Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.info:eu-repo/semantics/publishedVersio

Morphometric Relationships between Length and Weight of 109 Fish Species in the Caribbean Sea (French West Indies)

In total, 109 fish species (24,996 individuals)were sampled around Guadeloupe andMartinique Islands from October 2021 to September 2022 to estimate the morphometric relationships between total length and weight (LengthWeight Relationship: LWR) of each fish species according to potential spatial, temporal and sex differences. Of these species, this is the first time that the LWR was estimated in the Atlantic Ocean for 16 species. There is a significant relationship between length and weight for all tested species. For 83 tested species, the sex effect on the LWR showed significant sexual dimorphism for 24 species. Additionally, a link between the temporal effect and the reproduction period was tested for 68 species, of which 35 presented significant differences relative to the annual quarter of sampling. Finally, the geographical effect (i.e., the difference between samples from around Guadeloupe Island and those fromMartinique Island) was significant for 60 species. This island effect was significant for 25 species

Mangrove Restoration in the Vicinity of Oil and Gas Facilities: Lessons Learned From a Large-Scale Project

International audienceMangroves are critical ecosystems given their key role in conserving biodiversity, protecting coastlines from erosion and supporting coastal resources. They may be impacted by oil and gas activities, either directly or indirectly. Restoring them is therefore of prime importance. In the Mahakam Delta, oil and gas exploration and production have been conducted for more than 40 years. This industry has operated in a quasi-pristine area barely affected by its activities until the mid 80’s. Toward the late 1980’s and until 2000, the delta was subject to massive and rapid development of shrimp farming and by 2001, 80% of the delta mangroves were destroyed and most of it replaced by ponds used for aquaculture. During the 2000’s, shrimps production in the delta decreased due to lack of nutrients in ponds, and a drop in shrimp prices due to the rise of imports worldwide. Numerous ponds were abandoned in the delta. This economic situation generated social instabilities that could threaten the oil and gas industry in the region. Therefore, in order to better protect mangroves and optimize restoration of damaged areas, Total E&P Indonesie has embarked on a mangrove restoration initiative in the Mahakam delta aimed at understanding the restoration processes through both natural recolonization and planting techniques. The general methodology implemented has been to i) describe the land occupation by acquiring satellite images, interpreting aerial photos, conducting field work, and establishing GIS maps, ii) inventory fauna and flora (mangroves, birds, fish and benthic invertebrates, mammals, reptiles and others), iii) conduct a monitoring of naturally re-colonized areas, replanted areas and original forest on selected areas. Results show that natural recolonization of a mangrove area can be very quick under certain conditions (subject to availability of seeds and easy access to the area to be recolonized). But in areas where seeds cannot easily migrate and access, or where seed supply is too difficult, replanting remains the best option. Social aspects have also to be taken into account: replanting promote the local commitment to sustainable environmental conservation. This paper will detail the methodology, present the scientific results and discuss the lesson learned

Mangrove Restoration in the Vicinity of Oil and Gas Facilities: Lessons Learned From a Large-Scale Project

International audienceMangroves are critical ecosystems given their key role in conserving biodiversity, protecting coastlines from erosion and supporting coastal resources. They may be impacted by oil and gas activities, either directly or indirectly. Restoring them is therefore of prime importance. In the Mahakam Delta, oil and gas exploration and production have been conducted for more than 40 years. This industry has operated in a quasi-pristine area barely affected by its activities until the mid 80’s. Toward the late 1980’s and until 2000, the delta was subject to massive and rapid development of shrimp farming and by 2001, 80% of the delta mangroves were destroyed and most of it replaced by ponds used for aquaculture. During the 2000’s, shrimps production in the delta decreased due to lack of nutrients in ponds, and a drop in shrimp prices due to the rise of imports worldwide. Numerous ponds were abandoned in the delta. This economic situation generated social instabilities that could threaten the oil and gas industry in the region. Therefore, in order to better protect mangroves and optimize restoration of damaged areas, Total E&P Indonesie has embarked on a mangrove restoration initiative in the Mahakam delta aimed at understanding the restoration processes through both natural recolonization and planting techniques. The general methodology implemented has been to i) describe the land occupation by acquiring satellite images, interpreting aerial photos, conducting field work, and establishing GIS maps, ii) inventory fauna and flora (mangroves, birds, fish and benthic invertebrates, mammals, reptiles and others), iii) conduct a monitoring of naturally re-colonized areas, replanted areas and original forest on selected areas. Results show that natural recolonization of a mangrove area can be very quick under certain conditions (subject to availability of seeds and easy access to the area to be recolonized). But in areas where seeds cannot easily migrate and access, or where seed supply is too difficult, replanting remains the best option. Social aspects have also to be taken into account: replanting promote the local commitment to sustainable environmental conservation. This paper will detail the methodology, present the scientific results and discuss the lesson learned

