Rapid identification of <Emphasis Type="Italic">Salmo trutta</Emphasis> lineages by multiplex PCR utilizing primers tailored to discriminate single nucleotide polymorphisms (SNPs) of the mitochondrial control region

Analyses of the mtDNA control region sequence variation of the brown trout Salmo trutta through its distribution range have demonstrated five distinct phylogenetic lineages. In this work we report the design and implementation of a rapid and accurate molecular diagnostic procedure which allows the assignment of all major phylogenetic lineages. Our method relies on multiplex PCR that discriminates diagnostic single nucleotide polymorphisms (SNPs) characteristic of each lineage. The method is straightforward and easy to set up, involves a single reaction, yields data easy to interpret and does not pose significant risk for false positive/negative lineage assignment of a given individual. Panagotis K. Apostolou and Andreas Georgiadis contributed equally to this work.     

A chassis exchange terminal to reduce truck congestion at container terminals

Truck congestion for container terminals seems to be a worldwide unwanted phenomenon. In this paper we present and analyze a chassis exchange terminal concept to reduce the congestion. The terminal works as a kind of extended gate of a group of traditional container terminals. During the night containers are collected from these container terminals using chassis (or trailers). In daytime these containers on chassis are then collected and exchanged with export containers also on chassis. By exchanging the chassis we avoid extra handling of containers. As connecting and disconnecting to a chassis can be done in a short time, the chassis exchange terminal increases handling capacity substantially during peak hours. In this paper we analyze the concept for the Maasvlakte container terminals in Rotterdam. We investigate both the effect on waiting time, as well as the environmental effects.     

Unexpected inhibition of bradycardia pacing due to oversensing in ICD lead fracture associated with spurious tachyarrhythmia detection and discharges

Ιn a 76-year old man with a dual-chamber ICD implanted five years ago, dizzy spells and significant bradycardia on Holter were not initially recognized as inhibition of bradycardia pacing, due to oversensing. Hospital admission was deemed necessary only after repetitive ICD shocks attributed to right ventricular pace-sense lead fracture. The need to ensure adequate ICD antibradycardia backup pacing in pacing-dependent patients when deleterious sensing errors occur, cannot be overemphasized.     

Solvated protein–DNA docking using HADDOCK

Interfacial water molecules play an important role in many aspects of protein–DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein–DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein–DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein–DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein–DNA complexes.