This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS (PELagique GAScogne) integrated surveys ...over the 2004–2019 period. The samples were collected at night with a 200 µm mesh-size WP2 net fitted with a Hydrobios (back-run stop) mechanical flowmeter and hauled vertically from the sea floor to the surface, with the maximum depth set at 100 m when the bathymetry was deeper than this. The first dataset originates from samples collected from 2004 to 2016 and imaged on land with the ZooScan and is composed of 1 153 507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019 and imaged onboard the R/V Thalassa with the ZooCAM and is composed of 702 111 imaged and measured objects. The imaged objects are composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts ranging from 300 µm to 3.39 mm in equivalent spherical diameter which were individually imaged, measured and identified. Each imaged object is geolocated and associated with a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey-level-based features (8 bit encoding, 0 = black, 255 = white), including size, that were automatically extracted from each individual image. Each object was taxonomically identified using the web-based application Ecotaxa with built-in random-forest and CNN-based semi-automatic sorting tools, which was followed by expert validation or correction. The objects were sorted into 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data at individual-object granularity from which one can easily derive quantitative population and community descriptors such as abundances, mean sizes, biovolumes, biomasses and size structure. Each object's individual image is provided along with the data. These two datasets can be used in combination for ecological studies, as the two instruments are interoperable, or they can be used as training sets for ZooScan and ZooCAM users. The data presented here are available at the SEANOE dataportal: https://doi.org/10.17882/94052 (ZooScan dataset, Grandremy et al., 2023c) and https://doi.org/10.17882/94040 (ZooCAM dataset, Grandremy et al., 2023d).
•Exploration of energy density sources of variability: species, season, region, size.•Relationships between dry mass content and ED are strong but species specific.•Larger length, mass and ED at age ...in the English Channel than in the Bay of Biscay.•Sardine display larger energy reserves than anchovy.•Larger reserves are likely in link with larger spawning or maintenance costs.•A strong scaling of ED with size with a dome shape pattern for sardine.•Decrease of ED with size is discussed in link with feeding and spawning behaviours.
There is a growing interest in monitoring body condition of marine organisms in the context of the ecosystem approach to fisheries and global change. Fish condition is under the influence of environmental variability on seasonal scale, but also on longer timescales. It represents a good indicator of habitat quality or individual fitness, and is also a relevant parameter to evaluate energy transfer through the trophic chain. However, the sources of variability in fish condition need to be accurately understood and the significance of existing indices has to be correctly assessed. Here, we measured the energy density, a precise and global indicator of fish bioenergetic condition, for anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) in the Bay of Biscay and the English Channel, based on an extensive sampling design in 2014. First, we investigated the well-documented relationship between percent dry mass and energy density, and showed that such relationship is species specific. Second, we observed distinct patterns in bioenergetic condition between anchovy and sardine. Both species display similar minimum values at size or age but maximum are significantly higher for sardine, reflecting a higher energy storage capacity that scales more strongly with size. Third, we confirmed the large seasonal variability in energy density of both species. In the Bay of Biscay, energy density values for anchovy and sardine (age 1+) are 5.7 and 5.9 kJ g−1 (wet weight) in spring and 6.8 and 7.9 kJ g−1 in autumn, respectively. Our results revealed that fish from the English Channel display significantly higher energy density values in autumn (9.8 kJ g−1 for anchovy and 10.5 kJ g−1 for sardine) than those from the Bay of Biscay. When combined with size and weight at age it appears clearly that, after age 1, fish from the northern region display larger growth and energy reserves. This likely results from a higher zooplankton productivity in the English Channel or/and a selection pressure towards faster growing and faster reserve building individuals, to be able to survive a longer winter than in the Bay of Biscay. Finally, we described a dome shaped evolution of energy density with body size in case of sardine. Increase with size has been well documented but not the decrease at largest sizes. Several mechanisms may explain such a pattern, i.e. increasing investment in spawning, shift in diet or a metabolic trade-off between temperature and food availability, with regard to maintenance requirements.
ABSTRACT
Zooplankton analysis represents a bottleneck in marine ecology studies due to the difficulty to obtain zooplankton data. The last decades have seen the intense development of zooplankton ...imaging systems, to increase the zooplankton data spatio‐temporal resolution as well as enabling the combination of size, taxonomy, and functional traits in aquatic ecology studies. Here, we propose a benchmark between the ZooScan, a commercially available, laboratory‐based scanner, which analyses zooplankton preserved samples, and the ZooCAM, an in‐flow imaging system designed for on‐board live zooplankton imaging. Sixty‐one zooplankton samples collected over the Bay of Biscay in environments ranging from estuarine to offshore blue waters were imaged with both instruments. Zooplankton Normalized Biovolume‐Size Spectra slopes, mean sizes, abundances, and zooplankton community biogeographical patterns were computed for each instrument and compared at the taxonomic group, the sampling stations and the Bay of Biscay scales. Both instruments produced similar zooplankton variables by stations and by taxa and described similar zooplankton community compositions and biogeographical patterns, on the large mesozooplankton size range, i.e., 0.3–3.39 mm ESD. We conclude that the ZooCAM and the ZooScan data can be combined to generate long term or spatially resolved zooplankton time series. Our study shows that benchmarking imaging instruments or techniques (1) offers a robust assessment of interoperability between instruments, mitigating possible instrumental biases, and (2) may be of great interest in the case of instrumental obsolescence or breakdown, to choose the most conservative replacement solution in a long term time series framework.
