|
|
The effect of 6S-like RNAs on physiological differentiation of Streptomyces coelicolor
Burýšková, Barbora ; Bobek, Jan (advisor) ; Branny, Pavel (referee)
The variety of bacteria and their genomes sometimes causes conservation of homologue molecules to be displayed not in sequence but in secondary and tertiary structures. In the case of the regulatory 6S RNA, sequence homologues have been found in over 100 bacterial species so far. However, none were found in the genus Streptomyces. The unique genome of these soil- dwelling bacteria, known for their capacity to produce antibiotics, has a high G/C content and diverges substantially from distantly related bacteria. Yet in the non-coding 6S RNA it is the secondary structure that is crucial for its function. The 6S RNAs trap sigma factors by mimicking target promoter sequences in order to help with switching sets of expressed genes during developmental transitions. 6S-like RNA genes in Streptomyces coelicolor have been computationally predicted by comparison of in silico modelled secondary structures of known 6S RNAs. The aim of this thesis was the verification of these 6S-like RNA predictions. The experimental approach was based on RNA co-immunoprecipitation (RNA CoIP), as well as RT- PCR from RNA samples. The outcomes of this project are the detection of six novel ncRNA transcripts with possible 6S-like RNA functions, which also served as the wet-lab verification of the in silico prediction technique...
|
|
|
Expression of WT1 and its splicing variants in myeloid leukemias
Macháčková Lopotová, Tereza
3 Abstract Myeloid leukemias include malignant diseases characterized by clonal expansion of the myeloid cell lineage. While in case of chronic myeloid leukemia (CML), the main cause of the disease has already been identified - t(9;22) and the aktivity of the fusion product of the translocation BCR-ABL, acute myeloid leukemia (AML) has been associated with plenty of different translocations and mutations. The aim of this work was to contribute to the improvement of monitoring of patients with myeloid leukemias via detailed study of the panleukemic marker Wilms tumor gene 1 (wt1) expression. Prognostic value of wt1 expression has been proved for AML patients, however, it has not yet been confirmed for CML patients. Expression of different wt1 variants (more then 36 protein products) is known very poorly in both, AML and CML as well as in normal hematopoiesis. Most of the study is focused on CML, only limited parts are dedicated to AML. In the first part of the work, we clearly proved prognostic value of total wt1 mRNA expression for CML patients. Statistical evaluations revealed critical wt1 values which enable to specify prognosis of patients responding non-optimally to imatinib. Bcr-abl looses much of its prognostic value in these patients. Further, we have designed and optimized PCRs for selected wt1...
|
|
| |
|
|
The role of histone post-translational modifications in the regulation of gene expression in plants
Chromý, Jakub ; Čermák, Vojtěch (advisor) ; Holá, Dana (referee)
Chromatin structure, gene expression and consequently many important aspects of the plant development are under control of epigenetic regulation. Within epigenetic regulation, histones and their modifications play a pivotal role. The N-terminal tails of histones are dynamically modified by covalent post-translational modifications (PTMs). These modifications are key regulators modulating chromatin structure and thus regulating gene expression. In angiosperms, one of the processes finely regulated at the epigenetic level is the flowering. Flowering represents a very complex process, that is relevant for the study of epigenetic regulation as well as for practical application. In this work, I summarize current knowledge of the role of histone PTMs in the regulation of gene expression in plants, focused predominantly on two key regulators of flowering in Arabidopsis - FLC and FT.
|
|
|
Multifunctional protein CTCF and its role in regulation of gene expression
Pokorná, Linda ; Vacík, Tomáš (advisor) ; Vopálenský, Václav (referee)
CTCF is a ubiquitously expressed nuclear protein that binds to DNA through its central zinc finger domain. Thousands of CTCF binding sites have been identified throughout the human genome at gene promoters, in intergenic regions or in non-coding sequences. CTCF can function either as a positive or as a negative regulator of gene expression and is also involved in creating and maintaining long-range chromosomal interactions. Various developmentally important genes have been shown to be regulated by CTCF and its malfunction is frequently associated with developmental defects or diseases. CTCF undergoes various posttranslational modifications such as phosphorylation or SUMOylation which also affect its function in the regulation of gene expression. Keywords: CTCF, three dimensional genome, cohesin, regulation of gene expression, insulation, HOX genes
|
|
|
Molecular subgroups of medulloblastoma: the current consensus
Jarošová, Šárka ; Zíková, Martina (advisor) ; Nedvědová, Tereza (referee)
Medulloblastoma is the most common malignant brain tumor in children. In recent years, there has been a steady improvement in understanding of genetic and molecular heterogeneity of this tumor, that has led to better prognosis and improved targeted therapies. This thesis summarizes recent advances in molecular sub-grouping, and the associated gene mutation and copy number variations in medulloblastoma.
