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
Résumé : National audience
Congrès de la SPTC - Société de Pharmaco-Toxicologie Cellulaire
Paris, France

hal-01122677
https://hal.archives-ouvertes.fr/hal-01122677

Éditeur(s) : HAL CCSD Society for Range Management
Résumé : Grasslands and agroecosystems occupy one-third of the terrestrial area, but their contribution to the global carbon cycle remains uncertain. We used a set of 316 site-years of CO(2) exchange measurements to quantify gross primary productivity, respiration, and light-response parameters of grasslands, shrublands/savanna, wetlands, and cropland ecosystems worldwide. We analyzed data from 72 global flux-tower sites partitioned into gross photosynthesis and ecosystem respiration with the use of the light-response method (Gilmanov, T. G., D. A. Johnson, and N. Z. Saliendra. 2003. Growing season CO(2) fluxes in a sagebrushsteppe ecosystem in Idaho: Bowen ratio/energy balance measurements and modeling. Basic and Applied Ecology 4:167-183) from the RANGEFLUX and WORLDGRASSAGRIFLUX data sets supplemented by 46 sites from the FLUXNET La Thuile data set partitioned with the use of the temperature-response method (Reichstein, M., E. Falge, D. Baldocchi, D. Papale, R. Valentini, M. Aubinet, P. Berbigier, C. Bernhofer, N. Buchmann, M. Falk, T. Gilmanov, A. Granier, T. Grunwald, K. Havrankova, D. Janous, A. Knohl, T. Laurela, A. Lohila, D. Loustau, G. Matteucci, T. Meyers, F. Miglietta, J.M. Ourcival, D. Perrin, J. Pumpanen, S. Rambal, E. Rotenberg, M. Sanz, J. Tenhunen, G. Seufert, F. Vaccari, T. Vesala, and D. Yakir. 2005. On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Global Change Biology 11: 1.424-1439). Maximum values of the quantum yield (alpha = 75 mmol.mol(-1)), photosynthetic capacity (A(max) = 3.4 mg CO(2) . m(-2).s-1), gross photosynthesis (P(g,max) = 1.16 g CO(2) . m(-2).d(-1)), and ecological light-use efficiency (epsilon(ecol) = 59 mmol . mol(-1)) of managed grasslands and high-production croplands exceeded those of most forest ecosystems, indicating the potential of nonforest ecosystems for uptake of atmospheric CO(2). Maximum values of gross primary production (8 600 g CO(2) . m(-2).yr(-1)), total ecosystem respiration (7 900 g CO(2) . m(-2).yr(-1)), and net CO(2) exchange (2 400 g CO(2) . m(-2).yr(-1)) were observed for intensively managed grasslands and high-yield crops, and are comparable to or higher than those for forest ecosystems, excluding some tropical forests. On average, 80% of the nonforest sites were apparent sinks for atmospheric CO(2), with mean net uptake of 700 g CO(2) . m(-2).yr(-1) for intensive grasslands and 933 g CO(2) . m(-2).d(-1) for croplands. However, part of these apparent sinks is accumulated in crops and forage, which are carbon pools that are harvested, transported, and decomposed off site. Therefore, although agricultural fields may be predominantly sinks for atmospheric CO(2), this does not imply that they are necessarily increasing their carbon stock.
ISSN: 1550-7424

hal-01190754
https://hal.archives-ouvertes.fr/hal-01190754
DOI : 10.2111/rem-d-09-00072.1
PRODINRA : 214043

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
Continental rifts and passive continental margins show fundamental along-axis segmentation patterns that have been attributed to one or a number of different processes: extensional fault geometry, variable stretching along strike, preexisting lithospheric compositional and structural heterogeneities, oblique rifting, and the presence or absence of eruptive volcanic centers. The length and width scales of the rift stage fault-bounded basin systems change during the late evolution of the new plate boundary, and the role of magmatism may increase as rifting progresses to continental rupture. Along obliquely spreading ridges, first-order mid-ocean ridge geometries originate during the synrift stage, indicating an intimate relationship between magma production and transform fault spacing and location. The Gulf of Aden rift is a young ocean basin in which the earliest synrift to breakup structures are well exposed onshore and covered by thin sediment layers offshore. This obliquely spreading rift is considered magma-poor and has several large-offset transforms that originated during late stage rifting and control the first-order axial segmentation of the spreading ridge. Widely spaced geophysical transects of passive margins that produce only isolated 2-D images of crust and uppermost mantle structure are inadequate for evaluation of competing rift evolution models. Using closely spaced new geophysical and geological observations from the Gulf of Aden we show that rift sectors between transforms have a large internal variability over short distances (∼10 km): the ocean-continent transition (OCT) evolves from a narrow magmatic transition to wider zones where continental mantle is probably exhumed. We suggest that this small-scale variability may be explained (1) by the distribution of volcanism and (2) by the along-strike differences in time-averaged extension rate of the oblique rift system. The volcanism may be associated with (1) the long-offset Alula-Fartak Fracture Zone, which may enhance magma production on its younger side, or (2) channeled flow from the Afar plume material along the newly formed OCT and the spreading ridge. Oblique extension and/or hot spot interactions may thereby have a significant control on the styles of rifting and continental breakup and on the evolution of many magma-poor margins.
ISSN: 1525-2027

hal-00504866
https://hal.archives-ouvertes.fr/hal-00504866
https://hal.archives-ouvertes.fr/hal-00504866/document
https://hal.archives-ouvertes.fr/hal-00504866/file/G3-Leroy_al-2010.pdf
DOI : 10.1029/2009GC002963

