Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Negative Staining”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources
PubMed1997

Metal cations defibrillize the amyloid beta-protein fibrils.

Amyloid beta-protein (A beta) is the major constituent of amyloid fibrils composing beta-amyloid plaques and cerebrovascular amyloid in Alzheimer's disease (AD). We studied the effect of metal cations on preformed fibrils of synthetic A beta by Thioflavin T (ThT) fluorescence spectroscopy and electronmicroscopy (EM) in negative staining. The amount of cross beta-pleated sheet structure of A beta 1-40 fibrils was found to decrease by metal cations in a concentration-dependent manner as measured by ThT fluorescence spectroscopy. The order of defibrillization of A beta 1-40 fibrils by metal cations was: Ca2+ and Zn2+ (IC50 = 100 microM) > Mg3+ (IC50 = 300 microM) > Al3+ (IC50 = 1.1 mM). EM analysis in negative staining showed that A beta 1-40 fibrils in the absence of cations were organized in a fine network with a little or no amorphous material. The addition of Ca2+, Mg2+, and Zn2+ to preformed A beta 1-40 fibrils defibrillized the fibrils or converted them into short rods or to amorphous material. Al3+ was less effective, and reduced the fibril network by about 80% of that in the absence of any metal cation. Studies with A beta 1-42 showed that this peptide forms more dense network of fibrils as compared to A beta 1-40. Both ThT fluorescence spectroscopy and EM showed that similar to A beta 1-40, A beta 1-42 fibrils are also defibrillized in the presence of millimolar concentrations of Ca2+. These studies suggest that metal cations can defibrillize the fibrils of synthetic A beta.

Alzheimer Disease↗
PubMed1995

Visualization of TBP oligomers binding and bending the HIV-1 and adeno promoters.

The binding of the 28 kDa yeast TATA binding protein (yTBP) to the HIV and adeno major late promoters has been examined by electron microscopy (EM). Three different EM preparative methods were employed: direct mounting and shadowcasting of fixed samples, cryofixation and freeze-drying followed by shadowcasting, and negative staining of unfixed samples. Excellent agreement among the three methods was obtained. With ten yTBP monomers/DNA fragment, up to 25% of the DNA molecules contained easily distinguished protein particles at the TATA box and, less frequently, smaller particles were observed. Non-specific binding to DNA ends was common. The mass of the easily distinguished particles measured 63(+/- 5) kDa (cryofixation and shadowcasting) and 48(+/- 6) kDa (negative staining) indicating TBP dimerization. With 22 and 44 yTBP monomers/DNA, yTBP polymerization produced DNA-protein rods 9 nm wide and 20 to 30 nm long, frequently with two DNA strands exiting one end. Bending analysis revealed that yTBP dimers bend the DNA about the TATA box by 80 to 90 degrees. Although these protein ratios are relatively high, the structures formed demonstrate the propensity of yTBP to engage in protein-protein interactions.

Adenoviridae↗
PubMed1983

Frog skeletal muscle thick filaments are three-stranded.

A procedure has been developed for isolating and negatively staining vertebrate skeletal muscle thick filaments that preserves the arrangement of the myosin crossbridges. Electron micrographs of these filaments showed a clear periodicity associated with crossbridges with an axial repeat of 42.9 nm. Optical diffraction patterns of these images showed clear layer lines and were qualitatively similar to published x-ray diffraction patterns, except that the 1/14.3-nm meridional reflection was somewhat weaker. Computer image analysis of negatively stained images of these filaments has enabled the number of strands to be established unequivocally. Both reconstructed images from layer line data and analysis of the phases of the inner maxima of the first layer line are consistent only with a three-stranded structure and cannot be reconciled with either two- or four-stranded models.

Animals↗
PubMed1983

Morphology of cells and hemagglutinogens of Bordetella species: resolution of substructural units in fimbriae of Bordetella pertussis.

