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Biomedical subjects

D P Allison

Publications and source records attributed to D P Allison.

At least 19 recordsLinked to original sources
PubMed1997

Mapping individual cosmid DNAs by direct AFM imaging.

Individual cosmid clones have been restriction mapped by directly imaging, with the atomic force microscope (AFM), a mutant EcoRI endonuclease site-specifically bound to DNA. Images and data are presented that locate six restriction sites, predicted from gel electrophoresis, on a 35-kb cosmid isolated from mouse chromosome 7. Measured distances between endonuclease molecules bound to lambda DNA, when compared to known values, demonstrate the accuracy of AFM mapping to better than 1%. These results may be extended to identify other important site-specific protein-DNA interactions, such as transcription factor and mismatch repair enzyme binding, difficult to resolve by current techniques.

Animals↗
PubMed1996

Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules.

Direct imaging with the atomic force microscope has been used to identify specific nucleotide sequences in plasmid DNA molecules. This was accomplished using EcoRI (Gln-111), a mutant of the restriction enzyme that has a 1000-fold greater binding affinity than the wild-type enzyme but with cleavage rate constants reduced by a factor of 10(4). ScaI-linearized plasmids with single (pBS+) and double (pGEM-luc and pSV-beta-galactosidase) EcoRI recognition sites were imaged, and the bound enzyme was localized to a 50- to 100-nt resolution. The high affinity for the EcoRI binding site exhibited by this mutant endonuclease, coupled with an observed low level of nonspecific binding, should prove valuable for physically mapping large DNA clones by direct atomic force microscope imaging.

Binding Sites↗
PubMed1994

Stretched DNA structures observed with atomic force microscopy.

Double-stranded DNA molecules are occasionally found that appear to be straightened and stretched in atomic force microscope (AFM) images. Usually pBS+ plasmid and lambda DNA show relaxed structures with bends and kinks along the strands and have measured contour lengths consistent to about 5-7%; they also appear not to cross over each other, except in very high concentrations. The anomalous molecules observed here, compared with the majority of molecules in the preparation, show contour lengths increased by as much as 80% and have measured heights of about half that of normal relaxed DNA. Some molecules also appear to be in transition between stretched and relaxed forms. These observations are consistent with an uncoiling of the DNA helix without breakage of the covalent bonds in the deoxyribose-phosphate backbone.

Bacteriophage lambda↗
PubMed1992

Immobilization of DNA for scanning probe microscopy.

Reproducible scanning tunneling microscope and atomic force microscope images of entire molecules of uncoated plasmid DNA chemically bound to surfaces are presented. The chemically mediated immobilization of DNA to surfaces and subsequent scanning tunneling microscope imaging of DNA molecules demonstrate that the problem of molecular instability to forces exerted by the probe tip, inherent with scanning probe microscopes, can be prevented.

DNA, Bacterial↗
PubMed1992

Electrostatic spraying of DNA molecules for investigation by scanning tunneling microscopy.

We have investigated electrostatic spraying of DNA onto gold surfaces as an alternative sample-preparation technique for STM studies. Preliminary results show that a higher distribution of isolated strands as well as well ordered aggregates can be obtained with this technique when compared with electrodeposition or drop evaporation. In many places, the well ordered aggregates were found to cleave in a direction perpendicular to their length after repeated scanning in the same direction.

DNA↗
PubMed1992

Scanning tunneling microscopy of DNA: a novel technique using radiolabeled DNA to evaluate chemically mediated attachment of DNA to surfaces.

pBS+ plasmid deoxyribonucleic acid (DNA) was imaged by scanning tunneling microscopy (STM) after mounting microdroplets by aerosol deposition onto heated epitaxial gold surfaces. However, the instability of the adsorbate to forces exerted by the tunneling tip points out the need for more aggressive bonding of molecules to surfaces. We describe a sensitive assay for the qualitative and quantitative evaluation of chemical agents to influence binding of DNA to surfaces using 32P-labeled pBS+ plasmid DNA. We propose that such an assay can make an important contribution to immobilization techniques prior to STM imaging.

DNA↗
PubMed1992

Imaging isolated strands of DNA molecules by atomic force microscopy.

We have employed an atomic force microscope (AFM) to image in air isolated strands of pBS+ plasmid DNA adsorbed onto freshly cleaved mica. At a DNA concentration below 0.3 micrograms/ml isolated strands of the plasmid DNA are usually seen, while for concentrations higher than 3 micrograms/ml a uniform coverage of interconnected DNA strands was observed. We found that the contrast and the width of DNA were dependent upon humidity. When the relative humidity exceeds 60%, negative contrast images with strand widths 20 times the width of DNA are found, while positive contrast images with 7 to 10 times the width of DNA are found when the humidity is below 30%. By placing the AFM in an environment where the humidity could be controlled, we were able to switch between positive and negative contrasts.

Adsorption↗
PubMed1992

Atomic force microscopy of DNA on mica and chemically modified mica.

