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Methylation of viral RNA
Šimonová, Anna ; Macíčková Cahová, Hana (advisor) ; Sýkora, David (referee) ; Elleder, Daniel (referee)
Viruses are the major force that shapes the evolution of both pro- and eukaryotic organisms. They have a simple inner organization and contain only a few, usually well-described RNAs. In the case of +(ss)RNA viruses, their genomic RNA serves also as mRNA. This makes them a perfect model system for searching for new mRNA modifications as well as for understanding the role of already known modifications. In this work, Human Immunodeficiency Virus type 1 (HIV-1) from the Retroviridae family was used as a model system. In the following study, four representatives from the Picornaviridae family were tested for RNA methylation profile. To get the information, a combination of two techniques was developed, liquid chromatography- mass spectrometry (LC-MS) and sequencing techniques. Results of LC-MS reveal a surprisingly high amount of 1-methyladenosine (m1 A) in RNA isolated from HIV-1. Nevertheless, the m1 A mapping sequencing technique confirm m1 A position only in co-packed tRNA. This led to the recalculation of HIV-1 virion RNA composition. In the case of Picornaviridae, LC-MS revealed m1 A and 5-methylcytidine (m5 C) in two insect viruses (Sacbrood virus, SBV and Deformed wing virus, DWV). RNA seq techniques (m1 A mapping and bisulfite sequencing) confirmed the presence of m1 A and m5 C only in tRNA....
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Proteins mimicking epitopes of broadly neutralizing HIV-1 antibodies
Zosinčuková, Tereza ; Malý, Petr (advisor) ; Osička, Radim (referee)
HIV-1 is a dangerous retrovirus which represents one of the world's leading health problems. HIV-1 infection is incurable and without proper treatment by antiretroviral therapy it leads to death within several years. Despite intensive research, no HIV vaccine is currently available. This thesis presents a new and unique approach which has not been used for vaccine development yet. The promising strategy is based on small binding proteins that can elicit broadly neutralizing HIV-1 antibodies by mimicking their epitopes. The aim of this project was to select and characterize small binding proteins that can successfully mimic the surface of viral envelope glycoproteins that is recognized by the broadly neutralizing HIV-1 antibodies PGT121 and PGT126. Proteins were selected from a highly complex combinatorial protein library derived from a new type of scaffold called Myomedin. Firstly, the extent of the protein library was narrowed down using the ribosome display. Then the direct sandwich ELISA screening was applied to select scaffold variants that interact with the target antibodies. In total over 200 variants were tested and several promising candidates were found. These Myomedin variants were purified, biochemically and biophysically characterised and the best ones were used to immunize mice....
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Modulation of plasmacytoid dendritic cell function: role of immunoreceptors TIM-3 and BDCA-2
Font Haro, Albert ; Hirsch, Ivan (advisor) ; Němečková, Šárka (referee) ; Saláková, Martina (referee)
Albert Font Haro ABSTRACT Modulation of plasmacytoid dendritic cell function: role of immunoreceptors TIM-3 and BDCA-2 Plasmacytoid dendritic cells (pDCs) are key players in the antiviral response as well as in linking innate and adaptive immune response. They express endosomal toll-like receptors 7 and 9, which can detect ssRNA and unmethylated CpG DNA, respectively. Due to the constitutive expression of the transcription factor IRF7, pDCs are able to rapidly produce massive quantities of type I (α, β, ω) and type III (1, 2, 3, 4) interferons (IFN-I and IFN-III) as well as pro- inflammatory cytokines such as IL-1, IL-6 and TNF-α. After maturation, they also function as antigen-presenting cells. Despite intense research, the mechanisms of IFN and pro-inflammatory cytokines production and regulation are still poorly understood. Using the pDC cell line GEN2.2 and also primary human pDCs, we shed light on the role of kinases MEK and SYK in IFN-I production and regulation. We found that SYK is not only involved in the regulatory receptor (RR)-mediated BCR-like pathway that represents the negative regulation of IFN-I and IFN-III secretion but also in the positive TLR7/9-mediated signal transduction pathway that leads to IFN-I production, representing the immunogenic function. We also found that MEK plays a...
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Effects of heme arginate in HIV-1 acute infection and in latency reversal
Prakash, Shankaran ; Mělková, Zora (advisor) ; Hirsch, Ivan (referee) ; Hejnar, Jiří (referee)
The available antiretroviral compounds can effectively suppress the replication of HIV-1 and block the disease progression. However it is impossible to eradicate the virus from the organism as the HIV-1 integrated in the genome is not affected by the existing anti-HIV-1 drugs. Therefore, new latency reversing agents are being actively developed as part of "shock and kill" therapy to reactivate the provirus and clear the reservoir. Normosang (heme arginate; HA) is a human hemin- containing compound used to treat acute porphyria. Heme is physiologically catabolised by heme oxygenases to form iron (Fe2+ ), carbon monoxide (CO) and biliverdin that is further converted to bilirubin by biliverdin reductase. In this study, we have demonstrated that HA inhibited HIV-1 replication during the acute infection, which was accompanied by the inhibition of reverse transcription. On the other hand, HA synergised with phorbol myristyl acetate (PMA) and reactivated the HIV-1 provirus in ACH-2 cells and the HIV-1 "mini-virus" in Jurkat cell clones A2 and H12. HIV-1 ''mini-virus'' was reactivated also by HA-alone. Further, we have studied the effects of heme degradation products on latent HIV-1 reactivation when added individually. We employed addition of ascorbate to generate Fe2+ , resulting in an increased...
