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Nuclear magnetic resonance study of free and bound water fractions in normal lenses.

Proton NMR relaxation times T1 and T2 were determined for normal lenses excised from sexually mature animals from seven different species. Lenses were immersed in physiological buffer during measurements, and suppression methods were employed to null the buffer signal. This enabled selective analysis of lenticular water. Observed relaxation times were correlated with protein and water content. At 37 degrees C and 1.89 Tesla, single-exponential spin-lattice relaxation was observed, but spin-spin relaxation was found to be double-exponential. It was shown that the short-T2 fraction is proportional to protein concentration; this fraction was attributed to water bound to protein. The long-T2 fraction was attributed to free lenticular water. The amounts of free and bound water thus obtained were used in the spin-lattice relaxation rate equation for rapid exchange in a two-component system to calculate the magnitudes of the two corresponding T1 relaxation components.

Animals↗

POLYAN: a package for a polyparametric approach to cardio-respiratory variability signals analysis.

POLYAN, a computer program based on a point-and-click graphical user interface for easy and efficient polyparametric analysis of cardio-respiratory variability signals is described. The main tasks performed by the package are: univariate and bivariate spectral analysis on selected portions of the signals with the computation of some clinically relevant indices and baroreflex sensitivity assessment by the analysis of the relationship between systolic pressure and heart period signals. Some tools which help the analyst in the solution of common practical problems have been implemented to make analysis easier and more rigorous. Using Matlab language, POLYAN has the flexibility and expandability necessary for a research tool, which often requires implementation of new algorithms and computation of new parameters.

Computer Graphics↗

Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NMR signals of Anabaena 7120 vegetative [2Fe-2S]ferredoxin.

Two alternative T7 RNA promoter/polymerase systems have been employed for the heterologous expression of a plant-type [2Fe-2S]ferredoxin, Anabaena 7120 vegetative ferredoxin, in Escherichia coli at high levels (approximately 20 mg/liter of culture). One system was used when 15N-labeling the ferredoxin uniformly by growing E. coli with 15NH4Cl as the nitrogen source; the other was used in conjunction with auxotrophic host strains to enrich the protein selectively by incorporating 2H-, 13C-, and 15N-labeled amino acids. The labeled ferredoxin samples were studied by 1H, 2H, 13C, and 15N NMR spectroscopy. Results from 1H and 2H NMR studies of samples containing [2H alpha]Cys, [2H beta 2, beta 3]Cys, [13 C beta]-Cys, and [15N]Cys have confirmed previous cysteinyl proton resonance assignments (L. Skjeldal, W. M. Westler, B.-H. Oh, A. M. Krezel, H. M. Holden, B. L. Jacobson, I. Rayment, and J. L. Markley (1991) Biochemistry 30, 7363-7368). All four 13C NMR peaks arising from the four cysteinyl beta-carbons and all four 15N NMR peaks from the four cysteinyl nitrogens were resolved in spectra of both the oxidized and reduced ferredoxins. The nitrogen resonance of Cys46, which is located in a unique (Ala-Cys) dipeptide, was assigned by detection of 13Ci-15Ni+1 coupling in a ferredoxin sample with incorporated [13C']Ala and [15N]Cys. The nitrogen signal of Cys 41 was assigned tentatively on the basis of its chemical shift and T1 relaxation time. The cysteinyl beta-carbon resonances in the reduced state have been assigned to individual residues on the basis of correlations with their (previously assigned) beta-protons. The beta-carbons resonance from Cys46 in the oxidized state has been assigned by its correlation with the corresponding resonance in the reduced state; this was accomplished by following the progressive air oxidation of a protein sample reduced by dithionite in the presence of methyl viologen. The spin-lattice relaxation times of the beta-carbons of the two cysteines coordinated to Fe)III) were similar in the oxidized and reduced states. This suggests that the antiferromagnetic coupling present in the reduced cluster has little influence on the electronic relaxation time of the Fe(III). Studies of the temperature dependence of the 1H, 13C, and 15N signals of the cysteinyl ligands to the [2Fe-2S] cluster show that the slope of the temperature dependence (delta delta/delta T-1) can be different for different atom types within a given residue. For example, in the reduced ferredoxin, although delta delta/delta T-1 is positive for Cys49 1H beta 2 and 1H beta 3, it is negative for Cys49 13C beta. Although delta delta/delta T-1 is negative for protons of cysteines ligated to Fe(II) and positive for protons of cysteines ligated to Fe(III), it is positive for all the cysteinyl nitrogens.(ABSTRACT TRUNCATED AT 400 WORDS)

