Cross-validation of ELISA and a portable surface plasmon resonance instrument for IgG antibody serology with SARS-CoV-2 positive individuals.

We report on the development of surface plasmon resonance (SPR) sensors and matching ELISAs for the detection of nucleocapsid and spike antibodies specific to the novel coronavirus 2019 (SARS-CoV-2) in human serum, plasma and dried blood spots (DBS)

Developing common protocols to measure tundra herbivory across spatial scales

Understanding and predicting large-scale ecological responses to global environmental change requires comparative studies across geographic scales with coordinated efforts and standardized methodologies. We designed, applied and assessed standardized protocols to measure tundra herbivory at three spatial scales: plot, site (habitat), and study area (landscape). The plot and site-level protocols were tested in the field during summers 2014-2015 at eleven sites, nine of them comprising warming experimental plots included in the International Tundra Experiment (ITEX). The study area protocols were assessed during 2014-2018 at 24 study areas across the Arctic. Our protocols provide comparable and easy-to-implement methods for assessing the intensity of invertebrate herbivory within ITEX plots and for characterizing vertebrate herbivore communities at larger spatial scales. We discuss methodological constraints and make recommendations for how these protocols can be used and how sampling effort can be optimized to obtain comparable estimates of herbivory, both at ITEX sites and at large landscape scales. The application of these protocols across the tundra biome will allow characterizing and comparing herbivore communities across tundra sites and at ecologically relevant spatial scales, providing an important step towards a better understanding of tundra ecosystem responses to large-scale environmental change.CGB was funded by the Estonian Research Council (grant IUT 20-28), and the European Regional Development Fund (Centre of Excellence EcolChange). JDMS was supported by the Research Council of Norway (262064). OG and LB were supported by the French Polar Institute (program “1036 Interactions”) and PRC CNRS Russie 396 (program “ICCVAT”). DSH, NL, MAG, JB and JDR were supported by the Natural Sciences and Engineering Research Council (Canada). NL, MAG, JB and JDR were supported by the Polar Continental Shelf Program. NL was supported by the Canada Research Chair program and the Canada Foundation for Innovation. NL and JB were supported by Environment Canada and Polar Knowledge Canada. NL and MAG were supported by the Government of Nunavut, the Igloolik Community, and Université de Moncton. NL, MAG and JB were supported by the Northern Scientific Training Program. JMA was funded by Carl Tryggers stiftelse för vetenskaplig forskning and Qatar Petroleum (QUEX-CAS-QP-RD-18_19). IHM-S was funded by the UK Natural Environmental Research Council Shrub Tundra (NE/M016323/1) grant. ISJ was funded by the University of Iceland Research Fund. Fieldwork in Yamal peninsula (Erkuta, Sabetta and Belyi) for DE, NS and AS was supported by the Russian Foundation for Basic Research (No: 18-05-60261 and No: 18-54-15013), Fram Centre project YaES (No: 362259), the Russian Center of Development of the Arctic, and the “Yamal-LNG” company. Fieldwork in Utqiaġvik was supported by the U.S. Fish and Wildlife Service. Fieldwork in Svalbard was supported by the Norwegian Research Council (AFG No: 246080/E10), the Norwegian Polar Institute, Climate-ecological Observatory for Arctic Tundra – COAT, the Svalbard Environmental protection fund (project number 15/20), and the University Centre in Svalbard (UNIS) and the AB-338/AB-838 students of 2018. Sampling at Billefjorden was supported by GACR 17- 20839S

Annual and Seasonal Variation in Shorebird Abundance in the St. Lawrence River Estuary during Fall Migration

Many north American shorebird populations are declining. it is therefore urgent to identify major sites used during their annual cycle to achieve effective conservation measures. our objective was to expand some aspects of the knowledge base needed to assess the ecological value of the St. Lawrence River Estuary for shorebird conservation. Here, we present the results of the most intensive shorebird survey ever conducted in the St. Lawrence River Estuary during fall migration. Surveys were conducted between St-Jean-Port-Joli and St-Simon-sur-Mer, Quebec, Canada, in 2011 and 2012, from late June/early July through late november, corresponding to the migration period of all species potentially present in the study area. The Semipalmated Sandpiper (Calidris pusilla) was one of the two most abundant species during both years of our study (most abundant species, followed by Dunlin [Calidris alpina] and Black-bellied Plover [Pluvialis squatarola] in 2011; second to Blackbellied Plover in 2012). Considering the entire shorebird community, abundance of individuals peaked in early September. Peak abundance occurred earlier for adults than for juveniles. For most species, juveniles largely outnumbered adults. Juveniles were relatively less abundant in 2012 than in 2011. This reflected a general trend observed in northeastern north America between those years, suggesting a lower breeding success in 2012. Given its importance as a staging site for juvenile birds (study area used annually by up to a few hundred thousand shorebirds) and therein, its conservation value, we recommend that the St. Lawrence River Estuary should be included within the Western Hemisphere Shorebird Reserve network

