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Encystation and life cycle of free living amoebae of the genus Acanthamoeba spp.
Bínová, Eva ; Nohýnková, Eva (advisor) ; Dyková, Iva (referee) ; Ondriska, František (referee)
Amoebae of the genus Acanthamoeba spp. are free-living unicellular organisms found in disparate ecosystems all over the world. Due to their ability to invade human body, evade its defensive mechanisms and cause extensive tissue damage, Acanthamoeba infection can lead to serious, if rare, diseases, affecting most commonly the eye and the central nervous system. Specific therapy for Acanthamoeba infections is not available. A major reason for therapeutic failure in ameobiasis is the ability of the protist to differentiate into resistant stages. These are cysts, known to be formed under prolonged unfavorable conditions, both in the environment and the infected tissues, and the pseudocysts, less durable but rapidly formed under acute stress. The present thesis focuses on as yet unexplored mechanisms of resistance of cysts and pseudocysts. Moreover, further characteristics distinguishing cysts and pseudocysts as well as the processes involved in their formation are investigated. One of the issues addressed is a presence of protective carbohydrate compounds mannitol and trehalose that participate in defensive reactions against abiotic stress in many organisms. Although putative genes for enzymes of the trehalose and mannitol synthetic pathways are present in the genome of Acanthamoeba, only one of the...
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Evolution of brain size in birds
Straková, Barbora ; Němec, Pavel (advisor) ; Remeš, Vladimír (referee)
Vertebrates show dramatic interspecific variation in the size of their brains. The complexity of brains is considered to be the key factor of evolutionary success in Vertebrates, and therefore an evolutionary trend towards increasing brain size and coplexity is assumed. Large and complex brains evolved independently in birds and mammals. Birds have brains that are comparable in their relative size to the brains of mammals. However, in stark contrast to mammals, there is no general trend towards increase of brain size in birds. Relatively large brains have evolved independently in many avian lineages. Highly encephalised orders are parrots (Psittaciformes), woodpeckers and relatives (Piciformes), hornbills, hoopoe and wood hoopoes (Bucerotiformes), owls (Strigiformes), storks (Ciconiiformes) and several families of songbirds (Passeriformes), mainly bowerbirds (Ptilorhynchidae) and corvids (Corvidae). Otherhighlyencephalizedgroupsarenon-parasiticcuckoos(genusCentropus,Phaenicophaeus and Coua) and family Diomeidea and genus Pelecanus belonging to the clade water birds. Less encephalized groups include the basal lineages such as paleognaths and fowl (Galloanserae), and also pigeons (Columbiformes) and swifts, treeswifts and hummingbirds (Apodiformes). We suggest that this mosaic evolution is result of...
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Verification of species boundaries in clinically relevant Arthroderma species
Míková, Ivana ; Hubka, Vít (advisor) ; Dobiáš, Radim (referee)
The genus Arthroderma contains predominantly geophilic dermatophytes (naturally occuring in soil). Some species, especially those from Trichophyton terrestre complex, cause human and animal dermatomycosis. In the past, the species boundaries were determined mainly on the basis of biological species concept using in vitro mating experiments. But these nearly 70-years-old findings have not been tested by means of modern taxonomic methods. In total 194 species of the genus Arthroderma (including all available ex-type strains) originating predominantly in USA, Canada and Europe were studied in this thesis. They were mostly isolated from soil (n = 77), animals (n = 50), human clinical material (n = 41) and cave sediment (n = 9). The main goal of the thesis was to elucidate the species boundaries between species A. insingulare, A. lenticulare and A. quadrifidum, that were classified into the T. terrestre complex because of their seemingly identical asexual stage. Further, this work aimed to resolve the relationship between Arthroderma species using the multigene phylogeny and clarify which species are clinically relevant. A multigene phylogeny of the genus Arthroderma was based on the sequences of the ITS rDNA region, β-tubulin (TUB2) and translation elongation factor 1α (TEF1α) genes. The genus...
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Genetic diversity of two freshwater molluscs - Anisus vorticulus and Aplexa hypnorum - in central Europe
Buďová, Jana ; Černý, Martin (advisor) ; Štefka, Jan (referee)
The aim of my study was to sum up the data about genetic variability of freshwater gastropods living in temporary ponds. My model species were moss bladder snail (Aplexa hypnorum) and the critically endangered ramshorn snail (Anisus vorticulus). Genetic variability was investigated by two mtDNA and two nuclear markers. The differences in genetic variation at the COI gene follow the pattern of different catchments. However, these findings do not agree with the patterns derived from genetic markers ITS1 and 16S. The reasons for the differences between the different markers are discussed in several ways involving few possible historical scenarios, but also possible errors of laboratory methods. In this study, there was only little success in amplification and the most likely reason is the inhibitory effect of snail mucus on DNA amplification. Another problem that occurred when this work was to obtain the sequence of the parasite (fluke) instead Anisus gene using gastropod specific primers. In addition to genetic and related methodological part of this work is the third part concerning the evaluation of environmental factors periodic pools in the presence and absence of the species studied. The fourth part sis focused on the phylogenetical analyses of the european and american Aplexa linneages. Powered by TCPDF...
