Droits : All rights reserved by the source institution.

Droits : All rights reserved by the source institution.

Droits : All rights reserved by the source institution.

Droits : All rights reserved by the source institution.

Éditeur(s) : Inter-Research
Résumé : The species richness pattern of groundfish species in the entire northern Mediterranean Sea was examined at 3 spatial scales: region, large biogeographical zone and basin. We analysed 1914 trawl hauls collected using a single sampling design in the trawlable areas of the continental shelves between the Strait of Gibraltar and the Strait of Dardanelles (from 36.3 to 45.7 degrees N and 5.3 degrees W to 28 E). Spatial pattern in species diversity was assessed using complementary methods (Chao2 estimates of total species richness, mean species richness and beta diversity). No matter which scale was used, the expected longitudinally decreasing trend in species richness, which has been widely described in previous studies, did not appear when comparing estimates of total species richness per unit of area. Only the mean species richness pattern showed a moderate eastwards decrease at the largest spatial scale, but the trend progressively disappeared as the scale of analysis was reduced. In contrast to what is usually expected, our results suggest that Atlantic inflow does not play a key role in the present spatial pattern of fish species richness within the northern Mediterranean Sea. Furthermore, we show that the Aegean Sea can no longer be considered the least species-diverse zone in the northern Mediterranean Sea. Our results provide the first description of a quantitative 'reference state', with which the temporal changes in species richness patterns throughout the entire northern Mediterranean Sea can be compared in the future.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2007-07 , Vol. 341 , P. 191-203

Droits : 2007 Inter-Research
http://archimer.ifremer.fr/doc/2007/publication-3569.pdf
DOI:10.3354/meps341191
http://archimer.ifremer.fr/doc/00000/3569/

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 : 27 ref. *INRA Documentation Centre de Nancy (FRA) Diffusion du document : INRA Documentation Centre de Nancy (FRA)
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
absent
https://hal.archives-ouvertes.fr/hal-01190944

hal-01190944
https://hal.archives-ouvertes.fr/hal-01190944
PRODINRA : 85229

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
STUDY QUESTION: Can protein biomarkers of the male genital tract be identified in human seminal plasma? SUMMARY ANSWER: We identified potential biomarkers for each of the organs participating in the secretions of the human seminal plasma. WHAT IS KNOWN ALREADY: The seminal plasma fulfills critical functions for fertility by providing spermatozoa with a protective milieu, promoting their final maturation and modulating the immune responsiveness of the female reproductive tract. It is also considered to be a promising source of biomarkers of male infertility and/or pathologies of the male genital tract. STUDY DESIGN, SIZE, DURATION: This study combines proteomic analyses of normal seminal plasma together with transcriptomic gene expression profiling of human healthy tissues. MATERIALS, SETTING, METHODS: Non-liquefied seminal plasma proteins from a healthy donor were prefractionated using two sequential Proteominer™ libraries. Eight subproteome fractions were collected, trypsin digested and subjected to three successive mass spectrometry analyses for peptide characterization. The list of identified proteins was compared with and merged with other available data sets of the human seminal plasma proteome. The expression of corresponding genes was then investigated using tissue transcriptome profiles to determine where, along the male reproductive tract, these proteins were produced. Finally, tissue specificity of a selected subset of biomarker candidates was validated on human tissues. MAIN RESULTS AND THE ROLE OF CHANCE: We first performed a proteomic analysis of the human seminal plasma and identified 699 proteins. By comparing our protein list with other previous proteomic data sets, we found that 2545 unique proteins have been described so far in the human seminal plasma. We then profiled their expression at the gene level and identified 83 testis, 42 epididymis, 7 seminal vesicle and 17 prostate candidate protein markers. For a subset of testis-specific candidates, i.e. TKTL1, LDHC and PGK2, we further validated their germ cell expression and demonstrated that such markers could distinguish between semen from fertile and infertile men. LIMITATIONS, REASONS FOR CAUTION: While some of the markers we identified are well-known tissue-specific products, further dedicated studies to validate the biomarker status of new candidates will be required. Additionally, whether or not the abundance of these proteins is indeed decreased in some specific pathological situations remains to be determined. WIDER IMPLICATIONS OF THE FINDINGS: Using an integrative genomics approach, we identified biomarker candidates for each of the organs participating in the seminal plasma production. In this study, we essentially focused on germ cell markers and their potential application for the diagnosis of male infertility. Other types of markers also deserve a focused attention given their potential predictive value for various reproductive disorders, notably for prostate cancers. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the Proteomics Core Facility at Biogenouest and was funded by Conseil Régional de Bretagne, IBiSA and Agence de la Biomédecine grants. The authors declare that there exists a competing financial interest in this work that is related to a patent application on the use of identified germ cell-specific proteins in an antibody-based assay (Fertichip™) to predict the successful testicular biopsy outcomes in human non-obstructive azoospermia.
ISSN: 0268-1161

inserm-00814146
http://www.hal.inserm.fr/inserm-00814146
DOI : 10.1093/humrep/des360
PUBMED : 23024119

