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Results for “cell deconvolution”

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PubMed1995

Interaction of cytochrome c with cardiolipin: an infrared spectroscopic study.

The interactions of cytochrome c (cyt c) with cardiolipin, a major anionic phospholipid of mitochondrial membranes, and dioleoylphosphatidylglycerol (DOPG), have been compared by infrared (IR) spectroscopy. The Fourier self-deconvoluted IR spectra of the lipid carbonyl groups indicate that both cyt c3+ and cyt c2+ perturb and/or dehydrate the interfacial region of cardiolipin bilayers. Only a slight perturbation, if any, is observed in the interfacial region of DOPG bilayers. However, the phosphate head region of DOPG is perturbed by cyt c3+, which was not detected in cardiolipin. The results suggest that cytochrome c in both redox states can partially penetrate into cardiolipin but not into DOPG bilayers. The interaction of cyt c with cardiolipin and DOPG is mainly hydrophobic and electrostatic, respectively. The Fourier self-deconvoluted IR spectra in the amide I region reveal that ca. 10% of the cyt c3+ alpha-helix unfolds to random coil upon binding to cardiolipin bilayers. However, only very slight secondary structural changes, if any, were detected when cyt c3+ binds to DOPG bilayers.

Amides↗

PubMed2002

Autoimmune epitopes in messenger RNA.

Patients with systemic autoimmune disorders produce autoantibodies against sequence-specific conformational RNA epitopes on U1 snRNA, 28S rRNA, and transfer RNAs. The molecular basis for immunological reactivity with these highly abundant and stable RNAs is not understood. Here, we report the existence of discrete RNA epitopes in messenger RNAs that are generally less abundant and less stable than snRNAs and tRNAs. An iterative selection and amplification procedure using pooled autoimmune patient sera identified immunoreactive mRNA species. Following deconvolution of the pools to identify the reactive sera, several mRNAs recognized by these autoantibodies were cloned and sequenced. Detailed analysis using one particular serum indicated reactivity against the messages encoding alternative splicing factor (ASF/SF2) and calmodulin. Deletion and site-directed mutagenesis determined that an epitope recognized by this serum is located in a 17-base stem-loop structure common to both messages. This serum was then used to immunoprecipitate native mRNAs encoding ASF/SF2 and calmodulin from total HeLa cell RNA. Our results demonstrate that despite its low abundance and instability, messenger RNA is capable of reacting with autoantibodies generated during an autoimmune response. These data are consistent with direct presentation as a model to explain the generation of RNA conformation-specific autoantibodies.

Autoantibodies↗

PubMed1996

Metaphase and interphase mapping by FISH: improvement of chromosome banding and signal resolution in interphase nuclei by means of iterative deconvolution.

FISH images obtained with conventional epifluorescence microscopes are always blurred by glare and out of focus light emissions. In order to restore high contrast images, a procedure based on a modelling of the optical system in the microscope was developed and used for the processing of images acquired with a cooled CCD camera mounted on a fluorescence microscope. This procedure was tested on images of both mouse and human chromosomes stained with DAP1 and on images of interphase nuclei hybridized with pairs of cosmid probes. This method improves the definition and the sharpness of the DAPI G-banding and thus facilitates and speeds up the identification of chromosomes. When performed on images of interphase cell nuclei, this procedure allows the discrimination of fluorescent signals which appear partially overlapping on raw images. This significant improvement of spatial resolution is of particular interest for ordering sets of probes on DNA fibers.

Animals↗

PubMed1989

Pathophysiological features of the pulsatile secretion of biologically active luteinizing hormone in man.