Anabaena↗

Cell-free biosynthesis of multiple preprosomatostatins: characterization by hybrid selection and amino-terminal sequencing.

In vitro translation of mRNA isolated from islets of Langerhans results in the synthesis of three major preprosomatostatins of Mr 19 000, 18 000, and 16 000, each of which can be resolved into several isoelectric forms [Warren, T. G., & Shields, D. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 3729-3733]. Here we present further characterization of the somatostatin precursors by (i) hybrid selection translation of specific preprosomatostatin mRNAs, (ii) in vitro proteolytic processing of the nascent preprosomatostatins synthesized from hybrid-selected mRNAs, (iii) comparison of their tryptic peptides, and (iv) partial amino-terminal sequence analysis of the signal peptide regions. Hybrid selection experiments using specific cDNA clones demonstrated which preprosomatostatin species corresponded to previously characterized precursor cDNAs [Hobart, P., Crawford, R., Shen, L. P., Picket, R., & Rutter, W. J. (1980) Nature (London) 288, 137-141]; thus, the polypeptide encoded by plasmid pLaS1 corresponds to one form of the Mr 18 000 preprosomatostatins while one form of the Mr 16 000 preprosomatostatins is encoded by pLaS2. Analysis of the tryptic peptides demonstrated that the Mr 16 000 molecule possessed the mature hormone sequence at the carboxyl terminus, as had been shown for the Mr 19 000 and 18 000 precursors. Partial NH2-terminal sequence analysis (a) confirmed the data from hybrid selection and (b) demonstrated that the Mr 18 000 precursor contained a signal peptide manifesting amino acid heterogeneity at certain positions in the signal peptides of each preprosomatostatin. It is suggested that this heterogeneity might account, in part, for variants of the preprosomatostatin molecules.

Amino Acid Sequence↗

Identification of a developmentally regulated phase of postselection expansion driven by thymic epithelium.

To investigate events following the initiation of positive selection, we have used reaggregate organ cultures to follow the maturation of purified CD4+8+69+ thymocytes; these thymocytes represent a subpopulation of thymocytes which have already received positive selection signals. Using a dilution analysis of an FITC-based membrane-binding dye, 5-(and -6)-carboxyfluorescein diacetate succinimidyl ester, to allow a quantitative measure of proliferation, we show that while newly selected CD4+ and CD8+ cells are nondividing, both subsets subsequently undergo a wave of postpositive selection proliferation involving multiple cell divisions. Moreover, in the presence of fetal stromal cells, postselection expansion is more extensive in newborn thymocytes compared with adult thymocytes, suggesting that this phase of expansion is developmentally regulated. We also show that proliferation of CD4+ and CD8+ cells is seen in reaggregates of purified MHC class II+ thymic epithelial cells, while CD4+ and CD8+ cells generated from bcl-2 transgenic CD4+8+69+ thymocytes in the absence of stromal cell support survive but do not proliferate; this observation indicates that MHC class II+ thymic epithelial cells are both necessary and sufficient to mediate this wave of cell division. Finally, the maturation of CD4+8+69+ thymocytes and the subsequent proliferation of CD4+ and CD8+ cells occur in the presence of MHC-mismatched thymic stromal cells, suggesting that the later stages of positive selection and the associated postselection events do not depend on interactions with the same peptide/MHC complexes responsible for initiation.

