Information content of colored motifs in complex networks

We study complex networks in which the nodes of the network are tagged with different colors depending on the functionality of the nodes (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more so than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define the information content of the network. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward) it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements.Comment: 21 pages, 8 figures, to appear in Artificial Lif

Correlated fluctuations in the exciton dynamics and spectroscopy of DNA

The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between bases and the structure of the DNA environment. We model the effect of dynamical fluctuations in the environment and study correlation, which is present when multiple base pairs interact with the same mode in the environment. We find that the correlations strongly affect the exciton dynamics, and show how they are observed in the decay of the anisotropy as a function of a coherence and a population time in a non-linear optical experiment

Structure and Dynamics of the VAULT COMPLEX

Vaults are the largest ribonucleoprotein particles found in eukaryotic cells. The maincomponent of these 13 MDa structures is the Mr 100,000 major vault protein (MVP).In mammalian cells, about 96 copies of this protein are necessary to form one vaultparticle. Two additional proteins are associated with the complex, the so-called minorvault proteins of Mr 193,000 (VPARP) and Mr 240,000 (TEP1), as well as severaluntranslated RNA molecules of 86-141 bases. The components are arranged into ahollow barrel-like structure with each half representing eight arches, which are reminiscent to the arched vaulted ceilings of cathedrals. Therefore, when vaults werefirst observed as contaminants in a preparation of clathrin coated vesicles form rat liver,the large complexes were named ‘vaults’. The typical morphology and the individualvault constituents appear conserved throughout evolution, implying an important rolefor vaults in cellular metabolism. A number of functions have been suggested for theseunique particles, but the general idea is that vaults function in intracellular transportprocesses. Nevertheless, the precise cellular function of the vault complex has not yetbeen elucidated. In this study we attempted to gain insight in vault biogenesis,dynamics and their interaction with other cellular components in order to unravel thephysiological significance of vault

BMP-2 and BMP-4 signalling in the developing spinal cord of human and rat embryos

Bone morphogenetic proteins (BMPs) are multifunctional growth factors implicated in multiple biological events. Studies on mice, chickens and other experimental animals have shown that BMP signalling plays critical role in embryonic development, in particular in the neural patterning. In our study we comparatively evaluated BMP-2 and BMP-4 protein expression in the developing spinal cord of human and rat embryos. The human and rat embryos of Carnegie stages 14, 18 and 20 were embedded in paraffin and cut serially in transversal direction. BMP-2 and BMP-4 were detected by immunohistochemical staining. Spatial and temporal expression pattern of BMP-s during early stages of spinal cord development was similar in human and rat embryos. Higher expression of BMP-s was seen in the dorsal and lower expression in the ventral part of the developing spinal cord both in human and rat embryos. However, temporal difference in the expression of BMPs in the non-neural ectoderm between human and rat embryos was noted. Staining of BMP-s in the non-neural ectoderm adjacent to the developing spinal cord in the human embryos seemed to have a tendency to decrease from earlier to later developmental stages, while in rat embryos there was an opposite tendenc

Expression of Pax2 protein during the formation of the central nervous system in human embryos

Members of the paired box (Pax) gene family are expressed in distinctive regions of the developing central nervous system, supporting a role of neural patterning. In this study, Pax2 protein expression was examined in the developing neural tube by immunohistochemistry methods in 30 human embryos of Carnegiestages (CS) 10–20 collected after legal abortions. Pax2 expression was detected along the boundaries of main divisions of the developing brain and spinal cord. However, Pax2 expression was found to be stronger in the developing brain than in the spinal cord of the same young embryos in CS 10–14, which was the mostremarkable at CS 10. Pax2 expression was detected in the developing forebrain,midbrain and hindbrain. At later stages (CS 16–20) Pax2 expression was observed in the midbrain-hindbrain boundary and also in the developing diencephalon and cerebellum. In the wall of developing spinal cord Pax2 expression was detected in the ventricular, mantel and marginal layers. Pax2 staining was seen to increase throughout the later stages of spinal cord development and significantly stronger expression was found at CS 16–20 compared to CS 10. Furthermore, spatially restricted expression of Pax2 was observed along the compartmental dorsal-ventralaxis of the spinal cord as Pax2 staining was weaker in the ventricular layer of the ventral part of the developing spinal cord compared with developing area of dorsal part

Electromagnetic and mechanical characteristaion of ITER CS-MC conductors affected by transverse cyclic loading, part 3: mechanical properties

The magnetic field and current of a coil wound with a cable-in-conduit conductor causes a transverse force pushing the cable to one side of the conduit. This load causes elastic and plastic deformation with friction as well as heating due to friction. A special cryogenic press has been built to study the mechanical and electrical properties of full-size ITER conductors under transverse mechanical loading. The cryogenic press can transmit at 4.2 K cyclic forces of 650 kN/m to conductor sections of 400 mm length representative of the peak load on a 50 kA conductor at 13 T. In order to transmit the force directly onto the cable, the conduit is opened partly to allow the cable deformation. The force acting on the cable as well as the displacement are monitored simultaneously in order to determine the mechanical heat generation due to friction. The mechanical loss under load is investigated for the Nb3Sn, 45 kA, 10 and 13 T, central solenoid model cell conductors (CSMC). The mechanical heat generation is determined from the hysteresis in the measured curves of displacement versus applied force. The first results of the effect of some 40 loading cycles are presented and the two conductors are compared. A significant decrease of the cable mechanical heat generation after loading cycles is observed