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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↗

PubMed1996

A comparison of six deconvolution techniques.

We present results for the comparison of six deconvolution techniques. The methods we consider are based on Fourier transforms, system identification, constrained optimization, the use of cubic spline basis functions, maximum entropy, and a genetic algorithm. We compare the performance of these techniques by applying them to simulated noisy data, in order to extract an input function when the unit impulse response is known. The simulated data are generated by convolving the known impulse response with each of five different input functions, and then adding noise of constant coefficient of variation. Each algorithm was tested on 500 data sets, and we define error measures in order to compare the performance of the different methods.

Algorithms↗

PubMed1982

A method for in situ characterization of b- and c-type cytochromes in Escherichia coli and in complex III from beef heart mitochondria by combined spectrum deconvolution and potentiometric analysis.

An analytical technique for the in situ characterization of b- and c-type cytochromes has been developed. From evaluation of the results of potentiometric measurements and spectrum deconvolutions, it was concluded that an integrated best-fit analysis of potentiometric and spectral data gave the most reliable results. In the total cytochrome b content of cytoplasmic membranes from aerobically grown Escherichia coli, four major components are distinguished with alpha-band maxima at 77 K of 555.7, 556.7, 558.6 and 563.5 nm, and midpoint potentials at pH 7.0 of 46, 174, -75 and 187 mV, respectively. In addition, two very small contributions to the alpha-band spectrum at 547.0 and 560.2 nm, with midpoint potentials of 71 and 169 mV, respectively, have been distinguished. On the basis of their spectral properties they should be designated as a cytochrome c and a cytochrome b, respectively. In Complex III, isolated from beef heart mitochondria, five cytochromes are distinguished: cytochrome c1 (lambda m (25 degrees C) = 553.5 nm; E'0 = 238 mV) and four cytochromes b (lambda m (25 degrees C) = 558.6, 561.2, 562.1, 566.1 nm and E'0 = -83, 26, 85, -60 mV).

Animals↗

PubMed1988

Applications of a general method for deconvolution using compartmental analysis.

A method of deconvolution is illustrated using compartmental models. The approach can be used to determine an arbitrary unknown input function from a measured response and the impulse response of the system. Compartmental models are constructed to specify (a) the function fitting the response data and (b) the impulse response of the system. Simulation of these models is then used to construct the unknown input function.

Alanine↗

PubMed1983

Model-free deconvolution techniques for estimating vascular transport functions.

In this paper we present two methods which can be used to numerically deconvolve indicator dilution curves to obtain vascular transport functions. In the first method, direct algebraic deconvolution is made stable and practical by the damped least squares method. The second method involves a time-shift of the output curve which is based on the first and second moments of the input and output curves. This method is stable, computationally simple and can provide reasonable estimates of the transport function.

Animals↗

PubMed1995

Automatic analysis of cortical signals recorded with voltage-sensitive dyes using a forward-backward non-linear filtering technique and deconvolution.

A method for automatically analyzing cortical signals recorded with voltage-sensitive dyes and a photodiode array is described. First, a forward-backward non-linear filtering technique is used to eliminate the background noise and preserve the fast transients of the signals. Then the filtered signals are deconvoluted from their maximal values by using a gaussian function. The different components of the signals can be identified and characterized by their respective latencies, amplitudes, plateau durations, and slopes. These parameters can be used for subsequent statistical analysis. This automated method is much faster than a manual analysis because of the large number of responses that are optically recorded. Moreover, it can be easily applied to different experimental protocols and to other signals such as field potentials.

Animals↗

PubMed1993

Estimation of the secondary structure and conformation of bovine lens crystallins by infrared spectroscopy: quantitative analysis and resolution by Fourier self-deconvolution and curve fit.

