We experimentally evaluated the effect of predator removal on mallard (Anas platyrhynchos) duckling survival in south-central Saskatchewan, Canada, in 2000 and 2001. Previous predator-removal research has focused on nest success, but our study was the first to document an effect on duckling survival. We compared 4 control sites (no predator removal) with 4 treatment sites where professional trappers removed common nest predators. Survival of 686 ducklings from 78 broods was determined using radiotelemetry and periodic counts of ducklings. Duckling survival was higher on predator-removal sites relative to control sites in 2000 and 2001 and negatively correlated with hatch date in 2000. Results of analyses including and excluding hatch date as a covariate suggest that hatch date was confounded with predator removal (i.e., predator removal influenced hatch dates). Based on these results, we concluded that duckling survival was affected by predator removal in 2 ways. First, predator removal increased duckling survival by removing predators that likely caused total brood loss. Second, in-the-year hatch date was negatively correlated with duckling survival, earlier average hatch dates on predator-removal areas contributed to increased duckling survival. Combining the 2 effects and averaging over years, 30-day duckling survival was 0.573 (90% CI: 0.492 to 0.657) on predator-removal sites and 0.357 (90% CI: 0.275 to 0.456) on control sites. We concluded that predator-removal efforts conducted primarily to increase nest success of upland-nesting ducks also increased survival of mallard ducklings.

Effects of predator removal on mallard duckling survival

Spatial transcriptomics is a newly emerging field that enables high‐throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional biological studies to “in situ” biology, spatial transcriptomics can provide transcriptome‐scale spatial information. Currently, the ability to simultaneously characterize gene expression profiles of cells and relevant cellular environment is a paradigm shift for biological studies. In this review, recent progress in spatial transcriptomics and its applications in neuroscience and cancer studies are highlighted. Technical aspects of existing technologies and future directions of new developments (as of March 2023), computational analysis of spatial transcriptome data, application notes in neuroscience and cancer studies, and discussions regarding future directions of spatial multi‐omics and their expanding roles in biomedical applications are emphasized.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/advs.202206939

Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research

Modern neuroscience approaches including optogenetics, calcium imaging, and other genetic manipulations have facilitated our ability to dissect specific circuits in rodent models to study their role in neurological disease. These approaches regularly use viral vectors to deliver genetic cargo (e.g., opsins) to specific tissues and genetically-engineered rodents to achieve cell-type specificity. However, the translatability of these rodent models, cross-species validation of identified targets, and translational efficacy of potential therapeutics in larger animal models like nonhuman primates remains difficult due to the lack of efficient primate viral vectors. A refined understanding of the nonhuman primate nervous system promises to deliver insights that can guide the development of treatments for neurological and neurodegenerative diseases. Here, we outline recent advances in the development of adeno-associated viral vectors for optimized use in nonhuman primates. These tools promise to help open new avenues for study in translational neuroscience and further our understanding of the primate brain. 

https://doi.org/10.1016/j.crneur.2023.100086

Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system

. Conversion of natural grassland to cropland has been postulated as a cause for population declines among grassland birds. We evaluated nest-site habitat characteristics and landscape composition for three species of prairie-breeding shorebirds nesting across the agricultural landscape of prairie Canada. Nests of the Upland Sandpiper (Bartramia longicauda) and Willet (Tringa semipalmata) were found disproportionately in natural grazed (57%) or natural idled (21%) patches, whereas Marbled Godwit (Limosa fedoa) nests were in habitats in proportion to their availability on the landscape. We examined multiple landscape variables (proportions of crop, natural idled, natural grazed, and wetland habitats, edge density, and patch area) across a broad geographic scale, using relatively large samples of nests, and found no strong relationships. Neither nest-site habitat characteristics nor landscape-level effects influenced daily survival rates of Upland Sandpiper or Willet nests. Variation in landscape co...

https://bioone.org/journals/the-condor/volume-115/issue-1/cond.2012.110146/A-Spatial-Analysis-of-Factors-Affecting-Nesting-Success-of-Shorebirds/10.1525/cond.2012.110146.pdf

