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
Résumé : International audience
BOI1 and BOI2 are paralogs important for the actin cytoskeleton andpolar growth. BOI1 encodes a meiotic transcript isoform with an extended5-untranslated region predicted to impair protein translation. It is,however, unknown how the isoform is repressed during mitosis, and ifBoi1 is present during sporulation. By interpreting microarray data fromMATa cells, MATa/ cells, a starving MAT/ control, and a meiosis-impairedrrp6 mutant, we classified BOI1's extended isoform as earlymeiosis-specific. These results were confirmed by RNA-Sequencing, andextended by a 5-RACE assay and Northern blotting, showing that meioticcells induce the long isoform while the mitotic isoform remainsdetectable during meiosis. We provide evidence via motif predictions, anin vivo binding assay and genetic experiments that the Rpd3/Sin3/Ume6histone deacetylase complex, which represses meiotic genes duringmitosis, also prevents the induction of BOI1's 5-extended isoform inmitosis by direct binding of Ume6 to its URS1 target. Finally, we findthat Boi1 protein levels decline when cells switch from fermentation torespiration and sporulation. The histone deacetylase Rpd3 is conserved,and eukaryotic genes frequently encode transcripts with variable 5-UTRs.Our findings are therefore relevant for regulatory mechanisms involvedin the control of transcript isoforms in multi-cellular organisms.
ISSN: 0950-382X

hal-01122120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122120
DOI : 10.1111/mmi.12976
PUBMED : 25708805

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
This article corrects: The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1's meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae. Vol. 96, Issue 4, 861–874, Article first published online: 21 MAR 2015
ISSN: 0950-382X

hal-01299297
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01299297
DOI : 10.1111/mmi.13297
PUBMED : 25708805

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
[1] Zircons and monazites from 6 samples of the North Ayilari dextral shear zone (NAsz), part of the Karakorum fault zone (KFZ), have been dated with the U-Th-Pb method, using both ID-TIMS and SIMS techniques. The ages reveal (1) inheritance from several events spanning a long period between the late Archean and the Jurassic; (2) an Eocene-Oligocene magmatic event (similar to 35-32 Ma); (3) an Oligo-Miocene magmatic event (similar to 25-22 Ma), at least partly synkinematic to the right-lateral deformation; and (4) a period of metamorphism metasomatism (similar to 22-14 Ma) interpreted as thermal and fluid advection in the shear zone. The Labhar Kangri granite located similar to 375 km farther Southeast along the KFZ is dated at 21.1 +/- 0.3 Ma. Such occurrence of several Oligo-Miocene granites along the KFZ, some of which show evidence for synkinematic emplacement, suggests that the fault zone played an important role in the genesis and /or collection of crustal melts. We discuss several scenarios for the onset and propagation of the KFZ, and offset estimates based on the main sutures zones. Our preferred scenario is an Oligo-Miocene initiation of the fault close to the NA range, and propagation along most of its length prior to similar to 19 Ma. In its southern half, the averaged long-term fault-rate of the KFZ is greater than 8 to 10 mm/a, in good agreement with some shorter-term estimates based on the Indus river course, or Quaternary moraines and geodesy. Our results show the KFZ cannot be considered as a small transient fault but played a major role in the collision history.
ISSN: 0278-7407

hal-00412570
https://hal.archives-ouvertes.fr/hal-00412570
DOI : 10.1029/2007TC002184

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
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 Wiley-Blackwell
Résumé : Pervasive melting of the middle crust, as inferred in Tibet and the Altiplano, probably influences the deformation of the lithosphere. To constrain strain distribution in a pervasively molten crust, we analysed the deformation in an eroded analogue of these orogens. The Ribeira-Araçuaí orogen (SE Brazil) comprises a stack of allochthons containing large volumes of anatectic and magmatic rocks. The upper allochton (∼300 km long, 50–100 km wide and >10 km thick) involves peraluminous diatexites and leucogranites resulting from partial melting of the middle crust. It overlies another allochthon containing huge early- to syn-collisional plutons intruding metasediments. Both anatexites and magmatic intrusions display a pervasive strain-induced magmatic fabric. Homogeneous strain distribution suggests inefficient localization. U–Pb ages of ∼575 Ma imply that anatexite melting was synchronous to the early- to syn-collisional magmatism. Similarity in ages magmatic and solid-state fabrics indicates that intrusions and anatexites deformed coherently with solid-state rocks while still molten, in response to a combination of gravity-driven and collision-driven deformation.
ISSN: 0954-4879

hal-00404915
https://hal.archives-ouvertes.fr/hal-00404915
DOI : 10.1111/j.1365-3121.2007.00747.x

