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19 results on '"Kubát, Zdeněk"'

1. Sexy ways: the methodical approaches to study plant sex chromosomes

Author

Hobza, Roman, primary, Bačovský, Václav, additional, Čegan, Radim, additional, Horáková, Lucie, additional, Hubinský, Marcel, additional, Janíček, Tomáš, additional, Janoušek, Bohuslav, additional, Jedlička, Pavel, additional, Kružlicová, Jana, additional, Kubát, Zdeněk, additional, Rodríguez Lorenzo, José Luis, additional, Novotná, Pavla, additional, and Hudzieczek, Vojtěch, additional

Published
2024
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2. Sexy ways: approaches to studying plant sex chromosomes.

Author

Hobza, Roman, Bačovský, Václav, Čegan, Radim, Horáková, Lucie, Hubinský, Marcel, Janíček, Tomáš, Janoušek, Bohuslav, Jedlička, Pavel, Kružlicová, Jana, Kubát, Zdeněk, Lorenzo, José Luis Rodríguez, Novotná, Pavla, and Hudzieczek, Vojtěch

Subjects
SEX chromosomes, CHROMOSOME analysis, CHROMOSOME structure, MOLECULAR biology, PLANT epigenetics
Abstract

Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the specific genetic and epigenetic mechanisms responsible for shaping distinct sexes in plants. While the fundamental methods of molecular biology and genomics are generally employed for the analysis of sex chromosomes, it is often necessary to modify classical procedures not only to simplify and expedite analyses but sometimes to make them possible at all. In this review, we demonstrate how, at the level of structural and functional genetics, cytogenetics, and bioinformatics, it is essential to adapt established procedures for sex chromosome analysis. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia.

Author

Hubinský, Marcel, Hobza, Roman, Starczak, Marta, Gackowski, Daniel, Kubát, Zdeněk, Janíček, Tomáš, Horáková, Lucie, and Lorenzo, Jose Luis Rodriguez

Subjects
SEX chromosomes, DIOECIOUS plants, PLANT chromosomes, X chromosome, GENETIC regulation, METHYLCYTOSINE
Abstract

The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia , a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa.

Author

Jesionek, Wojciech, Bodláková, Markéta, Kubát, Zdeněk, Čegan, Radim, Vyskot, Boris, Vrána, Jan, Šafář, Jan, Puterova, Janka, and Hobza, Roman

Subjects
SEX chromosomes, Y chromosome, X chromosome, GENETIC sex determination, CHROMOSOME structure, TANDEM repeats, FLUORESCENCE in situ hybridization
Abstract

Background and Aims Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. Methods We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. Key Results We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. Conclusions The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage. [ABSTRACT FROM AUTHOR]

Published
2021
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9. Satellite DNA and Transposable Elements in Seabuckthorn ( Hippophae rhamnoides ), a Dioecious Plant with Small Y and Large X Chromosomes

Author

Puterová, Janka, Razumova, Olga, Martínek, Tomáš, Alexandrov, Oleg, Divashuk, Mikhail, Kubát, Zdeněk, Hobza, Roman, Karlov, Gennady, Kejnovský, Eduard, Puterová, Janka, Razumova, Olga, Martínek, Tomáš, Alexandrov, Oleg, Divashuk, Mikhail, Kubát, Zdeněk, Hobza, Roman, Karlov, Gennady, and Kejnovský, Eduard

Abstract

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome.We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes., Rakytník (Hippophae rhamnoides) je dvoudomý keř bežně používán ve farmaceutickém, kosmetickém a enviromentálním průmyslu jako zdroj oleje, minerálů a vitamínů. V této studii jsme analyzovali transpozony a satelity v jeho genomu. Vykonali jsme Illumina sekvenování a rekonstruovali jsme hlavní repetitivní DNA sekvence. Pro analýzu dat jsme vyvinuli nový bioinformatický přístup pro pokročilou analýzu satelitní DNA a ukázali jsme, že okolo 25% genomu tvoří satelitní DNA a asi 24% je tvořených transpozony, u kterých dominují Ty3/Gypsy a Ty1/Copia LTR retrotranspozony. FISH mapování odhalilo satelit akumulovaný na X chromozomu, Y specifický satelit a satelit akumulovaný na obou pohlavních chromozomech, přičemž většina satelitů byla nalzena na autosomech. Transpozibilní elementy byly umístněny většinou v subtelomerách všech chromozomů. 5S rDNA a 45S rDNA byly lokalizovány každá na jednom autosomálním lokusu. Přestože jsme demonstrovali malou velikost Y chromozomu a na něm akumulovanou satelitní DNA, nebyli jsme schopni odhadnou věk a rozsah degenerace Y chromozomu. Analýza dvoudomých příbuzných jako je např. Shepherdia by lépe objasnila evoluci pohlavních chromosomů.

