Features Of Superstructure Research Articles

Influence of DNA superstructural features and histones aminoterminal domains on mononucleosome and dinucleosome positioning

Mononucleosome and dinucleosome positioning was studied in the complexes between two DNA fragments of different lengths, both containing a strongly curved sequence from Crithidia fasciculata kinetoplast, and histone octamers either normal or lacking aminoterminal domains. The results obtained by Exo III and DNase I selective digestion were: 1. (a) The first and most stable nucleosome, formed with both types of histone octamers, is positioned on the curved sequence, showing a multiple dyad axis translational positioning with the same rotational phasing. This result is in very good agreement with the theoretical prediction, obtained by adopting a method developed by us, based on the evaluation of DNA distortion energy from the nucleotide sequence. 2. (b) The second nucleosome has two main different positions. The first one, near the extremity of the DNA fragment opposite to the curved sequence, presents a higher frequency in the case of normal nucleosome, whereas an intermediate position appears populated with a higher frequency in the case of the ‘tailless’ nucleosome.

Influence of DNA superstructural features and histone amino-terminal domains on nucleosome positioning

Nucleosome positioning has been studied on a strongly curved 268 by DNA fragment from a Crithidia fasciculata kinetoplast, complexed with a histone octamer either normal or lacking amino-terminal domains. A very similar nucleosome multiple positioning, with the same rotational phasing, has been found, by Exo III mapping, in both cases. The experimental positioning is in fairly good agreement with that predicted using a theoretical method based on DNA distortion energy, derived from the nucleotide sequence. Taking into account that nucleosomes, without histone amino-terminal domains, lack thirty percent of electrostatic interactions, these results suggest a dominant role on nucleosome positioning of DNA distortion energy with respect to modifications in histone domains.

Superstructural features of the upstream regulatory regions of two pea rbcS genes and nucleosomes positioning: theoretical prediction and experimental evaluation

Nucleosome positioning on two 384 bp DNA fragments, obtained from the upstream regulatory region of two pea rbcS genes, relevant in photoregulated transcription, was predicted using our theoretical method, based on the evaluation of the sequence dependent DNA bending energy. The theoretical prediction was checked by experimental evaluation of nucleosome positions after in vitro reconstitution, by mapping Exonuclease III-resistant borders and by digesting monomeric sequences with various restriction enzymes. Both approaches satisfactorily confirmed the theoretical predictions, showing that the nucleotide sequence intrinsic bendability has a dominant role in nucleosome positioning.

Different flexibility of the upstream regulatory regions of two differently expressed pea rbcS genes studied by theoretical evaluation of DNA distortion energy and cyclization kinetics

Different superstructural features of the upstream regulatory regions of the two pea genes rbcS- 3A and rbcS- E9 have been derived using a theoretical method, developed in our laboratory a few years ago, which evaluates the DNA distortion energy from a matrix of the deviations of the 16 possible dinucleotides from the standard B conformation. The theoretical analysis, which predicts different flexibilities of the regulatory regions of the two genes, is in satisfactorily good agreement with experimental evaluations from gel electrophoretic mobility and cyclization kinetics, suggesting a possible model to explain the largely different transcription efficiencies of the two genes.

Different superstructural features of the complexes between spermine and the light responsive elements of the pea genes rbcS-3A and rbcS-3.6. Gel elect

Different superstructural features of the complexes between spermine and the light responsive elements of the pea genes rbcS-3A and rbcS-3.6. Gel elect

Different superstructural features of the complexes between spermine and the light responsive elements of the two pea genes rbcS-3A and rbcS-3.6. Gel electrophoresis and circular dichroism studies

Two light responsive elements (LREs), DNA sequences, 62 base pairs long, relevant to the light control during transcription of the pea genes rbcS-3A and rbcS-3.6, were synthesized and ligated to obtain multimers with defined superstructural features. Their gel electrophoretic mobilities were studied in the presence of the tetracation, spermine, since it was previously suggested, on the basis of theoretical analysis, that spermine can increase DNA bending and thus could be useful in revealing DNA superstructural features. In fact, the difference between the curvatures of the two LREs, derived from gel electrophoresis retardation ratios, increases in the presence of spermine. Circular dichroism spectra of the complexes between spermine and the two LREs, at different neutralization ratios, show that the polyamine is able to induce the formation of asymmetric arrangements of complexes of molecules. The chirality of these complexes appears dramatically different for the two LREs, suggesting that their different superstructural features give rise to different interactions with the polyamine.

Different superstructural features of the light responsive elements of the pea genes rbcS-3A and rbcS-3.6

Analyses of the DNA sequences, named Light Responsive Elements (LREs), relevant in the photoactivation of the two pea genes rbcS-3A and rbcS-3.6, encoding the same protein but differently expressed, have been carried out, taking advantage of two complementary methods: a theoretical analysis, based on conformational energy calculations, and an experimental evaluation of LREs curvature, derived from gel electrophoretic mobilities of multimers of the LREs and of oligonucleotides corresponding to the three boxes in which they can be dissected. Theoretical and experimental analyses show that the curvature or the rbcS-3A LRE is larger than that of rbcS-3.6 LRE, and seems to be correlated with rbcS-3A higher transcription efficiency.

