Number of found documents: 438
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"Characterization of Pathogenic Variants of Mitochondrial Carriers and Transporters With the Use of Biochemical Methods: Revealing Novel Mutations and Deletions in Patient Samples, Assumed to be Associated With Rare Diseases."
BEHENSKY, Magdalena Maria
2022 - English
Research concerning orphan diseases pose a challenge to the scientific community, however, they are both of great interest and great necessity, leading to the improvement of treatment opportunities for the 263 to 446 million people affected worldwide and, subsequently, their quality of life. The presence of mitochondria in virtually all kinds of cells, with the exception of mature erythrocytes, make clinical diagnosis of mitochondrial diseases extremely challenging and difficult, as dysfunction in mitochondria can affect any organ, or even whole organ systems. A major challenge for modern medical science, is the identification of the genes affected, which cause specific rare diseases in humans. New technologies, such as next-generation sequencing, and, therefore, the possibility of identifying genetic variations, are rapidly proceeding. Consequently, available treatments, or genetic counseling can be found more often. SLC25A3 is a mitochondrial phosphate-carrier responsible for the transport of inorganic phosphate into the mitochondrial matrix, which is required for the final step of oxidative phosphorylation, and the process of aerobic synthesis of ATP. Alteration in this gene, located on chromosome 12q23.1, is known to cause PiC deficiency (OMIM 610773), which affects the heart-/muscle-specific phosphate-carrier isoform A (PiC-A) [19, 23, 24, 26]. The aim of the Master's Thesis, was to ascertain the impact of the mutation on the activity of the phosphate carrier, and the patient's resulting life expectancies. Previously, three mutations have been described in seven patients, as being homozygous, affecting exon 3A, with the exception of one, which is compound heterozygous and affecting exon 4. The four novel SLC25A3 mutations (p.Gly72Glu, p.Thr81Lys, p.Asp87Tyr, p.Ala124Pro) are homozygous, one (p.Gly72Glu) having been described previously [19,26,30]. In the context of this thesis, four patient samples were used for experimentation, each containing one of these homozygous mutations. SLC19A3 encodes the thiamine transporter 2 (hTHTR2), dysfunctions lead to recurrent encephalopathy, basal ganglia necrosis, generalized dystonia, severe disability and early death. Patients with changes in SLC19A3, located on the second chromosome (q36.3), show a considerable reduction of free-thiamine in cerebrospinal fluid and fibroblasts [34]. The clinical pathology of SLC19A3 is heterogeneous, and, likely, related to the age of onset [49]. Previously, Mayr et al. [27] reported various mutations associated with a thiamine pyrophosphokinase deficiency in encephalopathic children, as well as Kevelam et al. [70], who reported mutated SLC19A3 (p.Ser181Pro, p. Leu385Arg and p.Gly23Val) in patients with an early-infantile, lethal encephalopathy. Furthermore, Schänzer et al. [60], Whitford et al. [71] and Fl?nes et al. [63] have reported bigger partial deletions in SLC19A3. Assuming a partial deletion in the sequence of one of the patient samples, the main task of the second project was the determination of the edges, the localization of the breaking point, and further, the size of the deletion, and, whether this deletion has an impact on gene activity. Additionally, the influence of the location and size of the deletion on the overall condition of the patients was analyzed. Furthermore, a sample from a patient, who was previously identified as having a complete deletion of SLC19A3, was added to the experimentation for verification purposes. Finally, the newly found partial deletion and complete deletion were compared to the previously reported deletions. Large deletions of genes are of particular interest, due to their rarity. Large partial deletions, or even complete deletions are seldomly found and reported, as they are complicated to detect, and generally very rare. As in this case, sometimes, they are only detectable when searching in the non-coding region. Therefore, it is important to search in the right places. Research concerning orphan diseases pose a challenge to the scientific community, however, they