Éditeur(s) : American Geophysical Union
Résumé : As part of the French CLIPPER project, an eddy permitting model of the Atlantic circulation has been run for 22 years. The domain has open boundaries at Drake passage and at 30 degreesE, from Africa to Antarctica. The simulated mean circulation, as well as the eddy activity, is satisfactory for a 1/3 degrees model resolution, and the meridional heat transport at 30 degreesS is within the range estimated from observations. We use the "mixed" open boundary algorithm of Barnier et al. [1998], which has both a radiation condition and a relaxation to climatology. The climatological boundary forcing strongly constrains the solution in the whole domain. The model heat balance adjusts through the surface (heat flux retroaction term) more than the open boundaries. The radiation phase velocities calculated within the algorithm are analyzed. This shows, quite surprisingly, that both the eastern and western boundaries have a similar behavior, regardless of the preferred directions for advection (mainly eastward) and wave propagation (mainly westward). Our results confirm that open boundary algorithms behave differently according to the dynamics of the region considered. The passive boundary condition that Penduff et al. [2000] applied successfully in the north eastern Atlantic does not work in the present South Atlantic model. We emphasize the need for a careful prescription of the climatology at the open boundary, for which a new approach based on synoptic sections is implemented.
Journal of Geophysical Union - Research C - Oceans (0148-0227) (American Geophysical Union), 2001-10 , Vol. 106 , N. C10 , P. 22115-22129

Droits : 2001 American Geophysical Union
http://archimer.ifremer.fr/doc/2001/publication-454.pdf
DOI:10.1029/2000JC000376
http://archimer.ifremer.fr/doc/00000/454/

Éditeur(s) : HAL CCSD Cold Spring Harbor Laboratory Press
Résumé : International audience
The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein-coding mRNAs and a considerable amount of different noncoding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), which emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs, and a number of uncharacterized long noncoding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell-specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.
ISSN: 1355-8382

hal-00985894
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00985894
DOI : 10.1261/rna.043729.113
PUBMED : 24554440

Éditeur(s) : HAL CCSD
Résumé : International audience
Field trip Guidebook, CorseAlp 2011 Meeting of Geology

hal-00604006
https://hal.archives-ouvertes.fr/hal-00604006

Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The volume comprises some of the contributions presented during the 10th edition of the Alpine Meeting "CorseAlp 2011". It has been held in Saint Florent (Corsica) between 10th and 16th of April 2011 under the auspices of Societé Geologique de France, Società Geologica Italiana and the INGV (Istituto Nazionale di Geofisica e Vulcanologia) and with the collaboration of colleagues of Université de Corse (M.-M. Spella, M. and J. Ferrandini and L. Ciancaleoni) and the support of the city council of S. Florent. The meeting was framed in the series of "Alpine Workshops" e.g., Siegesmund et al. (2008), Handy and Rosenberg (2011), which are held every two years to develop interdisciplinary research on Alpine-type orogens. It hosted a variety of topical sessions from regional geology to process-oriented field and laboratory studies and gave the opportunity to collect multidisciplinary and multiscale approaches to geodynamic studies including continental rifting and ocean opening, oceanic and continental subduction, late- to post orogenic extension, exhumation of deep seated rocks, back-arc opening and microcontinent rotation, interfering orogenic-scale tectonics and surface processes, tectonics and seismic hazard within the Alpine chain and Mediterranean realms.
ISSN: 0040-1951

hal-00795580
https://hal.archives-ouvertes.fr/hal-00795580

Éditeur(s) : HAL CCSD
Résumé : International audience
Kisspeptins are well known as mediators of the coordinated communication between the brain-pituitary axis and the gonads in many vertebrates. To test the hypothesis that gonadal steroids regulate kiss1 and kiss2 mRNA expression in European sea bass (a teleost fish), we examined the brains of gonad-intact (control) and castrated animals, as well as castrated males (GDX) and ovariectomized females (OVX) that received testosterone (T) and estradiol (E2) replacement, respectively, during recrudescence. In GDX males, low expression of kiss1 mRNA is observed by in situ hybridization in the caudal hypothalamus (CH) and the mediobasal hypothalamus (MBH), although hypothalamic changes in kiss1 mRNA levels were not statistically different among the groups, as revealed by real-Time PCR. However, T strongly decreased kiss2 expression levels in the hypothalamus, which was documented in the MBH and the nucleus of the lateral recess (NRLd) in GDX T-Treated sea bass males. Conversely, it appears that E2 evokes lowkiss1mRNAin the CH, while there were cells expressing kiss2 in the MBH and NRLd in these OVX females. These results demonstrate that kisspeptin neurons are presumably sensitive to the feedback actions of sex steroids in the sea bass, suggesting that the MBH represents a major site for sex steroid actions on kisspeptins in this species. Also, recent data provide evidence that both positive and negative actions occur in key factors involved in sea bass reproductive function, including changes in the expression of gnrh-1/gonadotropin, cyp19b, er and ar genes and sex steroid and gonadotropin plasma levels in this teleost fish. © 2016. Published by The Company of Biologists Ltd.
Journal of Experimental Biology

hal-01406072
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01406072
DOI : 10.1242/jeb.137364
PUBMED : 27591305

