|
|
Biology and evolution of termite genus Neocapritermes (Blattodea: Termitoidea: Termitidae: Termitinae)
Cintulová, Eliška ; Šobotník, Jan (advisor) ; Jakub, Jakub (referee)
My thesis is a brief summary of knowledge on termites, especially genus Neocapritermes. It describes ecology, nutrition, caste patterns and phylogenetics of termites. In detail, it characterizes Neocapritermes taracua, its ecology and defensive behaviour of workers. The main topic is formulation of phylogenetic hypothesis concerning position of genus Neocapritermes and relatedness among particular species of the genus. My results suggest that Planicapritermes and Dentispicotermes are the closest relatives of Neocapritermes, perhaps inner taxa located within the genus.
|
|
|
Molekulární fylogeneze a genetická diverzita nejbližších příbuzných rodu Pisum
Bačovská, Nela
Phylogenetics has given us a unique possibility to learn the history of species evolution and their interconnection on the planet. Our earlier relience only on outter morphological features for taxon classification is now being completed and even replaced by molecular-biological studies for clarification. It is possible to use our knowledge when searching for geographical origins of organisms, their expansion and change of genetic information, which are all the needed foundations for species diversification. In this work we used the family Fabaceae for the study of evolutionary genetics. Then we chose Lathyrus neurolobus for further examination of the potential use of SSR and iPBS markers for Pisum intergenus studies.
|
|
|
Analýza variability genomů Nepovirů (GFLV a ArMV) v produkčních vinicích vinařské oblasti Morava
Eichmeier, Aleš
The disertation thesis was focused on the analysis of variability of two nepoviruses genomes, Grapevine fanleaf virus -- GFLV and Arabis mosaic virus -- ArMV. The thesis described single isolates of these nepoviruses and their until recently non-explored genome portions coded by RNA1 strand, the coding regions for 1BHel and 1EPol proteins precisely. The main topic of this thesis was the identification of infected plants that were infected by nepoviruses GFLV and ArMV. Based on design of specific primers there was established sequence homology of coding sequences. Another topic was the development and optimalization of diagnostic system for the efficient GFLV and ArMV detection. This work was based on hypothesis of very high level GFLV and ArMV genomes variability. The results were recieved mainly from sequencing analyses performed by capillary automatic sequencer ABI-PRISM 310 (Applied Biosystems, Carlsbad, USA). Obtained results were assessed with CLC Main Workbench 5 software (CLC Bio, Aarhus, Denmark). Real-time PCR TaqMan multiplex was also designed using this software. This real-time tool is able to detect and quantify both nepoviruses within one PCR reaction simultaneously. There were sequenced and analysed the genetic codes at the nucleotide level for MP 2B , 2CCP, 1BHel and 1EPol proteins in this work. The first one was assessed because of the development of real-time PCR TaqMan multiplex. In this case were sequenced 290 bp from 14 GFLV and ArMV isolates, the variability level was established in frame of nucleotides 71.7-97.6%. The partial genetic code for 2CCP was assessed in frame of 6 GFLV isolates and the variability was established in 935 bp fragment to 83-86% at the nucleotide level and 81-91% at the amino acid level. The partial genetic code for 1BHel was sequenced in frame of 6 isolates GFLV and the variability was established in 379 bp in frame of all accessible GFLV and ArMV isolates, the variability was established 86.4-98.9% at the nucleotide level and 96-100% at the aminoacid level. The partial genetic code for 1EPol protein was sequenced in 6 GFLV isolates in frame of 365 bp and the variability was established for all accessible sequences in GenBank/NCBI. The variability was established at the nucleotide level 79.5-100% and at the aminoacid level 91.4-100%. All received sequences longer than 300 bp were submitted to GenBank/NCBI. The obtained partial genetic codes for 1BHel a 1EPol proteins coded in RNA1 were unique at the time of publication. This work provided the important results which were used subsequently like source information for construction of vectors intended for the preparation of transgenic plants. Then the incurred grapevine would show resistance against GFLV. Moreover, based on results of this work there was created certified methodology of the real-time PCR TaqMan multiplex method which can be standartly used as an efficient diagnostic tool for simultaneous detection of GFLV and ArMV. This real-time system was succesfully compared with ELISA what would be interesting mainly for diagnostic laboratories engaged in the certification processes of propagation material.
