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tRNA synthetases as potential RNA capping enzymes
Říha, Jan ; Macíčková Cahová, Hana (advisor) ; Brázdovič, Filip (referee)
(EN) A novel type of non-canonical 5′ RNA caps, dinucleoside polyphosphate RNA caps, has recently been discovered in our laboratory. To elucidate the physiological role of these caps, more detailed information about their synthesis is essential. It has been already described that dinucleoside polyphosphate RNA caps (NpnN-RNA caps) can be accepted by RNA polymerase during transcription as a non-canonical initiating nucleotide (NCIN). However, the possibility that NpnN-RNA caps are created post- transcriptionally cannot be ruled out. The best candidates for post-transcriptional capping enzymes are aminoacyl-tRNA synthetases, which, besides their crucial role in translation, are responsible for the synthesis of free dinucleoside polyphosphates. In this thesis, four E. coli tRNA synthetases have been selected, cloned into plasmids, and purified using fast protein liquid chromatography (FPLC). Subsequently, selected tRNA synthetases have been tested for the production of free dinucleoside polyphosphate. These experiments have identified the optimal conditions for production of free dinucleoside polyphosphates, diadenosine tetraphosphate (Ap4A) particularly. The tRNA synthetases were then tested for their capabilities to form an RNA cap on in vitro transcribed radioactively labelled RNA. We found that...
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Employee’s Benefits
Matuška, František ; Říha, Jan (referee) ; Křížová, Zuzana (advisor)
The aim of this bachelor thesis is to describe benefits of employees and the manner in which they are used by employers and utilized by employees; it also concerns arguments for their utilization. The thesis examines tax and accounting aspects of the benefits of employees and determines a solution to the selected types of the benefits from the perspective of Czech legislation.
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Systems for file and directory synchronization
Říha, Jan ; Lattenberg, Ivo (referee) ; Pfeifer, Václav (advisor)
Bachelor's thesis is intent on snipping of systems for file and directory synchronization on various platforms. First part is addict to systems for mirroring, version control tools and web storage site. Second section put mind to address service. Third and last chapter apply to practical part with description of author script.
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Způsoby likvidace Lýkožrouta smrkového
ŘÍHA, Jan
The bachelor thesis deals with the morphology and life cycle of the spruce lichen-eater. The main focus is on measures to combat the spruce lichen-eater and an overview of such techniques and technologies designed for that. Here I describe the issue of swarming, wintering and what bark beetles have natural enemies. The bachelor's thesis describes how to treat the lichen-eater, how to prevent it, and mainly there are instructions on how to use individual technologies for its disposal. It is a mechanical technology of liquidation or even chemical liquidation. There is also a research overview of articles from international databases and extracts from them in my words. The aim of this work is to create a research overview of the biology and methods of disposal of the spruce lichen-eater.
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Intracellular dinucleoside polyphosphates and methods of their detection
Říha, Jan ; Macíčková Cahová, Hana (advisor) ; Šanderová, Hana (referee)
(EN) Dinucleoside polyphosphates are already known for more than 50 years, but their role inside a cell is still unclear. Some theories discuss their possible role as alarmones during stress conditions, others connect them to DNA damage or proliferation. One new theory is that dinucleoside polyphosphates act as 5' RNA caps. To elucidate their role in organisms, it is important to know their concentration in normal and stress conditions. This work will try to determine basal concentration in both bacterial and eukaryotic cells, and the changes of their concentration under stress conditions, from already known data. Measurement of concentration of any compound inside a cell depends on the used method. I also present basic overview of methods for detecting dinucleoside polyphosphates, from older luciferase- based techniques to new precise mass spectrometry-based techniques. Keywords: dinucleoside polyphosphates, Ap4A, RNA caps, cellular stress, LC-MS detection and quantification
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The design and cryptanalysis of the AES (Advanced Encyption Standard)
Říha, Jan ; Tůma, Jiří (advisor) ; Vábek, Jiří (referee)
Nazev prace: Konstrukce a kryptoanalyza AES (Advanced Encyption Standard) Autor: Jan Říha Katedra: Katedra Algebry Vedouci bakalafske prace: Doc. RNDr. Jin Tuma, DrSc. E-mail vedouciho bakalafske prace: Jiri.Tuma@mff.cuni.cz Abstrakt: V pfedlozene praci studujeme nejnovejsi symetrickou blokovou sifru AES. Nejprve se zabyvame vyvojem a vznikem sifry od vypsani souteze a2 po vyhlaseni vitezneho kandidata. Pote se venujeme jejf konstrukci, ve ktere se vyuziva nekterych netrivialnich poznatku algebry pfi praci s polynomy nad konecnym telesem. V teto kapitole je tez popsana prima inverzni sifra a ekvivalentni inverzni sifra slou^ici k desifrovani zasifrovanych dat. Ve tfeti kapitole zkoumame navrhovane implementace sifry AES na jednotlive platformy a nakonec rozebirame mozne utoky a odolnost Sifry AES vuci nim. Klicova slova: AES, sifra, implementace, kryptoanalyza Title: The design and cryptanalysis of the AES (Advanced Encyption Standard) Autor: Jan ftiha Department: Department of Algebra Supervisor: Doc. RNDr. Jin Tuma, DrSc. Supervisor's e-mail address: Jiri.Tuma@mff.cuni.cz Abstract: In the present work we study the newest symetric block cipher AES. At first we consider development and creation of the cipher from the start of selection proces till announcement of winning candidate. Then we turn to its...
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Advanced methods of Linear Cryptanalysis
Říha, Jan ; Rudolf, Bohuslav (advisor) ; Hojsík, Michal (referee)
In the present work we study advanced methods of linear cryptanalysis. At the beginning, we describe the principle of Matsui's linear cryptanalysis, the two basic algorithms - Algorithm 1 and Algorithm 2, against DES cipher. Further it is described a generalization of linear cryptanalysis and consequently partitioning and statistical cryptanalysis. Then it is followed by a look on the linear approximations over the correlation matrices. Furthermore, we study an improvement of Matsui's Algorithm 2 using Fast Fourier transform, based on circulant matrices theory. Finally we deal multidimensional linear cryptanalysis that uses multiple linear approximations and in the very end we propose an own design of improvement of multidimensional extension of Algorithm 2 by using Fast Fourier transform.
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