Published
2017

10. Overexpression of a flower-specific aerolysin-like protein from the dioecious plantRumex acetosaalters flower development and induces male sterility in transgenic tobacco

Author

Manzano, Susana, primary, Megías, Zoraida, additional, Martínez, Cecilia, additional, García, Alicia, additional, Aguado, Encarnación, additional, Chileh, Tarik, additional, López-Alonso, Diego, additional, García-Maroto, Federico, additional, Kejnovský, Eduard, additional, Široký, Jiří, additional, Kubát, Zdeněk, additional, Králová, Tereza, additional, Vyskot, Boris, additional, and Jamilena, Manuel, additional

Published
2016
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11. Overexpression of a flower-specific aerolysin-like protein from the dioecious plant Rumex acetosa alters flower development and induces male sterility in transgenic tobacco.

Author

Manzano, Susana, Megías, Zoraida, Martínez, Cecilia, García, Alicia, Aguado, Encarnación, Chileh, Tarik, López‐Alonso, Diego, García‐Maroto, Federico, Kejnovský, Eduard, Široký, Jiří, Kubát, Zdeněk, Králová, Tereza, Vyskot, Boris, and Jamilena, Manuel

Subjects
RUMEX acetosa, GENETIC overexpression, AEROLYSIN, FLOWER development, MALE sterility in plants, TOBACCO, TRANSGENIC plants
Abstract

Sex determination in Rumex acetosa, a dioecious plant with a complex XY1Y2 sex chromosome system (females are XX and males are XY1Y2), is not controlled by an active Y chromosome but depends on the ratio between the number of X chromosomes and autosomes. To gain insight into the molecular mechanisms of sex determination, we generated a subtracted cDNA library enriched in genes specifically or predominantly expressed in female floral buds in early stages of development, when sex determination mechanisms come into play. In the present paper, we report the molecular and functional characterization of FEM32, a gene encoding a protein that shares a common architecture with proteins in different plants, animals, bacteria and fungi of the aerolysin superfamily; many of these function as β pore-forming toxins. The expression analysis, assessed by northern blot, RT- PCR and in situ hybridization, demonstrates that this gene is specifically expressed in flowers in both early and late stages of development, although its transcripts accumulate much more in female flowers than in male flowers. The ectopic expression of FEM32 under both the constitutive promoter 35S and the flower-specific promoter AP3 in transgenic tobacco showed no obvious alteration in vegetative development but was able to alter floral organ growth and pollen fertility. The 35S:: FEM32 and AP3:: FEM32 transgenic lines showed a reduction in stamen development and pollen viability, as well as a diminution in fruit set, fruit development and seed production. Compared with other floral organs, pistil development was, however, enhanced in plants overexpressing FEM32. According to these effects, it is likely that FEM32 functions in Rumex by arresting stamen and pollen development during female flower development. The aerolysin-like pore-forming proteins of eukaryotes are mainly involved in defence mechanisms against bacteria, fungi and insects and are also involved in apoptosis and programmed cell death ( PCD), a mechanism that could explain the role of FEM32 in Rumex sex determination. [ABSTRACT FROM AUTHOR]

Published
2017
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12. Kompilátor zdrojového kódu pro PLC SIMATIC

Author

Pásek, Jan, Kaczmarczyk, Václav, Kubát, Zdeněk, Pásek, Jan, Kaczmarczyk, Václav, and Kubát, Zdeněk

Abstract

Tato diplomová práce popisuje nezávislý kompilátor pro aplikace STEP 7 a WinCC V7.0 společnosti SIEMENS. Kompilátor zpracovává zdrojový soubor generovaný ze STEP 7 a následně ukládá zpracovaná data do mezisouboru typu .xls. Data mezisouboru slouží jako zdrojová data pro funkce generující soubory s tagy, připravenými na import do WinCC V7.0. Pro vytvoření kompilátoru v prostředí Visual Studio 2010 byl použit programovací jazyk C#., The thesis discusses an independent compiler for STEP 7 and WinCC V7.0 applications of the SIEMENS company. The compiler processes source files generated in STEP 7 and subsequently saves the processed data in .xls type intermediatefiles. The data of the intermediatefiles serve as source data for functions generating files with tags to be imported into WinCC V7.0. The compiler was created using the C# programming language in Visual Studio 2010.