Éditeur(s) : Elsevier
Résumé : The multi-component aspect of species diversity of groundfish assemblages was examined on the basis of a set of experimental trawl surveys conducted on the east coast of Corsica. We analysed and compared the structuration of diversity within three different bathymetric strata: the continental shelf (60-120 m depth), the upper slope (250-400 m) and the lower slope (450-570 m). For each of these three bathymetric strata, we simultaneously analysed 12 indices that are theoretically complementary and relate to 4 diversity components: (1) the number of species, (2) rarity, (3) evenness and (4) taxonomic diversity. Principal component analysis based on Spearman's correlation coefficients was carried out to investigate empirical relationships between the selected indices. Our results showed not only that a single diversity index cannot provide a complete view of the groundfish diversity along the east coast of Corsica, but also that-in some cases-one index cannot even encapsulate a complete description of a specific diversity component. We also found that the nature and the number of independent diversity components slightly varied from one bathymetric stratum to another. The main differences-which mainly occurred in the deepest bathymetric stratum-might be associated with lower density of individuals and lower dominance of some species at deeper depths. Finally, this study is the first dealing with groundfish diversity in this area, which is currently characterized by one of the lowest fishing intensity rates in the northern Mediterranean Sea. It might be considered as a first '' reference state '' with a view to monitoring the spatio-temporal changes in species diversity patterns along the east coast of Corsica in the future. (C) 2007 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2007-12 , Vol. 88 , N. 1-3 , P. 120-132

Droits : 2007 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-3512.pdf
DOI:10.1016/j.fishres.2007.08.003
http://archimer.ifremer.fr/doc/00000/3512/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
o abstract
ISSN: 0168-8278

hal-01519257
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519257
DOI : 10.1016/S0168-8278(16)00178-1

Éditeur(s) : HAL CCSD Wiley Open Access
Résumé : Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
ISSN: 2045-7758

hal-01204216
https://hal.archives-ouvertes.fr/hal-01204216
DOI : 10.1002/ece3.1303
PRODINRA : 280886

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
We report the development of the ReproGenomics Viewer (RGV), a multi-and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
ISSN: 0305-1048

hal-01146120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120/file/nar.gkv345.full.pdf
PUBMED : 25883147

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Cell death of hepatocytes is a prominent characteristic in the pathogenesis of liver disease, while hepatolysis is a starting point of inflammation in hepatitis and loss of hepatic function. However, the precise molecular mechanisms of hepatocyte cell death, the role of the cytokines of hepatic microenvironment and the involvement of intracellular kinases, remain unclear. Tumor necrosis factor alpha (TNF-α) is a key cytokine involved in cell death or survival pathways and the role of RIPK1 has been associated to the TNF-α-dependent signaling pathway. We took advantage of two different deficient mouse lines, the RIPK1 kinase dead knock-in mice (Ripk1K45A) and the conditional knockout mice lacking RIPK1 only in liver parenchymal cells (Ripk1LPC-KO), to characterize the role of RIPK1 and TNF-α in hepatitis induced by concanavalin A (ConA). Our results show that RIPK1 is dispensable for liver homeostasis under steady-state conditions but in contrast, RIPK1 kinase activity contributes to caspase-independent cell death induction following ConA injection and RIPK1 also serves as a scaffold, protecting hepatocytes from massive apoptotic cell death in this model. In the Ripk1LPC-KO mice challenged with ConA, TNF-α triggers apoptosis, responsible for the observed severe hepatitis. Mechanism potentially involves both TNF-independent canonical NF-κB activation, as well as TNF-dependent, but canonical NF-κB-independent mechanisms. In conclusion, our results suggest that RIPK1 kinase activity is a pertinent therapeutic target to protect liver against excessive cell death in liver diseases. © The Author(s) 2016.
ISSN: 2041-4889

hal-01414916
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01414916
DOI : 10.1038/cddis.2016.362
PUBMED : 27831558

