A mitochondrial genome phylogeny of owlet moths (Lepidoptera: Noctuoidea), and examination of the utility of mitochondrial genomes for lepidopteran phylogenetics

A phylogenetic hypothesis for the lepidopteran superfamily Noctuoidea was inferred based on the complete mitochondrial (mt) genomes of 12 species (six newly sequenced). The monophyly of each noctuoid family in the latest classification was well supported. Novel and robust relationships were recovered at the family level, in contrast to previous analyses using nuclear genes. Erebidae was recovered as sister to (Nolidae+(Euteliidae+Noctuidae)), while Notodontidae was sister to all these taxa (the putatively basalmost lineage Oenosandridae was not included). In order to improve phylogenetic resolution using mt genomes, various analytical approaches were tested: Bayesian inference (BI) vs. maximum likelihood (ML), excluding vs. including RNA genes (rRNA or tRNA), and Gblocks treatment. The evolutionary signal within mt genomes had low sensitivity to analytical changes. Inference methods had the most significant influence. Inclusion of tRNAs positively increased the congruence of topologies, while inclusion of rRNAs resulted in a range of phylogenetic relationships varying depending on other analytical factors. The two Gblocks parameter settings had opposite effects on nodal support between the two inference methods. The relaxed parameter (GBRA) resulted in higher support values in BI analyses, while the strict parameter (GBDH) resulted in higher support values in ML analyses.

The evolutionary history of termites as inferred from 66 mitochondrial genomes

Termites have colonized many habitats and are among the most abundant animals in tropical ecosystems, which they modify considerably through their actions. The timing of their rise in abundance and of the dispersal events that gave rise to modern termite lineages is not well understood. To shed light on termite origins and diversification, we sequenced the mitochondrial genome of 48 termite species and combined them with 18 previously sequenced termite mitochondrial genomes for phylogenetic and molecular clock analyses using multiple fossil calibrations. The 66 genomes represent most major clades of termites. Unlike previous phylogenetic studies based on fewer molecular data, our phylogenetic tree is fully resolved for the lower termites. The phylogenetic positions of Macrotermitinae and Apicotermitinae are also resolved as the basal groups in the higher termites, but in the crown termitid groups, including Termitinae + Syntermitinae + Nasutitermitinae + Cubitermitinae, the position of some nodes remains uncertain. Our molecular clock tree indicates that the lineages leading to termites and Cryptocercus roaches diverged 170 Ma (153-196 Ma 95% confidence interval [CI]), that modern Termitidae arose 54 Ma (46-66 Ma 95% CI), and that the crown termitid group arose 40 Ma (35-49 Ma 95% CI). This indicates that the distribution of basal termite clades was influenced by the final stages of the breakup of Pangaea. Our inference of ancestral geographic ranges shows that the Termitidae, which includes more than 75% of extant termite species, most likely originated in Africa or Asia, and acquired their pantropical distribution after a series of dispersal and subsequent diversification events.

Comparative analysis and distribution of Omega-3 lcPUFA Biosynthesis genes in marine molluscs

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

Conserved gene structure and function of interleukin-10 in teleost fish

Interleukin-10 (IL-10) is an important immunoregulatory cytokine produced by various types of cells. Researchers describe here the isolation and characterization of olive flounder IL-10 (ofIL-10) cDNA and genomic organization. The ofIL-10 gene encodes a 187 amino acid protein and is composed of a five exon/four intron structure, similar to other known IL-10 genes. The ofIL-10 promoter sequence analysis shows a high level of homology in putative binding sites for transcription factors which are sufficient for transcriptional regulation ofIL-10. Important structural residues are maintained in the ofIL-10 protein including the four cysteines responsible for the two intra-chain disulfide bridges reported for human IL-10 and two extra cysteine residues that exist only in fish species. The phylogenetic analysis clustered ofIL-10 with other fish IL-10s and apart from mammalian IL-10 molecules. Quantitative real-time Polymerase Chain Reaction (PCR) analysis demonstrated ubiquitous ofIL-10 gene expression in the 13 tissues examined. Additionally, the induction of ofIL-10 gene expression was observed in the kidney tissue from olive flounder infected with bacteria (Edawardsiella tarda) or virus (Viral Hemorrhagic Septicemia Virus; VHSV). These data indicate that IL-10 is an important immune regulator that is conserved strictly genomic organization and function during the evolution of vertebrate immunity.

Study of surface evolution in the wheel-rail interface

This paper aims to trace surface evolution in the wheel-rail interface using data obtained from a twin-disc testing machine and the surface replication technique. Changes in the surface profile of the rail testing disc are explicitly analysed according to the wear mechanism, which helps elaborate a better understanding of the attrition of asperities during the wearing-in process of surface modification. The surface profile amplitude was seen to decrease during the initial running-in phase of the experiment cycle, and after reaching a saturation value, the profile amplitude then increased. Ultimately the results show that grinding will roughen the rail surface and the wheel-rail contact conditions will then remove this surface damage to some saturation value of the profile height. The variation in the rail surface profile beyond this point is then only dependant on the contact conditions which exist between the wheel and rail during normal operation.

