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Transplantation of insulin producing tissue is the only therapeutic method so far allowing type 1 diabetic patients to achieve long-term independence of insulin administration. Transplantation of isolated pancreatic islets (PI) into liver represents a safer but less effective alternative to whole-organ transplantation. This is caused by a significant loss of transplanted islets within a short time after transplantation due to the instant blood-mediated inflammatory reaction (IBMIR). This reaction is triggered by molecules of tissue factor, abundantly expressed on the surface of PI cells. Tissue factor activates directly the coagulation pathway leading to platelet aggregation, complement activation, and infiltration of islet graft by leukocytes which results in a destruction of up to 60 % of transplanted tissue, and a formation of ischemic areas of downstream lying liver tissue. Tissue factor also stimulates angiogenesis which makes it necessary for revascularization of PI after transplantation. Inhibition of tissue factor gene in isolated PI using RNA interference provides an opportunity for short-term suppression of tissue factor expression, leading to protection of PI in the early post-transplantation period without hindering the connection of capillaries to the recipient vascular system later...

The RNA interference (RNAi) mechanism can be used to reduce the expression of a selected gene in an organism. This method, discovered in 1998, has become the "gold standard" in basic biological research with overlaps to applied research and gene therapy in human medicine. For many reasons, RNAi is a suitable tool for the studies on biology of insects. RNAi is endowed with high sequence specificity, low costs, and easy application also in non-model species. Termites (Isoptera) are very sensitive to RNAi and this method is widely used to understand their physiology and ontogeny. The use of RNAi also has a potential in applied termite research and a significant number of publications have focused on the development of RNAi techniques as non-chemical pesticides against economically important termite species. This bachelor thesis aims to give a broad overview of the existing research on termites that uses the RNAi method.

The aim of this thesis was to study the role of Adenylate kinase 1 (Ak1) in the immune system of Drosophila melanogaster larvae upon the infection by parasitoid wasp Leptopilina boulardi. Using the immune specific Ak1 RNA interference, it was analyzed the effect of Ak1 reduction on the immune response and viability of Drosophila. The importance of Ak1 was also evaluated within the metabolism of immune cells. It has been shown that Ak1 is crucial in energy metabolism of immune cells and important for the proper functioning of immune system.

MicroRNAs are small regulating molecules of RNA that are encoded by orgamism's genome. Biogenesis of microRNA takes place partly in the nucleus and partly in the cytoplasm. Result of this biogenesis is a 22 nt long microRNA molecule. They are able to silence the genes thanks to sequence- specific degradation of a target mRNA or thanks to the repression of translation of target, complementary mRNA. In mammalian cells the mechanism of translational repression is more common. During this mechanism the microRNA molecule is not entirely complementary to 3'UTR of its target mRNA. Polyomaviruses are small, non-enveloped dsDNA viruses with a circular genome and icosahedral capsid composed of VP1 protein pentamers. These viruses belong in a group called onkoviruses, which can transform infected cells and contribute to development of serious illnesses such as Merkell cell carcinoma. Their genome encodes regulating proteins called T antigens, structural capsid proteins and also microRNAs. My main focus in this thesis will be SV40, MPyV, MCPyV, BKPyV and JCPyV encoded microRNA molecules. Key words: polyomaviruses, small interfering RNA, microRNA, siRNA, RNA interference, mouse polyomavirus, BK virus, JC virus, SV40

