AtlantECO Deliverable 2.1: AtlantECO-BASE1

This deliverable reports on Task 2.2 ‘Assembly of observations about microbiomes, plastics, the plastisphere and carbon fluxes’. It used protocols established in task 2.1 ‘Definition of common standards for the assembly of spatially explicit data’ to compile, quality-control and grid existing high-quality observations into a knowledge base of observations (D2.1). Data included into AtlantECO-BASE1 consisted of contributions from the five following data sources and tasks: Task 2.2.1 ‘Microbiome data from traditional microscopy (presence-absence, abundance and biomass)’, Task 2.2.2 ‘Microbiome data from state-of-the-art optical/imaging analysis’, Task 2.2.3 ‘Microbiome and plastisphere data from state-of-the-art genetic analyses’, Task 2.2.4 ‘Nano-, micro and macroplastics data from state-of-the-art sampling methods’, and Task 2.2.5 ‘Carbon flux data from estimated from high resolution bio-optical sensors’. Additional data contributions and mapping efforts from other partners and work packages (Task 2.3) are also included. A comprehensive list and description of all data sets collected can be found in the Appendix Tables to this document

Inhibition of 5′ to 3′ mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16

After deadenylation, most cytoplasmic mRNAs are decapped and digested by 5′ to 3′ exonucleases in Saccharomyces cerevisiae. Capped and deadenylated mRNAs are degraded to a lesser extent by 3′ to 5′ exonucleases. We have used a method, based on the electroporation of in vitro synthetised mRNAs, to study the relative importance of these two exonucleolytic pathways under stress conditions. We show that derepression of GCN4 upon amino acid starvation specifically limits the 5′-to-3′-degradation pathway. Because adenosine 3′-5′ biphosphate (pAp), which is produced by Met16p, inhibits this degradation pathway to a comparable extent, we were prompted to analyse the role of Met16p in this phenomenon. We show that the inhibitory effects of amino acid limitation on 5′ to 3′ mRNA degradation are absent in a met16 mutant. We therefore conclude that the GCN4 dependence of MET16 expression is responsible for the decrease in 5′ to 3′ digestion under stress conditions and that cells use pAp as a signal to limit 5′ to 3′ RNA degradation under stress conditions. Because 3′ to 5′ mRNA degradation is unaffected, the relative importance of this pathway in the decay of certain RNAs may be increased under stress conditions

Sédiments de dragage : variabilité des sédiments, retour d'expérience sur les pratiques de dragage et sur la valorisation à terre en France

International audienceL'accumulation de sédiments dans les ports, les chenaux d'accès, les canaux, les rivières et les fleuves empêche la circulation des bateaux et, lorsqu'ils sont pollués, impacte la qualité chimique des milieux aquatiques. Des opérations de dragage sont réalisées pour rétablir le bon usage ou la bonne qualité des eaux. En France, les quantités annuelles de sédiments dragués pour l'entretien des cours d'eau, fleuves et canaux sont de l'ordre de 5 millions de m3 et de l'ordre de 50 Mm3 pour les ports maritimes. La création de structures nouvelles génère également des quantités de sédiments de dragage non incluses dans ces chiffres. Les techniques de remise en suspension et/ou d'immersion sont les plus couramment utilisées, mais elles sont désormais restreintes, au titre de la réglementation sur l'eau. Les quantités gérées à terre (dépôts, régalage, valorisation en techniques routières, aménagement et comblement de carrière...) sont estimées à environ 2 Mm3/an pour les sédiments d'eau douce et de l'ordre de 5 Mm3/an pour les sédiments marins. Face à de tels volumes, l'enjeu est de permettre une gestion à terre sécurisée sur le plan environnemental et juridique. Le Grenelle de l'Environnement et la loi associée ont souligné la nécessité d'une amélioration de la gestion des sédiments. La caractérisation de la variabilité des sédiments de dragage vis-à-vis des transferts de contaminants est essentielle pour permettre de définir des filières de gestion à terre viables pour les gros volumes concernés. L'INERIS réalise actuellement un recueil de données et une étude statistique sur la variabilité physico-chimique des sédiments marins et terrestres à l'échelle nationale française, en teneur brute et en relargage. Cette étude s'appuie sur les données de Voies Navigables de France (VNF), des Agences de l'Eau, du Réseau national de surveillance de la qualité de l'Eau et des sédiments des POrts Maritimes (REPOM) de l'IFREMER et du projet SEDIMARD 83, de 1994 à 2008. Actuellement, l'étude rassemble 44 000 données portant sur la granulométrie, la teneur en carbone organique, en métaux toxiques, en composants organiques, sur des caractérisations microbiologiques, ainsi que sur des tests d'écotoxicologie pour un ensemble de 2500 échantillons de sédiments fluviaux et marins. Le tableau ci-dessous présente les teneurs minimales et maximales rencontrées dans les données à ce jour traitées. Cette étude s'est enrichie d'un retour d'expérience sur les pratiques des opérations de dragage et de valorisation à terre des sédiments au regard de l'impact potentiel sur le milieu aquatique. L'intervention de l'INERIS présentera les conclusions préliminaires de cette étude, qui s'achèvera fin décembre 2009

