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Biomedical subjects

R A Horowitz

Publications and source records attributed to R A Horowitz.

14 recordsLinked to original sources
PubMed1998

Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin.

The compaction level of arrays of nucleosomes may be understood in terms of the balance between the self-repulsion of DNA (principally linker DNA) and countering factors including the ionic strength and composition of the medium, the highly basic N termini of the core histones, and linker histones. However, the structural principles that come into play during the transition from a loose chain of nucleosomes to a compact 30-nm chromatin fiber have been difficult to establish, and the arrangement of nucleosomes and linker DNA in condensed chromatin fibers has never been fully resolved. Based on images of the solution conformation of native chromatin and fully defined chromatin arrays obtained by electron cryomicroscopy, we report a linker histone-dependent architectural motif beyond the level of the nucleosome core particle that takes the form of a stem-like organization of the entering and exiting linker DNA segments. DNA completes approximately 1.7 turns on the histone octamer in the presence and absence of linker histone. When linker histone is present, the two linker DNA segments become juxtaposed approximately 8 nm from the nucleosome center and remain apposed for 3-5 nm before diverging. We propose that this stem motif directs the arrangement of nucleosomes and linker DNA within the chromatin fiber, establishing a unique three-dimensional zigzag folding pattern that is conserved during compaction. Such an arrangement with peripherally arranged nucleosomes and internal linker DNA segments is fully consistent with observations in intact nuclei and also allows dramatic changes in compaction level to occur without a concomitant change in topology.

Animals↗
PubMed1998

Evaluation of a surgical debridement bur for use in periodontal surgery.

The Evian Debridement Bur facilitates two fundamental techniques in periodontal surgery--soft-tissue debridement and root planing. The bur debrides granulation and other soft tissues attached to the root or bone and removes hard deposits from root surfaces. It can also be used as an adjunct while performing crown-lengthening procedures and endodontic surgery. The bur is made with blunted flutes and, if used with a relatively light touch, will not cut into the alveolus and will not damage the tooth surface. This article reviews the use and advantages of this bur and shows its effect on the root surface at the ultrastructural level.

Dental Instruments↗
PubMed1997

Automated electron microscope tomography of frozen-hydrated chromatin: the irregular three-dimensional zigzag architecture persists in compact, isolated fibers.

The potential of electron microscope tomography as a tool for obtaining three-dimensional (3D) information about large macromolecular assemblies is greatly extended by automation of data collection. With the implementation of automated control of tilting, focusing, and digital image recording described here, tilt series of frozen-hydrated specimens can be collected with the requisite low dose. Long chromatin fibers were prepared in 90 mM monovalent ions to maintain a fully compact conformation, and after vitrification were completely contained within the ice layer. Tilt series of this material were recorded at 5 degrees tilt increments between +60 degrees and -60 degrees, with a cumulative dose of approximately 35 e-/A2 for the series. This extremely low dose data was successfully aligned, then reconstructed by weighted backprojection. The underlying architecture of the fibers is an irregular 3D zigzag of interconnected nucleosomes, with the linker DNA between successive nucleosomes in a largely extended conformation. The visualization of this structural motif within long, frozen-hydrated chromatin fibers at relatively high salt extends our previous studies on small fragments at low ionic strength and is in agreement with the observation of this architecture in chromatin fibers in situ in sectioned nuclei.

Animals↗
PubMed1997

Electron microscopy of chromatin.

Electron microscopy, with its ability to image DNA and nucleosomes, can provide a key visual link in the understanding of chromatin conformation. We discuss applications of EM to current chromatin research with emphasis on strategies that eliminate many of the potential problems associated with conventional EM preparative techniques. Cryo-electron microscopy (cryo-EM) of isolated chromatin, whereby samples are imaged "in solution" in thin vitrified films, is considered in detail, with emphasis on the recovery of three-dimensional information and on its application to linker DNA conformation and to salt-induced compaction. Factors that currently limit the technique, and the prospects of overcoming them, are also considered.

Chromatin↗
PubMed1997

The use of osteotomes for sinus augmentation at the time of implant placement.

The placement of endosseous dental implants is often hampered by the loss of alveolar bone. In the posterior maxilla, the presence of the maxillary sinus and less-dense bone present additional obstacles to successful implant placement. Existing methods of subantral augmentation require extensive surgical manipulation, often including a second surgical site for harvesting autogenous bone. The development of surgical osteotomes has facilitated the placement of implants in areas of minimal alveolar bone height in the posterior maxilla. This article describes the osteotome technique for sinus augmentation at the time of implant placement and presents a short-term evaluation of 34 implants placed in 18 patients.

Alveolar Bone Loss↗
PubMed1995

Chromatin organization re-viewed.