The secondary structure of six bovine lens protein fractions (two alpha, three beta and one gamma-crystallin) are examined in solution and in solid forms for the first time using FTIR spectroscopy. Films of the nuclear and cortical regions of the bovine lens are also examined. The structure is quantitatively estimated from the vibrational analysis of the resolution-enhanced amide-I profile achieved by Fourier self-deconvolution and linear least-squares curve-fit algorithm. All the protein fractions fold predominantly in a beta-pleated sheet structure with little or no alpha-helical domains in solution or in lyophilized solid form. These proteins also retain their predominant beta-sheet conformation in the cellular phospholipid environment of the lens, in conformity with the structure obtained for all the mammalian species examined to date. Despite structural homology, vibrational data indicate subtle structural differences within each class of the crystallins probably due to presence of several minor substructures/subconformations. Substantial high amounts of turns (approx. 40%) observed in the beta-fractions may have a fundamental implication in stabilizing the tertiary structure of the uniquely folded-proteins vital for the transparency of the lens. These proteins in solid KBr-matrix undergo a major structural change, induced primarily by ionic interactions which refold them in a helical conformation. IR spectroscopy together with band-narrowing procedures has proven to be an effective tool to obtain structural information of proteins in solution, as solid substrates or in a complex biological tissue, such as ocular lens.

Algorithms↗

PubMedDate not supplied

Combined deficits in the somatotropic and gonadotropic axes in healthy aging men: an appraisal of neuroendocrine mechanisms by deconvolution analysis.

We have employed deconvolution analysis of 24-h serum GH, LH, and FSH concentration profiles to evaluate the nature of age-associated changes in GH, LH, and FSH secretion and disappearance in healthy older individuals. Our findings indicate that healthy aging results in a diminished frequency of detectable GH secretory episodes and an apparent decrease in estimated GH half life in men. These combined effects lead to a significant reduction in mean serum GH concentrations over 24 h. In contrast, we find that LH secretory burst frequency tends to increase with a reciprocal decrease in amplitude as serum total and free testosterone concentrations decline during healthy aging. There is also a prolongation of LH secretory burst duration, and a putative increase in basal LH secretion rates. The changes in LH secretory dynamics are specific, because the half life of immunoradiometric LH and the mass of hormone secreted per burst are not altered. In contrast, the apparent half life of FSH increases with age, and the secretory burst duration may decrease. This spectrum of distinct neuroendocrine sequelae of aging has interesting implications to both investigative and therapeutic strategies for modifying the somatotropic and gonadotropic axes in aging individuals.

Adult↗

PubMed2003

Multicolor deconvolution microscopy of thick biological specimens.

One limitation in understanding disease at the cellular level has been the inability to efficiently analyze DNA on a cell-to-cell basis within the natural tissue context. However, DNA analyses at a single-cell resolution should be instrumental for the understanding of cancer cell biology, cancer evolution, for chromosomal mosaic analysis and rare cell events, and should provide otherwise inaccessible information on essential biological processes. Here we present a fluorescence in situ hybridization-based multicolor deconvolution technique for three-dimensional microscopy. We use up to seven different color channels for probe detection, which allows the simultaneous high-resolution localization of multiple point-like sources within a biological specimen with a thickness of up to 30 micro m. In addition, a DNA counterstain is used for volume labeling of the nuclei offering the opportunity for a simultaneous segmentation of nuclei. Furthermore, as the instrumentation consists of a standard fluorescence microscope it represents a low-cost method as compared to confocal microscopy.

Centromere↗

PubMed2002

Measurement of thin filament lengths by distributed deconvolution analysis of fluorescence images.

The lengths of the actin (thin) filaments in sarcomeres directly influence the physiological properties of striated muscle. Although electron microscopy techniques provide the highest precision and accuracy for measuring thin filament lengths, significant obstacles limit their widespread use. Here, we describe distributed deconvolution, a fluorescence-based method that determines the location of specific thin filament components such as tropomodulin (Tmod) or probes such as phallacidin (a phalloidin derivative). Using Tmod and phallacidin fluorescence, we were able to determine the thin filament lengths of isolated chicken pectoralis major myofibrils with an accuracy and precision comparable to electron microscopy. Additionally, phallacidin fluorescence intensity at the Z line provided information about the width of Z lines. Furthermore, we detected significant variations in thin filaments lengths among individual myofibrils from chicken posterior latissimus dorsai and embryonic chick cardiac myocytes, suggesting that a ruler molecule (e.g., nebulin) does not strictly determine thin filament lengths in these muscles. This versatile method is applicable to myofibrils in living cells that exhibit significant variation in sarcomere lengths, and only requires a fluorescence microscope and a CCD camera.

Actins↗

PubMed2000

Comparison of gas chromatography-pulsed flame photometric detection-mass spectrometry, automated mass spectral deconvolution and identification system and gas chromatography-tandem mass spectrometry as tools for trace level detection and identification.

