Distinct modes of promoter recognition by two iron starvation σ factors with overlapping promoter specificities

OrbS and PvdS are extracytoplasmic function (ECF) σ factors that regulate transcription of operons required for the biosynthesis of the siderophores ornibactin and pyoverdine in the B. cepacia complex and Pseudomonas spp., respectively. Here we show that promoter recognition by OrbS requires specific tetrameric -35 and -10 element sequences that are strikingly similar to those of the consensus PvdS-dependent promoter. However, whereas P. aeruginosa PvdS can serve OrbS-dependent promoters, OrbS cannot utilise PvdS-dependent promoters. To identify features present at OrbS-dependent promoters that facilitate recognition by OrbS, we carried out a detailed analysis of the nucleotide sequence requirements for promoter recognition by both OrbS and PvdS. This revealed that DNA sequence features located outside of the sigma binding elements are required for efficient promoter utilisation by OrbS. In particular, the presence of an A-tract extending downstream from the -35 element at OrbS-dependent promoters was shown to be an important contributor to OrbS specificity. Our observations demonstrate that the nature of the spacer sequence can have a major impact on promoter recognition by some ECF sigma factors through modulation of the local DNA architecture

Structural dynamics of a metal-organic framework induced by CO2 migration in its non-uniform porous structure

Stimuli-responsive behaviors of flexible metal-organic frameworks (MOFs) make these materials promising in a wide variety of applications such as gas separation, drug delivery, and molecular sensing. Considerable efforts have been made over the last decade to understand the structural changes of flexible MOFs in response to external stimuli. Uniform pore deformation has been used as the general description. However, recent advances in synthesizing MOFs with non-uniform porous structures, i.e. with multiple types of pores which vary in size, shape, and environment, challenge the adequacy of this description. Here, we demonstrate that the CO -adsorption-stimulated structural change of a flexible MOF, ZIF-7, is induced by CO migration in its non-uniform porous structure rather than by the proactive opening of one type of its guest-hosting pores. Structural dynamics induced by guest migration in non-uniform porous structures is rare among the enormous number of MOFs discovered and detailed characterization is very limited in the literature. The concept presented in this work provides new insights into MOF flexibility

Scaling determination of the nonlinear I-V characteristics for 2D superconducting networks

It is shown from computer simulations that the current-voltage ($I$-$V$) characteristics for the two-dimensional XY model with resistively-shunted Josephson junction dynamics and Monte Carlo dynamics obeys a finite-size scaling form from which the nonlinear $I$-$V$ exponent $a$ can be determined to good precision. This determination supports the conclusion $a=z+1$, where $z$ is the dynamic critical exponent. The results are discussed in the light of the contrary conclusion reached by Tang and Chen [Phys. Rev. B {\bf 67}, 024508 (2003)] and the possibility of a breakdown of scaling suggested by Bormann [Phys. Rev. Lett. {\bf 78}, 4324 (1997)].Comment: 6 pages, to appear in PR

Reactive organoallyl species generated from aryl halides and allene: allylation of alpha,beta-unsaturated aldehydes and cyclic ketones employing Pd/In transmetallation processes

Allylation of α,β-unsaturated aldehydes and cyclic ketones promoted by Pd/In transmetallation processes has been studied. The unsaturated aldehydes underwent regioselective 1,2-addition to afford secondary homoally alcohols. The reactions have been performed using Pd(OAc)2/PPh3 as catalytic system and metallic indium affording the products in good yields. The same transformation with unsaturated ketones proved to be less efficient, while saturated cyclic ketones delivered generally excellent yields in the presence of CuI. In these latter processes the presence of a distal heteroatom influences the reaction rate

Anisotropic Scaling in Threshold Critical Dynamics of Driven Directed Lines

The dynamical critical behavior of a single directed line driven in a random medium near the depinning threshold is studied both analytically (by renormalization group) and numerically, in the context of a Flux Line in a Type-II superconductor with a bulk current $\vec J$. In the absence of transverse fluctuations, the system reduces to recently studied models of interface depinning. In most cases, the presence of transverse fluctuations are found not to influence the critical exponents that describe longitudinal correlations. For a manifold with $d=4-\epsilon$ internal dimensions, longitudinal fluctuations in an isotropic medium are described by a roughness exponent $\zeta_\parallel=\epsilon/3$ to all orders in $\epsilon$, and a dynamical exponent $z_\parallel=2-2\epsilon/9+O(\epsilon^2)$. Transverse fluctuations have a distinct and smaller roughness exponent $\zeta_\perp=\zeta_\parallel-d/2$ for an isotropic medium. Furthermore, their relaxation is much slower, characterized by a dynamical exponent $z_\perp=z_\parallel+1/\nu$, where $\nu=1/(2-\zeta_\parallel)$ is the correlation length exponent. The predicted exponents agree well with numerical results for a flux line in three dimensions. As in the case of interface depinning models, anisotropy leads to additional universality classes. A nonzero Hall angle, which has no analogue in the interface models, also affects the critical behavior.Comment: 26 pages, 8 Postscript figures packed together with RevTeX 3.0 manuscript using uufiles, uses multicol.sty and epsf.sty, e-mail [email protected] in case of problem