Éditeur(s) : Amer Geophysical Union
Résumé : The temporal evolution and spatial distribution of surface salinity and colored detrital matter (cdm) were evaluated within and adjacent to the Amazon River Plume. Study objectives were as follows: first, to document the spatial coherence between Amazon discharge, salinity, cdm, and the nature of the salinity-cdm relationship; second, to document the temporal and spatial variability of cdm along the trajectory of the low-salinity Amazon Plume, and third, to explore the departure of cdm from conservative mixing behavior along the plume trajectory into the open ocean. Time series (2003-2007) of surface salinity estimated using the Advanced Microwave Scanning Radiometer-Earth Observing System and corresponding satellite cdm absorption (acdm) data documented a plume of freshened, colored water emanating from the Amazon. Salinity and acdm were generally coherent, but there were regions in which spatial patterns of salinity and acdm did not coincide. Salinity was oppositely phased with discharge, whereas acdm was in phase but lagged discharge and typically remained high after maximum discharge. Along the river plume trajectory, acdm was inversely correlated with salinity, yet there was considerable deviation from conservative mixing behavior during all seasons. Positive anomalies in a linear relationship between salinity and acdm corresponded to areas of enhanced satellite-retrieved net primary productivity, suggesting the importance of phytoplankton biomass or its subsequent remineralization as a source of cdm. Negative anomalies tended to predominate at the distal sections of the plume trajectories, an observation consistent with the process of photo-oxidation of cdm over observed time scales of days to weeks.
Journal Of Geophysical Research-oceans (0148-0227) (Amer Geophysical Union), 2011-07 , Vol. 116 , N. C00H02 , P. 14 p.

Droits : 2011 American Geophysical Union. All Rights Reserved.
http://archimer.ifremer.fr/doc/00041/15218/12593.pdf
DOI:10.1029/2011JC006989
http://archimer.ifremer.fr/doc/00041/15218/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome ofmajor phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of the proteome when cells switch from mitotic growth to meiotic development. We report a quantitative protein profiling analysis of yeast cell division and differentiation based on mass spectrometry. Information about protein levels was integrated with strand-specific tiling array expression data. We identified a total of 2366 proteins in at least one condition, including 175 proteins showing a statistically significant > 5-fold change across the sample set, and 136 proteins detectable in sporulating but not respiring cells. We correlate protein expression patterns with biological processes and molecular function by Gene Ontology term enrichment, chemoprofiling, transcription interference and the formation of double stranded RNAs by overlapping sense/antisense transcripts. Our work provides initial quantitative insight into protein expression in diploid respiring and differentiating yeast cells. Critically, it associates developmentally regulated induction of antisense long noncoding RNAs and double stranded RNAs with fluctuating protein concentrations during growth and development.
ISSN: 1874-3919

hal-01485858
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01485858/file/Becker%20et%20al.%20-%20The%20protein%20expression%20landscape%20of%20mitosis%20and%20me.pdf
DOI : 10.1016/j.jprot.2016.12.016

Éditeur(s) : Elsevier
Résumé : To better understand the recent motion of the Pacific plate relative to the Rivera plate and to better define the limitations of the existing Rivera-Pacific plate motion models for accurately predicting this motion, total-field magnetic data, multibeam bathymetric data and sidescan sonar images were collected during the BART and FAMEX campaigns of the N/O L'Atalante conducted in April and May 2002 in the area surrounding the Moctezuma Spreading Segment of the East Pacific Rise, located offshore of Manzanillo, Mexico, at 106 degrees 16'W, between 17.8 degrees N and 18.5 degrees N. Among the main results are: (1) the principle transform displacement zone of the Rivera Transform is narrow and well defined east of 107 degrees 15'W and these azimuths should be used preferentially when deriving new plate motion models, and (2) spreading rates along the Moctezuma Spreading Segment should not be used in plate motion studies as either seafloor spreading has been accommodated at more than one location since the initiation of seafloor spreading in the area of the Moctezuma Spreading Segment, or this spreading center is not a Rivera-Pacific plate boundary as has been previously assumed. Comparison of observed transform azimuths with those predicted by the best-fit poles of six previous models of Rivera-Pacific relative motion indicate that, in the study area, a significant systematic bias is present in the predictions of Rivera-Pacific motion. Although the exact source of this bias remains unclear, this bias indicates the need to derive a new Rivera-Pacific relative plate motion model.
Tectonophysics (0040-1951) (Elsevier), 2008-06 , Vol. 454 , N. 1-4 , P. 70-85

Droits : 2008 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2008/publication-4486.pdf
DOI:10.1016/j.tecto.2008.04.013
http://archimer.ifremer.fr/doc/00000/4486/