Atomic force microscopy (AFM) was used to image circular DNA adsorbed on freshly cleaved mica and mica chemically modified with Mg(II), Co(II), La(III), and Zr(IV). Images obtained on unmodified mica show coiling of DNA due to forces involved during the drying process. The coiling or super twisting appeared to be right handed and the extent of super twisting could be controlled by the drying conditions. Images of DNA observed on chemically modified surfaces show isolated open circular DNA that is free from super twisting, presumably due to strong binding of DNA on chemically modified surfaces.

Adsorption↗
PubMed1991

Electrochemically induced adsorption of radio-labeled DNA on gold and HOPG substrates for STM investigations.

In a scanning tunneling microscope (STM) electrochemical cell we have studied the effects of electrode potential on both the surface topography and the adsorption of deoxyribonucleic acid (DNA) to graphite and gold surfaces. Images of the surface of highly oriented pyrolytic graphite (HOPG), of the same area, in response to a positive increase in surface potential show degradation of the step edges with little change in the crystal plane. Images of the same area of a gold surface demonstrate the formation of and the progressive increase in nodular structures on the crystal planes, in response to increased potential, with little effect on the step edges. Using radio-labeled DNA we monitored electrochemical absorption onto HOPG and gold surfaces. Although at no applied potential and at negative surface potentials some DNA was bound, at positive potentials 3 to 5 times more DNA was incorporated onto both surfaces. DNA adsorbed to a surface at a positive potential was not removed by reversing the potential.

Adsorption↗
PubMed1991

Inhibited morphological terminal differentiation and enhanced proliferation of cultured mouse epidermal cells at different concentrations of dimethyl sulphoxide.

Dimethyl sulphoxide (DMSO), at concentrations of 1-2%, induces terminal differentiation in several different cell types in vitro and enhances the growth of newborn mouse epidermal cells in primary culture under conditions that also permit terminal differentiation. We have found that DMSO concentrations approaching 4% reversibly inhibited (with little overt toxicity) terminal differentiation of normal epidermal cells from newborn SENCAR mice. Cells cultured in medium containing 4% DMSO and calcium in excess of 1 mM did not stratify extensively or slough large amounts of keratinized debris into the medium as occurred in control cultures, nor did they form large numbers of squamous cells or keratin bundles, as revealed by light and electron microscopy. The number of detergent-insoluble cornified envelopes was similarly reduced. Long-term growth of epidermal colonies in secondary culture was optimum in 1% DMSO, this concentration also permitting normal terminal differentiation of these cells. Since DMSO had these effects on epidermal cells in vitro, it may also affect epidermal cell proliferation and terminal differentiation in vivo, an important consideration should DMSO ever be approved for topical use in the US.

Animals↗
PubMed1990

Scanning tunneling microscopy and spectroscopy of plasmid DNA.

We present scanning tunneling microscope (STM) images of uncoated deoxyribonucleic acid (DNA) electrochemically mounted on highly-oriented pyrolytic graphite (HOPG) and imaged in air. Images of linear abnormalities inherent to HOPG surfaces that can be confused with DNA are also presented. Scanning tunneling spectroscopic (STS) images generated by superimposing a small, high frequency ac bias onto the dc tunnel bias and recording the ac current signal were taken simultaneously with the topographic images. These spectroscopic images reveal contrast due to local conductivity variations and can be used to differentiate DNA molecules from graphite artifacts.

Carbon↗
PubMed1989

Synthesis of a more stable osmium ammine electron-dense DNA stain.

Specific DNA staining for electron microscopic observation is simplified by a shorter synthesis of the staining reagent. The new, more reliable reagent, osmium ammine-B, is stable for more than a year, dissolves completely in water, and does not require reoptimization of staining conditions for every batch, yet reproducibly gives strong contrast to DNA-containing structures.

Animals↗
PubMed1988

Antibodies to mouse lung capillary endothelium.

We are interested in developing monoclonal antibodies (MoAbs) that recognize specific cell types in the lung of BALB/c mice. Normal mouse lung homogenate was used to immunize F344 rats and hybridomas were produced by fusion of rat spleen cells with mouse myeloma SP 2/0. Two hybridomas were selected which produced MoAbs active in immunohistochemistry of lung cells. MoAb 273-34A and 411-201B both show extensive peroxidase staining of capillary endothelial cells within alveolar walls of lungs at the light microscopic level. To demonstrate cell specificity, immunoelectron microscopy with gold-labeled antibody was performed. Lightly fixed lungs were frozen and thin-sectioned before staining with MoAb and 5-nm gold particles coupled to secondary antibody. Quantitative analyses of these cryosections show that both antibodies, used at optimal concentrations, are specific for binding to capillary endothelial cells. More than 95% of the gold particles are associated with capillary endothelial cells on the thin side of the alveolar wall. When capillaries adjoined thick septa containing interstitial cells, about two thirds of the gold particles were associated with endothelial cells and about one quarter with interstitial cells. These MoAbs should be useful in studying the role of endothelial cells in toxic lung injury.

Animals↗
PubMed1987

Rat monoclonal antibodies to mouse lung components for analysis of fibrosis.