Animals↗

Single motor unit analysis from spatially filtered surface electromyogram signals. Part I: spatial selectivity.

The aim of the study was to compare experimentally, on the basis of single motor unit (MU) activities, the selectivity of different spatial filters commonly used to detect surface electromyogram (EMG) signals. Surface EMG signals were recorded from the biceps brachii and the upper trapezius muscle of five subjects using a two-dimensional (2D) electrode array consisting of 16 pin electrodes. The subjects performed isometric contractions at different elbow angles and shoulder abduction and flexion. The same monopolar surface EMG signals were filtered using longitudinal single and double differential, transverse single and double differential and normal double differential filters. From the single MU action potentials, extracted by automatic EMG decomposition, indexes of transverse (perpendicular with respect to the fibre direction) and longitudinal (along the fibre direction) selectivity were computed. The number of detected MUs was 46 for the upper trapezius, with the arms held in the sagittal plane, and 52 when the arms were held in the frontal plane; 85 MUs were identified from the biceps brachii contractions. The results showed that transverse selectivity was significantly higher for the 2D and transverse one-dimensional (1D) filters with respect to the 1D longitudinal filters, whereas longitudinal selectivity was higher (i.e. MU action potentials were shorter) for the 2D filter and the longitudinal double differential filter. In particular, the relative attenuation of potential amplitude moving 5 mm from the source was, on average (for the two muscles), 16.5% for the least selective filter in the transverse direction (longitudinal single differential) and 35.7% for the most selective one in the same direction (transverse double differential). The MU action potential duration was, on average, 13.8 ms for the most selective filter in the longitudinal direction (longitudinal double differential) and 18.7 ms for the least selective one (transverse double differential). The normal double differential filter resulted in spatial selectivity indexes that ware not statistically different in the two directions from those of the best filters in each direction.

Action Potentials↗

cDNA microarray analysis of multidrug resistance: doxorubicin selection produces multiple defects in apoptosis signaling pathways.

Doxorubicin plays an important role in the treatment of leukemias, lymphomas, and a variety of carcinomas. Tumor cell resistance to doxorubicin is often associated with expression of the multidrug resistance gene MDR1, which codes for the drug efflux pump P-glycoprotein, and a multidrug-resistant phenotype. Evidence from multiple sources suggests, however, that additional genes besides MDR1 are involved in development of multidrug resistance. To identify genes involved in the multidrug resistance phenotype, we created a 5760-gene cDNA microarray to search for differentially expressed genes between the human multiple myeloma cell line RPMI 8226 and its doxorubicin-selected sublines 8226/Dox6 and 8226/Dox40, both of which express MDR1 and are multidrug-resistant. The cDNA microarray results identified a set of differentially expressed genes, which included MDR1 as expected. Thirty Northern analyses were used to confirm the results of the cDNA microarrays; comparison with the microarray results showed a 90% agreement between the two techniques. Within the set of differentially expressed genes identified by the cDNA microarrays, 29 were of particular interest as they can participate in apoptotic signaling, particularly as mediated by ceramide and the mitochondrial permeability transition. The functional importance of these changes in gene expression is supported by their explanation of the 8226/Dox cell lines' cross-resistance to substances that are not P-glycoprotein substrates, such as Fas/CD95 ligand and staurosporine. We conclude that doxorubicin selection led to changes in gene expression that reduce the apoptotic response to death-inducing stimuli and thus contribute to the multidrug resistance phenotype.

Antibiotics, Antineoplastic↗

Selective and prolonged MRI enhancement by Mn-TPPS in an experimental rat brain tumour with peripheral benzodiazepine receptors.