Tick saliva contains a lot of biological active substances helping them to succesfully complete their feeding which is neccesary for their next development. Both proteinaceous and non-proteinaceous molecules including protease inhibitors are present in tick saliva. The biggest family of these proteases are serpins. Serpins are involved in many biological processes as blood coagulation, fibrinolysis, apoptosis or inflammation. The aim of this diploma work was to determine expression profiles of 10 serpins from nymphs of Ixodes ricinus fed for different times using quantitative real time PCR. For chosen genes (IRS 10, IRS 20) dsRNA for silencing of the gene was prepared and using RNA interference the role of these genes during tick (I. ricinus nymphs) feeding and transmission of Borrelia afzelii spirochetes, a vector of Lyme borreliosis, was evaluated.Tick saliva contains a lot of biological active substances helping them to succesfully complete their feeding which is neccesary for their next development. Both proteinaceous and non-proteinaceous molecules including protease inhibitors are present in tick saliva. The biggest family of these proteases are serpins. Serpins are involved in many biological processes as blood coagulation, fibrinolysis, apoptosis or inflammation. The aim of this diploma work was to determine expression profiles of 10 serpins from nymphs of Ixodes ricinus fed for different times using quantitative real time PCR. For chosen genes (IRS 10, IRS 20) dsRNA for silencing of the gene was prepared and using RNA interference the role of these genes during tick (I. ricinus nymphs) feeding and transmission of Borrelia afzelii spirochetes, a vector of Lyme borreliosis, was evaluated.

Charles University Faculty of Pharmacy in Hradec Králové Department od Biochemical Sciences Candidate: Bc. Robin Klieber Supervisor: PharmDr. Anna Jirkovská, Ph.D. Title of thesis: The use of RNA interference for the modification of DNA topoisomerase II levels in cancer cells and its influence on the antineoplastic effect of anthracyclines. Topoisomerase II (TOP II) is an enzyme that alters the topological state of the DNA double helix during physiological processes through the formation of transient DNA double strand breaks. Two TOP II isoforms are known: TOP IIα is essential for proper separation of chromosomes in mitotic cells, whereas TOP IIβ is primarily associated with gene transcription. Anthracycline antibiotics (ANT) belong to the group of topoisomerase poisons that stabilize the covalent complex of TOP II and DNA. This prevents the religation of the DNA double strand breaks and thus causes irreversible DNA damage leading to programmed cell death. Although ANTs are frequently administered in various antineoplastic protocols (hematooncological malignancies, hormone-dependent tumors and others), the therapy still possess a high risk of irreversible cardiotoxicity. The mechanism of cardiotoxicity remains unraveled. However, it has been previously discussed that TOP IIβ inhibition could play a...

Aim of this work was to study fatty acid synthesis pathway in the tick Ixodes ricinus. I have characterized tissues and stage expression profiles of three genes; acc (acetyl coenzyme A carboxylase), fas (fatty acid synthetase) and fabp (fatty acid binding protein) by qRT-PCR. Then expression of these genes was silenced by RNA interference and phenotypes observed during and after feeding in nymphs and adults. The pathway seems to be crutial for the ticks.

Uncontrolled spreading of genetically modified (GM) plants is one of the main concerns about their cultivation. Inducible RNA interference against an essential gene could be a tool for control of GM plants. After spraying with a chemical inducer, the essential gene will be silenced so the treated GM plant will die. For testing this strategy we chose two key enzymes of nitrogen metabolism, glutamate synthase (GOGAT) and glutamine synthetase (GS). GS processes ammonium ions into glutamine, then GOGAT transfers the amide group from glutamine to 2-oxoglutarate to form two glutamates. GS/GOGAT cycle is the main pathway for assimilation of ammonium ions, which could be toxic to plants in a higher concentration. Disruption of ammonium assimilation during photorespiration causes a strong inhibition of photosynthesis. The aim of this work was to describe the effects of silencing GOGAT and GS genes in Arabidopsis thaliana. To induce silencing, RNAi hairpin constructs under a control of constitutive or estradiol-inducible promoter were prepared. In selected independent transformants with the inducible hairpin against GOGAT, chlorosis and reduced growth were observed after the estradiol treatment in in vitro conditions. However, the spraying with estradiol was tricky, at the whole plant level, the induction of...

