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PubMed2000

Simulation-based medical planning for cardiovascular disease: visualization system foundations.

A technique for visualizing computational models along with volumetric imaging data in a real-time, interactive, simulation-based medical planning system for cardiovascular disease treatment is described. This technique involves an ordered rendering of faceted geometry and volumetric image data. We have developed a software system based on this image-fusion technique that is capable of capturing and representing the inherent anatomic constraints of an individual patient. Such constraints must be represented accurately in a medical planning system to ensure the validity of a potential procedure. A hypothetical clinical scenario is described for which vascular treatment plans were constructed pre-operatively without reference to the physical anatomic structure. These models were later embedded into patient-specific diagnostic MRA scans to establish the anatomic context for physiologic observations.

Algorithms↗

PubMed2000

A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent.

This study documents the feasibility of switching to an aprotic medium in sugar receptor research. The solvent change offers additional insights into mechanistic details of receptor--carbohydrate ligand interactions. If a receptor retained binding capacity in an aprotic medium, solvent-exchangeable protons of the ligand would not undergo transfer and could act as additional sensors, thus improving the level of reliability in conformational analysis. To probe this possibility, we first focused on hevein, the smallest lectin found in nature. The NMR-spectroscopic measurements verified complexation, albeit with progressively reduced affinity by more than 1.5 orders of magnitude, in mixtures of up to 50% dimethyl sulfoxide (DMSO). Since hevein lacks the compact beta-strand arrangement of other sugar receptors, such a structural motif may confer enhanced resistance to solvent exchange. Two settings of solid-phase activity assays proved this assumption for three types of alpha- and/or beta-galactoside-binding proteins, that is, a human immunoglobulin G (IgG) subfraction, the mistletoe lectin, and a member of the galectin family of animal lectins. Computer-assisted calculations and NMR experiments also revealed no conspicuous impact of the solvent on the conformational properties of the tested ligands. To define all possible nuclear Overhauser effect (NOE) contacts in a certain conformation and to predict involvement of exchangeable protons, we established a new screening protocol applicable during a given molecular dynamics (MD) trajectory and calculated population densities of distinct contacts. Experimentally, transferred NOE (tr-NOE) experiments with IgG molecules and the disaccharide Gal'alpha1-3Galbeta1-R in DMSO as solvent disclosed that such an additional crosspeak, that is, Gal'OH2--GalOH4, was even detectable for the bound ligand under conditions in which spin diffusion effects are suppressed. Further measurements with the plant lectin and galectins confirmed line broadening of ligand signals and gave access to characteristic crosspeaks in the aprotic solvent and its mixtures with water. Our combined biochemical, computational, and NMR-spectroscopical strategy is expected to contribute notably to the precise elucidation of the geometry of ligands bound to compactly folded sugar receptors and of the role of water molecules in protein--ligand (carbohydrate) recognition, with relevance to areas beyond the glycosciences.

Antimicrobial Cationic Peptides↗

PubMed2002

A neuroproteomic approach to targeting neuropeptides in the brain.

A novel universal neuropeptide display approach in the mass range of 300-5000 Da was developed to complement two-dimensional gel electrophoresis in the analysis of peptides and small proteins from brain tissue samples. For the analysis of neuropeptides we utilized on-line nanoscale capillary reversed phase liquid chromatography and electrospray ionization quadrupole-time of flight mass spectrometry. The method was employed for the analysis of a large number of peptides from three specific rat brain regions. Approximately 1500 peptides from each brain region were detected in the same analysis. Several of these peptides were sequenced using collision-induced dissociation and identified by database search tools. In addition, a method for comparing peptide elution profiles between samples was developed, to provide two- and three-dimensional computer graphics of the profiles and to pinpoint differences for statistical measurements. Among the characterized peptides were fragments from proteins such as hemoglobin, alpha-synuclein, stathmin, cyclophilin, actin, NADH dehydrogenase, cytochrome c oxidase and prosomatostatin, as well as the bioactive neuropeptides W-hemorphin-4, and LW-hemorphin-7. The present study showed that the combination of nanoscale reversed phase liquid chromatography and high-resolution tandem mass spectrometry provides a novel and powerful approach to investigate a large number of peptides and protein fragments in the brain.

Amino Acid Sequence↗

PubMed1984

The molecular structures and interactions of bovine and human gamma-crystallins.

