Browsing by Author "Dvorak, Pavel"
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Item Circulating and circular RNAs and the need for rationalization and synthesis of the research spiral(2019-03-06) Dvorak, Pavel; Leupen, Sarah; Soucek, PavelIn this essay, we aim to draw a short comparison between 2 important research topics – circular and circulating RNAs – and show how they are connected. The findings described here in the field of circular RNAs, which are still quite obscured by the rapidly expanding body of knowledge in biology, have added another dimension to our view of the process of gene expression, which is formed by a more complex network of molecule interactions than we previously thought. The term “circulating RNAs” refers to a broad spectrum of RNA fragments originating from different sources, such as physiologically dying cells, sites of inflammation or cancer cells, and fragments floating in human liquid tissues together with other elements. Fragments of nucleic acids circulating in blood are emerging as promising biomarkers in different medical conditions. Interestingly, circular RNAs have been found to be present in human blood and form a fraction of circulating RNAs. In addition to updating readers on these fast-developing areas of biology, we also stress the need for the study of complex networks of molecule interactions as whole structures (in unison with the thoughts of systems biology), as opposed to the trend toward searching for individual key player molecules. Fundamentally, we want to add to the rationalization and synthesis of new research findings in the scientific literature, because this direction is important not only for students, teachers and researchers, but also for the general population.Item Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates(MDPI, 2019-06-21) Dvorak, Pavel; Leupen, Sarah; Soucek, PavelSingle nucleotide polymorphisms located in 5' untranslated regions (50UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5' UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5' UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5' UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5' UTRs, such as GC content variation, hairpin structure conservation or 5' UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.