528 research outputs found
The Life and Work of the Historian and Teacher Zdenek Macek
No full textZdeněk Macek publikoval velké množství článku, týkajících se událostí první poloviny 20. století. Jako zdroj informací používal dobový tisk. Stal se průkopníkem v používání dobového tisku jako zdroje informací. Kromě mnoha článků ve sbornících je Zdeněk Macek autorem několika skript a středoškolských učebnic.
Předkládaná diplomová práce přináší zpracování odkazu této významné osobnosti plzeňského a hradeckého vysokého školství a vznikla z důvodu, aby tato osobnost neupadla v zapomnění.Katedra historieObhájenoZdeněk Macek published many articles concerning the events of the first half of the twentieth century. As a source of information, he used newspapers from the given historical time period. He became a pioneer of using this method as a source of information. Aside from many articles in compilations Zdeněk Macek is also the author of several university and high school textbooks.
The presented thesis brings an analysis of the legacy of this significant personality of the Pilsen and Hradec Králové university realm and was created for the purpose of remembering such an outstanding figure
Music lexicographer Jiří Fukač and the Brno School of Music Lexicography
No full textThe study summarizes the activity in the field of music lexicography of Jiří Fukač (1936–2002), professor of musicology at the Brno-based Masaryk University, who successfully resumed the activities of the Brno School of Music Lexicography, constituted chiefly by efforts of Gracian Černušák, Vladimír Helfert and Bohumír Štědroň. Already as a student Fukač collaborated as both author and organizer on the two-volume Československý hudební slovník osob a institucí (Czechoslovak Music Dictionary of Persons and Institutions, 1963, 1965). In 1966 he and Jiří Vysloužil initiated foundation of Kabinet hudební lexikografie (Office of Music Lexicography) and preparations for the new subject-focused dictionary project, later called Slovník české hudební kultury (Dictionary of Czech Music Culture) started. Fukač’s contribution was crucial and it was his tireless effort including writing texts of individual entries, editing texts by others and effecting his organizational skills, that finally lead to the successful completion of the project in 1997. The result undoubtedly presents a fundament in Czech music lexicography in both conception and extent. Then Jiří Fukač started to work on further projects of music lexicography: he actively participated in preparations and realization of the big lexicographical project of the Sudeten German Music Institute in Regensburg titled Lexikon zur deutschen Musikkultur (Böhmen, Mähren, Sudetenschlesien) published in Munich in 2000, where he was member of the scholarly board of the project and contributed to the conceptual and methodological preparations. In 2000 Fukač together with Petr Macek and Mikuláš Bek started preparations for the new web-based project of the Czech Music Dictionary of Persons and Institutions. A fatal illness didn't allow him to proceed further.The study summarizes the activity in the field of music lexicography of Jiří Fukač (1936–2002), professor of musicology at the Brno-based Masaryk University, who successfully resumed the activities of the Brno School of Music Lexicography, constituted chiefly by efforts of Gracian Černušák, Vladimír Helfert and Bohumír Štědroň. Already as a student Fukač collaborated as both author and organizer on the two-volume Československý hudební slovník osob a institucí (Czechoslovak Music Dictionary of Persons and Institutions, 1963, 1965). In 1966 he and Jiří Vysloužil initiated foundation of Kabinet hudební lexikografie (Office of Music Lexicography) and preparations for the new subject-focused dictionary project, later called Slovník české hudební kultury (Dictionary of Czech Music Culture) started. Fukač’s contribution was crucial and it was his tireless effort including writing texts of individual entries, editing texts by others and effecting his organizational skills, that finally lead to the successful completion of the project in 1997. The result undoubtedly presents a fundament in Czech music lexicography in both conception and extent. Then Jiří Fukač started to work on further projects of music lexicography: he actively participated in preparations and realization of the big lexicographical project of the Sudeten German Music Institute in Regensburg titled Lexikon zur deutschen Musikkultur (Böhmen, Mähren, Sudetenschlesien) published in Munich in 2000, where he was member of the scholarly board of the project and contributed to the conceptual and methodological preparations. In 2000 Fukač together with Petr Macek and Mikuláš Bek started preparations for the new web-based project of the Czech Music Dictionary of Persons and Institutions. A fatal illness didn't allow him to proceed further
