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PubMed1992

Use and misuse of multiple comparisons in animal experiments.

The objective of many animal experiments is to detect meaningful relationships among treatments and associated responses. Types of comparisons of means include pairwise multiple comparisons, planned orthogonal or nonorthogonal contrasts, and orthogonal polynomials. Some procedures are appropriate only for specific types of treatment designs and specific types of objectives. Pairwise, multiple comparisons are appropriate only for comparing unstructured, qualitative treatments. Planned comparisons partition the overall set of treatment effects into independent or nonindependent subsets, with special application to factorials. Orthogonal polynomial (regression) procedures assess relationships between quantitative treatments and response when a full range of responses or an optimal dose is of interest. Recommendations for appropriate use of each mean comparison procedure are illustrated using data from three Journal of Animal Science articles. Also mentioned are a number of computer graphics packages that provide creative ways to display biological relationships and can be linked to statistical packages for input and to word processors or 35-mm cameras for output.

Analysis of Variance↗
PubMed1998

Computer-generated three-dimensional reconstructions of serially sectioned mouse embryos.

We have been involved with a group of computer scientists and anatomists in the development of computer-based methodologies that not only combine the advantages of scanning electron microscopy and conventional histology, but provide the additional dimension of tissue recognition. The latter is achieved by the appropriate labelling of tissues and structures by delineation or 'painting'. Individually segmented anatomically defined tissues can be highlighted in a particular colour and viewed either in isolation or in combination with other appropriately labelled tissues and organs. Tissues can be shown in any orientation either as a transparent overlay on computer-generated histological sections or as 3-D images without the histological background. An additional feature of the system is that computer graphics technology combined with 3-D glasses now also allows the viewer to see the object under analysis in stereo. This facility has been found to be particularly helpful in drawing attention to topological relationships that had not previously been readily noted. As the mouse is now the mammalian model of choice in many areas of developmental research, it is of critical importance that a basic level of skill is available in the research community in the interpretation of serially sectioned material, for example, for the rapidly expanding field in which gene expression studies play a significant role. It is equally important that there is an understanding of the dynamic changes that occur in relation to the differentiation of the various organ systems seen in these early stages of development. What we emphasise here is the additional information that it is possible to gain from the use of this tool which, in our view, could not readily have been gained from the analysis of scanning electron micrographs or by studying conventional serial histological sections of similar stages of mouse embryonic development. The methodology has been developed as part of a large project to prepare a database of mouse developmental anatomy covering all stages from fertilisation to birth in order to allow the accurate spatial mapping of gene expression and cell lineage data onto the digital Atlas of normal mouse development. In this paper we show how this digital anatomical Atlas also represents a valuable teaching aid and research tool in anatomy.

Anatomy, Cross-Sectional↗
PubMed1993

A large screen digitizer system for radiation therapy treatment planning.

PURPOSE: This paper describes a new technique for manually drawing contours of anatomy over image data for the purposes of radiation therapy treatment planning. METHODS AND MATERIALS: A large area rear-projectible digitizer tablet is used together with a projection TV system to display computer graphics and image data. Large images of computed tomography or magnetic resonance cross-sections are displayed and the digitizer is used to directly trace outlines of important organs. Digitizer menus allow multiple functions for selecting images and structures, for changing the grayscale level and window, and for zooming and roaming the image. RESULTS: This device has been in clinical operation for many years and has proven to greatly increase the speed of entering cross-sectional outlines defined for serial computed tomography images sets. A small timing study of clinical usage demonstrates up to a factor of ten improvement in the speed of contour entry. CONCLUSION: For 3-dimensional radiation therapy, tumor, and target volumes, as well as important critical organs, must be delineated from serial sets of computed tomography or magnetic resonance images. Often 30 or more slices must be considered and the process of outlining structures on this number of slices can represent a significant fraction of the total treatment planning time. The device described in this paper greatly improve the ease and speed of manual contour entry for 3-dimensional radiation therapy planning.

Humans↗
PubMed1987

Chymotrypsin hydrolysis of X-phenyl hippurates. A quantitative structure-activity relationship and molecular graphics analysis.

The hydrolysis of a set of 28 X-phenyl hippurates by chymotrypsin was investigated. From the derived Km and kcat values a quantitative structure-activity relationship was developed. This equation shows that para substituents correlated by sigma- display only an electronic effect on the formation of the ES complex whereas meta hydrophobic substituents show a hydrophobic interaction correlated by pi in addition to their electronic effect. Meta polar substituents avoid contact with the enzyme and show only electronic effects on Km. Using the x-ray crystallographic coordinates for chymotrypsin and computer graphics, a model was constructed which is used to interpret the quantitative structure-activity relationship. As with a number of previously reported examples, we have found that when polar substituents have the option of binding to hydrophobic space or remaining in the aqueous phase they follow the latter possibility.

Binding Sites↗
PubMedDate not supplied

The visible animal project: a three-dimensional, digital database for high quality three-dimensional reconstructions.

The "Visible Animal Project" (VAP) is comprised of axial anatomic cryosections and corresponding CT and MR images of a mature dog. The digital database is used for the creation of three-dimensional computer graphics of canine anatomy. The technique of cryodissection is described in detail. The combining of the corresponding CT and MR images, and cryosections as well as the data processing for the creation of three-dimensional reconstructions is presented and examples are shown. For the first time a complete high-resolution three-dimensional database of a dog is available, which can be used as the base for further high quality three-dimensional reconstructions, similar to the "Visible Human Project" (VHP).

Anatomy, Cross-Sectional↗
PubMed1995

New representations of otolithic primary afferent spatial tuning--a re-processing of the Fernández & Goldberg (1976) data.

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.

Afferent Pathways↗
PubMed1995

Actin-actin contact: chemical cross-linking between actin and the 2.6-kDa peptide from subdomain 4 of actin.

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.

Actins↗
PubMed1991

Butyl conformational reorganization as a possible explanation for the longitudinal flexibility of the binding site of bacteriorhodopsin. The azulene and C-22 retinoid analogs.

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.

Azulenes↗
PubMed1998

Surface aggregation patterns of LDL receptors near coated pits. I. The radially convective diffusion and generalized insertion mechanism.

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.

Coated Pits, Cell-Membrane↗
PubMed1994

Site-directed mutagenesis of two highly conserved residues near the active site of phosphofructo-1-kinase.

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.

Amino Acid Sequence↗
PubMed1999

Three-dimensional morphometry in ultrasound.

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.

Adult↗
PubMed1991

Amino acid sequence of k Sci, the Bence Jones protein isolated from a patient with light chain deposition disease.

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.

Aged↗
PubMed1986

Molecular model of the interaction between the glucocorticoid receptor and the regulatory elements of inducible genes.

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.

Animals↗
PubMedDate not supplied

Calcium distribution and mobilization during depolarization in single cochlear hair cells. Imaging microscopy and fura-2.

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.

Animals↗
PubMed1991

Correlations between vertebral regional bone mineral density (rBMD) and whole bone fracture load.

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)

Adult↗
PubMedDate not supplied

Computer-aided three-dimensional reconstruction of the inner hair cells and their nerve endings in the guinea pig cochlea.

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.

Animals↗
PubMed1989

Crystallographic characterization and three-dimensional model of yeast Cu,Zn superoxide dismutase.

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.

Amino Acid Sequence↗