|
|
Prediction of p53 Protein Binding Sites
Radakovič, Jozef ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Protein p53 which is encoded by gene TP53 plays crucial role in cell cycle as a regulator of transcription of genes in cases when cell is under stress. Therefore p53 acts like tumor suppressor. Understanding the pathway of p53 regulation as well as predicting its binding sites on p53 regulated genes is one of the major concerns of modern research in genetics and bioinformatics. In first part of this project we aim to introduce basics from molecular biology to better understand the p53 protein pathway in gene transcription and introduction to analysis of prediction of p53 binding sites. Second part is about implementation and testing of tool which would be able to predict transcription factor binding sites for protein p53.
|
|
|
Functional analysis of the ERK signaling pathway in epithelial cells
Galvánková, Kristína ; Vomastek, Tomáš (advisor) ; Rösel, Daniel (referee)
The MAPK/ERK pathway, which is evolutionarily conserved in eukaryotes is one of the most intensively studied signaling pathways and consists of a three-tier cascade of Raf- MEK-ERK protein kinases. A variety of extracellular signals are transduced from receptors to hundreds of substrates by a series of sequential phosphorylations leading from Raf to MEK to ERK. The ERK pathway regulates a plethora of cell- and extracellular signal- specific responses such as gene expression, proliferation, differentiation, migration, and apoptosis. The proper execution of these physiological processes requires a precise temporal and spatial regulation of the pathway and disruption of the regulatory mechanisms leads to pathological consequence such as tumor transformation. Specificity and regulation of signal transduction are provided in part by the presence of isoforms at each level of the ERK signaling pathway. The functional differences between the effector protein kinases ERK1 and ERK2 have been controversial for a long time, but it is still unclear how important they are in achieving an appropriate cellular response. In this work, we focused on the functional characterization of ERK1 and ERK2 isoforms in MDCK epithelial cells. Specifically, we examined the effects of ERK2 inactivation on cell morphology and...
|
|
|
Where transcription meets translation
Hegrová, Karolína ; Krásný, Libor (advisor) ; Mašek, Tomáš (referee)
Transcription and translation are key steps in gene expression. The RNA polymerase (RNAP) plays a major role in the transcription process, while the ribosome is involved in translation. In bacteria, these two processes are not separated. RNAP and the ribosome interact, and its called transcription- translation coupling. In this thesis, I discuss the mechanism of transcription and translation, with the main focus on transcription-translation interactions. I divide these interactions into indirect, which are caused by regulátory molecules, and direct, where the ribosome directly binds with RNAP. When physical binding occurs, either a tight junction between these molecules occurs or a bridge is formed by transcription factors. Then I describe regulatory function of this connection and explain the exceptions where transcription and translation don't link. In the last part of the thesis, I focus on elongation factor Tu (EF-Tu), its important role in metabolism, its interactions with MreB protein, and how this factor is used by some bacteriophages. Finally, I mention its possible role in transcription-translation interactions. Key words: transcription, translation, transcription-translation coupling, RNA polymerase, ribosome, transcription factors, EF-Tu
|
|
|
Molecular mechanisms in the development of the cochlea
Procházková, Šárka ; Pavlínková, Gabriela (advisor) ; Novák, Josef (referee)
Molecular mechanisms in the development of the cochlea The cochlea is the primary structure for the perception of sound. A spiraled cochlear duct contains the auditory organ, the organ of Corti, is innervated by sensory neurons of the spiral ganglion. The organ of Corti contains hair cells, the sensory receptors of the inner ear, that are responsible for the mechano-transduction of sound waves into electrical signals. The development of the cochlea is regulated by the cellular and molecular processes, including cochlear outgrowth, cellular differentiation, and patterning. The precise coordination of multiple processes during the transformation of a flat embryonic epithelium into the cellular mosaic of the adult structure requires a multitude of transcription factors and signaling pathways. These regulatory networks dictate cell fate and timing decisions during cochlear development. Interestingly, these mechanisms operate as well during sensory epithelial cell regeneration after damage and during stem cell directed differentiation, making developmental studies instrumental for improving therapies for hearing impairment.
|
|
|
Algorithmic prediction of functional changes within protein sequence
TOLAR, Nikolas
The Following thesis provides a theoretical background to the biology of a naked mole-rat (Heterocephalus glaber), highlighting its unique characteristics that could potentially be explained by altered epigenetic mechanisms. In order to identify potentially functional evolutionarily changed sites in epigenetic modifiers, we developed a novel approach to protein scanning through the utilization of multiple-sequence alignments and protein annotations available in public databases. The key result is computer software and analysis of the obtained results, identifying candidate proteins with potentially altered functions.
|
|
|
Novel non-coding transcripts at imprinted loci in mammalian oocytes and embryos
NENIN, Nina
Aims of this thesis were to annotate novel transcripts within clusters of imprinted genes in mouse oocytes and embryo, to analyze expression changes of these transcripts during mouse embryonic development, to identify enriched sequence motifs and potential transcription factors binding sites at promoters of transcripts within imprinted gene clusters as well as transposable elements acting as promoters of these transcripts and to identify potential candidates for further functional studies, using bioinformatic methods.
|
|
|
Peak identification from ChIP-nexus data.