|
|
| |
|
|
Biological sequence classification utilizing lossless data compression algorithms
Kruml, Ondřej ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
Tato diplomová práce se zabývá možností využití bezeztrátových kompresních algoritmů ke klasifikaci biologických sekvencí. Nejdříve je představena literární rešerše o bezeztrátových kompresních algoritmech, která byla využita k výběru slovníkového algoritmu vytvořeného A. Lempelem a J. Zivem v roce 1976 (LZ77). Tento algoritmus je běžně používán k datové kompresi a v předkládané práci byl modifikován tak, aby umožnil klasifikaci biologických sekvencí. K algoritmu byly navrženy další modifikace, které rozvíjí jeho klasifikační možnosti. V průběhu práce byla sestavena sada datasetů biologických sekvencí, která umožnila podrobné testování algoritmu. Algoritmus byl porovnán s klasickými zarovnávacími metodami: Jukes-Cantor, Tamura a Kimura. Bylo ukázáno, že algoritmus dosahuje srovnatelných výsledků v oblasti klasifikace biologických sekvencí a dokonce je u 20% datasetů překonává. Lepší výsledky dosahuje zejména u sekvencí, jež jsou si vzájemně vzdálené.
|
|
|
Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
|
|
|
Bootstrap methods in phylogenetics
Sedlář, Karel ; Vohánka,, Jaroslav (referee) ; Škutková, Helena (advisor)
In recent decades, phylogenetic reconstruction has noted great development. It was achieved by using newly acquired molecular characteristics and processing that it began to be taken as an objective science. Rapid development showed that it is necessary to evaluate the results because new techniques provided phylograms from unreliable data. For these purposes, statistical sampling methods have been applied to the phylogeny, of which bootstrapping began later to dominate. However, it also has limitations, which should be considered during interpreting the results it provided to us. This work demonstrates by combining the principles of bootstrapping and consensus trees we can obtain phylograms with better properties than those of conventional phylograms.
|
|
|
Methods for phylogenetic supertree reconstruction
Kosíř, Kamil ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.
|
|
|
Biology and diversity of Cryptosporidium infecting squirrels (Sciuridae)
BARVÍŘ, Pavel
In total 399 samples from three species of squirrels (Sciurus vulgaris, Sciurus carolinensis and Callosciurus finlaysonii) were collected from 2010 to 2013. All samples were examined for the presence of Cryptosporidium using by molecular methods, which demonstrated by presence of Cryptosporidium specific DNA in 18 samples (4.5%). Out of them 12 samples were positive onCryptosporidium ferret genotype, 3 on Cryptosporidium skunk genotype, 1 on Cryptosporidium chipmunk genotype I and 2 samples onCryptosporidium ubiquitum. Statistical analyses did not reveal any influence of gender on the occurrence of Cryptosporidium. Juvenile individuals of squirrels from the family Sciuridae are more often infected by Cryptosporidium than the adult animals.
|
|
|
Diversity of Cryptosporidium spp. infecting rodents from subfamily Arvicolinae in the Czech Republic
HÁJKOVÁ, Ivana
Abstract In order to examine the prevalence of Cryptosporidium in wild Arvicolinae in the Czech Republic and understand the role that wild rodents play in the transmission of this parasite to humans and livestock, 152 faecal samples from 129 common voles (Microtus arvalis) and 23 bank voles (Clethrionomys glareolus) were collected on 9 localities in 2012. All samples were examined for presence of Cryptosporidium sp. using both the aniline-carbol-methyl violet staining method and molecular tools. The age, sex and faecal consistency were noted at the time of sampling. Microscopical examination revealed the presence Cryptosporidium sp. oocysts in 2 samples originated from common voles and 2 samples from bank voles. Genotyping was done through PCR amplification and characterization of the SSU rRNA and actin loci. Cryptosporidium specific DNA was detected in 10 samples (4 from common voles and 6 from bank voles) including those microscopically positive. Cryptosporidium infection was not linked to diarrhoea. Sequence and following phylogeny analyses revealed two new Cryptosporidium genotypes originated from bank voles and two new genotype from common vole, phylogeneticaly distinct from known species and genotypes. The host specificity needs to be verified by experimental infection in the future.
|
guest ::
