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Computer-aided three-dimensional reconstruction and morphometry of the outer hair cells of the guinea pig cochlea.

The outer hair cells and their nerve endings in the basal and third turns of the guinea pig cochlea were reconstructed three-dimensionally from serial thin sections by means of computer graphics, and morphometric data were obtained. The number of nerve endings in the third turn was two to three times greater than that in the basal turn. Many afferent and efferent terminals in the third turn did not demonstrate synaptic specialization. Presynaptic dense bodies were missing in the majority of outer hair cells in both basal and third turns. The morphologic arrangement of the subsurface cisternae and efferent fiber synapses on the side and base of the outer hair cells suggests a close functional relationship. The nerve fibers and cisternae may be involved in the contractile process of the cells. The volume of the outer hair cells in the first row of the basal turn was about 656 micron 3, and third turn, 1358 micron 3. The total count of mitochondria in the outer hair cells of the first row in the basal turn was 1425, and 1963 in the third turn. The density of mitochondria in the sensory cell in the basal turn was higher. The highest density was seen in the infranuclear region. The mitochondrial distribution patterns suggest that metabolic activity of the outer hair cells is higher in the basal turn than in the third turn and the energy requirement is greatest in the region close to nerve endings.

Animals↗
PubMed1997

New evaluation method for postoperative scar redness.

Even after successful operations, ugly postoperative skin scars are often distressing to patients and their parents. To judge the success of surgical methods and postoperative treatment, postoperative scars should be evaluated using a quantitative system. Height and width are easily measured, but scar redness is not. We have developed a simple and effective method for evaluating scar redness. According to the color definitions employed in computer graphics, each color can be expressed as RGB (red, green or blue) coordinates (r, g, b): 0 < or = r, g, b < or = 10. The degree of scar redness is defined by the following formula: redness score (RS) = (r1 - r0)2 + (g1 - g0)2 + (b1 - b0)2. Here, (r1, g1, b1) = coordinates of the scar color and (r0, g0, b0) = coordinates of the surrounding skin color. RS was evaluated in 59 children (35 males, 24 females; ages 1 month to 12 years old) who had scar redness after congenital cardiac surgery. For each patient, scar color and surrounding skin color was identified on the color sample table. Scar redness was also evaluated by the conventional grading method: 1 = mild, 2 = moderate and 3 = severe. The RS of the colored scars ranged from 4 to 100 (38 +/- 27). By the conventional grading method, 44 scars were grade 1, 15 grade 2 and none grade 3. RS was significantly higher among grade 2 than grade 1 patients, 52 +/- 25 and 33 +/- 27, respectively (P < 0.05). Given its subjectivity, the conventional grading method yields variable data surrounding skin color, moreover, is not considered. Our new evaluation method using RS effectively and accurately defines scar and skin colors, and allows quantitative studies of these factors.

Child↗
PubMed1987

Prothoracicotrophic hormone has an insulin-like tertiary structure.

A three-dimensional model of PTTH-II has been constructed using interactive computer graphics and energy, minimisation techniques, assuming homology with porcine insulin, the structure of which has been determined by X-ray analysis. The model shows that PTTH-II can assume an insulin-like tertiary structure, which is compact with the exception of the sequence variable NH2-terminal amino acids of the B chain. Most of the hydrophobic core residues including A2 Ile, A6 Cys, A11 Cys, A16 Leu, A20 Cys, B11 Leu, B15 Leu and B19 Cys are identical in PTTH-II and insulins. The glycines at A1, B8 and B23 allow the chain to assume the characteristic tertiary interactions of the insulin fold and although polypeptide chains are shorter at the COOH-termini of the A and B chains and extended at the NH2-terminus of the B chain, the insulin-like tertiary structure can still be assumed. It is unlikely that PTTH-II forms either dimers or hexamers, characteristic of porcine and human insulin, and the model is consistent with the inability of PTTH-II to bind anti-insulin antibodies or insulin receptors. A hydrophobic surface region of PTTH-II may be involved in intermolecular actions of physiological relevance. We discuss the implications of our model for evolution of this family of hormones and growth factors.

Animals↗
PubMed1988

Three-dimensional model of stellacyanin and its implications for electron transfer reactivity.

