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Epidemiological modeling of Covid-19
Schubert, Richard ; Kašpar, Jakub (referee) ; Mézl, Martin (advisor)
This thesis deals with the continuous epidemiological deterministic compartmental models and the COVID-19 pandemic modeling distinctive features. The effect of different probability distributions of individuals stay in compartments is studied numerically in relation to basic reproductive number and the final size of the epidemic, respectively. New model for a retrospective analysis of the first half of 2020 northern Italy epidemiological data is proposed. The model parameters estimation is performed using minimisation of weighted sum of squared residuals and the search through parameter space with BFGS algorithm implementation.
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Comparative and phylogenetic analysis of viruses in the University Hospital Brno
Švestková, Tereza ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This thesis is focused on the SARs-CoV-2 coronavirus associated with severe acute respiratory syndrome, which was first identified in 2019. This coronavirus caused a pandemic that affected almost the entire world. Knowledge of the genetic information is needed for vaccine development, to determine infectivity and to predict the evolution of SARs-CoV-2 variants. To obtain genetic information, RNA must be sequenced and these genomic sequences must be assembled. By comparing the assembled genomes, it is possible to find out which part of the organism has mutated. Phylogenetic analysis is performed on the basis of the concordance or divergence in the assembled genomes, which indicates the evolution of the organism and shows the evolutionary relationship with other organisms. The practical part is focused on the assembly of genomes from samples from patients in the University Hospital Brno and evaluation of the quality of the assembly. After the genomes are assembled, the next goal is to evaluate the variability and subsequent phylogenetic analysis.
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Analysis of coronavirus by QRT-PCR and possible therapy by nanoliposomal carriers of recombinant antigens
Krchová, Lenka ; doc. RNDr. Milan Bartoš. Ph.D. (referee) ; Turánek, Jaroslav (advisor)
This thesis deals with the study of coronaviruses, their diagnostics and subsequently the possible construction of a recombinant vaccine based on liposomal carriers of recombinant antigens. The experimental part of the thesis touches upon two levels. First, the diagnosis of SARS-CoV-2 virus was measured and investigated by real-time PCR. Biological material of a large number of patients was worked with. Together with the basic determination of the presence of the virus, the stability of the viral particle over time, its resistance to temperature changes, the effect of dilution of the carrier medium on the Ct value and other sub-experiments were investigated. From all the metadata, the most useful variant for pathogen diagnosis is finally evaluated. The experimental part is then followed by a possible therapy with recombinant vaccines. This issue is very topical and moves the whole professional community. Liposomes have been prepared which serve as carriers of bioactive substances in recombinant vaccines. The liposomes were homogenized by extrusion to the desired size and variously surface modified. Antigen binding, stability over time and possible degradation were investigated. Liposomes were characterized by DLS, nanoflow cytometry and electron microscopy.
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Impact of the COVID-19 Pandemic on Contruction Companies in the Czech Republic
Mudrych, Marek ; Všetečka, Jan (referee) ; Nováková, Jana (advisor)
The bachelor's thesis describes and evaluates the impact of the COVID-19 pandemic on construction companies in the Czech Republic using controlled interviews with representatives of companies and a questionnaire solution. The theoretical part generally describes problems caused by the coronavirus pandemic, which affect Czech construction industry. It is a description of the process of the pandemic in the Czech Republic, a description of selected anti-epidemic measures and government compensation bonuses. Part of the work is a description of the effects of the pandemic at the selected construction company and also prepared part of the documentation to management construction contract.
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Biophysical Characterization of Coronaviral nsp14 Inhibition
Trembulaková, Pavla ; Bouřa, Evžen (advisor) ; Dejmek, Milan (referee)
RNA virus SARS-CoV-2 caused worldwide pandemic of severe disease COVID-19 which lasted more than a year. Repair mechanisms of this virus during replication process significantly reduce efficiency of nucleotide analog drugs, eg. remdesivir. Nonstructural protein (nsp) 14 and nsp10 form a complex which acts as an exonuclease enzyme and will be furthrer referred to as an ExoN complex. This complex can probably cause lower efficiency of incorporation of nucleotide analogs compared to viruses without exonuclease enzymes. The two-protein complex with active site on nsp14 containing two magensium ions seems like a good target for testing potent inhobitors. Among possible inhibitors of SARS-CoV-2 exonuclease complex are isobavachalcone and sofalcone. According to published studies, those small organic molecules chelate magensium ions in active site of exonulease part in nsp14. This results in inactivation of ExoN complex active site in nsp14 structure and disables the catalytic function which acts as repairing element in RNA synthesis process. This tesis focuses on characterization of inhibition of protein complex nsp14 and nsp10 in presence of small selected molecules, isobavachalcone and sofalcone. Exonuclease activity assays in presence of various RNA substrates were performed. Furthermore, there have been...