The complexity of a matrix is in many cases the major limiting factor in the detection and identification of trace level analytes. In this work, the ability to detect and identify trace level of pesticides in complex matrices was studied and compared in three, relatively new methods: (a) GC-PFPD-MS where simultaneous PFPD (pulsed flame photometric detection) and MS analysis is performed. The PFPD indicates the exact chromatographic time of suspected peaks for their MS identification and provides elemental information; (b) automatic GC-MS data analysis using the AMDIS ("Automated Mass Spectral Deconvolution and Identification System") software by the National Institute of Standards and Technology; (c) GC-MS-MS analysis. A pesticide mixture (MX-5), containing diazinon, methyl parathion, ethyl parathion, methyl trithion and ethion was spiked, in descending levels from 1 ppm to 10 ppb, into soil and sage (spice) extracts and the detection level and identification quality were evaluated in each experiment. PFPD-MS and AMDIS exhibited similar performance, both superior to standard GC-MS, revealing and identifying compounds that did not exhibit an observable GC peak (either buried under the chromatographic background baseline or co-eluting with other interfering GC peaks). GC-MS-MS featured improved detection limits (lower by a factor of 6-8) compared to AMDIS and PFPD-MS. The GC-PFPD-MS-MS combination was found useful in several cases, where no reconstructed ion chromatogram MS-MS peaks existed, but an MS-MS spectrum could still be extracted at the elution time indicated by PFPD. The level of identification and confirmation with MS-MS was inferior to that of the other two techniques. In comparison with the soil matrix, detection limits obtained with the loaded sage matrix were poorer by similar factors for all the techniques studied (factors of 5.8, >6.5 and 4.0 for AMDIS, PFPD-MS and MS-MS, respectively). Based on the above results, the paper discusses the trade-offs between detectivity and identification level with the compared three techniques as well as other more traditional techniques and approaches.

Automation↗

PubMed2002

An expectation-maximisation algorithm for the deconvolution of the intrinsic distribution of single molecule's parameters.

Values obtained from single molecule techniques exhibit distinct distributions comprising an uncertainty due to random noise convoluted with the intrinsic distribution of the molecule's properties. In the fields of single molecule light microscopy and spectroscopy, force microscopy and spectroscopy as well as other techniques like electrophysiology, sophisticated data analysis algorithms are available which extract the interesting parameters and their uncertainties from the noisy data set. The intrinsic distributions of these parameters contain valuable information about the molecules' physical and chemical properties, that need to be deconvoluted from the data. Here, we present an expectation-maximisation (EM-) algorithm that estimates the intrinsic distribution in single molecule experiments. The performance is tested by using computer simulations and the application of the method is demonstrated for data from single molecule force spectroscopy.

Algorithms↗

PubMed1997

Noise deconvolution based on the L1-metric and decomposition of discrete distributions of postsynaptic responses.

A statistical approach to analysis of amplitude fluctuations of postsynaptic responses is described. This includes (1) using a L1-metric in the space of distribution functions for minimisation with application of linear programming methods to decompose amplitude distributions into a convolution of Gaussian and discrete distributions; (2) deconvolution of the resulting discrete distribution with determination of the release probabilities and the quantal amplitude for cases with a small number (< 5) of discrete components. The methods were tested against simulated data over a range of sample sizes and signal-to-noise ratios which mimicked those observed in physiological experiments. In computer simulation experiments, comparisons were made with other methods of 'unconstrained' (generalized) and constrained reconstruction of discrete components from convolutions. The simulation results provided additional criteria for improving the solutions to overcome 'over-fitting phenomena' and to constrain the number of components with small probabilities. Application of the programme to recordings from hippocampal neurones demonstrated its usefulness for the analysis of amplitude distributions of postsynaptic responses.

Animals↗

PubMed1988

Quantitation of collagen fragments and gelatin by deconvolution of polarimetry denaturation curves.