Synthesized Mn-TPPS, a paramagnetic metalloporphyrin, is expected to be a tumour specific contrast media for magnetic resonance (MR) imaging. We investigated the enhancing characteristics of Mn-TPPS using a transplanted rat C6 glioma model with peripheral type benzodiazepine (PBD) receptors since porphyrins are thought to possibly be endogenous ligands for PBD receptors. An Mn-TPPS enhancement study was then performed either with or without pretreatment while using peripheral and central type benzodiazepine receptor specific ligands (PK11195 and clonazepam, respectively). A signal intensity analysis disclosed the selective and prolonged enhancement of the brain tumour even at 17 h after the Mn-TPPS injection. This specific enhancement of the tumour, however, was not inhibited nor replaced by benzodiazepines. The tissue concentration of Mn-TPPS was significantly higher in the glioma tissue than the other tissues, while PK11195 pretreatment could not reduce the intratumoural Mn-TPPS concentration. A subcellular distribution study disclosed that Mn-TPPS was readily incorporated into the tumour cells. On the other hand, Mn-TPPS was not specifically distributed in the mitochondrial fraction where PBD receptors exist. The present study therefore indicates that Mn-TPPS could be incorporated into tumour cells and supports the potential use of this agent to improve the diagnostic specificity of MR imaging for brain tumours.

Animals↗

A novel sample labeling method with restriction display PCR for 60-mer oligonucleotide microarray.

OBJECTIVE: To investigate the value of restriction display PCR (RD-PCR) as a novel and expedient sample labeling method for high-density 60-mer oligonucleotide microarray. METHODS: Peripheral blood samples from three volunteers were collected and the total RNA was extracted from the peripheral blood mononuclear cells and labeled with RD-PCR protocol, followed by hybridization with Agilent Human 1B oligonucleotide microarrays in a two-color comparison format. The RNA from the same subject was divided into two aliquot and labeled with Cy3 and Cy5 respectively. The spots with significant difference between the foreground and local background intensities and those without significant difference between Cy5 and Cy3 signal intensities were selected for analysis. SPSS software was used to perform the statistical tests and plot generation. VSN packages were used under R language to remove the systematic array and dye biases. RESULTS: Totally 8744 common spots of the 3 microarrays were evaluated. The results demonstrated that RD-PCR could be a promising novel method for efficient labeling of microarray samples. Further analysis indicated the presence of adjustable biases derived from the array and incorporated dye in the labeling processes. The RD-PCR labeling showed better performance than the conventional approaches in regards to reproducibility of the quantitative signals for gene intensity and capability to label RNAs of lowly expressed genes. CONCLUSION: Given the evidence of the feasibility of using RD-PCR labeling in the field of high-density long oligonucleotide microarray, further optimization of the protocol may unleash the full potential of this novel labeling method.

Humans↗

Electron-nuclear interactions in two prototypical [2Fe-2S] proteins: selective (chiral) deuteration and analysis of (1)H and (2)H NMR signals from the alpha and beta hydrogens of cysteinyl residues that ligate the iron in the active sites of human ferredoxin and Anabaena 7120 vegetative ferredoxin.

A vertebrate ferredoxin (human ferredoxin) and a plant-type ferredoxin (the ferredoxin from the vegetative form of Anabaena 7120) were labeled selectively with deuterium at their active site cysteines. The recombinant proteins were produced in Escherichia coli and labeled by replacing natural abundance cysteine in the defined culture medium with (2)H(alpha)-cysteine, (2)H(beta2), (2)H(beta3)-cysteine, or (2)H(beta2)-cystine. The chiral labeled cystine ((2)H(beta2)-cystine) was prepared by selective hydrogen exchange catalyzed by cystathionine gamma-synthase. NMR spectra of these samples in their oxidized and reduced states support unambiguous identifications by atom type of (1)H and (2)H NMR signals from the cysteine alpha and beta hydrogens. These signals lie outside the normal diamagnetic spectral region as a result of interaction of the hydrogens with unpaired electron density from the iron-sulfur cluster, and their chemical shifts are highly dependent on local conformation at the active site. The very different chemical properties of the iron centers of plant-type and vertebrate ferredoxins reflect relatively small differences in the conformation of the iron-sulfur cluster ligands.

