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Normalisation algorithms for spatially resolved transcriptomic data
Nádvorníková, Bára ; Kolář, Michal (advisor) ; Abaffy, Pavel (referee)
Spatially resolved transcriptomics is a novel method that enables the study of gene expression in tissue samples without loss of spatial context. It can be used to map the distribution of mRNA to individual cells as well as subcellular locations. Data obtained using this method provide important insights into various aspects of biology, including embryology, oncology, or immunology. The functioning and mutual interaction of individual cells cannot be fully explained without knowledge of their exact location in the tissue. Due to the novelty of the method, reconciling the obtained information on gene expression and spatial arrangement of cells is currently a major challenge and bioinformatics approaches are still being established. The aim of this work is to map the current algorithms for the normalisation of spatially resolved transcriptomics data and to compare these algorithms based on available data sets. Eventually, selected algorithms will be implemented and integrated into the workflow used at IMG CAS. The work includes i. survey of available solutions, ii. selection of a suitable solution or design of a new one, iii. implementation of the solution and its testing on available data.
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The role of nitric oxide during embryonic wound healing and regeneration
Abaffy, Pavel ; Šindelka, Radek (advisor) ; Brábek, Jan (referee) ; Krylov, Vladimír (referee)
The study of the mechanisms that control wound healing is an attention-drawing area within the fields of biology and medicine. Wound healing can be usually defined as two basic types. The first type is adult wound healing, which is slow and results in the scar formation. The second type is referred to as embryonic wound healing, which is in contrast fast and scarless. Wound healing is a complicated process that includes many steps, which are regulated by various types of molecules. One of these important molecules is nitric oxide (NO). Its function is usually connected with the regulation of inflammation and angiogenesis during adult wound healing. However, there is currently no information on its role during embryonic wound healing, where the immune and vascular systems are not yet developed. In this work, we explore and describe the role of the NO during the healing of the early embryos. The highest concentration of the NO post wounding is produced during the first 30 minutes after injury. This applies to all developmental stages, from the blastula stage all the way to the swimming tadpole stage. The main role of the NO during embryonic wound healing is the regulation of the gene expression that is connected with the stress response and the regulation of cellular metabolism. Additionally, we...
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