A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi

The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing

Identification and certification of low indirect land use impact biomass for the eu bioeconomy

The EU Bioeconomy is considered an ambitious concept aiming at to promote several targets related to environmental, social and economic sustainability. One of the main concerns and risks associated with the development of a growing bioeconomy in the EU is the increasing demand for land to support additional biomass production. This increasing demand might be associated with a number of negative impacts such as for example deforestation, the loss of natural habitats and ecosystem services. The EU H2020 project STAR-ProBio aims at the development of a comprehensive framework for the sustainability assessment of biobased products. As part of this framework development, we are analyzing potential strategies for the production of biomass associated with low indirect impacts and a low demand for land, respectively. This paper highlights the main intermediate findings and describes potential next steps until the end of the STAR-ProBio project

Controls on the global distribution of contourite drifts: Insights from an eddy-resolving ocean model

Contourite drifts are anomalously high sediment accumulations that form due to reworking by bottom currents. Due to the lack of a comprehensive contourite database, the link between vigorous bottom water activity and drift occurrence has yet to be demonstrated on a global scale. Using an eddy-resolving ocean model and a new georeferenced database of 267 contourites, we show that the global distribution of modern contourite drifts strongly depends on the configuration of the world’s most powerful bottom currents, many of which are associated with global meridional overturning circulation. Bathymetric obstacles frequently modify flow direction and intensity, imposing additional finer-scale control on drift occurrence. Mean bottom current speed over contourite-covered areas is only slightly higher (2.2cm/s) than the rest of the global ocean (1.1cm/s), falling below proposed thresholds deemed necessary to re-suspend and redistribute sediments (10–15cm/s). However, currents fluctuate more frequently and intensely over areas with drifts, highlighting the role of intermittent, high-energy bottom current events in sediment erosion, transport, and subsequent drift accumulation. We identify eddies as a major driver of these bottom current fluctuations, and we find that simulated bottom eddy kinetic energy is over three times higher in contourite-covered areas in comparison to the rest o.f the ocean. Our work supports previous hypotheses which suggest that contourite deposition predominantly occurs due to repeated acute events as opposed to continuous reworking under average-intensity background flow conditions. This suggests that the contourite record should be interpreted in terms of a bottom current’s susceptibility to experiencing periodic, high-speed current events. Our results also highlight the potential role of upper ocean dynamics in contourite sedimentation through its direct influence on deep eddy circulation

Bathymetric Data Requirements for Operational Coastal Erosion Forecasting Using XBeach

There is an increasing interest in the broad-scale implementation of coastal erosion early warning systems (EWS) with the goal of enhancing community preparedness to extreme coastal storm wave events. These emerging systems typically rely on process-based models to predict the storm-induced morphological change. A key challenge with incorporating these models in EWSs is the need for up-to-date nearshore and surf zone bathymetry data, which is difficult to measure routinely, but potentially important for accurate erosion forecasting. This study evaluates the degree to which up-to-date bathymetry is required for accurate coastal erosion predictions using the morphodynamic model XBeach and, subsequently, whether a range of “representative” and/or “synthetic” bathymetries can be used for the bottom boundary, when a survey of the immediate pre-storm bathymetry is not available. Twelve storm events at two contrasting sites were modelled using six different bathymetry scenarios, including the expected “best case” bathymetry surveyed immediately pre-storm. These results indicate that alternative bathymetries can be used to obtain sub-aerial erosion predictions that are similar (and in some cases better) than those resulting from the use of an immediately pre-storm surveyed bathymetry, provided that rigorous model calibration is undertaken prior. This generalized finding is attributed to specific parametrizations in the XBeach model structure that are optimized during the calibration process to match the particular bottom boundary condition used. This study provides practical guidance for the selection of suitable nearshore bathymetry for use in operational coastal erosion EWSs