Knowledge of the three-dimensional structure of bovine gamma II-crystallin has provided the basis for building molecular models using computer graphics of two human gamma-crystallins, the sequences of which have recently been determined. The tertiary structures of these gamma-crystallins are predicted to be highly conserved. They have extensive networks of interacting charges on their surfaces, which may contribute to their thermodynamic stability and partially define the degree of water retention in the lens. The human crystallins appear to be more hydrophobic than the bovine molecule. All have arrangements of cysteine thiols which may be important as electron sinks and reserve redox potential in the normal lens but which may contribute to protein aggregation in cataract.

Amino Acid Sequence↗

PubMed1994

Computations of post-inductive dynamics in axolotl heart formation.

This paper reports modelling of heart localization in the axolotl (Ambystoma mexicanum). The region of heart specification in the mesoderm defined by classical induction from the endoderm is larger than the area of final myocardial differentiation. For localizing the area of differentiation within the area of specification, we postulate a reaction-diffusion system that arises within the mesoderm in response to induction from the endoderm. This mechanism generates a spatial pattern for two chemicals, an activator and an inhibitor, corresponding to the area of myocardial differentiation. We postulate a diffusible chemical rescuer, which is absent in the cardiac lethal mutant, and which is a precursor to the reaction-diffusion mechanism. The activator, inhibitor, rescuer, and product of endodermal induction are presented in an enzyme mechanism with rate equations similar to the Gierer-Meinhardt equations. These equations were solved numerically in both one and two spatial dimensions. We have attained quantitative agreement with the experimental data for sizes of tissue regions and for times to heartbeat. Experiments modelled include wild-type heart localization as well as both in vitro and in vivo rescue of cardiac lethal mesoderm with wild-type mesoderm. Based upon the parameters necessary to model heart localization, we make a series of predictions. We predict: a specific profile for the endodermal inducer gradient; the possibility of producing multiple hearts in vivo; and a greater contribution to the heart from the wild-type mesoderm for in vivo transplants with cardiac lethal mesoderm. We make some suggestions as to the possible chemical nature of the substances in the model. We indicate that the inhibitory field and mechanochemical theories are probably not as promising as reaction-diffusion for the mechanism of heart localization.

Ambystoma mexicanum↗

PubMed1985

Morphogenesis of human cardiac outflow.

The developmental anatomy of human cardiac outflow was studied in a series of 16 normal embryos (gestational days 29-39, crown-rump length 6-20 mm, stages 14-19). Structural features and kinetics during truncal septation (TS) were described from external photographs, serial histological sections, and computer graphic reconstructions of selected tissues. Early in the period studied, the tubular myocardium ensheathed the single cardiac lumen and spiralling conotruncal ridges, which were filled with mesenchymal cells during days 31-33. As TS began (late stage 16), the aorticopulmonary (AP) septum appeared across the dorsal wall of the aortic sac between arches IV and VI. Mesenchymal condensations formed within the AP septum, crossing the lumen bifurcation to extend along the truncal ridges to the myocardium. During days 35-37, the cephalic margin of the myocardium grew or folded in toward these mesenchymal condensations between the developing valves and within the nearby conal ridges, which appeared to fuse to separate the subvalvular outflow channels by day 39. These observations are consistent with studies in chicks and rats which suggest that mesenchymal condensations or cell death foci interact with the distal myocardial rim during TS to form a structural septation complex dividing the two arterial streams.

Aortic Valve↗

PubMed2007

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.

The knowledge of the access paths connecting interior of molecular systems with surrounding environment is important for the understanding of structurefunction relationships and engineering of molecules for biotechnological applications. CAVER is a computer program developed for calculations of tunnels, channels or pores in the biomolecules, inorganic materials and molecular ensembles. The algorithm performs a skeleton search based on a reciprocal distance function grid. The algorithm is implemented in the stand-alone version, web version and as plug-in for PyMol. CAVER is available from the website http://loschmidt.chemi.muni.cz/caver.

Algorithms↗

PubMed1995

Docking of congo red to the surface of crystalline cellulose using molecular mechanics.

A method for the docking of ligands to crystalline surfaces using molecular mechanics was developed and applied to study the molecular features of the adsorption of Congo Red to cellulose crystals. The docking procedure was based on a grid search exploring the surface repeat unit of the cellulose crystals using several orientations of Congo Red at each grid point. Results suggest a preferential adsorption of Congo Red onto certain faces of the cellulose crystals and that the lower energy conformers have a similar positioning and orientation with respect to the cellulose chains at the surface repeat unit.

Adsorption↗

PubMed1993

Variations in acoustical beam properties of intracoronary Doppler catheters.

