Microdomains of the C-type lectin DC-SIGN are portals for virus entry into dendritic cells

The C-type lectin dendritic cell (DC)–specific intercellular adhesion molecule grabbing non-integrin (DC-SIGN; CD209) facilitates binding and internalization of several viruses, including HIV-1, on DCs, but the underlying mechanism for being such an efficient phagocytic pathogen-recognition receptor is poorly understood. By high resolution electron microscopy, we demonstrate a direct relation between DC-SIGN function as viral receptor and its microlocalization on the plasma membrane. During development of human monocyte-derived DCs, DC-SIGN becomes organized in well-defined microdomains, with an average diameter of 200 nm. Biochemical experiments and confocal microscopy indicate that DC-SIGN microdomains reside within lipid rafts. Finally, we show that the organization of DC-SIGN in microdomains on the plasma membrane is important for binding and internalization of virus particles, suggesting that these multimolecular assemblies of DC-SIGN act as a docking site for pathogens like HIV-1 to invade the host

WATLAS: high-throughput and real-time tracking of many small birds in the Dutch Wadden Sea

Abstract Tracking animal movement is important for understanding how animals interact with their (changing) environment, and crucial for predicting and explaining how animals are affected by anthropogenic activities. The Wadden Sea is a UNESCO World Heritage Site and a region of global importance for millions of shorebirds. Due to climate change and anthropogenic activity, understanding and predicting movement and space-use in areas like the Wadden Sea is increasingly important. Monitoring and predicting animal movement, however, requires high-resolution tracking of many individuals. While high-resolution tracking has been made possible through GPS, trade-offs between tag weight and battery life limit its use to larger species. Here, we introduce WATLAS (the Wadden Sea deployment of the ATLAS tracking system) capable of monitoring the movements of hundreds of (small) birds simultaneously in the Dutch Wadden Sea. WATLAS employs an array of receiver stations that can detect and localize small, low-cost tags at fine spatial (metres) and temporal resolution (seconds). From 2017 to 2021, we tracked red knots, sanderlings, bar-tailed godwits, and common terns. We use parts of these data to give four use-cases revealing its performance and demonstrating how WATLAS can be used to study numerous aspects of animal behaviour, such as, space-use (both intra- and inter-specific), among-individual variation, and social networks across levels of organization: from individuals, to species, to populations, and even communities. After describing the WATLAS system, we first illustrate space-use of red knots across the study area and how the tidal environment affects their movement. Secondly, we show large among-individual differences in distances travelled per day, and thirdly illustrate how high-throughput WATLAS data allows calculating a proximity-based social network. Finally, we demonstrate that using WATLAS to monitor multiple species can reveal differential space use. For example, despite sanderlings and red knots roosting together, they foraged in different areas of the mudflats. The high-resolution tracking data collected by WATLAS offers many possibilities for research into the drivers of bird movement in the Wadden Sea. WATLAS could provide a tool for impact assessment, and thus aid nature conservation and management of the globally important Wadden Sea ecosystem

Additional file 13 of WATLAS: high-throughput and real-time tracking of many small birds in the Dutch Wadden Sea

Additional file 13. Data file with localizations to calculate home ranges for sanderling as shown in Fig. 9A. TAG represents Individual tag identity, TIME is UNIX time (s), X is the X-coordinate of localizations (m, UTM 31N), Y is the Y-coordinate of localizations (m, UTM 31N), NBS is the number of base stations used to calculate localizations, VARX is the Variance in X coordinates, VARY is the Variance in Y coordinates, COVXY is the Covariance between X and Y coordinates, ts is the timestamp (CET), tideID is the tidal cycle identity, tidaltime is the time past high tide (minutes), and waterlevel is the waterlevel at west-terschelling (cm)

Measurements of hydrodynamics, sediment, morphology and benthos on Ameland ebb-tidal delta and lower shoreface

A large-scale field campaign was carried out on the ebb-tidal delta (ETD) of Ameland Inlet, a basin of the Wadden Sea in the Netherlands, as well as on three transects along the Dutch lower shoreface. The data have been obtained over the years 2017-2018. The most intensive campaign at the ETD of Ameland Inlet was in September 2017. With this campaign, as part of KustGenese2.0 (Coastal Genesis 2.0) and SEAWAD, we aim to gain new knowledge on the processes driving sediment transport and benthic species distribution in such a dynamic environment. These new insights will ultimately help the development of optimal strategies to nourish the Dutch coastal zone in order to prevent coastal erosion and keep up with sea level rise. The dataset obtained from the field campaign consists of (i) single-and multi-beam bathymetry; (ii) pressure, water velocity, wave statistics, turbidity, conductivity, temperature, and bedform morphology on the shoal; (iii) pressure and velocity at six back-barrier locations; (iv) bed composition and macrobenthic species from box cores and vibrocores; (v) discharge measurements through the inlet; (vi) depth and velocity from X-band radar; and (vii) meteorological data. The combination of all these measurements at the same time makes this dataset unique and enables us to investigate the interactions between sediment transport, hydrodynamics, morphology and the benthic ecosystem in more detail. The data provide opportunities to calibrate numerical models to a high level of detail. Furthermore, the open-source datasets can be used for system comparison studies. The data are publicly available at 4TU Centre for Research Data at https://doi.org/10.4121/collection:seawad (Delft University of Technology et al., 2019) and https://doi.org/10.4121/collection:kustgenese2 (Rijkswaterstaat and Deltares, 2019). The datasets are published in netCDF format and follow conventions for CF (Climate and Forecast) metadata. The http://data.4tu.nl (last access: 11 November 2020) site provides keyword searching options and maps with the geographical position of the data

Measurements of hydrodynamics, sediment, morphology and benthos on Ameland ebb-tidal delta and lower shoreface

A large-scale field campaign was carried out on the ebb-tidal delta (ETD) of Ameland Inlet, a basin of the Wadden Sea in the Netherlands, as well as on three transects along the Dutch lower shoreface. The data have been obtained over the years 2017-2018. The most intensive campaign at the ETD of Ameland Inlet was in September 2017. With this campaign, as part of KustGenese2.0 (Coastal Genesis 2.0) and SEAWAD, we aim to gain new knowledge on the processes driving sediment transport and benthic species distribution in such a dynamic environment. These new insights will ultimately help the development of optimal strategies to nourish the Dutch coastal zone in order to prevent coastal erosion and keep up with sea level rise. The dataset obtained from the field campaign consists of (i) single-and multi-beam bathymetry; (ii) pressure, water velocity, wave statistics, turbidity, conductivity, temperature, and bedform morphology on the shoal; (iii) pressure and velocity at six back-barrier locations; (iv) bed composition and macrobenthic species from box cores and vibrocores; (v) discharge measurements through the inlet; (vi) depth and velocity from X-band radar; and (vii) meteorological data. The combination of all these measurements at the same time makes this dataset unique and enables us to investigate the interactions between sediment transport, hydrodynamics, morphology and the benthic ecosystem in more detail. The data provide opportunities to calibrate numerical models to a high level of detail. Furthermore, the open-source datasets can be used for system comparison studies. The data are publicly available at 4TU Centre for Research Data at https://doi.org/10.4121/collection:seawad (Delft University of Technology et al., 2019) and https://doi.org/10.4121/collection:kustgenese2 (Rijkswaterstaat and Deltares, 2019). The datasets are published in netCDF format and follow conventions for CF (Climate and Forecast) metadata. The http://data.4tu.nl (last access: 11 November 2020) site provides keyword searching options and maps with the geographical position of the data