This study is part of a project which aims to understand evolution of genetic code together with structural and functional analysis of prebiotic proteins. The repertoire of amino acids in the first proteins was probably developing in time and it influenced the development of structure and function of today's proteins. First amino acid alphabet was apparently only half of the size of present alphabet, which contains twenty amino acids. These ten amino acids were probably prebiotically available from endogenous and exogenous sources. This work includes cell-free expression and purification of two randomized protein libraries (containing approximately 1011 variants) with various amino acid composition and following comparison of their propensity to form secondary (using circular dichroism) and tertiary (using proteolytical analysis of sequences) structures. First library contains only ten probably prebiotically available amino acids; second library contains all twenty amino acids in today's genetic code. This project could help us understand benefits of genetic code expansion in terms of developing structure in protein sequences. The whole research could theoretically contribute a few basic questions not only in the fields of protein evolution but also in areas of synthetic biology or protein...

In the presented work we study the XML data evolution, reasons and consequences of XML schema evolution in particular. The thesis contains a survey of the existing approaches to this problem. The approach presented in this work extends the XSem conceptual model with the support for multiple versions of the model. Thanks to this extension, it is possible to define a set of changes between two versions of a schema. The thesis contains a description of an algorithm that compares two versions of a schema and produces a revalidation script in XSL.

Latitudinal diversity gradient is one of the oldest known trends in the distribution of life on the Earth. Scientists have been trying to find causes of its formation for more than two hundred years. There are several hypotheses suggested to explain this gradient. Recently, it is one of the main themes of discussion among ecologists and evolutionary biologists. By this Thesis, I will try to contribute to understanding of processes that generate the latitudinal diversity gradient. Particularly, I study if there is a relationship between ambient temperature and diversification rate. Is this relationship different for individual groups of animals? I choose birds as a model group. Specifically, these six families of birds: Accipitridae, Columbidae, Furnariidae, Picidae, Psittacidae and Strigidae. These groups include more than 1500 species. Each of them has the same universal gradient of diversity, with the highest diversity concentrated in the tropics. My objective was to find out, whether the universal gradients of bird's diversity had been shaped by the same historical processes. Or alternatively, whether different evolutionary trajectories had converged to the same gradients. The main outcome of my work is a discovery that some of the selected families diversified faster in warmer climates...

Bichirs, Polypteriformes, are a basal group of vertebrates with many unique characters as ganoid scales, fleshy pectoral fin, spiraculum or paired lung originated from ventral outpocketing from floor of pharynx. Among the most notable is also the dentition, which contatin teeth among whole area of oropharyngeal cavity. This arrangement is not easily call oral and pharyngeal, what is recently used e.g. for medaka, because it is only one dention with teeth on majority of oral as well as pharyngeal elements. This diploma thesis utilizes expression patterns of Dlx genes to visualize morphogenesis of dentition and pharyngeal arches in the Senegal Bichir (Polypterus senegalus). The very first developing teeth of oral dentition, as well as its further patterning were detected and accurately located using gene expression analyses. It was also discovered an interesting histological context connected with unique mouth opening mechanism during early development of teeth in oral cavity. Another discussion point is establishment of dorsoventral polarization in pharyngeal arches development of bichir based on results from Dlx gene expression analysis. Powered by TCPDF (www.tcpdf.org)

Subfamilies Rygmodinae and Sphaeridiinae together form approximately one third of the extant diversity within the family Hydrophilidae (Coleoptera: Polyphaga). Members of both these subfamilies inhabit wide spectrum of aquatic and terrestrial environments including specialized habitats such as phytotelmata, carrion or termite nests. So far, habitat shifts within these subfamilies have been only tested with a limited amount of taxa at the family level. Using a broader sampling and Bayesian and maximum likelihood methods, genus-level molecular phylogenetic analysis and divergence dating were performed. The dataset included 96 taxa, representing all major clades (genus groups) in both subfamilies, sequenced for two mitochondrial and two nuclear genes. A single shift from the aquatic to terrestrial environment in the Middle Jurassic was suggested, thus revealing both subfamilies and all tribes as ancestrally inhabiting decaying plant material and leaf litter. Secondary returns to aquatic habitats were suggested for two lineages of the Rygmodinae and several lineages belonging to tribes Coelostomatini and Megasternini. A single shift to flowers was revealed in the subfamily Rygmodinae. Similarly, single independent shifts to the inquiline lifestyle in tribes Omicrini and Megasternini were revealed. In...