The development of an in vitro bioassay of high specificity, sensitivity and precision for the measurement of low circulating concentrations of biologically active glycoprotein hormones has offered exciting new insights into the in vivo secretion and metabolic clearance of luteinizing hormone (LH) in various pathophysiological states. Moreover, the most recent combined application of the rat interstitial cell testosterone (RICT) bioassay and a novel multiple-parameter deonvolution model has allowed investigators to dissect plasma concentration profiles of bioactive LH into defined secretory bursts, which have numerically explicit amplitudes, locations in time, and durations, and are acted upon by determinable subject- and study-specific endogenous metabolic clearance rates. Here, we have: (i) reviewed the ability of the endogenous GnRH pulse signal to regulate the in vivo secretion of biologically active LH molecules as assessed in the RICT and by deconvolution mechanics; (ii) demonstrated that low-dose exogenous GnRH pulses effectively mimic spontaneous bioactive LH pulsatility; (iii) investigated the role of endogenous androgen and estrogen in modulating bioactive gonadotropin secretion in men and women; and (iv) described significant alterations in endogenous LH bioactivity in puberty and healthy aging.

Aging↗

PubMed1987

Infrared spectroscopic evidence of conformational transitions of an atrial natriuretic peptide.

The conformational properties of the atrial natriuretic peptide atriopeptin III were investigated by Fourier-transform infrared spectroscopy. Infrared spectra in the amide I region were analyzed quantitatively using deconvolution and band-fitting procedures. According to this analysis, in aqueous solution the monomeric peptide has a random structure. Binding to bilayer vesicles of dimyristoyl phosphatidylglycerol results in drastic conformational changes. The lipid-complexed atriopeptin III adopts a highly ordered structure of predominantly beta-sheets. A transition to a similar, but not identical, beta-structure occurs upon self-association of the peptide. The results of model experiments suggest that the binding of this atrial peptide to the target cell membrane is associated with the induction of beta-sheet structure and that it is this latter conformation that is predominant in the active form of the hormone.

Atrial Natriuretic Factor↗

PubMed2006

Measurement of desorption rates from octadecylsilyl bonded-phase HPLC particles and its characterization in terms of pore, surface, and film diffusion.

An instrument is developed to measure rates of desorption of solutes from particulate HPLC packing materials for processes that are quantitatively complete in a few tenths of a second. The instrument is a modified, pressure-driven, stopped-flow device. The major modifications include positioning a very short (0.6 mm) bed of the particles just upstream of the detector cell, eliminating the mixing chamber, and adding high-speed switching valves in order to allow sequential continuous flow of individual solutions. Instantaneous rate curves are measured for the desorption of 1,2-dimethyl-4-nitrobenzene (DMNB) from 12-microm-diameter porous particles of the bonded-phase packing Luna C-18 employing high linear velocities of the eluting solvent. The same experiment is performed for the nonsorbed compound phloroglucinol (PG) The PG rate curve is used in two ways (i.e., subtraction and deconvolution) in order to correct the observed rate curve of DMNB for experimental artifacts such as bed hold-up volume and instrument band broadening. The cumulative desorption rate curve of DMNB is obtained by integration. It is accurately described (R2 > 0.999) by a theoretical model that invokes both intraparticle diffusion (including both hindered pore diffusion and surface diffusion) and external film diffusion. The surface diffusion coefficient is (3.2 +/- 0.8) x 10(-6) cm(2)/s and the diffusion film thickness is 0.5 microm. The validity, of both the experimental technique and the theoretical model, is demonstrated by excellent agreement between a predicted and an observed chromatographic elution peak for DMNB on a 25-cm-long commercial column of Luna C-18.

Journal Article↗

PubMed1990

Computation of a three dimensional image of a periodic specimen from a single view of an oblique section.

We describe here a method for computing a three dimensional map of a periodic specimen from a single electron micrograph of an obliquely cut section. Neighbouring areas of such an image display successively the contents of the unit cell of the structure. The reconstruction procedure can be considered in two steps. The first step involves restacking of successive areas to produce an image akin to that produced by serial section reconstruction. The resolution normal to the section would, at this stage, be limited by the thickness of the section, since the micrograph represents a projection of the density in the section. However, because of the periodic nature of the specimen, the image contains redundant information, which can be used in an attempt to deconvolute the section thickness and thus produce improved resolution normal to the section. The computation can be carried out directly with the densities or more conveniently, particularly for three dimensional crystals, by using Fourier transforms. The approach, which is most powerful when the section is thin, is insensitive to the collapse of the section caused by electron irradiation. Striated muscle provides particularly suitable specimens for such analysis and we present, as examples, computed maps of the M-band of fish muscle and of insect flight muscle in rigor.

