Local sequence features that influence AP-1 cis-regulatory activity

In the genome, most occurrences of transcription factor binding sites (TFBS) have no cis-regulatory activity, which suggests that flanking sequences contain information that distinguishes functional from nonfunctional TFBS. We interrogated the role of flanking sequences near Activator Protein 1 (AP-1) binding sites that reside in DNase I Hypersensitive Sites (DHS) and regions annotated as Enhancers. In these regions, we found that sequence features directly adjacent to the core motif distinguish high from low activity AP-1 sites. Some nearby features are motifs for other TFs that genetically interact with the AP-1 site. Other features are extensions of the AP-1 core motif, which cause the extended sites to match motifs of multiple AP-1 binding proteins. Computational models trained on these data distinguish between sequences with high and low activity AP-1 sites and also predict changes in cis-regulatory activity due to mutations in AP-1 core sites and their flanking sequences. Our results suggest that extended AP-1 binding sites, together with adjacent binding sites for additional TFs, encode part of the information that governs TFBS activity in the genome.</jats:p

Dispersal and Re-Capture of Marked, Overwintering \u3ci\u3eTomicus Piniperda\u3c/i\u3e (Coleoptera: Scolytidae) From Scotch Pine Bolts

The pine shoot beetle (PSB), Tomicus piniperda is a recently established exotic pest of live pine in the southern Great Lakes of the U.S. and Canada. Scotch pine, Pinus sylvestris L. is the most susceptible pine species, but the adult also attacks several other North American species of Pinus. This research investigated the dispersal behavior of beetles emerging from overwintering sites to aid in the development of effective monitoring and management practices. Scotch pine logs with overwintering PSB were sprayed with fluorescent pigments to mark dispersing beetles. These logs were placed in piles in the centers of three circular trap arrays of 8-unit Lindgren traps, baited with a-pinene, and placed at distances of 50, 100,200, 300 and 400 meters from the center along equally spaced radii. An estimated average of 393 PSB, or 23.4% of the overwintering PSB, dispersed from each of three log piles during the initial spring dispersal flight, and 21.9% of these were captured in traps. Traps within 100 meters caught 56.0 to 67.8% of the marked PSB recovered. Most (95.3%) marked PSB were trapped within 400 meters, but 12 beetles (4.7%) were trapped 780-2,000 meters away in adjacent trap arrays. The dispersal pattern of the population, as indicated by trap catch, was to the northeast, in the direction of prevailing westerly/ southerly winds up to 4.77 mls daily average during beetle flight. Regression analysis suggests that the PSB within the experimental area had a predicted dispersal distance of 900 meters in an area that contained numerous traps. Dispersal distances may be greater under of conditions of strong and steady winds or iftraps or abundant host material removed fewer PSB from the dispersing population. The use of traps to monitor specific sites should consider the direction of prevailing winds. Trap catches of wild PSB suggest that optimal inter-trap spacing for efficient detection could be about 78 m

PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs

A large number of RNA binding proteins (RBPs) and miRNAs bind to the 3′ untranslated regions of mRNA, but methods to dissect their function and interactions are lacking. Here the authors introduce post-transcriptional regulatory element sequencing (PTRE-seq) to dissect sequence preferences, interactions and consequences of RBP and miRNA binding

Spectral Polarization and Spectral Phase Control of Time and Energy Entangled Photons

We demonstrate a scheme to spectrally manipulate a collinear, continuous stream of time and energy entangled photons to generate beamlike, bandwidth-limited fuxes of polarization-entangled photons with nearly-degenerate wavelengths. Utilizing an ultrashort-pulse shaper to control the spectral phase and polarization of the photon pairs, we tailor the shape of the Hong-Ou-Mandel interference pattern, demonstrating the rules that govern the dependence of this interference pattern on the spectral phases of the photons. We then use the pulse shaper to generate all four polarization Bell states. The singlet state generated by this scheme forms a very robust decoherence-free subspace, extremely suitable for long distance fiber-optics based quantum communication.Comment: 5 pages, 3 figure

ER Stress-Induced eIF2-alpha Phosphorylation Underlies Sensitivity of Striatal Neurons to Pathogenic Huntingtin

A hallmark of Huntington's disease is the pronounced sensitivity of striatal neurons to polyglutamine-expanded huntingtin expression. Here we show that cultured striatal cells and murine brain striatum have remarkably low levels of phosphorylation of translation initiation factor eIF2 alpha, a stress-induced process that interferes with general protein synthesis and also induces differential translation of pro-apoptotic factors. EIF2 alpha phosphorylation was elevated in a striatal cell line stably expressing pathogenic huntingtin, as well as in brain sections of Huntington's disease model mice. Pathogenic huntingtin caused endoplasmic reticulum (ER) stress and increased eIF2 alpha phosphorylation by increasing the activity of PKR-like ER-localized eIF2 alpha kinase (PERK). Importantly, striatal neurons exhibited special sensitivity to ER stress-inducing agents, which was potentiated by pathogenic huntingtin. We could strongly reduce huntingtin toxicity by inhibiting PERK. Therefore, alteration of protein homeostasis and eIF2 alpha phosphorylation status by pathogenic huntingtin appears to be an important cause of striatal cell death. A dephosphorylated state of eIF2 alpha has been linked to cognition, which suggests that the effect of pathogenic huntingtin might also be a source of the early cognitive impairment seen in patients

