Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch

Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the forming and melting of the aptamer terminal helix, the so called P1 stem, is essential for genetic control. The structural mechanisms by which this conformational change is modulated upon ligand binding mostly remain to be elucidated. Here, we used pulling molecular dynamics simulations to study the thermodynamics of the P1 stem in the add adenine riboswitch. The P1 ligand-dependent stabilization was quantified in terms of free energy and compared with thermodynamic data. This comparison suggests a model for the aptamer folding in which direct P1-ligand interactions play a minor role on the conformational switch when compared with those related to the ligand-induced aptamer preorganization

How can Dermanyssus gallinae (De Geer 1778) (Acari: Anactinotrichida: Dermanyssidae) walk upwards on slippery surfaces?

ABSTRACTScanning electron microscopy observations of the distal leg region of the poultry red mite Dermanyssus gallinae (De Geer 1778) identified the presence of a compound ambulacrum, the part of ..

Towards de novo RNA 3D Structure Prediction

RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which aim at the prediction of the three-dimensional (3D) native fold from the sole knowledge of the sequence. In a recent paper, we have introduced a scoring function for RNA structure prediction. Here, we analyze in detail the performance of the method, we underline strengths and shortcomings, and we discuss the results with respect to state-of-the-art techniques. These observations provide a starting point for improving current methodologies, thus paving the way to the advances of more accurate approaches for RNA 3D structure prediction

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

Introduction: Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. Methods In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Results Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Discussion and Conclusions Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations

the overall pulse model for water demand of aggregated residential users

Abstract The models for the end-user demand give a detailed description of the water request, which takes into account the consumes of each dwelling. Therefore, these approaches can model the water demand at WDS nodes by aggregating the single request of each user. The effectiveness of a novel approach the Overall Pulse model (OP)- to describe the aggregated water demand has been tested. In fact, the OP model, unlike the commonly used rectangular pulse models (e.g. PRP, NSRP), does not aim to reconstruct single demand pulses as they occur when home faucets and hydro-sanitary appliances are operated, but allows the generation of the water demand as it is observed at the house water meter. This feature makes the model very versatile, allowing the direct modeling of either a single user or of a group of n users. The possibility of 'pre-aggregation' of the water demand makes it easier to take into account the spatial variability of the model parameters. In the paper, the performance of the OP model is investigated, and to this aim the generated time series are compared with the observed ones of real users. In addition, the comparison of series obtained by means of the classical PRP approach and of the OP model show the effectiveness of the latter

An Innovative and Easy Method for Iron-Doped Titania Synthesis

In this work, photocatalytically active titanium oxide nanoparticles were synthesized for the treatment of contaminated water under visible light. Various Ag, Sr and Fe-based synthesis and doping techniques (mainly hydrothermal and sol-gel methods) were performed. Adsorptive and photocatalytic properties were studied by testing in batch mode for the decontaminating a synthetic methylene blue solution (used as a model contaminant) using a simple 13 W LED bulb as the light source. The best material in terms of both activity (high removal kinetics) and simplicity of synthesis was found to be titanium oxide doped with Fe via "solid-state"method. This method enabled the synthesis of titania nanoparticles about 70 nanometers in size with Fe3+ effectively substituting titanium atoms (Ti4+) in the crystalline bulk of titania. The pseudo-first-order kinetic model was found to represent the behavior of the experimental data

Drop test simulation and validation of a full composite fuselage section of a regional aircraft

Abstract In the aircraft industry, the use of fiber reinforced materials for primary structural components over metallic parts has increased up to more than 50% in the recent years, because of their high strength and high modulus to weight ratios, high fatigue and corrosion resistance. Currently, the need of lowering weight and fuel consumption is pushing the world's largest aircraft manufacturers in the design and building of structures entirely made of composites. Fuselage structure plays an important role in absorbing the kinetic energy during a crash. Through the deformation, crushing and damage of fuselage sub-floor structure, a survivable space inside the cabin area should be preserved during and after a crash impact in order to minimize the risk of passengers' injuries. In this work, a Finite Element (FE) model of a full-scale 95% composites made fuselage section of a regional aircraft under vertical drop test is presented. The experiment, conducted by the Italian Aerospace Research Centre (CIRA) with an actual impact velocity of 9.14 m/s in according to the FAR/CS 25, has been numerically simulated. Two ATDs (Anthropomorphic Test Dummies), both 50th percentile, seats and belts have been modelled to reproduce the experimental setup. The results of the simulation, performed by using LS-DYNA® explicit FE code, have been validated by correlation with the experimental ones. Such comparisons highlight that a good agreement has been achieved. The presented FE model allows verifying the structural behavior under a dynamic load condition and also estimating the passive safety capabilities of the designed structure. Since the experiment is expensive and non-repeatable, a FE model can be used for Certification by Analysis purposes since, if established, it is able to virtually demonstrate the compliance to the airworthiness rules

