French Research Institute for Exploitation of the Sea
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An updated non-intrusive, multi-scale, and flexible coupling interface in WRF 4.6.0
No full textThe Weather Research and Forecasting (WRF) model has been widely used for various applications, especially for solving mesoscale atmospheric dynamics. Its high-order numerical schemes and nesting capability enable high spatial resolution. However, a growing number of applications are demanding more realistic simulations through the incorporation of coupling with new model compartments and an increase in the complexity of the processes considered in the model. (e.g., ocean, surface gravity wave, land-surface, chemistry...). The present paper details the development and the functionalities of the coupling interface we implemented in WRF. It uses the Ocean-Atmosphere-Sea-Ice-Soil – Model Coupling Toolkit (OASIS3-MCT) coupler, which has the advantage of being non-intrusive, efficient, and very flexible to use. OASIS3-MCT has already been implemented in many climate and regional models. This coupling interface is designed with the following baselines: (1) it is structured with a 2-level design through 2 modules: a general coupling module, and a coupler-specific module, allowing to easily add other couplers if required, (2) variables exchange, coupling frequency, and any potential time and grid transformations are controlled through an external text file, offering great flexibility, (3) the concepts of “external domains” and “coupling mask” are introduced to facilitate the exchange of fields to/from multiple sources (different models, fields from different models/grids/zooms...). Finally, two examples of applications of ocean-atmosphere coupling are proposed. The first is related to the impact of ocean surface current feedback to the atmospheric boundary layer, and the second concerns the coupling of surface gravity waves with the atmospheric surface layer
The role of mantle inheritance and refertilization during breakup at magma-poor rifted margins: What can we learn from the SW-Australia margin?
No full textThe study of mantle-melt interactions at magma-poor rifted margins, accounting for about half of the world margins, is so far limited by the access to samples. Present concepts are therefore mainly based on studies of the Western Tethys and southern North Atlantic domain, and it remains unclear if they are applicable to other magma-poor rifted margins. Here, we present a study of well-preserved peridotites dredged along the southwestern Australian margin (Diamantina Zone). Our petrological data show that two types of peridotites occur: spinel lherzolite, which represents the inherited subcontinental mantle (SCLM) before the separation of Australia and Antarctica, and plagioclase peridotite formed by syn-rift melt entrapment at low pressure in the plagioclase stability field during mantle exhumation. The observed mantle types as well as the mantle-melt processes identified in the Diamantina peridotites are very similar to those documented in the Alpine-Apennine and Iberia margins. Hence, the Alpine/Iberia model of magma-poor rifted margins may be globally applicable and does not depend on the SCLM inheritance. Remnants of mantle inheritance may be preserved in the refertilized mantle, suggesting a progressive transition from an inherited to a refertilized mantle during breakup. Finally, this study highlights the role of inheritance and refertilization as the main features controlling final rifting and breakup at magma-poor rifted margins
Pleiotropic signaling of single-chain thyrostimulin (GPB5-GPA2) on homologous glycoprotein hormone receptors (ScFSHR, ScLHR, ScTSHR) in the elasmobranch Scyliorhinus canicula reproduction
No full textThe pituitary glycoprotein hormones (GPHs) control several physiological processes in vertebrates such as reproduction and metabolism. They include the luteinizing hormone (LH), the follicle-stimulating hormone (FSH), and the thyroid-stimulating hormone (TSH), which activate their cognate leucine-rich repeat G protein-coupled receptors (LGRs), LHR, FSHR, and TSHR. Each GPH consists of a common α subunit and a specific βFSH, βLH or βTSH subunit. More recently, two supplementary GPH proteins, GPA and GPB, were identified in nearly all bilaterians and are the ancestors of the pituitary GPH α- and β-subunits, respectively. Chondrichthyans (holocephalans and elasmobranchs), the sister group of bony vertebrates, are the most ancient clade to possess diversified GPH subunits. In the present study, GPA2, GPB5, TSHβ2, but not TSHβ1, and TSHR sequences have been identified in several elasmobranch genomes, and their 3D models were analyzed. Functional hormone-receptor interactions were studied in the small-spotted catshark (Scyliorhinus