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Molecular methods used for taxonomy and epidemiology of dermatophytes
Čmoková, Adéla ; Hubka, Vít (advisor) ; Hamal, Petr (referee)
In my bachelor thesis I have dealt with the role and aplication of the molecular methods in the taxonomy and epidemiology of the dermatophytes and the question of the species concepts in dermatophytes. In the first part, I focused on the evaluation of the advantages and disadvantages of the recent species concepts and their problematic application in dermatophytes. The second part is focused on the molecular methods that used genetic markers for phylogenetic analysis and species delineation within dermatophytes, e.g. the PCR-RFLP method, PCR-fingerprinting and DNA sequencing. I have evaluated the dicrimination power of the particular DNA sequence loci to distinguish closely related species. In the last part, I have summarized the molecular methods that have been used in the typization at the intraspecific level, e.g. microsatelite analysis, PCR-fingerprinting, multilocus sequence typing.
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Molekulárně-fylogenetická charakteristika izolátu Hymenolepis diminuta udržovaného v laboratorních podmínkáh
ŘEŽÁBKOVÁ, Lucie
The main goal of the present study was to confirm the possibility of cryptic diversity within Hymenolepis diminuta group of tapeworms. We used molecular-fylogenetic analyses for characterization of the intraspecific genetic diversity of five isolates of Hymenolepis diminuta. Further, we wanted to compare our isolate of H. diminuta that is tested for purposes of the helminth therapy with other isolates obtained from collaborative institutions. Our results showed no cryptic diversity within H. diminuta clade of the five isolates and confirmed that our isolate is really H. diminuta previously characterized only based on its morphology.
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Phylogenetic assesment of cultural characters
Gillová, Lucie ; Frynta, Daniel (advisor) ; Rexová, Kateřina (referee)
Phylogenetic methods have been used for analysing cultural characters extensively in the last ten years. This bachelor thesis starts with a brief overview and characteristics of the methods used for these analyses and then it deals with all three main fields where these methods have been applied. The first one of them is the analysis of manuscripts and their relations which is unique in that even non-cladistic methods bring usually good results. The second field discussed in this thesis is the anthropological characters, including both artefacts of material culture and various features of social orders. The last one deals with the analysis of languages and language families. In all the chapters, different approaches to different data are listed and the most important studies are described in detail. The thesis also attempts to find negative and positive sides of different approaches.
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Molecular-biological characterization of Potato virus M and Potato leafroll virus
Vaculík, Petr ; Čeřovská, Noemi (advisor) ; Fousek, Jan (referee)
The main aims of diploma thesis were: 1) The sequence analysis of the Czech isolate of Potato virus M (PVM) VIRUBRA 4/009 and phylogenetic analysis of PVM coat proteins sequences 2) The bacterial expression of recombinant triple gene block protein 1 (TGB1) of PVM derived from the Czech isolate VIRUBRA 4/007 3) The construction of expression cassette of Potato leafroll virus (PLRV) coat protein and its transformation into A. tumefaciens for transgenic PLRV resistant plant formation In theoretical part of the thesis the taxonomic classification, morphology, genomic structure and virus transmission are discussed. Furthermore, the main rules concerning the bacterial expression of recombinant proteins and construction of transgenic plants using A. tumefaciens are described. Methodical part is devoted to description of generally used molecular biological and immunochemical methods. The following results were obtained in the thesis: The complete nucleotide sequences of open reading frames coding for three movement proteins (Triple gene block -TGB), coat protein and NA-binding protein of PVM isolate VIRUBRA 4/009; phylogenetic analysis was performed; the TGB1 protein was expressed in bacterial cells and will be used for polyclonal antibodies raising. Finally, the expression cassette containing the PLRV...
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Predicting the Effect of Amino Acid Substitutions on Protein Function Using MAPP Method
Pelikán, Ondřej ; Vogel, Ivan (referee) ; Bendl, Jaroslav (advisor)
This thesis discusses the issue of predicting the effect of amino acid substitutions on protein function using MAPP method. This method requires the multiple sequence alignment and phylogenetic tree constructed by third-party tools. Main goal of this thesis is to find the combination of suitable tools and their parameters to generate the inputs of MAPP method on the basis of analysis on one massively mutated protein. Then, the MAPP method is tested with chosen combination of parameters and tools on two large independent datasets and consequently is compared with the other tools focused on prediction of the effect of mutations. Apart from this the web interface for the MAPP method was created. This interface simplifies the use of the method since the user need not to install any tools or set any parameters.
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Predictor of the Effect of Amino Acid Substitutions on Protein Function
Musil, Miloš ; Martínek, Tomáš (referee) ; Bendl, Jaroslav (advisor)
This thesis discusses the issue of predicting of the effect of amino acid substitutions on protein funkcion, based on phylogenetic analysis method, inspired by tool MAPP. Significant number of genetic diseases is caused by nonsynonymous SNPs manifested as single point mutations on the protein level. The ability to identify deleterious substitutions could be useful for protein engineering to test whether the proposed mutations do not damage protein function same as for targeting disease causing harmful mutations. However the experimental validation is costly and the need of predictive computation methods has risen. This thesis describes desing and implementation of a new in silico predictor based on the principles of evolutionary analysis and dissimilarity between original and substituting amino acid physico-chemical properties. Developed algorithm was tested on four datasets with 74,192 mutations from 16,256 sequences in total. The predictor yields up to 72 % accuracy and in the comparison with the most existing tools, it is substantially less time consuming. In order to achieve the highest possible efficiency, the optimization process was focused on selection of the most suitable (a) third-party software for calculation of a multiple sequence alignment, (b) overall decision threshold and (c) a set of physico-chemical properties.
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