High incidence of cryptic repeated elements in microsatellite flanking regions of galatheid genomes and its evolutionary implications

During the development of PCR primer sets for icrosatellite marker loci from enriched genomic libraries for three squat lobster species from Galatheidae (Decapoda: Anomura); Munida rugosa (Fabricius, 1775), M. sarsi (Huus, 1935), and Galathea strigosa (Linnaeus, 1761) (collectively known as squat lobsters), a number of unforeseen problems were encountered. These included PCR amplification failure, lack of amplification consistency, and the amplification of multiple fragments. Careful examination of microsatellite containing sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. BLAST analysis of these and other VNTR containing sequences (N 5 252) indicates that these cryptic elements can be grouped into families based upon sequence similarities. The unique features characterising these families suggest that different molecular mechanisms are involved. Of particular relevance is the association of microsatellites with mobile elements. This is the first reported observation of this phenomenon in crustaceans, and it also helps to explain why microsatellite primer development in galatheids has been relatively unsuccessful to date. We suggest a number of steps that can be used to identify similar problems in microsatellite marker development for other species, and also alternative approaches for both marker development and for the study of molecular evolution of species characterised by complex genome organisation. More specifically, we argue that new generation sequencing methodologies, which capitalise on parallel and multiplexed sequencing may pave the way forward for future crustacean research.

On the dissolution of non-metallic solid elements (sulfur, selenium, tellurium and phosphorus) in ionic liquids

Ionic liquids are shown to be good solvents for elemental sulfur, selenium, phosphorus and tellurium, and can be designed to maximise the solubility of these elements. The presence of the [S-3](center dot-) radical anion in diluted solutions of sulfur in some ionic liquids has been confirmed, and is the origin of their intense blue colour (cf. lapis lazuli).

Thermodynamic properties and atomistic structure of the dry amorphous silica surface from a reactive force field model

A force field model of the Keating type supplemented by rules to break, form, and interchange bonds is applied to investigate thermodynamic and structural properties of the amorphous SiO2 surface. A simulated quench from the liquid phase has been carried out for a silica sample made of 3888 silicon and 7776 oxygen atoms arranged on a slab similar to 40 angstrom thick, periodically repeated along two directions. The quench results into an amorphous sample, exposing two parallel square surfaces of similar to 42 nm(2) area each. Thermal averages computed during the quench allow us to determine the surface thermodynamic properties as a function of temperature. The surface tension turns out to be gamma=310 +/- 20 erg/cm(2) at room temperature and gamma=270 +/- 30 at T=2000 K, in fair agreement with available experimental estimates. The entropy contribution Ts-s to the surface tension is relatively low at all temperatures, representing at most similar to 20% of the surface energy. Almost without exceptions, Si atoms are fourfold coordinated and oxygen atoms are twofold coordinated. Twofold and threefold rings appear only at low concentration and are preferentially found in proximity of the surface. Above the glass temperature T-g=1660 +/- 50 K, the mobility of surface atoms is, as expected, slightly higher than that of bulk atoms. The computation of the height-height correlation function shows that the silica surface is rough in the equilibrium and undercooled liquid phase, becoming smooth below the glass temperature T-g.