In organisms, RNA interference serves as a defence mechanism against foreign nucleic acids. RNAi has a negative effect on translation, via the binding of small non-coding molecules to the complementary region of mRNA, resulting in its degradation. CRISPR, a new method of genetic engineering, is based upon modulating genetic expression via creating double-stranded breaks in target DNA, aided by a ribonucleoprotein complex, consisting of the prokaryotic endonuclease Cas9 and sgRNA. Both of the aforementioned methods can be utilised in functional analysis of proteins and the characterisation of metabolic pathways in organisms of interest. This work summarises the current state of knowledge regarding RNAi and CRISPR and their use in genome editing of parasitic protists.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a DNA tumor virus that has been associated with all epidemiological forms of Kaposi's sarcoma, primary effusion lymphoma (PEL) and multicentric Castleman disease (MCD). Like other herpesviruses, KSHV undergoes two phases of life cycle (latent and lytic replication). During latency, the viral genome persists as a circular episome in the nucleus of the host cell and only a few viral genes are expressed, namely LANA (latency- associated nuclear antigen), Kaposin, vFLIP (viral FLICE inhibitory protein), vCyclin, and vIRF3/LANA2 (viral interferon regulatory factor 3). These viral genes are responsible for regulation of host cell proliferation, prevention of apoptosis, facilitation of immune evasion, and maintenance of the extrachromosomal viral genome during cell divisions. vIRF3 is a multifunctional nuclear protein that is constitutively expressed in KSHV positive PEL cells and Castleman's disease tumors, which expression causes dramatic changes of critical host pathways that are involved in the regulation of apoptosis, cell cycle, antiviral immunity, and tumorigenesis. In our study, we have demonstrated and elucidated predicted mechanism, by which vIRF3 enhances transcription activity of c-Myc. Moreover, we have clarified the previously unappreciated...

RNA interference (RNAi) is a process mediated by small RNAs (sRNA), which is significantly involved in the regulation of gene expression in plants. Diverse RNAi pathways can be divided into two basic mechanisms, which are post-transcriptional and transcriptional gene silencing (PTGS and TGS). Production of sRNAs is dependent on the presence of a double-stranded RNA molecule (dsRNA), which is cleaved by one of DCL proteins to produce sRNAs usually of 21-24 nt in length. One strand of the sRNA is subsequently loaded onto AGO protein. During PTGS, the AGO-sRNA complex interacts with the target RNA based on its sequence complementarity to the sRNA and cleaves it or blocks its translation. In the case of TGS, AGO interacts with plant-specific RNA Pol V and its transcripts, which are again complementary to the sRNA. This interaction allows assembling of a protein complex facilitating DNA and histone methylation inhibiting RNA Pol II transcription. There are numerous ways the dsRNA can arise. A significant part of dsRNA cell production is dependent on synthesising the complementary strand of the dsRNA by RDR6 (RNA-dependent RNA polymerase 6). RDR6 is also involved in the process of the secondary sRNA formation. The significance of RDR6 during PTGS was examined using a GFP reporter gene either during...

Epigenetics is the study of heritable changes in gene activities that are not caused by changes in the DNA sequence. Epigenetic mechanisms can be employed at many levels, from transcription to translation. They include DNA methylation, histone modification, and with it connected chromatin modification, and RNA interference. The result is the change of chromatin conformation leading to decrease or increase of certain gene expression, X-chromosome inactivation or gene imprinting. Epigenetic regulation plays important role in etiopatogenesis of multifactorial diseases. Genetic predisposing factors (in autoimmune diseases there are genes of major histocompatibility complex) and environmental factors, which affect our genome just through epigenetic modifications, are involved in their manifestation. Key words: Epigenetic mechanisms, DNA methylation, histone modification, RNA interference, genomic imprinting, X-chromosome inactivation, multifactorial disease.

