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PCR Primer optimisation for amplification and sequencing PKD2 exons
KOZÁK, Kristián
The dominant type of the kidney polycystic disease affects a wide age spectrum and it represents certain limitations or complications for the patients, whether it concearns a finding of cysts in the organs, or up to renal insufficiency. After the familiarization of the characteristics, progress, diagnosies and therapy, I suggested new primers bounding the sections of the different exons of the PKD2 gene. I tested the new primers, as well as optimalized the temperatures of annealing of the primers by the gradient PCR. I then sent the amplified sections to sequencing and verified their identity. I managed to optimalize the primers for the amplification and further sequencing of the four exons of the PKD2 gene. One of these exons is also the exon 2, in which we can find the casual mutation which causes the autosomal dominant polycystic kidney disease ran in family, from which I gathered the samples for my research.
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Exploration of oncogenomic factors for prognostication and prevention of breast, ovarian, and colorectal cancers
Holý, Petr ; Souček, Pavel (advisor) ; Bouchal, Pavel (referee) ; Šulc, Miroslav (referee)
(Abstract) Cancer is now the leading cause of death in economically developer countries, with epidemiological indicators rising steadily on a global scale. This is mainly a result of socio- economic and demographic developments, particularly ageing populations or changes in lifestyle in some populations. Meanwhile, as absolute incidence and mortality rates are rising, the prevalence of cancer is also increasing, representing a heavy social and economic burden. Cancer research has received a great deal of attention from the scientific community, with molecular genetics in particular making the greatest recent progress. Thanks to modern methods of genome analysis, so-called genomics and other 'omics' disciplines, many biomarkers have been discovered, leading to better diagnosis, prognosis and more effective treatment with reduced incidence of adverse effects. However, there is still a long way to go in order to make the idea of personalised oncology, i. e., a precise therapeutic approach tailored to the individual patient, a reality. This paper examines three types of solid tumours. Firstly, breast cancer, which has the highest incidence worldwide in women, even overall. The next is colorectal cancer, which is the second and third most common cancer in women and men, respectively, and more common in...
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NANOBLAST: Python Tool for Raw Nanopore Signal Processing
Suriak, Martin ; Nykrýnová, Markéta
Oxford Nanopore Technologies’ sequencers enable direct real-time DNA/RNA sequencing. While numerous tools aid in analyzing the nanopore output data, offering functions such as visualizing raw signals with highlighted nucleotide positions, none provide a complete solution for exporting analyzed data into a clear, comprehensive file. In response, a Python tool has been developed to streamline various tasks. This includes searching for specific nucleotide sequences using BLAST, plotting raw signals with detected nucleotide bases, and generating a comprehensive file containing all essential information. The tool integrates components for handling raw nanopore data, extracting crucial information from the basecalling process using SAM file handlers, and utilizing a BLAST search engine. Employing a comprehensive algorithm, it can handle both the old FAST5 and the novel POD5 formats, enabling the identification of any nucleotide sequence and its corresponding signal.
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BacSeqer: Read simulator for bacterial RNA-Seq
Fialová, Adéla ; Sedlář, Karel
The RNA-Seq method has become a key tool in transcriptomics, providing deep insight into the genetic functioning of organisms. It is essential for understanding how genes are expressed, for discovering new gene variants and for understanding pathologies at the genetic level. RNA-Seq simulators are great for testing and validating bioinformatics tools, they offer a way to compare different computational algorithms and allow examining different sequencing protocols, parameter settings and sample sizes to ensure the most efficient use of resources. This study introduces BacSeqer, an RNA-Seq simulator specifically designed for bacterial transcriptomes with the aim of producing data that faithfully resembles those obtained in real experiments. It allows to take into account the specificities of the bacterial genome, especially an existence of only exons and their organization in operons that are not normally present in eukaryotes.