Breakdown of large-N quenched reduction in SU(N) lattice gauge theories

We study the validity of the large-N equivalence between four-dimensional SU(N) lattice gauge theory and its momentum quenched version--the Quenched Eguchi-Kawai (QEK) model. We find that the assumptions needed for the proofs of equivalence do not automatically follow from the quenching prescription. We use weak-coupling arguments to show that large-N equivalence is in fact likely to break down in the QEK model, and that this is due to dynamically generated correlations between different Euclidean components of the gauge fields. We then use Monte-Carlo simulations at intermediate couplings with 20 <= N <= 200 to provide strong evidence for the presence of these correlations and for the consequent breakdown of reduction. This evidence includes a large discrepancy between the transition coupling of the "bulk" transition in lattice gauge theories and the coupling at which the QEK model goes through a strongly first-order transition. To accurately measure this discrepancy we adapt the recently introduced Wang-Landau algorithm to gauge theories.Comment: 51 pages, 16 figures, Published verion. Historical inaccuracies in the review of the quenched Eguchi-Kawai model are corrected, discussion on reduction at strong-coupling added, references updated, typos corrected. No changes to results or conclusion

Post-ISCO Ringdown Amplitudes in Extreme Mass Ratio Inspiral

An extreme mass ratio inspiral consists of two parts: adiabatic inspiral and plunge. The plunge trajectory from the innermost stable circular orbit (ISCO) is special (somewhat independent of initial conditions). We write an expression for its solution in closed-form and for the emitted waveform. In particular we extract an expression for the associated black-hole ringdown amplitudes, and evaluate them numerically.Comment: 21 pages, 5 figures. v4: added section with numerical evaluation of the ringdown amplitude

Media representation of regulated incivilities: Relevant actors, problems, solutions and the role played by experts in the Flemish press

This article analyses the representations of regulated nuisance in a section of Flemish newspapers over time. It identifies the groups of people who have been successful in conveying messages in and through Flemish press news, and explores the way they have represented problems of, and suggested solutions to, regulated incivilities over the years. Furthermore, against the backdrop of newsmaking criminology, it considers whether and how crime and justice experts have contributed to shaping the Flemish media discourse on regulated incivilities over time. Overall the analysis of press news has found that the press, by giving coverage to the voices of local institutional actors, has promoted the criminalization of nuisance and, especially, of physical incivilities. The views of criminological experts, by contrast, have remained marginal. The article concludes by suggesting how such findings present a new set of empirical and conceptual challenges for newsmaking criminology, and more generally, for public criminology

Moduli, Scalar Charges, and the First Law of Black Hole Thermodynamics

We show that under variation of moduli fields $\phi$ the first law of black hole thermodynamics becomes $dM = {\kappa dA\over 8\pi} + \Omega dJ + \psi dq + \chi dp - \Sigma d\phi$, where $\Sigma$ are the scalar charges. We also show that the ADM mass is extremized at fixed $A$, $J$, $(p,q)$ when the moduli fields take the fixed value $\phi_{\rm fix}(p,q)$ which depend only on electric and magnetic charges. It follows that the least mass of any black hole with fixed conserved electric and magnetic charges is given by the mass of the double-extreme black hole with these charges. Our work allows us to interpret the previously established result that for all extreme black holes the moduli fields at the horizon take a value $\phi= \phi_{\rm fix}(p,q)$ depending only on the electric and magnetic conserved charges: $\phi_{\rm fix}(p,q)$ is such that the scalar charges $\Sigma ( \phi_{\rm fix}, (p,q))=0$.Comment: 3 pages, no figures, more detailed versio

Reduction of quantum noise in optical interferometers using squeezed light

We study the photon counting noise in optical interferometers used for gravitational wave detection. In order to reduce quantum noise a squeezed vacuum state is injected into the usually unused input port. Here, we specifically investigate the so called `dark port case', when the beam splitter is oriented close to 90{\deg} to the incoming laser beam, such that nearly all photons go to one output port of the interferometer, and only a small fraction of photons is seen in the other port (`dark port'). For this case it had been suggested that signal amplification is possible without concurrent noise amplification [R.Barak and Y.Ben-Aryeh, J.Opt.Soc.Am.B25(361)2008]. We show that by injection of a squeezed vacuum state into the second input port, counting noise is reduced for large values of the squeezing factor, however the signal is not amplified. Signal strength only depends on the intensity of the laser beam.Comment: 8 pages, 1 figur