|
|
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.
|
|
|
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.
|
|
|
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.
|
|
|
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...
|
|
|
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.
|
|
|
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.
|
|
|
Blood parasites of fish from Svalbard
POSPÍŠILOVÁ, Iva
This thesis reviews knowledge about diversity of blood parasites of fish. Blood smears of fish used in this study were obtained in Billefjorden (Svalbard archipelago, Arctic). Desseria myoxocephali, the type species of Desseria, is the only one parasite that was found in the smears. A partial 18S rDNA sequence of D. myoxocephali was prepared and phylogenetic analyses were computed. D. myoxocephali forms a lineage together with Dactylosoma ranarum and Babesiosoma stableri within adeleorinid clade.
|
|
|
Molecular analysis of the mitochondrial genom of \kur{Diuraphis noxia} (Aphididae)
CHUNDELOVÁ, Daniela
The complete sequence of mitochondrial DNA from Diuraphis noxia was obtained and characterized. The mitogenome contains a standard set of 13 protein-coding genes, 19 tRNA genes, 2 ribosomal RNA genes. A+T-rich and ?repets? regions in the same order as those of the other analyzed aphids. Comparison to mtDNAs from other Sternorrhyncha species obtained from GenBank revealed possible markers for studies on population differentiation. Phylogenetic analysis using parsimony and maximum likelihood confirmed the classification of Diuraphis noxia into the Aphididae.
|
|
|
Molecular identification and phylogeny of \kur{Chlorella} spp. production strains utilized in algal biotechnologies
VODIČKA, Tomáš
Green algae are quite important primary producers in fresh waters. The genus Chlorella represents one of algae most frequently utilized in algal biotechnologies to produce biomass, using either autotrophic or heterotrophic cultivation systems. It is than exploited as a food supplement for humans or animals. However, particular species within the genus are morphologically indistinguishable and molecular markers should be used to characterize production strains. This work is aimed to molecularly characterize three production strains of Chlorella for patent protection purposes and to specify their phylogenetic and taxonomic position.
|
|
| |
guest ::
