Complex organic molecules in protoplanetary disks

Context. Protoplanetary disks are vital objects in star and planet formation, possessing all the material, gas and dust, which may form a planetary system orbiting the new star. Small, simple molecules have traditionally been detected in protoplanetary disks; however, in the ALMA era, we expect the molecular inventory of protoplanetary disks to significantly increase.

Aims. We investigate the synthesis of complex organic molecules (COMs) in protoplanetary disks to put constraints on the achievable chemical complexity and to predict species and transitions which may be observable with ALMA.

Methods. We have coupled a 2D steady-state physical model of a protoplanetary disk around a typical T Tauri star with a large gas-grain chemical network including COMs. We compare the resulting column densities with those derived from observations and perform ray-tracing calculations to predict line spectra. We compare the synthesised line intensities with current observations and determine those COMs which may be observable in nearby objects. We also compare the predicted grain-surface abundances with those derived from cometary comae observations.

Results. We find COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances similar to 10(-6)-10(-4) that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, similar to 10(-12)-10(-7). Including the irradiation of grain mantle material helps build further complexity in the ice through the replenishment of grain-surface radicals which take part in further grain-surface reactions. There is reasonable agreement with several line transitions of H2CO observed towards T Tauri star-disk systems. There is poor agreement with HC3(N) lines observed towards LkCa 15 and GO Tau and we discuss possible explanations for these discrepancies. The synthesised line intensities for CH3OH are consistent with upper limits determined towards all sources. Our models suggest CH3OH should be readily observable in nearby protoplanetary disks with ALMA; however, detection of more complex species may prove challenging, even with ALMA "Full Science" capabilities. Our grain-surface abundances are consistent with those derived from cometary comae observations providing additional evidence for the hypothesis that comets (and other planetesimals) formed via the coagulation of icy grains in the Sun's natal disk.

The spotty donor star in the X-ray transient Cen X-4

We accurately determine the fundamental system parameters of the neutron star X-ray transient Cen X-4 solely using phase-resolved high-resolution UV-Visual Echelle Spectrograph spectroscopy. We first determine the radial-velocity curve of the secondary star and then model the shape of the phase-resolved absorption line profiles using an X-ray binary model. The model computes the exact rotationally broadened, phase-resolved spectrum and does not depend on assumptions about the rotation profile, limb-darkening coefficients and the effects of contamination from an accretion disc. We determine the secondary star-to-neutron star binary mass ratio to be 0.1755 ± 0.0025, which is an order of magnitude more accurate than previous estimates. We also constrain the inclination angle to be 32^{+8}_{-2} degrees. Combining these values with the results of the radial-velocity study gives a neutron star mass of 1.94^{+0.37}_{-0.85}M⊙ consistent with previous estimates. Finally, we perform the first Roche tomography reconstruction of the secondary star in an X-ray binary. The tomogram reveals surface inhomogeneities that are due to the presence of cool starspots. A large cool polar spot, similar to that seen in Doppler images of rapidly rotating isolated stars, is present on the Northern hemisphere of the K7 secondary star and we estimate that ~4 percent of the total surface area of the donor star is covered with spots.This evidence for starspots supports the idea that magnetic braking plays an important role in the evolution of low-mass X-ray binaries.

Making a Constitution in a Globalized World

This piece argues that constitutions must be documents which meet the needs and demands of the nation's people and that, as a nation's relationship with the world beyond its borders has increased in complexity in recent years, so individuals' expectations of their nation's constitutions have also increased considerably compared with the past. Using Northern Ireland as an exemplar, the chapter argues that Turkey has the potential to re-make itself through the adoption of a more modern, pluralistic and outward-looking constitution.