This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS integrated surveys, over the 2004–2019 ...period. The samples were collected at night, with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, hauled vertically from the sea floor to the surface with a maximum depth set at 100 m when the bathymetry is deeper. The first dataset originates from samples collected from 2004 to 2016, imaged on land with the ZooScan and is composed of 1,153,507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019, imaged on board the R/V Thalassa with the ZooCAM and is composed of 702,111 imaged and measured objects. The imaged objects is composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged, measured and identified. Each imaged object is geolocated, associated to a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction. The objects were sorted in 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data, at the individual object granularity, from which one can easily derive quantitative population and communities descriptors such as abundances, mean sizes, biovolumes, biomasses, and size structure. Each object’s individual image is provided along with the data. These two datasets can be used combined together for ecological studies as the two instruments are interoperable, or as training sets for ZooScan and ZooCAM users.
Downy mildew of grapevine (Vitis vinifera), caused by the oomycete Plasmopara viticola, is an important disease that is present in cultivation areas worldwide, and using resistant varieties provides ...an environmentally friendly alternative to fungicides. DOWNY MILDEW RESISTANT 6 (DMR6) from Arabidopsis is a negative regulator of plant immunity and its loss of function confers resistance to downy mildew. In grapevine, DMR6 is present in two copies, named VvDMR6-1 and VvDMR6-2. Here, we describe the editing of VvDMR6-1 in embryogenic calli using CRISPR/Cas9 and the regeneration of the edited plants. All edited plants were found to be biallelic and chimeric, and whilst they all showed reduced growth compared with non-transformed control plants, they also had reduced susceptibility to P. viticola. Comparison between mock-inoculated genotypes showed that all edited lines presented higher levels of salicylic acid than controls, and lines subjected to transformation presented higher levels of cis-resveratrol than controls. Our results identify VvDMR6-1 as a promising target for breeding grapevine cultivars with improved resistance to downy mildew.
Aims
The aim of this paper is to assess recent developments in non‐medical tramadol use, tramadol use disorder, illegal procurement and deaths.
Methods
This study used repeated cross‐sectional ...analysis of data collected nationwide from 2013 to 2018. Analysis was conducted through multisource monitoring of the French Addictovigilance Network of: (1) validated reports of high‐risk tramadol use, (2) record systems collecting information from toxicology experts investigating analgesic‐related deaths (DTA) and deaths related to substance abuse (DRAMES), and pharmacists for forged prescriptions (OSIAP), and (3) survey of drug users, with investigation of patterns of use while visiting addiction‐specialised institutions (OPPIDUM).
Results
Despite a plateauing level of tramadol exposure in the French population, the proportion of tramadol reports increased 1.7‐fold (187 cases in 2018, 3.2% (95% confidence interval CI: 2.74–3.63%), versus 1.9% (95% CI: 1.49–2.42% in 2013). Trends were similar in OSIAP: 11.9% of forged prescriptions in 2018 (95% CI: 10.56–13.45%); 1.7‐fold increase; in OPPIDUM: 0.76% (95% CI: 0.55–1.02); 2.2‐fold increase; and DRAMES: 3.2% of drug abuse‐related deaths in 2018 (95% CI: 1.89–5.16) versus 1.7% in 2013 (95% CI: 0.65–3.84). Tramadol was the primary opioid in analgesic‐related deaths in DTA (45% in 2018). Two profiles of high‐risk tramadol users were identified: (1) patients treated for pain or with tramadol persistence when pain disappeared (mainly women; mean age 44 years), and (2) individuals with non‐medical use for psychoactive effects (mainly men; mean age 36 years).
Conclusion
The triangulation of the data obtained through addictovigilance monitoring evidenced a recent increase in high‐risk tramadol use. These findings have a practical impact on the limitation of the maximal duration of tramadol prescriptions.
