3,267 research outputs found

    Fuzzy splicing systems

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    In this paper we introduce a new variant of splicing systems, called fuzzy splicing systems, and establish some basic properties of language families generated by this type of splicing systems. We study the “fuzzy effect” on splicing operations, and show that the “fuzzification” of splicing systems can increase and decrease the computational power of splicing systems with finite components with respect to fuzzy operations and cut-points chosen for threshold languages

    GRAPHICAL USER INTERFACE FOR BOUNDED-ADDITION FUZZY SPLICING SYSTEMS AND THEIR VARIANTS

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    A splicing system is one of the early theoretical proposals of the DNA-based computation device. The splicing operation starts when two DNA molecules are cut at specific subsequences with the presence of restriction enzymes: the first part is then connected to the second part of the other molecule, or vice versa, to produce splicing languages. Fuzzy with bounded-addition operation has been introduced as a restriction in splicing systems to increase the generative power of the languages generated. In this research, a graphical user interface is developed to generate all the splicing languages generated by bounded-addition fuzzy splicing systems and their variants. An algorithm is developed using JAVA and Visual Studio Code software in order to replace the time-consuming manual computation of the languages generated by bounded-addition fuzzy DNA splicing systems and their variants

    A unified mechanism for intron and exon definition and back-splicing.

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    The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes
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