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Orogenic wedges locally present chaotic tectonostratigraphic units that contain exotic blocks of various size, origin, age and lithology, embedded in a sedimentary matrix. The occurrence of ophiolitic blocks, sometimes huge, in such “mélanges” raises questions on (i) the mechanisms responsible for the incorporation of oceanic basement rocks into an accretionary wedge and (ii) the mechanisms allowing exhumation and redeposition of these exotic elements in “mélanges” during wedge growth.To address these questions, we present the results of a series of analogue experiments performed to characterize the processes and parameters responsible for accretion, exhumation and tectonosedimentary reworking of oceanic basement lithospheric fragments in an accretionary wedge.The experimental setup is designed to simulate the interaction between tectonics, erosion and sedimentation. Different configurations are applied to study the impact of various parameters, such as irregular oceanic floor due to structural inheritance, or the presence of layers with contrasted rheology that can affect deformation partitioning in the wedge (frontal accretion vs basal accretion) influencing its growth. Image correlation technique allows extracting instantaneous velocity field, and tracking of passive particles. By retrieving the particle paths determined from models, the pressure-temperature path of mélange units or elementary blocks can be discussed. The experimental results are then compared with observations from ophiolite-bearing mélanges in Taiwan (Lichi and Kenting mélanges) and Raman spectroscopy of carbonaceous material (RSCM) Thermometry data on rocks from the northern Apennines (Casanova mélange). A geological scenario is proposed following basic observations. The tectonic evolution of the retroside of doubly vergent accretionary wedges is mainly controlled by backthrusting and backfolding. The retro wedge is characterized by steep slopes that are prone to gravitational instabilities. It triggers submarine landslides inducing huge mass transfers. This erosion combined with backthrusting could favour exhumation of the ophiolitic fragments formerly accreted at the base of the wedge along the rough seafloor-sediments interface. Such an exhumed material can be reworked and deposited as debris- flows in proximal basins located at the foot of the retrowedge slope forming a tectono-sedimentary mélange. These syntectonic basins are continuously deformed and involved in prograding backthrusting-induced deformation.
ISSN: 0264-3707

hal-01395127
https://hal.archives-ouvertes.fr/hal-01395127
DOI : 10.1016/j.jog.2016.05.008

Éditeur(s) : HAL CCSD
Rendiconti della Societa Geologica Italianna, Nuova Serie

hal-00411132
https://hal.archives-ouvertes.fr/hal-00411132

Éditeur(s) : HAL CCSD
Résumé : CorseAlp 2011 was held in April 2011. A link to the website is here: CorseAlp 2011. The CorseAlp field trips were designed to introduce the participants to the general features of the geology of Alpine Corsica and to recent specific discoveries. Field trip 1 focused on the geology of the Ocean-Continent Transition preserved in the Monte San Petrone, in Central Corsica, which was subducted to eclogite facies conditions during the Alpine orogeny. Field Guide 1 itinerary: Bastia, Golo Valley, Piedicroce, M.S.Petrone and S.Florent.
Journal of the Virtual Explorer

hal-00689755
https://hal.archives-ouvertes.fr/hal-00689755

Éditeur(s) : HAL CCSD
Résumé : CorseAlp 2011 was held in April 2011. A link to the website is here: CorseAlp 2011. The CorseAlp field trips were designed to introduce the participants to the general features of the geology of Alpine Corsica and to recent specific discoveries. The three-day post-workshop field trip (Field trip 2) focused on the general architecture of Alpine Corsica in an EW transect between the Balagne region and Bastia. First day: The internal zones of Alpine Corsica: from Bastia to Saint Florent. Intinerary: Saint Florent, Serra di Pigno, Cima Malaspina, Patrimonio, Saint Florent. Second day: The Tenda massif and its eastern margin. Intinerary: Saint Florent, Casta, Fontana Porragghia, Rue de Morello, Fontana a Murello quarry; Fornali. Third day: The external zones of Alpine Corsica in the Balagne region. Intineray: Saint Florent, Colle di U'Vezzu, Ostriconi, Belgodere, San Sebastiano Chapel, San Colombano, Ponte Leccia, Francardo, Bastia.
Journal of the Virtual Explorer

