STORRE Community: This community contains the ePrints and eTheses produced by the Aquaculture staff and students.
http://hdl.handle.net/1893/12
This community contains the ePrints and eTheses produced by the Aquaculture staff and students.2024-03-22T03:05:34ZMapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics
http://hdl.handle.net/1893/35862
Title: Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics
Author(s): Andresen, Adriana M.S.; Taylor, Richard S.; Grimholt, Unni; Daniels, Rose Ruiz; Sun, Jianxuan; Dobie, Ross; Henderson, Neil C.; Martin, Samuel A.M.; Macqueen, Daniel J.; Fosse, Johanna H.
Abstract: Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.2024-03-01T00:00:00ZTranscriptomic 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.2023-09-01T00:00:00Z