SOLEIL Status Report

International audienceSOLEIL is both a synchrotron light source and a research laboratory at the cutting edge of experimental techniques dedicated to matter analysis down to the atomic scale, as well as a service platform open to all scientific and industrial communities. This French 2.75 GeV third generation synchrotron light source provides today extremely stable photon beams to 29 beamlines (BLs) complementary to ESRF. We report facility performance, ongoing projects and recent major achievements. A significant work was performed in order to secure the operation of the two canted 5.5 mm in-vacuum cryogenic permanent magnet undulators (CPMUs). Major R&D areas will also be discussed, and progress towards a lattice baseline for making SOLEIL a diffraction limited storage ring

Cross-Validation of ELISA and a Portable Surface Plasmon Resonance Instrument for IgG Antibodies Serology with SARS-CoV-2 Positive Individuals

We report on the development of surface plasmon resonance (SPR) sensors and matching ELISAs for the detection of nucleocapsid and spike antibodies specific against the novel coronavirus 2019 (SARS-CoV-2) in human serum, plasma and dried blood spots (DBS). When exposed to SARS-CoV-2 or a vaccine against SARS-CoV-2, the immune system responds by expressing antibodies at levels that can be detected and monitored to identify the fraction of the population potentially immunized against SARS-CoV-2 and support efforts to deploy a vaccine strategically. A SPR sensor coated with a peptide monolayer and functionalized with various sources of SARS-CoV-2 recombinant proteins expressed in different cell lines detected human anti-SARS-CoV-2 IgG in the nanomolar range. Nucleocapsid expressed in different cell lines did not significantly change the sensitivity of the assays, whereas the use of a CHO cell line to express spike ectodomain led to excellent performance. This bioassay was performed on a portable SPR instrument capable of measuring 4 biological samples within 30 minutes of sample/sensor contact and the chip could be regenerated at least 9 times. Multi-site validation was then performed with in-house and commercial ELISA, which revealed excellent cross-correlations with Pearson’s coefficients exceeding 0.85 in all cases, for measurements in DBS and plasma. This strategy paves the way to point-of-care and rapid testing for antibodies in the context of viral infection and vaccine efficacy monitoring

Effects of geolocators on hatching success, return rates, breeding movements, and change in body mass in 16 species of Arctic-breeding shorebirds.

19 pagesInternational audienceBackgroundGeolocators are useful for tracking movements of long-distance migrants, but potential negative effects on birds have not been well studied. We tested for effects of geolocators (0.8–2.0 g total, representing 0.1–3.9 % of mean body mass) on 16 species of migratory shorebirds, including five species with 2–4 subspecies each for a total of 23 study taxa. Study species spanned a range of body sizes (26–1091 g) and eight genera, and were tagged at 23 breeding and eight nonbreeding sites. We compared breeding performance and return rates of birds with geolocators to control groups while controlling for potential confounding variables.ResultsWe detected negative effects of tags for three small-bodied species. Geolocators reduced annual return rates for two of 23 taxa: by 63 % for semipalmated sandpipers and by 43 % for the arcticola subspecies of dunlin. High resighting effort for geolocator birds could have masked additional negative effects. Geolocators were more likely to negatively affect return rates if the total mass of geolocators and color markers was 2.5–5.8 % of body mass than if tags were 0.3–2.3 % of body mass. Carrying a geolocator reduced nest success by 42 % for semipalmated sandpipers and tripled the probability of partial clutch failure in semipalmated and western sandpipers. Geolocators mounted perpendicular to the leg on a flag had stronger negative effects on nest success than geolocators mounted parallel to the leg on a band. However, parallel-band geolocators were more likely to reduce return rates and cause injuries to the leg. No effects of geolocators were found on breeding movements or changes in body mass. Among-site variation in geolocator effect size was high, suggesting that local factors were important.ConclusionsNegative effects of geolocators occurred only for three of the smallest species in our dataset, but were substantial when present. Future studies could mitigate impacts of tags by reducing protruding parts and minimizing use of additional markers. Investigators could maximize recovery of tags by strategically deploying geolocators on males, previously marked individuals, and successful breeders, though targeting subsets of a population could bias the resulting migratory movement data in some species

Comment on “Global pattern of nest predation is disrupted by climate change in shorebirds”

International audienceKubelka et al. (Reports, 9 November 2018, p. 680) claim that climate change has disrupted patterns of nest predation in shorebirds. They report that predation rates have increased since the 1950s, especially in the Arctic. We describe methodological problems with their analyses and argue that there is no solid statistical support for their claims

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old