The limitations of coronary angiography in assessing the functional significance of coronary obstructions is well known. While the critical variable of coronary blood flow cannot be readily measured, intraluminal Doppler sonography offers useful related functional information on blood flow velocity. In order to fully evaluate Doppler signals it is essential to have exact knowledge of the transducer transmission characteristics and of the ultrasound beam topology. In an experimental set-up, the transmitter-receiver characteristics of five commonly used Doppler catheters were investigated. In comparing the beam characteristics we found inhomogeneities in the lateral beam spread. At a penetration depth of 3.0 mm the beam shape varied from a minimum of 1.25 mm up to a maximum of 3.5 mm. The mean was 2.25 mm. The different beam profiles of the investigated Doppler transducers cause an error in measuring the blood flow velocity. The blood flow velocity tends to be underestimated the more the vessel diameter and the blood flow velocity increase. Contrary to transducer design optimized for imaging, for spectral analysis of the Doppler signal it would be advantageous to have as broad a beam as possible in order to illuminate the entire vessel lumen.

Angioplasty, Balloon, Coronary↗

PubMed1982

Three-dimensional structure of the mammalian suprachiasmatic nuclei: a comparative study of five species.

The suprachiasmatic nuclei from five mammalian species (rat, hamster, cat, rhesus, and squirrel monkey) were reconstructed in three-dimensions by use of computer graphics and conventional histological techniques. The gross nuclear structures of the suprachiasmatic nuclei have complex three-dimensional geometries in every plane of orientation, and between the five species there are marked differences in the three-dimensional morphology of the suprachiasmatic nuclei. These dimensionally accurate reconstructions are discussed in relation to previous data suggesting morphological and/or functional specialization within specific regions of the suprachiasmatic nuclei.

Animals↗

PubMed1982

Axonal guidance during development of the great cerebral commissures: descriptive and experimental studies, in vivo, on the role of preformed glial pathways.

Do structures exist within the embryonic central nervous system that guide axons across the midline during development of the great cerebral commissures (corpus callosum, anterior commissure)? With the use of serial section and reconstructive computer graphic techniques we have found that during normal ontogeny of the mouse forebrain and before the arrival of the pioneer fibers of the corpus callosum at the midline, a population of primitive glial cells migrates medially (through the fused walls of the dorsal septum) from the ependymal zones of each hemisphere. At the midline, and well rostral to the lamina terminalis, these cells unite to form a bridgelike structure or "sling" suspended below the longitudinal cerebral fissure. The first callosal axons grow along the surface of this cellular bridge as they travel toward the contralateral side of the brain. The "sling" disappears neonatally. The fibers of the anterior commissure grow within the lamina terminalis along a different type of preformed glial structure. Movement of these axons occurs through an aligned system of glial processes separated by wide extracellular spaces. Do these transient glial tissues actually provide guidance cues to the commissural axons? Analyses of three situations in which the glial "sling" is genetically or surgically impaired or nonexistent indicate that this structure does, indeed, play an essential role in the development of the corpus callosum. We have analyzed (1) the embryonic stages of a congenitally acallosal mouse mutant (strain BALB/cCF), (2) several pouch stages of a primitive acallosal marsupial, Didelphys virginiana (opossum), and (3) animals in which the "sling" had been lesioned surgically through the uterine wall in the normal embryo (strain C57BL/6J). In the acallosal mouse mutant fusion of the septal midline is delayed by about 72 hours and the "sling" does not form. Although the would-be callosal axons approach the midline on schedule, they do not cross. Instead, the callosal fibers whirl into a pair of large neuromas adjacent to the longitudinal fissure. Similarly, in the opossum, fusion of the medial septal walls and formation of the glial "sling" are also lacking. However, in this species, instead of traveling dorsally, the "callosal" axons turn ventrally and pass contralaterally by way of the anterior commissure pathway. Surgical disunion of the glial "sling" also resulted in acallosal individuals. The callosal pathology in these affected animals mimicked exactly that of the genetically lesioned mutant. Our observations suggest that many different types of oriented glial tissues exist within the embryonic neural anlage. We propose that such tissues have the ability to influence the directionality of axonal movements and, thereby, play a crucial role in establishing orderly fiber projections within the developing central nervous system.

Agenesis of Corpus Callosum↗

PubMed1984

Studies on the factors that govern directionality of axonal growth in the embryonic optic nerve and at the chiasm of mice.

