Éditeur(s) : Elsevier
Résumé : The Okinawa Trough is a natural laboratory for the study of later Quaternary land-ocean interaction and paleoenvironmental changes. In this study we reconstruct the evolution of clay mineral assemblages in Core DGKS9604 retrieved from the central Okinawa Trough. Illite dominates the clay mineral compositions, with average contents above 60%. Clay mineral evolution since 28 ka is closely related to changes in sediment provenance and paleoenvironment. Sea level rise and the strength of the Kuroshio Current control the dispersal and deposition of clays on the East China Sea shelf and in the Okinawa Trough, and thus, determine the clay mineral compositions in the core sediments. During the late last glacial period (28.0-14.0 ka), the paleo-Changjiang River mouth was situated at the shelf edge close to the central Okinawa Trough and thus, together with the outer shelf, supplied large volumes of terrigenous sediments directly into the trough. From 14.0 to 8.4 ka influence from the Changjiang decreased while the mid-outer shelf of the East China Sea became the dominant sediment source to the central Okinawa Trough as sea level rose and the Changjiang river mouth migrated west. Strong sediment reworking and erosion at the shelf edge at 15-13 ka significantly increased the lateral transport of fine-grained shelf sediments to the central Okinawa Trough. Since ca. 8.4 ka clays from Taiwan have dominated the sediment flux to the site, coinciding with the re-entry of the Kuroshio Current into the trough. The increasing influence of the Changjiang-sourced sediments since 1.5 ka was probably related to the weakening of the Kuroshio Current and/or a higher river flux. (C) 2010 Elsevier B.V. All rights reserved.
Palaeogeography, Palaeoclimatology, Palaeoecology (0031-0182) (Elsevier), 2010-03 , Vol. 288 , N. 1-4 , P. 108-117

Droits : 2010 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00002/11367/7977.pdf
DOI:10.1016/j.palaeo.2010.01.040
http://archimer.ifremer.fr/doc/00002/11367/

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 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 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) : Elsevier Science Bv
Résumé : The late Quaternary paleoceanography and paleoenvironment in the Okinawa Trough, East China Sea, have been well reconstructed over the last decade, while in contrast the provenance of terrigenous sediments that have accumulated there remains enigmatic. In this study, rare earth elements (REE) were used to investigate provenance changes in sediments from Core DGKS9604, taken from the middle Okinawa Trough. Discrimination plots based on REE fractionation parameters suggest that the cored sediments have variable provenances over the last 30 ka, with the lower part (ca. 31-8.2 ka) ultimately originating mostly from the Changjiang (Yangtze River) and the upper part (7.1-0 ka) primarily from Taiwan. During the Last Glacial Maximum and early deglacial period, sea level was low and the main stream of the Kuroshio Current was deflected to the east of the Ryukyu Islands. As a result the Changjiang-derived sediments might have dominated sedimentation of the middle Okinawa Trough. However, since about 7 ka the main stream of the Kuroshio Current strengthened in the area of the trough, as sea level approximated the modern position. This caused near-bottom transport of fine-grained sediments from the continental margin to the trough to become weak and instead, Taiwan-derived terrigenous sediments dominated in the middle trough. The changing provenances of terrigenous sediments into the middle Okinawa Trough are closely related to the evolution of oceanic circulation and sea level in the East China Sea. Two tephra layers in the core have distinct REE compositions and correlate well with two volcanic eruptions at 7.6 and 25.8 ka in southern Japan. (C) 2010 Published by Elsevier B.V.
Marine Geology (0025-3227) (Elsevier Science Bv), 2010-09 , Vol. 275 , N. 1-4 , P. 212-220

Droits : 2010 Published by Elsevier B.V.
http://archimer.ifremer.fr/doc/00013/12459/9402.pdf
DOI:10.1016/j.margeo.2010.06.002
http://archimer.ifremer.fr/doc/00013/12459/

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
The etiology of congenital heart defect (CHD) combines environmental and genetic factors. So far, there were studies reporting on the screening of a single gene on unselected CHD or on familial cases selected for specific CHD types. Our goal was to systematically screen a proband of familial cases of CHD on a set of genetic tests to evaluate the prevalence of disease-causing variant identification. A systematic screening of GATA4, NKX2-5, ZIC3 and Multiplex ligation-dependent probe amplification (MLPA) P311 Kit was setup on the proband of 154 families with at least two cases of non-syndromic CHD. Additionally, ELN screening was performed on families with supravalvular arterial stenosis. Twenty-two variants were found, but segregation analysis confirmed unambiguously the causality of 16 variants: GATA4 (1 x), NKX2-5 (6 x), ZIC3 (3 x), MLPA (2 x) and ELN (4 x). Therefore, this approach was able to identify the causal variant in 10.4% of familial CHD cases. This study demonstrated the existence of a de novo variant even in familial CHD cases and the impact of CHD variants on adult cardiac condition even in the absence of CHD. This study showed that the systematic screening of genetic factors is useful in familial CHD cases with up to 10.4% elucidated cases. When successful, it drastically improved genetic counseling by discovering unaffected variant carriers who are at risk of transmitting their variant and are also exposed to develop cardiac complications during adulthood thus prompting long-term cardiac follow-up. This study provides an important baseline at dawning of the next-generation sequencing era.
ISSN: 1018-4813

hal-01404211
https://hal-univ-bourgogne.archives-ouvertes.fr/hal-01404211
DOI : 10.1038/ejhg.2015.105
PUBMED : 26014430