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Modelling of Cell Colony Dynamics
Bělehrádek, Stanislav ; Škutková, Helena (referee) ; Sedlář, Karel (advisor)
The content of the thesis is a description of intracellular processes responsible for cell cycle regulation and reactions of cells to external and internal stimuli. Thoroughly described are important signaling pathways with appropriate methods, which can be used to simulate them in silico. From these cellular processes, a cell cycle model is created and implemented in a tool programmed in C ++ with OpenGL used for visualization. The model is then tested for various cell processes including HeLa cells growth. Finally, the results are compared with the behavior of living cells.
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Morphological, immunohistochemical, and molecular analysis of leiomyocellular tumors of the female reproductive system
Gregová, Mária ; Dundr, Pavel (advisor) ; Mandys, Václav (referee) ; Škarda, Jozef (referee)
Introduction Leiomyoma with bizarre nuclei (LBN) and cellular leiomyoma (CL) are rare variants of uterine smooth muscle tumors. In diagnostic practice, LBN can be mistaken for leiomyosarcoma (LMS), while CL may mimic low grade endometrial stromal sarcoma (LG ESS). Careful evaluation of morphological features is necessary when making the diagnosis; in some borderline cases, immunohistochemical and molecular examinations may help. Literature data on molecular genetic alterations in LBN and CL is limited, but some of these tumors appear to share certain aberrations with classical leiomyomas (UL) and LMS. Aims The aim of the work is to expand the knowledge about smooth muscle tumors of the uterus, especially LBN and CL, and perform a complex morphological, immunohistochemical (IHC), and molecular evaluation of their features. The individual goals include: 1) confirmation of the hypothesized benign behaviour of LBN, 2) morphological analysis of LBN, 3) more detailed clarification of LBN tumorigenesis with a focus on the FH gene, 4) clarification of CL tumorigenesis, 5) the use of IHC FH antibody as a screening method to identify FH gene mutations, 6) the use of morphological evaluation and results of IHC examination to facilitate differential diagnostic balance between benign and malignant smooth muscle...
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Role of intestinal circadian clock in epithelial transport, proliferation, and tumourigenesis
Soták, Matúš ; Pácha, Jiří (advisor) ; Bendová, Zdeňka (referee) ; Herichová, Iveta (referee)
AABBSSTTRRAACCTT The molecular circadian clock enables anticipation of environmental changes. In mammals, clocks are ubiquitously present in almost all tissues and they are comprised of transcriptional-translational feedback loops of the so-called clock genes. The central clock represents the intrinsic pacemaker which is located in suprachiasmatic nuclei (SCN) of hypothalamus and synchronizes peripheral clocks. Clockwork system in alimentary tract and its regulatory link to intestinal functions are poorly understood. Therefore the objective of the thesis was to characterize molecular clock in particular parts of the rat intestine and to elucidate its link to the intestinal transport, regulation of cell cycle and neoplastic transformation in colonic tissue. We used quantitative RT-PCR (qPCR) to determine circadian profiles of mRNA expression of clock genes in the epithelium of duodenum, jejunum, ileum, and colon of rat. Furthermore, we analysed the expression of genes coding sodium chloride transporters and channels as well as cell cycle regulators in colon. To focus more precisely on different structures of intestinal epithelia we used laser capture microdissection. In addition, we performed Ussing chamber measurements to determine the colonic electrogenic transport. To study the contribution of circadian...
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The comparison of morphology, expression, epigenetic changes and mutations of HNF1B in solid tumors and non-neoplastic lesions.