A Spatial Analysis of Factors Affecting Nesting Success of Shorebirds in the Canadian Prairies

Wetlands in southern Alberta are often managed to benefit waterfowl and cattle production. Effects on other species usually are not examined. I determined the effect of managed wetlands on uplandnesting shorebirds in southern Alberta by comparing numbers of breeding willets (Catoptrophorus semipalmatus), marbled godwits (Limosa fedoa), and long-billed curlews (Numenius americanus) among areas of managed wetlands, natural wetland basins, and no wetland basins from 1995 to 2000. Surveys were carried out at 21 sites three times each year. Nine to ten of these areas (each 2 km2) were searched for nests annually from 1998–2000. Numbers of willets and marbled godwits and their nests were always highest in areas with managed wetlands, probably because almost all natural wetland basins were dry in this region in most years. Densities of willets seen during pre-incubation surveys averaged 2.3 birds/km2 in areas of managed wetlands, 0.4 in areas of natural wetland basins, and 0.1 in areas with no wetland basins. Nest densities of willets (one search each season) averaged 1.5, 0.9, and 0.3 nests/km2 in areas of managed, natural, and no wetland basins, respectively. Similarly, pre-incubation surveys averaged 1.6, 0.6, and 0.2 godwits/km2 in areas of managed, natural, and no wetland basins, and 1.2, 0.3, and 0.1 godwit nests/km2. For long-billed curlews, pre-incubation surveys averaged 0.1, 0.2, and 0.1 birds/km2, and 0, 0.2, and 0 nests/km2. Nest success was similar in areas with and without managed wetlands. Shallow managed wetlands in this region appear beneficial to willets and marbled godwits, but not necessarily to long-billed curlews. Only 8% of marked willets and godwits with nests in the area were seen or heard during surveys, compared with 29% of pre-laying individuals and 42% of birds with broods. This suggests that a low and variable percentage of these birds is counted during breeding bird surveys, likely limiting their ability to adequately monitor populations of these species. RESUME. Dans le sud de l’Alberta, des terres humides sont souvent amenagees de facon a favoriser la production de sauvagine et de betail. Habituellement, on n’etudie pas l’incidence de cet amenagement sur les autres especes. De 1995 a 2000, j’ai determine les effets des terres humides amenagees sur les oiseaux de rivage qui nichent dans les hautes terres dans le sud de l’Alberta en comparant le nombre de Chevaliers semipalmes (Catoptrophorus semipalmatus), de Barges marbrees (Limosa fedoa) et de Courlis a long bec (Numenius americanus) qui nichaient dans des secteurs de terres humides amenagees, des bassins de terres humides naturels et des secteurs sans terres humides. Des denombrements ont ete effectues dans 21 sites, trois fois par annee. Dans neuf ou dix de ces secteurs (2 km2 chacun), on a effectue une recherche annuelle des nids de 1998 a 2000. Le nombre de Chevaliers semipalmes, de Barges marbrees et de nids de ces especes etait toujours plus eleve dans les secteurs de terres humides amenagees, probablement parce que, la plupart de ces annees, presque tous les bassins de terres humides naturels etaient asseches dans cette Canadian Wildlife Service Avian Conservation and Ecology Ecologie et conservation des oiseaux 1(2): 2 http://www.ace-eco.org/vol1/iss2/art2/ region. Chez le Chevalier semipalme, pendant les denombrements effectues avant l’incubation, les densites se situaient en moyenne a 2,3 individus/km2 dans les secteurs de terres humides amenagees, a 0,4 dans les bassins de terres humides naturels et a 0,1 dans les secteurs sans bassins de terres humides. Le nombre moyen de nids (une recherche par saison) etait de 1,5, de 0,9 et de 0,3 nid/km2 respectivement dans chacun de ces secteurs. De meme, d’apres les denombrements precedant l’incubation, il y avait en moyenne 1,6, 0,6 et 0,2 Barge marbree/km2 dans les secteurs de terres humides amenagees, les bassins de terres humides naturels et les secteurs sans bassins de terres humides. Le nombre de nids de Barge marbree etait respectivement de 1,2, 0,3 et 0,1/km2. Dans le cas du Courlis a long bec, les releves precedant l’incubation ont permis de reperer en moyenne 0,1, 0,2 et 0,1 individu/km2, ainsi que 0, 0,2 et 0 nid/km2. Le succes de la nidification etait semblable dans les secteurs de terres humides amenagees et ceux ou il n’y en avait pas. La presence de terres humides amenagees peu profondes dans cette region semble benefique pour le Chevalier semipalme et la Barge marbree, mais pas necessairement pour le Courlis a long bec. Seulement 8 % des oiseaux marques (Chevaliers semipalmes et Barges marbrees) qui occupaient un nid dans la region ont ete vus ou entendus pendant les denombrements, comparativement a 29 % des individus presents avant la ponte et 42 % des oiseaux accompagnes de leur nichee. Ces resultats donnent a penser que le pourcentage des oiseaux de ces especes denombres pendant les denombrements d'individus nicheurs est faible et variable, ce qui limiterait l’efficacite de ceux-ci pour le suivi de ces especes.

