Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp, Andricus coriarius

The oak gallwasp Andricus coriarius is distributed across the Western Palaearctic from Morocco to Iran. It belongs to a clade of host-alternating Andricus species that requires host oaks in two sections of Quercus subgenus Quercus to complete its lifecycle, a requirement that has restricted the historic distribution and dispersal of members of this clade. Here we present nuclear and mitochondrial sequence evidence from the entire geographic range of A. coriarius to investigate the genetic legacy of longitudinal range expansion. We show A. coriarius as currently understood to be para- or polyphyletic, with three evolutionarily independent (but partially sympatric) lineages that diverged c. 10 million years ago (mya). The similarities in gall structure that have justified recognition of single species to date thus represent either strong conservation of an ancestral state or striking convergence. All three lineages originated in areas to the east of Europe, underlining the significance of Turkey, Iran and the Levant as 'cradles' of gallwasp evolution. One of the three lineages gave rise to all European populations, and range expansion from a putative Eastern origin to the present distribution is predicted to have occurred around 1.6 mya.     

The influence of an elastic tendon on the force producing capabilities of a muscle during dynamic movements

With increasing computer power, computer simulation of human movement has become a popular research tool. However, time to complete simulations can still be long even on powerful computers. One possibility for reducing simulation time, with models of musculo-skeletal system, is to simulate the muscle using a rigid tendon rather than the more realistic compliant tendon. This study examines the effect of tendon elasticity on muscle force output under different dynamic conditions. A single muscle, point mass model was used and simulations were performed varying the mass, the tendon length, the initial position, and the task. For simulations for relatively slow motion, as experienced for example in upper limb reaching motions or rising from a chair, tendon properties had little influence on muscle force, in contrast simulations of an explosive task similar to jumping or throwing tendon had a much larger effect.     

Mammalian DNA mismatch repair protects cells from UVB-induced DNA damage by facilitating apoptosis and p53 activation

DNA mismatch repair (MMR) is integral to the maintenance of genomic stability and more recently has been demonstrated to affect apoptosis and cell cycle arrest in response to a variety of adducts induced by exogenous agents. Comparing Msh2-null and wildtype mouse embryonic fibroblasts (MEFs), both primary and transformed, we show that Msh2 deficiency results in increased survival post-UVB, and that UVB-induced apoptosis is significantly reduced in Msh2-deficient cells. Furthermore, p53 phosphorylation at serine 15 is delayed or diminished in Msh2-deficient cells, suggesting that Msh2 may act upstream of p53 in a post-UVB apoptosis or growth arrest response pathway. Taken together, these data suggest that MMR heterodimers containing Msh2 may function as a sensor of UVB-induced DNA damage and influence the initiation of UVB-induced apoptosis, thus implicating MMR in protecting against UV-induced tumorigenesis.     

A note on the effect of auditory stimulation on the behaviour and welfare of zoo-housed gorillas

Auditory stimulation has long been employed as a form of therapy for humans and animals housed in institutions. Its effect on one of our closest-living relatives, the gorilla, however, is largely unknown. This study explored the effect of auditory stimulation on the behaviour and welfare of six gorillas housed in Belfast Zoo. All animals were exposed to three conditions of auditory stimulation: a control (no auditory stimulation), an ecologically relevant condition (rainforest sounds) and an ecologically non-relevant condition (classical music). The gorillas’ behaviour was recorded in each condition using a scan-sampling technique. There was no significant effect of the auditory environment on the gorillas’ behaviour, although animals tended to show more behaviours suggestive of relaxation (i.e. resting, sitting) and fewer behaviours typically associated with stress (i.e. aggression, abnormal behaviour) during the ecologically relevant, and, in particular, the non-relevant, conditions than the control. Overall, findings suggest that certain types of auditory stimulation may hold some merit as a method of enrichment for zoo-housed gorillas, although more long-term work with a larger number of animals is needed before firm conclusions can be drawn.     

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry

Background

Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential.

Results

We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons.

Conclusion

Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.