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Mammalian proteins carrying zinc finger arrays
Vobruba, Adam ; Svoboda, Petr (advisor) ; Mašek, Jan (referee)
A zinc finger is a small peptide motif stabilised by a single zinc ion, best known for its capability to specifically bind a 3-nucleotide sequence of DNA, depending on the exact amino acids present in the DNA-binding positions. Zinc fingers are unique in their ability to freely link together and form longer tandem arrays, which can bind DNA targets of any length and sequence determined by the combination of individual fingers. These arrays can easily mutate and be rebuilt to change binding specificity, allowing great flexibility and helping zinc fingers to their widespread presence in numerous endogenous proteins of various functions. This property of zinc finger arrays also made them a suitable tool for the creation of custom DNA- binding domains for genetic engineering. This thesis provides an overview of the discovery, structure and function of these domains and then reviews and discusses selected naturally occurring mammalian zinc finger proteins and their properties, showcasing diverse uses zinc finger arrays have been adapted for throughout evolution. The history and future of zinc fingers in artificial proteins created for gene therapy and research are discussed as well. Keywords: zinc finger, ZnF, KRAB, KZFP, CTCF, PRDM9, ZFN, mammals
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Growth factors in cultivated meat production
Janoušek, Jiří ; Rozbeský, Daniel (advisor) ; Mašek, Jan (referee)
The rapid expansion of global meat production poses severe environmental and ethical challenges, necessitating alternatives with reduced impacts. Cultivated meat, produced from animal cells in vitro, emerges as a promising solution. However, common cell culturing techniques using fetal bovine serum (FBS) are not sufficiently scalable for this purpose. The critical role of growth factors in replacing FBS is emphasized, with a focus on summarizing existing literature regarding their importance and potential for economically viable mass adoption. The described growth factor requirements of various cultivated meat production relevant cell types, as well as the potential improvements to the production processes, activity, or stability of the most important growth factors identified, are analyzed. Finally, alternative approaches to the use of growth factors are briefly explored. This work should provide a comprehensive overview of recombinant growth factor production and optimization as it pertains to the area of cultivated meat.
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Cohesive elements applied to advanced numerical simulation of concrete fracture
Veselý, Martin ; Mašek, Jan (referee) ; Miarka, Petr (advisor)
This bachelor’s thesis deals with the issue of a cohesive approach to modeling the fracture response of heterogeneous materials, such as concrete. This approach is one of the advanced methods for modeling fracture damage in heterogeneous materials. The first part introduces and describes the theoretical principles that need to be known and understood when modeling cohesive elements. In the practical part, single-element models were first created to verify the material properties of cohesive elements. Then complex geometry is created, which is subjected to a pressure test simulation. In conclusion, an evaluation of this approach to modeling in 2D is carried out.
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Simulation scenarios in NS2 demonstrating knowledge obtained in the MPKT course
Mašek, Jan ; Mlýnek, Petr (referee) ; Jeřábek, Jan (advisor)
The aim of the bachelor´s thesis is to develop simulation tasks for modeling of data networks. The tasks will be used in the course Modern communication technique (MKPT). The networks are simulated in the environment of Network Simulator 2 (NS2). A brief description of program environment NS2, as well as basics of Tcl language is mentioned in the introduction. Described is the possibility of simulation HTTP protocol in NS2 using OTcl PagePool classes. Totally six proposed tasks form the core of the thesis. The first task uses PagePool/Math and displays the simplest communication between client, server and cache. Next task uses PagePool/CompMath and it shows the communication between client, cache, Web server, FTP server and FTP client. The task, that uses PagePool/WebTraf class, simulates communication between two clients and three servers. The last three tasks are of different topologies and course of communication using PagePool/ProxyTrace. The exercises of this class are the most complicated and their input files allow defining whole communication. The outputs of exercises are given in graphs, log files of HTTP communication and the last task contains detailed instructions.
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Simulation of cryptographic algorithms using FPGA
Németh, František ; Mašek, Jan (referee) ; Smékal, David (advisor)
Bachelor thesis is dealing with a cipher standard AES and with a design of encryption and decryption components for AES in special modes of operation. Programming language is VHDL. In theoretical part of thesis is a further descriptions of AES and behaviour of block cipher operation modes. Furthermore the brief description of VHDL, FPGA and NetCOPE framework is a piece of theoretical part as well. The practical part contains designs which are made in developing environment Vivado from Xilinx. Programmed modes of operation are ECB, CBC, CTR and CFB. Simulation outputs and synthesis results are summerized in tables.
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Online interest point detector
Přibyl, Jakub ; Rajnoha, Martin (referee) ; Mašek, Jan (advisor)
This thesis focuses on online learning detector for long-term tracking of object in video sequence. The object is defined by a bounding box. The text describes different parts of the detector: object tracking, object detection and online learning detector. The main contribution of this work is creating extension of the OpenTLD program for parallel detection and tracking of multiple objects. The parallelization is then compared on two practical examples and the processor's impact on detection is compared. The best results were achieved with parallelization, where all objects were detected. The most accurate detection was in the case of sufficiently learned objects with the smallest shape change.
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Conditioning of Primary Systems for Solving by Flexibility Method
Sabelová, Katarína ; Mašek, Jan (referee) ; Frantík, Petr (advisor)
This bachelor thesis deals with effect of chosen basic determinate structure on solution of statically indeterminate structures obtained by using force method. Evaluation of basic determinate structure is based on conditioning of flexibility matrix, defined by three different condition numbers. Each of the four analyzed structures is examined in different way, due to their individual characteristics. As a result, few findings about dependence of conditioning of used basic structure on structures parameters and its effect on solution by force method were obtained.
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Computational tasks for Parallel data processing course
Horečný, Peter ; Rajnoha, Martin (referee) ; Mašek, Jan (advisor)
The goal of this thesis was to create laboratory excercises for subject „Parallel data processing“, which will introduce options and capabilities of Apache Spark technology to the students. The excercises focus on work with basic operations and data preprocessing, work with concepts and algorithms of machine learning. By following the instructions, the students will solve real world situations problems by using algorithms for linear regression, classification, clustering and frequent patterns. This will show them the real usage and advantages of Spark. As an input data, there will be databases of czech and slovak companies with a lot of information provided, which need to be prepared, filtered and sorted for next processing in the first excercise. The students will also get known with functional programming, because the are not whole programs in excercises, but just the pieces of instructions, which are not repeated in the following excercises. They will get a comprehensive overview about possibilities of Spark by getting over all the excercices.
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Indoor positioning system
Celeng, Michal ; Mašek, Jan (referee) ; Levek, Vladimír (advisor)
The work deals with the issue of indoor positiong system in the enviroment of the Android operating system, based on the efficient standard Bluetooth Low Energy, with conjunction of bluetooth beacons. The outcome of master‘s thesis is system topology, description of its components, standards needed for his creation and finally construction of the system.
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Static analysis of the office building
Golisová, Michaela ; Mašek, Jan (referee) ; Vlk, Zbyněk (advisor)
This bachelor thesis contains design and structural analysis of monolitic reinforced concrete frame structure of a high rise office building. Spatial bar model was created from my own design using RFEM software, in which it was then linearly statically analysed using Finite Element Method. RF - CONCRETE plug-in was used for prelminary design of necessary reinforcement.
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