The RNA interference is a mechanism, which allows cells to regulate their genes functions, to establish and maintain heterochromatin and to defend them against invasive nucleic acids. In plants, RNA interference is initiated by double-stranded RNA, which is processed by Dicer into small RNAs, usually 20-24nt long. These small RNAs form a complex with Argonaut protein that participates in different processes based on sequence complementarity. This complex can guide mRNA cleavage, translation blocking and chromatin modifications, resulting either into posttranscriptional silencing (by preventing translation of already existing mRNA, PTGS) or transcriptional silencing (by preventing transcription of mRNA, TGS). The first step of this thesis was to establish different ways of triggering PTGS and to evaluate their functionality and efficiency. The next step was a preparation of a system which would allow to study the transition from posttrancriptional to transcriptional silencing. These so called "indicator lines" should allow to observe the timing and dynamics of this process by utilizing fluorescent proteins. This system is also going to enable to evaluate, how different factors are involved in this process - one of the factors is RNA-dependent RNA polymerase 6 (RDR6) which plays an essential role in...

Translation initiation is the first step of protein synthesis that captures the flow of gene expression pathway in all living organisms. The advantage of regulation of gene expression at the level of translation initiation is that it allows for more rapid changes in the proteome and serves as the rate limiting step under certain conditions such as stress. This process is masterminded by many initiation factors. One of them, a multisubunit eukaryotic initiation factor 3 (eIF3), is a very efficient player in this field taking a part in the most of the initiation steps. The largest subunit of the eIF3 complex is called eIF3a p170 and TIF32 in mammals and yeast, respectively, and at least in yeast, it was shown to represent an essential constituent of the translational machinery. This work is based on all that has been learned about the eIF3a roles in translation initiation in the model organism of yeast Saccharomyces cerevisiae in effort to examine the degree of the functional conservation with its human ortholog. This is achieved by the RNAi-mediated knock-down of eIF3a in HeLa and HEK cell lines followed by variety of well established assays to monitor translational status of eIF3a depleted cells. In the first part, I describe optimization of the RNA interference protocol with respect to the choice...

Aim of this thesis was to shed light on the function(s) of Iba57 and Ssc1 proteins in both life cycle stages of T. brucei using RNA interference. Depletion of Ssc1 resulted in severe grow phenotype, decrease in activities of iron-sulphur cluster-containing enzyme aconitase but no increase in oxidative stress sensitivity or accumulation of ROS in mitochondrion. Down regulation of Iba57, specialized maturation factor of aconitase and homoaconitase, lead to depletion of aconitase, destabilization of Isa1 and increased sensitivity to oxidative stress and accumulation of ROS in both stages.

Two new genes encoding proteins Monolaris 1 and Monolaris 2 were isolated from tick Ixodes ricinus. Both cDNA fragments code for 94 aminoacid residues long protein with molecular mass 8,1kDa (Monolaris 1) and 8,3kDa (Monolaris 2). The function of Monolaris 1 was tested by using RNA interference in adult females of Ixodes ricinus that were subsequently fed on guinea-pigs. Body mass, egg mass and mortality were measured to evaluate the effect of gene silencing. Recombinant protein Monolaris 1 was prepared in bacterial expression system and antibodies against this protein were raised by immunization of a rabbit. Antibodies reacted with approximately 190kDa big protein in salivary gland, ovary and gut whereas monomer of Monolaris 1 was not detected in tick saliva, salivary glands and other tissues.

Influenza virus infection is one of the most current problems nowadays. Its unique ability to strongly inhibit cell immune response on many different levels and its pandemic potential make it a subject of interest of many research groups. The Influenza virus uses mainly NS1 protein to inhibit the immune response. NS1 protein is able, on one hand, to bind RNA and mask it against recognition by cellular sensors and other proteins. On the other hand, NS1 protein possesses a catalytic domain. Using this domain it interacts with many cellular proteins, interferes with signal transduction and guarantees successful infection. NS1 protein is one of principal pathogenicity instruments of the Influenza virus and it deserves appropriate attention.