Bártů, Michaela ; Dundr, Pavel (advisor) ; Mandys, Václav (referee) ; Škarda, Jozef (referee)
Introduction HNF1B is a tissue-specific transcription factor, which plays a crucial role in the embryological development of a number of organs, especially kidneys, gastrointestinal system, pancreas and billiary system. While the significance of HNF1B in the development of urinary tract malformations has already been well described, its role in the pathogenesis of solid tumors has not yet been elucidated. Based on the current data it seems that depending on the type of individual tumor HNF1B can either act as an oncogene or a tumor suppressor. However, the precise mechanism of how it exerts its influence is still unclear. Aims: The thesis focuses on expanding the knowledge of the significance of HNF1B changes in selected solid tumors and non-neoplastic lesions. The individual goals include: 1) determining the role which HNF1B plays in the pathogenesis of these lesions, 2) evaluating the significance of HNF1B for differential diagnosis, 3) analysis of the prognostic and predictive meaning of HNF1B, 4) mutation analysis of the HNF1B gene in all the tumor and non-tumor tissues with the aim to identify novel pathogenic mutations, 5) methylation analysis of the HNF1B promoter. Material and methods: Immunohistochemical examination with the antibody against HNF1B was performed on 516 samples of tumor and...
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lncRNA MIAT expression in cancer cells.
Jursová, Pavlína ; Eckschlager, Tomáš (advisor) ; Sztacho, Martin (referee)
LncRNAs have been shown, in many cases, to function as important regulators for gene expression and thus, they can play a critical role in various biological functions and disease processes including cancer. Myocardial infarction associated transcript (MIAT) is one of the non-coding RNAs first identified as lncRNA in 2006 and originally isolated as a candidate gene for myocardial infarction. This long non-coding RNA is also involved in other diseases such as diabetic retinopathy, paranoid schizophrenia or microvascular dysfunction. MIAT has also been identified as a carcinogenic regulator in many malignant tumors. Numerous researches have reported that MIAT silencing reduces cell viability, proliferation and invasivity and enhances cellular senescence and apoptosis of cancer cells. Therefore, it is considered a potential biomarker and therapeutic target in cancer. MIAT is involved in cellular processes through various mechanisms. It regulates alternative splicing, gene expression or functions through ceRNA mechanism and thus influences biological processes related to the tumor formation. Furthermore, in this study have been found that relative expression of MIAT was increased in Ewing sarcoma cell lines.
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Role of intestinal circadian clock in epithelial transport, proliferation, and tumourigenesis
Soták, Matúš
AABBSSTTRRAACCTT The molecular circadian clock enables anticipation of environmental changes. In mammals, clocks are ubiquitously present in almost all tissues and they are comprised of transcriptional-translational feedback loops of the so-called clock genes. The central clock represents the intrinsic pacemaker which is located in suprachiasmatic nuclei (SCN) of hypothalamus and synchronizes peripheral clocks. Clockwork system in alimentary tract and its regulatory link to intestinal functions are poorly understood. Therefore the objective of the thesis was to characterize molecular clock in particular parts of the rat intestine and to elucidate its link to the intestinal transport, regulation of cell cycle and neoplastic transformation in colonic tissue. We used quantitative RT-PCR (qPCR) to determine circadian profiles of mRNA expression of clock genes in the epithelium of duodenum, jejunum, ileum, and colon of rat. Furthermore, we analysed the expression of genes coding sodium chloride transporters and channels as well as cell cycle regulators in colon. To focus more precisely on different structures of intestinal epithelia we used laser capture microdissection. In addition, we performed Ussing chamber measurements to determine the colonic electrogenic transport. To study the contribution of circadian...
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Genomic instability in patient tumors due to excesive AID activity
Vaníčková, Karolína ; Drbal, Karel (advisor) ; Macůrek, Libor (referee)
AID is a member of APOBEC family of mutational enzymes. AID generates U:G mismatches in ssDNA by deaminating cytosine to uracil. In B cells error-prone repair of these mismatches induces a mutational burden in the process of somatic hypermutation of Ig locus during affinity maturation of immunoglobulins (Ig). AID also induces double-strand breaks during Ig class switch recombination or primary Ig diversification through templated gene conversion in some vertebrate species. AID might gain tumorigenic potential in case of insufficient regulation of induction and repair processes, causing genomic instability and possibly leading to tumorigenesis. AID is induced in epithelial tissues by proinflammatory cytokines via canonical NF-B pathway. Both exogenous factors (pathogens Helicobacter pylori or HCV), endogenous factors (bile acid) or even physiological state such as ovulation are the initiating factors. Thus, AID might be the link between inflammation and carcinogenesis. AID is expressed in different stages of carcinomas, mostly during the initial oncogenic transformation. Mice with ectopic AID expression develop lung, gastric, oral and hepatic carcinomas as well as melanomas. AID also regulates epithelial-mesenchymal transition in other tumors. AID is responsible for treatment resistance in both CML...
