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Biomedical subjects

P Penczek

Publications and source records attributed to P Penczek.

At least 37 records · Page 2Linked to original sources
PubMed1995

Automatic particle picking from electron micrographs.

A computer program for automatic particle picking based on textural methods is proposed. The technique relies on the evaluation of certain textural parameters for data windows containing single particles, and those containing undesirable material. These parameters are manipulated by a discriminant analysis routine for determining the rules of classification between the different categories. The effectiveness of the method was demonstrated by application to electron micrographs of 70S Escherichia coli ribosomes.

Algorithms↗
PubMed1995

Double-tilt electron tomography.

Fidelity of tomographic reconstructions is improved and reconstruction artifacts are reduced, without increasing the number of projections, by combining tilt series taken around two orthogonal axes. Test reconstructions were made from high-voltage EM of rat liver mitochondria in a 0.6 micron thick plastic section. A number of schemes for selecting tilt angles for the projections are compared. A new method for aligning fiducial markers is described. It uses an iterative algorithm to determine the shift, scale, in-plane rotation and tilt angle for each tilt image, enforcing agreement of the expected locations of the fiducial markers in 3D space. These 3D locations are used to find the orientation between two tilt series and to merge both sets of projections.

Animals↗
PubMed1994

Quaternary structure of Octopus vulgaris hemocyanin. Three-dimensional reconstruction from frozen-hydrated specimens and intramolecular location of functional units Ove and Ovb.

A frozen-hydrated sample of Octopus vulgaris hemocyanin was imaged at 0 degree and 40 degrees tilt angle under low dose conditions by transmission electron microscopy. A three-dimensional reconstruction by the method of random conical tilt series produced a three-dimensional volume to which a D5 symmetry was applied. Examination of serial sections in the volume and surface representation at various thresholds allowed the five arches containing functional unit Ovg to be localized at the interdimeric subunit groove. In another set of experiments specific polyclonal antibodies were used to label functional units Ovb and Ove in the cylinder wall. The observation of the negatively stained immunocomplexes showed that Ovb is located in the external tiers of functional units and Ove in the internal tier. These results suggest that the direction of the polypeptide chains in the cylinder wall may be only partially antiparallel. A model of the quaternary structure is proposed with the following features: (1) the external tiers of functional units comprise four units each (Ova-d) coming from a single polypeptide chain; (2) the internal tier comprises two functional units from each polypeptide chain (Ove-f); (3) the interdimeric subunit arches connect the two copies of a single functional unit (Ovg) located in each polypeptide chain.

Animals↗
PubMed1994

The internal compartmentation of rat-liver mitochondria: tomographic study using the high-voltage transmission electron microscope.

The three-dimensional organization of the internal compartments of conventionally fixed and embedded rat-liver mitochondria has been determined by tomographic reconstruction from tilt-series images collected on the Albany high-voltage electron microscope. The results indicate that the inner membranes of these organelles are predominantly tubular in the orthodox (expanded matrix) conformation, as previously suggested by scanning electron microscopy. In the condensed (contracted matrix) conformation, the intracristal space opens up into large irregularly shaped compartments which are connected to each other and to the external (intermembrane) space by tubes with approximately the same diameter (20 nm) as those observed in the orthodox state. These results raise several questions, in particular about the nature of the structural transitions that occur in the cristae during matrix expansion and contraction, and about the influence of inner-membrane shape on the diffusion of ions and metabolites between the intracristal and intermembrane compartments.

Animals↗
PubMed1993

Three-dimensional architecture of human alpha 2-macroglobulin transformed with methylamine.

A frozen-hydrated sample embedded in vitreous ice of human alpha 2-macroglobulin transformed by methylamine was imaged by cryoelectron microscopy and reconstructed in three dimensions. In the reconstruction, the cage-like architecture of this protease inhibitor is fully revealed with a clear visualization of two lozenge-shaped lateral walls connected by thin bridges. The shape and dimensions of the internal cavity normally containing the trapped protease(s) is described. The possible locations of the thiol ester sites and inter-subunit connections are also discussed.