Music lexicographer Jiří Fukač and the Brno School of Music Lexicography
No full textThe study summarizes the activity in the field of music lexicography of Jiří Fukač (1936–2002), professor of musicology at the Brno-based Masaryk University, who successfully resumed the activities of the Brno School of Music Lexicography, constituted chiefly by efforts of Gracian Černušák, Vladimír Helfert and Bohumír Štědroň. Already as a student Fukač collaborated as both author and organizer on the two-volume Československý hudební slovník osob a institucí (Czechoslovak Music Dictionary of Persons and Institutions, 1963, 1965). In 1966 he and Jiří Vysloužil initiated foundation of Kabinet hudební lexikografie (Office of Music Lexicography) and preparations for the new subject-focused dictionary project, later called Slovník české hudební kultury (Dictionary of Czech Music Culture) started. Fukač’s contribution was crucial and it was his tireless effort including writing texts of individual entries, editing texts by others and effecting his organizational skills, that finally lead to the successful completion of the project in 1997. The result undoubtedly presents a fundament in Czech music lexicography in both conception and extent. Then Jiří Fukač started to work on further projects of music lexicography: he actively participated in preparations and realization of the big lexicographical project of the Sudeten German Music Institute in Regensburg titled Lexikon zur deutschen Musikkultur (Böhmen, Mähren, Sudetenschlesien) published in Munich in 2000, where he was member of the scholarly board of the project and contributed to the conceptual and methodological preparations. In 2000 Fukač together with Petr Macek and Mikuláš Bek started preparations for the new web-based project of the Czech Music Dictionary of Persons and Institutions. A fatal illness didn't allow him to proceed further
Hochgenaue Massenspektrometrie zur Verbesserung genomischer Annotationen
No full textMajor improvements in DNA sequencing technologies during the last decade gave rise to “next generation sequencing” (NGS) technology, that enables routine sampling of entire genomes and transcriptomes of various organisms; however, the annotation of the raw genome sequence remains a big challenge for ab initio gene prediction programs. Experimental evidence of gene expression at the RNA and protein level can be used to train the machine learning algorithms and greatly improves accuracy of the resulting gene predictions. While NGS can provide gene expression data at the transcript level, translational evidence of genes on a large scale can only be addressed using mass spectrometry (MS)-based proteomics. Moreover, this technology is an indispensable tool to study regulatory post translational protein modifications (PTMs) such as phosphorylation. In this work I studied to what extent high accuracy MS-based proteomics can contribute to refining genome sequencing data, which is in focus of a fast-evolving research field termed “proteogenomics”. I first addressed the main parameters of a simple proteogenomic experiment, such as the actual false discovery rate of protein database search and sequence coverage of a bacterial genome using state-of-the-art MS technology. To that end I used a comprehensive proteome dataset of the model gram negative bacterium Escherichia coli, comprising its complete expressed proteome in exponential growth, and applied this approach to its well characterized genome. This analysis demonstrated a substantial underestimation of the false discovery rate in a commonly used proteogenomics workflow and pointed to the need for further improvement of sequence coverage in shotgun proteomic experiments. I further demonstrated the utility of proteogenomics in annotation of protein coding regions of a complex, eukaryotic genome on the example of Pristionchus pacificus, a model nematode increasingly used in evolutionary biology. The application led to the identification of several thousand novel peptide sequences that were used, together with transcriptomic data, to refine the existing genome annotation. Finally, I studied functional aspects of the refined P. pacificus proteome by using data from an in-depth phosphoproteomic study which enabled me to describe functional categories of detected P. pacificus phosphoproteins, to define its kinome and to perform a comparative analysis with