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Role of Rad18 in genome stability
Palek, Matouš ; Macůrek, Libor (advisor) ; Šolc, Petr (referee)
Rad18 is an E3 ubiquitin ligase well-known for its function in DNA damage tolerance (DDT). Especially, its role in translesion DNA synthesis, one of two DDT branches, was extensively studied in the past. Recently, Rad18 was shown to be involved in the repair of DNA double- strand breaks (DSBs) in mammalian cells. The role of Rad18 in human cells seems to be important since DSB repair as well as DDT pathway are essential for maintenance of genome stability. In this work, I introduce the function of Rad18 in both DDT pathways, translesion DNA synthesis (TLS) and template switching (TS). Then I summarize current knowledge about the role of human Rad18 in DSB repair. Finally, I describe potential involvement of Rad18 dysregulation in human cancer, since loss of genome integrity is an important driving force for tumorigenesis. Keywords: Rad18, genome stability, DNA double-strand break repair, tumorigenesis, DNA damage tolerance, translesion DNA synthesis, template switching.
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Important mechanisms of tumorigenesis and their role in chemoresistance of head and neck cancers
Zlámalová, Viktorie ; Šírová, Milada (advisor) ; Zíková, Martina (referee)
Head and neck squamous cell carcinoma (HNSCC) represents the sixth most common malignancy worldwide. Despite improvements in therapeutic outcomes due to advances in surgery, radiotherapy, chemotherapy, and imaging techniques, HNSCC still has high mortality rate. For patients who are not cured with surgery and radiotherapy, there are few effective treatment options. Although HNSCC is heterogeneous in nature, current molecular classification distinguishes only human papilloma virus positive and negative tumors. HNSCC in general are characterized by considerable resistance and high rate of locoregional recurrence. Loss of p53 control pathway and numerous alterations in components of intracellular signaling pathways are consistently observed throughout the majority of HNSCC cases, supporting uncontrolled proliferation. It was proven that common mutations in the HNSCC genome play major role in tumorigenesis as well as in resistance to chemotherapy. The aim of the thesis is to describe the important mechanisms in HNSCC, which are associated with mutations in epidermal growth factor receptor and p53, and those including PI3K/Akt/mTOR and Notch signaling pathways. Association of these pathways with chemoresistance to commonly used drugs and even to advanced targeted therapeutic agents was evidenced by many...
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Role of intestinal circadian clock in epithelial transport, proliferation, and tumourigenesis
Soták, Matúš
AABBSSTTRRAACCTT The molecular circadian clock enables anticipation of environmental changes. In mammals, clocks are ubiquitously present in almost all tissues and they are comprised of transcriptional-translational feedback loops of the so-called clock genes. The central clock represents the intrinsic pacemaker which is located in suprachiasmatic nuclei (SCN) of hypothalamus and synchronizes peripheral clocks. Clockwork system in alimentary tract and its regulatory link to intestinal functions are poorly understood. Therefore the objective of the thesis was to characterize molecular clock in particular parts of the rat intestine and to elucidate its link to the intestinal transport, regulation of cell cycle and neoplastic transformation in colonic tissue. We used quantitative RT-PCR (qPCR) to determine circadian profiles of mRNA expression of clock genes in the epithelium of duodenum, jejunum, ileum, and colon of rat. Furthermore, we analysed the expression of genes coding sodium chloride transporters and channels as well as cell cycle regulators in colon. To focus more precisely on different structures of intestinal epithelia we used laser capture microdissection. In addition, we performed Ussing chamber measurements to determine the colonic electrogenic transport. To study the contribution of circadian...
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