Image Processing, Computer-Assisted↗
PubMed1992

Alignment, classification, and three-dimensional reconstruction of single particles embedded in ice.

Cryo-electron microscopy of single biological particles poses new challenges to digital image processing due to the low signal-to-noise ratio of the data. New tools have been devised to deal with important aspects of 3-D reconstruction following the random-conical data collection scheme: (a) a new shift-invariant function has been derived, which promises to facilitate alignment and classification of single particle projections; (b) a new method of orientation search is proposed, which makes it possible to relate random-conical data sets to one another prior to reconstruction; and (c) the foundation is laid for a 3-D variance estimation which utilizes the oversampling of 3-D angular space by projections in the random-conical reconstruction scheme.

Algorithms↗
PubMed1992

Three-dimensional reconstruction of single particles embedded in ice.

Single particles embedded in ice pose new challenges for image processing because of the intrinsically low signal-to-noise ratio of such particles in electron micrographs. We have developed new techniques that address some of these problems and have applied these techniques to electron micrographs of the Escherichia coli ribosome. Data collection and reconstruction follow the protocol of the random-conical technique of Radermacher et al. [J. Microscopy 146 (1987) 113]. A reference-free alignment algorithm has been developed to overcome the propensity of reference-based algorithms to reinforce the reference motif in very noisy situations. In addition, an iterative 3D reconstruction method based on a chi-square minimization constraint has been developed and tested. This algorithm tends to reduce the effects of the missing angular range on the reconstruction, thereby facilitating the merging of random-conical data sets obtained from differently oriented particles.

Algorithms↗
PubMed1991

Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA.

A reconstruction, at 40 A, of the Escherichia coli ribosome imaged by cryo-electron microscopy, obtained from 303 projections by a single-particle method of reconstruction, shows the two subunits with unprecedented clarity. In the interior of the subunits, a complex distribution of higher mass density is recognized, which is attributed to ribosomal RNA. The masses corresponding to the 16S and 23S components are linked in the region of the platform of the small subunit. Thus the topography of the rRNA regions responsible for protein synthesis can be described.

Computer Graphics↗
PubMed1989

Analysis of the multi-channel epileptiform EEG using the Markov chains formalism.

A multi-level scheme of syntactic reduction of the epileptiform EEG data is briefly discussed and the possibilities it opens up in describing the dynamic behaviour of a multi-channel system are indicated. A new algorithm for the inference of a Markov network from finite sets of sample symbol strings is introduced. Formulae for the time-dependent state occupation probabilities, as well as joint probability functions for pairs of channels, are given. An exemplary case of analysis in these terms, taken from an investigation of anticonvulsant drug effects on EEG seizure patterns, is presented.

Algorithms↗
PubMed1987

The use of a multi-channel Kalman filter algorithm in structural analysis of the epileptic EEG.

An extension of the Kalman filter algorithm to the multi-channel case is presented and its application as a segmenting procedure in the analysis of the epileptic EEG is discussed. An analytical example of structural analysis, using the segments extracted by the proposed filter, is presented for a particular set of 4-channel EEG recordings. This analysis is shown to be especially fruitful if the autoregressive coefficients - a byproduct of the filtering procedure - are used to estimate the information flow between the channels by the calculation of partial as well as directed coherences for the representative segments.

Algorithms↗
PubMed1986

Segmentation of the epileptic EEG by means of a finite state automaton.

The aims and merits of the syntactical decomposition of the epileptic EEG are discussed in some detail. General assumptions in the design of segmenting algorithm--an essential part of the reduction of data program--are considered and a working example of segmenting routine is presented. This routine is designed as a finite state automaton, equivalent to a formal regular grammar. The performance of the routine on two sets of experimental data is presented and its intrinsic stability is shown in terms of cluster analysis of the segments produced. Means of extension of the proposed scheme to other cases of potential interest as well as possible applications in the higher level syntactical analysis are pointed out.

