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  • 1
    ISSN: 1573-4978
    Keywords: calorimetry ; chromatin-DNA ; fluorescence ; optical microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract New quantitative insights on the native high order chromatin-DNA structure existing within interphase nuclei are obtained by monitoring the effects of two common well-characterized fixatives, glutaraldehyde and ethanol/acetic acid mixture, at the level of the intranuclear DNA distribution and structures. Reproducible distinct levels of DNA fluorescence intensity and their intranuclear distribution are apparent in unfixed and fixed thymocytes by using DAPI and quantitative optical microscopy based on a charge coupled device. The fluorescent histograms correlated with the calorimetric thermograms on the very same thymocytes fixed and unfixed, establish an unequivocal baseline for the different levels of structural organization of the chromatin within the intact nucleus; namely their number, DNA packing ratio and fiber diameter. A systematic comparison among all the numerous models, being so far proposed for the quinternary and quaternary levels of DNA folding, to identifies the rope or ribbon-like and the chromonema as the ones that best fit with the in situ distribution.
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  • 2
    ISSN: 1573-4978
    Keywords: calf thymus chromatin ; chromatin high order structure ; fiber length ; X-ray small angle scattering
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This work investigates the structure of native calf thymus chromatin as a function of fiber length and isolation procedures by using X-ray small angle scattering technique. Two methods of chromatin isolation have been compared in order to better understand the differences reported by various authors in terms of chromatin high order structure. In addition to these experimental results the effects of shearing have also been studied. In order to explain the differences among these chromatin preparations we built several models of chromatin fibers (represented as a chain of spherical subunits) assuming increasing level of condensation at increasing salt concentrations. For all these fiber models the corresponding theoretical X-ray scattering curves have been calculated and these results have been used to explain the influence of fiber length on the scattering profiles of chromatin. The comparison between experimental and theoretical curves confirms that the high molecular weight chromatin-DNA prepared by hypotonic swelling of nuclei (without enzymatic digestion) displays a partially folded structure even at low ionic strength, whereas the low molecular weight chromatin-DNA prepared by a brief nuclease digestion appears very weakly folded at the same ionic conditions.
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  • 3
    ISSN: 1573-4978
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Modifications of the higher-order chromatin structure induced by polyamines have been quantitatively investigated in situ through a non-invasive biophysical approach using Differential Scanning Calorimetry and Quantitative Fluorescence Microscopy. Calorimetric and intensitometric profiles have been acquired for samples of native thymocytes, alternatively suspended in buffers, with or without natural polyamines (spermine and spermidine). The results here reported show that the structure and distribution of nuclear chromatin in situ considerably change upon the ionic composition of the environment. A quantitative analysis of this data and a comparison with previous results obtained from isolated chromatin fibers was carried out. Finally, an inverse relationship between chromatin condensation and nuclear volume was observed.
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  • 4
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 86 (1975), S. 71-81 
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: When resting confluent monolayers of WI-38 fibroblasts are trypsinized and replated at a lower density they are stimulated to proliferate again with an interval of 18 hours between replating and the onset of DNA synthesis. Trypsinization of resting cells causes a 40% loss of nuclear proteins as well as of cytoplasmic proteins. The amount of nuclear proteins remains low for the first six hours after the cells have been replated and then it increases rapidly, reaching the same level of non-trypsinized resting cells by ten hours after plating. The proteins that are lost from the nucleus immediately after trypsinization are chromatin-associated proteins and most of them are non-histone chromosomal proteins, although a modest loss of histones cannot be ruled out. The loss of non-histone chromosomal proteins from cells that have been trypsinized causes changes in the structure of chromatin that can be detected by circular dichroism and by viscosity measurements. These results show that cell trypsinization causes an extensive loss of proteins from chromatin and that the loss is restored only several hours after the cells have been replated at a lower density.
    Additional Material: 3 Ill.
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  • 7
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two-dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.
    Additional Material: 10 Ill.
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  • 8
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: A method for preparing samples suitable for calibrating scanning probe microscopes (SPM) and for eliminating any distortions in images is described. Samples consist of polystyrene particles organized in monolayers and bilayers with hexagonal-ordered domains. The monolayer is not uniform, but is characterized by areas without particles. These discontinuities allow the measurement of the thickness of the monolayer in order to calibrate the z axes, while the lattice constant of the domains can be used as a calibration standard for the x and y axes. The nondeformability of the particles after the deposition on the substrate has been studied by an optical microscope, equipped for interferometric measurements, scanning force microscopy, and scanning tunneling microscopy. The use of these standards directly as substrates for samples is proposed to correct the distortions in the SPM images. © 1996 American Institute of Physics.
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  • 9
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: An analysis of two-dimensional fast Fourier transform from images of periodical lattices (like highly oriented pyrolytic graphite) has been performed to understand and decouple the various parameters which account for distorted images in stylus microscopy. The effects of the various sources of image distortion have been described by means of linear maps and a mathematical approach has been developed to find the various correction coefficients resulting from the Fourier space analysis which restore the correct geometry of the images. Furthermore, the trend analysis of the distortion angle upon the scanning frequency shows the possibility of decoupling the role of "static'' and "time dependent'' distortion parameters. This possibility may be used for an a priori prediction of possible distortions in stylus microscopy and thus for a real-time correction of the images during scanning.
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  • 10
    ISSN: 0730-2312
    Keywords: histone acetylation ; chromatin structure ; circular dichroism ; ethidium bromide intercalation ; differential scanning calorimetry ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: The effect of histone acetylation was monitored on CHO chromatin structure, following the addition of 7 mM Na-butyrate to the cell culture medium. The properties of both control and hyperacetylated chromatins and nuclei were investigated by circular dichroism, ethidium bromide intercalation, differential scanning calorimetry, and affinity chromatography. Our results are compatible with modest but significant alterations in the various levels of chromatin organization, as a result of the charge neutralization of some lysine residues within the N-terminal region of the histonic octamer. Namely, large statistically significant differences do exist in the heat capacity thermograms of native nuclei, where unfolding into single nucleofilament of the highly packed native chromatin superfiber appears associated with acetylation; at the same time CD, EB, and affinity chromatography point to modest but consistent differences in the compactness of isolated nucleosomes and polynucleosomes. J. Cell. Biochem. 64:466-475. © 1997 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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