The morphology of cells and the hemagglutinogens isolated from cultures of Bordetella pertussis, Bordetella bronchiseptica, and Bordetella parapertussis were studied by electron microscopy with the negative-staining technique. Cells of all three species had long, thin (3 nm thick), peritrichously arranged fimbriae on the cell surface. Similar structures were found in purified hemagglutinogen preparations together with shorter fimbrial structures 3 nm thick and from 40 to 100 nm long. In one experiment, long, thin fimbriae isolated from B. pertussis were found to be arranged in a crystalline structure on the specimen grid after negative staining. Optical diffraction analysis with a filtering technique performed on micrographs of these structures revealed 12.5-nm-long substructures within individual fimbriae. Further analysis resolved each of these structures into three globules, a central globule 3.5 nm in diameter and two diametrically opposed globules 2.5 nm in diameter. Based on this substructural composition, it is suggested that subunits of the individual fimbriae are connected by fragile regions. The presence of such regions would explain the size heterogeneity of the filamentous structures observed in preparations of hemagglutinogens isolated from cultures of B. pertussis and B. bronchiseptica. The concept that the short filamentous structures present in purified preparations of hemagglutinogens originate from the surface fimbriae present on the cells is supported.

Bacterial Toxins↗
PubMed1992

Effects of surfactant apolipoproteins on liposome structure: implications for tubular myelin formation.

Tubular myelin is one of several forms of lung surfactant and may play an important role in its surface activity. To determine possible mechanisms of tubular myelin formation, we studied the effects of purified surfactant proteins (SP-A, SP-B, and SP-C) on large unilamellar dipalmitoylphosphatidylcholine-egg phosphatidylglycerol (7/3; wt/wt) liposomes. We studied different types of membrane interaction induced by the apolipoproteins and correlated these with the observed changes in ultrastructure. Aggregation was assessed by measurement of light absorbance, lysis, and fusion by measurement of the fluorescence emitted by water-soluble and lipid-soluble probes, respectively. Mixtures of the apolipoproteins and liposomes were examined in ultrastructural studies by negative staining and by thin sectioning. We found that each protein had a pronounced and distinct effect on liposome structure. SP-A caused aggregation, whereas SP-B and SP-C also caused extensive leakage of liposome contents (lysis) and some degree of lipid mixing (fusion). The disruptive effects of SP-B and to a lesser extent those of SP-C were correlated by negative staining with the appearance of bilayer disks, which tended to aggregate into large sheets. There was a marked synergy between SP-A and SP-B in the process of membrane fusion in the presence of calcium, which correlated with an early (10 min) and extensive rearrangement of the structures seen by electron microscopy followed by a delayed (24 h) appearance of small amounts of tubular myelin.

Animals↗
PubMed1991

Two-dimensional and epitaxial crystallization of a mutant form of yeast RNA polymerase II.

A mutant form of yeast RNA polymerase II that lacks the fourth and seventh largest subunits, referred to as pol II delta 4/7, crystallized on positively charged lipid layers. Both single-layered (two-dimensional) crystals and several multi-layered crystal forms were obtained. The two-dimensional crystals, preserved in negative stain, diffracted strongly to about 1/20 A-1 and more weakly to 1/13 A-1 resolution. A projection map computed from averaged Fourier transforms revealed four pol II delta 4/7 complexes per unit cell and further revealed a cleft on the surface of the complex similar to that previously observed in the structure of Escherichia coli RNA polymerase. One of the multi-layered crystal forms, preserved in negative stain, diffracted strongly beyond 1/15 A-1 resolution. Coherent diffraction from the multi-layered crystal is indicative of protein-protein interactions between layers and ordering in the third dimension.

Crystallization↗
PubMed2004

Detection of glutathione reductase after electrophoresis on native or sodium dodecyl sulfate polyacrylamide gels.

Commercial glutathione reductase (GR) from spinach and yeast (Saccharomyces cerevisiae) were stained on 7.5% native polyacrylamide gel electrophoresis (PAGE) gels or 15% sodium dodecyl sulfate (SDS)-PAGE gels with or without further purification by a 2',5'-ADP Sepharose 4B affinity column. For SDS-PAGE gels, the SDS was removed first by washing twice with 25% isopropanol in 10 mM Tris-HCl (pH 7.9) for 10 min. The gel was then dipped in a 50 mM Tris-HCl buffer (pH 7.9) containing 4.0 mM oxidized glutathione (GSSG), 1.5 mM NADPH, and 2 mM 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) for 20 min. The GR activity was negatively stained in the dark by a solution containing 1.2 mM 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and 1.6 mM phenazine methosulfate (PMS) for 5-10 min. The contrast between the clear zone of GR activity and the purple background was found in both native and SDS-PAGE gels. This negative staining method can detect GR as little as 0.064 units and 0.0032 units, respectively, for spinach and yeast sources. Under reduced SDS-PAGE gels, the GR activity band located on 72 kDa for spinach and 51 kDa for yeast. This fast and sensitive method could be used during enzyme purification and for characterization of GR from different sources under different physiological stages or conditions.

