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 : We have studied the phase transformation of forsterite to wadsleyite under shear stress at the Earth's transition zone pressure and temperature conditions. Two-step experiments were performed using a multi-anvil press. First, we hot pressed iron-free forsterite at 6 or 11 GPa and 1100 degrees C. Then we deformed a slab of this starting material using a direct simple shear assembly at 16 GPa and 1400 degrees C for 1, 15, 35, 40, or 60 min. Both the starting material and the deformed samples were characterized using optical and scanning electron microscopy including measurements of crystal preferred orientations (CPO) by electron back scattered diffraction (EBSD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FTIR). The phase transformation occurs very rapidly, in less than 1 min, and metastable forsterite relics are not observed after deformation. The grain size of wadsleyite is slightly smaller than the forsterite starting material. The water contents obtained from FTIR analyses in forsterite and wadsleyite are 65-124 wt ppm H2O and 114-736 wt ppm H2O, respectively, which are well below water solubility at similar conditions in the presence of free water. Wadsleyite aggregates display weak CPO patterns with [1 0 0] axes concentrated at low angle to the shear direction, [0 1 0] axes perpendicular to the shear plane and nearly random [0 0 1] axes. Only a few dislocations were observed in wadsleyite with TEM. This observation is consistent with the assumption that most dislocations formed during the initial high-stress stages of these stress-relaxation experiments, were consumed in the phase transformation, probably enhancing the transformation rate. CPO patterns vary as a function of the water content: with increasing water content the density of [1 0 0] axes parallel to the shear direction decreases, and the density of [0 0 1] axes increases. Viscoplastic self-consistent modeling of CPO evolution using previously reported glide systems for wadsleyite, i.e., [1 0 0]{0 k 1} and 1/2 (1 1 1){1 0 1}, cannot reproduce the measured CPO, unless the [0 0 1](0 1 0) system, for which dislocations have not been observed by TEM, is also activated. In addition, wadsleyite grain growth suggests the participation of diffusion-assisted processes in deformation. Calculated anisotropies for P and S-waves using measured CPO are always below 1%. This very low anisotropy is due to both the low finite strain achieved in the experiments, which leads to weak wadsleyite CPO, and to the diluting effect of added majorite. The present experiments emphasize the importance of stress, grain size evolution and water content in the forsterite to wadsleyite phase transformation and subsequent deformation in the transition zone.
ISSN: 0031-9201

hal-00617430
https://hal.archives-ouvertes.fr/hal-00617430
DOI : 10.1016/j.pepi.2010.11.001