Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli

Escherichia coli endoribonuclease E has a major influence on gene expression. It is essential for the maturation of ribosomal and transfer RNA as well as the rapid degradation of messenger RNA. The latter ensures that translation closely follows programming at the level of transcription. Recently, one of the hallmarks of RNase E, i.e. its ability to bind via a 5'-monophosphorylated end, was shown to be unnecessary for the initial cleavage of some polycistronic tRNA precursors. Here we show using RNA-seq analyses of ribonuclease-deficient strains in vivo and a 5'-sensor mutant of RNase E in vitro that, contrary to current models, 5'-monophosphate-independent, 'direct entry' cleavage is a major pathway for degrading and processing RNA. Moreover, we present further evidence that direct entry is facilitated by RNase E binding simultaneously to multiple unpaired regions. These simple requirements may maximize the rate of degradation and processing by permitting multiple sites to be surveyed directly without being constrained by 5'-end tethering. Cleavage was detected at a multitude of sites previously undescribed for RNase E, including ones that regulate the activity and specificity of ribosomes. A potentially broad role for RNase G, an RNase E paralogue, in the trimming of 5'-monophosphorylated ends was also revealed

T-cell responses in oiled guillemots and swans in a rehabilitation setting

This article has been accepted for publication in the Archives of Environmental Contamination and Toxicology. The final version can be accessed from the link below.This article has been made available through the Brunel Open Access Publishing Fund.Aquatic birds are commonly affected by oil spills. Despite rehabilitation efforts, the majority of rehabilitated common guillemots (Uria aalge) do not survive, whereas mute swans (Cygnus olor) tend to have higher post-release survival. Polyaromatic hydrocarbons (PAHs) present in crude oil and diesel are immunotoxic in birds affecting cell-mediated responses to immunogens. Because it is a target of PAH toxicity, T-lymphocyte response to controlled mitogen administration (phytohemagglutinnin test) was investigated in a scoping study as a potentially useful minimally invasive in vivo test of cell-mediated immunity. The test was performed on 69 mute swans and 31 common guillemots stranded on the Norfolk and Lincolnshire coastline and inland waterways in England (UK)either due to injury or to contamination with crude or diesel oil. T-lymphocyte response was significantly decreased in swans with greater oil scores. T-lymphocyte responses were also decreased in guillemots, but this finding was not statistically significant

Kerr-Newman Black Hole Thermodynamical State Space: Blockwise Coordinates

A coordinate system that blockwise-simplifies the Kerr-Newman black hole's thermodynamical state space Ruppeiner metric geometry is constructed, with discussion of the limiting cases corresponding to simpler black holes. It is deduced that one of the three conformal Killing vectors of the Reissner-Nordstrom and Kerr cases (whose thermodynamical state space metrics are 2 by 2 and conformally flat) survives generalization to the Kerr-Newman case's 3 by 3 thermodynamical state space metric.Comment: 4 pages incl 2 figs. Accepted by Gen. Rel. Grav. Replaced with Accepted version (minor corrections

Getting the Best of Both Worlds? Developing Complementary Equation-Based and Agent-Based Models

We argue that building agent-based and equation-based versions of the same theoretical model is a fruitful way of gaining insights into real-world phenomena. We use the epistemological concept of “models as isolations and surrogate systems” as the philosophical underpinning of this argument. In particular, we show that agent-based and equation-based approaches align well when used simultaneously and, contrary to some common misconceptions, should be considered complements rather than substitutes. We illustrate the usefulness of the approach by examining a model of the long-run relationship between economic development and inequality (i.e., the Kuznets hypothesis)

The Lippmann–Schwinger Formula and One Dimensional Models with Dirac Delta Interactions

We show how a proper use of the Lippmann–Schwinger equation simplifies the calculations to obtain scattering states for one dimensional systems perturbed by N Dirac delta equations. Here, we consider two situations. In the former, attractive Dirac deltas perturbed the free one dimensional Schrödinger Hamiltonian. We obtain explicit expressions for scattering and Gamow states. For completeness, we show that the method to obtain bound states use comparable formulas, although not based on the Lippmann–Schwinger equation. Then, the attractive N deltas perturbed the one dimensional Salpeter equation. We also obtain explicit expressions for the scattering wave functions. Here, we need regularisation techniques that we implement via heat kernel regularisation

Dilaton Quantum Cosmology with a Schrodinger-like equation

A quantum cosmological model with radiation and a dilaton scalar field is analysed. The Wheeler-deWitt equation in the mini-superspace induces a Schr\"odinger equation, which can be solved. An explicit wavepacket is constructed for a particular choice of the ordering factor. A consistent solution is possible only when the scalar field is a phantom field. Moreover, although the wavepacket is time dependent, a Bohmian analysis allows to extract a bouncing behaviour for the scale factor.Comment: 14 pages, 3 figures in eps format. Minors corrections, new figure