Chromatography, Affinity↗
PubMed1970

Quantitation, chemical characteristics, and ultrastructure of the three outer cell wall layers of a gram-negative bacterium.

The cell wall of the gram-negative marine pseudomonad (American Type Culture Collection 19855) consists of three layers: the loosely bound outer layer, the outer double-track layer, and the underlying layer. These three layers constitute 4.7, 7.9, and 6.1%, respectively, of the dry weight of the whole cells. All three layers contained protein, lipid, and carbohydrate. The loosely bound outer layer and underlying layer were lower in protein and lipid and higher in amino and nonamino carbohydrate than the outer double-track layer. All three layers contained proteins with similar amino acid compositions. Minicell-like forms attached to the ends of cells were separated with and fractionated from the units of loosely bound outer layer. Examination of negatively stained preparations by electron microscopy revealed the loosely bound outer layer to be composed largely of units ranging from 400 to 1000 nm in diameter. The outer double-track layer, by the same technique, appeared as large, usually rounded sheets, each with a distinct rim. Washing this layer changed the gross chemical composition but did not affect the bimolecular leaflet appearance in thin sections. The underlying layer, when negatively stained, appeared to be composed of a heterogeneous mixture of particles differing in size and shape. It was separated by gel filtration into a large fraction with a molecular weight range in excess of 20 x 10(6) to 40 x 10(6) and a small fraction with a lower range of molecular weight. The larger fraction contained both protein and hexosamine, whereas the smaller one contained protein and only traces of hexosamine. A cytochrome-like pigment separated with this latter fraction.

Journal Article↗
PubMed1989

The Sendai virus nucleocapsid exists in at least four different helical states.

Sendai virus nucleocapsids have been observed by electron microscopy to coexist in three different helical pitch conformations, 5.3, 6.8, and 37.5 nm. The 5.3- and 6.8-nm conformations are present both in uranyl acetate negatively stained preparations and in tantalum-tungsten metal-shadowed preparations, whereas the 37.5-nm conformation, which has not been previously reported, is present only in the shadowed preparations. The 5.3-nm pitch conformation appears to be a mixture of two discrete structural states, with a small difference in the twist of the structure between the two. We have used image reconstruction techniques on an averaged data set from eight negatively stained nucleocapsids to produce a three-dimensional reconstruction at 2.4-nm resolution of the structure in one of the 5.3-nm pitch states. There are 13.07 nucleocapsid protein (NP) subunits in each turn of the helix in this state. The helical repeat is 79.5 nm, containing 196 subunits in 15 turns of the left-handed 5.3-nm helix. The arrangement of subunits produces a 5.0-nm-diameter hollow core which forms an internal helical groove. The RNA accounts for about 3% of the mass of the nucleocapsid, and so its location is not conspicuous in the reconstruction. Because of the RNA remains associated with the NP subunits during mRNA transcription and genome replication, structural transitions in the nucleocapsid may determine the accessibility of the genome to polymerases. Alternatively, the large hollow core and internal helical groove we have reconstructed may allow access to the RNA even in the tightly coiled 5.3-nm pitch conformation.

Capsid↗
PubMed1979

Comparison of the ultrastructure of adrenaline and noradrenaline storage granules of bovine adrenal medulla.

