RNA editing in Trypanosoma brucei: characterization of gRNA U-tail interactions with partially edited mRNA substrates

Guide RNAs (gRNAs), key components of the RNA editing reaction in Trypanosoma brucei, direct the insertion and deletion of uridylate (U) residues. Analyses of gRNAs reveal three functional elements. The 5′-end of the gRNA contains the anchor, which is responsible for selection and binding to the pre-edited mRNA. The second element (the guiding region) provides the information required for editing. At the 3′-end of the gRNA is a non-encoded U-tail, whose function remains unclear. However, the cleavage–ligation model for editing proposes that the U-tail binds to purine-rich regions upstream of editing sites, thereby strengthening the interaction and holding onto the 5′ cleavage product. Our previous studies demonstrated that the U-tail interacts with upstream sequences and may play roles in both stabilization and tethering. These studies also indicated that the U-tail interactions involved mRNA regions that were to be subsequently edited. This raised the question of what happens to the mRNA–U-tail interaction as editing proceeds in the 3′→5′ direction. We examined gCYb-558 and its U-tail interaction with 5′CYbUT and two partially edited 5′CYb substrates. Our results indicate that the 3′-end of the U-tail interacts with the same sequence in all three mRNAs. Predicted secondary structures using crosslinking data suggest that a similar structure is maintained as editing proceeds. These results indicate that the role of the U-tail may also involve maintenance of important secondary structure motifs.

Comparison of the Ability of Partially N-Acetylated Chitosans and Chitooligosaccharides to Elicit Resistance Reactions in Wheat Leaves1

Chitin, a linear polysaccharide composed of (1→4)-linked 2-acetamido-2-deoxy-β-d-glucopyranose (GlcNAc) residues, and chitosan, the fully or partially N-acetylated, water-soluble derivative of chitin composed of (1→4)-linked GlcNAc and 2-amino-2-deoxy-β-d-glucopyranose (GlcN), have been proposed as elicitors of defense reactions in higher plants. We tested and compared the ability of purified (1→4)-linked oligomers of GlcNAc (tetramer to decamer) and of GlcN (pentamer and heptamer) and partially N-acetylated chitosans with degrees of acetylation (DA) of 1%, 15%, 35%, 49%, and 60% and average degrees of polymerization between 540 and 1100 to elicit phenylalanine ammonia-lyase (PAL) and peroxidase (POD) activities, lignin deposition, and microscopically and macroscopically visible necroses when injected into the intercellular spaces of healthy, nonwounded wheat (Triticum aestivum L.) leaves. Purified oligomers of (1→4)-linked GlcN were not active as elicitors, whereas purified oligomers of (1→4)-linked GlcNAc with a degree of polymerization ≥ 7 strongly elicited POD activities but not PAL activities. Partially N-acetylated, polymeric chitosans elicited both PAL and POD activities, and maximum elicitation was observed with chitosans of intermediate DAs. All chitosans but not the chitin oligomers induced the deposition of lignin, the appearance of necrotic cells exhibiting yellow autofluorescence under ultraviolet light, and macroscopically visible necroses; those with intermediate DAs were most active. These results suggest that different mechanisms are involved in the elicitation of POD activities by GlcNAc oligomers, and of PAL and POD activities by partially N-acetylated chitosan polymers and that both enzymes have to be activated for lignin biosynthesis and ensuing necrosis to occur.

Protein evolution on partially correlated landscapes.

We extend an earlier model of protein evolution on a rugged landscape to the case in which the landscape exhibits a variable degree of correlation (i.e., smoothness). Correlation is introduced by assuming that a protein is composed of a set of independent blocks or domains and that mutation in one block affects the contribution of that block alone to the overall fitness of the protein. We study the statistical structure of such landscapes and apply our theory to the evolution by somatic hypermutation of antibody molecules composed of framework and complementarity-determining regions. We predict the expected number of replacement mutations in each region.

Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I.

Previous biochemical studies have suggested a role for bacterial DNA topoisomerase (TOPO) I in the suppression of R-loop formation during transcription. In this report, we present several pieces of genetic evidence to support a model in which R-loop formation is dynamically regulated during transcription by activities of multiple DNA TOPOs and RNase H. In addition, our results suggest that events leading to the serious growth problems in the absence of DNA TOPO I are linked to R-loop formation. We show that the overexpression of RNase H, an enzyme that degrades the RNA moiety of an R loop, can partially compensate for the absence of DNA TOPO I. We also note that a defect in DNA gyrase can correct several phenotypes associated with a mutation in the rnhA gene, which encodes the major RNase H activity. In addition, we found that a combination of topA and rnhA mutations is lethal.

Correlation of the liquid–liquid equilibrium data for specific ternary systems with one or two partially miscible binary subsystems

This paper presents the results of a liquid–liquid equilibrium data correlation for 11 ternary systems which have not been previously fitted using the NRTL model or, when they have, the results presented in the literature are inconsistent with the experimental behavior of the system. These ternary systems include mixtures with one or two partially miscible pairs. During the correlation process, new restrictions were imposed on the values for the NRTL binary parameters to ensure correct prediction of the total or partial miscibility for the binary pairs involved. In addition, topological concepts related to the Gibbs stability test have been applied in order to validate the results in the whole range of compositions.

