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 : International audience
High-grade migmatitic and mylonitic gneisses from the Day Nui Con Voi massif in northern Vietnam record temperatures of 760-810 °C at pressures of 6-10 kbars. High temperature conditions have resulted in the development of major element diffusional profiles in garnet. Laser ablation ICP-MS analyses of trace elements indicate that REE and Hf closely followed Rayleigh-like fractionation trends but underwent significant post-crystallization modification. Light REE and to a lesser extent, HREE rim-to-rim zonation profiles show progressive flattening with the decreasing garnet size. Nd and Sm are completely homogenized in the crystals smaller than 1.5 mm, while Lu always preserves variable degrees of core-to-rim concentration gradient. The observed REE patterns are interpreted as resulting from the combination of protracted garnet growth of progressively smaller crystals and intracrystalline diffusion. This had profound influence on Sm-Nd geochronology and resulted in isochron ages ranging from 50 to 32 Ma. The youngest age was obtained for a sample, where all garnet crystals are smaller than 2 mm in which light REE profiles are completely or nearly completely homogenized. Thus, only the youngest age represents geologically meaningful event, and 31.7 ± 0.9 Ma age is interpreted as the best estimate of the resetting episode due to high temperature diffusional homogenization of light REE during early Oligocene metamorphism. Older Sm-Nd ages reflect mixed analyses of variably reset individual garnet crystals. Lu-Hf isotopic analyses of bulk garnet fractions, despite yielding high parent/daughter isotopic ratios appeared very scattered and did not allow defining isochron ages. Instead, apparent ages defined by whole rock and individual garnet fractions range from c. 80 to 160 Ma. Very old apparent ages are interpreted as being the consequence of intracrystalline Lu diffusion and preservation of the original Hf distribution, which leads to lower 176Lu/177Hf ratios, and thus steeper (older) isochrons. Back diffusion of Lu during commonly observed resorption played a subordinate role in modifying isotope systematics.
ISSN: 0009-2541

hal-00813949
https://hal.archives-ouvertes.fr/hal-00813949
DOI : 10.1016/j.chemgeo.2012.04.024

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Spinel lherzolite xenoliths from Mont Briancon, French Massif Central, retain evidence for multiple episodes of melt depletion and melt/fluid infiltration (metasomatism). Evidence for primary melt depletion is still preserved in the co-variation of bulk-rock major elements (MgO 38.7-46.1 wt.%; CaO 0.9-3.6 wt.%), and many samples yield unradiogenic bulk-rock Os isotope ratios (Os-187/Os-188 = 0.11541-0.12626). However, many individual xenoliths contain interstitial glasses and melt inclusions that are not in equilibrium with the major primary minerals. Incompatible trace element mass balance calculations demonstrate that metasomatic components comprise a significant proportion of the bulk-rock budget for these elements in some rocks, ranging to as much as 25%, of Nd and 40% of Sr Critically, for Re-Os geochronology, melt/fluid infiltration is accompanied by the mobilisation of Sulfide. Consequently, bulk-rock isotope measurements, whether using lithophile (e.g. Rb-Sr, Sm-Nd) or siderophile (Re-Os) based isotope systems, may only yield a perturbed and/or homogenised average of these multiple events.;Osmium mass balance calculations demonstrate that bulk-rock Os in peridotite is dominated by contributions from two populations of sulfide grain: (i) interstitial, metasomatic Sulfide with low [Os] and radiogenic Os-187/Os-188, and (ii) primary sulfides with high [Os] and unradiogenic Os-187/Os-188, which have been preserved within host silicate grains and shielded from interaction with transient melts and fluid. The latter can account for >97% of bulk-rock Os and preserve geochronological information of the melt from which they originally precipitated as an immiscible liquid. The Re-depletion model ages of individual primary sulfide grains preserve evidence for melt depletion beneath the Massif Central from at least 1.8 Gyr ago despite the more recent metasomatic event(s). (C) 2009 Elsevier Ltd. All rights reserved.
ISSN: 0016-7037

hal-00454537
https://hal.archives-ouvertes.fr/hal-00454537
DOI : 10.1016/j.gca.2009.09.031

Éditeur(s) : HAL CCSD American Association for the Advancement of Science
Résumé : International audience
Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6144 arthropod species from 0.48 hectare and extrapolated total species richness to larger areas on the basis of competing models. The whole 6000-hectare forest reserve most likely sustains 25,000 arthropod species. Notably, just 1 hectare of rainforest yields >60% of the arthropod biodiversity held in the wider landscape. Models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well. This lends credence to global estimates of arthropod biodiversity developed from plant models.
ISSN: 0036-8075

hal-00817285
https://hal.archives-ouvertes.fr/hal-00817285
https://hal.archives-ouvertes.fr/hal-00817285/document
https://hal.archives-ouvertes.fr/hal-00817285/file/1226727Revisedtext.pdf
DOI : 10.1126/science.1226727