The ultrastructure of the membranes of noradrenaline (NA) and adrenaline (A) granules of the bovine adrenal medulla (Terland, O., T. Flatmark, and H. Kryvi, Biochim, Biophys. Acta 553, 460--468 (1979)) was analyzed by transmission, negative staining and freeze-etch electron microscopy. The two types of storage granules can be distinguished mainly by two morphological criteria: (a) The NA-granules have a more electron dense matrix core than the A-granules, (b) the NA-granules revealed less asymmetry in the distribution of intramembrane particles (nPF:nEF = 4,5:1) than the A-granules (nPF:nEF = 9:1). Thus, the trilaminar structure, negative staining pattern and size distribution of the intramembrane particles of the two fracture faces on freeze-etch electron microscopy were very similar for the two types of granules. Freeze-etching revealed a wide range of the particle size distribution for both fracture faces in both types of granules, with an average diameter of 12.6 +/- 2.7 nm (A-granules) and 10.2 +/- 2.8 nm (NA-granules) for the E-fracture faces and 11.4 +/- 2.7 nm (A-granules) and 9.8 +/- 2.4 nm (NA-granules) for the P-fracture faces. Some of the particles on the P-fracture face (outer surface of the membrane) revealed a subunit structure, most clearly seen in the specimens of NA-granules. Morhpometric analyses of sectioned bovine adrenal medulla revealed that the chromaffin granules on an average account for approx. 13.5% of the cytoplasmic volume in the total population of chromaffin cells.

Adrenal Medulla↗
PubMed1984

Filipin as a cholesterol probe. II. Filipin-cholesterol interaction in red blood cell membranes.

Filipin, a mixture of polyene antibiotics which form complexes with cholesterol, perturbs membrane lipid organization, and causes hemolysis of erythrocytes, is increasingly used as a cytochemical probe for the distribution of cholesterol in cell membranes. We used light (phase-contrast, dark-field and fluorescence) and electron microscopical techniques (whole-mount shadowing, negative staining, and freeze-fracture) to study the interaction of filipin with unfixed and glutaraldehyde-fixed human red blood cell (RBC) membranes. Lysis time and extent depended upon the cholesterol:filipin (C:F) ratio. Lysis was prevented by osmotic protection with high MW dextran. Filipin treated cells fluoresced, but variation in fluorescence intensity among unfixed as well as among fixed cells was evident both at low and high C:F ratios. Negatively stained preparations of unfixed cells lysed on grids or in suspension revealed ring- or C-shaped filipin-induced lesions (FIL) equipped with a veil-like appendage; single FIL, and FIL fused by their veils into aggregates, were shed from membranes. FIL at the surface proper of shadowed whole-mounts and of freeze-etched preparations of prefixed cells appeared as single, dispersed or aggregated cylinders protruding to variable heights above the membrane's plane; aggregated FIL were shed from cells. The freeze-fracture appearance of FIL differed in membranes fixed before or after filipin treatment. E- and P-faces of post-fixed membranes exhibited cylindrical protrusions and depressions, respectively; in essence, the reverse was found in pre-fixed RBC. Both pre- and post-fixed membranes showed considerable variation in the number of FIL on individual cells whether incubated at high (1:1) or low (1:5) C:F ratios, or for a short (10 min) or a long (80-180 min) time. Aggregation and shedding of FIL was evident in all preparations. Thin layer chromatography of the incubation fluid after sedimentation of cells showed that membrane cholesterol was shed from incubated cells. The presented data question the feasibility of filipin as a probe for the topographical distribution of cholesterol in cell membranes.

Cholesterol↗
PubMed1978

Morphology of freeze-etched Treponema refringens (Nichols).

The freeze-etch technique was used to study the morphology of Treponema refringens (Nichols). There is a single band of cytoplasmic fibrils which follows a path in the form of a right-handed helix with a periodicity of 1500 nm around the body of the treponeme just below the cytoplasmic membrane. There are two major fracture planes, one located in the interior of the outer envelope and the second in the interior of the cytoplasmic membrane. The "blebs" or "surface protuberances", which are quite prominent in negative-stained preparations, were not evident with freeze-etch preparation, indicating they are not a part of the normal structure of this organism. The outer envelope in untreated cells was observed to closely fit the body of the treponeme, whereas the outer envelope of glutaraldehyde-treated cells had a loose, wrinkled appearance. Thus the "loose-fitting" outer envelope generally described for treponemes is most likely an artifact of preparation for negative-staining and thin-sectioning.

