On the stability of Dirac sheet configurations

Using cooling for SU(2) lattice configurations, purely Abelian constant magnetic field configurations were left over after the annihilation of constituents that formed metastable Q=0 configurations. These so-called Dirac sheet configurations were found to be stable if emerging from the confined phase, close to the deconfinement phase transition, provided their Polyakov loop was sufficiently non-trivial. Here we show how this is related to the notion of marginal stability of the appropriate constant magnetic field configurations. We find a perfect agreement between the analytic prediction for the dependence of stability on the value of the Polyakov loop (the holonomy) in a finite volume and the numerical results studied on a finite lattice in the context of the Dirac sheet configurations

Watching a superfluid untwist itself: Recurrence of Rabi oscillations in a Bose-Einstein condensate

The order parameter of a condensate with two internal states can continuously distort in such a way as to remove twists that have been imposed along its length. We observe this effect experimentally in the collapse and recurrence of Rabi oscillations in a magnetically trapped, two-component Bose-Einstein condensate of ^87Rb

Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites

The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in S. cerevisiae is qualitatively consistent with a `barrier nucleosome model', in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model, with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to ~1000 bp to each side.Comment: includes supporting materia

Cloning and expression of new microRNAs from zebrafish

MicroRNAs (miRNAs) play an important role in development and regulate the expression of many animal genes by post-transcriptional gene silencing. Here we describe the cloning and expression of new miRNAs from zebrafish. By high-throughput sequencing of small-RNA cDNA libraries from 5-day-old zebrafish larvae and adult zebrafish brain we found 139 known miRNAs and 66 new miRNAs. For 65 known miRNAs and for 11 new miRNAs we also cloned the miRNA star sequence. We analyzed the temporal and spatial expression patterns for 35 new miRNAs and for 32 known miRNAs in the zebrafish by whole mount in situ hybridization and northern blotting. Overall, 23 of the 35 new miRNAs and 30 of the 32 known miRNAs could be detected. We found that most miRNAs were expressed during later stages of development. Some were expressed ubiquitously, but many of the miRNAs were expressed in a tissue-specific manner. Most newly discovered miRNAs have low expression levels and are less conserved in other vertebrate species. Our cloning and expression analysis indicates that most abundant and conserved miRNAs in zebrafish are now known

Emergence of quasi-metallic state in disordered 2D electron gas due to strong interactions

The interrelation between disorder and interactions in two dimensional electron liquid is studied beyond weak coupling perturbation theory. Strong repulsion significantly reduces the electronic density of states on the Fermi level. This makes the electron liquid more rigid and strongly suppresses elastic scattering off impurities. As a result the weak localization, although ultimately present at zero temperature and infinite sample size, is unobservable at experimentally accessible temperature at high enough densities. Therefore practically there exists a well defined metallic state. We study diffusion of electrons in this state and find that the diffusion pole is significantly modified due to "mixture" with static photons similar to the Anderson - Higgs mechanism in superconductivity. As a result several effects stemming from the long range nature of diffusion like the Aronov - Altshuler logarithmic corrections to conductivity are less pronounced.Comment: to appear in Phys. Rev.

Non-linear effects and dephasing in disordered electron systems

The calculation of the dephasing time in electron systems is presented. By means of the Keldysh formalism we discuss in a unifying way both weak localization and interaction effects in disordered systems. This allows us to show how dephasing arises both in the particle-particle channel (weak localization) and in the particle-hole channel (interaction effect). First we discuss dephasing by an external field. Besides reviewing previous work on how an external oscillating field suppresses the weak localization correction, we derive a new expression for the effect of a field on the interaction correction. We find that the latter may be suppressed by a static electric field, in contrast to weak localization. We then consider dephasing due to inelastic scattering. The ambiguities involved in the definition of the dephasing time are clarified by directly comparing the diagrammatic approach with the path-integral approach. We show that different dephasing times appear in the particle-particle and particle-hole channels. Finally we comment on recent experiments.Comment: 28 pages, 6 figures (14ps-files

Quantum effects:heat flow in atomic bottlenecks

The Wiedemann–Franz law linking electrical and thermal conductance has now been verified experimentally in atomic junctions

The Glial Regenerative Response to Central Nervous System Injury Is Enabled by Pros-Notch and Pros-NFκB Feedback

Organisms are structurally robust, as cells accommodate changes preserving structural integrity and function. The molecular mechanisms underlying structural robustness and plasticity are poorly understood, but can be investigated by probing how cells respond to injury. Injury to the CNS induces proliferation of enwrapping glia, leading to axonal re-enwrapment and partial functional recovery. This glial regenerative response is found across species, and may reflect a common underlying genetic mechanism. Here, we show that injury to the Drosophila larval CNS induces glial proliferation, and we uncover a gene network controlling this response. It consists of the mutual maintenance between the cell cycle inhibitor Prospero (Pros) and the cell cycle activators Notch and NFκB. Together they maintain glia in the brink of dividing, they enable glial proliferation following injury, and subsequently they exert negative feedback on cell division restoring cell cycle arrest. Pros also promotes glial differentiation, resolving vacuolization, enabling debris clearance and axonal enwrapment. Disruption of this gene network prevents repair and induces tumourigenesis. Using wound area measurements across genotypes and time-lapse recordings we show that when glial proliferation and glial differentiation are abolished, both the size of the glial wound and neuropile vacuolization increase. When glial proliferation and differentiation are enabled, glial wound size decreases and injury-induced apoptosis and vacuolization are prevented. The uncovered gene network promotes regeneration of the glial lesion and neuropile repair. In the unharmed animal, it is most likely a homeostatic mechanism for structural robustness. This gene network may be of relevance to mammalian glia to promote repair upon CNS injury or disease

Norwalk Virus Shedding after Experimental Human Infection

Noroviruses are shed in feces up to 8 weeks after infection

Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.

The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation