National Repository of Grey Literature 18 records found  1 - 10next  jump to record: Search took 0.00 seconds. 
AGO-hook domains in RNA-directed DNA methylation in Arabidopsis thaliana
Teznerová, Kateřina ; Čermák, Vojtěch (advisor) ; Moravec, Tomáš (referee)
RNA-directed DNA methylation (RdDM) is an important pathway that regulates gene expression by inducing DNA methylation and is involved in regulation of gene expression and defence against invading DNA elements (especially transposons). Argonaut (AGO) proteins with small RNAs (sRNAs) that have sequence complementarity to the target DNA play a key role in the RdDM pathway. Domains called AGO-hooks are able to interact with Argonaut proteins. In plants, two proteins with AGO-hook domains are involved in the RdDM pathway: NRPE1 and SPT5L. Recently, a third protein, SPT6L, has been discovered at the investigator's site to be part of the Pol V complex (as well as the two proteins mentioned above). The role of SPT6L has not yet been described, but we hypothesize that it also plays a role in the RdDM pathway. This work focuses on the study of all three AGO-hook domains in Pol V complex and their involve in the RdDM pathway in Arabidopsis thaliana, from the preparation of mutants lacking different combinations of these AGO-hook domains to the study of their role and substitution in DNA methylation at different loci. Key words AGO-hook, Arabidopsis thaliana, NRPE1, SPT5L, SPT6L, siRNA, epigenetic chromatin labelling, Argonaut protein
The role of the AGO-hook domain of histone chaperone SPT6L in regulation of gene expression
Kašpar, Tomáš ; Čermák, Vojtěch (advisor) ; Převorovský, Martin (referee)
AGO-hook domains present in some eucaryotic proteins are crucial for a binding family of ARGONAUTE proteins (AGO). These AGO proteins are essential in many biological processes regulating gene expression by small RNA (sRNA), which is complementary to the gene that is supposed to be influenced. This thesis claims to find the function of the putative AGO-hook domain of the protein SPT6L. SPT6L is an elongation factor and histone chaperon of a complex of RNA polymerase II (Pol II) where it is acting in the epigenetic marking of histones. SPT6L of Arabidopsis thaliana is one of two paralogues of SPT6 proteins, that is characteristic of the presence of the AGO-hook domain. This is a plant specificity of this protein. What's more, the function of this domain remains unknown. Despite this, it could be assumed that this domain is necessary for binding of AGO proteins in the complex of Pol II, and by these interactions, it can enable guidance of regulation of chromatin modification, or it can co-transcriptionally influence nascent transcripts of Pol II by the sRNA. This thesis casts light on the function of the AGO-hook domain of SPT6L in A. thaliana in processes of gene regulation and protein interactions. It claims to confirm the interaction of the AGO-hook domain of SPT6L protein with AGO proteins and...
RNA interference in plants
Čermák, Vojtěch ; Fischer, Lukáš (advisor) ; Kulich, Ivan (referee)
The process of RNA interference allows cells to regulate functions of their genes. This process is usually initiated by the presence of double-stranded RNA within a cell. Such double-stranded RNA is diced by a specific protein called Dicer into duplexes of small RNAs, usually 20-25 nucleotides long. Single-stranded small RNAs, released from the duplexes, are the heart of RNA interference and they can be categorize into several groups according to their biogenesis. There are two groups of small RNAs in plants: miRNA and siRNA. Small RNAs can associate with a protein called Argonaut and guide it to the target molecule on the bases of sequence complementarity. The Argonaut-small RNA complex can act on itself or it can interact with other proteins in a wide spectrum of processes. The complex can slice the target mRNA (which can be handled by the sole Argonaut and small RNA), it can suppress translation or it can direct chromatin modifications. The phenomena of RNA interference can be found in almost all Eukaryotes where it can serve many functions, for example it can control cell differentiation, participate in stress responses, direct changes in chromatin and defend the organism against viruses. A diverse set of operating modes of RNA interference can be found in plants, which we are only at the...
Study of the mechanism of posttranscriptional and transcriptional transgene silencing in tobacco BY-2 cell line
Čermák, Vojtěch ; Fischer, Lukáš (advisor) ; Moravec, Tomáš (referee)
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...
Regulation of floral initiation in woody perennials
Čermák, Vladimír ; Mašková, Petra (advisor) ; Čermák, Vojtěch (referee)
Floral initiation is an important process for temperate woody perennials that affects the subsequent development of the flower. Although this process is well known in annual plants such as Arabidopsis thaliana, not much research has been done in woody plants. This review summarizes the knowledge about mechanisms of flowering induction in woody perennials, compared to the findings in model plants, especially A. thaliana, including factors involved in the regulation of the flowering process. In particular, FT-like genes and TFL1-like genes, which play an important role in the regulation of flowering induction, are discussed in detail. In temperate woody plants the dormancy period follows the floral induction before the floral development. Periodic regulation of this stage is controlled endogenously and, in addition to other factors, it is affected by expression of DAM genes. The genetic mechanisms regulating endodormancy release in woody perennials are similar to vernalization in herbs. Better understanding of processes such as the floral induction and endodormancy release can help us to develop cultivars with a modified flowering time.
Efficiency, predictability and liquidity in the commodity futures markets
Čermák, Vojtěch ; Krištoufek, Ladislav (advisor) ; Čech, František (referee)
This thesis examines efficiency of several CME commodity futures and its relation to market liquidity over the ten years period. The goal is to find ARMA model that is better than white noise in terms of forecasting power and carry out analysis of market liquidity if we find such model. This is done by comparing selected ARMA models to white noise. In order to do that, we use Diebolt - Mariano test on forecast errors obtained by pseudo out - of - sample analysis using rolling window with re - estimation. Concern of furhter analysis are factors, that can influence the DM statistics. Main findings are, that we are able to find such ARMA model for small enough time period within the ten years period for almost all commodities. For most commodities, this sub period is not long enough to violate efficient market hypothesis. Only for palladium and lean hog futures this period is longer than one year. These two futures shows strong signs of inefficiency, as its predictability is not out - weighted by liquidity restrictions.
Kinematic record of Jurassic obduction of oceanic crust in the West Carpathians
Čermák, Vojtěch ; Jeřábek, Petr (advisor) ; Vojtko, Rastislav (referee)
English abstract The bachelor thesis is focussed on problems of Jurassic subduction of Meliatic ocean in the region of the Western Carpathians. This oceanic domain opened during the Middle Triasic and closed at the end of Middle Jurassic. The existence of the oceanic domain in the Western Carpathians is documented by sedimentary rocks of oceanic origin glaucophane bearing basalts and serpentinized ultramafic rocks preserved in the area of the presumed suture zone. The chemical composition of metabasalts corresponds to the transition between the basalts of mid-oceanic ridges and basalts of island arcs. The metabasalts underwent high-pressure, low- temperature metamorphism, which proves their drag into to substantial depths during subduction and were later exhumed to structurally lower parts of the accretionary wedge. The research was focussed on identification of deformation record in units of the southern Gemeric Superunit, Meliata Unit (Borka Nappe) and Silicic Nappe. Four deformation events D1 - D4 were identified on the basis of structural analysis in the studied area. Deformation events D1 - D3 show distinct record in different units and are associated with roughly east- west direct of compression connected with the subduction of Meliatic oceanic plate, exhumation of its parts into an accretion complex...
Dynamics and variability of induced transgene silencing in tobacco cell line BY-2
Čermák, Vojtěch ; Fischer, Lukáš (advisor) ; Pečinka, Aleš (referee) ; Lafon Placette, Clément (referee)
RNA interference (RNAi) is an important mechanism regulating gene expression. In plants, RNAi is triggered by double-stranded RNA (dsRNA) which is processed into small RNAs (sRNAs), usually 21-24 nt long. The sRNAs are loaded into Argonaut (AGO) protein and recognize the target based on sequence complementarity. When the target is mRNA, they can slice it or block translation leading to posttranscriptional gene silencing (PTGS). When the target is DNA, they can induce DNA methylation and chromatin changes, which when present in the promoter can lead to transcriptional gene silencing (TGS). The individual components of RNAi are well described, but less is known about the impact of different types of dsRNA precursors on the dynamics of RNAi. To study these aspects of RNAi, we used tobacco BY-2 cell line expressing GFP reporter and inducible silencers. The silencers used different ways of triggering the dsRNA formation by transcripts from antisense (AS), unterminated sense (UT) and inverted repeat (IR) GFP sequence to initiate PTGS. Additionally, one IR silencer based on the CaMV 35S promoter initiated TGS. This allowed us to study RNAi from the beginning throughout the steady state level and till the recovery phase, all in the highly homogeneous system. Using this system, we described several features...
Adversarial examples design by deep generative models
Čermák, Vojtěch ; Neruda, Roman (advisor) ; Pilát, Martin (referee)
In the thesis, we explore the prospects of creating adversarial examples using various generative models. We design two algorithms to create unrestricted adversarial examples by perturbing the vectors of latent representation and exploiting the target classifier's decision boundary properties. The first algorithm uses linear interpolation combined with bisection to extract candidate samples near the decision boundary of the targeted classifier. The second algorithm applies the idea behind the FGSM algorithm on vectors of latent representation and uses additional information from gradients to obtain better candidate samples. In an empirical study on MNIST, SVHN and CIFAR10 datasets, we show that the candidate samples contain adversarial examples, samples that look like some class to humans but are classified as a different class by machines. Additionally, we show that standard defence techniques are vulnerable to our attacks.
Analysis of stock market sentiment with social media
Čermák, Vojtěch ; Baruník, Jozef (advisor) ; Vacek, Pavel (referee)
In the thesis, we explored prospects of extracting sentiment contained in Twitter messages. We proposed novel approach consisting of directly predicting the volatility on stock market by features obtained from the text documents using suitable document representation. We compared the performance of standard document vectorisation methods as well as a novel approach based on aggregating word vectors created by word embeddings. We showed that direct modelling of a market variable is possible with most of the proposed vectorisation techniques. In particular, the strong predictive power of aggregated word embeddings suggests that they are excellent sentiment representation, because they are independent of message volume and they capture well the semantical information in the tweets. Besides, our findings suggest that aggregating word embeddings vectorisation is viable approach even for large documents.

National Repository of Grey Literature : 18 records found   1 - 10next  jump to record:
See also: similar author names
11 Čermák, Vladimír
6 Čermák, Václav
Interested in being notified about new results for this query?
Subscribe to the RSS feed.