Experimental data were combined with computational methods in constructing a hypothetical three-dimensional model for the blue single copper protein Rhus stellacyanin (St). The known sequence of stellacyanin and its homology with plastocyanin (Pc) were used together with the results of spectroscopic studies of the protein that yielded the current assignment of two histidines, one cysteine and a disulfide sulfur as copper ligands in stellacyanin. By computer graphics and energy minimization the folding of the protein was predicted. The model structure is somewhat less regular than Pc as judged by surface area and energy comparisons, but it is a stable structure. Besides rotation of one imidazole ring the copper site undergoes no change even in the absence of the copper ion and the model shows that the site can be constructed with the four assumed copper ligands without forming a strained system. The structure also indicates that a carbonyl oxygen atom is near the copper, thus the site may have analogy to the Alcaligenes denitrificans azurin (Az) site, although the amino acid sequence is more homologous to that of Pc. The model indicates that aspartate 49, reductively labeled by Cr(III), is near the copper center and homologous to the site labeled by Cr(III) on Pc. Also homologous to Pc is a tyrosine residue adjacent to the aspartate. This tyrosine has been implicated in Pc electron transfer and thus is probably involved in electron transfer reactivity of St as well. The higher reactivity of St with small-molecule redox reagents compared to Az and Pc, may be due to the proximity of the above-mentioned aspartate 49 to the Cu, or the greater exposure of one of the Cu cysteine ligands, in the predicted structure as compared to that in the known Pc and Az structures.

Amino Acid Sequence↗
PubMed1991

Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c.

To understand the specificity and efficiency of protein-protein interactions promoting electron transfer, we evaluated the role of electrostatic forces in precollision orientation by the development of two new methods, computer graphics alignment of protein electrostatic fields and a systematic orientational search of intermolecular electrostatic energies for two proteins at present separation distances. We applied these methods to the plastocyanin/cytochrome c interaction, which is faster than random collision, but too slow for study by molecular dynamics techniques. Significant electrostatic potentials were concentrated on one-fourth (969 A2) of the plastocyanin surface, with the greatest negative potential centered on the Tyr-83 hydroxyl within the acidic patch, and on one-eighth (632 A2) of the cytochrome c surface, with the greatest positive potential centered near the exposed heme edge. Coherent electrostatic fields occurred only over these regions, suggesting that local, rather than global, charge complementarity controls productive recognition. The three energetically favored families of pre-collision orientations all directed the positive region surrounding the heme edge of cytochrome c toward the acidic patch of plastocyanin but differed in heme plane orientation. Analysis of electrostatic fields, electrostatic energies of precollision orientations with 12 and 6 A separation distances, and surface topographies suggested that the favored orientations should converge to productive complexes promoting a single electron-transfer pathway from the cytochrome c heme edge to Tyr-83 of plastocyanin. Direct interactions of the exposed Cu ligand in plastocyanin with the cytochrome c heme edge are not unfavorable sterically or electrostatically but should occur no faster than randomly, indicating that this is not the primary pathway for electron transfer.

Amino Acid Sequence↗
PubMed1989

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.

A new procedure for the analysis of the structure and molecular dynamics of duplex DNA is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the values of the conformational and helicoidal parameters for each structure entering the analysis using the method "Curves" developed by Lavery and Sklenar, J. Biomol. Str. Dyn. 6, 63 (1988), followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels, or "dials", for each IUPAC torsional parameter and "windows" on the range of values assumed by the linear and angular helicoidal parameters, and is presented in a form isomorphous with the structure per se. The complete time evolution of the conformational and helicoidal parameters of a DNA double helix can then be depicted in a set of six composite figures. Dynamical aspects of helix bending are also subsumed in this analysis. The procedure is illustrated with an analysis of the structures of canonical A and B forms of DNA and the 300 degrees K native dodecamer duplex d(CGCGAATTCGCG). The "dials and windows" are then used for a comprehensive analysis of 30 psec of molecular dynamics on the dodecamer in the vicinity of a canonical B-DNA energy minimum. This involves presentation of the time evolution of 206 conformational and 230 helicoidal parameters for the dodecamer. A number of interesting structural features can be recognized in the analysis, including crankshaft motions, BI - BII transitions, sugar repuckerings, and a description of spontaneous helix bending at what corresponds to the 1 degrees and 2 degrees "hinge points" indicated in the crystal structure. Our approach is expected to be directly useful for critical analysis of the effects of various assumptions about force field parameters, hydration and electrostatic effects and thus contribute to the development of reliable simulation protocols for nucleic acid systems. Extension of the method to present differential changes in conformational and helicoidal parameters is expected to be valuable for the analysis of structural and molecular dynamics studies of the reorganization and adaptation of DNA on complexation with various drugs and regulatory proteins.

Algorithms↗
PubMed1988

Model for the three-dimensional folding of 16 S ribosomal RNA.

