Near-inertial scattering by random flows

The impact of a turbulent flow on wind-driven oceanic near-inertial waves is examined using a linearised shallow-water model of the mixed layer. Modelling the flow as a homogeneous and stationary random process with spatial scales comparable to the wavelengths, we derive a transport (or kinetic) equation governing wave-energy transfers in both physical and spectral spaces. This equation describes the scattering of the waves by the flow which results in a redistribution of energy between waves with the same frequency (or, equivalently, with the same wavenumber) and, for isotropic flows, in the isotropisation of the wave field. The time scales for the scattering and isotropisation are obtained explicitly and found to be of the order of tens of days for typical oceanic parameters. The predictions inferred from the transport equation are confirmed by a series of numerical simulations. Two situations in which near-inertial waves are strongly influenced by flow scattering are investigated through dedicated nonlinear shallow-water simulations. In the first, a wavepacket propagating equatorwards as a result from the $\beta$-effect is shown to be slowed down and dispersed both zonally and meridionally by scattering. In the second, waves generated by moving cyclones are shown to be strongly disturbed by scattering, leading again to an increased dispersion.Comment: Accepted for publication in Phys. Rev. Fluid

Régulateurs transcriptionnels chez les archées hyperthermophiles et leurs virus (analyse moléculaire, fonctionnelle et génétique)

Chez les Archaea, tous les processus informationnels, transcription incluse, sont effectués par des protéines proches de celles des Eukarya. Alors que la machinerie transcriptionnelle des archées a été bien caractérisée structurellement et fonctionnellement, très peu d'informations sont disponibles sur la régulation de son activité. En travaillant à la fois avec des modèles cellulaires (crénarchée hyperthermophile Sulfolobus islandicus) et viraux, nous avons pu réaliser une étude approfondie de trois régulateurs transcriptionnels et mieux comprendre les mécanismes de régulation transcriptionnelle chez les archées. Au cours de cette thèse, deux régulateurs viraux, SvtR et AFV1p06, et un régulateur cellulaire, Sta1, ont été étudiés. Concernant SvtR, codé par le virus SIRV1 qui infecte S. islandicus, nous avons poursuivi la recherche précédente, qui avait permis de déterminer sa structure et sa fonction, en nous focalisant sur la caractérisation de l'ensemble de ses cibles dans le génome viral et sur l'étude de son mécanisme d'action. Pour cela, la séquence du site consensus reconnu par SvtR a été établie à l'aide de la mutagénèse systématique d'un de ses sites déjà caractérisés. Ce site est présent dans les promoteurs de dix gènes de SIRV1 montrant que SvtR pourrait réguler l'activité de plus de 20% des gènes viraux. Ses cibles incluent tous les gènes codant pour les protéines de la capside virale. L'analyse fonctionnelle réalisée sur une partie des sites de liaison de SvtR a permis de démontrer qu'il s'agit d'un régulateur polyvalent agissant, selon la cible, en tant que activateur ou répresseur transcriptionnel. En prenant comme modèle le promoteur du gène gp30, nous avons pu démontrer par plusieurs approches que la régulation de ce promoteur inclut la polymérisation de la protéine depuis son site de liaison principal jusqu à la TATA-box du promoteur. Il s agit d un mécanisme de régulation de transcription à distance original et inédit chez les archées. La structure de l autre régulateur viral étudié, AFV1p06, codé par le virus AFV1 qui infecte Acidianus hospitalis, révèle la présence au sein de cette protéine d un domaine en doigt de zinc C2H2, considéré jusqu à présent comme spécifique des eucaryotes. Nous avons démontré la capacité d AFV1p06 à se lier à l ADN avec une préférence pour les régions riches en GC. AFV1p06 est la première DNA binding protéine d archées de ce type caractérisée in vitro. Le troisième régulateur transcriptionnel, Sta1, est codé par le génome des Sulfolobales. Il est capable d activer la transcription de gènes viraux, ainsi que du gène chromosomique radA en réponse à un dommage à l ADN. Pour comprendre son rôle dans la cellule, nous avons tenté de réaliser, sans succès, un mutant knock-out du gène sta1 de S. islandicus RYE15A, ce qui indique que le gène sta1 serait un gène essentiel. L étude de l interaction hôte-virus sur le modèle S. islandicus LAL14/1 est un des sujets principaux de notre laboratoire. Le séquençage du génome de cette souche a ouvert la voie pour établir un système génétique. Plusieurs mutants KO de LAL14/1 (pyrEF-; CRISPR1) ont été construits. L impossibilité d inactiver un autre gène candidat, topR2, codant pour une réverse gyrase, indique qu il s agit d un gène essentiel. La construction du mutant CRISPR1 est la première étape pour obtenir un dérivé de LAL14/1 dépourvu de système CRISPR, un mutant très utile pour mieux comprendre l implication des CRISPRs dans le phénotype de résistance de LA14/1 au virus SIRV1 et leur rôle chez les archées en général. L ensemble des résultats de cette thèse contribue à la meilleure compréhension du fonctionnement moléculaire chez les archées et leurs virus.In Archaea cells all information processes, including transcription, are performed by the Eukarya-like proteins. While the transcriptional machinery of archaea has been well characterized structurally and functionally, very few information concerning the regulation of its activity is available. By working with both cell (crenarchaeota Sulfolobus islandicus) and viral models, we have performed an in-depth study of three transcriptional regulators: two viral regulators, SvtR and AFV1p06, and a cell regulator Sta1. The obtained results allow to better understand the mechanisms of transcriptional regulation in archaea. Concerning the protein SvtR encoded by the virus SIRV1 that infects S. islandicus, we continued the research project that had identified its structure and function. We were focused on identification and characterization of all of SvtR targets in the viral genome and on the study of the mechanisms of regulation. For this purpose, we established the sequence of consensus site recognized by SvtR using systematic mutagenesis of one of its previously characterized binding sites. This site is present in the promoters of 10 genes meaning that SvtR may regulate the activity of more than 20% of SIRV1 genes. Its targets include all known genes encoding proteins of the viral capsid. Functional analysis of SvtR has demonstrated that, according to the target, this protein is a versatile regulator acting as transcriptional activator or repressor. Taking as a model the gp30 gene promoter, we demonstrated by several approaches that regulation of this promoter includes the polymerization of the protein from its primary binding site towards the TATA-box. Such a mechanism of transcriptional regulation is new in archaea. Second, we performed a structural analysis of the protein AFV1p06 encoded by the virus AFV1 which infects Acidianus hospitalis. The structural analysis of AFV1p06 revealed the presence of a C2H2 zinc finger domain regarded hitherto as specific to eukaryotes. We demonstrated that AFV1p06 has ability to bind specifically to DNA sequences rich in GC. AFV1p06 is the first archaeal DNA binding protein with zinc finger domain characterized in vitro. The third transcriptional regulator, Sta1 is encoded by the genome of Sulfolobales. The protein RadA is able to activate the transcription of viral as well as chromosomal genes in response to DNA damage. To understand its role in the cell, we attempted, without success, to knockout the sta1 gene in S. islandicus RYE15A. This result indicates that the sta1 gene is probably essential. The strain S. islandicus LAL14 /1 is a model strain to study host-virus interaction in archaea. The sequencing of the genome of this strain opened the way to establish a genetic system for this model and allowed us to construct knockout mutants for several LAL14/1 genes (pyrEF-; CRISPR1). Our unsuccessful attempts to inactivate topR2, another candidate gene encoding reverse gyrase indicate that topR2 function could be essential. The construction of the CRISPR1 mutant opens the way to obtain a derivative of LAL14/1 entirely lacking the CRISPR system. Such a mutant will be very useful for the future studies of function and role of CRISPRs in archaea in general but also will allow to verify the hypothesis of involvement of CRISPRs in the phenotype of resistance of LA14/1 to SIRV1. All the results of this thesis contribute to an improved understanding of molecular mechanisms in archaeal cells and their viruses.PARIS-JUSSIEU-Bib.électronique (751059901) / SudocSudocFranceF

Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold

International audienceWhile the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers

On the concentration of near-inertial waves in anticyclones

An overlooked conservation law for near-inertial waves propagating in a steady background flow provides a new perspective on the concentration of these waves in regions of anticyclonic vorticity. The conservation law implies that this concentration is a direct consequence of the decrease in spatial scales experienced by an initially homogeneous wave field. Scaling arguments and numerical simulations of a reduced-gravity model of mixed-layer near-inertial waves confirm this interpretation and elucidate the influence of the strength of the background flow relative to the dispersion

Genomics and genetics of <em>Sulfolobus islandicus</em> LAL14/1, a model hyperthermophilic archaeon

The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin–antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus–host interactions and the CRISPR/Cas defence mechanism in Archaea

Lagrangian Time Series Models for Ocean Surface Drifter Trajectories

This paper proposes stochastic models for the analysis of ocean surface trajectories obtained from freely-drifting satellite-tracked instruments. The proposed time series models are used to summarise large multivariate datasets and infer important physical parameters of inertial oscillations and other ocean processes. Nonstationary time series methods are employed to account for the spatiotemporal variability of each trajectory. Because the datasets are large, we construct computationally efficient methods through the use of frequency-domain modelling and estimation, with the data expressed as complex-valued time series. We detail how practical issues related to sampling and model misspecification may be addressed using semi-parametric techniques for time series, and we demonstrate the effectiveness of our stochastic models through application to both real-world data and to numerical model output.Comment: 21 pages, 10 figure

Rapid injection of near-inertial shear into the stratified upper ocean at an Antarctic Circumpolar Current front