13. Kompilátor zdrojového kódu pro PLC SIMATIC

Author

Pásek, Jan, Kaczmarczyk, Václav, Kubát, Zdeněk, Pásek, Jan, Kaczmarczyk, Václav, and Kubát, Zdeněk

Abstract

Tato diplomová práce popisuje nezávislý kompilátor pro aplikace STEP 7 a WinCC V7.0 společnosti SIEMENS. Kompilátor zpracovává zdrojový soubor generovaný ze STEP 7 a následně ukládá zpracovaná data do mezisouboru typu .xls. Data mezisouboru slouží jako zdrojová data pro funkce generující soubory s tagy, připravenými na import do WinCC V7.0. Pro vytvoření kompilátoru v prostředí Visual Studio 2010 byl použit programovací jazyk C#., The thesis discusses an independent compiler for STEP 7 and WinCC V7.0 applications of the SIEMENS company. The compiler processes source files generated in STEP 7 and subsequently saves the processed data in .xls type intermediatefiles. The data of the intermediatefiles serve as source data for functions generating files with tags to be imported into WinCC V7.0. The compiler was created using the C# programming language in Visual Studio 2010.

14. Kompilátor zdrojového kódu pro PLC SIMATIC

Author

Pásek, Jan, Kaczmarczyk, Václav, Kubát, Zdeněk, Pásek, Jan, Kaczmarczyk, Václav, and Kubát, Zdeněk

Abstract

Tato diplomová práce popisuje nezávislý kompilátor pro aplikace STEP 7 a WinCC V7.0 společnosti SIEMENS. Kompilátor zpracovává zdrojový soubor generovaný ze STEP 7 a následně ukládá zpracovaná data do mezisouboru typu .xls. Data mezisouboru slouží jako zdrojová data pro funkce generující soubory s tagy, připravenými na import do WinCC V7.0. Pro vytvoření kompilátoru v prostředí Visual Studio 2010 byl použit programovací jazyk C#., The thesis discusses an independent compiler for STEP 7 and WinCC V7.0 applications of the SIEMENS company. The compiler processes source files generated in STEP 7 and subsequently saves the processed data in .xls type intermediatefiles. The data of the intermediatefiles serve as source data for functions generating files with tags to be imported into WinCC V7.0. The compiler was created using the C# programming language in Visual Studio 2010.

15. Knihovna FACEPLATE pro prostředí WinCC v11

Author

Pásek, Jan, Zezulka, František, Kubát, Zdeněk, Pásek, Jan, Zezulka, František, and Kubát, Zdeněk

Abstract

Prvním cílem této bakalářské práce bylo ověřit, za jakých podmínek lze uskutečnit migraci knihovny FACEPLATE z WinCC verze 7 do WinCC verze 11. Druhým cílem bylo vytvořit grafické objekty elektrovýzbroje knihovny FACEPLATE pro prostředí WinCC verze 11 SP2. Každý objekt v knihovně byl programově vybaven pro snadné navázání na stávající kód uložený v PLC. Poslední část práce je věnována ověření funkčnosti vytvořené knihovny na modelovém příkladu., The first goal of this Bc. work was to verify if and under what circumstances is it possible for the FACEPLATE library to migrate from WinCC version 7 into WinCC version 11. The second goal was to create graphical objects of electric equipment of the FACEPLATE library for the environment of WinCC version 11 SP2. Each object in the library was given a program for easy connect with code saved in PLC. The last part of the work is dedicated to verification of functionality of the created library using a model example.

