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Characterization of the distribution and dynamics of the antigen-presenting cells using MHC II-EGFP knock-in mouse model
Pačes, Jan ; Černý, Jan (advisor) ; Tlaskalová - Hogenová, Helena (referee)
Results of recent studies indicate that dendritic cells are capable of transporting commensal intestinal bacteria into the mammary glands, which ultimately leads to their occurrence in breast milk. We have therefore decided to evaluate the phenotype of immunologically relevant antigen presenting cells (APCs) present in the mammary glands and the small intestine, respectively and perform a comparison study. We also studied plasticity of these populations during lactation. In situ immunodetection and flow cytometry methods were used to determine phenotype. We succeeded in optimising the methods for preparation of samples for flow cytometry and microscopy. We thoroughly tested protocols for 3D visualisation of APC populations and quantitative image analysis for correlation with flow cytometry, further optimization is nevertheless needed. We found out that during lactation large numbers of MHC II+ cells cluster around the alveoli and milk ducts. These cells are of a distinctly dendritic shape and their phenotype does not correspond to the APCs in the surrounding tissue. A pronounced increase of APC cells in the mammary glands between the fourth and sixth days of lactation was observed, with the majority of these cells expressing the CD103 antigen typical for cell populations of immune cells of the...
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Endogenous retroviral elements and their functions in the human genome
Famfulíková, Mirka ; Pačes, Jan (advisor) ; Lichá, Irena (referee)
In addition to the coding sequences, the human genome contains a so noncoding DNA, among which we count transposable elements capable of transposition in the genome. The remnants of the past retrovirus infections - endogenous retroviruses (human endogenous retroviruses - HERVs) belong to the transposable elements, which contain the LTR sequences. Human endogenous retroviruses make up to 8% of the size of the human genome. The retroviruses are not only passive relicts, but they have gained some key functions - too. They increase the plasticity of the human genome and some HERV LTRs can serve as binding sites for transcription factors like. Env protein from the families HERV-W and HERV- FRD were coopted by the human genome and are nowadays expressed as proteins Syncitin-1 and Syncitin-2, which are necessary by the forming of human placenta. Unfortunately, the HERV elements can have a negative health impacts. In the last decades they are subject of a debate in connection with various diseases, such as multiple sclerosis, schizophrenia, HIV proliferation and some types of tumorigenesis. The role of HERVs in the human genome is not completely known yet and it is important to continue with their research. Powered by TCPDF (www.tcpdf.org)
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Current methods of genome analysis and their use in identification of genetic determinants of human diseases
Stránecký, Viktor ; Kmoch, Stanislav (advisor) ; Kleibl, Zdeněk (referee) ; Pačes, Jan (referee)
The study of rare genetic diseases presents unique opportunity to uncover the genetic and molecular basis of human traits and greatly helped to the identification of genes, to the elucidation of their function and to the characterization of metabolic pathways and cellular processes. Over the past decades, linkage analysis has been appropriate approach to search for the genes causing Mendelian diseases and contributed to the identification of many genes, but the genetic cause of many diseases remains unknown. New methods of studying the human genome, microarray technology and massively parallel sequencing (next generation sequencing), represent a way to efficiently identify the cause of genetically determined diseases, based on direct observation of mutations in the genome of affected individuals. These techniques replaced the traditional method of disease gene identification represented by linkage analysis and sequencing of candidate genes and have become the standard approach to elucidate the molecular basis of diseases. In this work, i describe the the results achieved by using these methods - identification of the genes underlying mucopolysacharidosis type IIIC, isolated defect of ATP synthase, Rotor syndrome, autosomal dominat ANCL and GAPO syndrome.
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Návrh Real-Time PCR testu pro detekci Aphibiocystidium ranae jako modelového druhu pro studium rhinosporidiózy
Přistoupilová, Anna ; Pačes, Jan (advisor) ; Vopálenský, Pavel (referee)
The aim of this thesis is to develop species-specific Real-Time PCR assay for detection of frog parasite Amphibiocystidium ranae as a model approach for studying rhinosporidiosis in human, caused by Rhinosporidium seeberi. Similarities of these parasites allow to study human rhinosporidiosis by analogy. Sequences of the gene for 18S rRNA of Amphibiocystidium ranae were analysed by multiple sequence alignment with sequences of closely related organisms found in GenBank nucleotide database. Amphibiocystidium ranae-specific regions were found and three primer sets were designed, two of them together with probe to increase specificity. Specificity was checked against GenBank nucleotide database and ribosomal RNA database SILVA. Primer sets were tested on samples taken from frogs. Specificity was confirmed by melting curve analysis. Amphibiocystidium ranae-specific Real-Time PCR assay was developed and can be used for detection of this parasite.
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Mechanismy kontroly endogenních retrovirů v hostitelské buňce.
Matoušková, Magda ; Hejnar, Jiří (advisor) ; Mělková, Zora (referee) ; Pačes, Jan (referee)
In my thesis I am dealing with human endogenous retroviruses (HERVs), which are involved in placenta development, and with porcine endogenous retroviruses (PERVs) in the context of the risk of their transmission to a patient xenotransplanted with a pig organ. We have shown DNA methylation to be an important silencing mechanism regulating HERV as well as PERV. (1) Whereas in placenta the demethylation of HERVs ERVWE1 and ERVFRDE1 is crucial for its correct function, in the testis it is connected with seminoma development. (2) It seems that methylation is partially responsible for low PERV expression in tissues and notably reduces the risk of zoonotic transmission during xenotransplantation. (3) However, the risk remains because in contrast with mouse and rat cells, some human cells are permissive to porcine retroviruses in vitro thanks to functional receptors and their inability to efficiently silence the integrated PERVs.
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Sequence analysis of SIX homeobox family in Craspedacusta sowerbyi
Vojta, Petr ; Pačes, Jan (advisor) ; Král, Jiří (referee)
Homeobox genes are generally known as key factors directing processes during the morphogenesis of organ systems. Recently, research of homeobox genes evolution has focused on evolutionary old groups of species, such as Cnidarians. ln Cnidarians, there are more homeobox genes compared with more complex organism, such as fruit flies. Several homeobox genes have also been described in plants and fungi. General opinion is that homeobox genes are a very old group of genes, originating even before the main kingdoms of multicellular organisms. Six homeobox genes that have been identified as homologues of Drosophila sine oculis, an important factor for compound-eye formation, take part in numerous developmental processes directed by the PAX-SIX-EYA signal pathway. ln Vertebratae, as representatives of Deuterostomes, there are six genes in three sub groups, whereas in Drosophila melanogaster, as a representative of Protostomes, three homologues have been described, always one for each subgroup. The ancestral six genes diverged even before the divergence of groups Bilateralia and Cnidaria. ln freshwater jellyfish Craspedacusta sowerbyi we distinguished both HD and SD regions for five SIX proteins. Four of these six genes of Craspedacusta sowerbyi belong to the established Six groups (Sixl/2, Six3/6 a Six4/5), where...
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Parsing Based on Programmed Grammars
Pačes, Jan ; Solár, Peter (referee) ; Meduna, Alexandr (advisor)
This thesis is researching methods of parsing based on programmed grammars. It modifies known algorithm of table driven non-recursive predictive parser for context-free grammars and applies it on programmed grammars. It studies strength of this method, focusing on some languages which are not context-free.
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