RNA Dynamics by NMR Spectroscopy

An ever-increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined—Lego like—than in proteins, hence the numerous revelations of RNA excited states.     

Metal content determination in four fish species from the Adriatic Sea

Concentrations of As, Cd, Cu, Hg and Pb were measured by atomic absorption spectrometry (AAS) in muscle tissues of four fish species: anchovy (Engraulis encrasicholus), mackerel (Scomber japonicus), red mullet (Mullus surmuletus) and picarel (Spicara smaris) from the Croatian waters of the Adriatic Sea during 2008 and 2009. Metal levels measured in anchovy were in the following ranges (mg kg⁻¹): As 0.01–54.8, Cd 0.001–0.02, Cu 0.001–6.29, Hg 0.001–0.52 and Pb 0.001–0.34 mg kg⁻¹. Metal ranges in red mullet were (mg kg⁻¹): As 0.01–70.9, Cd 0.002–0.85, Cu 0.001–57.3, Hg 0.001–2.07 and Pb 0.001–0.27 mg kg⁻¹. Metal level ranges measured in mackerel were (mg kg⁻¹): As 0.01–36.4, Cd 0.001–0.1, Cu 0.001–15.9, Hg 0.001–0.78 and Pb 0.002–0.24 mg kg⁻¹. In picarel, metal level ranges were (mg kg⁻¹): As 0.01–54.6, Cd 0.001–0.1, Cu 0.08–32.9, Hg 0.001–0.207 and Pb 0.001–0.46 mg kg⁻¹. Significant differences in metal concentrations were found among fish species. The results presented on metal contents in the examined species give an indication of the environmental conditions. Concentrations of Cd, Cu, Hg and Pb obtained were far below the established values by the European Community regulations. However, arsenic levels found in red mullet were higher than the recommended legal limits for human consumption and as such may present a human health issue.     

Performance Improvement Using Polarization Diversity in Precise Agriculture Communication Platform

The use of wireless sensor network (WSN) is essential for gathering data and implementation of information and control technologies in precision agriculture. The efficiency of such smart system strongly depends on WSN reliability and durability, which is highly influenced by wireless channel. Relaying of the collected data over the intermediate nodes has been proven as a good strategy for WSNs. In this paper we assume amplify-and-forward relaying strategy with variable gain amplification. In order to improve system performance we propose implementation of polarization diversity. It is assumed that all communication links are influenced by Rician fading. Thus, in the case of polarization diversity, link between the source and the relay is characterized as two correlated and non-identical Rician fading channels. In this paper, we present a novel analytical model for determining the outage probability of such system, which is applicable to various fading scenarios described with different Rician K factors and average signal to noise ratios (SNR), as well as different level of diversity signals correlation and cross-polar discrimination. Numerical results show that, using polarization diversity, improvements for the considered system performance can be realized with significantly lower SNR, despite a certain level of correlation and power unbalance between the diversity branches. In that manner, compared to the system with no diversity, the total needed transmit power for achieving the same level of system performances is reduced, and thus more energy efficient communication is enabled.     

Progressive Compression of 3D Mesh Geometry Using Sparse Approximations from Redundant Frame Dictionaries

In this paper, we present a new approach for the progressive compression of three‐dimensional (3D) mesh geometry using redundant frame dictionaries and sparse approximation techniques. We construct the proposed frames from redundant linear combinations of the eigenvectors of a combinatorial mesh Laplacian matrix. We achieve a sparse synthesis of the mesh geometry by selecting atoms from a frame using matching pursuit. Experimental results show that the resulting rate‐distortion performance compares favorably with other progressive mesh compression algorithms in the same category, even when a very simple, sub‐optimal encoding strategy is used for the transmitted data. The proposed frames also have the desirable property of being able to be applied directly to a manifold mesh having arbitrary topology and connectivity types; thus, no initial remeshing is required and the original mesh connectivity is preserved.     

The involvement of oxidative stress in ochratoxin A and fumonisin B1 toxicity in rats

The aim of this study was to find out whether very low doses of nephrotoxic and hepatotoxic mycotoxins ochratoxin A (OTA) and fumonisin B1 (FB1) induce oxidative stress in rat kidney and liver and whether their effect is synergistic. Rats were treated orally with OTA (5 ng/kg b.w. and 50 microg/kg b.w.) and FB1 (200 ng/kg b.w. and 50 microg/kg b.w.), or their combinations. Malondialdehyde (MDA) and protein carbonyls (PCs) concentration in kidney was affected with lower dose of OTA than in liver (p<0.05). FB1 did not affect MDA and PCs concentrations in the liver, while in the kidney both FB1 doses increased MDA concentration (p<0.05). The combination of the lower doses of OTA+FB1 increased the MDA and PCs concentration both in the liver and the kidney, compared to controls and animals treated with respective doses of mycotoxins (p<0.05). The combinations of mycotoxins reduced the catalase activity only in the kidney when compared to controls (p<0.05). In contrast to the increased kidney concentrations of MDA and PCs even with very low doses of OTA and FB1, the activity of catalase and SOD does not change. Combinations of OTA+FB1 affected almost all parameters, which indicates their potential to produce oxidative damage.     

Macro-azo-initiators having poly(ethylene glycol) units: Synthesis,characterization, and application to AB block copolymerization

Macro-azo-initiators (MAIs) having poly(ethylene glycol) (PEG) units were obtained by various multistep synthetic approaches. In the first stage, macro-azo-initiators of PEG type with azo groups inserted in the main chain were prepared. MAIs were then characterized by chemical analyses, spectral methods, ¹H-NMR, GPC, and DSC techniques. They were used in the free-radical bulk polymerization of dicyclohexylitaconate to synthesize AB block copolymers of poly(ethylene glycol-b-dicyclohexylitaconate) (PEG-b-PDCHI). © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65: 2173–2181, 1997     

WebFlow – a visual programming paradigm for Web/Java based coarse grain distributed computing

We present here recent work at NPAC aimed at developing WebFlow – a general purpose Web-based visual interactive programming environment for coarse grain distributed computing. We follow the 3-tier architecture with the central control and integration WebVM layer in tier-2, interacting with the visual graph editor applets in tier-1 (front-end) and the legacy systems in tier-3. WebVM is given by a mesh of Java Web servers such as Jeeves from JavaSoft or Jigsaw from MIT/W3C. All system control structures are implemented as URL-addressable servlets which enable Web browser-based authoring, monitoring, publication, documentation and software distribution tools for distributed computing. We view WebFlow/WEbVM as a promising programming paradigm and co-ordination model for the exploding volume of Web/Java software, and we illustrate it in a set of ongoing application development activities. © 1997 John Wiley & Sons, Ltd.