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 Springer-Verlag
Résumé : International audience
High-resolution borehole strainmeters are usually installed in tectonically active regions in order to detect slow-slip events, and to estimate slow transients related to earthquake swarms. However, they are also sensitive to other numerous influences, internal or external. Furthermore, the quality of their coupling to the rock through cementation, and the mechanical properties of the rock mass around them, have a critical influence on their records. Many of the existing strainmeters present such problems, and the correction for these effects often remains a challenge. In this paper, we present the analysis of the records of a high-resolution borehole dilatometer (Sacks–Evertson), located in the seismically active rift of Corinth (Greece) (station TRZ in the Trizonia island). We show that the instrument suffers from an only partial-solid coupling, and that the nearby sea tides have a direct (through elastic response) and indirect (through pore-pressure diffusion) effect on the dilatation signal, which adds up to the solid tidal strain source. We propose a methodology that allows, in a first step, to better separate the internal (solid tide) from the external (air pressure, sea level) influences, by calculating a frequency-dependent transfer function outside the range of the tidal periods. We then extrapolate this function, in particular at the tidal periods. In a second step, the resulting variation with frequency of the coupling coefficients with sea level led us to estimate the proportion of instrument not solidly cemented to rock (thus in contact with water pore pressure), which is about 90 % of the total height. Despite the small proportion of solid coupling, the sensor resolution remains very good up to a few tens of hours of a time period, thanks to the confining effects of the rocks on the local pore pressure. These results allow us to correct for the external effects, and reduce the associated variance by 80–90 % (in the period range of minutes to days). The empirical correction of the sea level effect could be explained using a simple Boussinesq’s approximation and 1D pore-pressure diffusion model, which contributed to better constraint of some of the poro-elastic parameters in the vicinity of the instrument. After correction, the solid tidal signal at the 24-h period is almost anti-correlated with those of the theoretical solid tide. This surprising result is consistent with a similar anti-correlation observed for the longest period surface waves (200 s) comparing the TRZ dilatometer signals to the strain measured by a nearby borehole strainmeter (MOK, 15 km). This could be related to the presence of a shallow fault close to the instrument, which would creep in response to seismic wave-related stress.
ISSN: 0033-4533

hal-01122853
https://hal.archives-ouvertes.fr/hal-01122853
DOI : 10.1007/s00024-013-0742-2