The predominant view of chromatin structure is that the beaded chain of nucleosomes is folded into a symmetrical helical fibre. Recently, however, direct evidence from cryoelectron microscopy and other imaging techniques confirms a non-symmetrical organization, consistent with modelling based on the heterogeneity of linker DNA lengths. This mode of chromatin folding is more compatible with the range of functional states in the living nucleus.

Journal Article↗
PubMed1995

Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy.

Cryoelectron microscopy has been used to examine the three-dimensional (3-D) conformation of small oligonucleosomes from chicken erythrocyte nuclei after vitrification in solutions of differing ionic strength. From tilt pairs of micrographs, the 3-D location and orientation of the nucleosomal disks, and the paths of segments of exposed linker can be obtained. In "low-salt" conditions (5 mM NaCl, 1 mM EDTA, pH 7.5), the average trinucleosome assumes the shape of an equilateral triangle, with nucleosomes at the vertices, and a length of exposed linker DNA between consecutive nucleosomes equivalent to approximately 46 bp. The two linker DNA segments converge at the central nucleosome. Removal of histones H1 and H5 results in a much more variable trinucleosome morphology, and the two linker DNA segments usually join the central nucleosome at different locations. Trinucleosomes vitrified in 20 mM NaCl, 1 mM EDTA, (the salt concentration producing the maximal increase in sedimentation), reveal that compaction occurs by a reduction in the included angle made by the linker DNA segments at the central nucleosome, and does not involve a reduction in the distance between consecutive nucleosomes. Frequently, there is also a change in morphology at the linker entry-exit site. At 40 mM NaCl, there is no further change in trinucleosome morphology, but polynucleosomes are appreciably more compact. Nevertheless, the 3-D zig-zag conformation observed in polynucleosomes at low salt is retained at 40 mM NaCl, and individual nucleosome disks remain separated from each other. There is no evidence for the formation of solenoidal arrangements within polynucleosomes. Comparison of the solution conformation of individual oligonucleosomes with data from physical measurements on bulk chromatin samples suggests that the latter should be reinterpreted. The new data support the concept of an irregular zig-zag chromatin conformation in solution over a range of ionic strengths, in agreement with other in situ (McDowall, A.W., J.M. Smith, and J. Dubochet. 1986, EMBO (Eur. Mol. Biol. Organ.) J.5: 1395-1402; Horowitz, R.A., D.A. Agard, J.W. Sedat, and C.L. Woodcock, 1994. J. Cell Biol. 125:1-10), and in vitro conclusions (van Holde, K., and J. Zlatanova. 1995. J. Biol. Chem. 270:8373-8376). Cryoelectron microscopy also provides a way to determine the 3-D conformation of naturally occurring chromatins in which precise nucleosome positioning plays a role in transcriptional regulation.

Animals↗
PubMed1994

The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon.

The three dimensional (3D) structure of chromatin fibers in sections of nuclei has been determined using electron tomography. Low temperature embedding and nucleic acid-specific staining allowed individual nucleosomes to be clearly seen, and the tomographic data collection parameters provided a reconstruction resolution of 2.5 nm. Chromatin fibers have complex 3D trajectories, with smoothly bending regions interspersed with abrupt changes in direction, and U turns. Nucleosomes are located predominantly at the fiber periphery, and linker DNA tends to project toward the fiber interior. Within the fibers, a unifying structural motif is a two nucleosome-wide ribbon that is variably bent and twisted, and in which there is little face-to-face contact between nucleosomes. It is suggested that this asymmetric 3D zig-zag of nucleosomes and linker DNA represents a basic principle of chromatin folding that is determined by the properties of the nucleosome-linker unit. This concept of chromatin fiber architecture is contrasted with helical models in which specific nucleosome-nucleosome contacts play a major role in generating a symmetrical higher order structure. The transcriptional control implications of a more open and irregular chromatin structure are discussed.

Animals↗
PubMed1993

A chromatin folding model that incorporates linker variability generates fibers resembling the native structures.

The "30-nm" chromatin fibers, as observed in eukaryotic nuclei, are considered a discrete level in a hierarchy of DNA folding. At present, there is considerable debate as to how the nucleosomes and linker DNA are organized within chromatin fibers, and a number of models have been proposed, many of which are based on helical symmetry and imply specific contacts between nucleosomes. However, when observed in nuclei or after isolation, chromatin fibers show considerable structural irregularity. In the present study, chromatin folding is considered solely in terms of the known properties of the nucleosome-linker unit, taking into account the relative rotation between consecutive nucleosomes that results from the helical twist of DNA. Model building based on this premise, and with a constant length of linker DNA between consecutive nucleosomes, results in a family of fiber- and ribbon-like structures. When the linker length between nucleosomes is allowed to vary, as occurs in nature, fibers showing the types of irregularity observed in nuclei and in isolated chromatin are created. The potential application of the model in determining the three-dimensional organization of chromatin in which nucleosome positions are known is discussed.