Mangrove Restoration in the Vicinity of Oil and Gas Facilities: Lessons Learned From a Large-Scale Project

International audienceMangroves are critical ecosystems given their key role in conserving biodiversity, protecting coastlines from erosion and supporting coastal resources. They may be impacted by oil and gas activities, either directly or indirectly. Restoring them is therefore of prime importance. In the Mahakam Delta, oil and gas exploration and production have been conducted for more than 40 years. This industry has operated in a quasi-pristine area barely affected by its activities until the mid 80’s. Toward the late 1980’s and until 2000, the delta was subject to massive and rapid development of shrimp farming and by 2001, 80% of the delta mangroves were destroyed and most of it replaced by ponds used for aquaculture. During the 2000’s, shrimps production in the delta decreased due to lack of nutrients in ponds, and a drop in shrimp prices due to the rise of imports worldwide. Numerous ponds were abandoned in the delta. This economic situation generated social instabilities that could threaten the oil and gas industry in the region. Therefore, in order to better protect mangroves and optimize restoration of damaged areas, Total E&P Indonesie has embarked on a mangrove restoration initiative in the Mahakam delta aimed at understanding the restoration processes through both natural recolonization and planting techniques. The general methodology implemented has been to i) describe the land occupation by acquiring satellite images, interpreting aerial photos, conducting field work, and establishing GIS maps, ii) inventory fauna and flora (mangroves, birds, fish and benthic invertebrates, mammals, reptiles and others), iii) conduct a monitoring of naturally re-colonized areas, replanted areas and original forest on selected areas. Results show that natural recolonization of a mangrove area can be very quick under certain conditions (subject to availability of seeds and easy access to the area to be recolonized). But in areas where seeds cannot easily migrate and access, or where seed supply is too difficult, replanting remains the best option. Social aspects have also to be taken into account: replanting promote the local commitment to sustainable environmental conservation. This paper will detail the methodology, present the scientific results and discuss the lesson learned

3D metrology with a laser tracker inside a vacuum chamber for NISP test campaign

International audienceIn the frame of the test of NISP instrument for ESA Euclid mission, the question was raised to perform a metrology measurement of different components during the thermal vacuum test of NISP instrument. NISP will be tested at Laboratoire d'Astrophysique de Marseille (LAM) in ERIOS chamber under vacuum and thermal conditions in order to qualify the instrument in its operating environment and to perform the final acceptance test before delivery to the payload. One of the main objectives of the test campaign will be the measurement of the focus position of NISP image plane with respect to the EUCLID object plane. To simulate the EUCLID object plane, a telescope simulator with a very well know focal distance will be installed in front of NISP into ERIOS chamber. We need to measure at cold and vacuum the position of reflectors installed on NISP instrument and the telescope simulator. From these measurements, we will provide at operational temperature the measurement of references frames set on the telescope simulator and NISP, the knowledge of the coordinates of the object point source provided by the telescope simulator and the measurement of the angle between the telescope simulator optical axis and NISP optical axis. In this context, we have developed a metrology method based on the use of a laser tracker to measure the position of the reflectors inside ERIOS. The laser tracker is installed outside the vacuum chamber and measure through a curved window reflectors put inside the chamber either at ambient pressure or vacuum pressure. Several tests campaigns have been done at LAM to demonstrate the measurement performance with this configuration. Using a well know reflectors configuration, we show that it is possible to correct the laser tracker measurement from the window disturbances and from the vacuum impact. A corrective term is applied to the data and allows retrieving the real coordinates of the reflectors with a bias lower than 30µm, which is lower than the laser tracker measurement uncertainties estimated at 60µm. No additional error term of the laser tracker measurement is observed when using the laser tracker with the curved window and in vacuum, comparing with a classical use of the laser tracker. With these test campaign, we have been able to demonstrate the possibility to use a laser tracker to measure in real time during a vacuum thermal test the position of different mechanical parts into a vacuum chamber with an accuracy better than 60µm