What are the forces residing at the presumptive chiasm of embryonic mice that control the directionality (i.e., side specificity) of the optic axons? In an attempt to answer this question, the overall trajectories of individual fascicles of early growing axons and the various environments that they encounter along their pathway have been charted from the eye through the nerve and into the base of the diencephalon. Serial sections and reconstructive computer graphic techniques were used for the analysis. The early optic axons (embryonic (E) day 13.5) arrive at the chiasm in a stereotyped topographic arrangement. However, the fiber array at the primitive chiasm is not retinotopically organized nor is it maintained with the same level of spatial precision as it is at the disc. Thus, the annular, inverted retinotopic contingent of "pioneering" axons that exists in the primitive nerve becomes reorganized at the chiasm into a crescent-shaped configuration, with fascicles from ventrotemporal and ventronasal retina at either side of the crescent and with fascicles from dorsal retina interposed. Because of their gross locations in the crescent, particular clusters of fibers, each largely originating from different retinal sectors, but "contaminated" with fibers from other regions, come in contact with different types of nonneuronal structures at the chiasm. One, a dense, knotlike glial formation that lies along the margin of the diencephalic-telencephalic junction, directs all adjacent (ventronasal) fibers contralaterally. The other, a discrete pathway of lengthy marginal glial processes, separated by an anastomotic system of large extracellular spaces, guides all nearby fibers from ventrotemporal retina ipsilaterally. The results suggest that fiber topography as well as local environmental factors may play important roles in guiding axons at the chiasm.

Animals↗

PubMed1990

Identification of pedicles of putative blue-sensitive cones in the human retina.

Cone photoreceptor pedicles from midperipheral regions of the human retina (6 mm from the foveal center) have been studied by light and electron microscopy. Three areas of cone pedicle mosaic were serially thin-sectioned, in the tangential plane, from the inner border of the outer plexiform layer to the emergence of the cone axons from the cone pedicles. Semithin sections were then collected from the cone axon level through the cone cell bodies to the cone inner segment level. Two hundred twenty-one cone pedicles were followed by this means to their respective inner segments. Eight percent of the cone pedicles were from cones with inner segment characteristics of the blue cones. All 221 cone pedicles were reconstructed by tracing images from electron micrographs. The cone pedicle locations, surface areas, telodendrial projections, and synaptic ribbons could then be measured by morphometry and analyzed by statistical methods. Some selected cone pedicles were reconstructed by computer graphics methods. The cone pedicles identified as belonging to the blue cone type could be distinguished from the surrounding longer wavelength types on the following morphological criteria: 1) they were smaller (50% the area of the surrounding pedicles), 2) they contained shorter synaptic ribbons, 3) they exhibited essentially no telodendrial contact to neighboring cone pedicles, 4) they were positioned slightly more vitread in the outer plexiform layer than neighboring pedicles, and 5) their irregular occurrence in the cone mosaic coincided with the distribution criteria established in our previous paper (Ahnelt et al: J. Comp. Neurol. 255:18-34, '87) for putative blue sensitive cones in midperipheral human retina.

Color Perception↗

PubMed1994

Horizontal cells and cone photoreceptors in primate retina: a Golgi-light microscopic study of spectral connectivity.

The relationship of primate horizontal cells (HC) to cone pedicles was assessed by superimposing the cone inner segment mosaic upon Golgi-impregnated HC dendritic terminal clusters in a light microscope (LM) study. The HI, HII, and HIII types of HC were identified, hand-drawn, photographed, and analyzed by computer graphics methods. Blue cone (B-cones) inner segments and their projected pedicles were distinguished from red (R-cones) and green (G-cones) cones on morphological criteria. Thus the inclusion or avoidance of B-cone pedicles by the various HC types' dendritic terminal clusters establishes whether there is any color specificity to their connections. In addition, we made counts of the number of dendritic terminals in the clusters going to cone pedicles in the various HCs' dendritic fields and plotted these against distances the cone pedicles lay from the cell body. In this way we could evaluate the weighting of spectral type of cone input. In general, the three HC types made the majority of their dendritic contacts with cones lying closest to their cell bodies at the center of their dendritic fields. However, HI and HIII cells, with their distinct terminal clusters, did not contact all the centrally located cones uniformly. They either avoided completely (HIII cells) or made only sparse dendritic connections (HI cells) with certain cones. The avoided or sparsely innervated cones were identified as B-cones. HII cells, on the other hand, with their more profuse and diffusely branched dendrites, appeared to contact all overlying cone pedicles and, in contrast to HI and HIII cells, directed a relatively larger number of dendrites to B-cone positions. Axon terminals of HII cells appeared to contact B-cones exclusively.

