The protein-protein interactions required for assembly of the Tn3 resolution synapse

The site‐specific recombinase Tn3 resolvase initiates DNA strand exchange when two res recombination sites and six resolvase dimers interact to form a synapse. The detailed architecture of this intricate recombination machine remains unclear. We have clarified which of the potential dimer‐dimer interactions are required for synapsis and recombination, using a novel complementation strategy that exploits a previously uncharacterized resolvase from Bartonella bacilliformis (“Bart”). Tn3 and Bart resolvases recognize different DNA motifs, via diverged C‐terminal domains (CTDs). They also differ substantially at N‐terminal domain (NTD) surfaces involved in dimerization and synapse assembly. We designed NTD‐CTD hybrid proteins, and hybrid res sites containing both Tn3 and Bart dimer binding sites. Using these components in in vivo assays, we demonstrate that productive synapsis requires a specific “R ” interface involving resolvase NTDs at all three dimer‐binding sites in res . Synapses containing mixtures of wild‐type Tn3 and Bart resolvase NTD dimers are recombination‐defective, but activity can be restored by replacing patches of Tn3 resolvase R interface residues with Bart residues, or vice versa . We conclude that the Tn3 /Bart family synapse is assembled exclusively by R interactions between resolvase dimers, except for the one special dimer‐dimer interaction required for catalysis

Detectability of non-differentiable generalized synchrony

Generalized synchronization of chaos is a type of cooperative behavior in directionally-coupled oscillators that is characterized by existence of stable and persistent functional dependence of response trajectories from the chaotic trajectory of driving oscillator. In many practical cases this function is non-differentiable and has a very complex shape. The generalized synchrony in such cases seems to be undetectable, and only the cases, in which a differentiable synchronization function exists, are considered to make sense in practice. We show that this viewpoint is not always correct and the non-differentiable generalized synchrony can be revealed in many practical cases. Conditions for detection of generalized synchrony are derived analytically, and illustrated numerically with a simple example of non-differentiable generalized synchronization.Comment: 8 pages, 8 figures, submitted to PR

A conserved role for Snail as a potentiator of active transcription

The transcription factors of the Snail family are key regulators of epithelial-mesenchymal transitions, cell morphogenesis, and tumor metastasis. Since its discovery in Drosophila ~25 years ago, Snail has been extensively studied for its role as a transcriptional repressor. Here we demonstrate that Drosophila Snail can positively modulate transcriptional activation. By combining information on in vivo occupancy with expression profiling of hand-selected, staged snail mutant embryos, we identified 106 genes that are potentially directly regulated by Snail during mesoderm development. In addition to the expected Snail-repressed genes, almost 50% of Snail targets showed an unanticipated activation. The majority of "Snail-activated" genes have enhancer elements cobound by Twist and are expressed in the mesoderm at the stages of Snail occupancy. Snail can potentiate Twist-mediated enhancer activation in vitro and is essential for enhancer activity in vivo. Using a machine learning approach, we show that differentially enriched motifs are sufficient to predict Snail's regulatory response. In silico mutagenesis revealed a likely causative motif, which we demonstrate is essential for enhancer activation. Taken together, these data indicate that Snail can potentiate enhancer activation by collaborating with different activators, providing a new mechanism by which Snail regulates development

Parties, promiscuity and politicisation: business-political networks in Poland

Research on post-communist political economy has begun to focus on the interface between business and politics. It is widely agreed that informal networks rather than business associations dominate this interface, but there has been very little systematic research in this area. The literature tends to assume that a politicised economy entails business-political networks that are structured by parties. Theoretically, this article distinguishes politicisation from party politicisation and argues that the two are unlikely to be found together in a post-communist context. Empirically, elite survey data and qualitative interviews are used to explore networks of businesspeople and politicians in Poland. Substantial evidence is found against the popular idea that Polish politicians have business clienteles clearly separated from each other according to party loyalties. Instead, it is argued that these politicians and businesspeople are promiscuous. Since there seems to be little that is unusual about the Polish case, this conclusion has theoretical, methodological, substantive and policy implications for other post-communist countries

Defect configurations and dynamical behavior in a Gay-Berne nematic emulsion

To model a nematic emulsion consisting of a surfactant-coated water droplet dispersed in a nematic host, we performed a molecular dynamics simulation of a droplet immersed in a system of 2048 Gay-Berne ellipsoids in a nematic phase. Strong radial anchoring at the surface of the droplet induced a Saturn ring defect configuration, consistent with theoretical predictions for very small droplets. A surface ring configuration was observed for lower radial anchoring strengths, and a pair of point defects was found near the poles of the droplet for tangential anchoring. We also simulated the falling ball experiment and measured the drag force anisotropy, in the presence of strong radial anchoring as well as zero anchoring strength.Comment: 17 pages, 15 figure

Effective index of refraction, optical rotation, and circular dichroism in isotropic chiral liquid crystals

This paper concerns optical properties of the isotropic phase above the isotropic-cholesteric transition and of the blue phase BP III. We introduce an effective index, which describes spatial dispersion effects such as optical rotation, circular dichroism, and the modification of the average index due to the fluctuations. We derive the wavelength dependance of these spatial dispersion effects quite generally without relying on an expansion in powers of the chirality and without assuming that the pitch of the cholesteric $P$ is much shorter than the wavelength of the light $\lambda$, an approximation which has been made in previous studies of this problem. The theoretical predictions are supported by comparing them with experimental spectra of the optical activity in the BP III phase.Comment: 15 pages and 7 figures. Submitted to PR

