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 Society for Biochemistry and Molecular Biology
Résumé : International audience
Chronic low grade inflammation is closely linked to obesity-associated insulin resistance. To examine how administration of the anti-inflammatory compound indomethacin, a general cyclooxygenase inhibitor, affected obesity development and insulin sensitivity, we fed obesity-prone male C57BL/6J mice a high fat/high sucrose (HF/HS) diet or a regular diet supplemented or not with indomethacin (±INDO) for 7 weeks. Development of obesity, insulin resistance, and glucose intolerance was monitored, and the effect of indomethacin on glucose-stimulated insulin secretion (GSIS) was measured in vivo and in vitro using MIN6 β-cells. We found that supplementation with indomethacin prevented HF/HS-induced obesity and diet-induced changes in systemic insulin sensitivity. Thus, HF/HS+INDO-fed mice remained insulin-sensitive. However, mice fed HF/HS+INDO exhibited pronounced glucose intolerance. Hepatic glucose output was significantly increased. Indomethacin had no effect on adipose tissue mass, glucose tolerance, or GSIS when included in a regular diet. Indomethacin administration to obese mice did not reduce adipose tissue mass, and the compensatory increase in GSIS observed in obese mice was not affected by treatment with indomethacin. We demonstrate that indomethacin did not inhibit GSIS per se, but activation of GPR40 in the presence of indomethacin inhibited glucose-dependent insulin secretion in MIN6 cells. We conclude that constitutive high hepatic glucose output combined with impaired GSIS in response to activation of GPR40-dependent signaling in the HF/HS+INDO-fed mice contributed to the impaired glucose clearance during a glucose challenge and that the resulting lower levels of plasma insulin prevented the obesogenic action of the HF/HS diet.
ISSN: 0021-9258

hal-01074835
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01074835
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01074835/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01074835/file/JBC-2013-525220v2-Kristiansen-POSTPRINT.pdf
DOI : 10.1074/jbc.M113.525220

Éditeur(s) : HAL CCSD
Résumé : International audience
Multiple chemicals are emitted in residential accommodation. Aggregate Daily Doses (ADD) (ng/kg-bw/d) were estimated for 32 semivolatile organic compounds (SVOCs) of different chemical families that are frequently detected in French dwellings in both air and settled dust. Daily doses were determined using steady-state models for the population, categorized into 11 age groups covering birth to age 30. Three routes of exposure were taken into account: dust ingestion, inhalation (gaseous and particulate phases) and dermal contact with the gaseous phase of air. Contamination levels were preferentially retrieved from large, nationwide representative datasets. A two-dimensional probabilistic approach was used to assess parametric uncertainty and identify the most influential factors. For children aged 2 to 3 years, ADD estimates spanned orders of magnitude, with median values ranging from 8.7 pg/kg-bw/d for 2,2′,3,4,4′-pentabromodiphenylether (BDE 85) to 1.3 μg/kg-bw/d for di-isobutyl phthalate (DiBP). Inhalation, ingestion and dermal pathway contributed at varying levels, and depending on compound, air was the dominant medium for 28 of the 32 compounds (either by inhalation or dermal contact). Indoor exposure estimate variance was mainly driven by indoor contamination variability, and secondarily by uncertainty in physical and chemical parameters. These findings lend support to the call for cumulative risk assessment of indoor SVOCs. © 2017 Elsevier Ltd
ISSN: 01604120

hal-01616433
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01616433
DOI : 10.1016/j.envint.2017.08.024
PUBMED : 28950160

Éditeur(s) : HAL CCSD
Résumé : International audience
Semi-volatile organic compounds (SVOCs) partition indoors between the gas phase, airborne particles, settled dust, and other surfaces. Unknown concentrations of SVOCs in the gas phase (Cg) can be predicted from their measured concentrations in airborne particles. In previous studies, the prediction of Cg depended largely on choosing a specific equation for the calculation of the particle/gas partition coefficient. Moreover, the prediction of Cg is frequently performed at a reference temperature rather than the real indoor temperature. In this paper, a probabilistic approach based on Monte Carlo simulation was developed to predict the distribution of SVOCs' Cg from their concentrations in airborne particles at the target indoor temperature. Moreover, the distribution of the particle/gas partition coefficient of each SVOC at the target temperature was used. The approach was validated using two measured datasets in the literature: the predicted Cg from concentrations measured in airborne particles and the measured Cg were generally of the same order of magnitude. The distributions of the Cg of 66 SVOCs in the French housing stock were then predicted. The SVOCs with the highest median Cg, ranging from 1 ng/m3 to > 100 ng/m3, included 8 phthalates (DEP, DiBP, DBP, DEHP, BBP, DMP, DiNP, and DMEP), 4 polycyclic aromatic hydrocarbons (fluorene, phenanthrene, fluoranthene, and anthracene), 2 alkylphenols (4-tert-butylphenol and 4-tert-octylphenol), 2 synthetic musks (galaxolide and tonalide), tributyl phosphate, and heptachlor. The nationwide, representative, predicted Cg values of SVOCs are frequently of the same order of magnitude in Europe and North America, whereas these Cg values in Chinese and Indian dwellings and the Cg of polybrominated diphenyl ethers in U.S. dwellings are generally higher. © 2016 Elsevier B.V.
Science of the Total Environment