|
|
|
The expression of TP53 gene at the mRNA level in patients with myelodysplastic syndrome
Šeborová, Karolína ; Beličková, Monika (advisor) ; Španielová, Hana (referee)
Myelodysplastic syndrome (MDS) is a heterogeneous group of diseases characterized by ineffective hematopoiesis which is caused by damage of differentiation of pluripotent haematopoietic stem cells. TP53 gene mutations are identified approximately in 10% of MDS and represent a negative prognostic factor. Altered TP53 gene expression may have similar effect as the mutation. Mutations or deregulated expression of this gene have an impact on many cellular processes including apoptosis, DNA repair, cell growth and angiogenesis. In this work, the expression mRNA levels of genes involved in p53 signalling pathway were studied in CD34+ pluripotent haematopoietic cells from bone marrow of patients with low- risk MDS. MDS patients showed increased expression of genes involved in apoptosis induction, regulation of cell cycle and DNA repair (BAX, BBC3, CCNE1, CDC25A, CDKN1A, FAS, GADD45A) as compared to healthy subjects. The patients with TP53 mutation had decreased expression of apoptotic genes (BAX, PIDD, TRAF2) and increased gene expression of apoptotic inhibitor (BCL2A1), indicating a reduced activity of apoptotic pathways and that way the pathological cell clone may gain a growth advantage. Deregulation of 21 genes (BAX, BBC3, EGR1, KAT2B, MDM2 etc.) was observed in patients with del (5q) compared to...
|
|
|
Production and secretion of virulence factors in Bordetella pertussis
Držmíšek, Jakub ; Večerek, Branislav (advisor) ; Petráčková, Denisa (referee)
Bordetella pertussis is a strictly human pathogen and causative agent of infectious respiratory disease called whooping cough. In order to establish successful infection and colonization of the host, B. pertussis uses a broad spectrum of virulence factors such as adhesins (filamentous hemagglutinin, pertactin, and fimbriae) and toxins (adenylate cyclase and pertussis toxins). In addition, the type 3 secretion system (T3SS) was also found in the genus Bordetella. In connection to our previous characterisation of B. pertussis strain lacking the gene encoding RNA chaperone Hfq (Δhfq), which proved that Hfq is required for T3SS functionality, the recombinant T3SS proteins BopB, BopD, BopC and BopN were purified to homogeneity. Next, the specific antibodies were obtained using purified recombinant proteins in order to study the production of the T3SS components in B. pertussis. Using refined anti- BopC antibodies it was for the first time shown that laboratory-adapted B. pertussis strain secretes BopC protein into medium. The recombinant translocators BopB and BopD were also used to examine their pore-forming activity using planar black lipid membranes. Based on the characterisation of hfq deletion mutant, having impaired production of membrane proteins when compared to the wild type, mass spectrometry...
|
|
| |
|
|
Effect of selected endocrine disruptors on the male mouse reproductive system in vivo
Žatecká, Eva ; Pěknicová, Jana (advisor) ; Kubelka, Michal (referee) ; Kaňka, Jiří (referee)
In our environment there are many compounds which can negatively influence humans and wildlife. Every day, a vast number of environmental pollutants are released into our environment and there is no way to avoid their exposure. Some of these compounds can even mimic endogenous hormones and interfere with our endocrine system (so called endocrine disruptors), which is the key regulatory system controlling almost all physiological processes in human and animal bodies. Also the reproductive system is largely regulated by various hormones, and their proper function is crucial for gamete formation, fertilization and embryo development. Environmental pollutants are therefore considered as one of the possible causes of increased infertility in human population. This prompted us to study the effect of two endocrine disruptors (tetrabromobisphenol A - TBBPA, and zearalenone - ZEA) on the male mouse reproductive system in vivo. According to our results, TBBPA is able to induce apoptosis as well as changes in the expression of selected testicular genes and sperm protamination. Our results also suggest that permanent exposure to TBBPA slightly enhances its effect in the next generation, depending on whether the parents have been affected or not. We hypothesized that differential protamination of the sperm DNA...
|
guest ::
