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Biomedical subjects

L D Harris

Publications and source records attributed to L D Harris.

At least 19 recordsLinked to original sources
PubMed1989

UvsY protein of bacteriophage T4 is an accessory protein for in vitro catalysis of strand exchange.

The uvsX and uvsY genes are essential to genetic recombination, recombination-dependent DNA synthesis and to the repair of DNA damage in bacteriophage T4. Purified UvsX protein has been shown to catalyze strand exchange and D-loop formation in vitro, but the role of UvsY protein has been unclear. We report that UvsY protein enhances strand exchange by UvsX protein by interacting specifically with UvsX protein: gene 32 protein (gp32) is not necessary for this effect and UvsY protein has no similar effect on the RecA protein of E. coli. UvsY protein, like UvsX protein, protects single-stranded DNA from digestion by nucleases, but, unlike UvsX protein, shows no ability to protect double-stranded DNA. UvsY protein enhances the rate of single-stranded-DNA-dependent ATP hydrolysis by UvsX protein, particularly in the presence of gp32 or high concentrations of salt, factors that otherwise reduce the ATPase activity of UvsX protein. The enhancement of ATP hydrolysis by UvsY protein is shown to result from the ability of UvsY protein to increase the affinity of UvsX protein for single-stranded DNA.

Adenosine Triphosphatases↗
PubMed1988

Formation of D loops by the UvsX protein of T4 bacteriophage: a comparison of the reaction catalyzed in the presence or absence of gene 32 protein.

The UvsX protein of T4 bacteriophage will catalyze the formation of D loops between linear single-stranded DNA (ssDNA) and homologous supercoiled double-stranded DNA (dsDNA) in the absence of T4 gene 32 protein (gp32). This reaction requires one monomer of UvsX protein per three nucleotides of ssDNA so that the ssDNA is completely covered with UvsX protein. Under these conditions, high rates of ATP hydrolysis are observed, and one-third of the products are joined paranemically. The reaction proceeds through a mechanism that creates homology-independent coaggregates of UvsX protein, dsDNA, and ssDNA. When UvsX protein is added to only 1 monomer per 8 nucleotides, but with 1 monomer of gp32 per 12 nucleotides, the rate of ATP hydrolysis is depressed, but D-loop formation is enhanced. Nearly all of the product is bound in plectonemic joints, and no coaggregated intermediates are formed. Coaggregate formation at high concentrations of UvsX protein is not inhibited by the presence of gp32; gp32 simply allows for efficient formation of D loops at such low concentrations of UvsX protein that coaggregates are not constructed. Electron microscopic visualization of the joint structures in this reaction reveals that both gp32 and UvsX protein are bound to the ssDNA. The single-stranded DNA binding (SSB) protein of Escherichia coli will substitute only partially for gp32: in the presence of SSB protein, D-loop formation can be catalyzed at one UvsX protein monomer per eight nucleotides, and it is accomplished without the formation of coaggregates, but a major portion of the product is joined paranemically.

Adenosine Triphosphatases↗
PubMed1988

DNA strand exchanges.

Biochemical and electron microscopic studies of the strand exchange reactions catalyzed by the RecA protein of Escherichia coli and the UvsX protein of T4 phage reveal that these reactions proceed in three distinct steps. The first step, termed joining, involves the assembly of RecA (or UvsX) protein onto a single-stranded DNA (ssDNA) molecule and the subsequent search for homology with a double-stranded DNA (dsDNA) partner and formation of a stable synapsis. In the second step (envelopment/exchange), the exchange of DNA strands occurs fueled by the hydrolysis of ATP. The third step (release of products) entails the resolution of the complexes and dissociation of the protein from the DNAs. The structure of the intermediates in the in vitro reactions catalyzed by the RecA and UvsX proteins is emphasized in this review. The results of pairing different DNA molecules in vitro (such as linear ssDNA pairing with linear or supertwisted dsDNA) are described. Paranemic joints represent a major pathway of joining between two DNA molecules which may involve, in some cases, most of the DNA substrate molecules. Since the nature of paranemic joints has only recently begun to be understood, the nature, role, and possible in vivo function of paranemic joining are considered.

DNA↗
PubMed1987

Visualization of the homologous pairing of DNA catalyzed by the bacteriophage T4 UvsX protein.

The uvsX gene product is essential for DNA repair and general recombination in T4 bacteriophage. The ability of UvsX protein to catalyze the homologous pairing of single-stranded DNA (ssDNA) with double-stranded DNA (dsDNA) in vitro was examined by electron microscopic (EM), nitrocellulose filter binding, and gel electrophoretic methods. Optimal joining was observed at ratios of UvsX protein:ssDNA of 2 nucleotides/protein monomer. At this level, the ssDNA was fully covered by UvsX protein as seen by EM, while the dsDNA appeared protein-free. Using this stoichiometry, the pairing of circular ssDNA with homologous supertwisted dsDNA was found to produce a high frequency of complexes in which a supertwisted dsDNA molecule was joined to a UvsX protein-ssDNA filament over a distance of less than 100 base pairs. These joints were labile to deproteinization and must have been paranemic. Pairing of linear ssDNA containing buried homology to the dsDNA produced identical structures. Pairing of fully homologous linear ssDNA and supertwisted dsDNA yielded D-loop joints (plectonemic) as seen by EM following deproteinization. Both the paranemic and the plectonemic joints were at sites of homology, as demonstrated by restriction cleavage of the complexes. Visualization of the joined complexes prior to deproteinization showed that 50% of the joints had the architecture of the paranemic joints, whereas in the remainder, a topologically relaxed dsDNA circle merged with the UvsX protein-ssDNA filament for a distance of 450 base pairs. The structure of the filament was not visibly altered in this region. These observations are similar, but not identical, to findings in parallel studies utilizing the RecA protein of Escherichia coli.