4 Neural crest-derived cellular cartilage is one of the defining characteristics of vertebrates. Elaboration of this tissue and its patterning allowed the evolution of jaws in the gnathostome lineage. Together these hallmarks helped jawed vertebrates become one of the dominant taxons in the animal kingdom. Lampreys, as basal jawless vertebrates, lie at a unique phylogenetic position that makes them ideal organisms for the study of evolution of vertebrate/gnathostome novelties. Larval lampreys possess a special oral skeleton composed of a tissue related to cartilage, termed mucocartilage. Despite considerable attention that has been paid to the evolutionary significance of mucocartilage, it is not yet clear, how this unique feature arises in development and to what extent it is homologous to gnathostome jaws. In this study, the development of oro-pharyngeal region was analyzed in the sea lamprey Petromyzon marinus. SEM imaging revealed shaping and topographic relationships of embryonic tissues, detailed plastic histology coupled with expression analyses of several molecular markers were used to describe origin, histogenesis and morphogenesis of mucocartilage. Furthermore, genetic regulation of the tissue was investigated in order to identify its unique or shared features. Mucocartilage is seen to...

The variability of the genome size reaches several grades even within relatively close groups of plants. The study of the genome size in the phylogenetic context provides interesting results which characterize the evolution of the individual groups of plants. In this respect, tropical plants have yet not been studied. Tropical genus Globba (ca. 100 species) belongs to an economically significant family Zingiberaceae. The diversity centre is found in Thailand but it spreads from east India and southern China up to Indonesia and the Philippines. It is a polyploid complex which exists in two cytotypes within one genus (2n = 32 a 2n = 48); it is characteristic minimally in three out of seven distinguished sections. The aim of this thesis has been a reconstruction of the group phylogeny, discovering the role of the polyploid and evaluation of the genome size evolution of the Globba genus in the phylogenetic context. To this end, modern biosystematic methods were used (flow cytometry, chromosome counting, sequencing of the nuclear and chloroplast DNA regions). Many types of software and statistical methods were used to process and interpret the data. In this group, the genome size was measured for the first time. Out of 87 individuals, the smallest size was measured with Globba nuda (2C = 1.11 pg). The...

Mitochondrion is believed to be an ubiquitous organelle which occurred about 1,5 billion years ago by a single endosymbiotic event. Mitochondria is mostly dependent on the protein import from cytosol thus the establishment of protein import machinery was essential for seizing the new endosymbiont. Possibilities of studying the evolution of protein import machineries are quite limited given that no "free living" mitochondria or amitochondriate organisms are known nowadays. One alternative is to study mitochondrial secondary reductive evolution of anaerobic parasitic protists. Giardia intestinalis is flagellated protozoan living in microaerofilic environment of the small intestine. It containes one of the most reduced mitochondrion (mitosome) described so far. Hence it serves as a great model for studying mitochondrial evolution. Although it is well understood that all mitosomal proteins are transported from cytosol, many aspects of protein import pathway remain elusive. While the main channel Tom40 is present in the outer membrane, two other main translocases (Sam50 which is required for betta-barrel assembly in the outer membrane and Tim17/22/23 which is essential for protein translocation through the inner membrane) have not been identified so far. Protein translocation through Tim17/22/23 channel...

Tree-based genetic programming (GP) has several known shortcomings: difficult adaptability to specific programming languages and environments, the problem of closure and multiple types, and the problem of declarative representation of knowledge. Most of the methods that try to solve these problems are based on formal grammars. The precise effect of their distinctive features is often difficult to analyse and a good comparison of performance in specific problems is missing. This thesis reviews three grammar-based methods: context-free grammar genetic programming (CFG-GP), including its variant GPHH recently applied to exam timetabling, grammatical evolution (GE), and LOGENPRO, it discusses how they solve the problems encountered by GP, and compares them in a series of experiments in six applications using success rates and derivation tree characteristics. The thesis demonstrates that neither GE nor LOGENPRO provide a substantial advantage over CFG-GP in any of the experiments, and analyses the differences between the effects of operators used in CFG-GP and GE. It also presents results from a highly efficient implementation of CFG-GP and GE.

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