Regulatory RNAs: A Universal Language for Inter-Domain Communication

In eukaryotes, microRNAs (miRNAs) have roles in development, homeostasis, disease and the immune response. Recent work has shown that plant and mammalian miRNAs also mediate cross-kingdom and cross-domain communications. However, these studies remain controversial and are lacking critical mechanistic explanations. Bacteria do not produce miRNAs themselves, and therefore it is unclear how these eukaryotic RNA molecules could function in the bacterial recipient. In this review, we compare and contrast the biogenesis and functions of regulatory RNAs in eukaryotes and bacteria. As a result, we discovered several conserved features and homologous components in these distinct pathways. These findings enabled us to propose novel mechanisms to explain how eukaryotic miRNAs could function in bacteria. Further understanding in this area is necessary to validate the findings of existing studies and could facilitate the use of miRNAs as novel tools for the directed remodelling of the human microbiota.     

The control of sea lice in Atlantic salmon by selective breeding

Sea lice threaten the welfare of farmed Atlantic salmon and the sustainability of fish farming across the world. Chemical treatments are the major method of control but drug resistance means that alternatives are urgently needed. Selective breeding can be a cheap and effective alternative. Here, we combine experimental trials and diagnostics to provide a practical protocol for quantifying resistance to sea lice. We then combined quantitative genetics with epidemiological modelling to make the first prediction of the response to selection, quantified in terms of reduced need for chemical treatments. We infected over 1400 young fish with Lepeophtheirus salmonis, the most important species in the Northern Hemisphere. Mechanisms of resistance were expressed early in infection. Consequently, the number of lice per fish and the ranking of families were very similar at 7 and 17 days post infection, providing a stable window for assessing susceptibility to infection. The heritability of lice numbers within this time window was moderately high at 0.3, confirming that selective breeding is viable. We combined an epidemiological model of sea lice infection and control on a salmon farm with genetic variation in susceptibility among individuals. We simulated 10 generations of selective breeding and examined the frequency of treatments needed to control infection. Our model predicted that substantially fewer chemical treatments are needed to control lice outbreaks in selected populations and chemical treatment could be unnecessary after 10 generations of selection. Selective breeding for sea lice resistance should reduce the impact of sea lice on fish health and thus substantially improve the sustainability of Atlantic salmon production.     

The impacts of cattle access points on deposited sediment levels in headwater streams in Ireland

Cattle access to streams has been linked globally with degradation of stream water quality, driven largely by bank erosion and resultant instream, fine sediment deposition. The majority of evidence on such effects is however based in arid and semiarid regions of the United States and Australia, with few studies relating to cool temperate climates such as Northwest Europe. In this study, “Quorer” resuspendable sediment samples were taken from riffle geomorphic units upstream (control) and at two points downstream (pressure and recovery) of cattle access points in headwater streams in agricultural catchments in Ireland to assess levels of deposited stream sediment. Samples were taken in April/May (2016) prior to the grazing season and in October (2016) at the end of the grazing season. Sites in good‐high ecological status catchments and less than good ecological status catchments were included in the study. Higher levels of sediment were found downstream of cattle access points in both good‐high status and less than good status catchments; however, the impacts of access points were spatially confined to, in most cases, the area immediately downstream of the point of access. There was a strong correlation between deposited sediment mass and organic matter (OM) mass, with levels of OM increasing linearly with deposited sediment mass. Levels of measured sediment were negatively correlated with riparian habitat health (measured using a qualitative habitat assessment). The results of this study highlight the need for measures to prevent cattle access to headwater streams where access points can be many in order to manage local habitat quality and downstream water quality issues.     

A miniature triaxial apparatus for investigating the micromechanics of granular soils with in situ X-ray micro-tomography scanning

The development of a miniature triaxial apparatus is presented. In conjunction with an X-ray micro-tomography (termed as X-ray μCT hereafter) facility and advanced image processing techniques, this apparatus can be used for in situ investigation of the micro-scale mechanical behavior of granular soils under shear. The apparatus allows for triaxial testing of a miniature dry sample with a size of \mathrm{8}\hspace{0.17em}\mathrm{mm}\times \mathrm{16}\hspace{0.17em}\mathrm{mm} (diameter \times height). In situ triaxial testing of a 0.4–0.8 mm Leighton Buzzard sand (LBS) under a constant confining pressure of 500 kPa is presented. The evolutions of local porosities (i.e., the porosities of regions associated with individual particles), particle kinematics (i.e., particle translation and particle rotation) of the sample during the shear are quantitatively studied using image processing and analysis techniques. Meanwhile, a novel method is presented to quantify the volumetric strain distribution of the sample based on the results of local porosities and particle tracking. It is found that the sample, with nearly homogenous initial local porosities, starts to exhibit obvious inhomogeneity of local porosities and localization of particle kinematics and volumetric strain around the peak of deviatoric stress. In the post-peak shear stage, large local porosities and volumetric dilation mainly occur in a localized band. The developed triaxial apparatus, in its combined use of X-ray μCT imaging techniques, is a powerful tool to investigate the micro-scale mechanical behavior of granular soils.