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Reverse genetics in anaerobic protists
Stojanovová, Darja ; Tachezy, Jan (advisor) ; Doležal, Pavel (referee)
This work is focused on reverese genetics of anaerobic protists, mainly T. vaginalis, G. intestinalis and E. histolytica and deals with techniques and experimental procedures of genome manipulation in these parasites. Both DNA and RNA can be manipulated and the gene function can be disclosed using methods of reverse genetics. The knowledge gained is useful in many ways. For example, using these techniques crucial aspects of biology of parasitic prostist are studied, providing basis for potential development of new drugs. Utilization of such methods also helps to understand the cellular and metabolic pathways and mechanisms, that could be very diverse or reduced in protists. The methods of reverse genetics that result in permanent and inheritable changes in DNA are, for instance, homologous recombination or DNA integration. There is also a transcriptional gene silencing (TGS) technique to stop gene expression even though the coding DNA remains unchanged. TGS could be realized by several mechanisms, for example by RNA interference. RNA interference pathway, commonly known as posttranscriptional gene silencing mechanism, causes the breakage of mRNA or stops its translation. Other techniques of gene silencing involve, e.g., the expression of antisense RNA, oligonucleotudes and ribozymes.
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The impact of Fam84b in retinal homeostasis
Raishbrook, Miles Joseph ; Procházka, Jan (advisor) ; Mašek, Jan (referee)
Fam84b is a largely unstudied protein, where its function in eukaryotic cells is unclear. This thesis work presents a FAM84B knockout mouse model and characterises the resulting retinal phenotype in detail. FAM84B KO mice were morphologically assessed by optical coherence tomography and histological processing, revealing dynamic changes stemming from the photoreceptor and pigmented epithelial layers. This potent phenotype progresses with age, spreading inwards towards the inner retinal layers, as well as laterally to adjacent retinal regions. Comparative localisation of standard retinal cell markers demonstrates that FAM84B KO retinal layering becomes increasingly disorganised, together with deformation of the retinal macrostructure. Due to this, KO mice experience reducing responses to light, as demonstrated by electroretinography, where overall retinal efficiency falls. Fam84b shows homology to the HRASLS enzyme family, which are capable of attenuating Ras-associated signalling. To investigate whether Fam84b possesses a similar function, the level of phosphorylated and activated downstream Ras effectors were compared between wild type and FAM84B KO mouse retinal lysates. A reduction of pERK1 (pY204) in KO lysates suggests that Fam84b holds some function related to this pathway downstream of Ras....
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The use of JavaScript MVC frameworks for creating web applications
KOLÁŘ, David
The objective of the bachelor thesis will be develop and describe issues related to JavaScritp MVC frameworks. How to simplify and streamline the work of the code when creating web applications in terms of client-side scripting. I will focus to compare the busiest frameworks, their advantages, disadvantages, when and why it pays to use. I will include in my selection AngularJS, React, Knockout and mention the other frameworks. The practical part will consist of examples particular frameworks while solving real problems. For this purpose, I will create a Web application, which will include an overview of their properties, and comparing the aforementioned examples.
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Reverse genetics in anaerobic protists
Stojanovová, Darja ; Tachezy, Jan (advisor) ; Doležal, Pavel (referee)
This work is focused on reverese genetics of anaerobic protists, mainly T. vaginalis, G. intestinalis and E. histolytica and deals with techniques and experimental procedures of genome manipulation in these parasites. Both DNA and RNA can be manipulated and the gene function can be disclosed using methods of reverse genetics. The knowledge gained is useful in many ways. For example, using these techniques crucial aspects of biology of parasitic prostist are studied, providing basis for potential development of new drugs. Utilization of such methods also helps to understand the cellular and metabolic pathways and mechanisms, that could be very diverse or reduced in protists. The methods of reverse genetics that result in permanent and inheritable changes in DNA are, for instance, homologous recombination or DNA integration. There is also a transcriptional gene silencing (TGS) technique to stop gene expression even though the coding DNA remains unchanged. TGS could be realized by several mechanisms, for example by RNA interference. RNA interference pathway, commonly known as posttranscriptional gene silencing mechanism, causes the breakage of mRNA or stops its translation. Other techniques of gene silencing involve, e.g., the expression of antisense RNA, oligonucleotudes and ribozymes.
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Utilization of genome editing technology to knock out \kur{dnd1} gene in sturgeons
VU THI, Trang
In this study, for the first time we used CRISPR/Cas9 gene editing technology in sturgeons i.e., sterlets (Acipenser ruthenus). The sequences of sgRNA and primers were designed based on published dnd1 sterlet sequence. Each pair of sgRNA oligos after ligation ready duplex DNA fragment was cloned into vector pX330-U6-Chimeric_BB-CBh-hSpCas9 backbone and thereafter the transformation to competent cells Escherichia coli DH5 was done. The plasmid carried sgRNA was extracted for downstream applications. We diluted extracted plasmid with 10% of 2 M KCl and injection into animal pole of fertilized eggs of sterlets at one to four-cell-stage, 4 hours post fertilization (hpf). At the same time, second microinjection with 2.5% FITC-biotin-dextrans was injected into vegetal pole for labelling PGCs. In the control groups, the eggs were only injected by 2.5% FITC into vegetal pole. PGCs of sterlet were visualized and photographed using a uorescent stereo microscope Leica M165 FC. To confirm the presence or deletion/insertion occurring in the target gene, we used MCE-202 MultiNA microchip electrophoresis system for DNA analysis, in which the targeted gene after amplifying by PCR was analyzed. Mutations in both treated and control embryos of sterlet were further assessed by Sanger sequencing of the PCR product. In present study, we successfully established basic protocols such as preparation of competent cells, construction of vector carrying sgRNA and its transformation into competent cells to carry out the CRISPR/Cas9 technology in sturgeons. Less number of PGCs was observed in embryos that were treated with CRISPR/Cas9; however, sequencing did not provide us a reliable evidence for mutation of the targeted gene probably due to an unspecific PCR. Therefore, more authentication of dnd1 knockout should be done in future by more specific PCR and repeated sequencing.
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