A theoretical model of the sequence dependent superstructures of DNA

A theoretical model of the sequence dependent superstructures of DNA is proposed on the basis of conformational energy calculations. The model appears to contain the basic physical features for translating the deterministic fluctuations of DNA bases sequences in superstructure elements. The general superstructural features, found in many examples of DNA biologically significative tracts we have investigated, suggest that large scale dynamics, as firstly shown by Careri in the case of enzymes, could be of relevance also in the case of DNA.

Educational Reform and the Dependency Paradigm: some considerations from Botswana

In common with many other African countries, newly independent Botswana attempted to redress problems in its education sector through the reforming agency of a national education commission. Slightly more than a decade has passed since the National Commission on Education of 1976 carried out its work, and now is an appropriate time to consider its impact. In carrying out this assessment, particular attention will be given to the area of junior secondary education. Furthermore, at this level, some useful insights into the process of reform and its limitations may be gleaned by focusing attention on the area of science education. The analytical framework of the assessment will be that of dependency theory. Although criticism of the pure dependency paradigm (see, for example, Blomstrom & Hettne, 1984), has been widespread, particularly its application to the analysis of superstructural features, it will be argued here that the Botswana economy can be described by the dependency model. Within the sphere of education, which is part of the superstructure, local resistance and adaptation appeared at certain key points of conflict to mitigate a simple centre-periphery picture. A pure dependency model, in which there are only puppets but no autonomous actors, does not fit Botswana education. Significant local initiatives, some reactionary, some progressive, emerged to produce what has the semblance of an equitable education system. Nonetheless, when probing deeper, evidence of structural inequality is still found. The first part of the paper considers the origins of the commission in the political context of the time. Next, the philosophy of the commission is examined and located within that of international educational planning circles. Conflict between the commission and one of its key working groups regarding the direction of junior secondary education is noted, although it is clear that the parties held similar views concerning the senior secondary endpoint of the education system. This part of the paper covers what might be seen as the first phase of post-independence education, in which only the topmost positions of the Ministry of Education were in local hands. It is argued that to this time a strong dependency relationship existed at all levels of the education system. The second phase is that where localisation spread to lower levels of decision-making, and covers the period to the introduction of new wider-based syllabuses in 1986. It is argued that this led to a shift in 'ownership' of

Spectroscopy of the radiation emitted by channeled particles—a new method of study of crystals

Studies of the properties of the radiation occurring in channeling of relativistic electrons and positrons, carried out over the last eight years, have shown that it is possible to study a number of properties of single crystals on the basis of the features of the radiation spectrum and the location and width of the spectral lines. The greatest success in this area has been achieved in determination of the Debye temperature of crystals, more accurate determination of the crystal potential, and determination of the density of electrons near crystal strings and planes. As a consequence of the localization of relativistic electrons or positrons near certain atomic planes or strings, the radiation spectrum of the channeled particles, in contrast to diffraction methods, carries direct information on the crystal potential. The method permits study of the correlation of thermal vibrations of the atoms in the lattice, and also of some features of superstructures and complex crystals.

Short-range order phenomena in lead-based perovskites

The electron diffraction patterns of many monocrystalline and polycrystalline lead-based perovskites have common superstructure features consisting of weak {h+1/2,k+1/2,O} spots, together with rods of diffuse scattering in 〈110〉 reciprocal lattice directions. These superstructure phenomena are thought to be associated with the short-range ordering of lead-site vacancies to form microregions with an I-centred 2ao x 2ao x 2ao superlattice.

Experimental High Resolution Dark Field Electron Microscopy

High resolution dark field (DF) images of the superstructures of the pyrrhotite (Fe1-xS) and bornite-digenite (Cu5FeS4-Cu9S5) series can be related to structure. Further, they provide more detail than bright field (BF) images. The same objective aperture size and stigmater settings were used for DF as for BF imaging; symmetrical arrangements of diffracted beams in the objective aperture were used. Images that can be related to structure were obtained at the defocus value giving the greatest image contrast, thereby enabling proper defocusing without requiring extensive through-focus series.For the minerals of interest, diffraction patterns consist of many superstructure reflections and a few subcell reflections. BF images contain primarily features of the superstructure, presumably because the subcell reflections fall far from the axis of the objective lens and thus are affected by spherical and chromatic aberrations and beam divergence. Likewise, DF images formed with a similar arrangement of beams as that in BF contain only features of superstructure, but with reverse contrast to BF.

The Double Diffraction Model for LEED-Intensity Spectra of the Clean Pt(100) Surface

Abstract The intensity spectra of the superstructure diffraction spots of the clean platinum (100) surface are presented for normal or nearly normal incidence. Their gross features are interpreted in terms of multiple diffraction contributions. It is shown that most of the maxima in the spectra can be explained by double diffraction processes from an idealized pure hexagonal surface layer and quadratic bulk layers. Alternative models in which the surface layer exchanges already all occuring reciprocal lattice vectors would predict additional peaks which, however, do not arise. Therefore superstructure features of the surface layer are assumed to be of second order. Thus double dif­fraction involving only idealized hexagonal and quadratic structures seems to dominate the diffraction behaviour of clean Pt(100).