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In search of DUSP specificity
Sladeček, Stanislava ; Novotný, Marian (advisor) ; Martínková, Natália (referee)
Dual specificity phosphatases (DUSP) are enzymes that dephosphorylate both phosphoserine/threonine and phosphotyrosine residues on one substrate. Most of them specifically dephosphorylate family mitogen-activated protein kinases (MAPK). Number of DUSPs increases with complexity of organisms and in human genome there are 25 DUSPs described. Some DUSPs can dephosphorylate only one protein while other interact with wider spectrum of substrates. Except for substrate specificity DUSPs differ in expression, subcellular localization etc. Although first DUSPs were described about 20 years ago, a clear factor responsible for their substrate specificity is not known. This works uses in silico methods to discover and describe similarities and differences between DUSPs which may be important in determining DUSP specificity. Key words: phosphatase, kinase, DUSP, MAPK, substrate specificity, conservation of residues, phylogenetic tree, in silico methods
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In search of DUSP specificity
Sladeček, Stanislava ; Novotný, Marian (advisor) ; Martínková, Natália (referee)
Dual specificity phosphatases (DUSP) are enzymes that dephosphorylate both phosphoserine/threonine and phosphotyrosine residues on one substrate. Most of them specifically dephosphorylate family mitogen-activated protein kinases (MAPK). Number of DUSPs increases with complexity of organisms and in human genome there are 25 DUSPs described. Some DUSPs can dephosphorylate only one protein while other interact with wider spectrum of substrates. Except for substrate specificity DUSPs differ in expression, subcellular localization etc. Although first DUSPs were described about 20 years ago, a clear factor responsible for their substrate specificity is not known. This works uses in silico methods to discover and describe similarities and differences between DUSPs which may be important in determining DUSP specificity. Key words: phosphatase, kinase, DUSP, MAPK, substrate specificity, conservation of residues, phylogenetic tree, in silico methods
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Consequences of an infectious disease on genetic information in DNA sequences in bats
Nováková, Markéta ; Martínková, Natália (advisor) ; Lučan, Radek (referee)
Whitenose syndrome is an emerging fungal disease of bats causing massive dieoffs in North American populations. The fungus causes lesions on bat skin, mainly on noses, ears and wing membranes. The infection by the fungus is accompanied by serious disruption of metabolism and hibernation physiology that is lethal to bats in North America. European bats seem to survive the disease in greater numbers. Since the fungus is probably of European origin, this study assumes that bats in Europe have developed inheritable defence mechanisms to the disease. The infection by the fungus serves as a strong selective pressure. We tested sequences of 7 genes for signs of positive selection using maximum likelihood approach. We detected past positive selection in the gene for transglutaminase 1.
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Fylogeneze vybraných druhů letounů Afriky na základě cytogenetického a molekulárního přístupu
Koubínová, Darina ; Zima, Jan (advisor) ; Macholán, Miloš (referee) ; Martínková, Natália (referee)
Phylogenetic relationships of a sample comprising 248 bats belonging to 19 species and four families (Hipposideridae, Rhinolophidae, Molossidae and Vespertilionidae) from Senegal (Western Africa) were investigated with the use of multi-locus sequence data and non- differentially stained chromosomes. The karyotypes of Hipposideros ruber, H. tephrus, H. jonesi and H. cyclops were described for the first time. The standard Hipposideros formula was recorded in H. tephrus, H. jonesi and H. ruber (2n = 32, FNa = 60, FN = 64). The karyotypes of H. cyclops (2n = 36, FN = 66) and H. gigas (2n = 52, FN = 64) substantially diverged from this typical chromosomal complement. Rhinolophus landeri and R. fumigatus shared the same diploid number (2n = 58), but differed in the chromosome morphology (R. fumigatus - FNa = 60, FN = 64; R. landeri - FNa = 64, FN = 68). Rhinolophus landeri was found karyotypically distinct to other African populations, thus signalling a possible presence of cryptic forms within this species. The karyotypes of Chaerephon pumilus and Mops condylurus had a 2n = 48, FN = 54 and were similar to other previously studied species of this chromosomally conservative family. Chromosomal, Bayesian, maximum likelihood and genetic distance analyses revealed an indication for the existence of cryptic...
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Strategický management ve společnosti Continental Matador Rubber, s.r.o.
Martinková, Natália
This work deals with an examination of strategic management of the company CONTINENTAL MATADOR RUBBER, s.r.o., division Conveyor belts. The business of division is focused on production and sale of conveyor belts and equipment. This work is divided in two parts. There is the theoretic part and the practice part, where the theoretic knowledge from the theoretic part is applied. The main purpose of this work is to propose the strategy for division Con-veyor belts, which is based on results of strategic analysis. Strategic analysis, used in this work, consists of analysis of outer environment, analysis of inner environment and summarizing SWOT analysis.
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Reconstructing phylogeny from patchy data of rodents
Martínková, Natália ; Moravec, J.
To reveal phylogeny of sparsely sequenced taxa, standard methods could not be successfully used due to patchy character of data and new methods had to be developed. We summarize such methods and present their funcionality on phylogeny of Arvicolini voles. Analyzing tree space with terraces, we have found that supermatrix approach is superior to supertree approach in extracting signal from data and determining a resolved and well-supported phylogeny. The most widely used program from Bayesian phylogeny inference fails to determine the correct lengths of branches in a large supermatrix with a lot of missing data, it still successfully determines the true tree topology.
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Multilocus phylogeny of Sciurini tree squirrels
Pečnerová, P. ; Martínková, Natália
Phylogenetic relationships inside the tribe Sciurini produce conflict between older morphological research and modern molecular studies. We provided a detailed phylogenetic analysis by incorporating eight loci and various methods of data processing. We used prevailing and user-friendly software packages (Geneious, BioEdit, MrBayes, ModelTest). Evolutionary history of Sciurini squirrels was examined by means of Bayesian inference of concatenated data set and six supertree construction methods. The concatenated data and supertrees generated by SuperTriplets, modified MinCut, standard MRP and veto supertree (without source tree correction) yielded similar results with taxa grouped according to their zoogeographic distribution. The genus Tamiasciurus formed a separate evolutionary lineage at the base of our trees and the other taxa gradually diverged into Palaearctic/Indomalayan, Nearctic and Neotropical groups. The other used methods, MinCut, Purvis-MRP and veto (with source tree correction) showed deviations from this pattern.
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Tree of life in a gappy genomic era
Martínková, Natália
Increasing volume of publicly available DNA sequence data enables comprehensive studies that address integrative questions. For these projects, bioinformatic analysis requires advanced methods and computational infrestructure. I present the character of DNA sequence matrices for multilocus datasets, which contain large portions of missing data. A condition critical for analysis of multilocus data is that datasets for all loci or genes need to have partially overlapping taxon sets. The work-flow for analysing such data differs between supermatrix and supertree estimation of species trees. In the supermatrix approach, aligned sequences for all genes are concatenated and the species tree is estimated directly from a partitioned matrix. In the supertree approach, gene sequence alignments are used for inference of gene trees. Those are then combined into a species supertree. Smaller projects could benefit from utilising all available information in the supermatrix. Larger projects should rely on supertree methods for computational optimisation.
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