a recent phosphoproteomics study of the model nematode Caenorhabditis elegans. Taken together, this work demonstrates the value of high accuracy MS based proteomics in refinement of genome sequencing data.Im Verlauf des letzten Jahrzehnts führten wesentliche Verbesserungen der Techniken zur DNA Sequenzierung zu einer neuen Generation von Sequenzierungstechnologien („next generation sequencing“, NGS), welche eine routinemäßige Sequenzierung ganzer Genome und Transkriptome verschiedenster Organismen ermöglichte. Die Annotation der Genomsequenz stellt nach wie vor eine Herausforderung für Programme zur ab initio Genvorhersage dar, welche auf Algorithmen des maschinellen Lernens basieren. Experimentelle Bestätigung von Genexpression auf RNA- und Proteinebene kann dazu verwendet werden, die Genauigkeit der Genvorhersagen enorm zu verbessern. Während NGS Technologien Genexpressionsdaten auf der Ebene der Transkription generieren, kann die Bestätigung der Translation global nur mittels Massenspektrometrie (MS)-basierter Proteomik analysiert werden. Darüber hinaus stellt diese Technologie ein unverzichtbares Werkzeug zur Untersuchung regulatorischer, posttranslationaler Proteinmodifikationen (PTM), wie zum Beispiel Phosphorylierung, dar. In dieser Arbeit untersuche ich, in welchem Umfang hochgenaue, MS-basierte Proteomik zur Verbesserung der Annotation von genomischen Sequenzierdaten beitragen kann, welches im Fokus einer sich rasant entwickelten Forschungszweigs namens „Proteogenomik“ steht. Zuerst untersuche ich grundlegende Parameter eines einfachen proteogenomischen Experimentes, wie zum Beispiel die eigentliche Fehlerrate (false discovery rate, FDR) und Sequenzabdeckung eines bakteriellen Genoms mittels modernster MS Technologie gewonnener Daten. Hierzu verwende ich einen umfassenden Proteomdatensatz des gram-negativen Modelbakteriums Escherichia coli, bestehend aus allen exprimierten Proteinen der exponentiellen Wachstumsphase, und wende diesen auf das sehr gut charakterisierte Genom des Bakteriums an. Dieser Versuch zeigte eine erhebliche Unterschätzung der Fehlerrate (FDR) einer häufig verwendeten Vorgehensweise, und deutete auf die Notwendigkeit hin, die Sequenzabdeckung MS-basierter Proteomik zu verbessern. Des Weiteren demonstriere ich den Nutzen eines proteogenomischen Experiments bei der Annotation Protein kodierender Bereiche eines komplexen, eukaryotischen Genoms am Beispiel des Fadenwurms Pristionchus pacificus, welcher vermehrt als Modellorganismus in der Evolutionsbiologie verwendet wird. Das Experiment führte zur Identifikation mehrerer Tausend, bisher unbekannter Peptidsequenzen. Diese wurden zusammen mit Transkriptionsdaten dazu verwendet, die existierende Annotation des Genoms zu verbessern. Abschließend betrachte ich die verbesserte Annotation des P. pacificus Proteoms, um dessen funktionelle Aspekte zu untersuchen. Dazu verwende ich Daten eines MS-basierten Experiments zur globalen Identifikation von Proteinphosphorylierungsstellen, um die phosphorylierten Proteine funktionell zu chrakterisieren, das Kinom des Organismus zu bestimmen und die gewonnenen Ergebnisse mit einer jüngst veröffentlichten Studie des Phosphoproteoms des Modellorganismus Caenorhabditis elegans zu vergleichen. Zusammengenommmen demonstriert diese Arbeit den Nutzen hochgenauer MS-basierter Proteomik in der Verbesserung von Genomsequenzierungsdaten
Post-Translational Regulation of Bacterial Physiology by Ser/Thr Kinases HipA and HipH - A Mass Spectrometry Study
No full textPost-translational modifications (PTMs) play an indispensable role in the rapid execution
of responses that regulate a number of biological functions. Protein Ser/Thr kinases
(STKs) are key regulators of vital cellular processes, including antibiotic tolerance,
metabolism, virulence, and stress response. Despite their importance, the molecular
mechanisms and targets of STKs are underinvestigated, especially in the context of
post-translational regulation in pathogenic bacteria. Antibiotic tolerance and persistence
are a major contributor to the relapse of many chronic infections and frequently result in
antibiotic overuse and the development of antibiotic resistance. One of the best-studied
drivers of persistence is a Ser/Thr kinase HipA, first characterized in Escherichia coli.
Multiple HipA-like kinases have been recently reported to be present in bacteria,
including pathogens such as Klebsiella pneumoniae, but their functions remain poorly
understood. In my thesis, I focused on elucidating the function of two such STKs, HipH
(YjjJ) in E. coli and HipA in K. pneumoniae to understand their potential role in regulating
cellular processes.
