Determination of the asymptotic shapes of sedimentation velocity patterns for reversibly polymerizing solutes

A simple method is described for the determination of the asymptotic boundary shape from a series of schlieren patterns taken during a sedimentation velocity experiment on a rapidly and reversibly associating solute. The form of the boundary so obtained reflects effects of sedimentation and chemical reaction but is free from effects of diffusion. The procedure is illustrated with analyses of experiments on diisopropyl fluorophosphate-inhibited α-chymotrypsin in 0.29 I phosphate, pH 7.9 (a monomer-dimer system), and on β-lactoglobulin A in 0.1 I acetate, pH 4.65 (a monomer-dimer-trimer-tetramer system). Asymptotic patterns so determined exhibit close agreement with those predicted by Gilbert theory.     

Revealing biases inherent in recombination protocols

Background  

The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing.     

Phylogenetic Analysis of theArenaviridae:Patterns of Virus Evolution and Evidence for Cospeciation between Arenaviruses and Their Rodent Hosts

Viruses of theArenaviridaecause hemorrhagic fevers and neurologic disease in humans. Historically, the arenaviruses have been divided into two complexes (LASV-LCMV, Tacaribe) through the use of antigenic typing. The phylogeny of theArenaviridaeas a whole has not been estimated previously due to a lack of sequence data for all members of the family. In this study, nucleocapsid protein gene sequence data were obtained for all currently known arenaviruses and used to estimate, for the first time, a phylogeny of the entire virus family. The LCMV-LASV complex arenaviruses are monophyletic and comprise three distinct lineages. The Tacaribe complex viruses also are monophyletic and occupy three distinct lineages. Comparisons of arenavirus phylogeny with rodent host phylogeny and taxonomic relationships provide several examples in which virus–host cospeciation is potentially occurring. The pathogenic arenaviruses do not appear to be monophyletic, suggesting that the pathogenic phenotype has arisen in multiple independent events during virus evolution.     

EFFECT OF THE SOUND GENERATED BY AN ACOUSTIC HARASSMENT DEVICE ON THE RELATIVE ABUNDANCE AND DISTRIBUTION OF HARBOR PORPOISES (PHOCOENA PHOCOENA) IN RETREAT PASSAGE, BRITISH COLUMBIA

We describe an experiment conducted to assess the impact of the sound generated by an acoustic harassment device (AHD) on the relative abundance and distribution of harbor porpoises ( Phocoena phocoena ) in Retreat Passage, British Columbia. During control periods when the AHD was inactive, the mean number of porpoises observed in the study area was 0.39 for broad area scans conducted with the naked eye and 0.48 for narrow sector scans conducted with binoculars. Abundance declined precipitously when the AHD was activated, to 0.007 porpoises per broad area scan and 0.018 per narrow sector scan. The mean number of porpoise resightings while tracking their movements also declined from 12.2 to 13.6 per sighting during control periods to 1.1–1.9 per sighting when the AHD was activated, which suggested that the few porpoises that ventured into the study area spent less time within it when the AHD was activated. The effect of the AHD diminished with distance. No porpoises were observed within 200 m of the AHD when it was activated. The number of sightings and resightings observed when it was activated was less than 0.2% of the number expected had there been no AHD effect at a range of 200–399 m, 1.4% the number expected at a range of 400–599 m, varied between 2.5% and 3.3% of the number expected at a range of 600–2,499 m, and was 8.1% the number expected at a range of 2,500–3,500 m, which suggested that the impact of the AHD extended beyond our maximum sighting range of 3.5 km.