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Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
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Consequences of perinatal insult on brain excitability in immature and adult rats
Fábera, Petr ; Mareš, Pavel (advisor) ; Pokorný, Jaroslav (referee) ; Ošlejšková, Hana (referee)
Perinatal insult may lead to a permanent impairment of brain function resulting in the development of epilepsy. Status epilepticus (SE) in immature rats leads to hippocampal hyperexcitability. The functional and morphological changes of the hippocampus are similar to those seen in human temporal lobe epilepsy. The excitability may be influenced by adenosine. Adenosine acts its anticonvulsant effect by activation of A1 receptors (A1R). The concentration of adenosine is regulated by adenosine kinase (ADK) present in two isoforms - ADK-L and -S. The main goal of the thesis is to elucidate the changes in A1R and ADK isoforms expression during intact brain development and after SE. A1R agonist 2-chloro-N6- cyclopentyladenosine (CCPA), as well as inhibition of ADK by 5-iodotubercidin (5-ITU), may bolster the anticonvulsant effect, but their action may correspond with the level of A1R and ADK. Hippocampal excitability in immature rats after LiCl-pilocarpine SE was studied by the model of hippocampal afterdischarges (ADs) and correlated with changes of A1R and ADK in the hippocampus. ADs demonstrated significantly decreased hippocampal excitability shortly after SE induction, whereas significant hyperexcitability accompanied by spontaneous seizures in older rats was shown. Increasing ADK-S expression...
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Vliv cytosolické nukleotidázy cN-IIIB na imunitní odpověď u \kur{Drosophila melanogaster}
DOLEJŠKOVÁ, Tereza
Adenosine is a key signal molecule of the metabolic switch, a crucial process of metabolic changes in Drosophila melanogaster upon parazitoid wasp infection. However, some components of the adenosine creation pathway have yet to be discovered. We studied a potential convertor of AMP to adenosine in immune response, cN-IIIB, a cytosolic nucleotidase known to accept the methylated RNA cap nucleotide 7-methylguanosine as a substrate and to protect cells against undesired incorporation of this nucleotide into nucleic acids. We suggest this trait can be potentially important in the metabolic switch.
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Study of adenosine effects on proliferation of BeWo cell line
Papírník, Josef ; Červený, Lukáš (advisor) ; Vokřál, Ivan (referee)
Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Josef Papírník Supervisor: doc. PharmDr. Lukáš Červený, Ph.D. Title of diploma thesis: Studium of adenosine on proiferation activity in BeWo cell line The placenta is a rapidly developing organ that provides nutrition, protection and environment for the growing fetus. Fetal development is dependent on the supply of nutrients from the mother's blood either by passive diffusion or mediated by transporters. One of the essential nutrients are nucleosides, which are known to promote DNA synthesis and thus the growth of certain tissues. In order to pass across the plasma membrane they need nukleoside transporters (NTs) because of its hydrophilic feature. Additionally Ado takes part in cell signaling. Its wide- ranging effects, including influencing proliferation, are mediated by its binding to adenosine receptors (ARs). The placenta expresses NTs and ARs, which means that it is equipped to uptake nucleosides from maternal blood and has ability to receive signals from the external environment via the adenosine molecule. However, the importance of nucleosides for placental growth has not been investigated yet. The aim of this thesis is to test the effect of nucleosides on the proliferation of...
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Study of adenosine effects on proliferation of JEG-3 cell line
Nguyen, Ngoc Duong ; Červený, Lukáš (advisor) ; Jirkovský, Eduard (referee)
Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology and Toxicology Student: Nguyen Ngoc Duong Supervisor: doc. PharmDr. Lukáš Červený, Ph.D. Title of diploma thesis: Effect of adenosine on the proliferation of JEG-3 cell line Adenosine is a purinergic signaling molecule that is used in nucleic acid synthesis. Transport of hydrophilic nucleosides through the plasma and/or organelle membranes is provided by equilibrative nucleoside transporters (ENTs), members of the SLC29A transporter family, and concentrative nucleoside transporters (CNTs), members of the SLC28A transporter family. The placenta is a complex and rapidly growing organ. It shows some patterns similar to tumors except for the fact that the placenta's growth is fully controlled. It was found that extracellular nucleosides support the proliferation of cancerous and some non-cancerous cells. The placenta expresses high levels of NTs which indicates the placenta's ability to take up the nucleosides from circulation, however, the contribution of this process to placental growth is known. The diploma thesis aims to test the effect of adenosine and other nucleosides on trophoblast proliferation. We evaluated whether adenosine and other nucleosides increase the proliferation of the choriocarcinoma-derived JEG-3 cell...