Dynamic investigation of an ancient masonry bell tower with operational modal analysis: a non-destructive experimental technique to obtain the dynamic characteristics of a structure

This paper shows the results of an experimental analysis on the bell tower of “Chiesa della Maddalena” (Mola di Bari, Italy), to better understand the structural behavior of slender masonry structures. The research aims to calibrate a numerical model by means of the Operational Modal Analysis (OMA) method. In this way realistic conclusions about the dynamic behavior of the structure are obtained. The choice of using an OMA derives from the necessity to know the modal parameters of a structure with a non-destructive testing, especially in case of cultural-historical value structures. Therefore by means of an easy and accurate process, it is possible to acquire in-situ environmental vibrations. The data collected are very important to estimate the mode shapes, the natural frequencies and the damping ratios of the structure. To analyze the data obtained from the monitoring, the Peak Picking method has been applied to the Fast Fourier Transforms (FFT) of the signals in order to identify the values of the effective natural frequencies and damping factors of the structure. The main frequencies and the damping ratios have been determined from measurements at some relevant locations. The responses have been then extrapolated and extended to the entire tower through a 3-D Finite Element Model. In this way, knowing the modes of vibration, it has been possible to understand the overall dynamic behavior of the structure.

Partial collapse of a ventilated stone façade: Diagnosis and analysis of the anchorage system

The mechanical behaviour of transventilated façades performed by natural stone is necessarily based on the correct execution of both anchoring elements on the stone cladding as in the ones corresponding to the enclosure support, either with brick masonry walls or reinforced concrete walls. In the case studied in the present work, the origin of the damages suffered on the façade of a building located in Alcoy has been analyzed, where the detachment of part of the outer enclosure occurred. This enclosure is a transventilated façade formed by Bateig Blue stone tiles. To this end, “in situ” tests of the anchoring systems employed have been performed, as well as laboratory tests of mechanical characterization of the material and of different types of anchor, comparing these results with those obtained in both the simplified analytical models of continuum mechanics as developed by the Finite Element Method (FEM).

Seismic behavior of a masonry chimney with severe cracking condition: preliminary study

This paper presents a structural analysis of a masonry chimney built in the 1940s, which is currently being cataloged as local interest heritage. This structure has not served any industrial purpose for the last thirty years. The chimney is located in the town of Agost (Alicante - Spain) and directly exposed to the prevailing winds from the sea, as it is approximately 12 km away from the waterfront and there are not any significant barriers, which could protect the structure against the wind. There are longitudinal cracks and fissures all along the shaft because of the chimney’s geometrical characteristics, the effect of the masonry creep and especially the lack of maintenance. Moreover, there is also a permanent bending deformation in the upper 1/3 of the height due to the wind pressure. A numerical analysis for the static behavior against gravity and wind loads was performed using the structure’s current conditions after a detailed report of its geometry, its construction system and the cracking pattern. Afterwards, the dynamic behavior was studied, i.e. a seismic analysis using both response spectra and accelerograms in order to examine the structural stability. This work shows the pre-monitoring analysis before any experimental testing. Using the current results the future test conditions will be determined (e.g. number of sensors and monitoring point location, excitation systems, etc) prior to a possible structural reinforcement by applying composite material (fiber reinforced polymers).

Moisture Distribution in Partially Saturated Concrete Studied by Impedance Spectroscopy

The moisture content and its spatial distribution has a great influence on the durability properties of concrete structures. Several non-destructive techniques have been used for the determination of the total water content, but moisture distribution is difficult to determine. In this paper impedance spectroscopy is used to study the water distribution in concrete samples with controlled and homogeneously distributed moisture contents. The technique is suitable for the determination of water distribution inside the sample, using the appropriate equivalent circuits. It is shown that using the selected drying procedures there is no change in the solid phase of the samples, although the technique can only be used for the qualitative study of variations in the solid phase when samples are too thick. The results of this work show that for a wide range of concrete percentages of saturation, from full to 18 % saturation, practically all the pores keep at least a thin layer of electrolyte covering their walls, since the capacitance measurement results are practically independent of the saturation degree.

Optimal model through identified frequencies of a masonry building structure with wooden floors

The paper presents the analysis of an important historical building: the Saint James Theater in the city of Corfù (Greece) actually used as the Municipality House. The building, located in the center of the city, is made of carves stones and is characterized by a stocky shape and by the presence of wooden floors. The study deals with the structural identification of such structure through the analysis of its ambient vibrations recorded by means of accelerometers with high accuracy. A full dynamic testing was developed using ambient vibrations to identify the main modal parameters and to make a non-destructive characterization of this building. The results of these dynamic tests are compared with the modal analysis of a complex finite element (FE) simulation of the structure. This analysis may present several problems and uncertainties for this stocky building. Due to the presence of wooden floors, the local modes can be highly excited and, as a consequence, the evaluation of the structural modal parameters presents some difficulties.