The lepidopteran innate immune response against RNA viruses remains poorly understood, while in other insects several studies have highlighted an essential role for the exo-RNAi pathway in combating viral infection. Here, by using deep-sequencing technology for viral small-RNA (vsRNA) assessment, we provide evidence that exo-RNAi is operative in the silkworm Bombyx mori against both persistent and pathogenic infection of B. mori cytoplasmic polyhedrosis virus (BmCPV) which is characterized by a segmented double-stranded RNA (dsRNA) genome. Further, we show that Dicer-2 predominantly targets viral dsRNA and produces 20-nucleotide (nt) vsRNAs, whereas an additional pathway is responsive to viral mRNA derived from segment 10. Importantly, vsRNA distributions, which define specific hot and cold spot profiles for each viral segment, to a considerable degree overlap between Dicer-2-related (19 to 21 nt) and Dicer-2-unrelated vsRNAs, suggesting a common origin for these profiles. We found a degenerate motif significantly enriched at the cut sites of vsRNAs of various lengths which link an unknown RNase to the origins of vsRNAs biogenesis and distribution. Accordingly, the indicated RNase activity may be an important early factor for the host's antiviral defense in Lepidoptera. Central to the defense of insects against RNA viruses is the triggering of the so-called exogenous RNA interference pathway (exo-RNAi), by which viral double-stranded RNA (dsRNA) is cleaved intracellularly into viral small interfering RNAs (siRNAs) that in turn silence homologous transcripts (1). It is established that Dicer-2, a cytoplasmic RNase III class enzyme, recognizes and cuts successively the dsRNA template to produce small interfering RNA duplexes of ϳ21 nucleotides (nt) characterized by a signature of 2-nt 3=-hydroxyl overhangs (2). These duplexes are subsequently incorporated into the effector complex RISC (RNA-induced silencing complex) via interactions with Argonaute-2, which, upon discarding one of the two strands (passenger strand), is followed by selection and cleavage of viral sequences bearing perfect complementarity to the remaining strand (guide strand) (1, 3). Dicer-2 may act upon the genome of the virus itself-as in the case of dsRNA viruses-and/or on viral replication and transcription intermediates, although structured, single-stranded RNA (ssRNA) may also be utilized (4). Interestingly, several deepsequencing data have revealed that approximately 18-to 30-nt viral small RNAs (vsRNAs) of infected insects are not evenly distributed along the genomes but map preferentially in distinct genomic areas (hot spots) versus genomic stretches with unmapped or less-mapped vsRNAs (cold spots) (4-13). The origin of these profiles, as well as the hypothetical functional distinction between vsRNAs deriving from hot or cold spots, remains substantially elusive, although hot spots near the end of the genome have been attributed to structured regulatory viral regions (14) and an RNAi decoy-like mechanism driven by abundant vsRNAs ...

The aim of this study is to investigate the dietary patterns which indicate the nutritional habits of Greek adults and their effects on serum 25(OH)D levels and quantitative ultrasound (QUS) parameters for bone health. This study is part of OSTEOS, an observational cross-sectional study. In total, 741 adults from rural and urban areas throughout Greece were recruited. A validated food frequency questionnaire (FFQ) was used for assessment of the population’s dietary habits. Serum 25(OH)D was measured by enzyme immunoassay; QUS parameters were assessed with an Achilles device. Principal component analysis (PCA) was carried out for dietary pattern determination, and univariate analysis of variance was used for the assessment of 25(OH)D, broadband ultrasound attenuation (BUA), speed of sound (SOS), and stiffness index (SI) determinants. Six dietary patterns explain 52.2% of the variability of Greek adults’ nutritional habits. The ‘vegetables–fruit’ dietary pattern explains the biggest rate of variability. Determinants of serum 25(OH)D are body mass index (BMI), elderly status, summer sun exposure, organized physical activity, a ‘healthy’ pattern in winter months, and adherence to a ‘sweet’ pattern. Determinants of QUS parameters are age, BMI, sedentary time, organized physical activity participation, and adherence to a ‘healthy’ pattern.

Strand biases reflect deviations from a null expectation of DNA evolution that assumes strand-symmetric substitution rates. Here, we present strong evidence that nearest-neighbour preferences are a strand-biased feature of bacterial genomes, indicating neighbour-dependent substitution asymmetries. To detect such asymmetries we introduce an alignment free index (relative abundance skews). The profiles of relative abundance skews along coding sequences can trace the phylogenetic relations of bacteria, suggesting that the patterns of neighbour-dependent substitution strand-biases are not common among different lineages, but are rather species-specific. Analysis of neighbour-dependent and codon-site skews sheds light on the origins of substitution asymmetries. Via a simple model we argue that the structure of the genetic code imposes position-dependent substitution strand-biases along coding sequences, as a response to GC mutation pressure. Thus, the organization of the genetic code per se can lead to an uneven distribution of nucleotides among different codon sites, even when requirements for specific codons and amino-acids are not accounted for. Moreover, our results suggest that strand-biases in replication fidelity of PolIII α-subunit induce substitution asymmetries, both neighbour-dependent and independent, on a genome scale. The role of DNA repair systems, such as transcription-coupled repair, is also considered.

No abstract

Analysis of DNA composition at several length scales constitutes the bulk of many early studies aimed at unravelling the complexity of the organization and functionality of genomes. Dinucleotide relative abundances are considered an idiosyncratic feature of genomes, regarded as a ‘genomic signature’. Motivated by this finding, we introduce the ‘Generalized Genomic Signatures’ (GGSs), composed of over- and under-abundances of all oligonucleotides of a given length, thus filtering out compositional trends and neighbour preferences at any shorter range. Previous works on alignment-free genomic comparisons mostly rely on k-mer frequencies and not on distance-dependent neighbour preferences. Therein, nucleotide composition and proximity preferences are combined, while in the present work they are strictly separated, focusing uniquely on neighbour relationships. GGSs retain the potential or even outperform genomic signatures defined at the dinucleotide level in distinguishing between taxonomic subdivisions of bacteria, and can be more effectively implemented in microbial phylogenetic reconstruction. Moreover, we compare DNA sequences from the human genome corresponding to protein coding segments, conserved non-coding elements and non-functional DNA stretches. These classes of sequences have distinctive GGSs according to their genomic role and degree of conservation. Overall, GGSs constitute a trait characteristic of the evolutionary origin and functionality of different genomic segments.