Sequence signature analysis of chromosome identity in three Drosophila species

BACKGROUND: All eukaryotic organisms need to distinguish each of their chromosomes. A few protein complexes have been described that recognise entire, specific chromosomes, for instance dosage compensation complexes and the recently discovered autosome-specific Painting of Fourth (POF) protein in Drosophila. However, no sequences have been found that are chromosome-specific and distributed over the entire length of the respective chromosome. Here, we present a new, unbiased, exhaustive computational method that was used to probe three Drosophila genomes for chromosome-specific sequences. RESULTS: By combining genome annotations and cytological data with multivariate statistics related to three Drosophila genomes we found sequence signatures that distinguish Muller's F-elements (chromosome 4 in D. melanogaster) from all other chromosomes in Drosophila that are not attributable to differences in nucleotide composition, simple sequence repeats or repeated elements. Based on these signatures we identified complex motifs that are strongly overrepresented in the F-elements and found indications that the D. melanogaster motif may be involved in POF-binding to the F-element. In addition, the X-chromosomes of D. melanogaster and D. yakuba can be distinguished from the other chromosomes, albeit to a lesser extent. Surprisingly, the conservation of the F-element sequence signatures extends not only between species separated by approximately 55 Myr, but also linearly along the sequenced part of the F-elements. CONCLUSION: Our results suggest that chromosome-distinguishing features are not exclusive to the sex chromosomes, but are also present on at least one autosome (the F-element) in Drosophila

Smooth geometries with four charges in four dimensions

A class of axially symmetric, rotating four-dimensional geometries carrying D1, D5, KK monopole and momentum charges is constructed. The geometries are found to be free of horizons and singulaties, and are candidates to be the gravity duals of microstates of the (0,4) CFT. These geometries are constructed by performing singularity analysis on a suitably chosen class of solutions of six-dimensional minimal supergravity written over a Gibbons-Hawking base metric. The properties of the solutions raise some interesting questions regarding the CFT.Comment: 1+32 pages, LaTeX, v2: references added, typographical errors correcte

A mathematical framework for critical transitions: normal forms, variance and applications

Critical transitions occur in a wide variety of applications including mathematical biology, climate change, human physiology and economics. Therefore it is highly desirable to find early-warning signs. We show that it is possible to classify critical transitions by using bifurcation theory and normal forms in the singular limit. Based on this elementary classification, we analyze stochastic fluctuations and calculate scaling laws of the variance of stochastic sample paths near critical transitions for fast subsystem bifurcations up to codimension two. The theory is applied to several models: the Stommel-Cessi box model for the thermohaline circulation from geoscience, an epidemic-spreading model on an adaptive network, an activator-inhibitor switch from systems biology, a predator-prey system from ecology and to the Euler buckling problem from classical mechanics. For the Stommel-Cessi model we compare different detrending techniques to calculate early-warning signs. In the epidemics model we show that link densities could be better variables for prediction than population densities. The activator-inhibitor switch demonstrates effects in three time-scale systems and points out that excitable cells and molecular units have information for subthreshold prediction. In the predator-prey model explosive population growth near a codimension two bifurcation is investigated and we show that early-warnings from normal forms can be misleading in this context. In the biomechanical model we demonstrate that early-warning signs for buckling depend crucially on the control strategy near the instability which illustrates the effect of multiplicative noise.Comment: minor corrections to previous versio

Mergers and Typical Black Hole Microstates

We use mergers of microstates to obtain the first smooth horizonless microstate solutions corresponding to a BPS three-charge black hole with a classically large horizon area. These microstates have very long throats, that become infinite in the classical limit; nevertheless, their curvature is everywhere small. Having a classically-infinite throat makes these microstates very similar to the typical microstates of this black hole. A rough CFT analysis confirms this intuition, and indicates a possible class of dual CFT microstates. We also analyze the properties and the merging of microstates corresponding to zero-entropy BPS black holes and black rings. We find that these solutions have the same size as the horizon size of their classical counterparts, and we examine the changes of internal structure of these microstates during mergers.Comment: 49 pages, 5 figures. v2 references adde