Cell Membrane↗
PubMed1976

Coated-vesicle shells, particle/chain material, and tubulin in brain synaptosomes. An electron microscope and biochemical study.

Coated vesicles (CVs), plain synaptic vesicles (PSVs), and nonvesicular flocculent material were isolated from synaptosomes and examined with goniometry and high-resolution electron microscopy after either negative staining or various biochemical procedures. The flocculent material (i.e. the presynaptic matrix material except CV shells) is largely composed of particulate or elongated (chainlike) structures; some of this material (here referred to as particle/chain material) is attached to PSVs. The results obtained were: (a) the proteinaceous properties of the CV coat (also referred to as CV shell) and the particle/chain material were demonstrated with chymotrypsin; (b) the CV shell, studied with various negative-staining techniques, differs from the particle/chain material since it has no 3-4-nm globular subunits and reacts differently to alkaline pH; (c) the particle/chain material consists of aggregates of 3-4-nm globular subunits, four of which yield 8-10-nm fine particles; and these particles can be further aggregated into chains 8-10 nm wide and up to 30-60 nm long showing a "hollow" core; (d) vinblastine sulfate induced ringlike or helical crystalloid precipitates closely resembling the vinblastine-induced microtubule crystals reported in the literature, but vinblastine had no effect on either the CV shell material or the particle/chain material.

Animals↗
PubMed1994

Three-dimensional model of Escherichia coli gyrase B subunit crystallized in two-dimensions on novobiocin-linked phospholipid films.

Two-dimensional crystals of the Escherichia coli DNA gyrase B subunit were obtained upon specific interactions with novobiocin linked phospholipid films. A three-dimensional surface model of the protein was generated by analysing images of tilted negatively stained crystals. The structure showed, at 2.5 to 3.0 nm resolution, two elongated arms organised as a V-shaped protein: the bottom of the V contains the novobiocin binding site, and the extremities of the arms mediate protein-protein interactions between the two monomers in the unit cell. Image analysis of frozen hydrated two-dimensional crystals resulted in a 1.0 nm resolution projection map that shows structural elements not revealed with negative staining. Electron microscopic structural data were compared with the crystallographic structure of the 43 kDa N-terminal fragment of the B subunit complexed with a non hydrolysable ATP analogue.

Binding Sites↗
PubMed1981

Periodic surface array in Caulobacter crescentus: fine structure and chemical analysis.

A periodic array structure on the cell surface of Caulobacter crescentus CB15 was revealed by electron microscopy of the cell envelope, using negative staining, thin-sectioning, and freeze-etching. This structural layer has been isolated from liquid cultures, in which large pieces of the two-dimensional array are shed by cells grown to high density. Often areas of intact array corresponding to the entire cell surface could be found. The hexagonally arranged structure was highly ordered and had an unusual degree of complexity, as determined by optical diffraction and computer processing of micrographs of negatively stained, isolated surface array. Filtered, reconstructed images were obtained from both normal and low-electron-dose micrographs demonstrating resolutions of 2.9 and 25 nm, respectively. Comparison by optical diffraction and image filtering of micrographs recorded by using either normal or minimal beam exposure techniques suggested that the lower-resolution features of the image are very stable to electron exposure. Gel electrophoresis indicated that isolated array preparations contain a number of polypeptides. It appears likely that more than one of these proteins are structural components of the array, in contrast to a single protein found in many bacterial surface arrays. The Caulobacter surface array is also unusual in that the repeated units are widely spaced with no apparent direct connection. Computer spatial averaging provided information about the shape and complexity of the connecting elements, and this was compared with some additional electron microscopic evidence of linking structures. Thin-sectioning studies confirmed the image features seen by other techniques, but the addition of tannic acid in the fixation procedure was required to visualize the structure. A comparison of these results with out current knowledge of the Caulobacter cell envelope suggests interesting questions about the biogenesis of this membrane structure and its involvement in the cell development process of this organism.

Bacteria↗
PubMed1976

The crystalline glycoprotein cell wall of the green alga Chlorogonium elongatum: a structural analysis.

