Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Climatic changes result in an increased in mean temperature and in a higher incidence of extreme weather events such as heat and cold waves. For ectotherms, such as insect parasitoids, the ability to remain active under extreme climatic conditions is a significant key to fitness. The body size of individuals, and in particular their surface to volume ratio, may play a role in their resistance to thermal conditions. The thermal tolerances are investigated of two closely-related sympatric parasitoid species [Aphidius avenae Haliday and Aphidius rhopalosiphi De Stefani-Perez (Hymenoptera: Aphidiinae)] that have a similar ecology but differ in body size and phenologies. The critical thermal limits of individuals are assessed in both sexes of each parasitoid species and the influence of surface-volume ratios on their thermal tolerances. Aphidius avenae is less resistant to low temperatures and more resistant to high temperatures than A. rhopalosiphi. The lower surface to volume ratio of A. avenae individuals may help them to remain active in summer when experiencing heat waves. However, body size is not the sole factor that plays a role in differences of thermal tolerance between species and body size may not be an adaptation to extreme temperatures but rather a by-product of developmental regulation. Closely related sympatric species from the same ecological guild can have different thermal tolerances that may allow them to occur within the same habitat. The present study also highlights the importance of clearly defining how to measure critical thermal limits to determine the thermal tolerance of a species.
ISSN: 0307-6962

hal-00589094
https://hal.archives-ouvertes.fr/hal-00589094
DOI : 10.1111/j.1365-3032.2010.00758.x

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : Permo-Triassic rift basins offer important hydrocarbon targets along the Atlantic margins. Their fill is dominated by continental red beds, comprising braided fluvial, alluvial fan, aeolian, floodplain and lacustrine facies. These relatively lightly explored basins span both the Atlantic and Tethyan domains and developed above a complex basement with inherited structural fabrics. Sparse data in offshore regions constrain understanding of depositional geometries and sedimentary architecture, further impeded by their deep burial beneath younger strata, combined with the effects of later deformation during continental breakup. This paper provides results from a multidisciplinary analysis of basins along the Atlantic margin. Regional seismic and well data, combined with geochemical provenance analysis from the European North Atlantic margins, are integrated with detailed outcrop studies in Morocco and Nova Scotia. The research provides new insights into regional basin tectonostratigraphic evolution, sediment fill, and reservoir distribution, architecture and quality at a range of scales. Regional seismic profiles, supported by key well data, indicate the presence of post-orogenic collapse basins, focused narrow rifts and low-magnitude multiple extensional depocentres. Significantly, Permo-Triassic basin geometries are different and more varied than the overlying Jurassic and younger basins. Provenance analysis using Pb isotopic composition of detrital K-feldspar yields new and robust controls on the sediment dispersal patterns of Triassic sandstones in the NE Atlantic margin. The evolving sedimentary architecture is characterized by detailed sedimentological studies of key outcrops of age equivalent Permian-Triassic rifts in Morocco and Nova Scotia. The interplay of tectonics and climate is observed to influence sedimentation, which has significant implications for reservoir distribution in analogue basins. New digital outcrop techniques are providing improved reservoir models, and identification of key marker horizons and sequence boundaries offers a potential subsurface correlation tool. Future work will address source and seal distribution within the potentially petroliferous basins.
Petroleum Geology: From Mature Basins to New Frontiers Proceedings of the 7th Petroleum Geology Conf

hal-00590618
https://hal.archives-ouvertes.fr/hal-00590618

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
The present study is a contribution to the "neXt50 challenge", a coordinated effort across C-HPP teams to identify the SO most tractable missing proteins (MPs) on each chromosome. We report the targeted search of 38 theoretically detectable MPs from chromosomes 2 and 14 in Triton X-100 soluble and insoluble sperm fractions from a total of 15 healthy donors. A targeted mass spectrometry-based strategy consisting of the development of LC-PRM assays (with heavy labeled synthetic peptides) targeting 92 proteotypic peptides of the 38 selected MPs was used. Out of the 38 selected MPs, 12 were identified with two or more peptides and 3 with one peptide after extensive SDS-PAGE fractionation of the two samples and with overall low-intensity signals. The PRM data are available via ProteomeXchange in PASSEL (PASS01013). Further validation by immunohistochemistry on human testes sections and cytochemistry on sperm smears was performed for eight MPs with antibodies available from the Human Protein Atlas. Deep analysis of human sperm still allows the validation of MPs and therefore contributes to the C-HPP worldwide effort. We anticipate that our results will be of interest to the reproductive biology community because an in-depth analysis of these MPs may identify potential new candidates in the context of human idiopathic infertilities.
ISSN: 1535-3893

hal-01681656
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01681656
DOI : 10.1021/acs.jproteome.7b00374

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 : International audience
Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein. PepPSy can also be used by biocurators to revisit the annotation of specific categories of proteins based on the 'omics' data housed by the system. In this study, it was used to prioritize 21 dubious protein-coding genes among the 616 annotated in neXtProt for reannotation.
DATABASE

hal-01342472
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01342472
DOI : 10.1093/database/baw070
PUBMED : 27173522

Éditeur(s) : HAL CCSD
Résumé : International audience
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome. © 2016 American Chemical Society.
Journal of Proteome Research

hal-01406074
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01406074
DOI : 10.1021/acs.jproteome.6b00400
PUBMED : 27444420