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 American Geophysical Union (AGU)
Résumé : International audience
[1] Zircons and monazites from 6 samples of the North Ayilari dextral shear zone (NAsz), part of the Karakorum fault zone (KFZ), have been dated with the U-Th-Pb method, using both ID-TIMS and SIMS techniques. The ages reveal (1) inheritance from several events spanning a long period between the late Archean and the Jurassic; (2) an Eocene-Oligocene magmatic event (similar to 35-32 Ma); (3) an Oligo-Miocene magmatic event (similar to 25-22 Ma), at least partly synkinematic to the right-lateral deformation; and (4) a period of metamorphism metasomatism (similar to 22-14 Ma) interpreted as thermal and fluid advection in the shear zone. The Labhar Kangri granite located similar to 375 km farther Southeast along the KFZ is dated at 21.1 +/- 0.3 Ma. Such occurrence of several Oligo-Miocene granites along the KFZ, some of which show evidence for synkinematic emplacement, suggests that the fault zone played an important role in the genesis and /or collection of crustal melts. We discuss several scenarios for the onset and propagation of the KFZ, and offset estimates based on the main sutures zones. Our preferred scenario is an Oligo-Miocene initiation of the fault close to the NA range, and propagation along most of its length prior to similar to 19 Ma. In its southern half, the averaged long-term fault-rate of the KFZ is greater than 8 to 10 mm/a, in good agreement with some shorter-term estimates based on the Indus river course, or Quaternary moraines and geodesy. Our results show the KFZ cannot be considered as a small transient fault but played a major role in the collision history.
ISSN: 0278-7407

hal-00412570
https://hal.archives-ouvertes.fr/hal-00412570
DOI : 10.1029/2007TC002184

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : 4 pages
International audience
This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.
ISSN: 1755-098X

hal-00823716
https://hal.archives-ouvertes.fr/hal-00823716
DOI : 10.1111/1755-0998.12095
PUBMED : 23521844

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.
ISSN: 0305-1048

Droits : http://creativecommons.org/licenses/by/
hal-01122128
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128/file/The%20conserved%20histone%20deacetylase.pdf
DOI : 10.1093/nar/gku1185

Éditeur(s) : HAL CCSD SpringerOpen
Résumé : The Karakorum Fault zone (KFZ) plays an important role in understanding the formation, evolvement and deformation of the Tibetan Plateau. The high-T dextral shearing metamorphic rocks, e.g., mylonites or mylonitized gneisses-granites, locally crop out along the southeastern part of the KFZ in the Ayila Ri'gyü Range area. The SHRIMP U-Pb dating of the syn-kinematic crystallized zircons indicates that the initial age of the KFZ is ∼27 Ma, ∼10 Ma older than previous results. The extensive high-T dextral shearing along the KFZ started at least at 27–20 Ma, accompanied by the syn-kinematic emplacement of leuco-granites. Deformation and concomitant fluid circulation during shearing most likely occurred as early as at 25–13 Ma. The KFZ probably grew from southeast to northwest along the fault as a result of continuous convergence between the India plate and Eurasia plate.
ISSN: 1001-6538

hal-00406402
https://hal.archives-ouvertes.fr/hal-00406402
DOI : 10.1007/s11434-007-0164-6