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

Résumé : La Petite Mer de Gavres est une zone conchylicole, classée salubre, et exploitée en pêche à pied, avec une commercialisation directe difficile à contrôler. A la suite de problèmes de salubrité rencontrés sur les coquillages de cette zone, une étude bactériologique a été réalisée par IFREMER de juin 1986 à septembre 1987, suivie en 1988 d'une comparaison des contaminations des différentes espèces de coquillages. Ces études montrent que l'insalubrité de certains coquillages de la petite Mer de Gavres est particulièrement évidente pour les fouisseurs (coques et palourdes). Malgré la proximité des sources de pollutions de la Rade de Lorient et la petitesse du bassin versant de la Petite Mer, c'est ce dernier qui la contamine, notamment aux abords du bourg de Riantec qui apparaît nettement insalubre. Cette pollution par les eaux douces d'un bassin versant très limité induit évidemment une forte saisonnalité des contaminations qui augmentent significativement en automne-hiver.

Droits : 1989 Ifremer
http://archimer.ifremer.fr/doc/00128/23945/21903.pdf
http://archimer.ifremer.fr/doc/00128/23945/

Éditeur(s) : HAL CCSD Le Cherche midi CNRS
Résumé : 192 pages
National audience
https://hal.archives-ouvertes.fr/hal-01118878

ISBN : 978-2-7491-4075-9
hal-01118878
https://hal.archives-ouvertes.fr/hal-01118878

Résumé : Tahiti’s pearl farming industry plays a major socio-economic role in French Polynesia. In an increasingly competitive market where the production of high quality pearls becomes essential, research can help secure and ensure sustainable production. In that context, Ifremer, in close collaboration with the “direction des resources marines” (French Polynesian government agency) has developed research projects on the “sustainable development of pearl farming”. This program is organized along 3 axes: (1) understanding the animal physiology and initiating a genetically selective breeding program of donor oysters; (2) understanding pearl oyster larvae dispersal and recruitment; (3) understanding the molecular mechanisms underlying biomineralization processes during shell and pearl formation. It is in this frame that we have developed a highthroughput Expressed Sequence Tags pyrosequencing program on the calcifying mantle, combined with proteomic analyses of the shell and pearl. We analyzed 276738 EST sequences, leading to the constitution of a P. margaritifera mantle transcripts catalogue of 82 sequences potentially involved in biomineralization. Our results provided direct evidence that our ESTs data set covers a large number of the matrix proteins of P. margaritifera. In addition, our proteomic analysis enabled us to retrieve, in silico, all the sequences from P. margaritifera involved in the biomineralization process already published on databases. Integration of these two methods allowed, for the first time, the global composition of calcifying tissue and calcified structures to be examined in tandem.
Recent Advances in Pearl Research—Proceedings of the International Symposium on Pearl Research 2011.Edited by Shugo Watabe, Kaoru Maeyama and Hiromichi Nagasawa. 2013. ISBN : 978-4-88704-158-5. pp.184-194

Droits : 2013 TERRAPUB. All rights reserved.
http://archimer.ifremer.fr/doc/00167/27840/26049.pdf
http://archimer.ifremer.fr/doc/00167/27840/

Éditeur(s) : HAL CCSD
Résumé : International audience
This study was designed to identify in the pearl oyster Pinctada margaritifera, used as a bio-accumulator, molecular biomarkers for the presence of heavy metals in the lagoon environment. Pearl oysters were exposed to 2 concentrations (1 and 10 μg L− 1) of cadmium (Cd) and chromium (Cr) compared to a control. Twelve target genes encoding proteins potentially involved in the response to heavy metal contamination with antioxidant, detoxification or apoptosis activities were selected. P. margaritifera accumulated Cd but not Cr, and mortality was related to the amount of Cd accumulated in tissues. In response to Cd-Cr contamination, metallothionein (MT) was significantly up-regulated by Cd-Cr at both concentrations, while 7 others (SOD, CAT, GPX, GSTO, GSTM, CASP, MDR) were down-regulated. Based on the development of these molecular tools, we propose that the pearl oyster, P. margaritifera, could be used as a sentinel species for heavy metal contamination in the lagoons of tropical ecosystems.
. Marine Pollution Bulletin

hal-01526382
https://hal.archives-ouvertes.fr/hal-01526382
DOI : 10.1016/j.marpolbul.2017.03.012
PUBMED : 28320509

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The ‘International Intercomparison Exercise of fCO₂ Systems’ was carried out in 1996 during the R/V Meteor Cruise 36/1 from Bermuda/UK to Gran Canaria/Spain. Nine groups from six countries (Australia, Denmark, France, Germany, Japan, USA) participated in this exercise, bringing together 15 participants with seven underway fugacity of carbon dioxide (fCO₂) systems, one discrete fCO₂ system, and two underway pH systems, as well as systems for discrete measurement of total alkalinity and total dissolved inorganic carbon. Here, we compare surface seawater fCO₂ measured synchronously by all participating instruments. A common infrastructure (seawater and calibration gas supply), different quality checks (performance of calibration procedures for CO2, temperature measurements) and a common procedure for calculation of final fCO₂ were provided to reduce the largest possible amount of controllable sources of error. The results show that under such conditions underway measurements of the fCO₂ in surface seawater and overlying air can be made to a high degree of agreement (±1 μatm) with a variety of possible equilibrator and system designs. Also, discrete fCO₂ measurements can be made in good agreement (±3 μatm) with underway fCO₂ data sets. However, even well-designed systems, which are operated without any obvious sign of malfunction, can show significant differences of the order of 10 μatm. Based on our results, no “best choice” for the type of the equilibrator nor specifics on its dimensions and flow rates of seawater and air can be made in regard to the achievable accuracy of the fCO₂ system. Measurements of equilibrator temperature do not seem to be made with the required accuracy resulting in significant errors in fCO₂ results. Calculation of fCO₂ from high-quality total dissolved inorganic carbon (CT) and total alkalinity (AT) measurements does not yield results comparable in accuracy and precision to fCO₂ measurements.
ISSN: 0304-4203

hal-01245605
https://hal.archives-ouvertes.fr/hal-01245605
DOI : 10.1016/S0304-4203(00)00080-3

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Bivalve larvae and hydrographic parameters were sampled over a range of spatio-temporal scales in a deep atoll lagoon. Bivalve larvae abundances were very high throughout the year: 18,550 m(-3) in average. Larvae were (i) concentrated at mid-depth with nocturnal ascent and diurnal descent, (ii) heterogeneously dispersed at the lagoon scale, (iii) subject to day-to-day variation in abundance and (iv) transferred between different parts of the lagoon providing evidence of intra-lagoonal connectivity. The primacy of physical factors was seen on large spatial scale with the diluting effect of water renewal and transfers by hydrodynamics. On smaller spatial scale, the primacy of biological processes was recognised, with larval swimming activity leading to dial vertical migration correlated with food concentration. Variations in larval abundance were driven by bivalve reproductive activity correlated with meteorological conditions (i.e. windy periods). Finally, relationship between bivalve larvae patterns and pearl oyster (Pinctada margaritifera) settlement structuring is discussed. (C) 2012 Elsevier Ltd. All rights reserved.
Marine Pollution Bulletin (0025-326X) (Pergamon-elsevier Science Ltd), 2012 , Vol. 65 , N. 10-12 , P. 453-462

Droits : 2012 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00101/21200/20690.pdf
DOI:10.1016/j.marpolbul.2011.12.028
http://archimer.ifremer.fr/doc/00101/21200/