We have derived a model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA, using interactive computer graphic methods. It is based on (1) the secondary structure derived from comparative sequence analysis, (2) the three-dimensional co-ordinates for the centers of mass of the 30 S subunit proteins, and (3) the locations of sites in 16 S rRNA that interact with specific ribosomal proteins, from footprinting and crosslinking studies. We present a detailed description of the derivation of the model. About 75% of the RNA chain is sufficiently constrained to provide a useful model. This contains most of the universally conserved core of the molecule. In all but a few instances, protected and crosslinked sites can be placed within or very close to their cognate proteins, while obeying stereochemical rules. The overall shape of the model and locations of specific regions of the RNA correspond well to data derived from electron micrographs of 30 S subunits, although such data were not used to construct the model. Phylogenetic variations in the structure are readily accommodated; as an example, we have modeled the 950-nucleotide mammalian mitochondrial 12 S rRNA by superimposing it on the E. coli structure. The three major RNA domains, as defined by secondary structure, appear to exist as autonomous structural units in three dimensions, for the most part. There is an extensive interface between the 5' and central domains, whereas the 3' major domain has relatively little apparent contact with the rest of the structure. The 5', central and 3' major domains form structures that resemble the body, platform and head, respectively, seen in electron micrographs of 30 S subunits. We discuss possible roles for the ribosomal proteins in stabilizing specific structural features of the RNA during ribosome assembly. The decoding site, as deduced from footprinting and crosslinking studies involving the tRNA anticodon stem-loop, is well-localized. Bases protected from chemical probing by the anticodon stem-loop line the cleft of the subunit. The conserved loop at position 530, which contains some of the bases protected by A site-bound tRNA, is remote (approx. 80 A) from the decoding site. Protection of these bases by the anticodon stem-loop is thus unlikely to be due to direct contact.

Base Sequence↗
PubMed1990

Molecular structure of flavocytochrome b2 at 2.4 A resolution.

The crystal structure of flavocytochrome b2 has been solved at 3.0 A resolution by the method of multiple isomorphous replacement with anomalous scattering. Area detector data from native and two heavy-atom derivative crystals were used. The phases were refined by the B.C. Wang phase-filtering procedure utilizing the 67% (v/v) solvent content of the crystals. A molecular model was built first on a minimap and then on computer graphics from a combination of maps both averaged and not averaged about the molecular symmetry axis. The structure was extended to 2.4 A resolution using film data recorded at a synchrotron and refined by the Hendrickson-Konnert procedure. The molecule, a tetramer of Mr 230,000, is located on a crystallographic 2-fold axis and possesses local 4-fold symmetry. Each subunit is composed of two domains, one binding a heme and the other an FMN prosthetic group. In subunit 1, both the cystochrome and the flavin-binding domain are visible in the electron density map. In subunit 2 the cytochrome domain is disordered. However, in the latter, a molecule of pyruvate, the product of the enzymatic reaction, is bound at the active site. The cytochrome domain consists of residues 1 to 99 and is folded in a fashion similar to the homologous soluble fragment of cytochrome b5. The flavin binding domain contains a parallel beta 8 alpha 8 barrel structure and is composed of residues 100 to 486. The remaining 25 residues form a tail that wraps around the molecular 4-fold axis and is in contact with each remaining subunit. The FMN moiety, which is located at the C-terminal end of the central beta-barrel, is mostly sequestered from solvent; it forms hydrogen bond interactions with main- and side-chain atoms from six of the eight beta-strands. The interaction of Lys349 with atoms N-1 and O-2 of the flavin ring is probably responsible for stabilization of the anionic form of the flavin semiquinone and hydroquinone and enhancing the reactivity of atom N-5 toward sulfite. The binding of pyruvate at the active site in subunit 2 is stabilized by interaction of its carboxylate group with the side-chain atoms of Arg376 and Tyr143. Residues His373 and Tyr254 interact with the keto-oxygen atom and are involved in catalysis. In contrast, four water molecules occupy the substrate-binding site in subunit 1 and Tyr143 forms a hydrogen bond to the ordered heme propionate group. Otherwise the two flavin-binding domains are identical within experimental error.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1993

Computer-aided socket design for trans-femoral amputees.

Computer-aided socket design (CASD) is a technique for the design of prosthetic sockets using the advantageous features of computer graphics and calculation. This paper describes a computer-aided technique used to design sockets for patients with trans-tibial lower limb amputations.

Amputees↗
PubMed1994

Computer-generated slide graphics on a shoestring budget.

The use of computer-generated slides in weekly didactic conferences and at regional and national meetings is commonplace. Though adding a professional look, the expense of computer-generated slides can be prohibitive. We herein present a simple technique for generating color slides that captures the professional look of computer-generated slides at a fraction of the cost.

Audiovisual Aids↗
PubMed1984

Three-dimensional vector graphics: a method for displaying results in a drug trial.

Three-dimensional computer graphics are used to depict multidimensional outcome measures in a clinical drug trial. This graphics approach was used in a study of 116 patients with active rheumatoid arthritis, in a randomized, double-blind 21-week comparison of placebo, oral gold, and injectable gold. Three health status components, physical disability, psychological status, and pain, were generated using the Arthritis Impact Measurement Scales (AIMS). Results were presented in a three-axis perspective, one axis for each component, plotting individual patient vectors for magnitude and direction on a 10 X 10 X 10 coordinate matrix. Vectors for each patient are plotted from time 1 (start) to time 2 (finish) over the 21-week trial period. Vector symbols were added for clarity and subgroup delineation. Vector displays show trends in treatment response that clarify and strongly reinforce the statistical results. It is concluded that three-dimensional vector graphics are a useful adjunct to the statistical analysis of clinical trial results. The graphics facilitate the visual interpretation of a complex data set, and clarify the analysis of the results for both the clinician and researcher.

Arthritis, Rheumatoid↗
PubMed1989

Historical evolution of disease mapping in general and specifically of cancer mapping.

The presentation of areal data in epidemiology is illustrated by such mapping techniques as dots (spots), shading (choropleth, thematic) and isolines (isopleths). Examples are also given of computer-assisted cartography (computer graphics) which employs hardware and software components of digital computers, together with the use of geographical and demographic base maps.

Cluster Analysis↗
PubMed1982

On-line microcomputer system for analysis of precordial maps.

An inexpensive system was developed for automated on-line analysis of ST segment heights, Q, R, and S heights and areas under these peaks, using an LSI-11 microcomputer. System accuracy was evaluated using a computer graphics technique which enabled magnification and labelling of the computed peaks on 60 maps from 17 patients. To compare the computer with hand analysis, the sigma ST (.06 seconds from S nadir) for 20 maps was calculated by three blinded observers. Correct computer evaluation occurred in all but five of 2058 leads. The mean observer sigma ST was 3.2 millivolts (range 0.77-7.5 mv). Mean inter-observer SD was +/-0.21 mv. The mean computer sigma ST was 3.5 mv (range 0.82-9.3 mv). The spread between computer and observer was +/-0.45 mv. Discrepancies between computer and observer were due to cumulative imprecision in observer measurements. This system has proven to be a practical and economic solution to handling the large volume of data accumulated with serial precordial mapping. It is considerably more precise than conventional hand analysis. Additionally, the system's versatility makes it ideally suited to many clinical and research functions.

Computers↗
PubMed1998

X-ray diffraction of food polysaccharides.

The morphologies of food polysaccharides described in this chapter illustrate the power of x-ray fiber diffraction in conjunction with computer modeling and sophisticated refinement techniques. On the other hand, the lack of information on structures such as xanthan reflects the inadequacy of the experimental techniques used to date. But the demands from academic and industrial sectors to investigate the molecular interactions in multicomponent systems, including protein-protein, protein-polysaccharide, polysaccharide-polysaccharide, and other complexes, are high and growing, because they have important food applications. These complexes are structurally more difficult than those solved in the past 40 years and it is improbable that any chosen system will be amenable for crystallographic investigation, crystals or fibers. Modern research facilities that include two-dimensional area detectors, millisecond exposures with synchrotron x-ray radiation, interactive computer graphics, sophisticated molecular dynamics calculations, unbelievably fast and inexpensive computers, and our own intellectual abilities are indispensable tools for the future of structural science in general and food polysaccharides in particular.

Carbohydrate Conformation↗
PubMed1986

Three-dimensional graphics display of X-ray angiography data.

A method for making three-dimensional computer graphics displays of in vivo blood vessels is described. Input data are taken from biplane X-ray angiograms using an image-processing system. A display list is built up which is then sent to a high-function graphics system. Real-time interaction is possible using a vector-refresh display where the blood vessel segments are shown as cylinders of the appropriate diameter. Realistic raster representations may be used to give the user insight into the overall topology of the network of vessels. The Winchester Graphics System is described together with explanations of the techniques employed.

Angiography↗
PubMed1983

Computerized medical records. A new resource for clinical decision making.

A computerized medical record changes the way a clinician practices medicine by presenting data about patients in multiple organized formats. A computerized record can be used to make it more difficult to overlook important findings. The computer can improve communication by informing both the patient and referring physicians of new data as they become available. Computer graphics or algorithms can be used to emphasize subtle trends. A computer data base can be used to aggregate data about selected patients to provide information about the natural history of disease and effect of treatment.

Computers↗
PubMed1999

Estimates of shape by eye, or, the little invariant that could.

Five experiments were conducted to test the hypothesis that observers apprehend specific constancies under change in perspective. The constancies were projective properties of ellipses pictured to slant and tilt in depth. Observers were asked to reproduce the static upright view of a moving pair of ellipses, using a computer graphics display and interface. Projective invariants for pairs of conics were computed on the observers' productions. A few experimental conditions revealed near-perfect performance. When pairs of coplanar ellipses were viewed under dynamic transformation in perspective, then invariants calculated on the observers' productions were a match--in value on average--to the invariants of the transforming ellipse pairs. It is proposed that measures of projective properties afford a family of techniques that can be applied to gauge acuity for complex shapes in the study of visual form perception.

Analysis of Variance↗