A method for quantitating nicked or shortened molecules (fragments) in pepsinized bovine type I collagen preparations using polarimetry thermal denaturation curves is described. The shortened molecules denature about 4 degrees C lower than intact collagen molecules. The analog output of a polarimeter was digitized and stored on a microcomputer disk. A BASIC program was written which retrieves the specific rotation data from the disk, smooths the data with a boxcar average, and plots the derivative of the denaturation curve. The derivative curve was deconvoluted by fitting three Gaussian curves to the derivative curve using published algorithms. The area of the Gaussian centered at 37 degrees C was proportional to the amount of collagen fragments. A good correlation between the amount of fragments determined by polarimetry and by a trypsin sensitivity assay was observed. The overall precision of the method was about 10% RSD, and the method was repeatable by multiple analysts. Application of the method to reconstituted fibrillar collagen samples showed that more fragments are generated when pepsin digestion time is lengthened. By fitting a fourth Gaussian component to the derivative curve, the method can also be used to determine relative amounts of denatured collagen (helix partially unwound but alpha chains not nicked). The detection limit for denatured collagen is about 20%.

Algorithms↗

PubMed2001

Spectral deconvolution and operational use of stripping ratios in airborne radiometrics.

Spectral deconvolution using stripping ratios for a set of pre-defined energy windows is the simplest means of reducing the most important part of gamma-ray spectral information. In this way, the effective interferences between the measured peaks are removed, leading, through a calibration, to clear estimates of radionuclide inventory. While laboratory measurements of stripping ratios are relatively easy to acquire, with detectors placed above small-scale calibration pads of known radionuclide concentrations, the extrapolation to measurements at altitudes where airborne survey detectors are used bring difficulties such as air-path attenuation and greater uncertainties in knowing ground level inventories. Stripping ratios are altitude dependent, and laboratory measurements using various absorbers to simulate the air-path have been used with some success. Full-scale measurements from an aircraft require a suitable location where radionuclide concentrations vary little over the field of view of the detector (which may be hundreds of metres). Monte Carlo simulations offer the potential of full-scale reproduction of gamma-ray transport and detection mechanisms. Investigations have been made to evaluate stripping ratios using experimental and Monte Carlo methods.

Air Pollution, Radioactive↗

PubMed2000

Image deconvolution for protein crystals.

The image deconvolution technique developed for non-biological samples, which is based on the weak-phase-object approximation and principle of maximum entropy, was applied to simulated images of the biotin-binding protein streptavidin. A slight modification of the technique was introduced to solve the problem caused by the special image formation condition for biological samples. It has been shown that the modified technique is effective.

Crystallography↗

PubMed1996

Quantitative analysis of multivariate data using artificial neural networks: a tutorial review and applications to the deconvolution of pyrolysis mass spectra.

The implementation of artificial neural networks (ANNs) to the analysis of multivariate data is reviewed, with particular reference to the analysis of pyrolysis mass spectra. The need for and benefits of multivariate data analysis are explained followed by a discussion of ANNs and their optimisation. Finally, an example of the use of ANNs for the quantitative deconvolution of the pyrolysis mass spectra of Staphylococcus aureus mixed with Escherichia coli is demonstrated.

Escherichia coli↗

PubMed1998

Bimodal granulocyte transit time through the human lung demonstrated by deconvolution analysis.

The lungs are an important site of granulocyte pooling. The aim of the study is to quantify pulmonary vascular granulocyte transit time using deconvolution analysis, as has previously been performed to measure pulmonary red cell transit time. Granulocyte and red cell studies were performed in separate groups of patients. Both cell types were labelled with Tc-99m, which for granulocyte labelling was complexed with hexamethylpropyleneamine oxime (HMPAO). The red cell impulse response function (IRF) was monoexponential with a median transit time of 4.3 s. The granulocyte IRF was biexponential in 19 of 22 subjects, 18 of whom had systemic inflammation (inflammatory bowel disease, systemic vasculitis or graft-vs-host disease) and four were controls without inflammatory disease. The median transit time of the fast component ranged from 20 to 25 s and of the slow component 120-138 s in the four patient groups. The fraction of cells undergoing slow transit correlated significantly with (a) mean granulocyte transit time and (b) the fraction showing shape change in vitro. We conclude that granulocyte transit time through the pulmonary circulation is bimodal and that shape-changed (activated) cells transit more slowly that non-activated cells. The size of the fraction undergoing slow transit is closely related to mean granulocyte transit time and is an important determinant of the size of the pulmonary vascular granulocyte pool.

Cell Movement↗