|
|
Methods to detect selection in DNA sequences
Procházka, Ondřej ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.
|
|
|
Evolutionary implications of innate immunity receptors polymorphism
Bainová, Zuzana ; Vinkler, Michal (advisor) ; Zajícová, Alena (referee)
Interactions between hosts and their parasites are considered to be one of the major forces driving animal evolution. It can be assumed that the evolutionary changes will occur especially in host molecules directly involved in these interactions. The first line of host defense is formed by innate immunity receptors among which also pattern recognition receptors (PRRs) belong. PRRs detect the presence of parasites at the beginning of their invasion by binding characteristic structures of their bodies (so called pathogen-associated molecular patterns, PAMPs, e. g. lipopolysaccharide, flagellin or peptidoglycans) or abnormal self molecules (damage-associated molecular patterns, DAMPs, e.g heat shock proteins). Although this mechanism of immune system activation is based on the recognition of ligands that are relatively evolutionarily conservative in pathogens, growing body of evidence suggests that PRRs are highly polymorphic on both interspecific and intraspecific level. High frequencies of minority alleles can be observed in most populations studied. It has been proven that particular alleles of many PRRs may associate with increased or decreased resistance to various infectious or autoimmunity diseases. Relationship between polymorphic receptor and a disease could be the main force, which shapes the...
|
|
|
Diversity and evolutionary significance of feather-degrading bacteria in birds
Kyptová, Markéta ; Javůrková, Veronika (advisor) ; Reif, Jiří (referee)
Although to date this fact has been widely neglected, avian plumage is inhabited by a wide range of bacteria able to utilize keratin, the basic structural unit of feathers. If these keratinophilic, so called feather-degrading bacteria (hereafter FDB) get out of control, it can lead to significant changes in the plumage structural properties, resulting in impaired thermoregulation, flight performance, and expression of plumage ornaments. These may have significant consequences on reproductive success and overall fitness of individual. Based on these facts, it is hypothesized that PDB pose strong selective pressure lying behind the evolution of defense mechanisms such as size and chemical composition of uropygial gland, deposition of pigments into the feathers, or molting strategies that have been observed to eliminate the negative effect of FDB. The aims of this bachelor thesis are, on the basis of available literature, to summarize findings related to overall diversity and characteristics of plumage bacteria, to evaluate their effect on quality of plumage and individual fitness, and also to assess a role of microorganism in the evolution of different life- strategies in birds. Finally, this bachelor thesis points out the shortcomings of recent studies and proposes the concept for future research...
|
|
|
Botany in Czech lands at the turn of the 20th century: theoretical aspects of the work of Josef Velenovský
Kaiprová, Sofie ; Čermáková, Lucie (advisor) ; Janko, Jan (referee)
The work is a literary research on the theoretical and evolutionary concepts in botany in the Czech environment at the turn of the 19th and 20th century with a focus on the work of Josef Velenovský (1858-1949). The work maps the historical context of Velenovský's work, deals with the transformations of Velenovský's vision of evolution and the most interesting aspects of his theoretical thinking about biology. At the beginning he fully acknowledges Darwin's theory, in the late age he holds a completely contradictory theory. Key words: history of botany, Josef Velenovský, evolutionary theory, natural selection, altruism
|
|
|
Diversity and evolutionary significance of feather-degrading bacteria in birds
Kyptová, Markéta ; Javůrková, Veronika (advisor) ; Reif, Jiří (referee)
Although to date this fact has been widely neglected, avian plumage is inhabited by a wide range of bacteria able to utilize keratin, the basic structural unit of feathers. If these keratinophilic, so called feather-degrading bacteria (hereafter FDB) get out of control, it can lead to significant changes in the plumage structural properties, resulting in impaired thermoregulation, flight performance, and expression of plumage ornaments. These may have significant consequences on reproductive success and overall fitness of individual. Based on these facts, it is hypothesized that PDB pose strong selective pressure lying behind the evolution of defense mechanisms such as size and chemical composition of uropygial gland, deposition of pigments into the feathers, or molting strategies that have been observed to eliminate the negative effect of FDB. The aims of this bachelor thesis are, on the basis of available literature, to summarize findings related to overall diversity and characteristics of plumage bacteria, to evaluate their effect on quality of plumage and individual fitness, and also to assess a role of microorganism in the evolution of different life- strategies in birds. Finally, this bachelor thesis points out the shortcomings of recent studies and proposes the concept for future research...