The taphonomy of Last Glacial–Interglacial Transition (LGIT) distal volcanic ash in small Scottish lakes

An extensive micro-tephrostratigraphic survey of three small lakes in the Scottish Inner Hebrides was conducted encompassing the Last Glacial–Interglacial Transition (LGIT). The lakes are highly contrasting in terms of lake area to catchment ratio, the presence or absence of stream inlets draining the catchment, and in the complexity of the catchment drainage network. A suite of distal Icelandic volcanic ashes was consistently detected in all three lakes, with three, namely Penifiler Tephra, Vedde Ash and Ashik Tephra, being common to all the lakes. These ashes were chosen to examine the taphonomic intercomparability of ash location and concentration among the lakes. Findings reveal that the part played by catchment inlets in determining ash concentration and within-basin location applies to microtephra layers as much as it does in studies of macrotephra layer thickness. The position of ash concentration maxima is also shown to vary significantly for different LGIT periods and may be a consequence of lake-level changes, especially during the early Holocene. High-resolution stratigraphic analysis through the Vedde Ash visible macrotephra at Loch Ashik reveals a high degree of complexity in taphonomic behaviour between the different geochemical components, with possible implications for the correct interpretation of the isochron position. The detection of multiple intact ash isochrons and the taphonomic processes responsible for their deposition should prove useful in future tephrostratigraphic surveys, as well as having applications within other palaeolimnological disciplines.

The current state of abortion law and practice in Northern Ireland

This paper reviews current abortion law and practice in Northern Ireland (NI). It explores the origins of NI's abortion law and its complexity in relation to current practice. it reviews issues relating to women seeking terminations in NI and Great Britain and reviews attempts by the Family Planning Association NI to require the Department of Health and Social Services and Public Safety NI to provide guidance for health professionals engaged in this practice. The paper also discusses some of the issues surrounding abortion in NI and seeks to explain why this subject is causing controversy and debate, especially following a judicial review in February and Marie Stopes opening a termination service in Belfast.

Neuropeptides in Helminths: Occurrence and Distribution

Nematode neuropeptide systems comprise an exceptionally complex array of similar to 250 peptidic signaling molecules that operate within a structurally simple nervous system of similar to 300 neurons. A relatively complete picture of the neuropeptide complement is available for Caenorhabditis elegans, with 30 flp, 38 ins and 43 nlp genes having been documented; accumulating evidence indicates similar complexity in parasitic nematodes from clades I, III, IV and V. In contrast, the picture for parasitic platyhelminths is less clear, with the limited peptide sequence data available providing concrete evidence for only FMRFamide-like peptide (FLP) and neuropeptide F (NPF) signaling systems, each of which only comprises one or two peptides. With the completion of the Schmidtea meditteranea and Schistosoma mansoni genome projects and expressed sequence tag datasets for other flatworm parasites becoming available, the time is ripe for a detailed reanalysis of neuropeptide signaling in flatworms. Although the actual neuropeptides provide limited obvious value as targets for chemotherapeutic-based control strategies, they do highlight the signaling systems present in these helminths and provide tools for the discovery of more amenable targets such as neuropeptide receptors or neuropeptide processing enzymes. Also, they offer opportunities to evaluate the potential of their associated signaling pathways as targets through RNA interference (RNAi)-based, target validation strategies. Currently, within both helminth phyla, the flp signaling systems appear to merit further investigation as they are intrinsically linked with motor function, a proven target for successful anti-parasitics; it is clear that some nematode NLPs also play a role in motor function and could have similar appeal. At this time, it is unclear if flatworm NPF and nematode INS peptides operate in pathways that have utility for parasite control. Clearly, RNAi-based validation could be a starting point for scoring potential target pathways within neuropeptide signaling for parasiticide discovery programs. Also, recent successes in the application of in planta-based RNAi control strategies for plant parasitic nematodes reveal a strategy whereby neuropeptide encoding genes could become targets for parasite control. The possibility of developing these approaches for the control of animal and human parasites is intriguing, but will require significant advances in the delivery of RNAi-triggers.

