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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Diversity and phylogeny of symbiotic partners in zeorin-containing red-fruited Cladonia species.
Steinová, Jana ; Škaloud, Pavel (advisor) ; Pérez-Ortega, Sergio (referee) ; Vondrák, Jan (referee)
Lichens are a classic example of mutualistic symbiotic associations, yet the views on lichen symbiosis have changed considerably during the last fifty years. Nowadays, lichens are generally understood to be microecosystems consisting of several symbiotic partners which contribute in different ways to the prosperity of the whole system and which differ by the strength of their bond to other symbiotic partners. The level of knowledge of the individual partners (mycobionts vs. photobionts vs. bacteria) varies greatly in terms of their specificity, diversity and in the forces that shape this diversity. The main aim of this work was to reveal the diversity of organisms participating in lichen symbiosis and to better understand the biological forces which shape this diversity. We worked with a relatively common lichen group, zeorin-containing red-fruited Cladonia species, and specifically, we focused on the mycobionts, photobionts and bacteria that participate in this association. During the course of the study, it became apparent that species delimitation, which is a fundamental requirement for accurate diversity estimates, is another topic that requires further research. Our analyses revealed that species circumscription of most of recently recognized Cladonia mycobionts cannot by supported by...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Species delimitation in lobose amoebae
Foučková, Martina ; Čepička, Ivan (advisor) ; Škaloud, Pavel (referee)
Lobose amoebae - amoebas that create lobopodia - are distributed among the supergroup Amoebozoa, Excavata, Rhizaria and the genus Anaeramoeba (Eukaryota incertae sedis). For their species delimitation (i.e., pinpointing boundaries between particular species), morphological features are used most often, such as the size and shape of the cell, appearance of the hyaloplasm, pseudopodia and subpseudopodia, granuloplasm with cytoplasmatic inclusions, number and size of nuclei, shape of the uroid and cysts if present. The morphological characteristics are easily documented using a light microscope. Ultrastructural features, such as the ultrastructure of nuclei and nucleoli, surface structures, and organelles, are used as well. Nowadays, species are also described and distinguished employing molecular methods, mostly analyses of the SSU rRNA and actin genes, COI barcoding, and ITS sequences, which allow detection of cryptic species. Before the sequencing era, RFLP, RAPD and isozymes methods were also used for delimitation of species. This thesis focuses on particular methods and features used for species delimitation of lobose amoebae on the basis of 125 selected species belonging to Amoebozoa (orders Acanthamoebida, Pellitida, Himatismenida, Dermamoebida, Thecamoebida, Vannellida, Dactylopodida,...
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Diversity and distribution of the Euastrum humerosum / didelta (Desmidiales) species complex
Kupčíková, Eva ; Šťastný, Jan (advisor) ; Kollár, Jan (referee)
From 23 European and North American strains Euastrum humerosum/didelta species complex (Desmidiales) I have obtained 3 lineages in molecular marker trnGucc group II intron. I did not acquire significant and homogenous results in SSU intron. It is probable that the lineages of trnGucc intron are very young. SEM revealed one central pore in cell wall and five bulges. The lineages were significantly different in their shape and dimensions. The lineages differentiated mainly in their length and breadth of the cells. The lineages inside morphotype E. humerosum differentiated in shape and dimensions of the polar lobe. The lineages inside morphotype E.didelta differentiated in shape and dimensions of the neck. That was ascertained using the geometric morphometrics with the measuring. Linear discriminant analysis of the desmids from literature revealed that is possible to partly discriminate groups of the varieties (E. humerosum var. parallelum and E. didelta in lineage A; two formae E. didelta f. val Piora and E. didelta f. latior in lineage B; E. didelta var. inermiforme and E. humerosum var. affine in lineage C). Key words: desmids, species, hidden diversity, molecular phylogenetics, geometric morphometrics, Euastrum, scanning electron microscopy
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Diversity and phylogeny of symbiotic partners in zeorin-containing red-fruited Cladonia species.
