A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome-wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome-wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long-term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome

Impact of calcium on salivary α-amylase activity, starch paste apparent viscosity and thickness perception

Thickness perception of starch-thickened products during eating has been linked to starch viscosity and salivary amylase activity. Calcium is an essential cofactor for α-amylase and there is anecdotal evidence that adding extra calcium affects amylase activity in processes like mashing of beer. The aims of this paper were to (1) investigate the role of salivary calcium on α-amylase activity and (2) to measure the effect of calcium concentration on apparent viscosity and thickness perception when interacting with salivary α-amylase in starch-based samples. α-Amylase activity in saliva samples from 28 people was assessed using a typical starch pasting cycle (up to 95 °C). The activity of the enzyme (as measured by the change in starch apparent viscosity) was maintained by the presence of calcium, probably by protecting the enzyme from heat denaturation. Enhancement of α-amylase activity by calcium at 37 °C was also observed although to a smaller extent. Sensory analysis showed a general trend of decreased thickness perception in the presence of calcium, but the result was only significant for one pair of samples, suggesting a limited impact of calcium enhanced enzyme activity on perceived thickness

Development of monotonic neuronal tuning in the monkey inferotemporal cortex through long-term learning of fine shape discrimination

Visual expertise in discriminating fine differences among a group of similar objects can be obtained through extensive long-term training. Here we investigated the neural bases of this superior capability. The inferotemporal cortex, located at the final stage along the ventral visual pathway, was a candidate site in monkeys because cells there respond to various complex features of objects. To identify the changes that underlie the development of visual expertise in fine discrimination, we created a set of parametrically designed object stimuli and compared the stimulus selectivity of inferotemporal cells between two different training histories. One group of recordings was conducted after the monkeys had been extensively trained for fine discrimination (fine-discrimination period) and the other after the monkeys had been exposed only for coarse discrimination (coarse-discrimination period). We found that the tuning of responses recorded in the fine-discrimination period was more monotonic in the stimulus parameter space. The stimuli located at the extreme in the parameter space evoked the maximum responses in a larger proportion of cells and the direction of response decrease in the parameter space was more consistent. Moreover, the stimulus arrangement reconstructed from the responses recorded during the fine-discrimination period was more similar to the original stimulus arrangement. These results suggest that visual expertise could be based on the development, in the inferotemporal cortex, of neuronal selectivity monotonically tuned over the parameter space of the object images

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

Structural studies of Langmuir and Langmuir-Blodgett films of functionalized surfactants

Structural studies of Langmuir and Langmuir-Blodgett films of functionalized surfactants show that the organization of surfactants is strongly dependent on cross-sectional match between the functionalized headgroup and the film-forming alkyl chain parts of the molecules. The organization of a particular functionalized surfactant with a slight cross-sectional mismatch between head and tail has been investigated by synchrotron radiation in floating monolayers and by atomic force microscopy (AFM) in Langmuir-Blodgett films. The transfer process was accompanied by an increase of the oblique unit cell area by 17% and by an increase of the average diameter of perfectly ordered domains from 3 nm to approximately 10 nm. We have calculated a number of likely packing patterns of alkyl chains and the lattice parameters of the Langmuir-Blodgett films are found to be consistent with one of these packings. For comparison, the results of preliminary studies on a functionalized surfactant with a severe cross-sectional mismatch between head and tail are presented, indicating that the tail is bent around the head group thereby preventing efficient packing of the alkyl chains

Design of a 5-station macromolecular crystallography beamline at MAX-Lab

A beamline for macromolecular crystallography is under construction at the Swedish synchrotron light source MAX-lab at Lund University in a collaborative effort between Denmark and Sweden. Of the 7 mrad horizontal wiggler fan emitted from the new superconducting multipole wiggler, the central 2 mrad will be used and split in three parts. The central 1 mrad will be used for a tunable station optimised for multi-wavelength anomalous diffraction experiments and on each side of the central fan there will be two fixed wavelength stations using different energies of the same part of the beam. These in total five stations can be used simultaneously and independently for collecting diffraction data