Palindromic complexity of trees

We consider finite trees with edges labeled by letters on a finite alphabet $\varSigma$. Each pair of nodes defines a unique labeled path whose trace is a word of the free monoid $\varSigma^*$. The set of all such words defines the language of the tree. In this paper, we investigate the palindromic complexity of trees and provide hints for an upper bound on the number of distinct palindromes in the language of a tree.Comment: Submitted to the conference DLT201

On Model Checking Boolean BI

The logic of bunched implications (BI), introduced by O'Hearn and Pym, is a substructural logic which freely combines additive and multiplicative implications. Boolean BI (BBI) denotes BI with classical interpretation of additives and its model is the commutative monoid. We show that when the monoid is finitely generated and propositions are recursively defined, or the monoid is infinitely generated and propositions are restricted to generator propositions, the model checking problem is undecidable. In the case of finitely related monoid and,generator propositions. the model checking problem is EXPSPACE-complete.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000270711900021&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Computer Science, Theory & MethodsEICPCI-S(ISTP)

The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin

The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site

Building and Combining Matching Algorithms

International audienceThe concept of matching is ubiquitous in declarative programming and in automated reasoning. For instance, it is a key mechanism to run rule-based programs and to simplify clauses generated by theorem provers. A matching problem can be seen as a particular conjunction of equations where each equation has a ground side. We give an overview of techniques that can be applied to build and combine matching algorithms. First, we survey mutation-based techniques as a way to build a generic matching algorithm for a large class of equational theories. Second, combination techniques are introduced to get combined matching algorithms for disjoint unions of theories. Then we show how these combination algorithms can be extended to handle non-disjoint unions of theories sharing only constructors. These extensions are possible if an appropriate notion of normal form is computable

The lack of protamine 2 (P2) in boar and bull spermatozoa is due to mutations within the P2 gene.

The nuclei of spermatozoa in all mammals examined so far contain P1 protamine. A second protamine variant, protamine P2, has to date been isolated only from human and murine spermatozoa where it represents the major fraction of basic nuclear protein. In order to elucidate the reason for this unusual distribution of the protamine variants among mammals we have investigated the expression of protamine P2 in boar and bull. It can be shown that also in these species protamine 2 is transcribed and translated on low levels. Various mutational events though have altered the primary structure of the protein: In boar, a deletion of 8 aminoacids has removed a sequence motif from the amino-terminus of the molecule, which highly probable is of functional relevance. The bovine sequence, as a consequence of numerous point mutations has accumulated neutral and hydrophobic aminoacids which reduce the affinity of the protamine 2 to DNA

On the Complexity of Counting the Hilbert Basis of a Linear Diophantine System

We investigate the computational complexity of counting the Hilbert basis of a homogeneous system of linear Diophantine equations. We establish lower and upper bounds on the complexity of this problem by showing that counting the Hilbert basis is #P-hard and belongs to the class #NP. Moreover, we investigate the complexity of variants obtained by restricting the number of occurrences of the variables in the system