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Left-right asymmetry specification in vertebrates
Vrúbel, Matěj ; Soukup, Vladimír (advisor) ; Fabian, Peter (referee)
The left-right body axis, along with the dorso-ventral and antero-posterior axis, is certainly very important, but at the same time the most neglected body axis of bilaterally symmetrical animals. The asymmetrical distribution of visceral organs along this body axis is vital for many animals. In vertebrates, this asymmetry becomes established at early embryonic stages. An essential role in this process is played by the organizer, which is responsible for the correct establishment of the left-right axis. Among vertebrates, organizers of left-right asymmetry are found in different parts of the embryonic body, and with few exceptions, they are composed of cells with motile cilia, which create an unidirectional leftward flow of extracellular fluids in the organizer. The flow is probably sensed by the cells that surround the left side of the organizer. These cells respond to the aforementioned mechanical stimulus by triggering the Nodal signaling pathway. This signaling cascade results in the left-sided expression of the Pitx2 gene, which specifies the left side of the embryonic body. It appears, that the role of Nodal signaling pathway in determining left-right asymmetry is not only present in all vertebrates, but also is probably ancestral to bilaterally symmetrical animals. Another mechanism ensuring...
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The role of vent genes family in early development and brain development
Fabian, Peter ; Kozmík, Zbyněk (advisor) ; Němec, Pavel (referee) ; Balaštík, Martin (referee)
6 III ABSTRACT (ENGLISH) In chordates, the central nervous system (CNS) is derived from the dorsal part of gastrula. Induced dorsal part of the embryo - the neural plate - gives rise to the neural tube or primordial brain. The developing dorsal part of the embryo is shaped by BMP/Smad signaling from the ventral part. Using the basal chordate amphioxus, we show here the conserved evolutionary role BMP/Smad signaling in axial cell fate determination. Pharmalogical inhibition of BMP/Smad signaling induces dorsalization of Branchiostoma floridae (amphioxus) and Oryzias latipes (medaka) embryos and expansion of neural plate markers. We provide evidence for the presence of the positive regulatory loop within the BMP/Smad signaling network of amphioxus. Thus, our data suggest that early emergence of a positive feedback loop within the BMP/Smad signaling network may represent a crucial molecular event in the evolutionary history of the chordate cell fate determination. The dorso-ventral body axis formation is mediated by genes of the vent family, which are the direct targets of BMP/Smad signaling. The function of vent gene family in early development is relatively well known, however, its role in developing CNS is not yet clear. Therefore, we decided to manipulate vox transcription factor, a vent family member....
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Refaktorizace editoru stromů TrEd
Fabian, Peter ; Žabokrtský, Zdeněk (advisor) ; Kruliš, Martin (referee)
Title: Refactoring tree editor TrEd Author: Peter Fabian Department: Institute of Formal and Applied Linguistics Supervisor: doc. Ing. Zdenek Zabokrtsky, Ph.D., Institute of Formal and Applied Linguistics Abstract: The main goal of the thesis was to refactor tree editor TrEd, improve its modularity, maintainability and make its further development less difficult. Static and dynamic analysis of TrEd have been performed in order to help us find acrid spots in the source code. More than 230 subroutines and data structures have been moved between packages, 50 new packages and a test suite with more than 1,300 tests have been created. A new coding style have been chosen for further development and most severe violations of this standard have been fixed. After the changes done on the source code, it have been analyzed again and the results have been compared with the previous state. Keywords: Tree Editor TrEd, Perl, code refactoring, code analysis
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The role of vent genes family in early development and brain development
Fabian, Peter ; Kozmík, Zbyněk (advisor) ; Němec, Pavel (referee) ; Balaštík, Martin (referee)
6 III ABSTRACT (ENGLISH) In chordates, the central nervous system (CNS) is derived from the dorsal part of gastrula. Induced dorsal part of the embryo - the neural plate - gives rise to the neural tube or primordial brain. The developing dorsal part of the embryo is shaped by BMP/Smad signaling from the ventral part. Using the basal chordate amphioxus, we show here the conserved evolutionary role BMP/Smad signaling in axial cell fate determination. Pharmalogical inhibition of BMP/Smad signaling induces dorsalization of Branchiostoma floridae (amphioxus) and Oryzias latipes (medaka) embryos and expansion of neural plate markers. We provide evidence for the presence of the positive regulatory loop within the BMP/Smad signaling network of amphioxus. Thus, our data suggest that early emergence of a positive feedback loop within the BMP/Smad signaling network may represent a crucial molecular event in the evolutionary history of the chordate cell fate determination. The dorso-ventral body axis formation is mediated by genes of the vent family, which are the direct targets of BMP/Smad signaling. The function of vent gene family in early development is relatively well known, however, its role in developing CNS is not yet clear. Therefore, we decided to manipulate vox transcription factor, a vent family member....
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Refaktorizace editoru stromů TrEd
Fabian, Peter ; Žabokrtský, Zdeněk (advisor) ; Kruliš, Martin (referee)
Title: Refactoring tree editor TrEd Author: Peter Fabian Department: Institute of Formal and Applied Linguistics Supervisor: doc. Ing. Zdenek Zabokrtsky, Ph.D., Institute of Formal and Applied Linguistics Abstract: The main goal of the thesis was to refactor tree editor TrEd, improve its modularity, maintainability and make its further development less difficult. Static and dynamic analysis of TrEd have been performed in order to help us find acrid spots in the source code. More than 230 subroutines and data structures have been moved between packages, 50 new packages and a test suite with more than 1,300 tests have been created. A new coding style have been chosen for further development and most severe violations of this standard have been fixed. After the changes done on the source code, it have been analyzed again and the results have been compared with the previous state. Keywords: Tree Editor TrEd, Perl, code refactoring, code analysis
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Interactive Data Visualization Tool
Fabian, Peter ; Babka, Vlastimil (referee) ; Parízek, Pavel (advisor)
The goal of the work was to design and implement a tool, which would allow the users to work with a graphical representation of statistic data easily in an interactive manner. The IVP tool supports both the basic adjustments of graphs and advanced modifications, which are either very hard or impossible to achieve in similar tools. However, the key feature of the tool is its extensibility. The particular graph types and the interactive features are implemented as plug-ins and their functionality is provided to the tool's core. The thesis also presents a description of the IVP tool's implementation details, user documentation, an overview of the existing graphing software and its comparison to the IVP tool.
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