Steinová, Jana ; Škaloud, Pavel (advisor) ; Pérez-Ortega, Sergio (referee) ; Vondrák, Jan (referee)
Lichens are a classic example of mutualistic symbiotic associations, yet the views on lichen symbiosis have changed considerably during the last fifty years. Nowadays, lichens are generally understood to be microecosystems consisting of several symbiotic partners which contribute in different ways to the prosperity of the whole system and which differ by the strength of their bond to other symbiotic partners. The level of knowledge of the individual partners (mycobionts vs. photobionts vs. bacteria) varies greatly in terms of their specificity, diversity and in the forces that shape this diversity. The main aim of this work was to reveal the diversity of organisms participating in lichen symbiosis and to better understand the biological forces which shape this diversity. We worked with a relatively common lichen group, zeorin-containing red-fruited Cladonia species, and specifically, we focused on the mycobionts, photobionts and bacteria that participate in this association. During the course of the study, it became apparent that species delimitation, which is a fundamental requirement for accurate diversity estimates, is another topic that requires further research. Our analyses revealed that species circumscription of most of recently recognized Cladonia mycobionts cannot by supported by...
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Diversity and distribution of the Euastrum humerosum / didelta (Desmidiales) species complex
Kupčíková, Eva ; Šťastný, Jan (advisor) ; Kollár, Jan (referee)
From 23 European and North American strains Euastrum humerosum/didelta species complex (Desmidiales) we have obtained 3 lineages in molecular marker trnGuuc group II intron. We did not acquire significant and homogenous results in SSU intron. It is probable that the lineages are very young. The lineages were significantly different in their shape and dimensions. We used the geometric morphometrics with the measuring of the lengths and breath of the semicells, isthmus and their ratios. The lineages differentiated in their dimensions and shape variable polar lobes and neck. SEM revealed the one central pore in cell wall on the contrary, with variant E. didelta var. bengalicum, which has two pores according the literature records. Key words: desmids, species, hidden diversity, molecular phylogenetics, geometric morphometrics, Euastrum, scanning electron microscopy
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Molecular genetic study of the emballonurid bats (Emballonuridae) of the Middle East and adjacent regions
Uvizl, Marek ; Benda, Petr (advisor) ; Vallo, Peter (referee)
The Middle East is occupied by three species of family Emballonuridae which are morfologically divided into several subspecies. Those could be defined only poorly and intraspecific diversity of these species is resolved unsatisfactorily. This is the reason why the molecular genetic analysis, which can revise the diversity on the new unused level, were used in this thesis. Based on data from sequencing of both mitochondrial and nuclear markers the phylogenetic analysis was performed. That analysis adds new information about interspecific and intraspecific relationships among populations of this family in this area. Bats (Chiroptera) of the family Emballonuridae are characterised by tail perforating the uropatagial membrane on its dorsal side in the half of its lenght and by reduction of the phalangi which makes long and narrow wing. The family is widespread circumtropically and is divided into two subfamilies. The subfamily Emballonurinae could be sometimes diveded into two tribes, new-world Diclidurini and old-world Emballonurini. The representatives of the subfamily Taphozoinae occur only in the Old World. Middle East is occupied by three species of this family. Coleura afra inhabits only southern Arabic peninsula and the populations from this area are ranked in subspecies C. a. gallarum....
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Evolutionary history of Parnassiinae
Kaman, Ondřej ; Čepička, Ivan (advisor) ; Král, David (referee)
This review is devoted to the evolutionary history of the Parnassiinae subfamily of the family Papilionidae and particularly to the nominate genus Parnassius which is the main group among the eight extant Parnassiinae genera. At first, the taxonomic concept, monophyly, and phylogenetic position of Parnassiinae are thoroughly discussed. It is shown that all its genera form three clades that are currently classified as tribes. Further, the estimated time of the divergence of Parnassiinae is given together with the description of all fossil taxa. The subsequent part is entirely focused on Parnassius whose internal phylogeny largely corroborates the traditional classification on eight subgenera, although the phylogenetic relationships among these clades remain mostly unresolved. All the clades are systematically discussed and interesting phylogenetic cases of species complexes and closely related taxa are analysed and supplemented by taxonomic remarks. The last three chapters are dedicated to the phylogeography of P. mnemosyne, P. apollo, and P. phoebus complex. Their evolutionary history is discussed in relation to glacial events in Pleistocene and warming of the climate in Holocene. The whole treatment attempts to integrate morphological, molecular, and biogeographical views together in order to provide a...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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