Members of the Chlamydomonaceae, mostly single-celled green algae, have been shown to contain a crystalline glycoprotein cell wall component. Most of the species examined fall into a class of algae whose walls have an identical crystalline unit cell. Chlorogonium elongatum has been chosen as a representative of this class in order to investigate in more detail its cell wall structure. The alga has a spindleshaped cell wall which retains its asymmetric shape on isolation. Sections from walls fized in the presence of tannic acid clearly reveal a regular subunit monolayer, about 20 nm thick, within the wall. Sodium dodecylsulphate (SDS) polyacrylamide gel electrophoresis shows the presence of at least 2 major glycoprotein species in the wall. Negatively stained purified cell walls demonstrate the crystalline nature of the cell wall. Optical diffraction of bright-field images and direct electron diffraction both give clear diffraction patterns whose spacings extend out to 3 nm and fall on a reciprocal lattice whose vectors describe a 2-dimensional unit cell within the wall 21.5 nm X 7.0 nm and an included angle of 80 degrees. Lattice defects within the cell wall are revealed by both negative staining and surface replication. Through-focal series were used to choose images with the optimal degree of underfocus for image processing. Linear integration and optical filtering of such images gave essentially the same result. A similar image was also obtained by computing the autocorrelation function of the amplitudes in the electron-diffraction pattern and the optical-diffraction pattern of the in-focus image. On the basis of these data a 2-dimensional model of the crystalline cell wall layer is presented.

Cell Wall↗
PubMed1986

Three-dimensional reconstruction of the connector of bacteriophage phi 29 at 1.8 nm resolution.

The three-dimensional reconstruction of the connector of bacteriophage phi 29 has been obtained from tilt series of negatively stained tetragonal ordered aggregates under low-dose conditions and up to a resolution of (1/1.8) nm-1. These connectors are built up as dodecamers of only one structural polypeptide (p10). Two connectors form the crystal unit cell, each one facing in the opposite direction with respect to the plane of the crystal and partially overlapping. The main features of the two connectors that build the unit cell were essentially the same, although they were negatively stained in slightly different ways, probably due to their situations with respect to the carbon-coated support grid. The main features of the phi 29 connector structure revealed by this three-dimensional reconstruction are: the existence of two clearly defined domains, one with a diameter of around 14 nm and the other narrower (diameter approximately equal to 7.5 nm); an inner hole running all along the structure (around 7 to 8 nm in height) with a cylindrical profile and an average diameter of 4 nm; a general 6-fold symmetry along the whole structure and a 12-fold one in the wider domain; a clockwise twist of the more contrasted regions of both domains from the narrower towards the wider domain (the direction of DNA encapsidation). These features are compatible with an active role for the connector in the process of DNA packaging.

Bacteriophages↗
PubMed1999

The Treponema denticola major sheath protein is predominantly periplasmic and has only limited surface exposure.

The recent discovery that the Treponema pallidum genome encodes 12 orthologs of the Treponema denticola major sheath protein (Msp) prompted us to reexamine the cellular location and topology of the T. denticola polypeptide. Experiments initially were conducted to ascertain whether Msp forms an array on or within the T. denticola outer membrane. Transmission electron microscopy (EM) of negatively stained and ultrathin-sectioned organisms failed to identify a typical surface layer, whereas freeze-fracture EM revealed that the T. denticola outer membrane contains heterogeneous transmembrane proteins but no array. In contrast, a lattice-like structure was observed in vesicles released from mildly sonicated treponemes; combined EM and biochemical analyses demonstrated that this structure was the peptidoglycan sacculus. Immunoelectron microscopy (IEM) subsequently was performed to localize Msp in T. denticola. Examination of negatively stained whole mounts identified substantial amounts of Msp in sonicated organisms. IEM of ultrathin-sectioned, intact treponemes also demonstrated that the preponderance of antigen was unassociated with the outer membrane. Lastly, immunofluorescence analysis of treponemes embedded in agarose gel microdroplets revealed that only minor portions of Msp are surface exposed. Taken as a whole, our findings challenge the widely held belief that Msp forms an array within the T. denticola outer membrane and demonstrate, instead, that it is predominantly periplasmic with only limited surface exposure. These findings also have implications for our evolving understanding of the contribution(s) of Msp/Tpr orthologs to treponemal physiology and disease pathogenesis.

Animals↗