Animals↗

PubMed1996

Redox dependent interactions of the metal sites in carbon monoxide-bound cytochrome c oxidase monitored by infrared and UV/visible spectroelectrochemical methods.

Spectroelectrochemical titration studies involving the binding of the infrared-active probe ligand carbon monoxide (CO) to the heme alpha 3/CuB site of bovine heart cytochrome c oxidase (CcO) have been reexamined. The spectroelectrochemical cell employed was constructed to monitor both the infrared (IR) and visible/Soret spectra of the CcO-CO complex as a function of the overall oxidation state of the enzyme. A number of commonly used electron transfer mediators were employed to shuttle electrons between the redox active sites within the enzyme and the electrode surface. The well-documented shift in the CO infrared stretch band maximum from 1963.3 cm-1 (CcO fully reduced) to 1965.5 cm-1 (CcO partially oxidized) was carefully titrated electrochemically. Deconvolution of the asymmetric CO stretches indicates the existence of two different states of CO vibrators within the enzyme, presumably due to two conformers which are present in a ratio of approximately 5:1. Upon incrementally stepping the potential from the fully reduced state to the partially oxidized state, we found it possible to follow the decrease in the intensity of the original pair of these conformers and the concomitant increase of a resultant pair while maintaining this 5:1 ratio between the conformers. By plotting the change in the deconvoluted CO peak intensities vs the redox potential, as well as the absorbance changes in the visible/Soret spectra vs the redox potential, we found not only that both fit an n = 1 electron process but also that the spectral changes tracked each other identically with experimental error. Furthermore, analysis of the second derivative of the Soret spectra allowed for the qualitative monitoring of the oxidation state of the Fe alpha site which again tracked identically to that of the CO shift in the IR region. These results would seem to confirm earlier suggestions that perturbing the oxidation state of Fe alpha causes a conformational change in the enzyme which affects the binding site for CO, namely heme alpha 3. As a consequence of the CO IR stretching frequencies changing by only 2 cm-1 during this redox titration, with no accompanying changes in half band width, we suggest that it is impossible that this small but significant change seen in the CO stretching frequencies could be due to an oxidation state change in CuB, given the known sensitivity of the CO stretching frequency to perturbations and the close proximity of Cu(B) to the CO binding site at heme alpha 3 (4.5 A). Therefore, it would appear that Cu(B) must remain reduced as long as CO is bound to the heme alpha 3 site. This is consistent with earlier proposals that Fe alpha 3 and Cu(B) are acting together as a two-electron donor to dioxygen.

Animals↗

PubMed2001

A dual path programmable array microscope (PAM): simultaneous acquisition of conjugate and non-conjugate images.

A programmable array microscope (PAM) incorporates a spatial light modulator (SLM) placed in the primary image plane of a widefield microscope, where it is used to define patterns of illumination and/or detection. We describe the characteristics of a special type of PAM collecting two images simultaneously. The conjugate image (Ic) is formed by light originating from the object plane and returning along the optical path of the illumination light. The non-conjugate image (Inc) receives light from only those regions of the SLM that are not used for illuminating the sample. The dual-signal PAM provides much more time-efficient excitation than the confocal laser scanning microscope (CLSM) and greater utilization of the available emission light. It has superior noise characteristics in comparison to single-sided instruments. The axial responses of the system under a variety of conditions were measured and the behaviour of the novel Inc image characterized. As in systems in which only Ic images are collected (Nipkow-disc microscopes, and previously characterized PAMs), the axial response to thin fluorescent films showed a sharpening of the axial response as the unit cell of the repetitive patterns decreased in size. The dual-signal PAM can be adapted to a wide range of data analysis and collection strategies. We investigated systematically the effects of patterns and unit cell dimensions on the axial response. Sufficiently sparse patterns lead to an Ic image formed by the superposition of the many parallel beams, each of which is equivalent to the single scanning spot of a CLSM. The sectioning capabilities of the system, as given by its axial responses, were similar for a given scan pattern and for processed pseudorandom sequence (PRS) scans with the same size of the unit cell. For the PRS scans, optical sectioning was achieved by a subtraction of an Inc image or, alternatively, a scaled widefield image from the Ic image. Based on the comparative noise levels of the two methods, the non-conjugate subtraction was significantly superior. A point spread function for Ic and Inc was simulated and properties of the optical transfer functions (OTFs) were compared. Simulations of the OTF in non-conjugate imaging did not suffer from the missing cone problem, enabling a high quality deconvolution of the non-conjugate side alone. We also investigated the properties of images obtained by subjecting the Ic and Inc data to a combined maximum likelihood deconvolution.