/pdf/upland-nesting-prairie-shorebirds-use-of-managed-wetland-3ippsitp37.pdf

Upland Nesting Prairie Shorebirds: Use of Managed Wetland Basins and Accuracy of Breeding Surveys

Breeding ecology of prairie nesting shorebirds: relationships with habitat, land use and predators

Cell-type-specific regulatory elements such as enhancers can direct expression of recombinant adeno-associated viruses (AAVs) to specific cell types, but this approach is limited by the relatively small packaging capacity of AAVs. In this study, we used spatial genomics to show that transcriptional crosstalk between individual AAV genomes provides a general method for cell-type-specific expression of large cargo by separating distally acting regulatory elements into a second AAV genome. We identified and profiled transcriptional crosstalk in AAV genomes carrying 11 different enhancers active in mouse brain. We developed spatial genomics methods to identify and localize AAV genomes and their concatemeric forms in cultured cells and in tissue, and we demonstrate here that transcriptional crosstalk is dependent upon concatemer formation. Finally, we leveraged transcriptional crosstalk to drive expression of a 3.2-kb Cas9 cargo in a cell-type-specific manner with systemically administered engineered AAVs, and we demonstrate AAV-delivered, minimally invasive, cell-type-specific gene editing in wild-type mice that recapitulates known disease phenotypes. Profiling transcriptional crosstalk between promoters and cell-type-specific enhancers allows large gene cargo delivery.

Spatial genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo.

Abstract A barrier to advancing engineered adeno-associated viral vectors (AAVs) for precision access to cell subtypes is a lack of high-throughput, high-resolution assays to characterize in vivo transduction profiles. In this study, we developed an ultrasensitive, sequential fluorescence in situ hybridization (USeqFISH) method for spatial transcriptomic profiling of endogenous and viral RNA with a short barcode in intact tissue volumes by integrating hydrogel-based tissue clearing, enhanced signal amplification and multiplexing using sequential labeling. Using USeqFISH, we investigated the transduction and cell subtype tropisms across mouse brain regions of six systemic AAVs, including AAV-PHP.AX, a new variant that transduces robustly and efficiently across neurons and astrocytes. Here we reveal distinct cell subtype biases of each AAV variant, including a bias of AAV-PHP.N toward excitatory neurons. USeqFISH also enables profiling of pooled regulatory cargos, as we show for a 13-variant pool of microRNA target sites in AAV genomes. Lastly, we demonstrate potential applications of USeqFISH for in situ AAV profiling and multimodal single-cell analysis in non-human primates. 

/pdf/spatial-transcriptomics-for-profiling-the-tropism-of-viral-18871nfa.pdf

Spatial transcriptomics for profiling the tropism of viral vectors in tissues

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Breeding ecology of prairie nesting shorebirds: relationships with habitat, land use and predators

Spatial genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo.

Spatial transcriptomics for profiling the tropism of viral vectors in tissues