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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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Gene order in eukaryotic genomes: an analysis using sequence-based gene expression data
Divina, Petr ; Forejt, Jiří (advisor) ; Pačes, Jan (referee) ; Mokrejš, Martin (referee)
ZÁVĚRY 61 6. ZÁVĚRY 6.1. Analýza genů exprimovaných v myším varleti a jejich uspořádání v genomu Pomocí expresního profilování metodou SAGE (sériová analýza genové exprese) byl vytvořen katalog genů exprimovaných ve varleti dospělých myší. Byly identifikovány poziční klastry genů na chromosomech obsahující geny s preferenční expresí ve varleti. Tyto klastry obsahovaly signifikantně vyšší počet genů než v náhodně vygenerovaných genomech. Geny specificky exprimované v somatických buňkách myšího varlete byly signifikantně obohacené na chromosomu X, což podporuje teorii o hromadění genů preferenčně exprimovaných v samčích tkáních na chromosomu X. Geny exprimované z chromosomu X byly ochuzené v transkriptomu celého myšího varlete, což je v souladu s představou o inaktivaci chromosomu X během prvního meiotického dělení. Byla vytvořena veřejně přístupná internetová databáze Mouse SAGE Site, která shromažďuje expresní data z myších tkání a buněčných liniích vytvořená pomocí metody SAGE. 6.2. Genový obsah chromosomu Z kura domácího Chromosom Z kura domácího byl signifikantně obohacený o geny preferenčně exprimované v samčím mozku. ZÁVĚRY 62 Geny s preferenční expresí v samičím mozku vykazovaly náznak ochuzení na chromosomu Z. Podobně, geny specificky exprimované ve vaječnících byly na chromosomu Z...
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The evolution of SARS-CoV-2 virus during the pandemic of COVID-19
Karban, Šimon ; Tachezy, Ruth (advisor) ; Pačes, Jan (referee)
Coronaviruses are animal and human viruses which, in the case of humans, cause respiratory diseases. The genome of coronaviruses is non-segmented and encodes several structural and several non-structural proteins. As their genome consists of single-stranded RNA in a positive sense, they encode RNA-dependent RNA polymerase. The origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is uncertain and may never be known. However, this thesis covers up-to-date knowledge and the arguments for the main theories on the emergence of this virus. The pandemic of disease COVID-19 caused by the SARS-CoV-2 had an enormous impact on the health and lives of people worldwide. The length and severity of the pandemic were caused by the characteristic of the virus, transmissibility and asymptomatic type of infection with severe symptoms in elderly and chronically ill individuals and the fast evolution of the virus after its appearance in humans. This thesis will describe important characteristics of the most important variants of the virus and changes which gave them a selection advantage. In the end, trends in the evolution of SARS-CoV-2 will be discussed. Keywords: SARS-CoV-2, Coronaviridae, variants, phylogeny, origin, evolution
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Gamma-delta T lymphocytes in adipose tissue
Sztoláriková, Adéla ; Krulová, Magdaléna (advisor) ; Pačes, Jan (referee)
T lymphocytes are a unique type of T lymphocytes which, because of their innate-like qualities, belong to the so-called innate lymphocytes. Although they are a relatively rare population of T lymphocytes in peripheral blood, they are enriched in many peripheral tissues where they participate in immune responses to infectious pathogens and cell transformation. In addition, they play a role in the development of several autoimmune disorders. Recently, non- immune functions of T lymphocytes in tissue repair and tissue homeostasis have also been emphasized. This work focuses on the characterization of T lymphocytes, especially those residing in adipose tissue. T lymphocytes regulate adipose tissue homeostasis and overall energy metabolism. The roles of T lymphocytes under physiological and non-physiological conditions are described, including their impact on the development of obesity and metabolic syndrome. The possible applications of these lymphocytes in the treatment of these diseases are also briefly mentioned.
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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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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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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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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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The effect of amino acid repertoire on protein structure and function
Treťjačenko, Vjačeslav ; Hlouchová, Klára (advisor) ; Obšil, Tomáš (referee) ; Pačes, Jan (referee)
To understand protein structure emergence is to comprehend the evolutionary transition from messy chemistry to the first heritable molecular systems. Early proteins were probably flexible in structure, promiscuous in activity and ambiguous in sequence. Moreover, first sequences were presumably composed of prebiotically plausible amino acids from endogenous and exogenous sources which form only a subset of the extant protein alphabet. Here we investigate the effect of most recent additions to the amino acid alphabet on protein structure/function relationship and the properties of random proteins as the evolutionary point-zero for the earliest sequences as well as for proteins emerging de novo from the non-coding parts of the genome. Random or never born proteins are of a special interest for the contemporary biology as they unveil the unexposed side of the protein sequence space. We constructed an in silico library of random proteins with the natural amino acid alphabet, analyzed its structure/disorder/aggregation content and selected 45 sequences for subsequent experimental preparation and biophysical characterization. We observed that structure content in random sequence space does not differ significantly from the natural proteins. However, the analyses of the aggregation propensity showed a...
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