Computers↗
PubMed1986

Syntactic analysis of the epileptic electroencephalogram.

A full-scale scheme of the multi-level syntactic analysis of the epileptic EEG is presented and discussed in detail. An exhaustive description of basic procedures necessary to obtain a meaningful description of any set of epileptic EEG recordings is given; these procedures include algorithms for extraction of various elementary peaks from the EEG signal, for segmentation of the recording, for classification of the segments found into distinct groups of characteristic patterns and, finally, for calculation of the Levenshtein distance between the individual recordings, each recording regarded as a string of symbols taken to represent different classes of patterns. An example of global analysis in terms of such a distance, performed on a typical set of epileptic EEG recordings, is supplied to prove the feasibility of the scheme proposed.

Algorithms↗
PubMed1985

Application of combined median-averaging filters to scintigraphic image processing.

Statistical and deterministic properties of median filters are briefly discussed and their inherent advantages as a prospective tool in scintigraphic data processing are pointed out. The ability of median filters of suppressing impulse noise while the edge-like features of an image are preserved, is demonstrated on phantom data. The residual high-frequency noise remaining after median filtering can be subsequently reduced by standard smoothing procedures. A simple algorithm, made up of the superposition of a median and an averaging filter, is presented and shown to be a promising candidate in the quest for fast and easy-to-implement processing routine.

Electronic Data Processing↗
PubMedDate not supplied

Three-dimensional reconstruction of Androctonus australis hemocyanin labeled with a monoclonal Fab fragment.

An immunocomplex formed by the 4 x 6 meric hemocyanin of the scorpion Androctonus australis with the monoclonal antibody L104 was studied by cryoelectron microscopy and subjected to three-dimensional (3D) reconstruction. The reconstructed particle reflects the structure of the immunocomplex in its hydrated state and is devoid of the flattening that was previously observed with a negatively stained preparation. A 3D fitting of the X-ray data of the Panulirus interruptus hemocyanin and of the Fab R19.9 to the reconstruction volume allowed the first quantitative measurement of the structural parameters of the antigen, and the localization of the epitope at the surface of subunit Aa6. The independent alignment of the Fabs and the hexamers provides a direct verification for the accuracy of the fit and allows the building of the most detailed model of a cheliceratan 4 x 6meric complex and its attached monoclonal antibodies.

Animals↗
PubMedDate not supplied

SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.

The SPIDER system has evolved into a comprehensive tool set for image processing, making use of modern graphics interfacing in the VMS and UNIX environment. SPIDER and WEB handle the complementary tasks of batch processing and visualization of the results. The emphasis of the SPIDER system remains in the area of single particle averaging and reconstruction, although a variety of other application areas have been added. Novel features are a suite of operations relating to the determination, modeling, and correction of the contrast transfer function and the availability of the entire documentation in hypertext format.

Animals↗
PubMedDate not supplied

Three-dimensional reconstruction of a complex of human alpha 2-macroglobulin with monomaleimido Nanogold (Au1.4nm) embedded in ice.

Cysteine 949 and glutamine 952 are known to be part of the thiol ester site of each of the four subunits of human alpha 2-macroglobulin (alpha 2M). The hydrolysis of this thiol ester bound to methylamine results in the incorporation of the amine and liberation of a free sulfhydryl group that can be specifically labeled. Therefore, a high-resolution marker specific for the sulfhydryl groups, the monomaleimido Nanogold (Au1.4nm) cluster was used to bind this amino acid. After cryoelectron microscopy, a three-dimensional reconstruction of the alpha 2M-Nanogold conjugates (alpha 2M-Au1.4nm) was achieved, revealing the internal location of the thiol ester sites in the transformed alpha 2M molecules. From this study we propose three possible locations for the cysteine 949.

Cysteine↗