DNA, Bacterial↗
PubMed1985

Three-dimensional cardiac anatomy and function in heart disease in adults: initial results with the dynamic spatial reconstructor.

The dynamic spatial reconstructor, or DSR, is a unique high-speed volume-imaging x-ray scanner based on computed tomographic principles. In this report, we present data obtained from the first feasibility DSR studies of adult patients with heart disease. Information from three patients--one with hypertrophic obstructive cardiomyopathy, one with calcific aortic valvular disease, and one with a left ventricular aneurysm--is described in detail. The mean DSR scanning time for each patient was 20 seconds, and the mean total irradiation to the sternum was 15.3 R. Transverse cross sections were reconstructed and then retrospectively reformatted to provide operator-selected oblique sections in space (for example, long-axis and short-axis sections of the left ventricle), to follow these sections through time (such as from end-diastole through end-systole), and to create three-dimensional displays (for instance, of the left ventricular chamber). Unique quantitative measurements of structure and function were made by using these images. For generation of most imaging data, only one injection of contrast material into the right side of the heart is necessary. Clinically useful three-dimensional dynamic imaging data can be acquired from adult patients with heart disease by using the DSR. Compared with conventional angiocardiography, DSR studies can provide information with less x-ray exposure and fewer angiographic injections.

Adult↗
PubMed1979

Display and visualization of three-dimensional reconstructed anatomic morphology: experience with the thorax, heart, and coronary vasculature of dogs.

A new method, termed reprojection, is used to visualize anatomic morphology contained within three-dimensional reconstructions made up of images of multiple parallel cross sections. This method involves the projection, either orthographically into a plane or radially onto a cylinder, of the volume picture elements (voxels) of the reconstruction. Orthographic reprojection images, formed by mathematically summing the magnitudes of the voxels along selected parallel paths through the reconstructed volume, are analagous to conventional radiographs formed by the passage of an X-ray beam through the volume. The reprojection image is a two-dimensional array of picture elements that is displayed on a television monitor using a digital-to-video scan converter. Also described are the techniques of noninvasive selective tissue dissolution and numerical dissection, whereby obscuring portions of the reconstructed volume are either partially "dissolved" or totally eliminated before reprojection. Utilizing these methods, anatomic information present in a three-dimensional reconstruction but not clearly seen in a reprojection image is rendered visible after removal of superposed structures. The usefulness of these methods is demonstrated utilizing three-dimensional reconstructions of the thorax, heart, and coronary arteries of dogs.

Animals↗
PubMed1979

Distribution of regional volumes and ventilation in excised canine lobes.

A linear elasticity solution for the gravitational deformation of excised lungs was obtained. The accuracy of our solution was examined by comparing predicted and measured displacements of markers glued to the surface of canine lower lobes. The equations describing the strains in a lobe were used to predict the distribution of regional volumes and the slope of phase III (S3) of a single-breath oxygen (SBO2) test. The analysis predicted a negative S3. However, S3 was found to be positive in the five lobes tested, suggesting that factors other than gravity were responsible for the observed pattern of ventilation. In SBO2 tests repeated with increasing delays at end inflation, S3 progressively decreased, became negative, and was eventually abolished. Our equations predicted the most negative observed S3 well. We conclude that continuum mechanics can be used to describe the gravitational deformation of lungs and the resulting effect on ventilation distribution.

Animals↗
PubMed1978

Regional lung expansion at total lung capacity in intact vs. excised canine lungs.

A computer-based biplane videoroentgenographic recording technique that determines the spatial coordinates of radiopaque lung parenchymal markers was used to compare regional lung expansion at total lung capacity (TLC) in the intact dog (prone and supine) and after removal from the chest. The reproducibility of the technique was examined by repeated determinations of intermarker distances at various static lung volumes during stepwise inflation and deflation of the lungs. Most of the variability in repeated determinations of intermarker distances at any lung volume was due to cardiogenic motion. When marker positions were determined repeatedly at the same phase of the cardiac cycle, the maximum coefficient of variation was less than 3% for a marker pair separated by 16.5 mm. At TLC, distances between all intralobar marker pairs in the intact thorax (prone and supine) and excised were highly linearly related (r = 0.96-0.99), whereas distances between interlobar marker pairs did not correlate as well (r = 0.77-0.86). We conclude that at TLC 1) the intact thorax does not distort the shape of the individual lobes from the state of isotropic expansion, and 2) in different body positions, overall lung shape may be different due to displacementof lobes relative to each other, but individual lobes remain uniformly expanded.

Animals↗