Animals↗

PubMed1987

Cell cycle perturbation of cultured C6 glioma cells following short-term contact with a low dose of ACNU.

The purpose of this study was to investigate the cell cycle perturbation of cultured C6 rat glioma cells induced by 1-(4-amino-2-methyl-5-pyrimidyl)methyl-3-(2-chloroethyl)3-nitrosourea hydrochloride (ACNU) using simultaneous flow cytometric measurements of DNA and bromodeoxyuridine (BrdU) content. A new graphic computer program permitted the quantification of cell density in hexagonal subareas and allowed the fraction of BrdU-labeled cells with mid-S phase DNA content (FLS) to be defined in a narrow window. The cell kinetic parameters such as cell cycle time (Tc) and S phase time (Ts) were estimated from a manually plotted FLS curve at 18 and 6 hr, respectively. The major effect of ACNU on the cell cycle was an accumulation of the cells in the G2M phase 12 to 24 hr posttreatment when compared to G2M traverse of untreated cells. For the two-dimensional analysis, cells were labeled with BrdU and then treated with ACNU, or treated with ACNU and then labeled with BrdU. It was concluded that the cells in the S and G2M phases at the time of ACNU administration progressed to mitosis but that the G1 phase cells accumulated in the subsequent G2M phase. Two-dimensional FCM analysis using BrdU provided a useful tool in studying cell cycle perturbation.

Animals↗

PubMed1993

Three-dimensional visualization of multi-channel volume data: the amSFP algorithm.

In this paper we present a three-dimensional visualization technique for multi-channel volume data. The technique simulates the physical process of fluorescence, hence its name: achromatic multi-channel simulated fluorescent process (amSFP). The data set is simulated as 3D distribution of different fluorescent dyes, where each channel is represented by a particular type of dye. Apart from the spatial density map, no additional characteristics about the data set have to be defined; no image segmentation is needed prior to visualization. The degree of interaction among the channels in the fluorescence process can be adapted to optimally render specific structures in the image. 3D multi-channel data can be obtained by a three-dimensional imaging device that is able to measure a number of physical quantities at a given location within a specimen. The fluorescence principle, the algorithm, and its implementation are presented. We have used the technique to investigate the relative spatial arrangement of blood vessels and astrocytes in the cat retina. The two components have been stained with different fluorescence dyes and recorded in a confocal light microscope to form a two-channel 3D data set.

Algorithms↗

PubMed1985

Three distinct epitopes within the loop region of hen egg lysozyme defined with monoclonal antibodies.

Five monoclonal antibodies specific for the loop region of hen egg lysozyme were prepared by immunisation with a synthetic conjugate of a proteolytic fragment of lysozyme coupled to bovine serum albumin. Their fine specificities were investigated using a panel of variant lysozymes and peptide fragments of lysozyme in a quantitative radio-immunoassay procedure. Knowledge of the structure of hen lysozyme to high resolution and the use of computer graphics enables the localisation of the epitopes recognised by the antibodies with some precision. The antibodies were shown to define three distinct, overlapping epitopes within what was previously considered to be a single antigenic site. These results are discussed in relation to current ideas of the antigenic nature of proteins and other recent studies in which anti-protein antibodies have been elicited by immunisation with small peptides.

Amino Acid Sequence↗

PubMed1985

beta s-Crystallin: structure and evolution of a distinct member of the beta gamma-superfamily.

The nucleotide sequence of the cDNA of bovine lens beta s-crystallin has been determined, and the derived amino acid sequence has been confirmed by amino acid compositions and partial sequences of the tryptic peptides of this monomeric protein. beta s-Crystallin has a length of 177 residues, corresponding to a mol. wt. of 20 773, and a blocked N-terminal serine. Comparison of beta s with the known sequences of other beta- and gamma-crystallins, and computer construction of a phylogenetic tree of these sequences, shows beta s to be more closely related to the monomeric gamma-crystallins than to the oligomeric beta-crystallins. Also the tertiary structure of beta s modelled by interactive computer graphics on the coordinates of gamma II-crystallin, revealed similarities with the gamma-crystallins which might explain its monomeric behavior: the presence of a very short N-terminal 'arm' as compared with the beta-crystallins; a distribution of charged residues on the surface as in the gamma-crystallins; and finally the nature of certain residues of its inter-domain contacts. beta s-Crystallin seems to be an old and isolated offshoot of the gamma-family, and, considering its ancient origin, might well be present in other, non-mammalian, vertebrate classes.

Amino Acid Sequence↗