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 Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Magnetic Resonance Imaging (MRI), a reference examination for cardiac morphology and function in humans, allows to image the cardiac right ventricle (RV) with high spatial resolution. The segmentation of the RV is a difficult task due to the variable shape of the RV and its ill-defined borders in these images. The aim of this paper is to evaluate several RV segmentation algorithms on common data. More precisely, we report here the results of the Right Ventricle Segmentation Challenge (RVSC), concretized during the MICCAI'12 Conference with an on-site competition. Seven automated and semi-automated methods have been considered, along them three atlas-based methods, two prior based methods, and two prior-free, image-driven methods that make use of cardiac motion. The obtained contours were compared against a manual tracing by an expert cardiac radiologist, taken as a reference, using Dice metric and Hausdorff distance. We herein describe the cardiac data composed of 48 patients, the evaluation protocol and the results. Best results show that an average 80% Dice accuracy and a 1cm Hausdorff distance can be expected from semi-automated algorithms for this challenging task on the datasets, and that an automated algorithm can reach similar performance, at the expense of a high computational burden. Data are now publicly available and the website remains open for new submissions (http://www.litislab.eu/rvsc/).
ISSN: 1361-8415

hal-01141170
https://hal.archives-ouvertes.fr/hal-01141170
PUBMED : 25461337

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 Elsevier
Résumé : International audience
Upon subduction, the oceanic crust transforms to blueschists and eclogites, with seismic properties that gradually become similar to those of the surrounding mantle. In order to evaluate the anisotropy of blueschists and glaucophane-bearing eclogites, the elastic constants of glaucophane single-crystal plates from the Sesia-Lanzo Zone (Aosta Valley, Western Alps) were measured using Brillouin spectroscopy at ambient conditions. The mean P- and S-wave velocities are 7.8 and 4.6 km s−1 respectively, and the anisotropy is high (38.1% (AVP) and 27.3% (AVS)). Glaucophane develops strong LPO, characterized by the [001]-axes concentrated sub-parallel to the lineation, and the {110} poles concentrated sub-perpendicular to the foliation in both blueschist and eclogite rocks. The measured LPO is in good agreement with viscoplastic selfconsistent numerical models. Seismic properties of glaucophane-bearing blueschist and eclogite are calculated by combining measured LPO and the single-crystal elastic moduli of glaucophane with the other main mineral constituents of the rock: mostly epidote for blueschist, and omphacite and garnet for eclogite. Blueschists present stronger anisotropies (AVP=16.1% and AVS=10.3%) than eclogites (AVP=2.9% and AVS=1.7%). The shear-wave splitting and resulting delay times for a 7-km thick layer of eclogite or blueschist are low for the eclogite (b0.03 s), but signi!cant for blueschist (0.16 s). Application to the subducted oceanic crust yields a decrease of velocity contrast with the surrounding mantle and of anisotropy at depth depending on the temperature of the slab. The details of the velocity variations in subducted oceanic crust are dif!cult to reconcile with the blueschist-eclogite transition as probed by exhumed metamorphic rocks and may require additional phases such as lawsonite or chemical variations such as oxidation state.
ISSN: 0040-1951

hal-00564518
https://hal.archives-ouvertes.fr/hal-00564518
DOI : 10.1016/j.tecto.2010.09.011

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a carcinogenic heterocyclic aromatic amine formed in cooked meats, is metabolically activated to electrophilic intermediates that form covalent adducts with DNA and protein. We previously identified an adduct of PhIP formed at the Cys34 residue of human serum albumin following reaction of albumin with the genotoxic metabolite 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (HONH-PhIP). The major adducted peptide recovered from a tryptic/chymotryptic digest was identified as the missed-cleavage peptide LQQC*[SO2PhIP]PFEDHVK, a [cysteine-S-yl-PhIP]-S-dioxide linked adduct. In this investigation, we have characterized the albumin adduction products of N-sulfooxy-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-sulfooxy-PhIP), which is thought to be a major genotoxic metabolite of PhIP formed in vivo. Targeted and data-dependent scanning methods showed that N-sulfooxy-PhIP adducted to the Cys34 of albumin in human plasma to form LQQC*[SO2PhIP]PFEDHVK at levels that were 8-10-fold greater than the adduct levels formed with N-(acetyloxy)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-acetoxy-PhIP) or HONH-PhIP. We also discovered that N-sulfooxy-PhIP forms an adduct at the sole tryptophan (Trp214) residue of albumin in the sequence AW*[PhIP]AVAR. However, stable adducts of PhIP with albumin were not detected in human hepatocytes. Instead, PhIP and 2-amino-1-methyl-6-(5-hydroxy)phenylimidazo[4,5-b]pyridine (5-HO-PhIP), a solvolysis product of the proposed nitrenium ion of PhIP, were recovered during the proteolysis, suggesting a labile sulfenamide linkage had formed between an N-oxidized intermediate of PhIP and Cys34 of albumin. A stable adduct was formed at the Tyr411 residue of albumin in hepatocytes and identified as a deaminated product of PhIP, Y*[desaminoPhIP]TK, where the 4-HO-tyrosine group bound to the C-2 imidazole atom of PhIP.
ISSN: 0893-228X

hal-01146777
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146777
DOI : 10.1021/acs.chemrestox.5b00075
PUBMED : 25815793