are both of great interest and great necessity, leading to the improvement of treatment opportunities for the 263 to 446 million people affected worldwide and, subsequently, their quality of life. The presence of mitochondria in virtually all kinds of cells, with the exception of mature erythrocytes, make clinical diagnosis of mitochondrial diseases extremely challenging and difficult, as dysfunction in mitochondria can affect any organ, or even whole organ systems. A major challenge for modern medical science, is the identification of the genes affected, which cause specific rare diseases in humans. New technologies, such as next-generation sequencing, and, therefore, the possibility of identifying genetic variations, are rapidly proceeding. Consequently, available treatments, or genetic counseling can be found more often. SLC25A3 is a mitochondrial phosphate-carrier responsible for the transport of inorganic phosphate into the mitochondrial matrix, which is required for the final step of oxidative phosphorylation, and the process of aerobic synthesis of ATP. Alteration in this gene, located on chromosome 12q23.1, is known to cause PiC deficiency (OMIM 610773), which affects the heart-/muscle-specific phosphate-carrier isoform A (PiC-A) [19, 23, 24, 26]. The aim of the Master's Thesis, was to ascertain the impact of the mutation on the activity of the phosphate carrier, and the patient's resulting life expectancies. Previously, three mutations have been described in seven patients, as being homozygous, affecting exon 3A, with the exception of one, which is compound heterozygous and affecting exon 4. The four novel SLC25A3 mutations (p.Gly72Glu, p.Thr81Lys, p.Asp87Tyr, p.Ala124Pro) are homozygous, one (p.Gly72Glu) having been described previously [19,26,30]. In the context of this thesis, four patient samples were used for experimentation, each containing one of these homozygous mutations. SLC19A3 encodes the thiamine transporter 2 (hTHTR2), dysfunctions lead to recurrent encephalopathy, basal ganglia necrosis, generalized dystonia, severe disability and early death. Patients with changes in SLC19A3, located on the second chromosome (q36.3), show a considerable reduction of free-thiamine in cerebrospinal fluid and fibroblasts [34]. The clinical pathology of SLC19A3 is heterogeneous, and, likely, related to the age of onset [49]. Previously, Mayr et al. [27] reported various mutations associated with a thiamine pyrophosphokinase deficiency in encephalopathic children, as well as Kevelam et al. [70], who reported mutated SLC19A3 (p.Ser181Pro, p. Leu385Arg and p.Gly23Val) in patients with an early-infantile, lethal encephalopathy. Furthermore, Schänzer et al. [60], Whitford et al. [71] and Fl?nes et al. [63] have reported bigger partial deletions in SLC19A3. Assuming a partial deletion in the sequence of one of the patient samples, the main task of the second project was the determination of the edges, the localization of the breaking point, and further, the size of the deletion, and, whether this deletion has an impact on gene activity. Additionally, the influence of the location and size of the deletion on the overall condition of the patients was analyzed. Furthermore, a sample from a patient, who was previously identified as having a complete deletion of SLC19A3, was added to the experimentation for verification purposes. Finally, the newly found partial deletion and complete deletion were compared to the previously reported deletions. Large deletions of genes are of particular interest, due to their rarity. Large partial deletions, or even complete deletions are seldomly found and reported, as they are complicated to detect, and generally very rare. As in this case, sometimes, they are only detectable when searching in the non-coding region. Therefore, it is important to search in the right places. Keywords: SLC25A3; rare genetic diseases; phosphate carrier; point mutation; mitochondrial diseases; PiC deficiency; SLC19A3; thiamine transporter 2; recurrent encephalopathy; basal ganglia necrosis; partial deletion; large deletion; complete deletion Available in the Digital Repository of University of South Bohemia.
"Characterization of Pathogenic Variants of Mitochondrial Carriers and Transporters With the Use of Biochemical Methods: Revealing Novel Mutations and Deletions in Patient Samples, Assumed to be Associated With Rare Diseases."

