Phylogeography of temperate plant species with the focus on Central Europe Ph.D. Thesis Hana Daneck Charles University Prague Faculty of Science Department of Botany Supervisor: Prof. RNDr. Karol Marhold, CSc. Consultant: Mgr. Tomáš Fér, Ph.D. Praha 2012 2 Summary This thesis presents contribution to clarification of postglacial history of temperate plant taxa in Europe with the focus on especially interesting region of Central Europe, for which diverse roles in postglacial plant histories were suggested. The first part of the thesis summarises general phylogeographical views and methodological approaches with the respect to species history after the last ice age in Europe. Further, the most important aspects of phylogeography of European temperate plant taxa are discussed. The second part contains a set of papers dealing with selected European temperate plant species, for which phylogeographical patterns throughout their present distribution area were inferred, including assumptions on the origin of their contemporary Central European populations and comparisons with another previously studied species. Paper 1: Phylogeographic pattern of the European forest grass species Hordelymus europaeus: cpDNA evidence. This paper presents phylogeographical pattern based on chloroplast haplotype variation covering the...

The aim of this semestral project is to try to study and describe work with sequences of proteins of different organisms, namely above all alligment sequences and evaluation of similarities of sequences. At the beginning of this work we deal with biochemistry of proteins, their constitution and structure. Further text go on with theory for work with sequential data, global, local and multiple assignment. At the last part we investigate possibilities of programme Matlab for aforesaid assignment.

Colouration is an important phenotypic trait of animals and plays a substantial role in the characteristics of individual animal species. The MC1R gene has an essential role in colouration. This thesis is focused on the study of sequence variability in this gene and subsequent phylogram formation in selected species, which are: Bos Primigenius Taurus, Sus Scrofa, Equus Caballus and Canis Lupus Familiaris. There were custom primers designed in Oligo for the selected exon sequence. Based on se-quencing, known polymorphisms in Canis Lupus Familiaris and Equus Caballus were detected. In Canis Lupus Familiaris sequence, there was a 790 A>G polymorphism. All of N sequenced samples (N = 10) carried the E (790AA) allele. In Equus Caballus se-quence, there was a 901 C>T polymorphism, with representatives of all genotypes nEE(901CC) = 2, nEe(901CT) = 2, nee(901TT) = 6. The thesis also provides a comprehensive overview of the phylogenetic tree for-mation process. For phylogenetic analysis, there were added sequences from other ani-mal species, gained from freely available genomic databases. The reconstruction took place in the MEGA X program with selected distance and sign methods. Only nodes with bootstrap support ≥ 70 could be interpreted. JC69 and HKY85 models were cho-sen as substitution models. The choice of models was statistically supported by testing likelihood in the Model Generator with P < 0,0001 support. The trees obtained by par-ticular methods were compared by the Pearson correlation coefficient.

In the plant kingdom, only about one tenth of the species have different sexes. Since plant sex chromosomes are in general younger (and not always distinguishable from autosomes) than animal sex chromosomes, it is interesting to analyze them. This data can then be used in agricultural research in terms of growing exlusively one type of sex or using sex-linked genes for breeding. Because of polyploidization and long-term selection of only agriculturaly advantageous features, it seems fit to find a model plant which has not been subjected to artificial selection and could be used for the study of natural genome evolution. In this study, we chose Mercurialis annua and its close relative Mercurialis huetii for comparative analysis of their genomes and sex chromosomes which seem to be undergoing the first stage of degeneration.

This master thesis deals with the detection and recognition of faces in the image. The content of this thesis is a description of methods that are used for the face detection and recognition. Method described in detail is the principal component analysis (PCA). This method is subsequently used in the implementation of face recognition in video sequence. In conjunction with the implementation work describes the OpenCV library package, which was used for implementation, specifically the C ++ API. Finally described application tests were done on two different video sequences.

This thesis follows up a cognitive psychological phenomenon, called boundary extension. This effect describes a situation, when we remember parts of a scene during scene perception, which could be located outside of the frame, but we actually did not see it. The literary review part offers up summary of fundamental findings of approximately thirty years of research of this phenomenon. The research part submits an experiment examining a boundary extension in panoramic photographs with respect to an effect of multiple factors, a sequence length (nine and thirteen frames), a type of sequence (indoor and outdoor), a target picture size (normal, close-up, wide-angle). This experiment is the first larger study of boundary extension in Czech population and the examined effect of factors was not experimentally verified in previous studies. Keywords Boundary extension, panoramic photographs, sequence length, type of sequence, target picture size

This thesis summarizes ways of representation of biological sequences and file formats used for sequence exchange and storage. Next part deals with techniques used for sequence pairwise alignment, followed by extension of these techniques to the problem of multiple sequence alignment. Additional methods are introduced, that are suboptimal, but on the other hand are able to compute results in reasonable time. Practical part of this thesis consists of implementing multiple sequence alignment application in Java programming language.

The majority of the mitochondrial proteins is synthetized on the cytosolic ribosomes in the form of the protein precursors bearing mitochondrion-targeting signal presequences. Once the protein precursor has reached the mitochondrial matrix the signal presequence is no longer necessary and is cleaved off by heterodimeric mitochondrial processing peptidase (MPP; α/β). Although the crystal structure of MPP is available, the MPP mechanism of function is still matter of discussion. An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the regulatory α-subunit of the yeast MPP. Wild-type and GRL-deleted MPP structures were studied both in the presence and absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the peptidase active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the α-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at...

In domesticated animals there are many different coat colours and mutations, often connected with pleiotropic effects. The aim of this thesis named The study of colour genes sequences in chinchilla based on homology of human and mice sequences was describe molecular genetic principles of pigmentation, introduce genes involved in melanogenesis and influencing a melanin function, their structure, mutations and mention other mutations which change the phenotype. Informations about alleles TYR, TYRP1, TYRP2/DCT, agouti, AGRP, gene group MCR (MC1R-MC5R) and more are focused on human (Homo sapiens), mouse (Mus musculus) and chinchilla (Chinchilla lanigera). In these three species was compared selected genes sequences TYR and TYRP2/DCT, results were studied, commented and mutations, which are very specific, but there are some analogs between human and mouse, were highlighted.

This master thesis purposes is create localization system using software defined radio. The purpose of this thesis is to create new localization system, which will be independent of existing systems. To create a localization system, we will use ADALM-PLUTO device to send and receive radio signals. This work contains a decription of serval possibilities how to create the localization system and description of their comunication.