To explore this, I applied state-of-the-art mass spectrometry-based quantitative
phosphoproteomics to gain new insights into the functions and substrates of these
kinases and fill crucial gaps in knowledge of bacterial physiology and pathogenesis. I
first reviewed recent advances in quantitative phosphoproteomics to highlight the utility
of LC-MS/MS technologies combined with quantitative proteomics strategies to
investigate dynamic phosphorylation changes during various biological processes. I
then applied this technology to study HipA-family Ser/Thr kinase HipH (YjjJ) in E. coli.
Using quantitative phosphoproteomics based on stable isotope labeling by amino acids
in cell culture (SILAC) and in vitro kinase assay, I demonstrated that HipH
phosphorylates specific targets such as the ribosomal protein RpmE and the carbon
storage regulator CsrA. Therefore, HipH plays an important role in regulating ribosome
assembly, cell division, and central carbon metabolism, but it does not confer antibiotic
tolerance like its homolog HipA. I have also shown that HipH cross-talks with other
bacterial kinases, revealing a complex network of regulatory interactions. The final part
of my work focused on Klebsiella pneumoniae, a major cause of antibiotic-resistant
VIII
nosocomial infections worldwide. I demonstrated that overproduced K. pneumoniae
HipA (HipAkp) is toxic to both E. coli and K. pneumoniae, and this toxicity can be rescued
by overproduction of the antitoxin HipBkp. Importantly, I showed that HipAkp
overproduction leads to increased tolerance against ciprofloxacin, linking HipA activity
to antibiotic persistence in this organism. Through proteome and phosphoproteome
analyses, I confirmed that HipAkp has Ser/Thr kinase activity, auto-phosphorylates at
S150, and shares multiple substrates with its E. coli counterpart. I performed a
comprehensive analysis of the K. pneumoniae phosphoproteome with HipAkp
overproduction to generate the largest dataset of phosphorylated proteins for this
bacterium.
Overall, my work provides an in-depth analysis of the roles of the two HipA-like kinases
in antibiotic tolerance and metabolism, offering new insights into their functions and
regulatory networks. These findings also provide a foundation for future research on
post-translational regulation of bacterial physiology
Work safety in production processes located in Poland
No full textThis article presents selected aspects connected to work safety, related to production facilities in Poland, where production lines are installed as new, or transferred from other locations. The author focuses on ensuring work safety from the moment the decision of is made by company authorities, through the transfer of all production means and their commissioning to a regular production stage. The article contains the review of legislation, literature on technology transfer as well as researches and experiences of the author gained during his cooperation with international companies from the
industries like food, energy, automotive and others
Impact of phosphoproteomics on studies of bacterial physiology
No full textProtein phosphorylation on serine, threonine and tyrosine is recognized as a major tool of signal transduction in bacteria. However, progress in the field has been hampered by the lack of global and site-specific data on bacterial phosphoproteomes. Recent advances in mass spectrometrybased proteomics have encouraged bacteriologists to start using powerful gel-free approaches for global detection of phosphorylated proteins. These studies have generated large data sets of proteins phosphorylated on serine, threonine and tyrosine, with identified phosphorylation sites which represent an excellent starting point for in-depth physiological characterization of kinases and their substrates. The list of phosphorylated proteins inspired a number of physiological studies in which the identity of the phosphorylation site facilitated the elucidation of molecular mechanisms of signaling and regulation. Bacterial phosphoproteomics also provided interesting insights into the evolutionary aspects of protein phosphorylation. The field is rapidly embracing quantitative mass spectrometry strategies, comparing phosphoproteome dynamics in changing conditions and aiming to reconstruct the entire regulatory networks by linking kinases to their physiological substrates
Site-specific analysis of bacterial phosphoproteomes
No full textProtein phosphorylation on serine, threonine and tyrosine is established as an important regulatory modification in bacteria. A growing number of studies employing mass spectrometry-based proteomics report large protein phosphorylation datasets, providing precise evidence for in-vivo phosphorylation that is especially suitable for functional follow-up. Here, we provide an overview of the strategies currently used in bacterial phosphoproteomics, with an emphasis on gel-free proteomics and approaches that enable global detection of phosphorylation sites in bacterial proteins. The proteomics technology has matured sufficiently to permit routine characterization of phosphoproteomes and phosphopeptides with high sensitivity; we argue that the next challenge in the field will be the large-scale detection of protein kinase and phosphatase substrates and their integration into regulatory networks of the bacterial cell
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