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 Coastal Education and Research Foundation
Résumé : The present work concerns cuspate spits: slightly symmetrical geomorphic features growing along the shoreline in shallow waters. We develop a new formulation for the dynamics of cuspate spits. Our approach relies on classical paradigms such as a conservation law to the shoreface scale and an explicit formula for alongshore sediment transport. We derive a non-linear diffusion equation and a fully explicit solution for the growth of cuspate spits. From this general expression, we found interesting applications to quantify shoreline dynamics in the presence of cuspate spits. In particular, we point out a simple method for the datation of a cuspate spit given a limited number of input parameters. Furthermore, we develop a method to quantify the mean alongshore diffusivity along a shoreline perturbed by well-defined cuspate spits of known sizes. Finally, we introduce a formal relationship between the geometric characteristics (amplitude, length) of cuspate spits, which reproduce the self-similarity of these geomorphic features.
ISSN: 0749-0208

hal-01234952
https://hal.archives-ouvertes.fr/hal-01234952
DOI : 10.2112/SI70-009.1

Éditeur(s) : HAL CCSD
Résumé : International audience
Among infertile couples, approximately half have to face with male infertility. In men with non-obstructive azoospermia, surgical retrieval testicular sperm extraction (TESE) of spermatozoa can be attempted, but with low success rates. A specific biomarker that could predict residual spermatogenesis would obviously be of interest before performing TESE. Thus, our aim was to identify biomarkers of residual spermatogenesis in seminal plasma of patients with non-obstructive azoospermia (NOA) using an isotope-coded protein label (ICPL)-based proteomic strategy coupled with conventional protein assay. This retrospective study was conducted in 40 men with NOA at the University Hospital of Nantes and Proteomics Core facility Biogenouest - Inserm U1085 - IRSET, Rennes, France. Comparative ICPL proteomic screening of frozen seminal plasma and correlation with TESE outcome allowed the identification of some differentially expressed proteins. Among them, lectin galactoside-binding, soluble 3 binding protein (LGALS3BP) expression was further confirmed using conventional protein assay, and its interest as a predictor of TESE outcome was then evaluated and compared with conventional clinical and hormonal markers of residual spermatogenesis. Among the 12 differentially expressed proteins identified with comparative ICPL proteomic strategy, seminal LGALS3BP expression was found to be significantly higher in men with successful TESE. Finally, comparative ICPL proteomic screening of seminal plasma appears to be a promising approach for the identification of biomarkers of residual spermatogenesis. LGALS3BP, associated with clinical and hormonal markers, could potentially be used as a predictive marker of successful TESE outcome in patients with NOA.
Andrology

inserm-00818514
http://www.hal.inserm.fr/inserm-00818514
DOI : 10.1111/j.2047-2927.2012.00059.x
PUBMED : 23427166

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Aim : To assess gaps in the representation of taxonomic, phylogenetic and functional diversity among coastal fishes in Mediterranean marine-protected areas (MPAs).
ISSN: 1366-9516

hal-01135644
https://hal.archives-ouvertes.fr/hal-01135644
DOI : 10.1111/ddi.12280

Éditeur(s) : HAL CCSD
Résumé : International audience
The present work concerns cuspate spits: slightly symmetrical geomorphic features growing along the shoreline in shallow waters. We develop a new formulation for the dynamics of cuspate spits. Our approach relies on classical paradigms such as a conservation law to the shoreface scale and an explicit formula for alongshore sediment transport. We derive a non-linear diffusion equation and a fully explicit solution for the growth of cuspate spits. From this general expression, we found interesting applications to quantify shoreline dynamics in the presence of cuspate spits. In particular, we point out a simple method for the datation of a cuspate spit given a limited number of input parameters. Furthermore, we develop a method to quantify the mean alongshore diffusivity along a shoreline perturbed by well-defined cuspate spits of known sizes. Finally, we introduce a formal relationship between the geometric characteristics (amplitude, length) of cuspate spits, which reproduce the self-similarity of these geomorphic features.
13th International Coastal Symposium
Durban, South Africa

hal-01006569
https://hal.archives-ouvertes.fr/hal-01006569
https://hal.archives-ouvertes.fr/hal-01006569/document
https://hal.archives-ouvertes.fr/hal-01006569/file/JCR_SI_70_009_Bouchette_et_al.pdf