Mitochondrial metagenomics: letting the genes out of the bottle

‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity

Hydrogen maser oscillation at 10 K

A low temperature atomic hydrogen maser was developed using frozen atomic neon as the storage surface. The maser has been operated in the pulsed mode at temperatures from 6 K to 11 K and as a self-excited oscillator from 9 K to 10.5 K

Representing the Process of Machine Tool Calibration in First-order Logic

Machine tool calibration requires a wide range of measurement techniques that can be carried out in many different sequences. Planning a machine tool calibration is typically performed by a subject expert with a great understanding of International standards and industrial best-practice guides. However, it is often the case that the planned sequence of measurements is not the optimal. Therefore, in an attempt to improve the process, intelligent computing methods can be designed for plan suggestion. As a starting point, this paper presents a way of converting expert knowledge into first-order logic that can be expressed in the PROLOG language. It then shows how queries can be executed against the logic to construct a knowledge-base of all the different measurements that can be performed during machine tool calibration

Considering Manufacturability in the Design of Deployable Origami-Adapted Mechanisms

Primary barriers to greater implementation of deployable origami-adapted mechanisms are their manufacturability and robustness. This paper discusses manufacturability in the design of such mechanisms through presenting and examining three examples. Manufacturability lessons gathered from these examples include the importance of joint-panel interfaces and how techniques and approaches for origami-adapted design can be customized to meet the needs of a specific product. As the manufacturability of deployable origami-adapted products is addressed and improved, their robustness will also improve, thereby enabling greater use of origami-adapted design

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

Remarks on the Basic Plan of the Terminal Abdominal Structures of the Males of Winged Insects

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Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge

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