Towards OWL-based Knowledge Representation in Petrology

This paper presents our work on development of OWL-driven systems for formal representation and reasoning about terminological knowledge and facts in petrology. The long-term aim of our project is to provide solid foundations for a large-scale integration of various kinds of knowledge, including basic terms, rock classification algorithms, findings and reports. We describe three steps we have taken towards that goal here. First, we develop a semi-automated procedure for transforming a database of igneous rock samples to texts in a controlled natural language (CNL), and then a collection of OWL ontologies. Second, we create an OWL ontology of important petrology terms currently described in natural language thesauri. We describe a prototype of a tool for collecting definitions from domain experts. Third, we present an approach to formalization of current industrial standards for classification of rock samples, which requires linear equations in OWL 2. In conclusion, we discuss a range of opportunities arising from the use of semantic technologies in petrology and outline the future work in this area.Comment: 10 pages. The paper has been accepted by OWLED2011 as a long presentatio

The first preparative solution phase synthesis of melanotan II

Melanotan II is a synthetic cyclic heptapeptide used to prevent a sunlight-induced skin cancer by stimulating the skin tanning process. In this paper we report the first solution phase synthesis of the title compound. The hexapeptide sequence has been assembled by [(2+2)+1+1] scheme. After removing the orthogonal protection, a carbodiimide mediated lactamization, involving the ε-amino group of lysine and γ-carboxy group of aspartic acid, led to a cyclic intermediate. Appending N-acetylnorleucine concluded the assembly of melanotan II molecule. Protection of the lateral groups in arginine and tryptophan was omitted for atom and step economy reasons. The total synthesis of melanotan II was accomplished in 12 steps with 2.6% overall yield, affording >90% pure peptide without using preparative chromatography

First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species

The extant reptiles are one of the most diverse clades among terrestrial vertebrates and one of a few groups with instances of parthenogenesis. Due to the hybrid origin of parthenogenetic species, reference genomes of the parental species as well as of the parthenogenetic progeny are indispensable to explore the genetic foundations of parthenogenetic reproduction. Here, we report on the first genome assembly of rock lizard Darevskia valentini, a paternal species for several parthenogenetic lineages. The novel genome was used in the reconstruction of the comprehensive phylogeny of Squamata inferred independently from 7369 trees of single-copy orthologs and a supermatrix of 378 conserved proteins. We also investigated Hox clusters, the loci that are often regarded as playing an important role in the speciation of animal groups with drastically diverse morphology. We demonstrated that Hox clusters of D. valentini are invaded with transposons and contain the HoxC1 gene that has been considered to be lost in the amniote ancestor. This study provides confirmation for previous works and releases new genomic data that will contribute to future discoveries on the mechanisms of parthenogenesis as well as support comparative studies among reptiles