Temperature trends and recent decline in body size of the stone marten Martes foina in Denmark

We studied a sample of 131 skulls of the stone marten Martes foina that were collected in Denmark between 1858 and 1999. Data were available for 37 years, but collection effort was not uniform throughout the study period and annual sample size varied between 1 and 27. We used principal component analysis (PCA) to combine the information of four skull measurements into a single variable (PC1). PC1 was then corrected for factors that significantly affected it (sex and longitude), and residual PC1 was used for further analysis in which we calculated trends in PC1 values during the study period. During the study period there was an increase in mean annual temperature in Denmark, but this increase was not continuous, as there was slight decrease in temperature between 1947 and 1965.We found that skull size (and by implication body size) of the stone marten in Denmark had two periods of decrease and these two periods coincide with the periods of increase in mean annual temperature. These results may indicate that body size of the stone marten is sensitive to the change in ambient temperature, either due to a change in food availability that was caused by the increase in temperature, or decreased its size in accordance with Bergmann's rule.     

Soluble minerals in chemical evolution

The adsorption of 5-AMP onto solid CaSO₄ · 2H₂O was studied in a saturated suspension as a function of pH and electrolyte concentration. The adsorption is pH-dependent and is directly correlated with the charge on the 5-AMP molecule which is determined by the state of protonation of the N-1 nitrogen of the purine ring and the phosphate oxygens. It is proposed that the binding that occurs between the nucleotide and the salt is electrostatic in nature. The adsorption decreases with increasing ionic strength of the solution which means that in a fluctuating environment of wetting and drying cycles, a biomolecule similar to 5-AMP could be expected to desorb during the drying phase. The results indicate that CaSO₄ · 2H₂O can serve as a concentrating surface for biomolecules. The significance of this is discussed with regard to the possible role of soluble minerals and their surfaces in a geochemical model consistent with the evolution of the Earth and the origin of life.     

Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach

Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next‐generation sequencing to allow such large‐scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large‐scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost‐effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.     

Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches

Synonymous variations, which are defined as codon substitutions that do not change the encoded amino acid, were previously thought to have no effect on the properties of the synthesized protein(s). However, mounting evidence shows that these "silent" variations can have a significant impact on protein expression and function and should no longer be considered "silent". Here, the effects of six synonymous and six non-synonymous variations, previously found in the gene of ADAMTS13, the von Willebrand Factor (VWF) cleaving hemostatic protease, have been investigated using a variety of approaches. The ADAMTS13 mRNA and protein expression levels, as well as the conformation and activity of the variants have been compared to that of wild-type ADAMTS13. Interestingly, not only the non-synonymous variants but also the synonymous variants have been found to change the protein expression levels, conformation and function. Bioinformatic analysis of ADAMTS13 mRNA structure, amino acid conservation and codon usage allowed us to establish correlations between mRNA stability, RSCU, and intracellular protein expression. This study demonstrates that variants and more specifically, synonymous variants can have a substantial and definite effect on ADAMTS13 function and that bioinformatic analysis may allow development of predictive tools to identify variants that will have significant effects on the encoded protein.     

Global assessment of marine biodiversity potentially threatened by offshore hydrocarbon activities

Increasing global energy demands have led to the ongoing intensification of hydrocarbon extraction from marine areas. Hydrocarbon extractive activities pose threats to native marine biodiversity, such as noise, light, and chemical pollution, physical changes to the sea floor, invasive species, and greenhouse gas emissions. Here, we assessed at a global scale the spatial overlap between offshore hydrocarbon activities and marine biodiversity (>25,000 species, nine major ecosystems, and marine protected areas), and quantify the changes over time. We discovered that two‐thirds of global offshore hydrocarbon activities occur in areas within the top 10% for species richness, range rarity, and proportional range rarity values globally. Thus, while hydrocarbon activities are undertaken in less than one percent of the ocean's area, they overlap with approximately 85% of all assessed species. Of conservation concern, 4% of species with the largest proportion of their range overlapping hydrocarbon activities are range restricted, potentially increasing their vulnerability to localized threats such as oil spills. While hydrocarbon activities have extended to greater depths since the mid‐1990s, we found that the largest overlap is with coastal ecosystems, particularly estuaries, saltmarshes and mangroves. Furthermore, in most countries where offshore hydrocarbon exploration licensing blocks have been delineated, they do not overlap with marine protected areas (MPAs). Although this is positive in principle, many countries have far more licensing block areas than protected areas, and in some instances, MPA coverage is minimal. These findings suggest the need for marine spatial prioritization to help limit future spatial overlap between marine conservation priorities and hydrocarbon activities. Such prioritization can be informed by the spatial and quantitative baseline information provided here. In increasingly shared seascapes, prioritizing management actions that set both conservation and development targets could help minimize further declines of biodiversity and environmental changes at a global scale.     

Modeling the effects of enclosure size on geometry learning

Several recent studies have shown that chickens, fish, and humans trained to find a reward in a corner of a rectangular enclosure with distinctive features rely more on the geometry of the enclosure in small enclosures and rely more on the features in large enclosures. Here, these results are modeled using a recent associative model of geometry learning [Miller, N.Y., Shettleworth, S.J., 2007. Learning about environmental geometry: an associative model. J. Exp. Psychol. Anim. B 33, 191–212]. By adjusting the salience of either geometric or featural information or both the model is capable of reproducing much of the data on the effects of enclosure size on geometry learning.