First-principles study of nucleation, growth, and interface structure of Fe/GaAs

We use density-functional theory to describe the initial stages of Fe film growth on GaAs(001), focusing on the interplay between chemistry and magnetism at the interface. Four features appear to be generic: (1) At submonolayer coverages, a strong chemical interaction between Fe and substrate atoms leads to substitutional adsorption and intermixing. (2) For films of several monolayers and more, atomically abrupt interfaces are energetically favored. (3) For Fe films over a range of thicknesses, both Ga- and As-adlayers dramatically reduce the formation energies of the films, suggesting a surfactant-like action. (4) During the first few monolayers of growth, Ga or As atoms are likely to be liberated from the interface and diffuse to the Fe film surface. Magnetism plays an important auxiliary role for these processes, even in the dilute limit of atomic adsorption. Most of the films exhibit ferromagnetic order even at half-monolayer coverage, while certain adlayer-capped films show a slight preference for antiferromagnetic order.Comment: 11 two-column pages, 12 figures, to appear in Phys. Rev.

Spin injection into a ballistic semiconductor microstructure

A theory of spin injection across a ballistic ferromagnet-semiconductor-ferromagnet junction is developed for the Boltzmann regime. Spin injection coefficient $\gamma$ is suppressed by the Sharvin resistance of the semiconductor $r_N^*=(h/e^2)(\pi^2/S_N)$, where $S_N$ is the Fermi-surface cross-section. It competes with the diffusion resistances of the ferromagnets $r_F$, and $\gamma\sim r_F/r_N^*\ll 1$ in the absence of contact barriers. Efficient spin injection can be ensured by contact barriers. Explicit formulae for the junction resistance and the spin-valve effect are presented.Comment: 5 pages, 2 column REVTeX. Explicit prescription relating the results of the ballistic and diffusive theories of spin injection is added. To this end, some notations are changed. Three references added, typos correcte

Polyamine plays key role in different osmotic stress responses of wheat-rye 1BL/1RS translocation lines

It is well demonstrated that wheat-rye 1BL/1RS translocated chromosome leads to some valuable novel traits such as disease resistance, high yield and functional stay-green after anthesis. To understand the physiological mechanism of 1BL/1RS translocation responsible for osmotic stress, two wheat cultivars, CN12 and CN17, carrying the translocated chromosome and MY11 without the translocated chromosome were employed in the study. During 5-day osmotic stress, fresh weight inhibition, chlorophyll content, soluble protein content, MDA concentration, antioxidant enzymes activity and free polyamines content were examined. CN12 and CN17, especially cultivar CN17, registered greater biomass and minor oxidative damage compared with their wheat parent. Meanwhile, the concentration of Spd and Spm in CN17 was significantly higher than the others. In addition, we found a positive correlation of fresh weight inhibition (FWI) and Put concentration, and a negative one with the parameters (Spd + Spm): Put ratio, indicating the importance of higher polyamine (Spd and Spm) accumulation on the adaptation to osmotic stress. Therefore, we proposed that the accumulation of higher polyamines (Spd and Spm) should play an important role on the adaptation of 1BL/1RS translocation lines to osmotic stress and might be important factors for the origin of novel traits introduced by 1BL/1RS

Understanding Group Structures and Properties in Social Media

Abstract. The rapid growth of social networking sites enables people to connect to each other more conveniently than ever. With easy-to-use social media, people contribute and consume contents, leading to a new form of human interaction and the emergence of online collective behav-ior. In this chapter, we aim to understand group structures and proper-ties by extracting and profiling communities in social media. We present some challenges of community detection in social media. A prominent one is that networks in social media are often heterogeneous. We intro-duce two types of heterogeneity presented in online social networks and elaborate corresponding community detection approaches for each type, respectively. Social media provides not only interaction information but also textual and tag data. This variety of data can be exploited to profile individual groups in understanding group formation and relationships. We also suggest some future work in understanding group structures and properties. Key words: social media, community detection, group profiling, het-erogeneous networks, multi-mode networks, multi-dimensional networks

Discrete cilia modelling with singularity distributions

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system