French Research Institute for Exploitation of the Sea
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Characterisation of the eddy-driven variability inshore of the Agulhas Current using Sea Surface Temperature observations
No full textOff the east coast of South Africa, coastal waters inshore of the Agulhas Current are largely affected by oceanic mesoscale turbulence, primarily in the form of meanders such as Natal Pulses and Durban Eddies. This study utilises forty years of modern, high-resolution satellite sea surface temperature (SST) data, offering both improved spatial detail and a longer time series than previous products, to characterise these eddies using an automated meander detection algorithm. Notably, automated detection has never before been applied to Durban Eddies, and Natal Pulses have not been analysed using such a high-resolution, long-term SST dataset. The algorithm successfully estimated the daily position of the inshore edge and core of the Agulhas Current and the “first occurrence” of Agulhas waters for the period of the study —the latter defined as the initial emergence of Agulhas Current waters in a filament or plume associated with Natal Pulses. The analysis reveals that the inshore edge of the Agulhas Current is not subject to seasonal variation but is significantly influenced by the presence of Natal Pulses and Durban Eddies. The first occurrence of Agulhas Current waters was only detected during the passage of Natal Pulses. Results indicate increased variability in regions south of 29.8°S, with Natal Pulses showing an increase in size and surface lifespan in the southern region. Conversely, Durban Eddies exhibit a decrease in size and surface lifespan as they propagate southward. Furthermore, seasonal SST anomalies are generally small, with cold events more frequent; Natal Pulses cause higher variability, while Durban Eddies maintain relative stability
ReefTEMPS: The Pacific Islands Coastal Temperature Network
No full textWhile the rise in global ocean temperature continues its course, reaching 1.45+/- 0.12 °C above pre-industrial level according to the World Meteorological Organization in 2023, marine heat waves frequencies and intensities increase. Consequently, coral reef ecosystems which are among the most vulnerable environments are strongly impacted with dystrophic events and corals experiencing increasing frequencies of bleaching events. That has devastating consequences for the Pacific Island Countries and Territories (PICTS) that strongly rely on these ecosystems. In-situ observation remains the best alternative for providing accurate characterization of long-term trends and extremes in these shallow environments. This paper presents the coastal temperature dataset of the ReefTEMPS monitoring network in which moored stations are implemented over a number of PICTS over a wide region in the Western and Central South Pacific from New Caledonia to French Polynesia. These in situ temperature time series are unique in several ways: in the length of some historical stations dating back to 1958 for the oldest, thus providing more than 65 years of daily data; in the number of countries sampled (16 PICTS) ; and in the variety of coral ecosystems monitored (from atolls to high islands and from barrier reef’s external slopes to shallow and narrow lagoons). Measurement devices have evolved over the years to provide increasingly precise and frequent observations so that the ReefTEMPS network was endorsed as a French National Observation Service in 2020, a label ensuring quality controlled and open access data of long-term observations. All stations are publicly available in ASCII or formatted NetCDF files, either on the ReefTEMPS dedicated Information System which also allows quick visualisation of time series, or in the SEANOE marine data platform. All links and accesses to these temperature time series are provided herein. The quality control and longevity of these temperature time series allows diagnosing long-term trends, highlighting the influence of multiple processes on temperature dynamics (e.g., internal waves, cyclones, seasonal and climate modes) and documenting the time evolution of extreme events. All files are made publicly available in dedicated SEANOE repositories (DOI provided herein)
Heterochromatin protein 1 (HP1) of Schistosoma mansoni: non-canonical chromatin landscape and oviposition effect
No full textBACKGROUND Heterochromatin protein 1 (HP1) is widespread in several organisms playing a role in control of gene expression by heterochromatin formation and maintenance of silent chromatin. Schistosoma mansoni is a human parasite that is responsible for Schistosomiasis, a tropical neglected disease in the tropical and subtropical areas in the world, where the intermediate host Biomphalaria glabrata is present. OBJECTIVES In this study we attempted to investigate if the SmHP1 is enriched in S. mansoni chromatin in cercariae larvae stage, compared with another larvae stage sporocysts and its importance for S. mansoni life cycle progression and parasite oviposition. METHODS We used ChIPmentation with commercial antibody ab109028 that passed in-house quality control. We also used RNA interference, mice infection and histology. FINDINGS Our data show that S. mansoni HP1 enrichment is non-canonical with a peak at the transcription end sites of protein coding genes. We did not find strong differences in SmHP1 chromatin landscapes between sporocysts and cercariae. Knockdown of SmHP1 in schistosomula and in vivo experiments in mice unexpectedly increased parasite oviposition. MAIN CONCLUSIONS Our results suggest that SmHP1 may influence chromatin structure in a non-canonical way in S. mansoni stages and may play a role in regulation of parasite ovipositio
Impact of altimeter-buoy data-pairing methods on the validation of Sentinel-3A coastal significant wave heights