Research concerning orphan diseases pose a challenge to the scientific community, however, they are both of great interest and great necessity, leading to the improvement of treatment opportunities ...

BEHENSKY, Magdalena Maria
Jihočeská univerzita v Českých Budějovicích, 2022

'The Animal and Human World in Cormac McCarthy and Jack London's Works'
BENÍČKOVÁ, Kamila
2022 - English
Available in the Digital Repository of University of South Bohemia.
'The Animal and Human World in Cormac McCarthy and Jack London's Works'

BENÍČKOVÁ, Kamila
Jihočeská univerzita v Českých Budějovicích, 2022

Postmodern Space in Contemporary British Fiction (Graham Swift)
MYKYTYN, Kristýna
2022 - English
Práce se pokusí definovat prostor ve vybraných románech současného britského autora Grahama Swifta. Teoretická část práce nejprve nastíní společenskou, politickou a literární situaci 20. století a představí literární prostředky používané v moderní, postmoderní a současné britské literatuře. Dále se práce zabývá změnou vnímání prostoru, teorií postmoderního chronotopu a vedle Grahama Swifta jsou představeni i další nejvýznamnější autoři současné britské literatury. Jádrem práce je literárněvědná analýza prostoru a krajiny románů Země vod (1983) a Mimo tento svět (1988). Cílem práce je porovnání použití postmoderních prvků a analýza vlivu historie a krajiny na osud hrdinů vybraných románů. The thesis aims to reflect on space in selected novels by contemporary British writer Graham Swift. The theoretical part of the thesis will first outline the social, political and literary situation of the 20th century and introduce the literary tools used in modern, postmodern and Contemporary British literature. Furthermore, the thesis deals with the change in the perception of space, the theory of postmodern chronotope, and besides Graham Swift, other most important writers of Contemporary British literature are introduced. The core of the thesis is a literary analysis of the space and landscape of the novels Waterland (1983) and Out of This World (1988). The aim is to compare the usage of postmodern elements and analyse the influence of history and landscape on the fate of the heroes of selected novels. Keywords: postmodernismus; současná britská próza; Graham Swift; Země vod; Mimo tento svět; prostor; britská fikce; chronotop Available in the Digital Repository of University of South Bohemia.
Postmodern Space in Contemporary British Fiction (Graham Swift)

Práce se pokusí definovat prostor ve vybraných románech současného britského autora Grahama Swifta. Teoretická část práce nejprve nastíní společenskou, politickou a literární situaci 20. století a ...

MYKYTYN, Kristýna
Jihočeská univerzita v Českých Budějovicích, 2022

The Present Perfect Tense as a Critical Issue in Teaching of English in the Lower Secondary School Curriculum
ALTMAN, Nela
2022 - English
Tato diplomová práce se zabývá předpřítomným časem jako kritickým místem kurikula 2. stupně základních škol. Předpřítomný čas v anglickém jazyce byl identifikován učiteli jako kritické místo v rámci projektu IPUP KA7 - Inovace přípravy učitelů pro praxi. Tento fakultní projekt zkoumal tzv. kritická místa kurikula a byl založen na akčním výzkumu, který se stal podkladem pro tuto diplomovou práci. V teoretické části diplomová práce nejprve definuje kritická místa obecně a poté konkrétní kritické místo analyzuje z lingvistického a didaktického hlediska. V empirické části se věnuje metodologii výzkumu a stanovuje jeho fáze, které dále realizuje. Součástí empirické části je konfrontace poznatků teoretiků v oblasti výuky předpřítomného času s praxí učitelů a z toho vzniklá doporučení do praxe. Tato doporučení jsou aplikována na modelovou výukovou hodinu, jejímž cílem je navrhnout řešení jak toto kritické místo překonávat. This diploma thesis examines the Present Perfect tense as a critical issue in the curriculum at the lower secondary schools. The Present Perfect tense in English was identified by teachers as a critical issue in the IPUP KA7 project - Inovace přípravy učitelů pro praxi. This faculty project investigated critical issues in the curriculum and included action research that provided the basis for this thesis. In the theoretical section, the thesis first defines critical issues in general and then analyses our chosen specific critical issue (the Present Perfect tense) from a linguistic and methodological point of view. In the empirical section, it discusses the research methodology and sets out the stages of the research, which it then implements. The empirical section includes an examination of the findings of scholars in the field of teaching the Present Perfect tense in comparison with teachers' practical classroom experience and also includes resulting recommendations for practice. These recommendations are applied to a model lesson to suggest solutions on how to overcome this critical issue. Keywords: kritické místo kurikula; kurikulum; RVP; SERR; předpřítomný čas; výuka gramatiky; akční výzkum Available in the Digital Repository of University of South Bohemia.
The Present Perfect Tense as a Critical Issue in Teaching of English in the Lower Secondary School Curriculum

Tato diplomová práce se zabývá předpřítomným časem jako kritickým místem kurikula 2. stupně základních škol. Předpřítomný čas v anglickém jazyce byl identifikován učiteli jako kritické místo v rámci ...

