Neotrygon vali, a new species of the blue-spotted maskray complex (Myliobatoidei: Dasyatidae)

The blue-spotted maskray from Guadalcanal Island (Solomon archipelago) is distinct by its colour patterns from Neotrygon kuhlii with which it was previously confused, and belongs to a genetic lineage clearly separate from all other known species in the genus Neotrygon. It is here described as a new species, Neotrygon vali sp. nov., on the basis of its nucleotide sequence at the cytochrome oxidase 1 (CO1) gene locus. It is diagnosed from all other known species in the genus Neotrygon by the possession of nucleotide T at nucleotide site 420 and nucleotide G at nucleotide site 522 of the CO1 gene.

Estimation of the in vivo recombination rate for a plant RNA virus

Phylogenomic evidence suggested that recombination is an important evolutionary force for potyviruses, one of the larger families of plant RNA viruses. However, mixed-genotype potyvirus infections are marked by low levels of cellular coinfection, precluding template switching and recombination events between virus genotypes during genomic RNA replication. To reconcile these conflicting observations, we evaluated the in vivo recombination rate (r g) of Tobacco etch virus (TEV; genus Potyvirus, family Potyviridae) by coinfecting plants with pairs of genotypes marked with engineered restriction sites as neutral markers. The recombination rate was then estimated using two different approaches: (i) a classical approach that assumed recombination between marked genotypes can occur in the whole virus population, rendering an estimate of r g = 7.762×10−8 recombination events per nucleotide site per generation, and (ii) an alternative method that assumed recombination between marked genotypes can occur only in coinfected cells, rendering a much higher estimate of r g = 3.427×10−5 recombination events per nucleotide site per generation. This last estimate is similar to the TEV mutation rate, suggesting that recombination should be at least as important as point mutation in creating variability. Finally, we compared our mutation and recombination rate estimates to those reported for animal RNA viruses. Our analysis suggested that high recombination rates may be an unavoidable consequence of selection for fast replication at the cost of low fidelity.

Conformational changes at the nucleotide pocket of motor proteins monitored by electron paramagnetic resonance spectroscopy

A fundamental goal in the field of motor proteins is to identify the conformational changes associated with the hydrolysis of the physiological substrate, ATP, and to define how these conformational changes are modulated by binding to the polymer track and translated into biologically useful movement. We have used electron paramagnetic resonance (EPR) spectroscopy to monitor conformational changes at the nucleotide-binding site of myosin- and kinesin-family motors. A novel set of nucleotide-analog EPR spin probes were synthesized and used to localize a spin moiety at the nucleotide site. This allows a reporter group to be placed with high specificity at the ATP binding site. Our results indicate that the nucleotide-binding site of myosin motors opens when the motor binds to its polymer roadway, actin, while that of kinesin closes on binding to microtubules (MTs). However, the transition is not all-or-none. There is instead an equilibrium between open and closed conformations. The different conformational changes in the two motor families can be correlated with differences in their biochemical cycles. Thus, we can now define the relationship between nucleotide-site structure, biochemistry and polymer binding for the two motors.