hal-01467547
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467547
DOI : 10.1016/j.scitotenv.2016.10.074
PUBMED : 27788447

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Diploid budding yeast undergoes rapid mitosis when it ferments glucose, and in the presence of a non-fermentable carbon source and the absence of a nitrogen source it triggers sporulation. Rich medium with acetate is a commonly used pre-sporulation medium, but our understanding of the molecular events underlying the acetate-driven transition from mitosis to meiosis is still incomplete. We identified 263 proteins for which mRNA and protein synthesis are linked or uncoupled in fermenting and respiring cells. Using motif predictions, interaction data and RNA profiling we find among them 28 likely targets for Ume6, a subunit of the conserved Rpd3/Sin3 histone deacetylase-complex regulating genes involved in metabolism, stress response and meiosis. Finally, we identify 14 genes for which both RNA and proteins are detected exclusively in respiring cells but not in fermenting cells in our sample set, including CSM4, SPR1, SPS4 and RIM4, which were thought to be meiosis-specific. Our work reveals intertwined transcriptional and post-transcriptional control mechanisms acting when a MATa/α strain responds to nutritional signals, and provides molecular clues how the carbon source primes yeast cells for entering meiosis. Our integrated genomics study provides insight into the interplay between the transcriptome and the proteome in diploid yeast cells undergoing vegetative growth in the presence of glucose (fermentation) or acetate (respiration). Furthermore, it reveals novel target genes involved in these processes for Ume6, the DNA binding subunit of the conserved histone deacetylase Rpd3 and the co-repressor Sin3. We have combined data from an RNA profiling experiment using tiling arrays that cover the entire yeast genome, and a large-scale protein detection analysis based on mass spectrometry in diploid MATa/α cells. This distinguishes our study from most others in the field-which investigate haploid yeast strains-because only diploid cells can undergo meiotic development in the simultaneous absence of a non-fermentable carbon source and nitrogen. Indeed, we report molecular clues how respiration of acetate might prime diploid cells for efficient spore formation, a phenomenon that is well known but poorly understood.
ISSN: 1874-3919

hal-01122122
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122122
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122122/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122122/file/Integrated%20RNA-%20and%20protein%20profiling%20of%20fermentation.pdf
DOI : 10.1016/j.jprot.2015.01.015

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Investigation of an eclogite xenolith, discovered in a Cretaceous granite from the Central Domain of the Dabieshan massif in eastern China, yields new petrological insights into the high to ultrahigh-pressure metamorphism, experienced by the Qinling-Dabie orogen. Prior to inclusion as a xenolith in the granite during the Early Cretaceous, this eclogite xenolith had recorded a complex metamorphic evolution that complies with subduction and exhumation processes experienced by the continental crust of the South China Block. Well-preserved mineral parageneses substantiate the prograde and retrograde stages revealed by inclusions in porphyroblastic garnet and zoned minerals such as garnet, comphacite and amphibole in the matrix. The relatively low P/T re-equilibration during a latemetamorphic stage was textually inferred by the presence of aluminous and calcic-subcalcic amphiboles such as katophorite, edenite, taramite and pargasite as main matrix phases. According to our U/Pb, Rb/Sr and new 40Ar/39Ar geochronological results, namely 109 ± 1 and 112 ± 2 Ma plateau ages for muscovite and amphiboles, respectively, two successive but distinct cooling stages account for the thermal history of the granite–migmatite gneiss dome that forms the Central Dabieshan Domain. We argue that prior to the Cretaceous doming, the Central Dabieshan Domain experienced a tectono-metamorphic evolution similar to that observed in the high-pressure to ultra high-pressure units developed in the Southern Dabieshan Domain and Hong'an massif.
ISSN: 1437-3254

hal-00104224
https://hal-insu.archives-ouvertes.fr/hal-00104224
https://hal-insu.archives-ouvertes.fr/hal-00104224/document
https://hal-insu.archives-ouvertes.fr/hal-00104224/file/Lin-IntJEarthSciences-2007.pdf
DOI : 10.1007/s00531-006-0129-z