Novel dermaseptin, adenoregulin and caerin homologs from the Central American red-eyed leaf frog, Agalychnis callidryas, revealed by functional peptidomics of defensive skin secretion

By integrating systematic peptidome and transcriptome studies of the defensive skin secretion of the Central American red-eyed leaf frog, Agalychnis callidryas, we have identified novel members of three previously described antimicrobial peptide families, a 27-mer dermaseptin-related peptide (designated DRP-AC4), a 33-mer adenoregulin-related peptide (designated ARP-AC1) and most unusually, a 27-mer caerin-related peptide (designated CRP-AC1). While dermaseptin and adenoregulin were originally isolated from phyllomedusine leaf frogs, the caerins, until now. had only been described in Australian frogs of the genus, Litoria. Both the dermaseptin and adenoregulin were C-terminally amidated and lacked the C-terminal tripeptide of the biosynthetic precursor sequence. In contrast, the caerin-related peptide, unlike the majority of Litoria analogs. was not C-terminally amidated. The present data emphasize the need for structural characterization of mature peptides to ensure that unexpected precursor cleavages and/or post-translational modifications do not produce mature peptides that differ in structure to those predicted from cloned biosynthetic precursor cDNA. Additionally, systematic study of the secretory peptidome can produce unexpected results such as the CRP described here that may have phylogenetic implications. It is thus of the utmost importance in the functional evaluation of novel peptides that the primary structure of the mature peptide is unequivocally established - something that is often facilitated by cloning biosynthetic precursor cDNAs but obviously not reliable using such data alone. (C) 2008 Elsevier Masson SAS. All rights reserved.

A density functional theory study of the surface relaxation and reactivity of Cu2O(100)

Density functional theory has been used to investigate the surface relaxation of Cu2O(100) and the adsorption of NO. The calculations indicate the formation of surface copper dimers on relaxation coupled with a large contraction of the spacing between the first and second layers. Local density of states for atoms in the top three layers shows that the third layer copper atoms have the greatest change in bonding character. Adsorption energies have been calculated for the N-down and O-down adsorption of NO on the Cu2O(100) surface. These indicate that N-down adsorption is favoured and that in this case NO-lattice oxygen interactions dominate the adsorbate structure. (C) 2000 Elsevier Science B.V. All rights reserved.

Assignment methods for incidence calculus

Incidence calculus is a mechanism for probabilistic reasoning in which sets of possible worlds, called incidences, are associated with axioms, and probabilities are then associated with these sets. Inference rules are used to deduce bounds on the incidence of formulae which are not axioms, and bounds for the probability of such a formula can then be obtained. In practice an assignment of probabilities directly to axioms may be given, and it is then necessary to find an assignment of incidence which will reproduce these probabilities. We show that this task of assigning incidences can be viewed as a tree searching problem, and two techniques for performing this research are discussed. One of these is a new proposal involving a depth first search, while the other incorporates a random element. A Prolog implementation of these methods has been developed. The two approaches are compared for efficiency and the significance of their results are discussed. Finally we discuss a new proposal for applying techniques from linear programming to incidence calculus.

A comprehensive comparison between generalized incidence calculus and Dempster-Shafer theory of evidence.

Dealing with uncertainty problems in intelligent systems has attracted a lot of attention in the AI community. Quite a few techniques have been proposed. Among them, the Dempster-Shafer theory of evidence (DS theory) has been widely appreciated. In DS theory, Dempster's combination rule plays a major role. However, it has been pointed out that the application domains of the rule are rather limited and the application of the theory sometimes gives unexpected results. We have previously explored the problem with Dempster's combination rule and proposed an alternative combination mechanism in generalized incidence calculus. In this paper we give a comprehensive comparison between generalized incidence calculus and the Dempster-Shafer theory of evidence. We first prove that these two theories have the same ability in representing evidence and combining DS-independent evidence. We then show that the new approach can deal with some dependent situations while Dempster's combination rule cannot. Various examples in the paper show the ways of using generalized incidence calculus in expert systems.

Constructing probabilistic ATMS using extended incidence calculus

This paper discusses the relations between extended incidence calculus and assumption-based truth maintenance systems (ATMSs). We first prove that managing labels for statements (nodes) in an ATMS is equivalent to producing incidence sets of these statements in extended incidence calculus. We then demonstrate that the justification set for a node is functionally equivalent to the implication relation set for the same node in extended incidence calculus. As a consequence, extended incidence calculus can provide justifications for an ATMS, because implication relation sets are discovered by the system automatically. We also show that extended incidence calculus provides a theoretical basis for constructing a probabilistic ATMS by associating proper probability distributions on assumptions. In this way, we can not only produce labels for all nodes in the system, but also calculate the probability of any of such nodes in it. The nogood environments can also be obtained automatically. Therefore, extended incidence calculus and the ATMS are equivalent in carrying out inferences at both the symbolic level and the numerical level. This extends a result due to Laskey and Lehner.