Animals↗

PubMed1998

High affinity ligands from in vitro selection: complex targets.

Human red blood cell membranes were used as a model system to determine if the systematic evolution of ligands by exponential enrichment (SELEX) methodology, an in vitro protocol for isolating high-affinity oligonucleotides that bind specifically to virtually any single protein, could be used with a complex mixture of potential targets. Ligands to multiple targets were generated simultaneously during the selection process, and the binding affinities of these ligands for their targets are comparable to those found in similar experiments against pure targets. A secondary selection scheme, deconvolution-SELEX, facilitates rapid isolation of the ligands to targets of special interest within the mixture. SELEX provides high-affinity compounds for multiple targets in a mixture and might allow a means for dissecting complex biological systems.

Blood Proteins↗

PubMed1988

Multiwavelength method for measuring concentration of free cytosolic calcium using the fluorescent probe indo-1.

It is assumed that the spectra of fluorescent probes indo-1 and fura-2 in the cytoplasm are linear combinations of the spectra of calcium-bound and free probes with weight factors proportional to the concentrations of these forms. When the concentration of calcium is measured by the dual-wavelength method, the above assumption is employed without testing. A multiwavelength method for measuring free cytosolic calcium concentration is described in the present study. The method is based on the registration of the fluorescence spectra of the probe with an optical multichannel analyzer and deconvolution of the spectra into components, corresponding to free and bound forms of the probe. A mismatch is also calculated to allow estimation of deconvolution accuracy. It was found that the spectra, recorded in aqueous calibration solution with varying calcium concentrations, can be deconvoluted into components, obtained both in the absence of calcium and at its saturating concentration. When the spectrum of the probe in the cytoplasm is deconvoluted into the same components the mismatch is higher. When aqueous calibration is used, the cytosolic calcium concentration determined by the dual-wavelength method is dependent considerably on the selected wavelengths. Our data indicate that this phenomenon may be associated with the lower polarity of cytoplasm compared to the aqueous calibration solution. Addition of either ethanol or glycerol into the calibration medium results in a considerable decrease in the mismatch. The optimal concentration of ethanol is 22-32%, and depends on the type and condition of cells tested. It is shown that the use of calibration spectra obtained in aqueous solutions leads to considerable overestimation of cytosolic calcium concentration.

Calcium↗

PubMed2000

Synthesis of a small library of phenylalkylamide derivatives as melatoninergic ligands for human mt1 and MT2 receptors.

Focused small libraries of melatonin receptor ligands from arylalkylamine derivatives were synthesised by combinatorial chemistry using the mix and split method in the solid phase. A library of 108 compounds was then synthesised from 12 arylalkyl amines and nine carboxylic acids. The compound mixtures were evaluated on chicken brain melatonin and recombinant human mt1 and MT2 receptors. Deconvolution of the most potent mixture demonstrated the superiority of 3-methoxy and 2,5-dimethoxy substitution on the phenyl ring with isopropyl, propyl and ethyl amido chains. Several compounds with nanomolar affinity for human melatonin receptors were obtained.

Amides↗

PubMed1999

Genetic live vaccines mimic the antigenicity but not pathogenicity of live viruses.

