Development of the nanobody display technology to target lentiviral vectors to antigen-presenting cells

Lentiviral vectors (LVs) provide unique opportunities for the development of immunotherapeutic strategies, as they transduce a variety of cells in situ, including antigen-presenting cells (APCs). Engineering LVs to specifically transduce APCs is required to promote their translation towards the clinic. We report on the Nanobody (Nb) display technology to target LVs to dendritic cells (DCs) and macrophages. This innovative approach exploits the budding mechanism of LVs to incorporate an APC-specific Nb and a binding-defective, fusion-competent form of VSV. G in the viral envelope. In addition to production of high titer LVs, we demonstrated selective, Nb-dependent transduction of mouse DCs and macrophages both in vitro and in situ. Moreover, this strategy was translated to a human model in which selective transduction of in vitro generated or lymph node (LN)-derived DCs and macrophages, was demonstrated. In conclusion, the Nb display technology is an attractive approach to generate LVs targeted to specific cell types

River gauging at global scale using optical and passive microwave remote sensing

Recent discharge observations are lacking for most rivers globally. Discharge can be estimated from remotely sensed floodplain and channel inundation area, but there is currently no method that can be automatically extended to many rivers. We examined whether automated monitoring is feasible by statistically relating inundation estimates from moderate to coarse (>0.05°) resolution remote sensing to monthly station discharge records. Inundation extents were derived from optical MODIS data and passive microwave sensors, and compared to monthly discharge records from over 8000 gauging stations and satellite altimetry observations for 442 reaches of large rivers. An automated statistical method selected grid cells to construct “satellite gauging reaches” (SGRs). MODIS SGRs were generally more accurate than passive microwave SGRs, but there were complementary strengths. The rivers widely varied in size, regime, and morphology. As expected performance was low (R  0.6. The best results (R > 0.9) were obtained for large unregulated lowland rivers, particularly in tropical and boreal regions. Relatively poor results were obtained in arid regions, where flow pulses are few and recede rapidly, and in temperate regions, where many rivers are modified and contained. Provided discharge variations produce clear changes in inundated area and gauge records are available for part of the satellite record, SGRs can retrieve monthly river discharge values back to around 1998 and up to present

Day versus night use of forest by red and roe deer as determined by Corine Land Cover and Copernicus Tree Cover Density: assessing use of geographic layers in movement ecology

Diel use of forest and open habitats by large herbivores is linked to species-specific needs of multiple and heterogeneous resources. However, forest cover layers might deviate considerably for a given landscape, potentially affecting evaluations of animals’ habitat use. We assessed inconsistency in the estimates of diel forest use by red and roe deer at GPS location and home range (HR) levels, using two geographic layers: Tree Cover Density (TCD) and Corine Land Cover (CLC). We first measured the classification mismatch of red and roe deer GPS locations between TCD and CLC, also with respect to habitat units’ size. Then, we used generalized Least Squares models to assess the proportional use of forest at day and night at the GPS location and HR levels, both with TCD and CLC. About 20% of the GPS locations were inconsistently classified as forest or open habitat by the two layers, particularly within smaller habitat units. Overall proportion of forest and open habitat, though, was very similar for both layers. In all populations, both deer species used forest more at day than at night and this pattern was more evident with TCD than with CLC. However, at the HR level, forest use estimates were only marginally different between the two layers. When estimating animal habitat use, geographic layer choice requires careful evaluation with respect to ecological questions and target species. Habitat use analyses based on GPS locations are more sensitive to layer choice than those based on home ranges.publishedVersio

Back and forth: day–night alternation between cover types reveals complementary use of habitats in a large herbivore

Context The Complementary Habitat Hypothesis posits that animals access resources for different needs by moving between complementary habitats that can be seen as ‘resource composites’. These movements can occur over a range of temporal scales, from diurnal to seasonal, in response to multiple drivers such as access to food, weather constraints, risk avoidance and human disturbance. Within this framework, we hypothesised that large herbivores cope with human-altered landscapes through the alternate use of complementary habitats at both daily and seasonal scales. Objectives We tested the Complementary Habitat Hypothesis in European roe deer (Capreolus capreolus) by classifying 3900 habitat-annotated movement trajectories of 154 GPS-monitored individuals across contrasting landscapes. Methods We considered day-night alternation between open food-rich and closed refuge habitats as a measure of complementary habitat use. We first identified day–night alternation using the Individual Movement - Sequence Analysis Method, then we modelled the proportion of day–night alternation over the year in relation to population and individual characteristics. Results We found that day-night alternation is a widespread behaviour in roe deer, even across markedly different landscapes. Day–night alternation followed seasonal trends in all populations, partly linked to vegetation phenology. Within populations, seasonal patterns of open/closed habitat alternation differed between male and female adults, but not in juveniles. Conclusion Our results support the Complementary Habitat Hypothesis by showing that roe deer adjust their access to the varied resources available in complex landscapes by including different habitats within their home range, and sequentially alternating between them in response to seasonal changes and individual life history.publishedVersio

Back and forth: day–night alternation between cover types reveals complementary use of habitats in a large herbivore