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We report paleomagnetic results from four overlapping stratigraphic sections (55 flows) through the lava pile in Tjörnes peninsula (North Iceland). The initial aim of our study was to check the existence of intermediate directions previously interpreted as belonging to the Matuyama-Brunhes geomagnetic reversal (MBR), and complete this record with Thellier-Thellier paleointensity determinations and 40Ar/39Ar radioisotopic dating. The directional results corroborate the findings by Kristjánsson et al. (1988): a sequence of reversed, transitional, normal, and transitional polarity (R-T-N-T) is found in each section. The polarity change is characterized by a jump from reversed virtual geomagnetic poles (VGPs) to a quasi-cluster of transitional VGPs located over China, followed by a second jump to a cluster of normal polarity before moving again towards intermediate polarities. Reversely magnetized flows exhibit a magnetic mineralogy well suited for paleointensity determination. Of these 25 flows, 20 yielded paleointensity estimates of good quality. Unfortunately, the systematic presence of coarse multidomain (MD) titanomagnetite in the transitional and normal polarity flows hampered paleointensity estimates for these flows. The Virtual Dipole Moments (VDM) calculated for the reversed polarity flows vary from 4.9 to 7.0 × 1022 Am2 with an arithmetic mean value of 5.5 ± 0.8 × 1022 Am2. This value is identical to the mean VDM obtained for the 0.3-5 Ma time window and thus strengthens the conclusion that the recent geomagnetic field strength is anomalously high compared to that older than 0.3 Ma. 40Ar/39Ar isochron ages were obtained with the incremental heating technique on groundmass separates or phenocryst-poor whole rock samples. Six of the transitionally magnetized lavas yielded isochron ages that are indistinguishable from one another at the 95% confidence level. The weighted average age is 862 ± 51 ka. In the upper part of this volcanic sequence, the normally magnetized flows yielded a weighted average age of 787 ± 40 ka. This finding supports the conclusion that a geomagnetic excursion within the Matuyama chron is recorded in the lower part of the Tjörnes volcanic sequence, whereas only the latest portion of the MBR is recorded by flows in the upper part of the lava pile. This conclusion is supported via comparison of the VGPs obtained from the lavas with those predicted by a geomagnetic field model.
ISSN: 0012-821X

hal-00618515
https://hal.archives-ouvertes.fr/hal-00618515
https://hal.archives-ouvertes.fr/hal-00618515/document
https://hal.archives-ouvertes.fr/hal-00618515/file/Camps-epsl2011.pdf
DOI : 10.1016/j.epsl.2011.07.026

Éditeur(s) : HAL CCSD IOP Publishing
Résumé : The Bureau International des Poids et Mesures (BIPM), Sevres, France, hosted the 7th International Comparison of Absolute Gravimeters (ICAG) and the associated Relative Gravity Campaign (RGC) from August to September 2005.;ICAG 2005 was prepared and performed as a metrological pilot study, which aimed:;(1) To determine the gravity comparison reference values;;(2) To determine the offsets of the absolute gravimeters; and;(3) As a pilot study to accumulate experience for the CIPM Key Comparisons.;This document presents a complete and extensive review of the technical protocol and data processing procedures. The 1st ICAG-RGC comparison was held at the BIPM in 1980-1981 and since then meetings have been organized every 4 years.;In this paper, we present an overview of how the meeting was organized, the conditions of BIPM gravimetric sites, technical specifications, data processing strategy and an analysis of the final results. This 7th ICAG final report supersedes all previously published reports.;Readings were obtained from participating instruments, 19 absolute gravimeters and 15 relative gravimeters. Precise levelling measurements were carried out and all measurements were performed on the BIPM micro-gravity network which was specifically designed for the comparison.
ISSN: 0026-1394

hal-00644529
https://hal.archives-ouvertes.fr/hal-00644529
DOI : 10.1088/0026-1394/48/5/003

Éditeur(s) : HAL CCSD American Geophysical Union - AGU
Résumé : without
InterRidge News

hal-00464150
https://hal.archives-ouvertes.fr/hal-00464150

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
ISSN: 0022-0345

hal-01545481
https://hal.archives-ouvertes.fr/hal-01545481
DOI : 10.1177/0022034513482941