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Adenosine metabolism and its role in cell physiology
Neumannová, Kateřina ; Novotný, Jiří (advisor) ; Hansíková, Jana (referee)
Adenosine is not just a major component of important molecules such as ATP, RNA or cAMP, but also has its own signaling function. Therefore, its extracellular level is strictly maintained by balance in its formation, degradation and transport. Both inside and outside the cell adenosine is formed mainly through degradation of ATP and is eliminated by two enzymes, adenosine kinase and adenosine deaminase. Transport of adenosine through the cell membrane is provided by nucleoside transporters, which are either equilibrative or concentrative according to the mechanism of transfer. All three processes described above contribute to maintaining adenosine level under normal conditions and its increase in pathological situations. Extracellular adenosine as a signal molecule binds to adenosine receptors (subtypes A1, A2A, A2B, A3) that affect many cellular signaling pathways via G-proteins. By these pathways adenosine regulates energy homeostasis, controls the function of various organs and also modulates the nervous and immune system and thus it may participate in a number of pathological processes. Pharmacological affecting of specific adenosine receptors or enzymes involved in its metabolism can serve as an effective therapy. Some drugs based on this system are already in use, others are being tested, and many...
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The influence of perinatal hypoxia on motoric development on laboratory rat and means of therapy
Vachovcová, Sylva ; Mareš, Pavel (advisor) ; Stuchlík, Aleš (referee)
Severe perinatal hypoxia represents a substantial brain injury in human newborns. This Diploma thesis is focused on long-term motor outcome of laboratory rat after moderate perinatal hypoxia. We described some behavioral test for detection motor development and presented the influence of perinatal hypoxia on central nervous system. We also discussed an effect of agonists and antagonists of adenosine A1 receptor in brain. The aim of an experimental part was an evaluation of long-term motor behavior in rats affected by perinatal hypoxia. To cause perinatal hypoxia we put pregnant female rats to a hypoxic (10% O2) normobaric room in 11th day of their gestation. The pregnant female rats stayed in hypoxic room until they gave a birth and 6 more days after birth with their litters. For classification of motor development we used battery of tests of motor coordination. These tests correspond to the level of development of the rat. Then a group of rats with perinatal hypoxia was treated by a single administration of an agonist of adenosine A1 receptor 2-chloro-N(6)- cyclopentyladenosin (CCPA) in postnatal day 14. The animals affected by perinatal hypoxia show motor deficits in 3 from 4 selected behavioral tests. Otherwise, this motor behavior was no longer detected in young adults. The rats affected by...
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Molecular mechanisms of sleep homeostasis
Dvořáková, Tereza ; Spišská, Veronika (advisor) ; Rydzyková, Tereza (referee)
Sleep is an essential physiological process driven by a circadian system with its main endogenous pacemaker in the suprachiasmatic nucleus of hypothalamus (SCN) and by sleep homeostasis, a process reflecting time spent awake. This work is focused on basic characteristics of sleep, describes the two process model of sleep regulation and sleep homeostasis theory which connects synaptic plasticity with sleep. Next it describes the function and principles of the circadian system including the synthesis of melatonin and the principles of homeostatic sleep regulation. Within the sleep homeostasis, the focus is on the role of dopamine, prostaglandin D2 and especially adenosine. Next are discussed genes involved in sleep homeostasis and connecting it with synaptic plasticity. Last are mentioned alterations in homeostatic regulation of sleep in people suffering from depression and the final chapter focuses on the interactions between circadian and homeostatic process, particularly on the role of clock genes in sleep homeostasis. Key words: sleep, circadian system, sleep homeostasis, adenosine
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Genomic Data Mining Techniques
Jaša, Petr ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
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