13:00
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Lucie
Červenková
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B3
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doc.Ing. Filip Lankaš, Ph.D.
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Temperature dependent structure, dynamics and deformability of DNA A-tracts
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detail
Temperature dependent structure, dynamics and deformability of DNA A-tracts
DNA A-tracts are sequences of several adenines (A) or thymines (T) which do not contain a TA dinucleotide. They induce bending to the DNA double helix and exhibit peculiar structural properties. In the genome, A-tracts prevent nucleosome formation, contributing to the regulation of gene expression. At elevated temperatures, A-tracts undergo a premelting transition in which they loose their salient features, becoming structurally more similar to canonical B-DNA. However, the microscopic mechanism of the transition is not fully understood. In my work I set out to investigate the mechanism of premelting by means of atomic-resolution molecular dynamics simulations of A-tracts at different temperatures. The analysis of the simulated data should provide insight into the changes of A-tract structure and mechanical stiffness associated with premelting. The results will help understand the mechanisms of gene regulation in thermophilic organisms and may also be useful in the design of artificial DNA nanostructures.
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13:15
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Bc.
Jaroslav
Kurfürst
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M2
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Mgr. Jan Pačes, Ph.D.
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Rozšíření databáze kuřecích endogenních retrovirů
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detail
Rozšíření databáze kuřecích endogenních retrovirů
Majority of eukaryotic genomes is composed of DNA repetitive sequences. Part of them are retroviral elements. They are remnants of the retroviral genomes that in the past infected the eukaryotic organisms in question, reversed transcribed and integrated into the host DNA. For example, retroviral elements comprizes up to ten per cent of the human genome. Recently, we constructed database of the human retroviral elements. Now we want to compare the human elements with retroviral elements of other eukaryotic genomes. In the course of this study we are expanding the existing database of chicken elements with the elements of the newly sequenced Gallus gallus genome.
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13:30
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Bc.
Eva
Matoušková
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M2
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doc.Ing. Filip Lankaš, Ph.D.
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Structure and dynamics of naked and nucleosomal DNA containing pyrimidine-pyrimidone (6-4) photoproduct
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detail
Structure and dynamics of naked and nucleosomal DNA containing pyrimidine-pyrimidone (6-4) photoproduct
Ultraviolet radiation from the Sun can produce a covalent linkage between two adjacent pyrimidine bases in DNA to form pyrimidine (6-4) pyrimidone photoproduct. In my project I study DNA containing the pyrimidine dimer in naked oligomers and in nucleosomes, and two control DNA oligomers without the dimer. The systems were simulated by the molecular dynamics method with the OL15 force field for DNA and with explicit inclusion of water and ions. The DNA dynamics was analysed by measuring hydrogen bonds in the dimer and other parameters describing the structure. I also performed cluster analysis to identify separate conformational states. The results indicate that damaged DNA in the nucleosome exhibits more pronounced conformational dynamics that the naked undamaged DNA. This may provide mechanistic explanation of the observed high binding affinity of the UV-DDB repair protein to nucleosomal DNA.
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13:45
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Bc.
Anna
Pavlů
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M2
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prof. Ing. Tomáš Ruml, CSc.
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Crosslink and MS spectra generator for the study of M-PMV matrix protein
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detail
Crosslink and MS spectra generator for the study of M-PMV matrix protein
The matrix protein of the Mason-Pfizer monkey virus is the N-terminal part of its structural polyprotein Gag. The matrix protein determines where the immature virus particles assemble and later it is crucial for the interaction with the plasma membrane during budding. During the self-assembly the matrix protein forms oligomers. The locations where the matrix monomers interact with each other can be studied by crosslinking mass spectrometry. However, these crosslinked peptides are generally of low abundance and in turn are poorly identifiable in the MS spectra. To mitigate this disadvantage, a software tool has been developed to simulate the process of protein crosslinking which is followed by computing theoretical MS spectra of the crosslinked fragments and finally, comparing those to the experimental MS spectra.
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14:00
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Bc.
Jiří
Reiniš
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B1
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Mgr. Jan Pačes, Ph.D.
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Analysis of expression of human and mouse endogenous retroviruses in thymus
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detail
Analysis of expression of human and mouse endogenous retroviruses in thymus
Endogenous retroviruses comprise millions of discrete genetic loci integrated into the genomes of all vertebrates. These genetic loci represent past retroviral infections and their ability to integrate into the chromosomal DNA of germ-line cells has endowed retroviruses with the potential to be fixed in the genomes during evolution. Despite the fact that endogenous retroviruses lost this ability to infect other cells, presence of strong promotors in their sequences allows them to express some of their genes in host cells.
In this work, we study gene expression of human and mouse ERVs in the thymus in context of autoimmune diseases. We analyze RNAseq data and compare expression patterns of ERVs in thymus to those in other tissues. Single cell RNAseq data from mTECs is analyzed to obtain detailed expression patterns. Our aim is to assess to what extent are HERVs included in the presentation of self antigens during negative selection of T cells and discuss what are the implications in autoimmune disorders. Results from this diploma work will be integrated into the internationally acclaimed database of endogenous retroviruses HERVd.
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14:15
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Anna
Vavříková
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M1
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Mgr. Jan Pačes, Ph.D.
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Detection of expression of human endogenous retroviruses in different tissues
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detail
Detection of expression of human endogenous retroviruses in different tissues
Endogenous retroviruses comprise millions of discrete genetic loci integrated into the genomes of all vertebrates. These genetic loci represent past retroviral infections and their ability of integration into the chromosomal DNA of germ-line cells has endowed retroviruses with the potential to be fixed in the genomes during evolution. Despite the fact that endogenous retroviruses lost theis abitily to infect other cells, presence of strong promotors in their sequences allows them to express some of their genes in host cells. Results from this bachelor work are integrated into the internationally acclaimed database of endogenous retroviruses HERVd.
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14:30
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Martina
Zoubková
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B2
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RNDr. Michal Kolář, Ph.D.
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Simulace ribozomálního proteinu eS7
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detail
Simulace ribozomálního proteinu eS7
The presentation is about simulation of a ribosomal protein eS7 and its mutation, where a valine is replaced by phenylalanine. Ribosomes serve as a site of protein synthesis. Mutation is a change in genetic sequence and it can have an impact on the function of a protein. The studied mutation causes Diamond–Blackfan anemia in humans. We hope that the research will shed some light on the molecular cause of this illness.The purpose of this study is to test, if the mutation causes a structural change of the eS7. Such a change may affect the protein function.
Simulations are performed in Linux environment using GROMACS (GROningen MAchine for Chemical Simulations) program package. Same conditions apply for the two – native and mutated – protein simulations.
During the evaluation, we analyze the RMSD (Root-Mean-Square-Deviation) of a protein and of several its parts in time t. Previous simulations of both proteins did not reveal any fundamental changes of the protein structure, but these simulations were too short to be conclusive. Another, longer, simulations are currently running. These should be long enough to provide more data to make a better evaluation of the mutation effect.
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