The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin

We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$ between the in and outgoing DNA strands. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the vertical distance $d$ has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded volume borderline or missing H1 histones which can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values

Unwrapping of DNA-protein complexes under external stretching

A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and the dynamics of the unwrapping process by computer simulation and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered, i.e. there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent to nucleosome. There is a clear winding number and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated to discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.Comment: 8 pages, 7 figure

DNA folding: structural and mechanical properties of the two-angle model for chromatin

We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N. Whitaker. 1993. PNAS 90:9021-9025) that describes the chromatin fiber geometry in terms of the entry-exit angle of the nucleosomal DNA and the rotational setting of the neighboring nucleosomes with respect to each other. We explore analytically the different structures that arise from this building principle, and demonstrate that the geometry with the highest density is close to the one found in native chromatin fibers under physiological conditions. On the basis of this model we calculate mechanical properties of the fiber under stretching. We obtain expressions for the stress-strain characteristics which show good agreement with the results of recent stretching experiments (Cui, Y., and C. Bustamante. 2000. PNAS 97:127-132) and computer simulations (Katritch, V., C. Bustamante, and W. K. Olson. 2000. J. Mol. Biol. 295:29-40), and which provide simple physical insights into correlations between the structural and elastic properties of chromatin.Comment: 23 pages, 6 figures, to be published in Biophys.

A Circular Dichroic Study of Cu (II) -Ribonuclease Complexes

The visible and ultraviolet circular dichroic (CD) spectra resulting from the interaction of ribonuclease with successive Cu(I1) ions have been recorded under a variety of conditions. At pH 7 in the presence of 0.16 M KC1 a broad, negative band was found in the visible region. This band increased in intensity and changed in shape as successive coppers were added. The circular dichroic spectra could be analyzed in terms of two kinds of binding sites: a single strong site with CD minimum at about 710 nm, and four weaker sites with CD minimum at about 600 nm. The binding constants observed are close to those obtained by more conventional means. Carboxymethylation of one histidine results in loss of one of the weaker sites. In 0.01 M salt, only the 600-nm band is seen. Binding at pH 9.6 differed in that saturation did not occur until about 33 sites had been filled. The presence of tetra coordination at this pH was indicated by the shift of the primary d-d transition down to 530 nm. Additional structure in the visible and near ultraviolet CD was now present in the form of a negative band at 355 nm and, for the first two Cu(II)‘s added, a positive one at 480 nm. Strong positive bands were observed at 251 and 305 nm for all pH values ≥7. These are tentatively ascribed to charge transfer complexes between Cu(I1) and the peptide backbone. The relationship of the Cu(II)-ribonuclease CD spectra to those of natural, copper-containing metalloproteins, both “blue” and “non-blue”, is discussed, with special emphasis on the oxyhemocyanins

The two-angle model and the phase diagram for Chromatin

We have studied the phase diagram for chromatin within the framework of the two-angle model. Rather than improving existing models with finer details our main focus of the work is getting mathematically rigorous results on the structure, especially on the excluded volume effects and the effects on the energy due to the long-range forces and their screening. Thus we present a phase diagram for the allowed conformations and the Coulomb energies

The role of psychosocial factors and treatment need in dental service use and oral health among adults in Norway

Objectives - This study aimed to explore whether population characteristics were associated with the use of dental services, individual's personal oral health practices, dental caries and oral health‐related impacts using the revised Andersen's behavioural model as the theoretical framework. Methods - This cross‐sectional study included participants from a Norwegian general population (N = 1840; 20‐79 years) included in the Tromstannen—Oral Health in Northern Norway (TOHNN) study. The variables included in the model were social structure (income, education, urbanization), sense of coherence (SOC), enabling resources (difficulties accessing the dentist, declined treatment, dental anxiety), treatment need, use of dental services, toothbrushing frequency, sugary soda drink consumption, decayed teeth and oral health‐related impacts (OHIP‐14). Structural equation modelling was used to test the direct and indirect effects within Andersen's behavioural model of access and health outcomes. Results - Andersen's behavioural model fit the data well and explained a large part of the variance in use of dental services (58%), oral health‐related impacts (48%) and, to a lesser extent, decayed teeth (12%). More social structures and a stronger SOC was associated with more enabling resources, which in turn, was associated with more use of dental services. Social structures were not directly associated with use of dental services or decayed teeth but were predictive of oral health‐related impacts. A stronger SOC was associated with more frequent toothbrushing, less soda drink consumptions, fewer decayed teeth and less oral health‐related impacts. Self‐perceived need did not predict dental attendance but was associated with decayed teeth. A less frequent use of dental services, less frequent toothbrushing and more frequent sugary soda drink consumption were associated with more decayed teeth. Decayed teeth were not associated with oral health‐related impacts. Conclusion - The findings suggests that, in addition to focusing on reducing socioeconomic inequalities in relation to oral health in the Norwegian population, it is also important to consider how people perceive their own resources (eg financial, psychological, social) as well as their access to dental care in order to support regular dental attendance and potentially, in turn, enhance oral health

Intrinsic Low Temperature Paramagnetism in B-DNA

We present experimental study of magnetization in $\lambda$-DNA in conjunction with structural measurements. The results show the surprising interplay between the molecular structures and their magnetic property. In the B-DNA state, $\lambda$-DNA exhibits paramagnetic behaviour below 20 K that is non-linear in applied magnetic field whereas in the A-DNA state, remains diamagnetic down to 2 K. We propose orbital paramagnetism as the origin of the observed phenomena and discuss its relation to the existence of long range coherent transport in B-DNA at low temperature.Comment: 5 pages, 4 figures, submitted to Physical Review Letters October 200

Organized condensation of worm-like chains

We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a wrapping state is transformed into a complex multi-leafed, rosette structure as the adhesion energy is reduced. The statistical mechanics of the "melting" of a rosette can be mapped into an exactly soluble one-dimensional many-body problem.Comment: 15 pages, 2 figures in a pdf fil

To what extent does smoking affect gingival bleeding response to supragingival plaque? Site‐specific analyses in a population‐based study

Background and objective - The aim of this study was to investigate the influence of smoking on the site‐specific association between bleeding on gingival probing and supragingival plaque and to assess whether this differs in different regions of the dentition. Methods - Data from a representative sample of 1911 adults (20‐79 years old) in Northern Norway were analyzed. Periodontal examinations consisted of full‐mouth recordings of periodontal probing depth (PD), bleeding on probing (BOP), and presence of supragingival plaque. Smoking status and background characteristics were self‐reported by questionnaire. The association between plaque and BOP was assessed in several three‐level (subject, tooth, and site) random intercept logistic regression models adjusted for PD, smoking status, socioeconomic factors, and body mass index. In a further model, it was assessed whether the association between supragingival plaque and BOP differed in different parts of the dentition. Results - For plaque‐free sites, bleeding tendency was lower in smokers, the odds ratio (OR) was 0.773 with a 95% confidence interval of 0.678‐0.881 as compared to non‐smokers (OR: 1; ref., P 2(4)= 32.043, P Conclusions - Smoking considerably attenuates the site‐specific association between plaque and BOP with a dose‐dependent effect. The effect of smoking did not differ across tooth types

Die quantitative Bestimmung des Paraffins in den hochsiedenden Destillaten des Rohpetroleums

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