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : Reconstruction of Northern African monsoon between 6.2 and 4.9 Ma and possible relationships with Late Miocene events. Mineralogical and geochemical investigations have been realized on ODP Site 659 in order to better understand the detrital sedimentation of the Cap Verde plateau and to reconstruct African monsoon intensity variations between 6.2 and 4.9 Ma. Time intervals corresponding to an intensification of the summer African monsoon rainfall are associated to a reduction of eolian input from the Sahara and an intensification of the African river input. The reflooding of the Mediterranean Sea at the end of the Messinian salinity crisis (MSC) (5.33 Ma) is correlated to a greater aridity in the Sahara.
ISSN: 1631-0713

hal-00412151
https://hal.archives-ouvertes.fr/hal-00412151
DOI : 10.1016/j.crte.2008.07.005

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.
ISSN: 0305-1048

Droits : http://creativecommons.org/licenses/by/
hal-01122128
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128/file/The%20conserved%20histone%20deacetylase.pdf
DOI : 10.1093/nar/gku1185

Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.
ISSN: 1535-9476

hal-00682837
https://hal.archives-ouvertes.fr/hal-00682837
DOI : 10.1074/mcp.M111.012682
PUBMED : 21997732

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes. The results of expression quantitative trait locus (eQTL) analyses were also replicated with a Gene Expression Omnibus (GEO) data set. The effects of eQTLs on overall survival (OS) and disease-free survival (DFS) were evaluated. RESULTS: Five ancestry-related SNPs were identified as cis-eQTLs in the DNA polymerase beta (POLB) gene (false discovery rate [FDR]<0.01). The homozygous/heterozygous genotypes containing the African allele showed higher POLB expression than the homozygous white allele genotype (P<.001). A replication study using a GEO data set validated all 5 eQTLs and also showed a statistically significant difference in POLB expression based on genetic ancestry (P=.002). An association was observed between these eQTLs and OS (P<.037; FDR<0.0363) as well as DFS (P=.018 to.0629; FDR<0.079) for oral cavity and laryngeal cancer patients treated with platinum-based chemotherapy and/or radiotherapy. Genotypes containing the African allele were associated with poor OS/DFS in comparison with homozygous genotypes harboring the white allele. CONCLUSIONS: Analyses show that ancestry-related alleles could act as eQTLs in HNSCC and support the association of ancestry-related genetic factors with survival disparities in patients diagnosed with oral cavity and laryngeal cancer. (C) 2016 American Cancer Society.
ISSN: 0008-543X

hal-01519253
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519253
DOI : 10.1002/cncr.30457
PUBMED : 27906459

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We analyze in this study a new set of marine data including 3D local tomography, 1992-2008 relocated earthquakes and two recent multichannel seismic lines to characterize the deformation style in the collision area offshore east Taiwan. We have mapped in detail the Mohos of the converging plates as well as the subduction interface with a resolution never reached before. We show that the sharp continental subduction of the Eurasia plate, beneath the middle part of the Central Range, indents the Philippine Sea plate (PSP) as attested by intra-oceanic slicing and incipient subduction of the PSP beneath the east coast of Taiwan. The westernmost part of the PSP slab is probably experiencing a beginning of break-off as attested by NW-trending en-échelon shear zones beneath the southern slope of the southern Ryukyu arc (SRA). These en-échelon shear zones have a sinistral component favored by the "collision-free" subduction of the PSP north of 24°30′N. The down-faulting of the subduction interface forms ramps along which earthquakes clusterize. Three M7 subduction earthquakes occurred offshore Suao city along these ramps with a recurrence interval of about 40 years: 1920 Mw7.7, 1963 Mw7.2 and 2002 Mw7.1 events. The 1966 Mw6.0-7.5 earthquakes sequence likely outlines a WNW-ESE left-lateral intra-slab shear zone. The SRA upper plate accommodates the complex geometry and deformation of the subducting PSP through seismic deformation. Shallow high velocities fringing the Luzon volcanic arc (LVA) beneath the Longitudinal Valley and north of the southernmost Ryukyu forearc basins are interpreted as relics of the LVA forearc basement squeezed in the collision zone. Based on the accommodation of a large part of the convergence through shortening within the PSP and the subsequent segmentation of the shallow subduction interface, we consider that the nucleation of a Mw ≥ 8 earthquake along the southernmost Ryukyu megathrust is unlikely.
ISSN: 0040-1951

hal-00853365
https://hal.archives-ouvertes.fr/hal-00853365
https://hal.archives-ouvertes.fr/hal-00853365/document
https://hal.archives-ouvertes.fr/hal-00853365/file/publallemandifremer.pdf
DOI : 10.1016/j.tecto.2013.03.020