Six rat monoclonal antibodies to mouse lung membrane fraction have been characterized. Each has unique binding properties and can be used to stain particular lung components in paraffin sections. One antibody, 133-13A, recognizes a 100-kDa glycoprotein on lung tumor cells, but stains only macrophage-like cells in normal or fibrotic lung sections as determined by immunogold electron microscopy. The monoclonal antibody 273-34A binds to a 112-kDa protein on the surface of normal mouse lung fibroblasts. Immunogold electron microscopy demonstrates antibody binding to capillary endothelial cells, but not to fibroblasts. Type I, or Type II cells. Staining of fibrotic sections with MoAb 273-34A is dramatically enhanced over staining of normal lung. A third antibody, 370-8A, gives a general staining pattern throughout normal lung that is intensified in fibrotic lung. Another MoAb 328-41A mediates intense nuclear fluorescence of lung tumor cells and cells in lung sections. It binds to 14- and 17-kDa proteins that may be high mobility group (HMG) nuclear proteins. Enzyme inhibition studies and immunofluorescence staining patterns on normal lung indicate that elastin may be the target of MoAb 328-35B. MoAb 327-5B binds to normal mouse lung fibroblasts and red blood cell membranes. These last three MoAbs stain macrophages in fibrotic lung, but give a general pattern of light epithelial cell stain in normal lung sections indicating macrophage engulfment of the normal cell antigen during fibrosis. These antibodies should be useful in identifying cell types and molecular mechanisms involved in early stages of fibrosis induced by different chemical insults.

Animals↗
PubMed1986

The intracellular fate of [3H]benzo[a]pyrene diol epoxide diastereomers localized in vivo in SENCAR mouse epidermis: a quantitative electron microscopic study.

The intracellular localization of topically applied anti and syn diastereomers of racemic benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE) was investigated in SENCAR mouse epidermis using conventional electron microscopic (EM) autoradiography. The shaved backs of adult mice were treated in vivo with the active skin tumor initiator anti [3H]BPDE or with its stereoisomer syn [3H]BPDE, which is inactive as an initiator. After 3, 12 and 24 h of exposure, thin sections of the treated skin were prepared for high resolution autoradiography to determine the intracellular distributions of radioactivity bound within the epidermis. For each treatment and exposure time, the interfollicular area of epidermis examined by EM encompassed 350-700 keratinocytes, and extended from the basal lamina to the innermost keratinizing layer at a magnification that permitted basal and suprabasal cell populations to be distinguished in situ following autoradiography. Statistical analysis of the distributions of silver grains localized over keratinocytes at 3-, 12- and 24-h timepoints revealed that 27.2% of the carcinogenic anti [3H]BPDE grains occurred over epidermal nuclei, which was significantly more (P less than 0.001) than 20.0% of the non-carcinogenic syn [3H]BPDE grains associated with nuclei at all timepoints examined. In the basal cell population at the 3-h time point 33% of both racemic diastereomers were found within nuclei; at 12 and 24 h of exposure the nuclear association of anti [3H]BPDE grains increased (P less than 0.01) to 39% and 47% respectively, while the nuclear-associated syn [3H]BPDE grains remained at 29% and 33%. The localization of [3H]BPDE observed in our experiments suggests that the epidermal cell nucleus may be an important intracellular target for anti BPDE.

Administration, Topical↗
PubMed1983

Electron microscopic comparison of the sequences of single-stranded genomes of mammalian parvoviruses by heteroduplex mapping.

The sequence homologies among the linear single-stranded genomes of several mammalian parvoviruses have been studied by electron microscopic analysis of the heteroduplexes produced by reannealing the complementary strands of their DNAs. The genomes of Kilham rat virus, H-1, minute virus of mice and LuIII, which are antigenically distinct non-defective parvoviruses, have considerable homology: about 70% of their sequences are conserved. The homologous regions map at similar locations in the left halves (from the 3' ends) of the genomes. No sequence homology, however, is observed between the DNAs of these nondefective parvoviruses and that of bovine parvovirus, another non-defective virus, or that of defective adenoassociated virus, nor between the genomes of bovine parvovirus and adenoassociated virus. This suggests that only very short, if any, homologous regions are present. From our results, we predict an evolutionary relationship among Kilham rat virus, H-1, minute virus of mice and LuIII. It is interesting to note that, although LuIII was originally isolated from a human cell line and is specific for human cells in vitro, its genome has sequences in common only with the rodent viruses Kilham rat virus, minute virus of mice and H-1, and not with the other two mammalian parvoviruses tested.

Base Sequence↗
PubMed1983

Membrane-bound fractions of R6K plasmid DNA in Escherichia coli.

The intracellular location of plasmid DNA has been of interest in an effort to understand the maintenance of these molecules. We have employed a simple procedure which enables us to isolate from exponentially grown cells on sucrose gradients membrane-complexed forms of R6K plasmid DNA. Electron micrographs identified the complexing of membrane fractions to circular forms of R6K DNA. Biochemical studies of the complexed R6K molecules showed the presence of membrane-specific proteins and suggested that complexing of R6K DNA was primarily with inner membrane fractions of Escherichia coli.

Bacterial Proteins↗