Studying grapevine (Vitis vinifera) innate defense mechanisms is a prerequisite to the development of new protection strategies, based on the stimulation of plant signaling pathways to trigger ...pathogen resistance. Two transcriptional coactivators (VvNPR1.1 and VvNPR1.2) with similarity to Arabidopsis thaliana NPR1 (Non-Expressor of PR genes 1), a well-characterized and key signaling element of the salicylic acid (SA) pathway, were recently isolated in Vitis vinifera. In this study, functional characterization of VvNPR1.1 and VvNPR1.2, including complementation of the Arabidopsis npr1 mutant, revealed that VvNPR1.1 is a functional ortholog of AtNPR1, whereas VvNPR1.2 likely has a different function. Ectopic overexpression of VvNPR1.1 in the Arabidopsis npr1-2 mutant restored plant growth at a high SA concentration, Pathogenesis Related 1 (PR1) gene expression after treatment with SA or bacterial inoculation, and resistance to virulent Pseudomonas syringae pv. maculicola bacteria. Moreover, stable overexpression of VvNPR1.1-GFP in V. vinifera resulted in constitutive nuclear localization of the fusion protein and enhanced PR gene expression in uninfected plants. Furthermore, grapevine plants overexpressing VvNPR1.1-GFP exhibited an enhanced resistance to powdery mildew infection. This work highlights the importance of the conserved SA/NPR1 signaling pathway for resistance to biotrophic pathogens in V. vinifera.
Aims
The French Ministry of Health scheduled opioid cough suppressants as prescription‐only drugs on 12 July 2017. The present study assessed the impact of this regulation on the diversion modalities ...of the concerned drugs and the related drug pholcodine by analysing the national OSIAP (Ordonnances Suspectes Indicateur d'Abus Possible) database.
Methods
Medical prescriptions with at least 1 mention of codeine, dextromethorphan, ethylmorphine, noscapine or pholcodine for cough suppression recorded in 2013–2019 were extracted from OSIAP. Annual mentioning rates were estimated by dividing numbers of mentions over those of prescriptions recorded the year considered. A descriptive analysis compared the characteristics of prescriptions before and after 12 July 2017.
Results
Overall, 832 mentions of the requested drugs were retrieved on 827 prescription forms. Codeine was the most frequent (n = 809, 8.7%) with 6 additional mentions of codeine/ethylmorphine combination, followed by dextromethorphan (n = 11, 0.1%) and pholcodine (n = 6, 0.1%). There was no mention of noscapine. Annual mentioning rates varied between 0 and 0.3% for all drugs except codeine. Codeine mentioning rates ranged between 0.3% (n = 2) and 0.7% (n = 9) before 12 July 2017 and increased to 10.1% (n = 61) thereafter in 2017, 16.1% (n = 314) in 2018, and 19.8% (n = 414) in 2019. The profile of subjects evolved accordingly with an increased male/female ratio (10.0 vs. 1.5 before) and decreased age (23 vs. 40 y before, P < .001).
Discussion
The sharp increase of recourse to falsified prescription forms indicates that codeine diversion continues despite restricted access, whereas the other drugs studied do not seem to have been impacted.
Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. ...Here, wide SARS-CoV-2 immunoprofiling in Wuhan COVID-19 convalescents combining serological, cellular, and monoclonal antibody explorations revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor-binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.
Coxsackievirus A16 (CV-A16;
) is an enterovirus (EV) type associated with hand, foot, and mouth disease (HFMD) in children. To investigate the spatial spread of CV-A16, we used viral sequence data ...sampled during a prospective sentinel surveillance of HFMD in France (2010 to 2014) and phylogenetic reconstruction. A data set of 168 VP1 sequences was assembled with 416 publicly available sequences of various geographic origins. The CV-A16 sequences reported were assigned to two clades, genogroup B and a previously uncharacterized clade D. The time origins of clades B and D were assessed in 1978 (1973 to 1981) and 2004 (2001 to 2007), respectively. The shape of the global CV-A16 phylogeny indicated worldwide cocirculation of genetically distinct virus lineages over time and across geographic regions. Phylogenetic tree topologies and Bayes factor analysis indicated virus migration. Virus transportation events in clade B within Europe and Asia and between countries of the two geographic regions were assessed. The sustained transmission of clade D viruses over 4 years was analyzed at the township level in France and traced back to Peru in South America. Comparative genomics provided evidence of recombination between CV-A16 clades B and D and suggested an intertype recombinant origin for clade D. Time-resolved phylogenies and HFMD surveillance data indicated that CV-A16 persistence is sustained by continuing virus migration at different geographic scales, from community transmission to virus transportation between distant countries. The results showed a significant impact of virus movements on the epidemiological dynamics of HFMD that could have implications for disease prevention.
Coxsackievirus A16 is one of the most prevalent enterovirus types in hand, foot, and mouth disease outbreaks reported in Southeast Asia. This study is based on epidemiological and viral data on HFMD caused by CV-A16 in a European country. The phylogeographic data complemented the syndromic surveillance with virus migration patterns between geographic regions in France. The results show how viral evolutionary dynamics and global virus spread interact to shape the worldwide pattern of an EV disease. CV-A16 transmission is driven by movements of infected individuals at different geographic levels: within a country (local dynamics), between neighboring countries (regional dynamics), and between distant countries (transcontinental dynamics). The results are consistent with our earlier data on EV-A71 and confirm the epidemiological interconnection of Asia and Europe with regard to EV infections.
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