Leishmania of the subgenus Viannia are protozoan parasites transmitted by phlebotomine sandflies (Diptera: Phlebotominae). They occur in tropical and subtropical areas in South America, where they cause cutaneous and mucocutaneous leishmaniasis. In this thesis, we studied developmental pattern of Viannia group and factors affecting its development within the sand fly gut. First, we investigated Leishmania braziliensis development within the Lutzomyia longipalpis digestive tract. Using GFP-labeled strain we demonstrated peripylar development: promastigotes escaped from the endoperitrophic space, colonized the hindgut and then migrated anteriorly. Four morphological forms were found within the Lu. longipalpis digestive tract: elongated nectomonads, short nectomonads, metacyclic promastigotes and paramastigotes. Furthermore, using the histological methods we demonstrated parasite attachment in pylorus region, while there were only free promastigotes in the midgut; neither form was found attached to the midgut epithelium. The next part was devoted to the effect of temperature on Viannia in Lu. longipalpis. We compared development of two closely related species L. peruviana and L. braziliensis at 20 řC and 26 řC. Leishmania braziliensis developed well in both temperatures tested, L. peruviana developed...

Several biological principles such as epigenetic changes, RNA interference, epithelial-mesenchymal transition, and cancer stem cell formation have been recently connected to the pathobiology of tumors. All these phenomena have, along with genetic changes, a significant impact on the neoplastic transformation and/or tumor progression. Authors report a review of the above mentioned "nongenetic" processes and their effect on the neoplastic transformation, and the appearance, behavior, prognosis, and therapy of tumors. Future diagnostic and therapeutic perspectives are also discussed.

Aim of this work was to find out how mitochondrial processing peptidases are working in the mitochondrion of Trypanosoma brucei. I have shown by RNA interference that mitochondrial processing peptidase (MPP) and mitochondrial intermediate peptidase (MIP) are essential for procyclic stages. Moreover, processing of human frataxin in T. brucei has a similar pattern as in human cells.

Since many people all around the world are suffering from genetic disorders, modern therapeutic approaches are focused on the search of new pharmaceutical products. These products will be able to act on the gene level, more accurately on the nucleotide sequences themselves. RNA interference (RNAi) is an evolutionary conserved process that is caused by double stranded RNA (dsRNA). MicroRNA (miRNA) and small interfering RNA (siRNA) are the most important dsRNAs, which have been identified so far. Short (19-25 bp) non-coding dsRNAs are responsible for regulation of cellular development, heterochromatin formation and genomic stability in eukaryotes. Most importantly they are able to silence cognate genes. Therefore, they can provide new insights into the gene function and pathway analysis. Furthermore, they are believed to be new potential targets for diagnosis and therapeutics, especially for the treatment of genetic disorders, which can be caused by nucleotides insertions, deletions and translocations.

In this study, I utilized the defined (target) sequence for transcription factor NHR-25 and GFP as a marker to visualize where nhr-25 is active during the development in vivo. After obtaining worm strains carrying these constructs, the expression pattern was analyzed and the specificity of the expression was tested by means of RNAi.

In this study was shown by RNA interference that YCF 45 gene of putative chloroplast origin is not essential for surviving of procyclic Trypanosoma brucei. Three different construct bearing HA-tagged YCF 45 protein that differs on their N-terminus were generated to reveal the localization of the protein in the cell. Spliced leader acceptor site of YCF 45 mRNA was identified and in comparison to annotated data new start codon was proposed. Fylogeny tree was made to shed some light on the origin of this gene.

The aim of this work was to characterise the influence of adenosine on imaginal disc cell line Cl8+ of Drosophila. I prepared stable cell lines with the overexpression or RNA interference of genes coding adenosine receptor AdoR (CG9753) and adenosine transporter DmENT2 (CG11045) in D. melanogaster. These cell lines were subsequently used to test their response to extracellular adenosine signal by the measurement of cell viability and level of second messengers cAMP and Ca2+ in Cl8+ cells.