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Phylogenetic analysis and molecular detection of coronaviruses
MARHOUNOVÁ, Lucie
The aim of this bachelor thesis was to get acquainted with the creation of phylogenetic trees, which describe the relationships between coronaviruses and compare and assess the suitability of used and designed primers for the detection of a new type of coronavirus SARS-CoV-2. According to phylogenetic trees, it is possible to determine the evolutionary relationship of the studied organisms, which during evolution are subject to changes in their sequences, so-called mutations. These changes determine their development. The theoretical part of the bachelor thesis was focused on general acquaintance with viruses and subsequently coronaviruses and a new type of coronavirus SARS-CoV-2. SARS-CoV-2 has posed and continues to pose a major threat to the world. Furthermore, the issue of phylogenetics and finally the PCR detection method were discussed. In the practical part, phylogenetic trees were created using the computer program MEGA-X using the Neighbor-Joining method, which examined the phylogenetic relationships between coronaviruses focused mainly on SARS-CoV-2. The nearest coronaviruses of this new type of SARS-CoV-2 coronavirus were further compared using special BLAST software, which reported the percent agreement of the studied sequences. During these analyzes, SARS-CoV-2 was found to be most like the bat coronavirus RaTG13. Primers that are commonly used to detect SARS-CoV-2 are not disclosed, therefore primers from the CoVrimer web application have been used, where primers that have been used for scientific research are available. These were compared with the primers designed by the author. The design was performed as part of a bachelor's thesis using a special application Pirmer-BLAST. The primers obtained from the CoVrimer application were not designed to comprehensively distinguish all SARS-CoV-2 variants studied.
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A test of "object permanence" in Paridae and effect of neophobia and individual explorative strategies on success in solving object permanence tasks
Marhounová, Lucie ; Landová, Eva (advisor) ; Sedláček, František (referee)
Object permanence (OP) is a cognitive ability that enables animals to mentally represent the existence of hidden objects even if they can not be perceived by senses. In humans, OP develops during six qualitative stages, in which the understanding of relationships between objects in space and time changes. Current research shows that primates, some carnivores and several species of birds also acquire various degrees of this ability depending on their social life and foraging strategies. Many studies of OP have focused on food-storing birds but yet only in the Corvidae family. Therefore we decided to test this ability in two species of the Paridae family, food-storing coal tit (Periparus ater, N=23) and non-storing great tit (Parus major, N=24) to find out which stage they can achieve and whether there is a difference between these species in relation to their caching ability. Our results suggest that food-storing coal tits search for completely hidden objects significantly better than great tits. Most of the great tits were not able to solve this task. However, the upper limit for both species is probably Stage 4 because coal tits probably solved OP tasks with more screens randomly or used alternative strategies rather than mental representation. Substantial interindividual variability in the...
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A test of "object permanence" in Paridae and effect of neophobia and individual explorative strategies on success in solving object permanence tasks
Marhounová, Lucie ; Landová, Eva (advisor) ; Sedláček, František (referee)
Object permanence (OP) is a cognitive ability that enables animals to mentally represent the existence of hidden objects even if they can not be perceived by senses. In humans, OP develops during six qualitative stages, in which the understanding of relationships between objects in space and time changes. Current research shows that primates, some carnivores and several species of birds also acquire various degrees of this ability depending on their social life and foraging strategies. Many studies of OP have focused on food-storing birds but yet only in the Corvidae family. Therefore we decided to test this ability in two species of the Paridae family, food-storing coal tit (Periparus ater, N=23) and non-storing great tit (Parus major, N=24) to find out which stage they can achieve and whether there is a difference between these species in relation to their caching ability. Our results suggest that food-storing coal tits search for completely hidden objects significantly better than great tits. Most of the great tits were not able to solve this task. However, the upper limit for both species is probably Stage 4 because coal tits probably solved OP tasks with more screens randomly or used alternative strategies rather than mental representation. Substantial interindividual variability in the...
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Cognition test for testing object permanence in birds and primates
Marhounová, Lucie ; Landová, Eva (advisor) ; Veselý, Petr (referee)
Object permanence is a cognitive ability to mentally represent the existence and the movement of hidden objects. This phenomenon is being developed since birth in six different stages following the development of the sensorimotor intelligence. Not only the humans but also the other animals possess a certain notion of hidden objects and acquire various degrees of this ability depending on their life strategies. This thesis summarizes the research conducted up to the present in the field of the object permanence within the infant developmental psychology, but particularly in the animal world with the emphasis on the taxa where this ability has been most researched, that is in primates and birds. This thesis also recapitulates the types of the cognitive tasks used in the object permanence research and compares the methods of experiments applied to the humans, the primates and the birds. Part of this thesis also involves a phylogenetic reconstruction estimate of the ancestral character status in terms of the object permanence and testing the progress dependance of such character in relation to the selected ecological factors in primates.
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