ALTMAN, Nela
Jihočeská univerzita v Českých Budějovicích, 2022

Politické tendence ve vybrané romantické poezii
RILLICH, Jan
2022 - English
Tato práce se zabývá analýzou vybrané anglické romantické poezie z hlediska politických postojů autorů. V práci jsou rozebrána a zasazena do kontextu dobových politických událostí díla více básníků tohoto období. Hlavními tématy jsou politická pravice a levice, konflikt monarchismu a republikánství a kritika institucionalizovaného náboženství tak, jak jsou nazírány romantickými básníky. V případech, kdy se stejnou otázkou zabývá více autorů, jsou jejich přístupy porovnány. This thesis analyses selected poetry of English Romantic poets in terms of their political opinions. The works of various poets are scrutinised and put into the context of important political events of the period. The main topics discussed are the left-right political spectrum, the conflict between monarchism and republicanism, and the critique of institutionalised religion in how the Romantic poets perceive them. In cases where more poets show interest in the same question, their ideas are compared. Keywords: Romantismus; poezie; politika; anarchismus; náboženství; ateismus; revoluce; Británie; Francie; Amerika; Wordsworth; Coleridge; Southey; Byron; Shelley; Keats Available in the Digital Repository of University of South Bohemia.
Politické tendence ve vybrané romantické poezii

Tato práce se zabývá analýzou vybrané anglické romantické poezie z hlediska politických postojů autorů. V práci jsou rozebrána a zasazena do kontextu dobových politických událostí díla více básníků ...

RILLICH, Jan
Jihočeská univerzita v Českých Budějovicích, 2022

Analysis of Games and Films Inspired by Or Spin-Offs of The Godfather
DAVID, Tomáš
2022 - English
V této inovativní studii bude student zkoumat filmy a hry, které vykazují intertextuální vztah s vlivnou filmovou sérií Kmotr ze 70. let minulého století. Jak hry, tak filmy budou studovány metodou specifické aplikace teorií intertextuality, které budou prezentovány a aplikovány. Rozmanitost použitých žánrů poslouží jako příklad stále se rozšiřujících žánrů textů hodných vážného akademického zkoumání a analýzy. In this innovative study, the student will examine films and games which exhibit an intertextual relationship with the influential Godfather film series from the 1970s. Both games and films will be under study specifically applying theories of intertextuality which will be both presented and applied. The variety of genres approached will serve as an example of the ever expanding genres of texts worthy of rigorous academic investigation and analysis. Keywords: Adaptace; mafie; videohry; filmy; kinematografie Available in the Digital Repository of University of South Bohemia.
Analysis of Games and Films Inspired by Or Spin-Offs of The Godfather

V této inovativní studii bude student zkoumat filmy a hry, které vykazují intertextuální vztah s vlivnou filmovou sérií Kmotr ze 70. let minulého století. Jak hry, tak filmy budou studovány metodou ...

DAVID, Tomáš
Jihočeská univerzita v Českých Budějovicích, 2022

Development of DiCre parental lineage of \kur{Babesia divergens }
REICHENSDÖRFEROVÁ, Dominika
2022 - English
Babesia divergens is a tick-transmitted parasite of the order Piroplasmida, an important causative agent of bovine and human babesiosis. Even though Babesia represent an important worldwide veterinary threat and an emerging risk to humans, some of the fundamental principles of their parasitic lifestyle are still poorly understood. One of the approaches, which help us to better understand the biology of Babesia parasites and their interaction with hosts or vectors, is functional genomics. Hence, the aim of this thesis is to establish a DiCre parental lineage of B. divergens that may provide the absent genome editing technique of conditional gene knock-out. Such a tool will help to functionally characterize essential genes/proteins and validate them as novel targets for the yet missing specific treatment. We have selected and identified an eligible recipient locus in the B. divergens genome into which a DiCre cassette will be integrated via homology recombination. We have validated and determined the optimal concentration of WR99210 and G-418 for their use as selection markers for transfected B. divergens cultures. Finally, we have designed and constructed the plasmid vector containing the DiCre cassette for the generation of DiCre parental B. divergens lineage that may be universally applicable to functionally validate any genes/proteins of interest. Babesia divergens is a tick-transmitted parasite of the order Piroplasmida, an important causative agent of bovine and human babesiosis. Even though Babesia represent an important worldwide veterinary threat and an emerging risk to humans, some of the fundamental principles of their parasitic lifestyle are still poorly understood. One of the approaches, which help us to better understand the biology of Babesia parasites and their interaction with hosts or vectors, is functional genomics. Hence, the aim of this thesis is to establish a DiCre parental lineage of B. divergens that may provide the absent genome editing technique of conditional gene knock-out. Such a tool will help to functionally characterize essential genes/proteins and validate them as novel targets for the yet missing specific treatment. We have selected and identified an eligible recipient locus in the B. divergens genome into which a DiCre cassette will be integrated via homology recombination. We have validated and determined the optimal concentration of WR99210 and G-418 for their use as selection markers for transfected B. divergens cultures. Finally, we have designed and constructed the plasmid vector containing the DiCre cassette for the generation of DiCre parental B. divergens lineage that may be universally applicable to functionally validate any genes/proteins of interest. Keywords: B. divergens; DiCre cassette; DiCre parental B. divergens lineage; treatment; Gibson assembly Available in the Digital Repository of University of South Bohemia.
Development of DiCre parental lineage of \kur{Babesia divergens }

Babesia divergens is a tick-transmitted parasite of the order Piroplasmida, an important causative agent of bovine and human babesiosis. Even though Babesia represent an important worldwide veterinary ...

