Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs

Small nucleolar RNAs (snoRNAs) and microRNAs are two classes of non-protein-coding RNAs with distinct functions in RNA modification or post-transcriptional gene silencing. In this study, we introduce novel insights to RNA-induced gene activity adjustments in human cells by identifying numerous snoRNA-derived molecules with miRNA-like function, including H/ACA box snoRNAs and C/D box snoRNAs. In particular, we demonstrate that several C/D box snoRNAs give rise to gene regulatory RNAs, named sno-miRNAs here. Our data are complementing the increasing number of studies in the field of small RNAs with regulatory functions. In massively deep sequencing of small RNA fractions we identified high copy numbers of sub-sequences from >30 snoRNAs with lengths of ≥18 nt. RNA secondary structure prediction indicated for a majority of candidates a location in predicted stem regions. Experimental analysis revealed efficient gene silencing for 11 box C/D sno-miRNAs, indicating cytoplasmic processing and recruitment to the RNA silencing machinery. Assays in four different human cell lines indicated variations in both the snoRNA levels and their processing to active sno-miRNAs. In addition we show that box D elements are predominantly flanking at least one of the sno-miRNA strands, while the box C element locates within the sequence of the sno-miRNA guide strand

Material Flow Analysis: A tool to support environmental policy decision making. Case-studies on the city of Vienna and the Swiss lowlands

This paper discusses the use of Material Flow Analysis (MFA) as a tool to support policy decision making in the field of resource and environmental management. In terms of policy, MFA can be used for early recognition, priority setting, to analyse and improve the effectiveness of measures and to design efficient material management strategies in view of sustainability. MFA has a high potential to be implemented as a guiding tool at the regional level, for example as part of a regional environmental management and audit system or as a part of the Local Agenda 21 process. Material management based on MFA is complementary to traditional environmental and resource management strategies, which have tended to focus heavily on specific environmental compartments, and measure the concentration of substances in various media. MFA, in contrast, provides an overview of the total system by linking the anthroposphere (that part of the biosphere in which humans' activities take place) with the environment. This system approach shifts the focus away from the back-end so-called 'filter strategies' to more pro-active front-end measures. MFA examines short- and long-term loadings rather than concentrations and highlights current and potential material accumulations, called material stocks. These stocks represent either potential environmental problems (e.g. large stocks of hazardous materials) or a potential source of future resources (e.g. urban mining). In this way, MFA can assist precautionary policy making by highlighting future environmental or resource issue problems without relying on signals of environmental stress. The objective of materials management is: firstly, to analyse material flows and stocks; secondly, to evaluate these results; and thirdly, to control material flows in view of certain goals such as sustainable development. MFA is an excellent tool for the first objective and is well suited to generate a base for the other two objectives. MFA results can be compared against environmental standards or can be interpreted using assessment or indicator methodologies (such as environmental impact assessment or ecological footprints). Selected results from two studies, carried out for the city of Vienna (substance management) and the Swiss lowlands (timber management), illustrate the use of MFA as a tool for early recognition (resource depletion and environmental quality), for priority setting and for effective policy making

Bacterial degradation of large particles in the southern Indian Ocean using in vitro incubation experiments

International audienceLarge particles (> 60 mm) were collected at 30 and 200 m water depth by in situ pumps in the southern Indian Ocean in January–February 1999. The samples were incubated under laboratory conditions with their own bacterial assemblages for 7–17 days in batches under oxic conditions in the dark. Particulate and dissolved fractions of organic carbon , amino acids, sugars and lipids, as well as bacterial production were quantified over time. During the experiments, 32–38% and 43–50% of total organic carbon (TOC) was mineralized and considered as labile material in the Polar Front Zone (PFZ) and Sub-Antarctic region (SAr), respectively. This material was utilized with a bacterial growth efficiency (BGE) of 10–21% (PFZ) and 12–17% (SAr), with the lower values being observed for surface samples (30 m). These results imply that most (79–90%) of the incorporated carbon from large particles was respired as CO 2. The study revealed that the initial relative abundance of the three main classes of organic matter, including sugars, amino acids and lipids, varied greatly between SAr and PFZ, with sugars being more abundant in SAr (15–19% of TOC) than in PFZ (8–9% of TOC). In the PFZ, mineralization rates of amino acids and lipids were two to ten fold higher than those of sugars, whereas the opposite was observed in SAr biodegradation experiments. Moreover, our results suggested that organic carbon is mineralized by bacteria more rapidly in the euphotic zone of the SAr than the PFZ. The differences observed between the two sites may be related to the more rapid dissolution of silica as well as the higher temperatures and bacterial production encountered in SAr waters. The bacterial processes apparently affect the composition of material sinking to the ocean interior.

The Green Edge cruise: investigating the marginal ice zone processes during late spring and early summer to understand the fate of the Arctic phytoplankton bloom

The Green Edge project was designed to investigate the onset, life, and fate of a phytoplankton spring bloom (PSB) in the Arctic Ocean. The lengthening of the ice-free period and the warming of seawater, amongst other factors, have induced major changes in Arctic Ocean biology over the last decades. Because the PSB is at the base of the Arctic Ocean food chain, it is crucial to understand how changes in the Arctic environment will affect it. Green Edge was a large multidisciplinary, collaborative project bringing researchers and technicians from 28 different institutions in seven countries together, aiming at understanding these changes and their impacts on the future. The fieldwork for the Green Edge project took place over two years (2015 and 2016) and was carried out from both an ice camp and a research vessel in Baffin Bay, in the Canadian Arctic. This paper describes the sampling strategy and the dataset obtained from the research cruise, which took place aboard the Canadian Coast Guard ship (CCGS) Amundsen in late spring and early summer 2016. The sampling strategy was designed around the repetitive, perpendicular crossing of the marginal ice zone (MIZ), using not only ship-based station discrete sampling but also high-resolution measurements from autonomous platforms (Gliders, BGC-Argo floats …) and under-way monitoring systems. The dataset is available at https://doi.org/10.17882/86417 (Bruyant et al., 2022)

The Green Edge cruise: Understanding the onset, life and fate of the Arctic phytoplankton spring bloom

Abstract. The Green Edge project was designed to investigate the onset, life and fate of a phytoplankton spring bloom (PSB) in the Arctic Ocean. The lengthening of the ice-free period and the warming of seawater, amongst other factors, have induced major changes in arctic ocean biology over the last decades. Because the PSB is at the base of the Arctic Ocean food chain, it is crucial to understand how changes in the arctic environment will affect it. Green Edge was a large multidisciplinary collaborative project bringing researchers and technicians from 28 different institutions in seven countries, together aiming at understanding these changes and their impacts into the future. The fieldwork for the Green Edge project took place over two years (2015 and 2016) and was carried out from both an ice-camp and a research vessel in the Baffin Bay, canadian arctic. This paper describes the sampling strategy and the data set obtained from the research cruise, which took place aboard the Canadian Coast Guard Ship (CCGS) Amundsen in spring 2016. The dataset is available at https://doi.org/10.17882/59892 (Massicotte et al., 2019a)