No full textSea state information is critical for a broad range of human activities (e.g. shipping, marine energy, marine engineering) most of them being concentrated along the coastal zone. Satellite altimeter records of significant wave heights (SWH) represent the largest source of sea state observations available to date. However, the quality of altimeter observations is reduced in the coastal zone due to surface heterogeneity within the radar signal footprint. Major difficulties to assess the performance of coastal altimetry in the coastal zone are the reduced number of valid altimeter records and the increased sea state variability, which have recently fostered the development of new methods to pair and compare nearby altimeter and buoy data. In this study, we use a high-resolution numerical wave model implemented over the European coastal waters in order to characterize the spatial variability of sea states in the proximity of coastal in situ buoys, we explore different model-based data-pairing methods to account for coastal sea state variability and we assess their impact on the validation of Sentinel-3A 20Hz SWH measurements. Three Sentinel-3A processing modes are considered: the pseudo low rate mode processing, the SAR processing and the Low Resolution with Range Migration Correction (LR-RMC) processing. Our results indicate major impacts of data-pairing methods on the Sentinel-3A coastal validation and reveals the contribution of more frequent low SWH conditions, poorly resolved by radar altimeters, in the coastal zone as an additional source of errors in coastal altimetry
Estimating the variability of deep ocean particle flux collected by sediment traps using satellite data and machine learning
No full textThe gravitational pump plays a key role in the ocean carbon cycle by exporting sinking organic carbon from the surface to the deep ocean. Deep sediment trap time-series provide unique measurements of this sequestered carbon flux. Sinking particles are influenced by physical short-term spatio-temporal variability, which inhibits the establishment of a direct link to their surface origin. In this study, we present a novel machine learning tool, designated as Unetsst-ssh, which is capable of predicting the catchment area of particles captured by sediment traps moored at a depth of 3000 m above the Porcupine Abyssal Plain (PAP), based solely on surface data. The machine learning tool was trained and evaluated using Lagrangian experiments in a realistic CROCO numerical simulation. The conventional approach of assuming a static 100–200 km box over the sediment trap location, only yields an average prediction of ∼25 % of the source region, whilst Unetsst-ssh predicts ∼50 %. Unetsst-ssh was then applied to satellite observations to create a 20-year catchment area dataset, which demonstrates a stronger correlation between the PAP site deep particle fluxes and surface chlorophyll concentration, compared with the conventional approach. However, predictions remain highly sensitive to the local deep dynamics which are not observed in surface ocean dynamics. The improved identification of the particle source region for deep ocean sediment traps can facilitate a more comprehensive understanding of the mechanisms driving the export of particles from the surface to the deep ocean, a key component of the biological carbon pump
Poroelastic and viscoelastic properties of soft materials determined from AFM force relaxation and force-distance curves
No full textIn the field of tissue engineering, determining the mechanical properties of hydrogels is a key prerequisite to develop biomaterials mimicking the properties of the extracellular matrix. In mechanobiology, understanding the relationships between the mechanical properties and physiological state of cells is also essential. Time-dependent mechanical characterization of these soft materials is commonly achieved by atomic force microscopy (AFM) experiments in liquid environment. However, the determination of an appropriate model to correctly interpret the experimental data is often missing, making it difficult to extract quantitative mechanical properties. Here, force relaxation and force-distance curves were combined to elucidate the origin of dissipative processes involved in hydrogels and cells, before applying the relevant poroelastic or viscoelastic theory to model the curves. By using spherical AFM tips, analytical equations were developed to transform these curves into mechanical parameters by describing the relationships between the exerted force and the elastic, poroelastic or viscoelastic responses of semi-infinite and finite-thickness materials. Poroelastic behavior was evidenced for a thermoresponsive hydrogel and a set of poroelastic parameters was extracted from the force relaxation curves. In contrast, cells exhibited viscoelastic properties characterized by a single power-law relaxation over three-decade time scales. In addition, compressive modulus and fluidity exponent of cells were obtained by fitting force relaxation curves and approach-retraction force-distance curves. This combined theoretical and experimental framework opens a rigorous way toward quantitative mechanical properties of soft materials by (1) systematically determining the origin of their relaxation mechanisms, (2) defining the theoretical models to correctly interpret the experimental data, (3) using analytically solved equations to extract the mechanical parameters
Health Risks Status for Two Seaweeds of Economic Interest in Northwest Africa