The anomaly line bundle of the self-dual field theory

In this work, we determine explicitly the anomaly line bundle of the abelian self-dual field theory over the space of metrics modulo diffeomorphisms, including its torsion part. Inspired by the work of Belov and Moore, we propose a non-covariant action principle for a pair of Euclidean self-dual fields on a generic oriented Riemannian manifold. The corresponding path integral allows to study the global properties of the partition function over the space of metrics modulo diffeomorphisms. We show that the anomaly bundle for a pair of self-dual fields differs from the determinant bundle of the Dirac operator coupled to chiral spinors by a flat bundle that is not trivial if the underlying manifold has middle-degree cohomology, and whose holonomies are determined explicitly. We briefly sketch the relevance of this result for the computation of the global gravitational anomaly of the self-dual field theory, that will appear in another paper.Comment: 41 pages. v2: A few typos corrected. Version accepted for publication in CM

Relativistic Hydrodynamic Evolutions with Black Hole Excision

We present a numerical code designed to study astrophysical phenomena involving dynamical spacetimes containing black holes in the presence of relativistic hydrodynamic matter. We present evolutions of the collapse of a fluid star from the onset of collapse to the settling of the resulting black hole to a final stationary state. In order to evolve stably after the black hole forms, we excise a region inside the hole before a singularity is encountered. This excision region is introduced after the appearance of an apparent horizon, but while a significant amount of matter remains outside the hole. We test our code by evolving accurately a vacuum Schwarzschild black hole, a relativistic Bondi accretion flow onto a black hole, Oppenheimer-Snyder dust collapse, and the collapse of nonrotating and rotating stars. These systems are tracked reliably for hundreds of M following excision, where M is the mass of the black hole. We perform these tests both in axisymmetry and in full 3+1 dimensions. We then apply our code to study the effect of the stellar spin parameter J/M^2 on the final outcome of gravitational collapse of rapidly rotating n = 1 polytropes. We find that a black hole forms only if J/M^2<1, in agreement with previous simulations. When J/M^2>1, the collapsing star forms a torus which fragments into nonaxisymmetric clumps, capable of generating appreciable ``splash'' gravitational radiation.Comment: 17 pages, 14 figures, submitted to PR

The baryonic collapse efficiency of galaxy groups in the RESOLVE and ECO surveys

We examine the z = 0 group-integrated stellar and cold baryonic (stars + cold atomic gas) mass functions (group SMF and CBMF) and the baryonic collapse efficiency (group cold baryonic to dark matter halo mass ratio) using the RESOLVE and ECO survey galaxy group catalogs and a GALFORM semi-analytic model (SAM) mock catalog. The group SMF and CBMF fall off more steeply at high masses and rise with a shallower low-mass slope than the theoretical halo mass function (HMF). The transition occurs at the group-integrated cold baryonic mass Mbary cold ~ 1011 M. The SAM, however, has significantly fewer groups at the transition mass ∼1011 M and a steeper low-mass slope than the data, suggesting that feedback is too weak in low-mass halos and conversely too strong near the transition mass. Using literature prescriptions to include hot halo gas and potential unobservable galaxy gas produces a group BMF with a slope similar to the HMF even below the transition mass. Its normalization is lower by a factor of ∼2, in agreement with estimates of warm-hot gas making up the remaining difference. We compute baryonic collapse efficiency with the halo mass calculated two ways, via halo abundance matching (HAM) and via dynamics (extended all the way to three-galaxy groups using stacking). Using HAM, we find that baryonic collapse efficiencies reach a flat maximum for groups across the halo mass range of Mhalo ~ 1011.4 - 12 M, which we label “nascent groups.” Using dynamics, however, we find greater scatter in baryonic collapse efficiencies, likely indicating variation in group hot-to-cold baryon ratios. Similarly, we see higher scatter in baryonic collapse efficiencies in the SAM when using its true groups and their group halo masses as opposed to friends-of-friends groups and HAM masses

Consensus and ordering in language dynamics

We consider two social consensus models, the AB-model and the Naming Game restricted to two conventions, which describe a population of interacting agents that can be in either of two equivalent states (A or B) or in a third mixed (AB) state. Proposed in the context of language competition and emergence, the AB state was associated with bilingualism and synonymy respectively. We show that the two models are equivalent in the mean field approximation, though the differences at the microscopic level have non-trivial consequences. To point them out, we investigate an extension of these dynamics in which confidence/trust is considered, focusing on the case of an underlying fully connected graph, and we show that the consensus-polarization phase transition taking place in the Naming Game is not observed in the AB model. We then consider the interface motion in regular lattices. Qualitatively, both models show the same behavior: a diffusive interface motion in a one-dimensional lattice, and a curvature driven dynamics with diffusing stripe-like metastable states in a two-dimensional one. However, in comparison to the Naming Game, the AB-model dynamics is shown to slow down the diffusion of such configurations.Comment: 7 pages, 6 figure