Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 19 of 19 for “"functional RNA"”.
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Computational Identification of Noncoding Driver Mutations Based On Impact On Rna Processing
… the relation between noncoding mutations and functional RNA motifs. The goals for this study, therefore, were to identify RNA motifs that were significantly associated with the presence of somatic, noncoding mutations and to predict the functional impact of noncoding variants. The analysis was …
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Communication between layers in biological transcriptional networks
… (copying) of a gene and the production of the functional RNA or protein that the gene encodes. Therefore, ChIP-chip data provides powerful insight on how genes and gene products (i.e., proteins, RNA) interact and regulate one another in the underlying network of the cell. Much of the current …
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Genome wide search for pseudo knotted non-coding RNAs
Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To …
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RNA structure analysis : algorithms and applications
… thesis, efficient algorithms for aligning RNA secondary structures and mining unknown RNA motifs are presented. As the major contribution, a structure alignment algorithm, which combines both primary and secondary structure information, can find the optimal alignment between two given …
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Enhancing RNA Foundation Models via Secondary Structure Modelling
… life, yet their application to Ribonucleic Acid (RNA) is uniquely challenged by its functional dependence on complex structure. Modelling this intricate sequence-structure-function relationship represents a vital problem in computational biology. This thesis aims to resolve three core impediments …
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Characterization of Negeviruses and insect virome interactions during co-infection in cell culture
… from Aedes albopictus. C7/10 cells have a dysfunctional RNA interference response, while Aag2 cells have a functional RNA interference pathway and pre-existing chronic infections with two ISVs: CFAV and PCLV. Homologous exclusion will be tested through additional infectious clones of …
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Computational studies of the self-cleavage mechanism in the glmS ribozyme
Ribozymes are catalytically functional RNA molecules. To overcome the lack of structural and chemical diversity, ribozymes employ several interesting strategies for catalysis. The glmS ribozyme regulates the level of glucosamine-6-phosphate (GlcN6P) in bacteria by catalyzing a self-cleavage …
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Thermodynamics of neutral sets and sequence length changes in the genotype-phenotype map of RNA secondary structure
The genotype-phenotype (GP) map of RNA secondary structure connects RNA sequences and the corresponding folded molecular structures. This relationship is required for modelling the evolution of functional RNA structures. In this thesis, we fill two gaps in the understanding of the RNA GP map: we …
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Sequence determinants of pri-miRNA processing
MicroRNAs (miRNAs) are short RNAs that regulate many processes in physiology and pathology by guiding the repression of target messenger RNAs. For classification purposes, miRNAs are defined as ~22 nt RNAs that are produced by the cleavage of endogenously transcribed hairpins. From a cellular …
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Genotypic and Phenotypic Determinants of Japanese Encephalitis Virus Geographical Expansion
… (mosquito larvae derived cell line lacking a functional RNA interference response) from 24-48 hours post infection compared to the other viral isolates. In nature, an increased viral multiplication efficiency of GI-b viruses in mosquitoes may have resulted in a shortened extrinsic incubation …
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Structural RNA Homology Search and Alignment Using Covariance Models
Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and …
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Study Of Protein-Rna Interactions Using Fluorescence Resonance Energy Transfer (fret) And Single-Molecule Fret
<p>In the cell, RNA and protein, interact to form ribonucleoprotein complexes (RNPs) that have vital structural, catalytic and regulatory roles. Despite their functional importance, the mechanistic details and dynamics of RNPs are poorly understood. Single-molecule Fluorescence Resonance Energy …
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Assembling The Building Blocks For A Unified Splicing Code
… processing of this code: DNA is transcribed to RNA, which is translated to proteins. In eukaryotes, DNA is transcribed to pre-mRNA. Subsequently, a single pre-mRNA can encode for different proteins by selectively including or excluding protein-coding and non-coding RNA fragments from the final …
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Telomerase : a tumor marker in the peripheral blood of colorectal cancer patients
… activity of a treatment. Telomerase is an RNA-dependant DNA polymerase that synthesises telomeric DNA sequences on the tip of chromosomes and is widely considered to be one of the most abundant and common tumour markers. Telomerase consists of two components; one is the functional RNA …
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Trashing old notions: the significance of small tRNAs in Trichomonas vaginalis extracellular vesicles and implications for host-parasite communication
… for infection. However, the contribution of EV RNA cargo to the infection process remains unclear, which inspired the three experimental chapters of this study. The first chapter compared sRNA-seq data from EVs and their originating cells. The analysis revealed that while cells and EVs had …
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Genome engineering in saccharomyces cerevisiae
… been proposed as a sustainable and renewable alternative to the traditional petrochemical industry. Saccharomyces cerevisiae is one of the most widely used microbial cell factories, to produce ethanol as the first generation of biofuel. To enable this yeast as a producer for 1-butanol, which is a …
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Biochemical and structural studies of RNA damage and repair in bacteria
… endonucleases which typically target RNA molecules that are necessary for translation mainly, tRNAs and rRNAs which can result in their loss of function. In order to respond to RNA damage, some organisms have developed RNA repair systems which can heal and seal the cleaved RNA molecule …
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Control of Cardiac Remodelling during Ageing and Disease by Epigenetic Modifications and Modifiers
… in DNA cytosine modifications, long non-coding RNA (lncRNA) expression and histone tail lysine methylation marks – epigenetic marks with central roles in transcriptional regulation in many biological systems. I examined how these changes correlate with alterations in the CM transcriptome during …
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Detektion funktioneller RNAs in Genomsequenzen
… bewährter Werkzeuge wird eine Pipeline zur fRNA-Vorhersage in kompletten Genomsequenzen entwickelt. Das Programm ermöglicht sowohl die Vorhersage neuer, bisher unbekannter fRNAs, als auch die Vorhersage der Mitglieder bereits bekannter Familien. Hierbei ist kein Expertenwissen zu den …