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Bioinformatics study of the third generation sequencing platforms applied on a thermophile
Umair, Mohammad ; Řeháková, Veronika ; Buchtikova, Iva ; Bezdicek, Matej ; Obruca, Stanislav ; Sedlář, Karel
This study compares the efficiency of Pacific Biosciences technology (PacBio) and Oxford Nanopore Technology (ONT) in sequencing, assembling, and annotating the Aneurinibacillus sp AFn2 bacterium. We aim to evaluate the performance based on contiguity, depth, and functional annotation of the resulting genome. Using ONT we generated 152,047 long reads assembling into 2 contigs with total base count of 0.4 billion which provided us efficient assembly while PacBio produced 139,701 reads, assembling into 21 contigs with a total base count of 1.4 billion. Functional annotation revealed differences in the number of coding sequences, with PacBio detecting more comprehensive gene sets than ONT. The comparative analysis done in this research shows the strengths and limitations of both the platforms, with ONT providing higher assembly contiguity and PacBio offering greater detail in genetic content. We aim to offer insights of both the sequencing technologies, guiding researchers in selecting the appropriate technology.
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Profiling of T-cell receptor rearrangements in type 1 diabetes and celiac disease research
Obermaierová, Anna ; Froňková, Eva (advisor) ; Volejníková, Jana (referee)
This thesis discusses the detection of T-lymphocyte receptor rearrangements (TCR) with NGS methods and its significance in autoimmune disorders such as type 1 diabetes (T1D) and celiac disease. The first part introduces sequencing methods of TCRs and highlights the breakthrough that came with the advent of NGS. The second part then describes various approaches to utilizing these methods in medicine, with special attention dedicated to the endeavour of finding biomarkers for two closely related autoimmune disorders: T1D and celiac disease.
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Metatranscriptomic evaluation dashboard using BiBakery.
Hýl, Jan ; Jurečková, Kateřina (referee) ; Bartoň, Vojtěch (advisor)
Metatranscriptomic analysis provides information about the currently expressed genes of an organism at the time the sample is collected. The boom in the study of genes came with the development of sequencing technologies and other technological advances. This thesis discusses nucleic acids and their importance in genetics. It explores the concepts of metatranscriptome, metagenome and microbiome. It describes the Illumina sequencing method and introduces software suitable for metatranscriptomic analysis. Subsequently, the work includes the creation of a test dataset, the creation of a dashboard for data visualization, and the testing of this dashboard using the test dataset.
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Hybrid mapping for plasmid content determination in NGS data
Pražáková, Martina ; Vítková, Helena (referee) ; Nykrýnová, Markéta (advisor)
This bachelor's thesis is focused on hybrid mapping for determining the presence of plasmids in NGS data. The beginning of the thesis is dedicated to theory, firstly, various sequencing technologies are described, with a greater emphasis on the Illumina platform and nanopore sequencing. Next, methods for assembling sequences and bacterial genome are explained. In the second part of the thesis, the process of processing nanopore data is outlined, along with the proposal of a procedure for determining the presence of plasmids in NGD data and it's implementation .
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Read simulator for bacterial RNA-Seq
Fialová, Adéla ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
This thesis is dedicated to the analysis of the bacterial genome, measurement of its expression mainly by RNA-Seq technology and simulation of RNA-Seq data. The first part of the thesis provides a theoretical background on the structure of the bacterial genome, its expression and methods to study it, including modern sequencing techniques. Several selected simulators of RNA-Seq data are also mentioned. In the second part, the actual simulator implementation is presented, designed to take into account the characteristics of the bacterial genome, in particular the presence of operons.
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Advanced Methods for Genome Annotation and Functional Description of Non-Model Organisms in Biotechnology Research
Musilová, Jana ; Friedel, Caroline (referee) ; Šafránek,, David (referee) ; Sedlář, Karel (advisor)
Komplexní znalost genomu a fenotypu biotechnologicky využitelných bakterií je pro jejich uplatněnění klíčová, přesto přístupy k zevrubnému poznání těchto organismů převážně chybí. Cílem disertační práce je proto navržení nových výpočetních metod pro popis genomových a funkčních vlastností zaměřených na nemodelové bakterie. Úvodní část práce se věnuje metodám anotace genomu. Zahrnuje vývoj nové pipeline pro hybridní sestavování celého genomu, její aplikaci na různé bakterie a následnou identifikaci zájmových oblastí genomu těchto bakterií. Následující část rozebírá metody funkčního popisu se zaměřením na přístupy ke studiu genové regulace. Podrobně jsou shrnuty aktuální přístupy a je představen nový balíček pro odvozování genových regulačních sítí a Booleovských sítí včetně jeho testování.
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