Wear particle analysis and the evolution of the plastically deformed layer on Australian rail steel

Particle analysis methodology is presented, together with the morphology of the wear debris formed during rolling contact fatigue. Wear particles are characterised by their surface topography and in terms of wear mechanism. Rail-wheel materials are subjected to severe plastic deformation as the contact loading progresses, which contributes to a mechanism of major damage in head-hardened rail steel. Most of the current methodologies involve sectioning of the rail-wheel discs to trace material damage phenomena such as crack propagation and plastic strain accumulation. This paper proposes methodology to analyse the development of the plastically deformed layer by sectioning wear particles using the focussed ion beam (FIB) milling method. Moreover, it highlights the processes of oxidation and rail surface delamination during unlubricated rolling contact fatigue.

Ortho-Dihydroxyl-9,10-anthraquinone dyes as visible-light sensitizers that exhibit a high turnover number for hydrogen evolution

Pt/TiO2 sensitized by the cheap and organic ortho-dihydroxyl-9,10-anthraquinone dyes, such as Alizarin and Alizarin Red, achieved a TON of approximately 10 000 (TOF > 250 h−1 for the first ten hours) during >80 hours of visible light irradiation (>420 nm) for photocatalytic hydrogen evolution when triethanolamine was used as the sacrificial donor. The stability and activity enhancements can be attributed to the two highly serviceable redox reactions involving the 9,10-dicarbonyl and ortho-dihydroxyl groups of the anthracene ring, respectively

Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes

Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The “distances” used in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view.

Perpendicularly oriented MoSe2/graphene nanosheets as advanced electrocatalysts for hydrogen evolution

By increasing the density of exposed active edges, the perpendicularly oriented structure of MoSe2 nanosheets facilitates ion/electrolyte transport at the electrode interface and minimizes the restacking of nanosheets, while the graphene improves the electrical contact between the catalyst and the electrode. This makes the MoSe2/graphene hybrid perfect as a catalyst in the hydrogen evolution reaction (HER). It shows a greatly improved catalytic activity compared with bare MoSe2 nanosheets.

Does size matter? An assessment of quota market evolution and performance in the Great Barrier Reef fin-fish fishery

In fisheries managed using individual transferable quotas (ITQs) it is generally assumed that quota markets are well-functioning, allowing quota to flow on either a temporary or permanent basis to those able to make best use of it. However, despite an increasing number of fisheries being managed under ITQs, empirical assessments of the quota markets that have actually evolved in these fisheries remain scarce. The Queensland Coral Reef Fin-Fish Fishery (CRFFF) on the Great Barrier Reef has been managed under a system of ITQs since 2004. Data on individual quota holdings and trades for the period 2004-2012 were used to assess the CRFFF quota market and its evolution through time. Network analysis was applied to assess market structure and the nature of lease-trading relationships. An assessment of market participants’ abilities to balance their quota accounts, i.e., gap analysis, provided insights into market functionality and how this may have changed in the period observed. Trends in ownership and trade were determined, and market participants were identified as belonging to one out of a set of seven generalized types. The emergence of groups such as investors and lease-dependent fishers is clear. In 2011-2012, 41% of coral trout quota was owned by participants that did not fish it, and 64% of total coral trout landings were made by fishers that owned only 10% of the quota. Quota brokers emerged whose influence on the market varied with the bioeconomic conditions of the fishery. Throughout the study period some quota was found to remain inactive, implying potential market inefficiencies. Contribution to this inactivity appeared asymmetrical, with most residing in the hands of smaller quota holders. The importance of transaction costs in the operation of the quota market and the inequalities that may result are discussed in light of these findings

Evolution of a ~2.7 Ga large igneous province: A volcanological, geochemical and geochronological study of the Agnew Greenstone Belt, and new regional correlations for the Kalgoorlie Terrane (Yilgarn Craton, Western Australia)

