Processing of RNA Containing 8-Oxo-7,8-Dihydroguanosine (8-oxoG) by the Exoribonuclease Xrn-1

Understanding how oxidatively damaged RNA is handled intracellularly is of relevance due to the link between oxidized RNA and the progression/development of some diseases as well as aging. Among the ribonucleases responsible for the decay of modified (chemically or naturally) RNA is the exonuclease Xrn-1, a processive enzyme that catalyzes the hydrolysis of 5′-phosphorylated RNA in a 5′→3′ direction. We set out to explore the reactivity of this exonuclease towards oligonucleotides (ONs, 20-nt to 30-nt long) of RNA containing 8-oxo-7,8-dihydroguanosine (8-oxoG), obtained via solid-phase synthesis. The results show that Xrn-1 stalled at sites containing 8-oxoG, evidenced by the presence of a slower moving band (via electrophoretic analyses) than that observed for the canonical analogue. The observed fragment(s) were characterized via PAGE and MALDI-TOF to confirm that the oligonucleotide fragment(s) contained a 5′-phosphorylated 8-oxoG. Furthermore, the yields for this stalling varied from app. 5–30% with 8-oxoG located at different positions and in different sequences. To gain a better understanding of the decreased nuclease efficiency, we probed: 1) H-bonding and spatial constraints; 2) anti-syn conformational changes; 3) concentration of divalent cation; and 4) secondary structure. This was carried out by introducing methylated or brominated purines (m1G, m6,6A, or 8-BrG), probing varying [Mg2+], and using circular dichroism (CD) to explore the formation of structured RNA. It was determined that spatial constraints imposed by conformational changes around the glycosidic bond may be partially responsible for stalling, however, the results do not fully explain some of the observed higher stalling yields. We hypothesize that altered π-π stacking along with induced H-bonding interactions between 8-oxoG and residues within the binding site may also play a role in the decreased Xrn-1 efficiency. Overall, these observations suggest that other factors, yet to be discovered/established, are likely to contribute to the decay of oxidized RNA. In addition, Xrn-1 degraded RNA containing m1G, and stalled mildly at sites where it encountered m6,6A, or 8-BrG, which is of particular interest given that the former two are naturally occurring modifications.

Responses in area hMT+ reflect tuning for both auditory frequency and motion after blindness early in life

Previous studies report that human middle temporal complex (hMT+) is sensitive to auditory motion in early-blind individuals. Here, we show that hMT+ also develops selectivity for auditory frequency after early blindness, and that this selectivity is maintained after sight recovery in adulthood. Frequency selectivity was assessed using both moving band-pass and stationary pure-tone stimuli. As expected, within primary auditory cortex, both moving and stationary stimuli successfully elicited frequency-selective responses, organized in a tonotopic map, for all subjects. In early-blind and sight-recovery subjects, we saw evidence for frequency selectivity within hMT+ for the auditory stimulus that contained motion. We did not find frequency-tuned responses within hMT+ when using the stationary stimulus in either early-blind or sight-recovery subjects. We saw no evidence for auditory frequency selectivity in hMT+ in sighted subjects using either stimulus. Thus, after early blindness, hMT+ can exhibit selectivity for auditory frequency. Remarkably, this auditory frequency tuning persists in two adult sight-recovery subjects, showing that, in these subjects, auditory frequency-tuned responses can coexist with visually driven responses in hMT+.

Spatial Self-Organization Resolves Conflicts Between Individuality and Collective Migration

Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the behavior of each individual will differ due to existing genetic and non-genetic variation within the population. It remains unclear how this individuality is managed to achieve collective behavior. We quantified individuality in bands of clonalEscherichia colicells that migrate collectively along a channel by following a self-generated gradient of attractant. We discovered that despite substantial differences in individual chemotactic abilities, the cells are able to migrate as a coherent group by spontaneously sorting themselves within the moving band. This sorting mechanism ensures that differences between individual chemotactic abilities are compensated by differences in the local steepness of the traveling gradient each individual must navigate, and determines the minimum performance required to travel with the band. By resolving conflicts between individuality and collective migration, this mechanism enables populations to maintain advantageous diversity while on the move.

Rotational Motion Modelling for Numerical Analysis of Electric Machines

The paper presents a brief review of the movement modelling methods of electric machines and the two most common used torque calculation techniques. After the classification of single-layer moving band methods, a low computation cost and an easily realisable new variant of this movement modelling technique is proposed. To study the accuracy of proposed moving band technique equipped with Arkkio's method and Maxwell's stress tensor method for torque calculation an international benchmark problem used. Further, to check the applicability, the proposed method has been used to analyse a three-phase switched reluctance motor. The results of proposed method have been compared to analytical and numerical results.