Graph splicing systems

AbstractIn this paper, extended graph splicing systems are defined. It is shown that when strings are represented as linear graphs, any recursively enumerable set can be generated by an extended graph splicing system. It is also shown that the computational completeness of extended graph splicing systems can be proved under some constraints too

The Jones polynomial and graphs on surfaces

The Jones polynomial of an alternating link is a certain specialization of the Tutte polynomial of the (planar) checkerboard graph associated to an alternating projection of the link. The Bollobas-Riordan-Tutte polynomial generalizes the Tutte polynomial of planar graphs to graphs that are embedded in closed oriented surfaces of higher genus. In this paper we show that the Jones polynomial of any link can be obtained from the Bollobas-Riordan-Tutte polynomial of a certain oriented ribbon graph associated to a link projection. We give some applications of this approach.Comment: 19 pages, 9 figures, minor change

Topological gravity on plumbed V-cobordisms

An ensemble of cosmological models based on generalized BF-theory is constructed where the role of vacuum (zero-level) coupling constants is played by topologically invariant rational intersection forms (cosmological-constant matrices) of 4-dimensional plumbed V-cobordisms which are interpreted as Euclidean spacetime regions. For these regions describing topology changes, the rational and integer intersection matrices are calculated. A relation is found between the hierarchy of certain elements of these matrices and the hierarchy of coupling constants of the universal (low-energy) interactions. PACS numbers: 0420G, 0240, 0460Comment: 29 page

Splicing Systems from Past to Future: Old and New Challenges

A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing systems, introduced by P\u{a}un and subsequently developed by many researchers in both linear and circular case of splicing definition. In particular, we will present recent results on this topic and how they stimulate new challenging investigations.Comment: Appeared in: Discrete Mathematics and Computer Science. Papers in Memoriam Alexandru Mateescu (1952-2005). The Publishing House of the Romanian Academy, 2014. arXiv admin note: text overlap with arXiv:1112.4897 by other author

An orchestrated intron retention program in meiosis controls timely usage of transcripts during germ cell differentiation

Global transcriptome reprogramming during sper-matogenesis ensures timely expression of factors in each phase of male germ cell differentiation. Sper-matocytes and spermatids require particularly exten-sive reprogramming of gene expression to switch from mitosis to meiosis and to support gamete morphogenesis. Here, we uncovered an extensive alternative splicing program during this transmeiotic differentiation. Notably, intron retention was largely the most enriched pattern, with spermatocytes showing generally higher levels of retention compared with spermatids. Retained introns are characterized by weak splice sites and are enriched in genes with strong relevance for gamete func-tion. Meiotic intron-retaining transcripts (IRTs) were exclusively localized in the nucleus. However, differ-ently from other developmentally regulated IRTs, they are stable RNAs, showing longer half-life than properly spliced transcripts. Strikingly, fate-mapping experiments revealed that IRTs are recruited onto polyribosomes days after synthesis. These studies reveal an unexpected function for regulated intron retention in modulation of the timely expression of select transcripts during spermatogenesis