Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes

Metagenomic shotgun sequencing, using Illumina technology, and de novo genome assembly of mixed field-collected amples of invertebrates readily produce mitochondrial genome sequences, allowing rapid identification and quantification of species diversity. However, intraspecific genetic variability present in the specimen pools is lost during mitogenome assembly, which limits the utility of ‘mitochondrial metagenomics’ for studies of population diversity. 2. Using 10 natural communities (>2600 individuals) of leaf beetles (Chrysomelidae), DNA variation in the mitochondrial cox1-5’ ‘barcode’ was compared for Sanger sequenced individuals and Illumina shotgun sequenced specimen pools. 3. Generally, only a single mitochondrial contig was assembled per species, even in the presence of intraspecific variation. Ignoring ambiguity from the use of two different assemblers, the cox1 barcode regions from these assemblies were exact nucleotide matches of a Sanger sequenced barcode in 90.7% of cases, which dropped to 76.0% in assemblies from samples with large intra and interspecific variability. Nucleotide differences between barcodes from both data types were almost exclusively in synonymous 3rd codon position, although the number of affected sites was very low, and the greatest discrepancies were correlated with poor quality of Sanger sequences. 4. Unassembled shotgun reads were also used to score single nucleotide polymorphisms and to calculate intraspecific nucleotide diversity (pi) for all available populations at each site. These values correlated with Sanger sequenced cox1 variation but were significantly higher. 5. Overall, the assemblage-focused shotgun sequencing of pooled samples produced nucleotide variation data comparable to the well-established specimen-focused Sanger approach. The findings thus extend the application of mitochondrial metagenomics of complex biodiversity samples to the estimation of diversity below the species level

Metagenome skimming of insect specimen pools: potential for comparative genomics

Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from lowcoverage sequencing by “genome skimming,” which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and knownrepeatelementsof high and low complexity, includingnumerous copies ofrRNAandhistone genes.Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous “clusters” of scaffolds mapped to the same genomic site revealed intraand/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The “metagenome skimming” approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomic

Automated Certification of Authorisation Policy Resistance

Attribute-based Access Control (ABAC) extends traditional Access Control by considering an access request as a set of pairs attribute name-value, making it particularly useful in the context of open and distributed systems, where security relevant information can be collected from different sources. However, ABAC enables attribute hiding attacks, allowing an attacker to gain some access by withholding information. In this paper, we first introduce the notion of policy resistance to attribute hiding attacks. We then propose the tool ATRAP (Automatic Term Rewriting for Authorisation Policies), based on the recent formal ABAC language PTaCL, which first automatically searches for resistance counter-examples using Maude, and then automatically searches for an Isabelle proof of resistance. We illustrate our approach with two simple examples of policies and propose an evaluation of ATRAP performances.Comment: 20 pages, 4 figures, version including proofs of the paper that will be presented at ESORICS 201

FUSE Spectra of the Black Hole Binary LMC X-3

Far-ultraviolet spectra of LMC X-3 were taken covering photometric phases 0.47 to 0.74 in the 1.7-day orbital period of the black-hole binary (phase zero being superior conjunction of the X-ray source). The continuum is faint and flat, but appears to vary significantly during the observations. Concurrent RXTE/ASM observations show the system was in its most luminous X-ray state during the FUSE observations. The FUV spectrum contains strong terrestrial airglow emission lines, while the only stellar lines clearly present are emissions from the O VI resonance doublet. Their flux does not change significantly during the FUSE observations. These lines are modelled as two asymmetrical profiles, including the local ISM absorptions due to C II and possibly O VI. Velocity variations of O VI emission are consistent with the orbital velocity of the black hole and provide a new constraint on its mass.Comment: 12 pages including 1 table, 4 diagrams To appear in A

Education for collaboration: the influence of the third space on professional boundaries

The delivery of integrated care requires the establishment of effective professional relationships that foster collaborative working across health systems. Evidence for how to prepare practitioners to work in those settings is limited. By exploring an innovative postgraduate Programme for Integrated Child Health (PICH) this article highlights the conditions by which effective collaboration can be encouraged. Our qualitative evaluation of PICH involved one-to-one semi-structured interviews with 23 postgraduate general practice and paediatric trainees and their mentors. We analysed the data using the concept of the ‘third space’, where multiple discourses between individuals with diverse professional backgrounds occur, enabling creative exploration of tensions inherent in new ways of working in order to identify enablers and barriers to collaboration. Our analysis identified three themes that enabled collaboration: effective communication, boundary work and educational spaces; and four themes that were barriers: traditional hierarchical professional identities, curriculum design, financial systems and workplace spaces. PICH demonstrated the value of educational spaces and their role in enabling collaborative practice, as participants explored their professional identities and those of other disciplines. Structural factors in the workplace which inhibit collaborative practice were also evident. We conclude by proposing a model for collaborative learning in third spaces based upon the recognition that, while educational programmes alone will not lead to change, they have the potential to inform the development of productive workplace spaces that will be required if collaborative practice in healthcare is to become a reality

The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera

International audienceWe describe the mitochondrial genome of Hydropsyche pellucidula Curtis 1834, which is first described for the suborder Annulipalpia and the first in the order Trichoptera to show a non-canonical gene order. The mitogenome was obtained by de novo assembly of shotgun sequenced total genomic DNA using Illumina Miseq technology, which produced an average coverage of 115× and a minimum coverage of 48×. The mitochondrial genome includes 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The genome is characterized by a rearrangement in the relative position of protein-coding and ribosomal genes. This mitogenome sequence will be useful for studying the family Hydropsychidae, which is commonly used for freshwater pollution biomonitoring

Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained via masstrapping, many of which will be new species, could be incorporated routinely in phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures via mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from ~500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined, only minor topological changes are induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, whilst the ecological sample expands the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA ‘superbarcodes’ for testing hypotheses regarding global patterns of diversity

High-Resolution spectroscopy of the low-mass X-ray binary EXO 0748-67

We present initial results from observations of the low-mass X-ray binary EXO 0748-67 with the Reflection Grating Spectrometer on board the XMM-Newton Observatory. The spectra exhibit discrete structure due to absorption and emission from ionized neon, oxygen, and nitrogen. We use the quantitative constraints imposed by the spectral features to develop an empirical model of the circumsource material. This consists of a thickened accretion disk with emission and absorption in the plasma orbiting high above the binary plane. This model presents challenges to current theories of accretion in X-ray binary systems.Comment: 5 pages, 4 figures, accepted by A&A letters, XMM special issu