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
Résumé : National audience
Des expériences dans un bassin de 30 m x 30 m ont été réalisées dans l'objectif de caractériser la dynamique d'un courant d'arrachement et les évolutions morphologiques associées. La plage de sable fin (diamètre médian 166 microns) couvrait la largeur du bassin (30 m en longshore ) pour un profil total de 20 m cross-shore . La formation de courants sagittaux a été forcée par une houle frontale (spectre de Jonswap) avec un déficit d'énergie au centre du bassin. Une séquence accrétive complète de plage intermédiaire à simple barre (selon classification de WRIGHT & SHORT, 1984) a été reproduite. La barre s'est progressivement tridimensionnalisée en forme de croissant puis s'est connectée au haut de plage avec la présence de deux chenaux profonds qui se sont ensuite comblés pour obtenir une plage à terrasse au bout de plusieurs dizaines d'heures. L'association des mesures hydrodynamiques et morphodynamiques montre que le comblement des chenaux est alimenté par le haut de plage.
XI èmes Journées Nationales Génie Côtier - Génie Civil
Sables d'Olonne, France

hal-00861953
https://hal.archives-ouvertes.fr/hal-00861953

Éditeur(s) : Elsevier
Résumé : The fining upward trend commonly described on levees of turbidite systems can be either attributed to changes in the sediment supply (external forcing = allocyclic) or changes in the spillover processes related to the growth of the levee (internal forcing = autocyclic). However the real causes remain speculative and difficult to demonstrate. Knowledge of vertical change in flow velocity (or grain size) in turbidity currents, of the turbidity current's height, as well as the growth rate of a levee are theoretically sufficient to describe the evolution of the grain size of a leveed turbidite sequence deposited by spillover processes. A piston core (MD99-2344) retrieved on the right levee of the Petit-Rhone neofan, sampled an 8.50 m long turbidite sequence containing more than one hundred turbidite beds and showing a marked fining upward trend. With the help of two profiles describing respectively the vertical velocity [Stacey, M. and Bowen, A.J., 1988b. The vertical structure of turbidity currents and a necessary condition for self-maintenance, Journal of Geophysical Research, pp. 3543-3553.] and the vertical grain size [Migeon, S., 2000. Dunes geantes et levees sedimentaires en domaine marin profond: approche morphologique, sismique et sedimentologique. PhD Thesis, Universite Bordeaux 1, Talence, France, 288 pp.] of a turbidity current, and a simple graphical method, we test several hypotheses on the height of the turbidity current and on the grain size at the bottom of the turbidity current and we attempt to reproduce the vertical fining upward trend. Our results show that the fining upward trend of the turbidite facies can be explained by the aggradation of the turbidite levee and the gradual confinement of the turbidity currents in the channel. This is, therefore, an autocyclical phenomenon. However a high frequency variability of the grain size overprinted on the trend cannot be explained by internal forcing and is believed to be allocyclical, depending on changes to the sediment input. The vertical grain-size profile allows more realistic flow conditions to be determined and shows that the vertical velocity profile does not describe the ability of turbidity current to transport sediment. This simple graphical method allows a better understanding and quantification of the forcing on turbidite deposits and improves description of the characteristics of the turbidity currents from the grain size of the deposits.
Marine Geology (0025-3227) (Elsevier), 2006-12 , Vol. 234 , N. 1-4 , P. 191-213

Droits : 2006 Elsevier
http://archimer.ifremer.fr/doc/2006/publication-2311.pdf
DOI:10.1016/j.margeo.2006.09.019
http://archimer.ifremer.fr/doc/00000/2311/