The development of an effective HIV vaccine is both a pressing and a formidable problem. The most encouraging results to date have been achieved using live-attenuated immunodeficiency viruses. However, the frequency of pathogenic breakthroughs has been a deterrent to their development. We suggest that expression libraries generated from viral DNA can produce the immunologic advantages of live vaccines without risk of reversion to pathogenic viruses. The plasmid libraries could be deconvoluted into useful components or administered as complex mixtures. To explore this approach, we designed and tested several of these genetic live vaccines (GLVs) for HIV. We constructed libraries by cloning overlapping fragments of the proviral genome into mammalian expression plasmids, then used them to immunize mice. We found that inserting library fragments into a vector downstream of a secretory gene sequence led to augmented antibody responses, and insertion downstream of a ubiquitin sequence enhanced cytotoxic lymphocyte responses. Also, fragmentation of gag into subgenes broadened T-cell epitope recognition. We have fragmented the genome by sequence-directed and random methods to create libraries with different features. We propose that the characteristics of GLVs support their further investigation as an approach to protection against HIV and other viral pathogens.

AIDS Vaccines↗

PubMed2000

High-Resolution Laser Photoacoustic Spectroscopy of HSiF(3): The 5nu(1) and 6nu(1) Overtone Bands.

A spectrum of HSiF(3) has been recorded at room temperature with a gas pressure of 20-50 Torr in the near-infrared region. A laser photoacoustic spectrometer consisting of a longitudinal resonant cell coupled to a titanium:sapphire ring laser was employed. The 5nu(1) and 6nu(1) overtone bands of H(28)SiF(3) associated with the Si-H stretching have been observed at high resolution (3 x 10(-2) cm(-1)) in the regions 10 900-10 960 and 12 875-12 925 cm(-1), respectively. About 450 lines of the 5nu(1)-0 band have been assigned (J </= 45, K = 3p </= 18). Within each J cluster of the P and R branches, the K structure has been deconvoluted. A set of parameters characterizing the upper vibration-rotation structure has been obtained. Perturbations have been evidenced for K = 9 and 15. The characterization of the perturbed 6nu(1)-0 band was limited to J </= 38, and effective parameters have been determined with no detailed information on the K structure. Most perturbations are supposedly due to the cubic anharmonic constant φ(144) linking nnu(1) to (n - 1)nu(1) + 2nu(4) (n = 5, 6) and to their accompanying interacting rovibrational states. Copyright 2000 Academic Press.

Journal Article↗

PubMed2026

Uncovering the diagnostic potential of seminal fluid beyond fertility: cfDNA methylation analysis for the detection of clinically significant prostate cancer.

Research on the potential use of seminal fluid as a liquid biopsy for prostate cancer detection has been limited due to challenges associated with acquisition of this bodily fluid in clinical studies. Here we sought to expand on our previous analysis, which demonstrated high levels of prostate-derived cell free DNA (cfDNA) in seminal fluid in presumed healthy individuals, to a much larger cohort that included participants with prostate cancer. A total of 279 men scheduled for prostate biopsy were enrolled over 4 months across 12 sites. Prior to their biopsy, participants mailed a seminal fluid sample collected at home to the laboratory, from which cfDNA was extracted and underwent methylation analysis. Consistent with our earlier study in healthy individuals, we observed an abundance of high molecular weight (HMW) cfDNA in all samples. Tissue-of-origin deconvolution revealed that granulocytes and sperm were the principal contributors to seminal fluid cfDNA, while prostate-derived cfDNA was present at abundances readily detectable with current technologies. The nucleosomal fraction was very pronounced in some but not all samples and was determined to be correlated with the relative sperm signal. The sperm signal was also observed to be associated with an increase in small insert sizes (< 125 bp) in the sequenced libraries. Unsupervised clustering revealed two distinct populations driven by the abundance of sperm and granulocytes. Since summarizing at the genomic region level confounded tissues of different origins, fragment-level DNA methylation features were used to characterize and quantify the prostate cancer related signal, and features associated with clinically significant prostate cancer were identified. This study expands on our previous work to further characterize seminal fluid and highlights its potential as a promising liquid biopsy medium for the detection and monitoring of clinically significant prostate cancer.

