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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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Earlier evolutionary dead-ends, now the creators of a reproductive strategy: the origin and reproduction of the all-male water frog lineage Pelophylax esculentus
Doležálková, Marie ; Choleva, Lukáš (advisor) ; Mikulíček, Peter (referee) ; Kratochvíl, Lukáš (referee)
Asexual modes of reproduction are usually based on the principle of copying (cloning) DNA from the female and passing it on to the offspring. For most asexually reproducing vertebrates the progeny develop from an unreduced and often unfertilised egg. This is driven by the mechanisms of parthenogenetic and gynogenetic reproduction. While in the former the clonal germ cell develops spontaneously and separately, in the latter a sexual partner is needed to activate the cleavage of the ovum, although without the fusion of the sperm and egg. Therefore in both cases there is no fertilization and the clonal progeny consist solely of daughters, hence the majority of previous studies have only focused on asexual female lineages. However, on rare occasions asexual clonal males can arise when the right fertilization occurs. Whilst these offspring are usually infertile, fertile diploid asexual males have been discovered in just three genera of hybrid origin in vertebrates. One of these unique cases is the European water frog complex of the genus Pelophylax, whose distribution includes the Czech Republic. In areas around the upper Odra River populations of hybrid males were recently discovered who form stable all-male lineages, similar to those formed by asexual females. The results of this study show that males produce...
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Earlier evolutionary dead-ends, now the creators of a reproductive strategy: the origin and reproduction of the all-male water frog lineage Pelophylax esculentus
Kaštánková, Marie
Asexual modes of reproduction are usually based on the principle of copying (cloning) DNA from the female and passing it on to the offspring. For most asexually reproducing vertebrates the progeny develop from an unreduced and often unfertilised egg. This is driven by the mechanisms of parthenogenetic and gynogenetic reproduction. While in the former the clonal germ cell develops spontaneously and separately, in the latter a sexual partner is needed to activate the cleavage of the ovum, although without the fusion of the sperm and egg. Therefore in both cases there is no fertilization and the clonal progeny consist solely of daughters, hence the majority of previous studies have only focused on asexual female lineages. However, on rare occasions asexual clonal males can arise when the right fertilization occurs. Whilst these offspring are usually infertile, fertile diploid asexual males have been discovered in just three genera of hybrid origin in vertebrates. One of these unique cases is the European water frog complex of the genus Pelophylax, whose distribution includes the Czech Republic. In areas around the upper Odra River populations of hybrid males were recently discovered who form stable all-male lineages, similar to those formed by asexual females. The results of this study show that males produce...
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Earlier evolutionary dead-ends, now the creators of a reproductive strategy: the origin and reproduction of the all-male water frog lineage Pelophylax esculentus
Kaštánková, Marie
Asexual modes of reproduction are usually based on the principle of copying (cloning) DNA from the female and passing it on to the offspring. For most asexually reproducing vertebrates the progeny develop from an unreduced and often unfertilised egg. This is driven by the mechanisms of parthenogenetic and gynogenetic reproduction. While in the former the clonal germ cell develops spontaneously and separately, in the latter a sexual partner is needed to activate the cleavage of the ovum, although without the fusion of the sperm and egg. Therefore in both cases there is no fertilization and the clonal progeny consist solely of daughters, hence the majority of previous studies have only focused on asexual female lineages. However, on rare occasions asexual clonal males can arise when the right fertilization occurs. Whilst these offspring are usually infertile, fertile diploid asexual males have been discovered in just three genera of hybrid origin in vertebrates. One of these unique cases is the European water frog complex of the genus Pelophylax, whose distribution includes the Czech Republic. In areas around the upper Odra River populations of hybrid males were recently discovered who form stable all-male lineages, similar to those formed by asexual females. The results of this study show that males produce...
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Identification of key regulators of gene expression in mammalian oocyte and embryo
Jansová, Denisa ; Šušor, Andrej (advisor) ; Gahurová, Lenka (referee) ; Lin, Chih-Jen Lance (referee)
Mammalian oocyte is a highly differentiated cell which gives rise to an embryo after fertilization. Importantly, fully-grown oocytes become transcriptionally inactive at the end of the growth phase. During following stages of development, i. e. meiotic maturation of the oocyte and early embryonic development, only transcripts previously synthesized and stored are used. The tight correlation between mRNA distribution and subsequent protein localization and function provides a mechanism of spatial and temporal regulation of gene expression used by various cell types. However, not much is known about mRNA localization and translation in the mammalian oocyte and early embryo. The aim of my thesis was to determine the localization of transcripts and components of translational machinery in the mammalian oocyte and embryo and to uncover the mechanisms of spatiotemporal regulation of translation as a prerequisite for correct oocyte and embryo development. We have shown that nuclei of both mouse and human oocytes contain RNA molecules and RNA binding proteins. Following the nuclear envelope breakdown (NEBD), translational hot-spots occur in the area surrounding the nuclear region. We suppose that mRNAs previously retained in the nucleus are released to the cytoplasm during NEBD and their subsequent...
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Methods of Molecular Biology in Predictive Diagnostics of Her/neu in Stomach Cancer
Důra, Miroslav ; Staněk, Libor (advisor) ; Gemperle, Jakub (referee)
Stomach cancer is a malignant neoplastic disease, which is caused by malignant transformation of the gastric mucosal epithelium. Elderly patients are more frequently affected, the majority of the patients are males. Stomach cancer has some typical features like minor symptomatology and early metastasis founding. Nowadays, a mild decrease of incidence is registered. Treatment of stomach cancer depends on its location and stage. Because of its relative chemo- and radioresistance, surgical resection is the only one potentially curable method, although there is high number of recurrences. An amplification and overexpression of HER2 receptor is detected in approximately 10 - 20 % patients with stomach cancer. This overexpression correlates with worse prognosis of disease. Treatment with a monoclonal antibody named trastuzumab, Herceptin® could significantly elongate their life. Trastuzumab is now widely and successfully used for the treatment of female patients with breast carcinoma. Detection of HER2 amplification is there needed. Treatment with trastuzumab can be useful only when HER2 positivity of tumor is determined. This determination should be made by a reliable test with sufficient sensitivity and specificity. The aim of this work is to summarize the methods of molecular biology that are used in...
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Earlier evolutionary dead-ends, now the creators of a reproductive strategy: the origin and reproduction of the all-male water frog lineage Pelophylax esculentus
Doležálková, Marie ; Choleva, Lukáš (advisor) ; Mikulíček, Peter (referee) ; Kratochvíl, Lukáš (referee)
Asexual modes of reproduction are usually based on the principle of copying (cloning) DNA from the female and passing it on to the offspring. For most asexually reproducing vertebrates the progeny develop from an unreduced and often unfertilised egg. This is driven by the mechanisms of parthenogenetic and gynogenetic reproduction. While in the former the clonal germ cell develops spontaneously and separately, in the latter a sexual partner is needed to activate the cleavage of the ovum, although without the fusion of the sperm and egg. Therefore in both cases there is no fertilization and the clonal progeny consist solely of daughters, hence the majority of previous studies have only focused on asexual female lineages. However, on rare occasions asexual clonal males can arise when the right fertilization occurs. Whilst these offspring are usually infertile, fertile diploid asexual males have been discovered in just three genera of hybrid origin in vertebrates. One of these unique cases is the European water frog complex of the genus Pelophylax, whose distribution includes the Czech Republic. In areas around the upper Odra River populations of hybrid males were recently discovered who form stable all-male lineages, similar to those formed by asexual females. The results of this study show that males produce...
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