Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.     

Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex

The blue-emissive antibody EP2-19G2 that has been elicited against trans-stilbene has unprecedented ability to produce bright luminescence and has been used as a biosensor in various applications. We show that the prolonged luminescence is not stilbene fluorescence. Instead, the emissive species is a charge-transfer excited complex of an anionic stilbene and a cationic, parallel pi-stacked tryptophan. Upon charge recombination, this complex generates exceptionally bright blue light. Complex formation is enabled by a deeply penetrating ligand-binding pocket, which in turn results from a noncanonical interface between the two variable domains of the antibody.     

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.     

The mineral content affects vertebral morphology in underyearling smolt of Atlantic salmon (Salmo salar L.)

This study investigated the individual variation in vertebral morphology and mineral content (as % of bone dry weight) in rapid growing underyearling smolt (n = 33) twelve weeks after transfer to seawater. The smolt, which were reared in triplicate tanks, had a large individual variation in vertebral bone mineral content (Tank A: 36.2% min, 45.2% max, 39.6% mean. Tank B: 32.6% min, 46.6% max, 40.0% mean. Tank C: 38.5% min, 47.9% max, 42.4% mean), and were subdivided into two groups based on mean within each tank: high mineral content (HMC, above tank mean, n = 15) and low mineral content (LMC, below tank mean, n = 18). Vertebrae of smolt with a low mineral content were more compressed in the anterior–posterior direction (HMC vertebral length/dorso-ventral diameter ratio 0.83, LMC 0.80). This was related to a change in the growth direction of the vertebral cone. This change occurred around transfer to seawater and was characterised by an increased angle between the wall of the cone of the vertebrae and the cranial–caudal axis, and gave the vertebrae a compressed appearance. Smolt with a high mineral content were significantly longer (HMC 28.1 cm, LMC 26.5 cm) and heavier (HMC 270 g, LMC 210 g) twelve weeks after transfer to seawater.