The thick package of ~2.7 Ga mafic and ultramafic lavas and intrusions preserved among the Neoarchean of the Kalgoorlie Terrene in Western Australia provides valuable insight into geological processes controlling the most prodigious episode of growth and preservation of juvenile continental crust in Earth’s history. Limited exposure of these rocks results in uncertainty about their age, physical and chemical characteristics, and stratigraphic relationships. This in turn prevents confident correlation of regional occurrences of mafic and ultramafic successions (both intrusive and extrusive) and hinders the interpretation of tectonic setting and magmatic evolution. A recent stratigraphic drilling program of the Neoarchean stratigraphy of the Agnew Greenstone Belt in Western Australia has provided continuous exposures through a c. 7 km thick sequence of mafic and ultramafic units. In this study, we present a volcanological, lithogeochemical and chronological study of the Agnew Greenstone Belt, and provide the first pre-2690 Ma regional correlation across the Kalgoorlie Terrane. The Agnew Greenstone Belt records ~30 m.y. of episodic ultramafic-mafic magmatism that includes two cycles, each defined by a komatiite that is overlain by units that become more evolved and contaminated with time. The sequence is divided into nine conformable packages, each consisting of stacked subaqueous lava flows and comagmatic intrusions, as well as two sills without associated extrusions. Lavas, with the exception of intercalations between two units, form a layer-cake stratigraphy and were likely erupted from a system of fissures tapping the same magma source. The komatiites are not contaminated by continental crust ([La/Sm]PM ~0.7) and are of the Al-undepleted Munro-type. Crustal contamination is evident in many units (Songvang Basalt, Never Can Tell Basalt, Redeemer Basalt, and Turrett Dolerite), as judged by [La/Sm]>1, negative Nb and Ti anomalies, and geochemical mixing trends towards felsic contaminants. Crystal fractionation was also significant, with early olivine and chromite (Mg#>65) followed by plagioclase and clinopyroxene removal (Mg<65), and in the most evolved case, titanomagnetite accumulation. Three new TIMS dates on granophyric zones of mafic sills and one ICP-MS date from an interflow felsic tuff are presented and used for regional stratigraphic correlation. Cycle I magmatism began at ~2720 Ma and ended ~2705 Ma, whereas cycle II began ~2705 Ma and ended at 2690.7±1.2 Ma. Regional correlations indicate the western Kalgoorlie Terrane consists of a remarkably similar stratigraphy that can be recognised at Agnew, Ora Banda and Coolgardie, whereas the eastern part of the terrane (e.g., Kambalda Domain) does not include cycle I, but correlates well with cycle II. This research supports an autochthonous model of greenstone formation, in which one large igneous province, represented by two complete cycles, is constructed on sialic crust. New stratigraphic correlations for the Kalgoorlie Terrane indicate that many units can be traced over distances >100 km, which has implications for exploration targeting for stratigraphically hosted ultramafic Ni and VMS deposits.

Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar

TERMINAL EAR1-like (TEL) genes encode putative RNA-binding proteins only found in land plants. Previous studies suggested that they may regulate tissue and organ initiation in Poaceae. Two TEL genes were identified in both Populus trichocarpa and the hybrid aspen Populus tremula × P. alba, named, respectively, PoptrTEL1-2 and PtaTEL1-2. The analysis of the organisation around the PoptrTEL genes in the P. trichocarpa genome and the estimation of the synonymous substitution rate for PtaTEL1-2 genes indicate that the paralogous link between these two Populus TEL genes probably results from the Salicoid large-scale gene-duplication event. Phylogenetic analyses confirmed their orthology link with the other TEL genes. The expression pattern of both PtaTEL genes appeared to be restricted to the mother cells of the plant body: leaf founder cells, leaf primordia, axillary buds and root differentiating tissues, as well as to mother cells of vascular tissues. Most interestingly, PtaTEL1-2 transcripts were found in differentiating cells of secondary xylem and phloem, but probably not in the cambium itself. Taken together, these results indicate specific expression of the TEL genes in differentiating cells controlling tissue and organ development in Populus (and other Angiosperm species).

Comparative genomic analysis of human Chlamydia pneumoniae isolates from respiratory, brain and cardiac tissues

Chlamydia pneumoniae is an obligate intracellular bacterium implicated in a wide range of human diseases including atherosclerosis and Alzheimer's disease. Efforts to understand the relationships between C. pneumoniae detected in these diseases have been hindered by the availability of sequence data for non-respiratory strains. In this study, we sequenced the whole genomes for C. pneumoniae isolates from atherosclerosis and Alzheimer's disease, and compared these to previously published C. pneumoniae genomes. Phylogenetic analyses of these new C. pneumoniae strains indicate two sub-groups within human C. pneumoniae, and suggest that both recombination and mutation events have driven the evolution of human C. pneumoniae. Further fine-detailed analyses of these new C. pneumoniae sequences show several genetically variable loci. This suggests that similar strains of C. pneumoniae are found in the brain, lungs and cardiovascular system and that only minor genetic differences may contribute to the adaptation of particular strains in human disease.

Thermal evolution of the submonolayer near-surface alloy of ZnPd on Pd (111)

We have performed a high-resolution synchrotron radiation photoelectron spectroscopy study of the initial growth stages of the ZnPd near-surface alloy on Pd(111), complemented by scanning tunnelling microscopy data. We show that the chemical environment for surfaces containing less than half of one monolayer of Zn is chemically distinct from subsequent layers. Surfaces where the deposition is performed at room temperature contain ZnPd islands surrounded by a substrate with dilute Zn substitutions. Annealing these surfaces drives the Zn towards the substrate top-layer, and favours the completion of the first 1 : 1 monolayer before the onset of growth in the next layer.