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Integration site distribution of expressed proviruses
Miklík, Dalibor ; Hejnar, Jiří (advisor) ; Kejnovský, Eduard (referee) ; Indik, Stanislav (referee)
To establish efficient expression of their genes, retroviruses integrate proviral copies into the genomes of the cells they have infected. Epigenetic events, however, silence expression of the integrated proviruses. This silencing protects host cells from harmful viral spread, but also creates a reservoir of latent proviruses that subsequently hinders the cure of retroviral (e.g., HIV-1) infections. Furthermore, the silencing of retrovirus-derived integrative vectors complicates their application in transgenesis and gene therapy. The goal of this thesis is to describe the interaction between retroviral expression and host (epi)genomic environment at the site of proviral integration. To pursue the goal, we sought to define the (epi)genomic environment of the proviruses, which expression is not affected by the epigenetic silencing. Diverse retroviral vectors derived from avian sarcoma and leukosis virus (ASLV), murine leukemia virus (MLV), and human immunodeficiency virus type 1 (HIV-1) were used as model retroviral systems, and expression stability of the vectors in human cell lines was examined. In order to identify the features unique to integration sites of the active proviruses, we sorted the cells positive for the proviral expression, identified their proviral integration sites, and compared them to...
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Interaction of HIV-1 infection and expresion of endogenous retroviruses
Machač, David ; Elleder, Daniel (advisor) ; Drda Morávková, Alena (referee)
The aim of this bachelor thesis is to describe the effect of HIV-1 on the expression of HERV proviruses in infected cells, how the presence of HERV transcripts and proteins can affect the replication cycle of HIV-1, the composition, structure and infectivity. These interactions may have negative but also positive effects on HIV-1 infectivity. For example, the mutual presence of HIV-1 and HERV proteins encoded by the gag genes responsible for the capsid, nucleocapsid, and virion matrix, may mix together, and form aberrant capsids that will not play a correct role in the HIV-1 replication cycle. Further, due to the phenomenon called viral pseudotyping, HERV envelope glycoproteins could be incorporated into the HIV-1 membrane. This could be a pathway, how the HIV-1 could theoreticaly extend the tropism to other cells than only CD4 T-lymphocytes, macrophages and dedritic cells. Key Words: HERV, HIV-1, virus pseudotypes, retrovirus replication
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Effects of heme arginate in HIV-1 acute infection and in latency reversal
Prakash, Shankaran ; Mělková, Zora (advisor) ; Hirsch, Ivan (referee) ; Hejnar, Jiří (referee)
The available antiretroviral compounds can effectively suppress the replication of HIV-1 and block the disease progression. However it is impossible to eradicate the virus from the organism as the HIV-1 integrated in the genome is not affected by the existing anti-HIV-1 drugs. Therefore, new latency reversing agents are being actively developed as part of "shock and kill" therapy to reactivate the provirus and clear the reservoir. Normosang (heme arginate; HA) is a human hemin- containing compound used to treat acute porphyria. Heme is physiologically catabolised by heme oxygenases to form iron (Fe2+ ), carbon monoxide (CO) and biliverdin that is further converted to bilirubin by biliverdin reductase. In this study, we have demonstrated that HA inhibited HIV-1 replication during the acute infection, which was accompanied by the inhibition of reverse transcription. On the other hand, HA synergised with phorbol myristyl acetate (PMA) and reactivated the HIV-1 provirus in ACH-2 cells and the HIV-1 "mini-virus" in Jurkat cell clones A2 and H12. HIV-1 ''mini-virus'' was reactivated also by HA-alone. Further, we have studied the effects of heme degradation products on latent HIV-1 reactivation when added individually. We employed addition of ascorbate to generate Fe2+ , resulting in an increased...
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Effect of restriction factors on replication of hepatitis B virus
Kunteová, Kateřina ; Hirsch, Ivan (advisor) ; Sýkora, Michal (referee)
Specific aim of this bibliographic research is to elucidate the effects of cellular restriction factors on HBV replication. The work will specially analyze the role of the innate and natural immunity and to compare the effect of analogical or identical restriction factors on HBV and HIV-1 replication. Because of the central role of cccDNA for virus persistence in human organism, the work will study the effects of restriction factors on its possible destruction and eradication and a possible HBV cure. The research will also be focused on the effect of restriction factors during acute, chronic and occult infection. Powered by TCPDF (www.tcpdf.org)
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Functional genome analysis using the retroviral integration sites permissive for provirus expression in human cells
Miklík, Dalibor ; Hejnar, Jiří (advisor) ; Španielová, Hana (referee)
The expression of retroviral genes depends on the establishment of the provirus - the DNA copy of retroviral genome integrated into the host genome. The transcriptional state of provirus is then influenced by the environment at the site of integration. The phenomenon of proviral silencing is an obstacle to the usage of retroviral vectors and a barrier to the eradication of human immunodeficiency virus type 1 (HIV-1) from infected individuals. Taking advantage of single cell clones bearing one provirus, this diploma thesis investigates the distribution of (epi)genomic features at the sites occupied by stably expressed proviruses. In total, long-term expression profiles of 245 and 255 clones carrying avian sarcoma-leucosis virus (ASLV) and HIV-1, respectively, were obtained. The database-based analysis of 42 integration sites of ASLV and three integration sites of HIV-1 proviruses shows that proviral stable expression highly correlates with the transcriptional start sites (TSS) at the sites of integration. Histone marks characteristic for the proximity of active TSSs and regulatory elements at the sites of integration of stably expressed proviruses confirm this finding. The results presented in this thesis could inspire other analyses investigating the relationship between the integration site and the...
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