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
Human exposure to dechloranes has been evaluated in Western Europe (France) with the analysis of Dechlorane Plus (DP), Dechloranes (Dec) 602, 603 and 604, Chlordene Plus (CP) and Mirex in 48 serum samples collected between 2003 and 2005. While no production source has been identified in Europe until now, detection frequencies for all investigated dechloranes were high, except for Dec 604 which was below detection limit for all samples. The mean DP concentration was 1.40±1.40ng/g lipid weight (lw), lower than levels reported in serum from Chinese population, but higher than levels reported in Canadian human milk. To the best of our knowledge, this is the first time that ∑5dechlorane levels are reported for human serum. A specific pattern of contamination was found (Dec 603>DP>Mirex>Dec 602>CP) compared to other biota samples that have been analyzed from Europe, with Dec 603 as the most abundant dechlorane (mean level: 2.61±2.63ng/g lw). Dec 603 and CP levels were correlated with age and with levels of some bioaccumulative organochlorine pesticides (OCPs). These results indicate that bioaccumulation properties should be further investigated and taken in consideration when assessing human exposure to dechloranes. For comparison purposes, polybrominated diphenyl ether (PBDE) levels were also measured for BDE-47, -99, -100, -153 and -154 in the serum samples. As expected, BDE-47 and BDE-153 were the major congeners with mean levels of 2.06±1.80ng/g lw and 1.39±0.97ng/g lw, respectively. The mean ∑5PBDE levels (4.32±2.99ng/g lw) were in the range typical of Western Europe levels, but lower than the mean ∑5dechlorane levels (6.24±4.16ng/g lw). These results indicate that the attention to dechloranes should be continued if research indicates toxicological concerns.
ISSN: 0160-4120

hal-01004642
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01004642
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01004642/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01004642/file/Levelssur dechloranes_and_polybrominated_diphenyl_ethers_accepted.pdf
DOI : 10.1016/j.envint.2013.12.014

Éditeur(s) : HAL CCSD IOP Publishing
Résumé : During November 2011 a EURAMET key comparison of absolute gravimeters was organized in the Underground Laboratory for Geodynamics in Walferdange, Luxemburg. The comparison assembled 22 participants coming from 16 countries and four different continents. The comparison was divided into two parts: a key comparison that included six National Metrology Institutes or Designated Institutes, and a pilot study including all participants. The global result given by the pilot study confirms that all instruments are absolutely coherent with each other. The results obtained in the key comparison confirm a good agreement between the NMI instruments. Finally, a link to ICAG-2009 shows also that the NMI gravimeters are stable in time. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
ISSN: 0026-1394

hal-00795586
https://hal.archives-ouvertes.fr/hal-00795586
DOI : 10.1088/0026-1394/49/1A/07014

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD IOP Publishing
Résumé : We present the results of the third European Comparison of Absolute Gravimeters held in Walferdange, Grand Duchy of Luxembourg, in November 2011. Twenty-two gravimeters from both metrological and non-metrological institutes are compared. For the first time, corrections for the laser beam diffraction and the self-attraction of the gravimeters are implemented. The gravity observations are also corrected for geophysical gravity changes that occurred during the comparison using the observations of a superconducting gravimeter. We show that these corrections improve the degree of equivalence between the gravimeters. We present the results for two different combinations of data. In the first one, we use only the observations from the metrological institutes. In the second solution, we include all the data from both metrological and non-metrological institutes. Those solutions are then compared with the official result of the comparison published previously and based on the observations of the metrological institutes and the gravity differences at the different sites as measured by non-metrological institutes. Overall, the absolute gravity meters agree with one another with a standard deviation of 3.1 µGal. Finally, the results of this comparison are linked to previous ones. We conclude with some important recommendations for future comparisons.
ISSN: 0026-1394

hal-00853755
https://hal.archives-ouvertes.fr/hal-00853755
DOI : 10.1088/0026-1394/50/3/257