The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication, but essential for the production of infectious virus.

Non-coding regions of viral RNA (vRNA) genomes are critically important in the regulation of gene expression. In particular, pseudoknot (PK) structures, which are present in a wide range of RNA molecules, have a variety of roles. The 5' untranslated region (5' UTR) of foot-and-mouth disease virus (FMDV) vRNA is considerably longer than in other viruses from the picornavirus family and consists of a number of distinctive structural motifs that includes multiple (2, 3 or 4 depending on the virus strain) putative PKs linked in tandem. The role(s) of the PKs in the FMDV infection are not fully understood. Here, using bioinformatics, sub-genomic replicons and recombinant viruses we have investigated the structural conservation and importance of the PKs in the FMDV lifecycle. Our results show that despite the conservation of two or more PKs across all FMDVs, a replicon lacking PKs was replication competent, albeit at reduced levels. Furthermore, in competition experiments, GFP FMDV replicons with less than two (0 or 1) PK structures were outcompeted by a mCherry FMDV wt replicon that had 4 PKs, whereas GFP replicons with 2 or 4 PKs were not. This apparent replicative advantage offered by the additional PKs correlates with the maintenance of at least two PKs in the genomes of FMDV field isolates. Despite a replicon lacking any PKs retaining the ability to replicate, viruses completely lacking PK were not viable and at least one PK was essential for recovery of infections virus, suggesting a role for the PKs in virion assembly. Thus, our study points to roles for the PKs in both vRNA replication and virion assembly, thereby improving understanding the molecular biology of FMDV replication and the wider roles of PK in RNA functions.

Effect of Trail Bifurcation Asymmetry and Pheromone Presence or Absence on Trail Choice by Lasius niger Ants.

During foraging, ant workers are known to make use of multiple information sources, such as private information (personal memory) and social information (trail pheromones). Environmental effects on foraging, and how these interact with other information sources, have, however, been little studied. One environmental effect is trail bifurcation asymmetry. Ants forage on branching trail networks and must often decide which branch to take at a junction (bifurcation). This is an important decision, as finding food sources relies on making the correct choices at bifurcations. Bifurcation angle may provide important information when making this choice. We used a Y-maze with a pivoting 90° bifurcation to study trail choice of Lasius niger foragers at varying branch asymmetries (0°, [both branches 45° from straight ahead], 30° [branches at 30° and 60° from straight ahead], 45°, 60° and 90° [one branch straight ahead, the other at 90°]). The experiment was carried out either with equal amounts of trail pheromone on both branches of the bifurcation or with pheromone present on only one branch. Our results show that with equal pheromone, trail asymmetry has a significant effect on trail choice. Ants preferentially follow the branch deviating least from straight, and this effect increases as asymmetry increases (47% at 0°, 54% at 30°, 57% at 45°, 66% at 60° and 73% at 90°). However, when pheromone is only present on one branch, the graded effect of asymmetry disappears. Overall, however, there is an effect of asymmetry as the preference of ants for the pheromone-marked branch over the unmarked branch is reduced from 65%, when it is the less deviating branch, to 53%, when it is the more deviating branch. These results demonstrate that trail asymmetry influences ant decision-making at bifurcations and that this information interacts with trail pheromone presence in a non-hierarchical manner.