Animals↗
PubMed1993

Transitions between in situ and isolated chromatin.

We show that the mechanism by which chromatin displaying higher-order structure is usually isolated from nuclei involves a transition to an extended nucleosomal arrangement. After being released from nuclei, chromatin must refold in order to produce the typical chromatin fibers observed in solution. For starfish sperm chromatin with a long nucleosome repeat (222 bp), isolated fibers are significantly wider than those in the nucleus, indicating that the refolding process does not regenerate the native higher-order structure. We also propose that for typical eukaryotic nuclei, the concept that the native state of the (inactive) bulk of the genome is a chromatin fiber with defined architecture be reconsidered.

Animals↗
PubMed1992

Alternative staining methods for Lowicryl sections.

A number of stains and stain combinations have been identified that, when used with the hydrophilic resin Lowicryl K11M, produce marked improvements over aqueous uranyl and lead salts (UA-Pb) in terms of low granularity, specificity, and range of components contrasted. Three test specimens, tobacco mosaic virus (TMV), starfish sperm, and cultured mouse fibroblasts, were used to evaluate stain characteristics. UA-Pb showed a preference for nuclei acids, which were stained specifically by osmium ammine-B at pH 1.5. A number of stain combinations in which UA was followed or preceded by salts containing barium, manganese, tungsten, molybdenum, and vanadium provided excellent staining of protein-containing components, each stain combination being unique in terms of the degree to which specific components were discriminated. These stains were particularly effective for visualizing internal components of the nucleus where a number of fibrillar and particulate structures not seen with UA-Pb were well contrasted.

Acrylic Resins↗
PubMed1991

Ultrastructure of chromatin. I. Negative staining of isolated fibers.

The ultrastructure of chromatin fibers isolated from erythrocyte nuclei of Necturus maculosus and contrasted with a number of negative stains is described. Long (greater than 1000 nm) fibers are prepared under ionic conditions that promote fiber integrity, fixed with glutaraldehyde and negatively stained with aurothioglucose, ammonium molybdate, methylamine tungstate, sodium phosphotungstate, uranyl acetate and a uranyl acetate-sodium phosphotungstate sequence. All stains yield images of '30 nm' chromatin fibers, but aurothioglucose gives the most consistent diameter measurements (33 nm, S.D. 3.5 nm), and provides the clearest images of individual nucleosomes. Regions of fiber showing structural order are seen with all stains. The most commonly observed is a regular pattern of oblique cross-striations consistent with the visualization of the 'top' or 'bottom' of a helical structure. There is a significant relationship between fiber diameter and the cross-striation angle, consistent with an extensible chromatin fiber. Examination of power spectra prepared from selected ordered regions confirms the visual impressions, and indicates a striation spacing ranging from 11 nm to 18 nm, and dependent on the stain type. Fibers allowed to unfold slightly in a buffer containing 50 mM monovalent ions show evidence of a two-stranded helix-like organization. These results are discussed in terms of current models for the structure of the chromatin fiber.

Animals↗
PubMed1990

Ultrastructural preservation of nuclei and chromatin: improvement with low-temperature methods.

The ultrastructure of chromatin has been examined in nuclei prepared by a variety of low-temperature methods. Embedding glutaraldehyde (GA)-fixed nuclei in Lowicryl K4M or K11M following dehydration by the progressive lowering of temperature (PLT) method, or in K11M following spray freezing and freeze substitution (FS), produces chromatin fibres that have, in situ, a diameter close to the in vivo state, and show internal structural details consistent with patterns of nucleosome packing previously observed only in preparations of isolated fibres. This is a temperature-dependent effect; fibres conventionally dehydrated and embedded in Lowicryl at 0 degrees C or in conventional epoxy resin at 60 degrees C have lower and less uniform diameters, and lack internal structural details. Of the techniques used, spray freezing followed by FS resulted in the most notable improvement over conventional methods. Inclusion of GA during FS of rapidly frozen, unfixed nuclei in methanol does not result in cross-linking of nuclear proteins. In acetone, however, cross-linking by GA occurs at -45 degrees C, or at lower temperatures if the water content of the acetone-based FS media is kept deliberately high. Substitution regimes employing GA alone or in combination with uranyl acetate and/or osmium tetroxide do not result in fibre morphologies comparable to either prefixed or unfixed nuclei substituted in additive-free substitution media. Whole fibroblasts show excellent preservation of nuclei and the nuclear/cytoplasmic interface after spray freezing followed by FS and low-temperature embedding.

Animals↗