16. Kompilátor zdrojového kódu pro PLC SIMATIC

Author

Pásek, Jan, Kaczmarczyk, Václav, Kubát, Zdeněk, Pásek, Jan, Kaczmarczyk, Václav, and Kubát, Zdeněk

Abstract

Tato diplomová práce popisuje nezávislý kompilátor pro aplikace STEP 7 a WinCC V7.0 společnosti SIEMENS. Kompilátor zpracovává zdrojový soubor generovaný ze STEP 7 a následně ukládá zpracovaná data do mezisouboru typu .xls. Data mezisouboru slouží jako zdrojová data pro funkce generující soubory s tagy, připravenými na import do WinCC V7.0. Pro vytvoření kompilátoru v prostředí Visual Studio 2010 byl použit programovací jazyk C#., The thesis discusses an independent compiler for STEP 7 and WinCC V7.0 applications of the SIEMENS company. The compiler processes source files generated in STEP 7 and subsequently saves the processed data in .xls type intermediatefiles. The data of the intermediatefiles serve as source data for functions generating files with tags to be imported into WinCC V7.0. The compiler was created using the C# programming language in Visual Studio 2010.

17. Knihovna FACEPLATE pro prostředí WinCC v11

Author

Pásek, Jan, Zezulka, František, Kubát, Zdeněk, Pásek, Jan, Zezulka, František, and Kubát, Zdeněk

Abstract

Prvním cílem této bakalářské práce bylo ověřit, za jakých podmínek lze uskutečnit migraci knihovny FACEPLATE z WinCC verze 7 do WinCC verze 11. Druhým cílem bylo vytvořit grafické objekty elektrovýzbroje knihovny FACEPLATE pro prostředí WinCC verze 11 SP2. Každý objekt v knihovně byl programově vybaven pro snadné navázání na stávající kód uložený v PLC. Poslední část práce je věnována ověření funkčnosti vytvořené knihovny na modelovém příkladu., The first goal of this Bc. work was to verify if and under what circumstances is it possible for the FACEPLATE library to migrate from WinCC version 7 into WinCC version 11. The second goal was to create graphical objects of electric equipment of the FACEPLATE library for the environment of WinCC version 11 SP2. Each object in the library was given a program for easy connect with code saved in PLC. The last part of the work is dedicated to verification of functionality of the created library using a model example.

18. Kompilátor zdrojového kódu pro PLC SIMATIC

Author

Pásek, Jan, Kaczmarczyk, Václav, Kubát, Zdeněk, Pásek, Jan, Kaczmarczyk, Václav, and Kubát, Zdeněk

Abstract

Tato diplomová práce popisuje nezávislý kompilátor pro aplikace STEP 7 a WinCC V7.0 společnosti SIEMENS. Kompilátor zpracovává zdrojový soubor generovaný ze STEP 7 a následně ukládá zpracovaná data do mezisouboru typu .xls. Data mezisouboru slouží jako zdrojová data pro funkce generující soubory s tagy, připravenými na import do WinCC V7.0. Pro vytvoření kompilátoru v prostředí Visual Studio 2010 byl použit programovací jazyk C#., The thesis discusses an independent compiler for STEP 7 and WinCC V7.0 applications of the SIEMENS company. The compiler processes source files generated in STEP 7 and subsequently saves the processed data in .xls type intermediatefiles. The data of the intermediatefiles serve as source data for functions generating files with tags to be imported into WinCC V7.0. The compiler was created using the C# programming language in Visual Studio 2010.

19. Kompilátor zdrojového kódu pro PLC SIMATIC

Author

Pásek, Jan, Kaczmarczyk, Václav, Kubát, Zdeněk, Pásek, Jan, Kaczmarczyk, Václav, and Kubát, Zdeněk

Abstract

Tato diplomová práce popisuje nezávislý kompilátor pro aplikace STEP 7 a WinCC V7.0 společnosti SIEMENS. Kompilátor zpracovává zdrojový soubor generovaný ze STEP 7 a následně ukládá zpracovaná data do mezisouboru typu .xls. Data mezisouboru slouží jako zdrojová data pro funkce generující soubory s tagy, připravenými na import do WinCC V7.0. Pro vytvoření kompilátoru v prostředí Visual Studio 2010 byl použit programovací jazyk C#., The thesis discusses an independent compiler for STEP 7 and WinCC V7.0 applications of the SIEMENS company. The compiler processes source files generated in STEP 7 and subsequently saves the processed data in .xls type intermediatefiles. The data of the intermediatefiles serve as source data for functions generating files with tags to be imported into WinCC V7.0. The compiler was created using the C# programming language in Visual Studio 2010.

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