Preliminary Report of Three-Dimensional Reconstructive Intraoperative C-Arm in Percutaneous Vertebroplasty

Objective: Percutaneous vertebroplasty (PVP) is usually carried out under three-dimensional (2D) fluoroscopic guidance. However, operative complications or bone cement distribution might be difficult to assess on the basis of only 2D radiographic projection images. We evaluated the feasibility of performing an intraoperative and postoperative examination in patients undergoing PVP by using three-dimensional (3D) reconstructive C-arm. Methods: Standard PVP procedures were performed on 14 consecutive patients by using a Siremobil Iso-C 3D and a multidetector computed tomography machine. Post-processing of acquired volumetric datasets included multiplanar reconstruction (MPR) and surface shaded display (SSD). We analyzed intraoperative and immediate postoperative evaluation of the needle trajectory and bone cement distribution. Results: The male: female ratio was 2: 12; mean age of patients, 70 (range, 77-54) years; and mean T score,-3.4. The mean operation time was 52.14 min, but the time required to perform and post-process the rotational acquisitions was 7.76 min. The detection of bone cement distribution and leakage after PVP by using MPR and SSD was possible in all patients. However, detection of the safe trajectory for needle insertion was not possible. Conclusion: 3D rotational image acquisition can enable intra- or post-procedural assessment of vertebroplasty procedures for the detection of bone cement distribution and leakage. However, it is difficult to assess the safe trajectory for needle insertion. Key Words: Vertebroplasty · Intraoperative 3D imaging · Complication · Feasibility

Social Institutions and Economic Inequality Modeling the onset of the Kuznets Curve

Theoretical models of the Kuznets Curve have been purely analytical with little contribution to the timing of the process and to the presence of additional mechanisms affecting its timing. This paper proposes an agent-based version of Acemoglu and Robinsons model of the political economy of the Kuznets Curve. In extending their analytical framework we include heterogeneity of agents' income and a mating mechanism that together represent elements of social mobility. These two simple changes proved to be enough to shed light on the length and timing before high inequality implies regime change. Thus, this work may contribute to an effective empirical assessment of the Kuznets curve as it explicitly considers the time dimension of the process and the e ects of considering social dynamics

Simple, Fast and Accurate Implementation of the Diffusion Approximation Algorithm for Stochastic Ion Channels with Multiple States

The phenomena that emerge from the interaction of the stochastic opening and closing of ion channels (channel noise) with the non-linear neural dynamics are essential to our understanding of the operation of the nervous system. The effects that channel noise can have on neural dynamics are generally studied using numerical simulations of stochastic models. Algorithms based on discrete Markov Chains (MC) seem to be the most reliable and trustworthy, but even optimized algorithms come with a non-negligible computational cost. Diffusion Approximation (DA) methods use Stochastic Differential Equations (SDE) to approximate the behavior of a number of MCs, considerably speeding up simulation times. However, model comparisons have suggested that DA methods did not lead to the same results as in MC modeling in terms of channel noise statistics and effects on excitability. Recently, it was shown that the difference arose because MCs were modeled with coupled activation subunits, while the DA was modeled using uncoupled activation subunits. Implementations of DA with coupled subunits, in the context of a specific kinetic scheme, yielded similar results to MC. However, it remained unclear how to generalize these implementations to different kinetic schemes, or whether they were faster than MC algorithms. Additionally, a steady state approximation was used for the stochastic terms, which, as we show here, can introduce significant inaccuracies. We derived the SDE explicitly for any given ion channel kinetic scheme. The resulting generic equations were surprisingly simple and interpretable - allowing an easy and efficient DA implementation. The algorithm was tested in a voltage clamp simulation and in two different current clamp simulations, yielding the same results as MC modeling. Also, the simulation efficiency of this DA method demonstrated considerable superiority over MC methods.Comment: 32 text pages, 10 figures, 1 supplementary text + figur

Thermodynamical Metrics and Black Hole Phase Transitions

An important phase transition in black hole thermodynamics is associated with the divergence of the specific heat with fixed charge and angular momenta, yet one can demonstrate that neither Ruppeiner's entropy metric nor Weinhold's energy metric reveals this phase transition. In this paper, we introduce a new thermodynamical metric based on the Hessian matrix of several free energy. We demonstrate, by studying various charged and rotating black holes, that the divergence of the specific heat corresponds to the curvature singularity of this new metric. We further investigate metrics on all thermodynamical potentials generated by Legendre transformations and study correspondences between curvature singularities and phase transition signals. We show in general that for a system with n-pairs of intensive/extensive variables, all thermodynamical potential metrics can be embedded into a flat (n,n)-dimensional space. We also generalize the Ruppeiner metrics and they are all conformal to the metrics constructed from the relevant thermodynamical potentials.Comment: Latex, 25 pages, reference added, typos corrected, English polished and the Hawking-Page phase transition clarified; to appear in JHE