The impact on the upper ocean of the passage of a short, intense storm over a Southern Ocean site, in proximity to an Antarctic Circumpolar Current front, is characterized. The storm causes a wind-induced deepening of the mixed layer and generates an inertial current. Immediate post-storm observations indicate a mixed layer extending to approximately 50 m depth. Subsequent measurements show the upper-ocean to have re-stratified, injecting near-inertial shear in stratified waters within 1 day of the storm's passage. This time scale for the development of near-inertial shear is one order of magnitude shorter than that predicted by the ?-dispersion paradigm. The observed rapid changes in upper-ocean stratification point to the existence of an as yet undocumented, efficient mechanism for injection of near-inertial shear into the stratified ocean that is in turn associated with enhanced turbulence and mixing

2019 French oceanographic cruises report

This document reports on the French oceanographic cruises conducted in 2019. It was produced by Ifremer's Sismer (French acronym for Scientific information systems for the Sea) service which, in its role as the national oceanographic Data Center, is responsible inter alia for managing metadata, the data from French marine research cruises and updating the related information. It presents the french fleet's activity in 2019 and provides dynamic access to cruise information through the new research cruise catalogue: http://campagnes.flotteoceanographique.fr/.Ce document présente le bilan des campagnes océanographiques françaises conduites en 2019. Il a été réalisé par le Sismer (Systèmes d’Informations Scientifiques pour la MER), service de l’Ifremer, qui, dans sa fonction de centre national de données océanographiques, a, entre autres, la responsabilité de gérer les métadonnées, les données issues des campagnes à la mer françaises et donc de maintenir à jour l’information relative. Il présente l’activité 2019 de la flotte française et permet un accès dynamique à l’information des campagnes par l’intermédiaire du catalogue des campagnes : http://campagnes.flotteoceanographique.fr/

2013 French oceanographic cruises report

This document reports on the French oceanographic cruises conducted in 2013. It provides a detailed description of SISMER'S role in archiving cruise information and oceanographic data. It also gives an overall view of the French ocean research fleet's vessels and how they are used and provides dynamic access to cruise information through the web portal CALLED Nautilus: http://www.ifremer.fr/sismer/index_UK.htm. This report has been drawn up by IFREMER, and more specifically by the SISMER department in charge of managing cruise data. The electronic version of this document is available at the following address: http://www.ifremer.fr/sismer/UK/doc_UK.htm. Clicking on the hypertext links gives direct access to the cruise descriptions. The various reports for French oceanographic cruises are also available via IFREMER'S institutional archive, Archimer, at: http://archimer.ifremer.fr/default.jsp?la=en.Ce document présente le bilan des campagnes océanographiques françaises réalisées en 2013. Il décrit en détail le rôle du SISMER en matière d’archivage de l’information campagne et des données océanographiques. Il présente une vision globale des navires composant la flotte océanographique française et de leur utilisation et permet un accès dynamique à l’information des campagnes par l’intermédiaire du portail WEB Nautilus : http://www.ifremer.fr/sismer/index_FR.htm. Ce bilan a été réalisé par l’IFREMER, et notamment par le SISMER qui a la responsabilité de gérer l’information des campagnes. La version électronique de ce document se trouve à l’adresse suivante : http://www.ifremer.fr/sismer/FR/doc_FR.htm. Elle permet un accès direct aux descriptifs de campagne par l’intermédiaire de liens hypertextes. Les différents bilans des campagnes océanographiques françaises sont également disponibles sur le site Archimer, archive institutionnelle de l’ IFREMER, à l’adresse suivante : http://archimer.ifremer.fr/

2014 French oceanographic cruises report

This document reports on the French oceanographic cruises conducted in 2014. It was drawn up by IFREMER, and more specifically by the SISMER (French acronym for marine scientific information systems) department which is in charge of managing cruise data. It provides a detailed description of the role of the various players managing French ocean-going facilities and of the means to archive cruise information and oceanographic data. It presents the fleet's activity in 2014 and provides dynamic access to cruise information through the web portal CALLED Nautilus: http://www.ifremer.fr/sismer/index_UK.htm. Previous years' reports for French oceanographic cruises are also available via the Archimer website IFREMER'S INSTITUTIONAL archive, at: http://archimer.ifremer.fr/index.jsp?la=en.Ce document présente le bilan des campagnes océanographiques françaises réalisées en 2014. Il a été réalisé par l’IFREMER, et notamment par le SISMER (Systèmes d’Informations Scientifiques pour la MER) qui a la responsabilité de gérer l’information des campagnes. Il décrit en détail le rôle des différents acteurs en matière de gestion des moyens navals français et des moyens d’archivage de l’information des campagnes et des données océanographiques. Il présente l’activité 2014 de la flotte et permet un accès dynamique à l’information des campagnes par l’intermédiaire du portail WEB Nautilus : http://www.ifremer.fr/sismer/index_FR.htm. Les bilans des campagnes océanographiques françaises des années antérieures sont également disponibles sur le site Archimer, archive institutionnelle de l’IFREMER, à l’adresse suivante : http://archimer.ifremer.fr/