Anabaena↗

Spectrotemporal analysis and cochlear hearing impairment: effects of frequency selectivity, temporal resolution, signal frequency, and rate of modulation.

The detection of 500- or 2000-Hz pure-tone signals in unmodulated and modulated noise was investigated in normal-hearing and sensorineural hearing-impaired listeners, as a function of noise bandwidth. Square-wave modulation rates of 15 and 40 Hz were used in the modulated noise conditions. A notched noise measure of frequency selectivity and a gap detection measure of temporal resolution were also obtained on each subject. The modulated noise results indicated a masking release that increased as a function of increasing noise bandwidth, and as a function of decreasing modulation rate for both groups of listeners. However, the improvement of threshold with increasing modulated noise bandwidth was often greatly reduced among the sensorineural hearing-impaired listeners. It was hypothesized that the masking release in modulated noise may be due to several types of processes including across-critical band analysis (CMR), within-critical band analysis, and suppression. Within-band effects appeared to be especially large at the higher frequency region and lower modulation rate. In agreement with previous research, there was a significant correlation between frequency selectivity and masking release in modulated noise. At the 500-Hz region, masking release was correlated more highly with the filter skirt and tail measures than with the filter passband measure. At the 2000-Hz region, masking release was correlated more with the filter passband and skirt measures than with the filter tail measure. The correlation between gap detection and masking release was significant at the 40-Hz modulation rate, but not at the 15-Hz modulation rate. The results of this study suggest that masking release in modulated noise is limited by frequency selectivity at low modulation rates, and by both frequency selectivity and temporal resolution at high modulation rates. However, even when the present measures of frequency selectivity and temporal resolution are both taken into account, significant variance in masking release still remains unaccounted for.

Acoustic Stimulation↗

Signal selection in high-resolution NMR by pulsed field gradients. I. Geometrical analysis.

A geometrical description for the selection of coherence transfer pathways in high resolution NMR by the application of pulsed field gradients along three orthogonal directions in space is presented. The response of the spin system is one point of the three-dimensional Fourier transform of the sample volume affected by a sequence of field gradients. The property that a pathway is retained (or suppressed) when a sequence of field gradients is applied is expressed by the property of vectors, representing the pathway and the sequence, respectively, to be orthogonal (or not orthogonal). Ignoring imperfections of RF pulses, and with the exception of sensitivity enhanced experiments and experiments where the relevant coherence order is zero while field gradients are applied, it is shown that at most only half of the relevant pathways, as compared to a phase cycled experiment, are retained when field gradients are used for signal selection.

Artifacts↗

Signal selection by cortical feedback.

By modifying patterns of activity in the midbrain and thalamus, cortical feedback may be involved in selecting sensory signals for further analysis.

Animals↗

Species-specific differences in expression of G-protein-coupled receptor kinase (GRK) 7 and GRK1 in mammalian cone photoreceptor cells: implications for cone cell phototransduction.

Desensitization plays an important role in the rapid termination of G-protein signaling pathways. This process, which involves phosphorylation by a G-protein-coupled receptor kinase (GRK) followed by arrestin binding, has been studied extensively in the rod photoreceptor cell of the mammalian retina. In contrast, less is known regarding desensitization in cone photoreceptor cells, which occurs more rapidly than in rod cells. Recently, our laboratory has cloned a novel GRK family member, GRK7, from the retina of a cone-dominant mammal, the 13-lined ground squirrel. Here we report the cloning of GRK7 from rod-dominant pig and human retinas, suggesting that this kinase plays a role in human visual signaling. Because GRK1 (rhodopsin kinase), the GRK that mediates rhodopsin desensitization in the rod cell, is reportedly expressed in both rods and cones, a detailed comparison of the localization of the two kinases is a necessary step toward determining their potential roles in cone visual signaling. Immunocytochemical analysis using antibodies selective for these two GRKs unexpectedly demonstrated species-specific differences in GRK7 and GRK1 expression in cones. In pigs and dogs, cones express only GRK7, whereas in mice and rats, we detected only GRK1 in cones. These results suggest that either GRK7 or GRK1 may participate in cone opsin desensitization, depending on the expression pattern of the kinases in different species. In contrast, GRK7 and GRK1 are coexpressed in monkey and human cones, suggesting that coordinate regulation of desensitization by both kinases may occur in primates.