hal-00688971
https://hal.archives-ouvertes.fr/hal-00688971

Éditeur(s) : HAL CCSD
Résumé : Corsica is located in the Mediterranean sea, about 90 km from the Italian coast of Tuscany and 175 km from the French Riviera. This relatively large island stretches for 180 km in the north-south direction and 85 Km east-west. The rugged landscape, with a mean elevation of ca. 500 m and the highest point at 2710 m (Monte Cinto) is interrupted only by a major plain along the east coast. CorseAlp 2011 was held in April 2011. A link to the website is here: CorseAlp 2011. The CorseAlp field trips were designed to introduce the participants to the general features of the geology of Alpine Corsica and to recent specific discoveries. Field trip 1 focused on the geology of the Ocean-Continent Transition preserved in the Monte San Petrone, in Central Corsica, which was subducted to eclogite facies conditions during the Alpine orogeny. The three days post-workshop field trip (Field trip 2) focused on the general architecture of Alpine Corsica in an EW transect between the Balagne region and Bastia. The main topics of Field trip 1 and 2 allow discussion about the overall evolution of Alpine Corsica in the framework of Mediterranean geodynamics, with a focus on the most controversial aspects.
Journal of the Virtual Explorer

hal-00688965
https://hal.archives-ouvertes.fr/hal-00688965

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The Alps/Apennines system, as well as many collisional orogens through the world, shows a finite deformation produced during a long geological history which involves numerous superimposed tectonic events. As a result, complex and often contrasted reconstructions for the setting and tectonics of the different stages of the growing and interfering Alps/Apennines system have been proposed. To enlight some of the geometric and kinematic signatures related to past geodynamics in the composite Alps(Corsica)/Apennines system, we analyse the major deformation processes, their superimposition, and resulting finite structural geometries in the currently growing Taiwan orogenic system. The Taiwan island and its offshore northward and southward prolongations represent the emerged and the sub-marine parts of an orogenic wedge related to the interactions between the Eurasian and the Philippine Sea and recording different subduction settings. Using the Taiwan actualistic geodynamic scenarios and the related first-order geometric-kinematic constraints, we will attempt a reconstruction of the tectonic evolution for the Corsica/Apennines orogenic system foregrounding the key role of continental subduction and subduction reversal during such evolution.
ISSN: 1437-3254

hal-00617149
https://hal.archives-ouvertes.fr/hal-00617149
DOI : 10.1007/s00531-010-0598-y

Éditeur(s) : Springer
Résumé : Series of sensitivity tests were performed with a z-coordinate, global eddy-permitting (1/4 degrees) ocean/sea-ice model (the ORCA-R025 model configuration developed for the DRAKKAR project) to carefully evaluate the impact of recent state-of-the-art numerical schemes on model solutions. The combination of an energy-enstrophy conserving (EEN) scheme for momentum advection with a partial step (PS) representation of the bottom topography yields significant improvements in the mean circulation. Well known biases in the representation of western boundary currents, such as in the Atlantic the detachment of the Gulf Stream, the path of the North Atlantic Current, the location of the Confluence, and the strength of the Zapiola Eddy in the south Atlantic, are partly corrected. Similar improvements are found in the Pacific, Indian, and Southern Oceans, and characteristics of the mean flow are generally much closer to observations. Comparisons with other state-of-the-art models show that the ORCA-R025 configuration generally performs better at similar resolution. In addition, the model solution is often comparable to solutions obtained at 1/6 or 1/10 degrees resolution in some aspects concerning mean flow patterns and distribution of eddy kinetic energy. Although the reasons for these improvements are not analyzed in detail in this paper, evidence is shown that the combination of EEN with PS reduces numerical noise near the bottom, which is likely to affect current-topography interactions in a systematic way. We conclude that significant corrections of the mean biases presently seen in general circulation model solutions at eddy-permitting resolution can still be expected from the development of numerical methods, which represent an alternative to increasing resolution.
Ocean Dynamics (1616-7341) (Springer), 2006-12 , Vol. 56 , N. 5-6 , P. 543-567

Droits : © Springer 2006. Part of Springer Science+Business Media
http://archimer.ifremer.fr/doc/2006/publication-3514.pdf
DOI:10.1007/s10236-006-0082-1
http://archimer.ifremer.fr/doc/00000/3514/