Role of topological exclusion in formation and organization of chromosomal territories

Chromosomes of eukaryotic organisms are composed of chromatin loops. Using Monte Carlo simulations we investigate how the topological exclusion between loops belonging to different chromosomes affects chromosome behaviour. We show that in a confined space the topological exclusion limiting catenation between loops belonging to different chromosomes entropically drives the formation of chromosomal territories. The same topological exclusion in a connection with interchromosomal binding via transcription factories explains why actively transcribed genes are found preferentially at the peripheries of their chromosomal territories. This paper is based in part on the results presented in J. Dorier and A. Stasiak, Nucl. Acids Res. 37 (2009), 6316 and 38 (2010), 7410.

Quantum similarity topological indices definition, analysis and comparison with classical molecular topological indices

Es mostra que, gracies a una extensió en la definició dels Índexs Moleculars Topològics, s'arriba a la formulació d'índexs relacionats amb la teoria de la Semblança Molecular Quàntica. Es posa de manifest la connexió entre les dues metodologies: es revela que un marc de treball teòric sòlidament fonamentat sobre la teoria de la Mecànica Quàntica es pot connectar amb una de les tècniques més antigues relacionades amb els estudis de QSPR. Es mostren els resultats per a dos casos d'exemple d'aplicació d'ambdues metodologies

A topological invariant to predict the three-dimensional writhe of ideal configurations of knots and links.

We present herein a topological invariant of oriented alternating knots and links that predicts the three-dimensional (3D) writhe of the ideal geometrical configuration of the considered knot/link. The fact that we can correlate a geometrical property of a given configuration with a topological invariant supports the notion that the ideal configuration contains important information about knots and links. The importance of the concept of ideal configuration was already suggested by the good correlation between the 3D writhe of ideal knot configurations and the ensemble average of the 3D writhe of random configurations of the considered knots. The values of the new invariant are quantized: multiples of 4/7 for links with an odd number of components (including knots) and 2/7 plus multiples of 4/7 for links with an even number of components.

Topological comparison of methods for predicting transcriptional cooperativity in yeast

Background: The cooperative interaction between transcription factors has a decisive role in the control of the fate of the eukaryotic cell. Computational approaches for characterizing cooperative transcription factors in yeast, however, are based on different rationales and provide a low overlap between their results. Because the wealth of information contained in protein interaction networks and regulatory networks has proven highly effective in elucidating functional relationships between proteins, we compared different sets of cooperative transcription factor pairs (predicted by four different computational methods) within the frame of those networks. Results: Our results show that the overlap between the sets of cooperative transcription factors predicted by the different methods is low yet significant. Cooperative transcription factors predicted by all methods are closer and more clustered in the protein interaction network than expected by chance. On the other hand, members of a cooperative transcription factor pair neither seemed to regulate each other nor shared similar regulatory inputs, although they do regulate similar groups of target genes. Conclusion: Despite the different definitions of transcriptional cooperativity and the different computational approaches used to characterize cooperativity between transcription factors, the analysis of their roles in the framework of the protein interaction network and the regulatory network indicates a common denominator for the predictions under study. The knowledge of the shared topological properties of cooperative transcription factor pairs in both networks can be useful not only for designing better prediction methods but also for better understanding the complexities of transcriptional control in eukaryotes.

Topological locking restrains replication fork reversal.

Two-dimensional agarose gel electrophoresis, psoralen cross-linking, and electron microscopy were used to study the effects of positive supercoiling on fork reversal in isolated replication intermediates of bacterial DNA plasmids. The results obtained demonstrate that the formation of Holliday-like junctions at both forks of a replication bubble creates a topological constraint that prevents further regression of the forks. We propose that this topological locking of replication intermediates provides a biological safety mechanism that protects DNA molecules against extensive fork reversals.

Topological computation of local cohomology multiplicities.

We express the Lyubeznik numbers of the local ring of a complex isolated singularity in terms of Betti numbers of the associated real link.

Raman scattering and photoluminescence analysis of silicon on insulator structures obtained by single and multiple oxygen implants

An analysis of silicon on insulator structures obtained by single and multiple implants by means of Raman scattering and photoluminescence spectroscopy is reported. The Raman spectra obtained with different excitation powers and wavelengths indicate the presence of a tensile strain in the top silicon layer of the structures. The comparison between the spectra measured in both kinds of samples points out the existence in the multiple implant material of a lower strain for a penetration depth about 300 nm and a higher strain for higher penetration depths. These results have been correlated with transmission electron microscopy observations, which have allowed to associate the higher strain to the presence of SiO2 precipitates in the top silicon layer, close to the buried oxide. The found lower strain is in agreement with the better quality expected for this material, which is corroborated by the photoluminescence data.

Raman microstructural analysis of silicon-on-insulator formed by high dose oxygen ion implantation: As-implanted structures

A microstructural analysis of silicon-on-insulator samples obtained by high dose oxygen ion implantation was performed by Raman scattering. The samples analyzed were obtained under different conditions thus leading to different concentrations of defects in the top Si layer. The samples were implanted with the surface covered with SiO2 capping layers of different thicknesses. The spectra measured from the as-implanted samples were fitted to a correlation length model taking into account the possible presence of stress effects in the spectra. This allowed quantification of both disorder effects, which are determined by structural defects, and residual stress in the top Si layer before annealing. These data were correlated to the density of dislocations remaining in the layer after annealing. The analysis performed corroborates the existence of two mechanisms that generate defects in the top Si layer that are related to surface conditions during implantation and the proximity of the top Si/buried oxide layer interface to the surface before annealing.

Edge excitations and topological order in rotating Bose gas

The edge excitations and related topological orders of correlated states of a fast rotating Bose gas are studied. Using exact diagonalization of small systems, we compute the energies and number of edge excitations, as well as the boson occupancy near the edge for various states. The chiral Luttinger-liquid theory of Wen is found to be a good description of the edges of the bosonic Laughlin and other states identified as members of the principal Jain sequence for bosons. However, we find that in a harmonic trap the edge of the state identified as the Moore-Read (Pfaffian) state shows a number of anomalies. An experimental way of detecting these correlated states is also discussed.

Topological magnetic irreversibility in superconducting Pb samples of various shapes

The magnetic-field dependence of the magnetization of cylinders, disks, and spheres of pure type-I superconducting lead was investigated by means of isothermal measurements of first magnetization curves and hysteresis cycles. Depending on the geometry of the sample and the direction and intensity of the applied magnetic field, the intermediate state exhibits different irreversible features that become particularly highlighted in minor hysteresis cycles. The irreversibility is noticeably observed in cylinders and disks only when the magnetic field is parallel to the axis of revolution and is very subtle in spheres. When the magnetic field decreases from the normal state, the irreversibility appears at a temperature-dependent value whose distance to the thermodynamic critical field depends on the sample geometry. The irreversible features in the disks are altered when they are submitted to an annealing process. These results agree well with very recent high-resolution magneto-optical experiments in similar materials that were interpreted in terms of transitions between different topological structures for the flux configuration in the intermediate state. A discussion of the relative role of geometrical barriers for flux entry and exit and pinning effects as responsible for the magnetic irreversibility is given.

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.