Context The Complementary Habitat Hypothesis posits that animals access resources for different needs by moving between complementary habitats that can be seen as ‘resource composites’. These movements can occur over a range of temporal scales, from diurnal to seasonal, in response to multiple drivers such as access to food, weather constraints, risk avoidance and human disturbance. Within this framework, we hypothesised that large herbivores cope with human-altered landscapes through the alternate use of complementary habitats at both daily and seasonal scales. Objectives We tested the Complementary Habitat Hypothesis in European roe deer (Capreolus capreolus) by classifying 3900 habitat-annotated movement trajectories of 154 GPS-monitored individuals across contrasting landscapes. Methods We considered day-night alternation between open food-rich and closed refuge habitats as a measure of complementary habitat use. We first identified day–night alternation using the Individual Movement - Sequence Analysis Method, then we modelled the proportion of day–night alternation over the year in relation to population and individual characteristics. Results We found that day-night alternation is a widespread behaviour in roe deer, even across markedly different landscapes. Day–night alternation followed seasonal trends in all populations, partly linked to vegetation phenology. Within populations, seasonal patterns of open/closed habitat alternation differed between male and female adults, but not in juveniles. Conclusion Our results support the Complementary Habitat Hypothesis by showing that roe deer adjust their access to the varied resources available in complex landscapes by including different habitats within their home range, and sequentially alternating between them in response to seasonal changes and individual life history

Global raster dataset on historical coastline positions and shelf sea extents since the Last Glacial Maximum

Motivation: Historical changes in sea level caused shifting coastlines that affected the distribution and evolution of marine and terrestrial biota. At the onset of the Last Glacial Maximum (LGM) 26 ka, sea levels were >130 m lower than at present, resulting in seaward-shifted coastlines and shallow shelf seas, with emerging land bridges leading to the isolation of marine biota and the connection of land-bridge islands to the continents. At the end of the last ice age, sea levels started to rise at unprecedented rates, leading to coastal retreat, drowning of land bridges and contraction of island areas. Although a growing number of studies take historical coastline dynamics into consideration, they are mostly based on past global sea-level stands and present-day water depths and neglect the influence of global geophysical changes on historical coastline positions. Here, we present a novel geophysically corrected global historical coastline position raster for the period from 26 ka to the present. This coastline raster allows, for the first time, calculation of global and regional coastline retreat rates and land loss rates. Additionally, we produced, per time step, 53 shelf sea rasters to present shelf sea positions and to calculate the shelf sea expansion rates. These metrics are essential to assess the role of isolation and connectivity in shaping marine and insular biodiversity patterns and evolutionary signatures within species and species assemblages. Main types of variables contained: The coastline age raster contains cells with ages in thousands of years before present (bp), representing the time since the coastline was positioned in the raster cells, for the period between 26 ka and the present. A total of 53 shelf sea rasters (sea levels <140 m) are presented, showing the extent of land (1), shelf sea (0) and deep sea (NULL) per time step of 0.5 kyr from 26 ka to the present. Spatial location and grain: The coastline age raster and shelf sea rasters have a global representation. The spatial resolution is scaled to 120 arcsec (0.333° × 0.333°), implying cells of c. 3,704 m around the equator, 3,207 m around the tropics (±30°) and 1,853 m in the temperate zone (±60°). Time period and temporal resolution: The coastline age raster shows the age of coastline positions since the onset of the LGM 26 ka, with time steps of 0.5 kyr. The 53 shelf sea rasters show, for each time step of 0.5 kyr, the position of the shelf seas (seas shallower than 140 m) and the extent of land. Level of measurement: Both the coastline age raster and the 53 shelf sea rasters are provided as TIFF files with spatial reference system WGS84 (SRID 4326). The values of the coastline age raster per grid cell correspond to the most recent coastline position (in steps of 0.5 kyr). Values range from 0 (0 ka, i.e., present day) to 260 (26 ka) in bins of 5 (0.5 kyr). A value of “no data” is ascribed to pixels that have remained below sea level since 26 ka. Software format: All data processing was done using the R programming language

Global raster dataset on historical coastline positions and shelf sea extents since the Last Glacial Maximum

Abstract Motivation Historical changes in sea level caused shifting coastlines that affected the distribution and evolution of marine and terrestrial biota. At the onset of the Last Glacial Maximum (LGM) 26 ka, sea levels were >130?m lower than at present, resulting in seaward-shifted coastlines and shallow shelf seas, with emerging land bridges leading to the isolation of marine biota and the connection of land-bridge islands to the continents. At the end of the last ice age, sea levels started to rise at unprecedented rates, leading to coastal retreat, drowning of land bridges and contraction of island areas. Although a growing number of studies take historical coastline dynamics into consideration, they are mostly based on past global sea-level stands and present-day water depths and neglect the influence of global geophysical changes on historical coastline positions. Here, we present a novel geophysically corrected global historical coastline position raster for the period from 26 ka to the present. This coastline raster allows, for the first time, calculation of global and regional coastline retreat rates and land loss rates. Additionally, we produced, per time step, 53 shelf sea rasters to present shelf sea positions and to calculate the shelf sea expansion rates. These metrics are essential to assess the role of isolation and connectivity in shaping marine and insular biodiversity patterns and evolutionary signatures within species and species assemblages. Main types of variables contained The coastline age raster contains cells with ages in thousands of years before present (bp), representing the time since the coastline was positioned in the raster cells, for the period between 26 ka and the present. A total of 53 shelf sea rasters (sea level

Wherever I may roam-Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents

Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activit

Wherever I may roam—Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents

Human activity and associated landscape modifications alter the movements of ani-mals with consequences for populations and ecosystems worldwide. Species perform-ing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement ex-pression, using the standardized metric Intensity of Use, reflecting both the directional-ity and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topogra-phy, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strong-est driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric- based movement expression across widely distributed populations of a deer genus, contribut-ing to the understanding and prediction of animals' responses to human activity.publishedVersio