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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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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 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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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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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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Unveiling hidden species diversity in desmids (Desmidiales, Viridiplantae)
Šťastný, Jan ; Neustupa, Jiří (advisor) ; F.M. Coesel, Peter (referee) ; Kaštovský, Jan (referee)
The delineation of desmid species was traditionally based on purely morphological features. However, a frequent misinterpretation of morphological variability in desmids has led in the past to extensive taxonomical confusion within this important group of green algae which complicates the interpretation of their biodiversity in freshwater ecology, biogeography and biomonitoring. Consequently, I focused in this thesis predominantly on a previously neglected issue, the application of polyphasic approaches in the species-level taxonomy of desmids. In the most studies, a combination of both traditional morphological and modern molecular phylogenetic and geometric morphometric methods has been used to evaluate the taxonomy of selected desmid species, particularly representatives of the morphologically complex genera Micrasterias and Xanthidium. In two papers, I used the combination of traditional morphological and autecological data to clear up the taxonomy of several morphologically less prominent desmid taxa. Generally, the results of the thesis demonstrated that the way we recently see the diversity and distribution of desmids should be thoroughly changed. The real species diversity is mostly distinctly finer than that estimated by classical morphological taxonomy, often corresponds to varieties of...
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Molecular phylogeny and evolutionary trends in Hieracium (Asteraceae, Lactuceae)
Krak, Karol ; Fehrer, Judith (advisor) ; Zozomová, Judita (referee) ; Nieto Feliner, Gonzalo (referee)
The hawkweed subgenus Hieracium s. str. is notoriously known for its extreme morphological variability and variation in ploidy levels that is associated with differences in modes of reproduction. Extensive past hybridization is supposed for the subgenus, but recent hybridization was evidenced only in few cases. The subgenus attracts the attention of botanists already for more than a century. Therefore the species diversity is largely examined and the taxonomy of the subgenus is well elaborated, although several contradictory taxonomic concepts exist. However the relationships among the species are unknown and haven't been studied yet. The investigation of these relationships from a phylogenetic perspective using molecular approaches was the main aim of the presented thesis. Basic species (both diploid and polyploid), representing morphologically unique taxa, that are supposed to be the basic evolutionary units of the subgenus were studied. The sequences of two intergenic spacers of the cpDNA (trnT-trnL and trnV-ndhC) and the external transcribed spacer of the nuclear ribosomal DNA (nrDNA ETS) were analyzed. Moreover, three new low-copy nuclear markers with higher variability than nrDNA and cpDNA markers were developed and their suitability for phylogenetic studies in Hieracium s. str. was...
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