Humans↗

PubMed1988

Moment analysis of drug disposition in kidney: transcellular transport kinetics of p-aminohippurate in the isolated perfused rat kidney.

The mean renal epithelial cell residence time, Tcell, was defined as a model-independent characteristic of the transcellular transport process in the isolated perfused kidney. The transcellular transport process includes transport at the basolateral membrane, diffusion in the cytosol, and transport at the brush border membrane. The parameter Tcell represents the mean time for the drug secreted from the tubules to pass through the renal epithelial cells, and is calculated as the difference of the mean urinary transit time between secreted drug and inulin in the single-pass perfusion system. Therefore, the urinary excretion rate-time course is indispensable to evaluate Tcell. p-Amino-hippuric acid was used as a model compound. The bovine erythrocytes in the perfusate kept the isolated kidney in an almost constant physiological condition, including secretion function. The renal vein outflow curves were also analyzed by the use of moments. The dispersion in the catheter was corrected by a deconvolution. The apparent secretion intrinsic clearance and the apparent volume of distribution were calculated from the moments. The present method will be useful for analysis of the transcellular transport mechanism and the effect of disease states on renal transport of drugs.

Aminohippuric Acids↗

PubMed1989

Fourier transform infrared spectroscopic investigation of rhodopsin structure and its comparison with bacteriorhodopsin.

FT-IR spectroscopy has been used to investigate the conformation of rhodopsin in bovine rod outer segment membranes, dispersed in aqueous suspension in both 2H2O and H2O. Detailed analysis of the amide I band was made, using second-derivative and deconvolution procedures. The frequency of the major amide I component is consistent with the presence of predominantly alpha-helices within the rhodopsin structure. A spectroscopic change occurs at acidic pH with the membranes in both 2H2O and H2O. The results for the membranes dispersed in H2O at pH 7 were used to estimate a value of 0.67 for w (amide II/amide I intensity ratio in H2O). This value of w gives an estimate of the unexchanged amide protons, in rhodopsin, of 51%. The extent of amide proton exchange at acidic p2H (p2H 5 and 2), in 2H2O was also determined. The conformation of rhodopsin in its unbleached and bleached states was investigated but no significant difference in the secondary structure was observed. A comparison, after second-derivative and deconvolution analysis, of the spectra of rhodopsin with that of bacteriorhodopsin shows that both proteins exhibit a similar number of amide I components. However, with bacteriorhodopsin the amide I band occurs at a higher frequency. Bacteriorhodopsin under similar conditions, in 2H2O, has 20% more unexchanged amide protons than does rhodopsin.

Animals↗

PubMed1997

Selection of a histidine-containing inhibitor of gelatinases through deconvolution of combinatorial tetrapeptide libraries.

A fully automated peptide synthesizer was used to generate tetrapeptide sublibraries from 24 natural and nonnatural amino acids, from which new inhibitors of gelatinases (matrix metalloproteinases MMP-2 and MMP-9) were selected as potential anticancer drugs. MMP-2 and MMP-9 from mouse Balbc/3T3 fibroblasts conditioned media were assayed in their linear range response by zymography to quantify inhibition at each step of the tetrapeptide library deconvolution. The histidine-epsilon-amino caproic acid-beta-alanine-histidine (His-epsilon Ahx-beta Ala-His) sequence was found to yield optimal inhibition of both MMP-2 and MMP-9. Inhibition by selected tetrapeptides was also evaluated with two other techniques, a native type IV collagen degradation assay and a fluorogenic enzymatic assay, confirming the tetrapeptide potency. The His-epsilon Ahx-beta Ala-His tetrapeptide also inhibited purified human MMP-2 and MMP-9 and the corresponding enzymes present in conditioned media from human tumour cells. Finally, the length of the spacer between the two terminal histidines was found to be crucial to the inhibitory potential. This approach may thus be considered as a-successful strategy to yield specific peptide or pseudopeptide inhibitors, although their potency remains moderate, since it was measured before any chemical optimization was undertaken.

3T3 Cells↗