Ribosomes initiating translation of the hbs mRNA protect it from 5′-to-3′ exoribonucleolytic degradation by RNase J1

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Additional Layer of Regulation via Convergent Gene Orientation in Yeasts

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Controlling Bragg gaps induced by electric boundary conditions in phononic piezoelectric plates

International audienceA Phononic Crystal (PC), constituted of a homogeneous piezoelectric plate covered by a 1Dperiodic arrangement of thin metallic electrodes on both surfaces, is studied. The application ofElectric Boundary Conditions (EBCs) on the electrodes enables the propagation control of theultrasonic guided waves in the PC. The band structure is investigated for different EBCs: theelectrodes are either at a floating potential or they are alternately short-circuited and at a floatingpotential. In the latter case, a Bragg gap appears for the fundamental S$_0$ guided Lamb mode. Theseresults are verified experimentally and compared to finite element calculations. A physical interpretationis also given, relying on the symmetry of the electric potential fields associated with theseguided mode

Hybridization bandgap induced by an electrical resonance in piezoelectric metamaterial plates

International audienceWe demonstrate numerically and experimentally the opening of a locally resonant bandgap in an active phononic crystal (PC) made of a homogeneous piezoelectric plate covered by a 1D periodic array of thin electrodes connected to inductive shunts. The application of periodic electrical boundary conditions (EBCs) enables an at will tailoring of the dispersion properties of the PC plate, thus leading to a control of the dispersion of the propagating guided elastic waves in the plate. Depending on the nature of the EBCs, several bandgaps open up, the most important being a Hybridization Bandgap (HBG) in the subwavelength regime. The PC behaves as a locally resonant metamaterial. The HBG originates from the interaction of propagating elastic waves (Lamb modes) with an electrical resonant mode whose dispersion can be effectively described through an equivalent transmission line model

No-Go Decay mRNA cleavage in the ribosome exit tunnel produces 5′-OH ends phosphorylated by Trl1

International audienceThe No-Go Decay (NGD) mRNA surveillance pathway degrades mRNAs containing stacks of stalled ribosomes. Although an endoribonuclease has been proposed to initiate cleavages upstream of the stall sequence, the production of two RNA fragments resulting from a unique cleavage has never been demonstrated. Here we use mRNAs expressing a 3′-ribozyme to produce truncated transcripts in vivo to mimic naturally occurring truncated mRNAs known to trigger NGD. This technique allows us to analyse endonucleolytic cleavage events at single-nucleotide resolution starting at the third collided ribosome, which we show to be Hel2-dependent. These cleavages map precisely in the mRNA exit tunnel of the ribosome, 8 nucleotides upstream of the first P-site residue and release 5′-hydroxylated RNA fragments requiring 5′-phosphorylation prior to digestion by the exoribonuclease Xrn1, or alternatively by Dxo1. Finally, we identify the RNA kinase Trl1, alias Rlg1, as an essential player in the degradation of NGD RNAs

Cytoplasmic Control of Sense-Antisense mRNA Pairs

Transcriptome analyses have revealed that convergent gene transcription can produce many 3′-overlapping mRNAs in diverse organisms. Few studies have examined the fate of 3′-complementary mRNAs in double-stranded RNA-dependent nuclear phenomena, and nothing is known about the cytoplasmic destiny of 3′-overlapping messengers or their impact on gene expression. Here, we demonstrate that the complementary tails of 3′-overlapping mRNAs can interact in the cytoplasm and promote post-transcriptional regulatory events including no-go decay (NGD) in Saccharomyces cerevisiae. Genome-wide experiments confirm that these messenger-interacting mRNAs (mimRNAs) form RNA duplexes in wild-type cells and thus have potential roles in modulating the mRNA levels of their convergent gene pattern under different growth conditions. We show that the post-transcriptional fate of hundreds of mimRNAs is controlled by Xrn1, revealing the extent to which this conserved 5′-3′ cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression