Both piRNA and siRNA Pathways Are Silencing Transcripts of the Suffix Element in the Drosophila melanogaster Germline and Somatic Cells

In the Drosophila melanogaster germline, the piRNA pathway silences retrotransposons as well as other transcribed repetitive elements. Suffix is an unusual short retroelement that was identified both as an actively transcribed repetitive element and also as an element at the 3′ ends of the Drosophila non-LTR F element. The copies of suffix that are F element-independent are far more actively transcribed than their counterparts on the F element. We studied the patterns of small RNAs targeting both strands of suffix in Drosophila ovaries using an RNase protection assay and the analysis of the corresponding RNA sequences from the libraries of total small RNAs. Our results indicate that suffix sense and antisense transcripts are targeted mainly by 23–29 nucleotides in length piRNAs and also by 21 nucleotides in length siRNAs. Suffix sense transcripts actively form longer RNA species, corresponding either to partial digestion products of the RNAi and Piwi pathways or to another RNA silencing mechanism. Both sense and antisense suffix transcripts accumulated in the ovaries of homozygous spn-E, piwi and aub mutants. These results provide evidence that suffix sense and antisense transcripts in the germ line and soma are targeted by both RNAi and Piwi pathways and that a Dicer-independent pathway of biogenesis of siRNAs could exist in Drosophila cells

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis

The trophodynamics of Southern Ocean Electrona (Myctophidae) in the Scotia Sea

The Scotia Sea is one of the most productive regions of the Southern Ocean, but its surface waters are experiencing a rapid increase in temperature, which may be changing the behaviour and distribution of many myctophids and their prey species. Electrona antarctica and Electrona carlsbergi are two of the most abundant myctophids in the region, but their ecology is poorly understood and their response to ongoing environmental change is difficult to determine. This study investigated spatial and temporal patterns in their abundance, population structure and diets using mid-water trawl nets deployed across the Scotia Sea during spring, summer and autumn. E. antarctica was the most numerically abundant species (0.09–0.21 ind. 1,000 m−3), with greatest concentrations occurring in the sea-ice sectors. E. carlsbergi occurred in more northern regions, comprising densities of 0.02–0.11 ind. 1,000 m−3. There was evidence of seasonal variation in depth distribution, size-related sexual dimorphism and size-specific vertical stratification for both species. Latitudinal trends in sex ratio and female body size were apparent for E. antarctica. Its diet varied between regions, seasons and size classes, but overall, Euphausia superba, Metridia spp. and Themisto gaudichaudii were the dominant prey items. E. carlsbergi appeared not to recruit in the Scotia Sea. Its diet was dominated by copepods, particularly Rhincalanus gigas and Metridia spp., but regional, seasonal and ontogenetic variations were evident. This study contributes to our understanding of how mid-water food webs are structured in the Southern Ocean and their sensitivity to ongoing environmental change