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Computer three-dimensional reconstruction of serial sections is currently an active area of research. In this paper we combine computer graphics, image processing and biomedical techniques to reconstruct a stereo model of intraglandular lymphatic vessels, veins, arteries and ducts from serial microsections of the human submandibular gland.
In 1976 Fernández & Goldberg published detailed results of the polarization vectors for squirrel monkey primary otolithic afferents (1). Each vector represented the direction in three-dimensional space of the linear acceleration which caused maximum facilitation of the otolith afferent. The published plots were separate views of the projections of the polarization vectors of all the individual neurons in the superior (mainly utricular) and inferior (mainly saccular) divisions of the vestibular nerve. There were distinctly different clusters of vectors for each division. We have used new computer graphic procedures to re-process these data and show the data three-dimensionally in relation to the major planes of the head.
Previously, we demonstrated that the 2.6-kDa peptide extending from Arg177 to Tyr198 in subdomain 4 of rabbit skeletal actin bound to actin itself, inhibited the elongation of actin filament, and severed F-actin. The corresponding segment in actin, therefore, is thought to contain the most critical actin-actin contact [Hori, K. and Morita, F. (1992) J. Biochem. 112, 401-408; Hori, K., Itoh, T., Takahashi, K., and Morita, F. (1994) Biochim. Biophys. Acta 1186, 35-42]. In this paper, we report on the binding site in actin for the 2.6-kDa peptide studied by using a zero-length cross-linker, 1-ethyl-3(3-dimethylaminopropyl)carbodiimide (EDC). We conducted limited digestion of actin cross-linked with the 125I-labeled 2.6-kDa peptide with various proteases, and developed peptide maps. The cross-linked region of the 2.6-kDa peptide was found to be within the region of Ala114 to Glu167 in actin by identifying the radioactive peptide fragments. The region was further restricted by isolation of radioactive peptide from alpha-chymotryptic digest of the cross-linked actin. The binding site of the 2.6-kDa peptide was finally assigned to be within the 24 amino acid segment from Ala144 to Glu167, which lies in subdomain 3 of actin. Using computer graphics, actin-actin contact provided by the two segments was suggested to be along the left-handed genetic helix of actin filament.
The UV-VIS absorption data of four bacteriorhodopsin (BR) analogs formed from azulene-retinals of varying polyene chain length show that the one-bond-shortened to one-bond-lengthened analogs possess comparable opsin shift values to that of BR. A two-bond-shortened analog exhibited a much smaller opsin shift. These data, combined with those reported for the C-22 retinal analog (Tokunaga et al., 1977, Biophys. J. 19, 191-198) were analyzed by molecular modelling and computer graphics in terms of a model where conformational flexibility of the appended butyl is the controlling factor in determining ease of pigment formation and protein/substrate interaction.
In this paper we formulate a mathematical model for the receptor mediated endocytotic cycle under the influence of diffusion, radial convection, and generalized receptor reinsertion. The steady state radial concentration function of unbound receptors admits an explicit representation. This can be expressed as a functional of the insertion rate, the diffusion coefficient, and the flow strength. Using the referred functional we study the influence of the aforementioned mechanisms on the surface aggregation pattern of low density lipoprotein (LDL) receptors near coated pits. We perform that analysis on both a theoretical level and by means of simulated receptor aggregation patterns obtained by computer graphics techniques. We conclude that radially convective diffusion in combination with suitable characterizations of the insertion mode are consistent with reported cell surface aggregation patterns.
Mutations of either of two highly conserved residues near the active site of Escherichia coli phosphofructokinase, Ile-126 or Asn-128, produce no changes in the Km for ATP, relatively small changes in kcat, and a large increase in the Km for fructose 6-P, despite the fact that these residues are not directly involved in substrate binding. A computer graphics analysis of the three-dimensional structure suggests that the mutations effect the orientation of Arg-252, a residue important both for fructose 6-P binding and for catalysis.
The clinical use of three-dimensional (3D) ultrasound has rapidly spread to many specialities over the last ten years. The reason is easy to see, namely that single two-dimensional (2D) scans are often difficult to interpret and the mental correlation of multiple 2D scans to form a 3D image of anatomical morphology is taxing and uncertain. The rapid development of techniques for the realtime tracking of the spatial position and orientation of ultrasound probes and the development of computer graphics techniques for the presentation of anatomical images have made 3D ultrasound a realistic diagnostic tool. The authors describe the range of methods of data acquisition and display and provide illustrations of some current clinical applications.
