Cargo-specific effects of hypoxia on clathrin-mediated trafficking

Clathrin-associated trafficking is a major mechanism for intracellular communication, as well as for cells to communicate with the extracellular environment. A decreased oxygen availability termed hypoxia has been described to influence this mechanism in the past. Mostly biochemical studies were applied in these analyses, which miss spatiotemporal information. We have applied live cell microscopy and a newly developed analysis script in combination with a GFP-tagged clathrin-expressing cell line to obtain insight into the dynamics of the effect of hypoxia. Number, mobility and directionality of clathrin-coated vesicles were analysed in non-stimulated cells as well as after stimulation with epidermal growth factor (EGF) or transferrin in normoxic and hypoxic conditions. These data reveal cargo-specific effects, which would not be observable with biochemical methods or with fixed cells and add to the understanding of cell physiology in hypoxia. The stimulus-dependent consequences were also reflected in the final cellular output, i.e. decreased EGF signaling and in contrast increased iron uptake in hypoxia.</p

Spatial synchrony in the response of a long range migratory species ( Salmo salar ) to climate change in the North Atlantic Ocean

International audienceA major challenge in understanding the response of populations to climate change is to separate the effects of local drivers acting independently on specific populations, from the effects of global drivers that impact multiple populations simultaneously and thereby synchronize their dynamics. We investigated the environmental drivers and the demographic mechanisms of the widespread decline in marine survival rates of Atlantic salmon (Salmo salar) over the last four decades. We developed a hierarchical Bayesian life cycle model to quantify the spatial synchrony in the marine survival of 13 large groups of populations (called stock units, SU) from two continental stock-groupings (CSG) in North America (NA) and Southern Europe (SE) over the period 1971-2014. We found strong coherence in the temporal variation in post-smolt marine survival among the 13 SU of NA and SE. A common North Atlantic trend explains 37% of the temporal variability of the survivals for the 13 SU and declines by a factor 1.8 over the 1971-2014 time series. Synchrony in survival trends is stronger between SU within each CSG. The common trends at the scale of NA and SE capture 60% and 42% of the total variance of temporal variations, respectively. Temporal variations of the post-smolt survival are best explained by the temporal variations of sea surface temperature (SST, negative correlation) and net primary production indices (PP, positive correlation) encountered by salmon in common domains during their marine migration. Specifically, in the Labrador Sea/Grand Banks for NA populations 26% and 24% of variance is captured by SST and PP, respectively and in the Norwegian Sea for SE populations 21% and 12% of variance is captured by SST and PP, respectively. The findings support the hypothesis of a response of salmon populations to large climate induced changes in the North Atlantic simultaneously impacting populations from distant continental habitats

ICES. 2023. Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA).

The ICES Working Group on Southern horse mackerel, anchovy and sardine (WGHANSA) assessed the status of anchovy in Atlantic Iberian waters (ane.27.9a; western and southern components) and horse mackerel in Atlantic Iberian waters (hom.27.9a) in the May meeting. The status of anchovy in Bay of Biscay (ane.27.8), sardine in southern Celtic Seas and the English Channel (pil.27.7), sardine in Bay of Biscay (pil.27.8abd) and sardine in Cantabrian Sea and Atlantic Iberian waters (pil.27.8c9a) will be assessed in the November meeting. The status of jack mackerel in Subdivision 10.a.2 (Azores grounds) (jaa.10.a2) won’t be assessed this year, since the advice is provided biannually. The stock of anchovy in Bay of Biscay (ane.27.8) has been above Blim since the reopening of the fishery in 2010. SSB in 2023 has been estimated as the second highest of the historical series. Recruitment (age 1 biomass at the beginning of the year) in 2024 is estimated above the average of the time-series. Harvest rates (catch/SSB) have been stable in the last years. The stock of anchovy in Atlantic Iberian waters (ane.27.9a) is composed by the western component (distributed in areas 9.a North, Central–North, and Central–South) and the southern component (distributed in area 9.a South). The advice is provided for the two components separately for the management calendar from July to June next year. Based on the MSE work developed for each component, the advice is based for the first time on constant harvest rate rules. For the western component, the combined PELACUS and PELAGO acoustic biomass estimate is used as an indicator of stock development and the advice is based on the stock indicator for 2023, multiplied by a constant harvest rate of 0.25, with no biomass safeguard. For the southern component, the relative SSB from an analytical assessment conducted with GADGET is used as the index of stock size development and the advice is based on the stock indicator for 2023, multiplied by a constant harvest rate of 0.5 with a biomass safeguard. In the last years sardine in the Bay of Biscay (pil.27.8abd) shows a decreasing trend in SSB. In 2023 spawning-stock biomass is estimated below MSY Btrigger, Bpa and above Blim. Since 2013 the fishing mortality has been oscillating above FMSY and Fpa, and below Flim. The advice for sardine in southern Celtic Seas and the English Channel (pil.27.7) is based on the PELTIC survey biomass index in the total area. The index ratio indicates an increase of 62% in 2023 compared with the two previous years. The biomass (age 1+) of sardine in Atlantic Iberian waters (pil.27.8c9a) in 2023 is estimated to be above MSY Btrigger, Bpa and Blim for the fourth consecutive year. Fishing mortality in 2022 is below FMSY. ICES advice is based on the ICES MSY advice rule. However, the catch options explored for 2024 include several harvest control rules that were assessed by ICES as precautionary. The SSB of horse mackerel in Atlantic Iberian waters (hom.27.9a) fluctuated from 1992 (the beginning of the assessment) to 2013 and afterwards has increased continuously to historical maximum values in 2023. In 2023 SSB is estimated at 1 214 200 tonnes, well above MSY Btrigger, Bpa, and Blim. Fishing mortality has been below FMSY over the whole time-series, with a decreasing trend in the last years. Recruitment shows a decreasing trend from 2017 to 2021 but is still above the average of the time series. The lack of the survey index in 2019 and 2020 is reflected in larger confidence intervals for SSB and recruitment in the last years. The jack mackerel in Subdivision 10.a.2 (Azores grounds) (jaa.10.a2) is classified in category 5 and advice is provided biannually. The latest advice for this stock was provided last year.This work was mainly funded by a European Union-Next Generation EU project. Agreement of the Ministry of Agriculture, Fishing and Food, as well as the Spanish Research Council (CSIC) through the Spanish Oceanographic Institute (IEO). Project Math4Fish: New tools for mathemat-ical modelling in stock assessment of spanish fisheries

Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces

A hierarchical life cycle model for Atlantic salmon stock assessment at the North Atlantic basin scale

This working paper is derived from:Olmos, M. 2019. Investigating the drivers of Atlantic salmon populations decline in the North Atlantic basin. Thèse de doctorant d’Agrocampus Ouest, COMUE Université Bretagne Loire. Soutenue le 22 Mars 2019.Olmos, M., Massiot-Granier, F., Prévost, E., Chaput, G., Bradbury, I. R., Nevoux, M., & Rivot, E. (2019). Evidence for spatial coherence in time trends of marine life history traits of Atlantic salmon in the North Atlantic. Fish and Fisheries, 20(2), 322-342. https://doi.org/10.1111/faf.1234

DELMOGES. Cartes de distribution saisonnières et interannuelles des principales proies des dauphins communs dans le GdG à partir des données existantes

Le projet Delmoges vise à produire de nouvelles connaissances écologiques et halieutiques, pour réduire les captures accidentelles de dauphins dans le golfe de Gascogne (GdG). Ce livrable présente les cartes produites par un modèle hiérarchique de la distribution saisonnière et interannuelle des principales proies des dauphins, les petits poissons pélagiques. Le modèle intègre 3 types de données : présence-absence et biomasse de poissons des campagnes scientifiques et présences de poissons par les données de pêche. Le modèle a fourni pour la première fois une description quantitative de la dynamique spatiale saisonnière de la sardine et des pêcheries associées. Les principales zones de distribution de la sardine étaient côtières, de l'embouchure de la Gironde au sud-ouest de la Bretagne. La sardine était en moyenne distribuée sur une plus large zone sous forme de petits agrégats au printemps. Elle semblait se concentrer dans ses zones de distribution principales en été et se disperser vers le large en automne, mais dans une moindre mesure qu’au printemps. Les pêcheries étaient concentrées dans les zones de distribution principale de la sardine à la côte, et étaient plus intenses en été, puis à l’automne et moins intenses au printemps. Après avoir intégré les données hivernales, l’application de notre modèle à l’anchois, et son couplage avec les distributions de dauphins communs devrait à terme permettre d'améliorer notre compréhension des interactions entre les petits poissons pélagiques et les dauphins et d’évaluer leur influence sur les captures accidentelles

A Bayesian hierarchical model to unravel the spatial covariations in the response of Atlantic salmon populations to climate change in the North Atlantic Ocean

RésuméInternational audienc

A Bayesian hierarchical model to unravel the spatial covariations in the response of Atlantic salmon populations to climate change in the North Atlantic Ocean

RésuméInternational audienc

Assessing spatial deposition of aquatic subsidies by insects emerging from agricultural streams

International audienceThe role of winged aquatic insects that emerge from streams and subsidize terrestrial ecosystems has been demonstrated for natural forest landscapes, but almost no information is available for intensive agricultural landscapes. This study is the first to estimate aquatic subsidies provided by flying insects that emerge from streams and land on cropland. We investigated three major groups of aquatic insects - Trichoptera, Ephemeroptera and Chironomidae (Diptera) - that emerged from 12 third-order temperate, agricultural streams. We simultaneously monitored their emergence using floating traps and their terrestrial dispersal using passive interception traps. We estimated that the annual aquatic emerging dry mass (DM) of these groups varied from 1.4-7.5 g m(-2) yr(-1), depending on the stream. We used a Bayesian approach to estimate parameters of the terrestrial dispersal function of each group. We combined emerging DM and the dispersal parameters to estimate how terrestrial deposition of aquatic insect DM varied with increasing distance from streams. The results highlighted that emerging DM and dispersal to land could be higher in intensive agricultural landscapes than that previously described in natural settings. We estimated that 12.5 kg ha(-1) yr(-1) of winged aquatic insect DM fell to the ground 0-10 m from stream edges, composed mainly of Ephemeroptera and Trichoptera. We also estimated that 2.2 kg DM ha(-1) yr(-1) fell 10-50 m from the stream, especially small-bodied species of Chironomidae, throughout the year, except for the coldest weeks of winter. By influencing aquatic insect communities that emerge from streams, intensive agricultural practices change the magnitude and spatial extent of aquatic subsidy deposition on land. Implications for terrestrial food webs and ecosystem services provided to agriculture are discussed