|
|
|
Reception od Darwin in biology
Richter, Jiří ; Markoš, Anton (advisor) ; Flegr, Jaroslav (referee)
Reception of Darwin in biology conveys a story of evolutionary biology with emphasis on the divergent reception of Charles Darwin's theories by biologists in the past 150 years. Given the influence of Darwin's thought, a unique tradition has emerged in the scientific field. Every fifty years starting from the publishing of The Origin of Species, scientists gather to celebrate Charles Darwin as a thinker and a person. An immense amount of literature on Darwin and evolutionary biology has been produced by authors and publishers worldwide, thus the recurring commemorative events provide a fine start to the historical survey of Darwinism and are used as such in Reception of Darwin in biology.
|
|
|
Evolutionary implications of innate immunity receptors polymorphism
Bainová, Zuzana ; Vinkler, Michal (advisor) ; Zajícová, Alena (referee)
Interactions between hosts and their parasites are considered to be one of the major forces driving animal evolution. It can be assumed that the evolutionary changes will occur especially in host molecules directly involved in these interactions. The first line of host defense is formed by innate immunity receptors among which also pattern recognition receptors (PRRs) belong. PRRs detect the presence of parasites at the beginning of their invasion by binding characteristic structures of their bodies (so called pathogen-associated molecular patterns, PAMPs, e. g. lipopolysaccharide, flagellin or peptidoglycans) or abnormal self molecules (damage-associated molecular patterns, DAMPs, e.g heat shock proteins). Although this mechanism of immune system activation is based on the recognition of ligands that are relatively evolutionarily conservative in pathogens, growing body of evidence suggests that PRRs are highly polymorphic on both interspecific and intraspecific level. High frequencies of minority alleles can be observed in most populations studied. It has been proven that particular alleles of many PRRs may associate with increased or decreased resistance to various infectious or autoimmunity diseases. Relationship between polymorphic receptor and a disease could be the main force, which shapes the...
|
|
|
The role of nest in reproduction of the Great Reed Warbler
Jelínek, Václav ; Procházka, Petr (advisor) ; Krist, Miloš (referee) ; Trnka, Alfréd (referee)
7 Abstract Bird nests protect eggs and nestlings, allowing the parents to leave their offspring and subsequently return to them. Their thermoregulatory properties reduce energetic costs of incubation and brooding of nestlings. For all these reasons, nests are key structures for the reproduction of a majority of avian species and as such they should be subject to natural selection. Several hypotheses describing selection pressures which affect the size of nests or some of their parts have been suggested. In my PhD thesis, I investigated some of them in the great reed warbler (Acrocephalus arundinaceus) - an open nesting passerine species with very variable nest size. For this purpose, I used a large dataset of several hundred measured great reed warbler nests, nest enlargement experiments and an experiment with artificial nests. In accordance with previous studies, we did not find that nest size affects the probability of common cuckoo (Cuculus canorus) brood parasitism, while it was influenced by other factors, such as timing of breeding, reed density around the nest and nest visibility from the nearest potential cuckoo perch site. More interestingly, we found that cuckoos adjust their nest-searching strategy in relation to availability of host nests. When host nests were scarce, cuckoos parasitized all of...
|
|
|
Eugenics in the Czech Countries in the First Half of the 20th Century
MEZEROVÁ, Kristýna
The thesis defines Czech eugenics in the 1. half of the 20. of the century. For understanding Czech eugenics, I outlined the development eugenics from its beginnings. The work presents main themes czech eugenics, for example degeneration of the human race, ways for its regeneration, establishment of eugenic marital revision or the importace of medical examinations before marriage. The thesis also presents most famous Czech eugenics. The thesis focuses on the German racial, its main Themis such as sterilization and euthanasia. The thesis compares the Czech eugenics and other similar movements. It is a theoretical work, the research here is applied primarily to the historical method, in particular, the analysis of the literary sources, which are primarily works of Czech, published in the 1. half of the 20. of the century. Also uses the comparative method when comparing the eugenics of the Czech and other similar movements. In the work are used in particular in Czech, but also an literary sources. The work attempts to answer the following research questions: 1. How was the Czech the eugenic movement and who led him? 2. What were the main themes of the Czech eugenic movement? 3. What were the similarities, or of the cooperation of the Czech movement with foreign eugenics associations? She worked on the Czech eugenic movement German racial hygiene? 4. That circumstances contributed to the demise of the Czech eugennic movement?
|
|
|
Methods to detect selection in DNA sequences
Procházka, Ondřej ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.
|
guest ::