Superhydrophobic coatings as anti-icing systems for small aircraft

Traditional anti-icing/de-icing systems, i.e., thermal and pneumatic, in most cases require a power consumption not always allowable in small aircraft. Therefore, the use of passive systems, able to delay the ice formation, or reduce the ice adhesion strength once formed, with no additional energy consumption, can be considered as the most promising solution to solve the problem of the ice formation, most of all, for small aircraft. In some cases, the combination of a traditional icing protection system (electrical, pneumatic, and thermal) and the passive coatings can be considered as a strategic instrument to reduce the energy consumption. The effort of the present work was to develop a superhydrophobic coating, able to reduce the surface free energy (SFE) and the work of adhesion (WA) of substrates, by a simplified and non-expensive method. The developed coating, applied as a common paint with an aerograph, is able to reduce the SFE of substrates by 99% and the WA by 94%. The effects of both chemistry and surface morphology on the wettability of surfaces were also studied. In the reference samples, the higher the roughness, the lower the SFE and the WA. In coated samples with roughness ranging from 0.4 and 3 μm no relevant variations in water contact angle, nor in SFE andWA were observed

Analytical Model of Connected Bi-Omega: Robust Particle for the Selective Power Transmission Through Sub-Wavelength Apertures

Cataloged from PDF version of article.In this paper, we present a new analytical model of the connected bi-omega structure consisting of two bi-omega particles connected together through their arms. A single bi-omega particle consists of a pair of regular equal omegas with mirror symmetry. Assuming the individual bi-omega particle electrically small, the equivalent circuit is derived, in order to predict its resonant frequency. Then, two bi-omega particles are connected together, obtaining a symmetric structure that supports two fundamental modes, with even and odd symmetries, respectively. The proposed analytical model, then, is used to develop a procedure allowing the design of the particle for a desired resonant frequency. The effectiveness of the proposed analytical model and design guidelines is confirmed by proper comparisons to full-wave numerical and experimental results. We also demonstrate through a proper set of experiments that the resonant frequencies of the connected bi-omega particle depend only on the geometrical and electrical parameters of the omegas and are rather insensitive to the practical scenario where the particle itself is actually used, e.g. in free-space, rectangular waveguide or across an aperture in a metallic screen

Raman-scattered O VI Features in the Symbiotic Nova RR Telescopii

RR Tel is an interacting binary system in which a hot white dwarf (WD) accretes matter from a Mira-type variable star via gravitational capture of its stellar wind. This symbiotic nova shows intense Raman-scattered O VI 1032 and 1038 features at 6825 ˚A and 7082 ˚A. We present high-resolution optical spectra of RR Tel taken in 2016 and 2017 with the Magellan Inamori Kyocera Echelle (MIKE) spectrograph at Magellan-Clay telescope, Chile. We aim to study the stellar wind accretion in RR Tel from the profile analysis of Raman O VI features. With an asymmetric O VI disk model, we derive a representative Keplerian speed of > 35 km s−1 , and the corresponding scale < 0.8 au. The best-fit for the Raman profiles is obtained with a mass loss rate of the Mira M˙ ∼ 2 × 10−6 M yr−1 and a wind terminal velocity v∞ ∼ 20 km s−1 . We compare the MIKE data with an archival spectrum taken in 2003 with the Fibre-fed Extended Range Optical Spectrograph (FEROS) at the MPG/ESO 2.2 m telescope. It allows us to highlight the profile variation of the Raman O VI features, indicative of a change in the density distribution of the O VI disk in the last two decades. We also report the detection of O VI recombination lines at 3811 ˚A and 3834 ˚A, which are blended with other emission lines. Our profile decomposition suggests that the recombination of O VII takes place nearer to the WD than the O VI 1032 and 1038 emission region.Fil: Heo, J. E.. Observatorio Gemini; Chile. Universidad de La Serena; Chile. Sejong University; Corea del SurFil: Lee, H. W.. Universidad de Sejong; Corea del SurFil: Angeloni, R.. Universidad de La Serena; ChileFil: Palma, Tali. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Departamento de Astrofísica Estelar; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Di Mille, F.. Observatorio Las Campanas; Chil