Éditeur(s) : Elsevier
Résumé : The composition of the glacial vegetation of southern French plains has been a matter of debate for several decades. Vegetation is considered as steppic according to French and Spanish lacustrine pollen records whereas cave deposits suggest the presence of mesothermophilous trees through the Last Glacial Maximum. In our paper, we display new palynological records from marine sediments of the Gulf of Lions. They indicate the presence of Abies, Picea and deciduous Quercus in the Gulf of Lions, certainly located in the drainage basins of the Pyreneo-Languedocian rivers. These populations that were sensitive to short climatic events during Marine Isotopic Stage 2 could have been linked to northeastern Spanish and southeastern French relicts already evidenced by phylogenetic data. These trees were absent from the Rhone drainage basin during the deglaciation and certainly also disappeared from the Pyreneo-Languedocian drainage basins from ca 17 to 15 ky cal BP. Finally, the Last Glacial Maximum does not appear as stable, cold and dry as previously thought.
Quaternary Science Reviews (0277-3791) (Elsevier), 2007-04 , Vol. 26 , N. 7-8 , P. 1037-1054

Droits : 2007 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-2804.pdf
DOI:10.1016/j.quascirev.2006.12.009
http://archimer.ifremer.fr/doc/00000/2804/

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
This study describes a laboratory experiment on rip current circulations over a moveable bed. Rip current characteristics over eight contrasting nature-like beach morphologies are investigated. The seabed varied from reasonably alongshore uniform to strongly alongshore nonuniform with crescentic patterns and bar-rip morphologies, representative of a full morphological down-state sequence. The same offshore shore-normal waves were generated by the wavemaker for the eight situations with the same mean water level to study the sensitivity of rip current characteristics as a function of the beach morphology only. In each case, a 30 to 60 min video run was used to track a large number of drifters released within the surf zone. Results show the presence of classic rip current patterns with counterrotating cells and a relatively narrow offshore-directed jet varying from shore-normal to strongly skewed. Wave-driven circulations were strongly unstable. Computed standard deviations of flow intensity and direction provide high-resolution information on the spatial variability of rip current instabilities. Highly pulsating and weakly directionally variable offshore-directed flow is observed in the rip neck for well-developed bar-rip morphologies that turns into a weakly pulsating and highly directional variable rip current flow with decreasing beach alongshore nonuniformity. Proposing a definition of rip current intensity based on the rip current circulation geometry, rip current intensity was found to linearly increase with increasing measure of beach alongshore nonuniformity within both the low-energy and moderate-energy rip current regimes. To date, our laboratory experiment provides the first extensive quantitative rip current information during a full down-state sequence for a given wave condition.
ISSN: 0148-0227

hal-00602920
https://hal.archives-ouvertes.fr/hal-00602920
DOI : 10.1029/2010JC006343

Éditeur(s) : HAL CCSD World Scientific
Résumé : The present paper presents a laboratory experiment of rip current circulations over a moveable bed. The rip current characteristics over four distinct beach morphologies, exhibiting more or less developed nature-like bar-rip morphology,were investigated. For each video run, the same off shore shore-normal waves were generated by the wave maker with the same mean water level in order to study the sensitivity of the rip current characteristics as a function of the beach morphology only. In each case, a 1-hour video run was used to track a large number (~30) of drifters released within the surf zone. Image coordinates were then rectifie d to still water level Cartesian coordinates to compute drifter velocities, mean characteristics and surf zone rete ntion rates. Results show the presence of classic rip current patterns with counter-rotating cells and a relatively narrowoffshore-directed jet with, for three of the situations, a reasonably symmetric shape. Non-surprisingly, it was found that rip current intensity increases with increasing relative depth of the rip channel. The wave-driven circulations were strongly unstable. Computed standard deviation in fl ow intensity and direction provides high resolution information on the spatial variability of the rip current insta bilities with, for instance, highly-pulsating and weakly directionally variable offshore-directed flow in the rip channel. Conversely to what was previously hypothesized in the literature, there was hardly trace of vortices being shed offs hore and drifters exiting the surf zone compartment were not systematically caught by a pulsating jet. The cause for drifter exiting the semi-enclosed surf zone compartment remains, however, elusive and deserves further investigations. The computed surf zone retention rates (~90%) were of the order of those previously observed in the field, with no clear relationship with the mean rip current velocity or relative depth of the rip channel. Further video-runs will have to be analyzed to explore potential explanations
Proceedings of Coastal Dynamics 2009 Impacts of Human Activities on Dynamic Coastal Processes

ISBN : 978-981-4282-46
hal-00854534
https://hal.archives-ouvertes.fr/hal-00854534