canicula) and showed that conditioned media from cells expressing the recombinant single-chain ScGPB5-ScGPA2 were more effective than independent subunits in activating ScTSHR, ScFSHR, and ScLHR. Expression profiles were analyzed by real-time PCR, in situ hybridization, and immunohistochemistry along the male genital tract, other male and female tissues, and female tissues. A broader tissue distribution expression was observed for tshr and gpa2 than for gpb5, which was mainly observed in the testes. In testis, expression of tshr and gpb5 by Sertoli cells and of gpa2 by germ cells suggested paracrine/autocrine functions of GPA2/GPB5/GPHR signaling during spermatogenesis. This study complements the data on GPA2 and GPB5 by studying a chondrichthyan of phylogenetic interest for understanding the evolution of endocrine regulation in vertebrates
Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues
No full textSince the 1990s, the Pacific oyster Magallana gigas has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole-genome analysis. Identification of the best method for extraction of high molecular weight (HMW) DNA and development of accurate bioinformatic pipelines for its characterization are now required. To this end, we evaluated and compared six HMW methods and one conventional DNA extraction kit for their ability to extract OsHV-1 DNA from M. gigas -infected tissues. We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole-genome and “adaptive sampling” (AS) sequencing approaches. Finally, we evaluated the efficiency of bioinformatics tools for de novo assembly and consensus calling to generate accurate OsHV-1 genomes. The HMW DNA extraction kit coupled with ONT sequencing and dedicated bioinformatics tools allowed us to produce accurate OsHV-1 genomes compared to those assembled using Illumina technology. The AS approach allowed up to 60% enrichment for viral data, and the long reads generated by ONT allowed the characterization of OsHV-1 isomers. Together with its portability, this sequencing shows great promise as a diagnostic tool for the characterization of unculturable aquatic viruses directly from host tissues. IMPORTANCE Many aquatic viruses threaten commercially valuable species and cause significant economic losses during outbreaks. To improve our understanding of the origin, transmission patterns and spread of these viruses, additional genomic data are essential. However, genomic characterization of unculturable large DNA viruses is a major challenge. In the present study, we have successfully evaluated the ability of ONT sequencing and adaptive sequencing (AS) to sequence and assemble the complete OsHV-1 genome. Our results show that it is now possible to sequence the whole genome of large DNA viruses directly from infected host tissue, without the need for prior in vitro propagation or prior laboratory steps for virus enrichment
Crotalia jafari: a new weakly calcified holococcolithophore genus and species from the Southwest Indian Ocean
No full textWe here describe a distinctive weakly calcified holococcolithophore Crotalia jafari gen. et sp. nov. from the Southwest Indian Ocean phytoplankton. The coccospheres of Crotalia jafari measure 8–15 ?m in diameter, and possess 430–538 coccoliths, with each coccolith measuring less than 1 ?m in diameter. The coccoliths are tightly attached to each other by an organic layer. Their central area appears open. Finger-shaped extensions are present in the peripheral coccoliths, and stretch from the hexagonal surface layer towards the basal plate. The basal plate is flat and composed of irregular wall fabric. The crystallites of the coccoliths are small. These morphological features make this holococcolithophore unique among the extant and fossil coccolithophores. The described species is therefore placed into the new genus ‘Crotalia’. This study also suggests that high diversity of weakly calcified (and still undescribed) holo- and heterococcolithophores may exist in the Southern Ocean, which requires additional careful observation
Evaluation of joint recommendations on the landing obligation, technical measures, and conservation measures necessary for compliance with obligations under Union environmental legislation (STECF 24-04)
No full textCommission Decision of 25 February 2016 setting up a Scientific, Technical and Economic Committee for Fisheries, C(2016) 1084, OJ C 74, 26.2.2016, p. 4–10. The Commission may consult the group on any matter relating to marine and fisheries biology, fishing gear technology, fisheries economics, fisheries governance, ecosystem effects of fisheries, aquaculture or similar disciplines. This report contains a review of Joint Recommendations submitted by Member States Regional Groups for the implementation of the Landing Obligation in 2024 and beyond