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 Royal Society, The
Résumé : International audience
To forecast marine disease outbreaks as oceans warm requires new environmental surveillance tools. We describe an iterative process for developing these tools that combines research, development and deployment for suitable systems. The first step is to identify candidate host–pathogen systems. The 24 candidate systems we identified include sponges, corals, oysters, crustaceans, sea stars, fishes and sea grasses (among others). To illustrate the other steps, we present a case study of epizootic shell disease (ESD) in the American lobster. Increasing prevalence of ESD is a contributing factor to lobster fishery collapse in southern New England (SNE), raising concerns that disease prevalence will increase in the northern Gulf of Maine under climate change. The lowest maximum bottom temperature associated with ESD prevalence in SNE is 128C. Our seasonal outlook for 2015 and long-term projections show bottom temperatures greater than or equal to 128C may occur in this and coming years in the coastal bays of Maine. The tools presented will allow managers to target efforts to monitor the effects of ESD on fishery sustainability and will be iteratively refined. The approach and case example highlight that temperature-based surveillance tools can inform research, monitoring and management of emerging and continuing marine disease threats.
ISSN: 0080-4622

Droits : http://creativecommons.org/licenses/by/
hal-01282834
https://hal-univ-perp.archives-ouvertes.fr/hal-01282834
https://hal-univ-perp.archives-ouvertes.fr/hal-01282834/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01282834/file/20150208.full.pdf
DOI : 10.1098/rstb.2015.0208

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Projections of climate change impacts on coral reefs produced at the coarse resolution (~1°) of Global Climate Models (GCMs) have informed debate but have not helped target local management actions. Here, projections of the onset of annual coral bleaching conditions in the Caribbean under Representative Concentration Pathway (RCP) 8.5 are produced using an ensemble of 33 Coupled Model Intercomparison Project phase-5 models and via dynamical and statistical downscaling. A high-resolution (~11 km) regional ocean model (MOM4.1) is used for the dynamical downscaling. For statistical downscaling, sea surface temperature (SST) means and annual cycles in all the GCMs are replaced with observed data from the ~4-km NOAA Pathfinder SST dataset. Spatial patterns in all three projections are broadly similar ; the average year for the onset of annual severe bleaching is 2040–2043 for all projections. However, downscaled projections show many locations where the onset of annual severe bleaching (ASB) varies 10 or more years within a single GCM grid cell. Managers in locations where this applies (e.g., Florida, Turks and Caicos, Puerto Rico, and the Domini-can Republic, among others) can identify locations that represent relative albeit temporary refugia. Both downscaled projections are different for the Bahamas compared to the GCM projections. The dynamically downscaled projections suggest an earlier onset of ASB linked to projected changes in regional currents, a feature not resolved in GCMs. This result demonstrates the value of dynamical downscaling for this application and means statistically downscaled projections have to be interpreted with caution. However, aside from west of Andros Island, the projections for the two types of downscaling are mostly aligned; projected onset of ASB is within AE10 years for 72% of the reef locations.
ISSN: 1354-1013

Droits : http://creativecommons.org/licenses/by-nc/
hal-01223492
https://hal-univ-perp.archives-ouvertes.fr/hal-01223492
https://hal-univ-perp.archives-ouvertes.fr/hal-01223492/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01223492/file/Hooidonk_et_al-2015-Global_Change_Biology.pdf
DOI : 10.1111/gcb.12901

Éditeur(s) : HAL CCSD SpringerOpen
Résumé : The Karakorum Fault zone (KFZ) plays an important role in understanding the formation, evolvement and deformation of the Tibetan Plateau. The high-T dextral shearing metamorphic rocks, e.g., mylonites or mylonitized gneisses-granites, locally crop out along the southeastern part of the KFZ in the Ayila Ri'gyü Range area. The SHRIMP U-Pb dating of the syn-kinematic crystallized zircons indicates that the initial age of the KFZ is ∼27 Ma, ∼10 Ma older than previous results. The extensive high-T dextral shearing along the KFZ started at least at 27–20 Ma, accompanied by the syn-kinematic emplacement of leuco-granites. Deformation and concomitant fluid circulation during shearing most likely occurred as early as at 25–13 Ma. The KFZ probably grew from southeast to northwest along the fault as a result of continuous convergence between the India plate and Eurasia plate.
ISSN: 1001-6538

hal-00406402
https://hal.archives-ouvertes.fr/hal-00406402
DOI : 10.1007/s11434-007-0164-6

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 Public Library of Science
Résumé : International audience
Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of mammals.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01233552
https://hal.archives-ouvertes.fr/hal-01233552
https://hal.archives-ouvertes.fr/hal-01233552/document
https://hal.archives-ouvertes.fr/hal-01233552/file/journal.pone.0133314.pdf
DOI : 10.1371/journal.pone.0133314

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