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 American Society for Biochemistry and Molecular Biology
Résumé : International audience
2-Amino-9H-pyrido[2,3-b]indole (AαC) is a carcinogenic heterocyclic aromatic amine formed during the combustion of tobacco. AαC undergoes bioactivation to form electrophilic N-oxidized metabolites that react with DNA to form adducts, which can lead to mutations. Many genotoxicants and toxic electrophiles react with human serum albumin (albumin); however, the chemistry of reactivity of AαC with proteins has not been studied. The genotoxic metabolites, 2-hydroxyamino-9H-pyrido[2,3-b]indole (HONH-AαC), 2-nitroso-9H-pyrido[2,3-b]indole (NO-AαC), N-acetyloxy-2-amino-9H-pyrido[2,3-b]indole (N-acetoxy-AαC), and their [(13)C6]AαC-labeled homologues were reacted with albumin. Sites of adduction of AαC to albumin were identified by data-dependent scanning and targeted bottom-up proteomics approaches employing ion trap and Orbitrap MS. AαC-albumin adducts were formed at Cys(34), Tyr(140), and Tyr(150) residues when albumin was reacted with HONH-AαC or NO-AαC. Sulfenamide, sulfinamide, and sulfonamide adduct formation occurred at Cys(34) (AαC-Cys(34)). N-Acetoxy-AαC also formed an adduct at Tyr(332). Albumin-AαC adducts were characterized in human plasma treated with N-oxidized metabolites of AαC and human hepatocytes exposed to AαC. High levels of N-(deoxyguanosin-8-yl)-AαC (dG-C8-AαC) DNA adducts were formed in hepatocytes. The Cys(34) was the sole amino acid of albumin to form adducts with AαC. Albumin also served as an antioxidant and scavenged reactive oxygen species generated by metabolites of AαC in hepatocytes; there was a strong decrease in reduced Cys(34), whereas the levels of Cys(34) sulfinic acid (Cys-SO2H), Cys(34)-sulfonic acid (Cys-SO3H), and Met(329) sulfoxide were greatly increased. Cys(34) adduction products and Cys-SO2H, Cys-SO3H, and Met(329) sulfoxide may be potential biomarkers to assess exposure and oxidative stress associated with AαC and other arylamine toxicants present in tobacco smoke
ISSN: 0021-9258

hal-01169796
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01169796
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01169796/file/Manuscript_KP_JBC_REV_050515_final_TC.pdf
DOI : 10.1074/jbc.M115.646539
PUBMED : 25953894

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : CABI:20153174020
Understanding how plants are constructed - i.e., how key size dimensions and the amount of mass invested in different tissues varies among individuals - is essential for modeling plant growth, carbon stocks, and energy fluxes in the terrestrial biosphere. Allocation patterns can differ through ontogeny, but also among coexisting species and among species adapted to different environments. While a variety of models dealing with biomass allocation exist, we lack a synthetic understanding of the underlying processes. This is partly due to the lack of suitable data sets for validating and parameterizing models. To that end, we present the Biomass And Allometry Database (BAAD) for woody plants. The BAAD contains 259634 measurements collected in 176 different studies, from 21084 individuals across 678 species. Most of these data come from existing publications. However, raw data were rarely made public at the time of publication. Thus, the BAAD contains data from different studies, transformed into standard units and variable names. The transformations were achieved using a common workflow for all raw data files. Other features that distinguish the BAAD are: (i) measurements were for individual plants rather than stand averages; (ii) individuals spanning a range of sizes were measured; (iii) plants from 0.01-100 m in height were included; and (iv) biomass was estimated directly, i.e., not indirectly via allometric equations (except in very large trees where biomass was estimated from detailed sub-sampling). We included both wild and artificially grown plants. The data set contains the following size metrics: total leaf area; area of stem cross-section including sapwood, heartwood, and bark; height of plant and crown base, crown area, and surface area; and the dry mass of leaf, stem, branches, sapwood, heartwood, bark, coarse roots, and fine root tissues. We also report other properties of individuals (age, leaf size, leaf mass per area, wood density, nitrogen content of leaves and wood), as well as information about the growing environment (location, light, experimental treatment, vegetation type) where available. It is our hope that making these data available will improve our ability to understand plant growth, ecosystem dynamics, and carbon cycling in the world's vegetation.
ISSN: 0012-9658

hal-01535227
https://hal.archives-ouvertes.fr/hal-01535227
DOI : 10.1890/14-1889.1
PRODINRA : 306122