytic methods for epidemiological risk assessment.

The authors measure the efficacy of three methods for predicting the time to infection for susceptible individuals in a population undergoing an HIV epidemic. The methods differ in whether they require detailed information of the contact network and whether they require knowledge of the initial source of infection. Efficacy is evaluated using simulations for 20 different contact patterns. Only the risk score that uses both kinds of information accounts for more than 15 per cent of individual variability. The efficacy of this score ranges from 10 per cent in very unstructured populations to 60 per cent for spatially localized contact networks. This improved performance may be explained by the larger fraction of the total variability not due to the disease dynamics. When all variables are dichotomized, the two poorer methods produce odds ratios between 1.4 and 2.3. The odds ratio for the risk score with full information ranges from 2.5 to 17. Risk assessment protocols and intervention programmes are encouraged to assess contact patterns and detect sources of infection.

Analysis of Variance↗
PubMed1996

Analysis of total lipid extracts from human liver by 13C and 1H nuclear magnetic resonance spectroscopy.

Lipid extracts of liver tissue from normal donors and from patients with acute liver failure were analyzed by 13C NMR and 1H NMR at 9.4 T. The spectra allowed estimation of (i) the free fatty acid to total fatty acid chains ratio, (ii) the polyunsaturated to monounsaturated lipids ratio, (iii) the glycerophospholipids to triacylglycerols ratio, (iv) the total cholesterol to total fatty acids molar ratio, (v) the acylcholesterol to cholesterol ratio, (vi) the phosphatidylcholine to phosphatidylethanolamine molar ratio, and (vii) the unsaturation ratio of the fatty acid chains. The values obtained for normal livers agree with literature data on lipid composition obtained by other techniques. The two pathologic livers differ from the normal in the composition of some lipids and show a higher free fatty acid to total fatty acid chains ratio and a lower polyunsaturated to monounsaturated lipid ratio, a lower acylcholesterol to cholesterol ratio, and a lower phosphatidylcholine to phosphatidylethanolamine ratio, whereas the ratio of total cholesterol to fatty acids and the unsaturation ratio remained unchanged. The detailed assignment of the 13C NMR spectra of lipid extracts from normal and pathologic human liver may contribute to direct future research programs on 13C NMR spatially localized spectroscopy of the liver in vivo.

Cholesterol↗
PubMed1995

An in vivo 31P magnetic resonance spectroscopy study of uridine excess in rats fed orotic acid.

Spatially localized 31P NMR spectroscopy was used to assay in vivo the liver of intact rats fed orotic acid (OA) in a diet which produces hepatic steatosis. Twenty-three sets of multiple volume spectra were obtained from twenty-one 265- to 315-g female rats after 0-9 days of feeding either a 1% OA/64% sucrose diet (12 rats) or a 65% sucrose control diet (9 rats). The intensity of the in vivo diphosphodiester resonance ascribed to UDP-hexos(amin)es increased and the phosphomonoester resonance decreased in intensity prior to fatty infiltration. High resolution NMR spectroscopy of extracts of these livers indicated that the UDP-hexos(amin)e peak included four different UDP-sugars including UDP-N-acetylglucosamine (UDP-glcNAc), and that lower phosphocholine (P-Cho) accounted for the lower phosphomonoester resonance in vivo. Increased UDP-glcNAc is thought to reflect impaired lipoprotein glycosylation as a mechanism for hepatic steatosis in orotic acid feeding. P-Cho deficiency has been shown to be due to an increased rate of phosphatidylcholine synthesis. Low P-Cho concentration has been shown to be associated with lipid accumulation in a choline-deficient diet, but was not previously associated with hepatic steatosis in OA feeding. Changes in phosphorus metabolites were observed 2 days prior to development of fatty liver. HPLC assay of uridine nucleotides showed a good correlation between magnetic resonance spectroscopy and HPLC quantitation. In this study there were two biochemical correlates of impaired hepatic lipid secretion detectable by in vivo assay with 31P NMR spectroscopy. This method has application for noninvasive assays in ornithine transcarbamylase-deficient patients.

Animals↗
PubMed1993

Enhancer regions responsible for temporal and cell-type-specific expression of a spore coat gene in Dictyostelium.

The extracellular spore coat of Dictyostelium discoideum is composed of three major proteins, SP96, SP70, and SP60, encoded by the cotA, cotB, and cotC genes, respectively. The spore coat proteins are coordinately synthesized in prespore cells shortly after aggregation, stored in prespore vesicles during the slug stage, and secreted during encapsulation of spores. We have ligated various portions of the upstream region of cotB to lacZ such that a protein consisting of the first nine amino acids of SP70 fused to beta-galactosidase is synthesized in prespore cells. Individual cells that accumulate the enzyme can be observed in situ during early aggregation due to the sensitivity of the assay. We have found that prespore cells first appear in a random distribution throughout the aggregates with no indication of spatial localization. They subsequently sort out from prestalk cells that form a tip on the aggregates. The cotB regulatory region was subdivided into a proximal and a distal region, each of which could independently direct proper temporal and cell-type control. Transcriptional activity directed by these two regions appears to be additive in the full-length regulatory region. The proximal region was shown to be complex in that removal of certain portions partially reduced transcriptional activity while removal of other portions abolished all activity. Nevertheless, cells transformed with constructs showing attenuated activity expressed the fusion gene at the proper time in development and the activity was localized to prespore cells. The cis-acting regions responsible for all aspects of cotB regulation appear to be closely opposed within the minimal essential sequence of the proximal region.

Animals↗
PubMed1993

Homeobox-containing genes in teratocarcinoma embryoid bodies: a possible role for Hox-D12 (Hox-4.7) in establishing the extraembryonic endoderm lineage in the mouse.

We wish to identify genes involved in mediating early lineage decisions in the mouse embryo. F9 teratocarcinoma cells treated with retinoic acid (RA) in suspension culture develop into embryoid bodies (EBs) with an outer layer of visceral endoderm. In order to identify genes that are involved in establishing this extraembryonic endoderm lineage we have employed a PCR-based approach using cDNAs from early EBs as templates. PCR reactions were performed with degenerate oligonucleotide primers coding for the highly conserved regions of the homeodomains of the Drosophila Antennapedia, bicoid, and zerknüllt proteins. Among the PCR products were representatives of previously identified mouse genes, including Hox-A5 (1.3), A1 (1.6), A9 (1.7), B8 (2.4), B2 (2.8), C8 (3.1), and D12 (4.7). Whole mount in situ hybridization analysis, performed to examine the temporal and spatial distribution of transcripts, suggests a possible role for the Hox-D12 gene during endoderm differentiation in F9 EBs. Whereas the expression patterns of several other homeobox genes are essentially uniform throughout the aggregates, Hox-D12 expression is restricted to the outer surface of early EBs at a time when lineage decisions may be occurring. In order to establish the relationship between the Hox-D12 expression pattern and the role of RA in inducing F9 EB differentiation, we examined PSA-1 EBs that differentiate in the absence of added RA. PSA-1 EBs show similar temporal and spatial localization of Hox-D12 when compared to F9 EBs. These data suggest that the pattern of Hox-D12 expression correlates with endoderm differentiation and not with RA treatment and point to a possible role for homeobox-containing genes during the early stages of mouse embryogenesis.

Amino Acid Sequence↗