Drahoňovská, Lucie ; Převorovský, Martin (advisor) ; Gahurová, Lenka (referee)
Proteins play a very important role in live organisms. Their roles are for example structural, transport, regulatory or catalytic. What genes will be expressed, what proteins will be made and at what rate can have a strong impact on the function or even health of the organism. Gene expression is significantly regulated by transcription factors, whose activity may cause multiple diseases or disorders (Latchman 1997). Studying those factors and their function is therefore very important. Several methods were developed to this cause, ChIP-chip, ChIP-seq, ChIP-exo and ChIP-nexus. They enable us to study the binding sites of transcription factors and other DNA-binding proteins with various degrees of resolution. In this thesis I am going to describe the above mentioned methods and peak callers, softwares used for analysis of data obtained by those methods. I will also attempt to do peak calling of ChIP-nexus data of Cbf11 protein and compare the outcomes.
|
|
|
Potential of genetic engineering for breeding plants tolerant to abiotic stresses: cold resistance in rice
Lotová, Gabriela ; Lipavská, Helena (advisor) ; Janská, Anna (referee)
With increasing population and climate change, there has been an increase in efforts to breed more efficient crops. Genetic engineering has opened unprecedented breeding possibilities in developing plants with desired traits. Transgenic crops with better qualities, including resistance to adverse environmental conditions, can contribute to solving problems of hunger and malnutrition in developing countries. Although society perceives genetically modified crops rather negatively, these crops are widely used as feed for livestock and outside Europe also for human nutrition. Because of the complexity of resistance to abiotic stress, the utility of genetic manipulations for the breeding of resistant plants was previously not anticipated. However, it turned out that modification of the stress signalling cascade or transcription factors can lead to success. This thesis summarizes the possibilities of genetic modification of crops, which may result in better tolerance to cold, and is mainly focused on rice. Part of the work deals with transduction of cold signal, whose modification can also result in increased tolerance to cold. Another part deals with transcription factors that activate expression of low temperature- resistant genes. The greatest attention is paid to CBF/DREB transcription factors that...
|
|
|
Chromatin immunoprecipitation of selected transcription factors
Smetanová, Jitka ; Vališ, Karel (advisor) ; Převorovský, Martin (referee)
The TEAD family of transcription factors regulates expression of genes affecting cell proliferation, differentiation and apoptosis. The activity of a particular transcription factor called TEAD1 is regulated by the Hippo signalling pathway. The Hippo pathway has been implicated to play a role in cancer suppression, however its precise mechanism remains unclear. MYC and GLUT1, genes which are coding two key regulators of glycolysis, were recently described as potential targets of the Hippo signalling pathway in human leukemia cells. In this diploma thesis, I tried to confirm the proposed interaction of the transcription factor TEAD1 with regulatory sequences of MYC and GLUT1 genes using chromatin immunoprecipitation (ChIP) analysis in human leukemic cells. However, I failed to successfully isolate TEAD1 complexes using ChIP. So, I discuss in my diploma thesis also possible reasons for this outcome, including biological and methodological issues. (In Czech) Key words: Transcriptional regulation, TEAD transcription factors, chromatin immunoprecipitation, leukemia
|
|
|
The transcription factor C/EBPƴ as a novel regulator in mast cell development and function
Jedlička, Marek ; Alberich Jorda, Meritxell (advisor) ; Černý, Jan (referee)
Mast cells contribute to the activities of innate and adaptive branches of the immune system. They participate in pro-inflammatory responses to a wide range of pathogens, such as parasites, bacteria, and other foreign agents. These beneficial properties are in contrast to the contribution of mast cells to certain pathologies, such as asthma, allergy, autoimmune disorders, anaphylaxis, and systemic mastocytosis. Thorough knowledge of mast cell biology in health and disease is critical for the development of new therapeutic approaches. However, molecular mechanisms that control mast cell development and function are still incompletely defined. Our preliminary data indicate that the transcription factor C/EBP is a key player in mast cell biology. Here, using in vitro and in vivo models, we determine how C/EBP regulates the commitment of hematopoietic progenitors towards mast cells, and modulates mast cells function. These efforts provide novel insights to the role of C/EBP in hematopoiesis, and contribute to a better understanding of the mechanisms governing mast cell biology. Key words Mast cells, C/EBP, transcription factors, bone marrow-derived mast cell cultures, mast cell development, Cebpg conditional knockout mice
|
guest ::