Mangrove Restoration in the Vicinity of Oil and Gas Facilities: Lessons Learned From a Large-Scale Project

International audienceMangroves are critical ecosystems given their key role in conserving biodiversity, protecting coastlines from erosion and supporting coastal resources. They may be impacted by oil and gas activities, either directly or indirectly. Restoring them is therefore of prime importance. In the Mahakam Delta, oil and gas exploration and production have been conducted for more than 40 years. This industry has operated in a quasi-pristine area barely affected by its activities until the mid 80’s. Toward the late 1980’s and until 2000, the delta was subject to massive and rapid development of shrimp farming and by 2001, 80% of the delta mangroves were destroyed and most of it replaced by ponds used for aquaculture. During the 2000’s, shrimps production in the delta decreased due to lack of nutrients in ponds, and a drop in shrimp prices due to the rise of imports worldwide. Numerous ponds were abandoned in the delta. This economic situation generated social instabilities that could threaten the oil and gas industry in the region. Therefore, in order to better protect mangroves and optimize restoration of damaged areas, Total E&P Indonesie has embarked on a mangrove restoration initiative in the Mahakam delta aimed at understanding the restoration processes through both natural recolonization and planting techniques. The general methodology implemented has been to i) describe the land occupation by acquiring satellite images, interpreting aerial photos, conducting field work, and establishing GIS maps, ii) inventory fauna and flora (mangroves, birds, fish and benthic invertebrates, mammals, reptiles and others), iii) conduct a monitoring of naturally re-colonized areas, replanted areas and original forest on selected areas. Results show that natural recolonization of a mangrove area can be very quick under certain conditions (subject to availability of seeds and easy access to the area to be recolonized). But in areas where seeds cannot easily migrate and access, or where seed supply is too difficult, replanting remains the best option. Social aspects have also to be taken into account: replanting promote the local commitment to sustainable environmental conservation. This paper will detail the methodology, present the scientific results and discuss the lesson learned

Avoiding falsely low creatinine concentrations measured in patients treated with N-acetylcysteine for acetaminophen intoxication using enzymo-amperometric method - An in vitro and in vivo study

International audienceBACKGROUND: Circulating creatinine is a biomarker of paramount importance in clinical practice. In cases of acetaminophen (APAP) intoxication, the antidote, N-acetylcysteine (NAC), interferes with commonly used creatininase-peroxidase methods. This study aimed to assess whether creatininase-amperometric methods were affected in this context. METHODS: This study includes in vitro interference tests, involving four creatinine assays using NAC-spiked plasma pools and an in vivo retrospective study comparing creatininase-peroxidase and creatininase-amperometric measurements in patients presenting with NAC-treated APAP poisoning. RESULTS: Creatininase-peroxidase method was impacted by NAC interference in a clinically-significant manner at therapeutic NAC levels (basal value recovery of 80 % and 70 % for 500 and 1000 mg.L(-1) of NAC, respectively), surpassing the desirable Reference Change Value (RCV%). Enzymo-amperometric methods were not impacted. Among patients, a mean bias of -45.2 ± 28.0 % was observed for the peroxidase detection method compared to the amperometric in those who received NAC prior plasma sampling and -2.7 ± 5.4 % in those who did not. CONCLUSIONS: Our findings indicate that enzymo-amperometric creatinine assays remain unaffected by NAC interference due to the absence of the peroxidase step in the analytical process. Therefore, these methods are suitable to prevent spurious hypocreatininemia in APAP intoxicated patients undergoing NAC therapy