No full textSeaweeds hold significant potential for human nutrition due to its high content of essential minerals and trace elements. In Africa, the development of the blue economy promotes their sustainable exploitation. However, harmful elements such as arsenic (As), lead (Pb), and cadmium (Cd) can accumulate in seaweeds, posing potential health risks upon consumption. Meristotheca senegalensis and Hypnea musciformis, two seaweeds of economic interest in Senegal, were collected in various locations, and their concentrations of essential nutrients, heavy metals, and transition metals were analyzed. Notably, cadmium levels in all samples exceeded established toxicity thresholds. A health risk assessment was performed, evaluating non-carcinogenic and carcinogenic risks through estimated daily intakes, target hazard quotients, hazard indexes, and carcinogenic risks. For adults, a low daily intake of seaweed (0.1 g day-1) posed no significant health risk over long-term exposure. High (8 g day-1) and medium (4 g day-1) daily intake levels posed no risk for adults and children, respectively, over 6-month exposure. In addition, seaweed represents a valuable iron source for preventing deficiency in Senegalese populations. Such intake levels could be incorporated into agro-food products for trace element enrichment. Nevertheless, for children, site-specific selection is critical to avoid carcinogenic risks over prolonged exposure. Seaweed offers a valuable opportunity for addressing food and nutrition security as well as promoting economic growth within Africa’s blue economy. However, careful scientific evaluation, particularly regarding site selection, is essential to ensure safe and sustainable uses, especially in countries like those in Africa, where marine pollution monitoring is often limited
Ichnologic and sedimentologic datasets from the Ediacaran–Cambrian Chapel Island Formation, Newfoundland, Canada
No full textExtensive ichnologic and sedimentologic datasets were gathered from six localities (Fortune Head, Fortune North, Grand Bank Head, Lewin's Cove, Little Dantzic Cove, and Point May) of the Ediacaran–Cambrian Chapel Island Formation at Burin Peninsula, south-eastern Newfoundland, eastern Canada. 1,708.2 m of sedimentary strata were logged at a centimeter scale (1:40) using a Jacob staff, in addition to 11.08 m of strata reported at a millimeter scale (1:1.67). Sedimentary logs focus on: (1) bed geometry; (2) bed thickness; (3) bed grain size; (4) sandstone/ mudstone ratio; and (5) sedimentary structures. For each log, trace-fossil datasets were reported, consisting of: (1) bioturbation intensity in cross-section (1,596 data points); (2) bed surface bioturbation intensity (1,481 data points); (3) stratigraphic position of individual trace fossils; (4) trace-fossil width (3,164 data points); (5) trace-fossil depth (1,539 data points); and (6) ichnotaxonomic classification (3,510 trace fossils identified at ichnospecies rank). The datasets are of importance to researchers interested in the palaeoecological signals depicted in this classic Ediacaran–Cambrian succession or in the compilation of worldwide data for deciphering macro-evolutionary trends in early animal life
Diversity and biogeography of the bacterial microbiome in glacier-fed streams
No full textThe rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth’s major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem
Product user manual. For Multi-Year WAVE In Situ Product INSITU_GLO_WAV_DISCRETE_MY_013_045
No full textThis document is the user manual for the Multi-Year WAVE In Situ product INSITU_GLO_WAV_DISCRETE_MY_013_045 (see Table 1). This guide describes the data product files, the available services to access them, and how to use these files and services. This product integrates observations aggregated and validated from the Regional EuroGOOS consortium (Arctic-ROOS, BOOS, NOOS, IBI-ROOS, MONGOOS) and Black Sea GOOS as well as from National Data Centers (NODCs), JCOMM global systems (OceanSITES, DBCP) and the Global telecommunication system (GTS) used by the Metoffices. The In Situ TAC relies on observing systems maintained by institutes that are not part of the In Situ TAC and Copernicus Marine Service is not contributing to the maintenance and setting up of the observing systems it uses. Data are distributed on full level (no interpolation) and are available in a dedicated directory to waves (INSITU_GLO_WAV_DISCRETE_MY_013_045) of Copernicus Marine Service Dissemination System in one or two files per platform. The Multi-Year WAVE product is a global product and provides two kinds of files: one with integrated parameters computed from the wave spectrum (e.g. significant wave height, peak period, mean direction) or zero crossing parameters (e.g. maximum wave height, mean height) and another one with the spectral information when available (scalar spectrum and directional functions like mean direction and angular spreading depending on the frequency). The files with integrated parameters contain also other physical and meteorological variables measured by the same platform. The complete list of variables distributed by the In Situ TAC can be found in the Copernicus Marine In Situ TAC physical parameters list (https://doi.org/10.13155/53381). This product is updated twice a year after a validation process carried out at centralized level by the Production Unit and described in detail in the Quality Information Document CMEMS-INS-QUID-013_045 (https://catalogue.marine.copernicus.eu/documents/QUID/CMEMS-INS-QUID-013_045.pdf). Since December 2020, files with wave spectra are included in the Multi-Year WAVE product. Since 2023, hourly data is delivered in a dedicated dataset: cmems_obs-ins_glo_wav_my_na_PT1H. More detailed information can be obtained from the Copernicus Marine Service web page (https://marine.copernicus.eu/) and the In Situ TAC web page (http://www.marineinsitu.eu/). Information on operational issues on products and services can be found on our User Notification Service. If you have any questions, please contact u