No abstract

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.

The postural adaptation impairments of patients with Parkinson's disease (PD) suggest that the basal ganglia may be important for quickly modifying muscle activation patterns when the direction of perturbation or stance conditions suddenly change. It is unknown whether their particular instability to backward postural perturbations is due to specific abnormalities of parkinsonian postural muscle synergies in that direction and not present in other directions. In the present study, we test this hypothesis by comparing the patterns of leg and trunk muscle activation in 13 subjects with PD and 13 control subjects in response to eight randomly presented directions of horizontal surface translations while standing with either narrow or wide stance. The direction of maximum activation for each muscle was similar for PD and control subjects, suggesting that the basal ganglia is not critical for programming externally triggered postural synergies. However, antagonist muscle activation was earlier and larger in PD than in control subjects, resulting in coactivation. PD subjects also did not increase the magnitude of muscle activation as much as did control subjects when changing from wide to narrow stance. These results are consistent with the hypothesis that PD results in an inability to shape the pattern and magnitude of postural muscle responses for changes in perturbation direction and in stance position.

This study provides comprehensive validation of the 14-item Mediterranean Diet Adherence Screener (14-MEDAS) in an adult population from Greece (GR), Portugal (PT), Italy (IT), Spain (SP), Cyprus (CY), Republic of North Macedonia (NMK), and Bulgaria (BG). A moderate association between the 14-MEDAS and the reference food diary was estimated for the entire population (Pearson r = 0.573, p-value < 0.001; Intraclass Correlation Coefficient (ICC) = 0.692, p-value < 0.001) with the strongest correlation found in GR, followed by PT, IT, SP, and CY. These results were supported by kappa statistics in GR, PT, IT, and SP with ≥50% of food items exhibiting a fair or better agreement. Bland–Altman analyses showed an overestimation of the 14-MEDAS score in the whole population (0.79 ± 1.81, 95%Confidence Interval (CI) 0.61, 0.96), but this value was variable across countries, with GR, NMK, and BG exhibiting the lowest bias. Taking all analyses together, the validation achieved slightly better results in the Mediterranean countries but a definitive validation ranking order was not evident. Considering growing evidence of the shift from Mediterranean Diet (MD) adherence and of the importance of culture in making food choices it is crucial that we further improve validation protocols with specific applications to compare MD adherence across countries.