STORRE
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The STORRE digital repository system captures, stores, indexes, preserves, and distributes digital research material.2024-03-19T01:20:12ZTranscriptomic landscape of Atlantic salmon (Salmo salar L.) skin
http://hdl.handle.net/1893/35860
Title: Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin
Author(s): Sveen, Lene R; Robinson, Nicholas; Krasnov, Aleksei; Daniels, Rose Ruiz; Vaadal, Marianne; Karlsen, Christian; Ytteborg, Elisabeth; Robledo, Diego; Salisbury, Sarah; Dagnachew, Binyam; Lazado, Carlo C; Tengs, Torstein
Abstract: In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from 4 distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the lateral line, obtained from 2 Atlantic salmon (150 g). High-quality frozen tissue sections were obtained by embedding tissue in optimal cutting temperature media prior to freezing and sectioning. Further, we generated libraries and spatial transcriptomic maps, achieving a minimum of 80 million reads per sample with mapping efficiencies ranging from 79.3 to 89.4%. Our analysis revealed the detection of over 80,000 transcripts and nearly 30,000 genes in each sample. Among the tissue types observed in the skin, the epithelial tissues exhibited the highest number of transcripts (unique molecular identifier counts), followed by muscle tissue, loose and fibrous connective tissue, and bone. Notably, the widest nodes in the transcriptome network were shared among the epithelial clusters, while dermal tissues showed less consistency, which is likely attributable to the presence of multiple cell types at different body locations. Additionally, we identified collagen type 1 as the most prominent gene family in the skin, while keratins were found to be abundant in the epithelial tissue. Furthermore, we successfully identified gene markers specific to epithelial tissue, bone, and mesenchyme. To validate their expression patterns, we conducted a meta-analysis of the microarray database, which confirmed high expression levels of these markers in mucosal organs, skin, gills, and the olfactory rosette.2023-11-01T00:00:00ZOrganized B cell sites in cartilaginous fishes reveal the evolutionary foundation of germinal centers
http://hdl.handle.net/1893/35859
Title: Organized B cell sites in cartilaginous fishes reveal the evolutionary foundation of germinal centers
Author(s): Matz, Hanover; Taylor, Richard S.; Redmond, Anthony K.; Hill, Thomas M.; Ruiz Daniels, Rose; Beltran, Mariana; Henderson, Neil C.; Macqueen, Daniel J.; Dooley, Helen
Abstract: The absence of germinal centers (GCs) in cartilaginous fishes lies at odds with data showing that nurse sharks can produce robust antigen-specific responses and affinity mature their B cell repertoires. To investigate this apparent incongruity, we performed RNA sequencing on single nuclei, allowing us to characterize the cell types present in the nurse shark spleen, and RNAscope to provide in situ cellular resolution of key marker gene expression following immunization with R-phycoerythrin (PE). We tracked PE to the splenic follicles where it co-localizes with CXCR5high centrocyte-like B cells and a population of putative T follicular helper (Tfh) cells, surrounded by a peripheral ring of Ki67+ AID+ CXCR4+ centroblast-like B cells. Further, we reveal selection of mutations in B cell clones dissected from these follicles. We propose that the B cell sites iden tified here represent the evolutionary foundation of GCs, dating back to the jawed vertebrate ancestor.2023-07-01T00:00:00ZSingle cell genomics as a transformative approach for aquaculture research and innovation
http://hdl.handle.net/1893/35858
Title: Single cell genomics as a transformative approach for aquaculture research and innovation
Author(s): Daniels, Rose Ruiz; Taylor, Richard S.; Robledo, Diego; Macqueen, Daniel J.
Abstract: Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up-step in biological information compared to long-established ‘bulk’ methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non-model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under-characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology.2023-09-01T00:00:00ZKripke, Quine, the 'Adoption Problem' and the Empirical Conception of Logic
http://hdl.handle.net/1893/35857
Title: Kripke, Quine, the 'Adoption Problem' and the Empirical Conception of Logic
Author(s): Boghossian, Paul; Wright, Crispin
Abstract: Recently, there has been a significant upsurge of interest in what has come to be known as the 'Adoption Problem', first developed by Saul Kripke in 1974. The problem purports to raise a difficulty for Quine’s anti-exceptionalist conception of logic. In what follows, we first offer a statement of the problem and argue that, so understood, it depends upon natural but resistible assumptions. We then use that discussion as a springboard for developing a different adoption problem, arguing that, for a significant class of basic logical principles, there is indeed a difficulty in seeing how they might be ‘freely adopted,’ thereby vindicating something close to the spirit of Kripke’s original claim. This first part of our argument will enforce a significant qualification of Quine’s claim that basic logical principles can be empirically confirmed. In the concluding sections of the paper, we turn to the question, specifically, of the empirical revisability of logic, arguing that when proper attention is paid to the role of reasoning in theory revision, it does indeed emerge that anti-exceptionalism, in full generality, is untenable.2024-01-01T00:00:00Z