Superconducting microstrip detectors

Superconducting NbN microstrip counters feature radiation hardness two orders of magnitude higher than conventional Si strip detectors, spatial resolution limited only by lithographic techniques (0.1 - 2 microns), intrinsic signal rise time of 2 ps, and signal transport over large distances without losses. The aim of this proposal is to improve understanding of the physics of such detectors and to establish their large- scale feasibility

The transition from the adiabatic to the sudden limit in core level photoemission: A model study of a localized system

We consider core electron photoemission in a localized system, where there is a charge transfer excitation. The system is modelled by three electron levels, one core level and two outer levels. The model has a Coulomb interaction between these levels and the continuum states into which the core electron is emitted. The model is simple enough to allow an exact numerical solution, and with a separable potential an analytic solution. We calculate the ratio r(omega) between the weights of the satellite and the main peak as a function of the photon energy omega. The transition from the adiabatic to the sudden limit takes place for quite small photoelectron kinetic energies. For such small energies, the variation of the dipole matrix element is substantial and described by the energy scale Ed. Without the coupling to the photoelectron, the corresponding ratio r0(omega) is determined by Ed and the satellite excitation energy dE. When the interaction potential with the continuum states is introduced, a new energy scale Es=1/(2Rs^2) enters, where Rs is a length scale of the interaction potential. At threshold there is typically a (weak) constructive interference between intrinsic and extrinsic contributions, and the ratio r(omega)/r0(omega) is larger than its limiting value for large omega. The interference becomes small or weakly destructive for photoelectron energies of the order Es. For larger energies r(omega)/r0(omega) therefore typically has a weak undershoot. If this undershoot is neglected, r(omega)/r0(omega) reaches its limiting value on the energy scale Es.Comment: 18 pages, latex2e, 13 eps figure

Retention of a cell adhesion complex at the paranodal junction requires the cytoplasmic region of Caspr

An axonal complex of cell adhesion molecules consisting of Caspr and contactin has been found to be essential for the generation of the paranodal axo-glial junctions flanking the nodes of Ranvier. Here we report that although the extracellular region of Caspr was sufficient for directing it to the paranodes in transgenic mice, retention of the Caspr–contactin complex at the junction depended on the presence of an intact cytoplasmic domain of Caspr. Using immunoelectron microscopy, we found that a Caspr mutant lacking its intracellular domain was often found within the axon instead of the junctional axolemma. We further show that a short sequence in the cytoplasmic domain of Caspr mediated its binding to the cytoskeleton-associated protein 4.1B. Clustering of contactin on the cell surface induced coclustering of Caspr and immobilized protein 4.1B at the plasma membrane. Furthermore, deletion of the protein 4.1B binding site accelerated the internalization of a Caspr–contactin chimera from the cell surface. These results suggest that Caspr serves as a “transmembrane scaffold” that stabilizes the Caspr/contactin adhesion complex at the paranodal junction by connecting it to cytoskeletal components within the axon

D1D5 microstate geometries from string amplitudes

We reproduce the asymptotic expansion of the D1D5 microstate geometries by computing the emission amplitudes of closed string states from disks with mixed D1D5 boundary conditions. Thus we provide a direct link between the supergravity and D-brane descriptions of the D1D5 microstates at non-zero string coupling. Microscopically, the profile functions characterizing the microstate solutions are encoded in the choice of a condensate for the twisted open string states connecting D1 and D5 branes.Comment: 21 pages; added reference

Experimental entanglement verification and quantification via uncertainty relations

We report on experimental studies on entanglement quantification and verification based on uncertainty relations for systems consisting of two qubits. The new proposed measure is shown to be invariant under local unitary transformations, by which entanglement quantification is implemented for two-qubit pure states. The nonlocal uncertainty relations for two-qubit pure states are also used for entanglement verification which serves as a basic proposition and promise to be a good choice for verification of multipartite entanglement.Comment: 5 pages, 3 figures and 2 table