Light chain Sci was isolated from the urine of a patient affected by light chain deposition disease with an apparent exclusive localization to the kidney. Sci protein is an intact light chain: it consists of 214 amino acid residues and has an Mr of 23.65. Its complete primary structure has been determined by sequence analysis of the corresponding tryptic peptides and by partially sequencing the intact protein. Sequence comparison shows that Sci protein is strictly related to the light chains of kIIIa family (88% structural identity) which are usually expressed in autoimmune rheumatoid syndromes. Computer graphics model suggests a perturbation in k Sci three-dimensional structure due to the unusual replacement of residues 53 and 77.
Binding sites for the glucocorticoid receptor in an ecdysone-inducible gene from Drosophila melanogaster and in the chicken vitellogenin gene are described. A comparison with other binding sites for the glucocorticoid receptor, which have been analyzed by methylation protection experiments, shows they can be classified into three groups. The first group exhibits two blocks of contact points in two subsequent turns of the DNA helix, and includes only functional regulatory elements. The second group shows an identical contact with the hexanucleotide 5'-TGTYCT-3', but only half the contact points in the other turn of the helix, whereas the third group of sites exhibits only the contact points within the conserved hexanucleotide. An analysis of the hydrogen-bonding potential of the DNA base pairs along the major groove of 10 binding sites shows a very well-conserved pattern and a twofold rotational symmetry, suggesting that the array of hydrogen bonds may be a relevant aspect of sequence recognition by hormone receptors. A representation of the binding sites and contact points by computer graphics suggests the interaction of a receptor dimer, in a head-to-head arrangement, with two subsequent turns of the B-DNA helix within the glucocorticoid regulatory elements.
Intracellular distribution of cytoplasm-free Ca2+ concentrations ((Ca2+)i) and dynamic changes during stimulation of viable hair cells were studied using digital imaging microscopy and the Ca2(+)-sensitive dye fura-2. (Ca2+)i was visualized on pseudo-colour images and three-dimensional computer graphics. In the resting state, the intra-cellular distribution of (Ca2+)i in both the outer and inner hair cells was heterogeneous, and the amount of (Ca2+)i in most of the peripheral cytoplasm just beneath the plasma membrane was greater than that throughout the entire cytoplasm. Cell depolarization, induced by elevated K+, led to an increase in (Ca2+)i in the outer hair cells. The increase in (Ca2+)i was not observed under conditions of depolarization in Ca2(+)-free medium. These observations are interpreted to mean that the increase in (Ca2+)i is induced by depolarization with the result that there is an influx of extracellular Ca2+ into the cytoplasm. When Mn2+ was applied during depolarization, a fluorescence quenching occurred. By such means the site of Ca2+ channels was elucidated.
Wear resistance has been a problem for the posterior application of resin composites. This study evaluated and compared the wear characteristics of two conventional and two packable composites. Opposing enamel wear was also measured. One traditional hybrid composite-Herculite XR (HXR), one micro-filled composite-Heliomolar (HM) and two packable composites-Filtek P60 (P60) and Surefil (SF) were formed into disks (n = 10) and used as substrates for the wear test. Enamel was harvested from extracted human third molars and machined into cusps with a 5-mm spherical radius (n = 40). The Oregon Health Sciences University oral wear simulator was used to evaluate abrasive wear and attrition of the composite materials and wear of the opposing enamel. The resulting enamel wear facets were measured and recorded in mm2 using optical scanning methods and a computer graphics program. Abrasion and attrition of the composite substrates were measured using a profilometer. Both sets of data were subjected to ANOVA and multiple comparison tests to determine significant differences. After wear testing, scanning electron micrographs were made using representative composite samples from each group. The packable composites showed significantly less attrition and abrasive wear (p < 0.001) than the conventional controls. The microfilled composite HM resulted in significantly lower enamel wear (p < 0.001) than the materials HXR and P60 but was not significantly different from the packable composite SF at the alpha = 0.05 level. The results of this in-vitro study suggest that packable composites may have improved wear resistance over some conventional composites. Clinical studies are needed to evaluate packable composites over time.