Animals↗

Selection of the order of autoregressive models for spectral analysis of Doppler ultrasound signals.

Autoregressive modelling includes a model identification procedure, that is, it is necessary to choose the order of the autoregressive (AR) process that best describes the given finite record (frame) of the signal. Four previously suggested procedures to choose the "best order" of AR processes have been tested: The "first zero crossing" of the autocorrelation function (FZC), the "final prediction error" (FPE), "Akaike's information criterion" (AIC), and the "criterion autoregressive transfer-function" (CAT). It was found that: (i) For more than 98% of the 1280 frames of Doppler signals analyzed the order selected by the various criteria was ten or less. (ii) For the same records of Doppler signals, FPE, AIC and CAT behave in a very similar manner, but the FZC criterion underestimates the order in relation to the others. (iii) For true AR processes, the order selected is frequently different from the true AR order when frames of 64 samples are used. When more samples are used FPE, AIC and CAT tend to select the correct order. (iv) The effect on the spectral estimate of using too high a model order is usually insignificant, while using too low an order can change the estimate more dramatically, that is, overestimating the model order is better than underestimating it.

Analysis of Variance↗

Correlation spectroscopy of minor fluorescent species: signal purification and distribution analysis.

We are performing experiments that use fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) to monitor the movement of an individual donor-labeled sliding clamp protein molecule along acceptor-labeled DNA. In addition to the FRET signal sought from the sliding clamp-DNA complexes, the detection channel for FRET contains undesirable signal from free sliding clamp and free DNA. When multiple fluorescent species contribute to a correlation signal, it is difficult or impossible to distinguish between contributions from individual species. As a remedy, we introduce "purified FCS", which uses single molecule burst analysis to select a species of interest and extract the correlation signal for further analysis. We show that by expanding the correlation region around a burst, the correlated signal is retained and the functional forms of FCS fitting equations remain valid. We demonstrate the use of purified FCS in experiments with DNA sliding clamps. We also introduce "single-molecule FCS", which obtains diffusion time estimates for each burst using expanded correlation regions. By monitoring the detachment of weakly-bound 30-mer DNA oligomers from a single-stranded DNA plasmid, we show that single-molecule FCS can distinguish between bursts from species that differ by a factor of 5 in diffusion constant.

Computer Simulation↗

Methodology utilizing MS signal intensity and LC retention time for quantitative analysis and precursor ion selection in proteomic LC-MALDI analyses.

This study describes a methodology for performing relative quantitation in large-scale proteomic sample comparisons using an LC-MALDI mass spectrometry analytical platform without the use of isotope tagging reagents. The method utilizes replicate analyses of a sample to create a profile of constituent components that are aligned based on LC elution time and mass. Once components from individual runs have been grouped as common "features", the Student's t test is used to determine which components are systematically different between samples. In this study, five HPLC runs of human plasma were compared to five HPLC runs of human serum. About 3889 components were detected in all 10 runs. Of these, 1831 corresponded to approximately 100 known serum proteins, based on MS/MS analysis of one run each from serum and plasma. As expected, fibrinogen alpha, beta, and gamma chains accounted for many of the most significant differences. Therefore, using MALDI, samples containing thousands of peptides can be compared in a minimal amount of time. Moreover, the results of the comparison can be used to guide further MS/MS mode sample interrogation in a result dependent manner.

Animals↗