REICHENSDÖRFEROVÁ, Dominika
Jihočeská univerzita v Českých Budějovicích, 2022

Calculation of vibrational SFG spectra from molecular dynamics simulations
MUSIL, Patrik
2022 - English
In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. The key part of the thesis was significant improvement of the original codes used by the group of Prof. Marie-Pierre Gaigeot to post-process ab initio molecular dynamics trajectories to predict vibrational SFG spectra and apply it to classical molecular dynamics simulations. Particular attention was paid to modifying and optimizing the code for processing much larger systems (number of molecules) and much longer trajectories (longer simulation times), allowing to take advantage of classical simulations to work on larges scales than the ab initio simulations. The code also integrates calculations of contributions from water O-H bonds and surface hydroxyls. As a new feature, calculation of cross-correlations among molecules was implemented. The performance of the resulting codes is verified and the influence of classical molecular simulation parameters, as well as parameters entering the SFG spectra calculations, on the calculated vibrational SFG spectra is studied for fluorite/water interface. In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. The key part of the thesis was significant improvement of the original codes used by the group of Prof. Marie-Pierre Gaigeot to post-process ab initio molecular dynamics trajectories to predict vibrational SFG spectra and apply it to classical molecular dynamics simulations. Particular attention was paid to modifying and optimizing the code for processing much larger systems (number of molecules) and much longer trajectories (longer simulation times), allowing to take advantage of classical simulations to work on larges scales than the ab initio simulations. The code also integrates calculations of contributions from water O-H bonds and surface hydroxyls. As a new feature, calculation of cross-correlations among molecules was implemented. The performance of the resulting codes is verified and the influence of classical molecular simulation parameters, as well as parameters entering the SFG spectra calculations, on the calculated vibrational SFG spectra is studied for fluorite/water interface. Keywords: computer simulations; solid-liquid interface; nonlinear optics; sum-frequency generation; spectroscopy Available in the Digital Repository of University of South Bohemia.
Calculation of vibrational SFG spectra from molecular dynamics simulations

In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. ...

MUSIL, Patrik
Jihočeská univerzita v Českých Budějovicích, 2022

Analysis of the dicyemid diversity using amplicon sequencing
FLEGROVÁ, Tereza
2022 - English
Using amplicon sequencing, this study reveals dicyemid diversity around the world as well as within individual cephalopod hosts. A wide number of samples of multiple species were collected to reflect true dicyemid diversity. Heterogeneity primers were designed in order to improve the sequencing performance of the Illumina platform. A complex bioinformatic pipeline was implemented to process non-overlapping reads. The species delimitation methods were used to categorize occurring dicyemid types. Using the output of implemented methods, dicyemid diversity was assessed, proposing new trends opposing the current methodology. Keywords: amplikonové sekvenování; dicyemida; populační diverzita; illumina Available in the Digital Repository of University of South Bohemia.
Analysis of the dicyemid diversity using amplicon sequencing

Using amplicon sequencing, this study reveals dicyemid diversity around the world as well as within individual cephalopod hosts. A wide number of samples of multiple species were collected to reflect ...

FLEGROVÁ, Tereza
Jihočeská univerzita v Českých Budějovicích, 2022

mTOR-regulated translation during first the wave of inner cell generation in mouse preimplantation embryos
ČERNÁ, Pavlína
2022 - English
The aim of this master thesis was to investigate the role of mTOR and connected pathways in early mouse preimplantation development. The aim of this master thesis was to investigate the role of mTOR and connected pathways in early mouse preimplantation development. Keywords: mouse preimplantation development; trophectoderm; primitive endoderm; epiblast; mTOR signalling pathway Available in the Digital Repository of University of South Bohemia.
mTOR-regulated translation during first the wave of inner cell generation in mouse preimplantation embryos

The aim of this master thesis was to investigate the role of mTOR and connected pathways in early mouse preimplantation development....

ČERNÁ, Pavlína
Jihočeská univerzita v Českých Budějovicích, 2022

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