To assess the significance of regional quantitative computed tomography measurements of bone density with respect to mechanical strength in the human lumbar spine, 58 vertebrae (from 12 males, 10 females) were scanned in vitro with multiple-thin-slice quantitative computed tomography and then compressed to fracture. With computer graphics, 18 specific regions of physical density and 10 combination averages of density were identified within each vertebral body. To ensure the statistical independence of data, the individual vertebral specimens were assigned to one of three groups (T11-L1, L2-L3, or L4-L5). Use of best-subsets procedures resulted in regression models to predict fracture strength. These models used specific regional density values and often the age and sex of the donors. The correlation coefficients that resulted from the multiple regression models ranged from r = 0.88 to r = 0.95. When the density values were multiplied by the minimum cross-sectional area of the vertebral body, similar regional density averages were selected, and the predictive values were slightly improved (r = 0.94-0.97). The heterogeneity of the density samples (measured as standard deviation) in multiple regression fashion also produced strong correlation coefficients (r = 0.88-0.94). The bone density in an anterior cylinder of the midplane region, the location measured most often in quantitative computed tomography densitometry, was strongly correlated (r = 0.85) to fracture load for the T12-L1 group (N = 20), but was not significant for the other two groups of vertebrae. The cancellous bone density from the female data was not found to be significantly different from the male data set.(ABSTRACT TRUNCATED AT 250 WORDS)
The inner 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. The inner hair cells showed narrowing below the cuticular plate and gradual increase in size toward the base where the surface was indented by nerve attachments. The sizes of the afferent nerve endings were in the range of 0.9 to 3.2 microns in cross section. Large endings were fewer and were located mainly on the pillar cell side, whereas small endings were numerous and were located on the modiolar side. The number of afferent nerve endings on a single cell in the basal turn averaged 26 and in the third turn, 17. All the afferent fibers were unbranched, most of them innervated a single cell, and 81% of them formed synapses with distinct synaptic bodies in the inner hair cells. A few afferent endings formed membrane specializations with two adjacent inner hair cells but the synaptic body was seen in only one cell. The number of efferent endings, from 0.08 to 2.0 micron in diameter, was about nine in the basal turn and was seven in the third turn. No significant difference was seen between the basal and third turns in cell shape, proportion of afferent to efferent endings, nor in morphology of synapses.
The Cu,Zn superoxide dismutase from yeast was crystallized in the orthorhombic space group P21212 with unit cell dimension a = 105.1 A,b = 142.2 A, c = 62.1 A. The crystals grow in 25 mM citrate, 10 mM phosphate buffer pH 6.5, and 6% (W/V) polyethylene glycol, with a Vm of 3,4 A3/dalton, for two dimers/asymmetric unit. The crystals were unstable in the mother liquor, but were stabilized by transfer to a 35% polyethylene glycol solution. This crystalline form diffracts at high resolution and is suitable for determination of the atomic structure. The three dimensional structure of the yeast enzyme could be model-built by computer graphics techniques using the bovine enzyme atomic coordinates as template. The proposed model requires removal of some salt bridges and non equivalence of the metal-binding sites in the subunits, in line with reported functional properties of the yeast enzyme.
Using available computer graphics software programs, a novice can develop a presentation. Going beyond the basics, however, requires knowledge of the use of the elements of design: fonts, colors, and graphics. This article describes how to select fonts and colors and provides guidelines for use of pictures and graphs. Guidelines for use of default settings and templates, and considerations related to the use of animation, sound, and projection are included. Examples are provided to demonstrate important points and creating a polished, professional product.
OBJECTIVE: The Virtual Tape Measure for the Operating Microscope (VTMOM) was created to assist surgeons in making accurate 3D measurements of anatomical structures seen in the surgical field under the operating microscope. The VTMOM employs augmented reality techniques by combining stereoscopic video images with stereoscopic computer graphics, and functions by relying on an operator's ability to align a 3D graphic pointer, which serves as the end-point of the virtual tape measure, with designated locations on the anatomical structure being measured. The VTMOM was evaluated for its baseline and application performances as well as its application efficacy. METHODS: Baseline performance was determined by measuring the mean error (bias) and standard deviation of error (imprecision) in measurements of non-anatomical objects. Application performance was determined by comparing the error in measuring the dimensions of aneurysm models with and without the VTMOM. Application efficacy was determined by comparing the error in selecting the appropriate aneurysm clip size with and without the VTMOM. RESULTS: Baseline performance indicated a bias of 0.3 mm and an imprecision of 0.6 mm. Application bias was 3.8 mm and imprecision was 2.8 mm for aneurysm diameter. The VTMOM did not improve aneurysm clip size selection accuracy. DISCUSSION AND CONCLUSION: The VTMOM is a potentially accurate tool for use under the operating microscope. However, its performance when measuring anatomical objects is highly dependent on complex visual features of the object surfaces.
A short review of the author's computer-graphics developments since 1976 is presented. Some of the major developments in these programs are reviewed and a description is provided of some of the more recent tools that can be used for electron-density map interpretation. These tools include a secondary-structure template-building system that works in conjunction with a new sequence-decoration system.
The photographic method of recording computer graphics is now very much an automated procedure using film recorders, as compared with the old technique of photographing directly off the coloured video display. There are at present three types of film recorder available: terminal driven, direct drive and optical-font imager. Theoretical and practical information is given on each of these recorders based on the author's practical experience.