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Effect of selected compounds on NMPylation of nsp9 SARS-CoV-2 catalyzed by NiRAN domain of nsp12 SARS-CoV-2
Fedák, Michal ; Šilhán, Jan (advisor) ; Vaněk, Ondřej (referee)
SARS-CoV-2 pandemic that begun in the end of 2019 caused over 770 milion confirmed cases of infection and almost 7 milion deaths worliwide. Despite pandemic being suppressed thanks to vaccines and restriction measures, the research of new medication targeting this virus continues. One of the possible targets of SARS-CoV-2 is nonstructural protein 9 (nsp9), which is essential for virus repliation. Just recently it was revealed that this protein can covalently bind nukleoside monophosphate (NMPylation) or RNA chain of various length (RNAylation). These reactions are catalyzed by nidovirus RNA-dependent RNA polymerase (RdRp) asociated nucleotidyltransferase (NiRAN) domain of nonstuctural protein 12 (nsp12). RNAylation of nsp9 showed to be crucial step in synthesis of RNA cap. The function of NMPylation was not jet revealed, but it is believed that this modification of nsp9 could play a role in priming of RNA synthesis. Some studies have already investigated inhibition of NMPylation. In this diploma thesis recombinant nsp9 was prepared and used in NMPylation reactions. Negative effect of DMSO on nsp9 NMPylation was observed. Three compounds (saquinavir, darunavir and conivaptan) selected based on the results of in silico studies did not show ability to inhibit NMPylation of nsp9. Next, it was confirmed...
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Vývoj nezaměstnanosti v ČR v letech 2020-2021
Svobodová, Tereza
The diploma thesis deals with the development of unemployment in the territory of the Czech Republic in the period 2020–2021. The aim of the thesis is to reflect the changes in unemployment rate in the given territory as a result of government restrictions in order to protect the public health of the population in connection with the spread of the SARS-CoV-2 virus. Based on secondary data of the unemployment rate, the thesis interprets the numerical transformation of the growth of unemployment across the regions of the Czech Republic. These knowledges are placed in the context of temporal events of interventions in the economy. The results of the analytical part proved that the anti-epidemic measures is-sued as part of the prevention of the covid-19 disease had an effect on increased unemployment. The national average of the unemployment rate increased by 1.1 p. p. as of 31 December 2020. At the same time, based on the results, it can be stated that there are differentiations between regions, which are dependent on the struc-ture of the industry and their share of employment in the given industry. The high-est year-on-year increase as of 31 December 2020 was recorded in the district of Karlovy Vary by 3.4 p. p., the smallest in the district of Prachatice by 0.3 p. p.
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COVID-19 and kidney diseases
Stanovský, Samuel ; Čertíková-Chábová, Věra (advisor) ; Zahrádka, Ivan (referee)
In clinical practice, SARS-CoV-2 virus infection and COVID-19 disease are mainly associated with dominant respiratory disorders of varying severity, from minor events such as upper respiratory tract infections to life-threatening respiratory failure. However, COVID-19 can not only be seen as a respiratory infection, but the possibility of systemic involvement should also be considered. One of the internal organs that can be directly affected by the virus is the kidneys. Renal damage from the SARS-CoV-2 virus can occur in completely intact kidneys or can affect kidneys with pre-existing nephropathy. In addition, patients with manifest renal disease are considered at higher risk for the COVID-19 than healthy population due to the often-significant immunosuppressive pharmacotherapy that might be a part of various nephropathy treatment regimens.
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The evolution of SARS-CoV-2 virus during the pandemic of COVID-19
Karban, Šimon ; Tachezy, Ruth (advisor) ; Pačes, Jan (referee)
Coronaviruses are animal and human viruses which, in the case of humans, cause respiratory diseases. The genome of coronaviruses is non-segmented and encodes several structural and several non-structural proteins. As their genome consists of single-stranded RNA in a positive sense, they encode RNA-dependent RNA polymerase. The origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is uncertain and may never be known. However, this thesis covers up-to-date knowledge and the arguments for the main theories on the emergence of this virus. The pandemic of disease COVID-19 caused by the SARS-CoV-2 had an enormous impact on the health and lives of people worldwide. The length and severity of the pandemic were caused by the characteristic of the virus, transmissibility and asymptomatic type of infection with severe symptoms in elderly and chronically ill individuals and the fast evolution of the virus after its appearance in humans. This thesis will describe important characteristics of the most important variants of the virus and changes which gave them a selection advantage. In the end, trends in the evolution of SARS-CoV-2 will be discussed. Keywords: SARS-CoV-2, Coronaviridae, variants, phylogeny, origin, evolution
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Design and evaluation of potential viral methyltransferase inhibitors
Kocek, Hugo ; Nencka, Radim (advisor) ; Grantz Šašková, Klára (referee)
A global pandemic of SARS-CoV-2 confirmed the pandemic potential of the Coronaviridae family and pointed out the need for novel antiviral drugs. The SARS-CoV-2 pandemic has been tamed thanks to mRNA vaccines; however, monoclonal antibodies and small molecules such as nirmatrelvir (protease inhibitor), remdesivir (polymerase inhibitor), or molnupiravir (mutagen) are currently also available. It is worth noting that remdesivir and molnupiravir were previously investigated as antivirals against different pathogens. SARS-CoV-2 encodes 16 non-structural proteins, and two of them - methyltransferases (MTases) nsp14 and nsp16 - participate in RNA capping as the virus must mimic the host's mRNA to evade the cellular antiviral sensors (e.g., IFIT1) and replicate. These MTases are structurally very similar to those of SARS-Co-V; therefore, we might expect that inhibitors of SARS-CoV-2 MTases could be used in the future against different coronaviruses. For the reasons mentioned above, this thesis focuses on developing novel MTase inhibitors targeting SARS-CoV-2 nsp14 and nsp16. The design was based on S-adenosyl-L-homocysteine (SAH; endogenous inhibitor of MTases) and an in silico compound library was constructed with various replacements for SAH's amino acid moiety. The potential inhibitory activity was...
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