How the mollusc got its scales: Convergent evolution of the molluscan scleritome

Radiation of dramatically disparate forms among the phylum Mollusca remains a key question in metazoan evolution, and requires careful evaluation of homology of hard parts throughout the deep fossil record. Enigmatic early Cambrian taxa such as Halkieria and Wiwaxia (in the clade Halwaxiida) have been proposed to represent stem-group aculiferan molluscs (Caudofoveata+Solenogastres+Polyplacophora), as complex scleritomes were considered to be unique to aculiferans among extant molluscs. The 'scaly-foot gastropod' (Neomphalina: Peltospiridae) from hydrothermal vents of the Indian Ocean, however, also carries dermal sclerites and thus challenges this inferred homology. Despite superficial similarities to various mollusc sclerites, the scaly-foot gastropod sclerites are secreted in layers covering outpockets of epithelium and are largely proteinaceous, while chiton (Polyplacophora: Chitonida) sclerites are secreted to fill an invaginated cuticular chamber and are largely calcareous. Marked differences in the underlying epithelium of the scaly-foot gastropod sclerites and operculum suggest that the sclerites do not originate from multiplication of the operculum. This convergence in different classes highlights the ability of molluscs to adapt mineralized dermal structures, as supported by the extensive early fossil record of molluscs with scleritomes. Sclerites of halwaxiids are morphologically variable, undermining the assumed affinity of specific taxa with chitons, or the larger putative clade Aculifera. Comparisons with independently derived similar structures in living molluscs are essential for determining homology among fossils and their position with respect to the enigmatic evolution of molluscan shell forms in deep time.

Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.

Chapter Three – Host–Parasite Interactions and the Evolution of Immune Defense

Parasites and pathogens are ubiquitous and act as an important selection pressure on animals. Here, drawing primarily on our own research, mostly on insects, we illustrate how host-parasite interactions have played a role in the evolution of a range of phenomena, including animal coloration, social behavior, foraging ecology, sexual selection, and life-history tradeoffs, as well as how variation in host behavior and ecology can drive variation in parasitism risk and host allocation of resources to immunity and other antiparasite defenses. We conclude by identifying key areas for future study.

The emergence of DNA methylation as a key modulator of aberrant cell death in prostate cancer

It is now well established that cancer cells exhibit a number of genetic defects in the machinery that governs programmed cell death and that sabotage of apoptosis is one of the principal factors aiding in the evolution of the carcinogenic phenotype. A number of studies have implicated aberrant DNA methylation as a key survival mechanism in cancer, whereby promoter hypermethylation silences genes essential for many processes including apoptosis. To date, studies on the methylation profile of apoptotic genes have largely focused on cancers of the breast, colon and stomach, with only limited data available on prostate cancer. Here we discuss the major developments in the field of DNA methylation and its role in the regulation of aberrant apoptosis in prostate cancer. The most significant advances have involved the discovery of apoptotic gene targets of methylation, including XAF1, (fragile histidine triad (FHIT ), cellular retinol binding protein 1 (CRBP1), decoy receptor 1(DCR1), decoy receptor 2 (DCR2 ), target of methylation-induced silenceing 1 (TMS1), TNF receptor superfamily, member 6 (FAS), Reprimo (RPRM) and GLI pathogenesis-related 1 (GLIPR1). These genes are reported to be hypermethylated in prostate cancer and some offer potential as diagnostic and prognostic markers. We also introduce the concept of an 'apoptotic methylation signature' for prostate cancer and evaluate its potential in a diagnostic, prognostic and therapeutic setting.

Content Validity in Landscape Valuation: A transdisciplinary approach to valuing the landscape of the peninsula of Sorrento, Italy.

This paper addresses the representation of landscape complexity in stated preferences research. It integrates landscape ecology and landscape economics and conducts the landscape analysis in a three-dimensional space to provide ecologically meaningful quantitative landscape indicators that are used as variables for the monetary valuation of landscape in a stated preferences study. Expected heterogeneity in taste intensity across respondents is addressed with a mixed logit model in Willingness to Pay space. The results suggest that the integration of landscape ecology metrics in a stated preferences model provides useful insights for valuing landscape and landscape changes

Stated preference methods and landscape ecology indicators: an example of transdisciplinarity in landscape economic valuation

This paper addresses the representation of landscape complexity in stated preferences research. It integrates landscape ecology and landscape economics and conducts the landscape analysis in a three-dimensional space to provide ecologically meaningful quantitative landscape indicators that are used as variables for the monetary valuation of landscape in a stated preferences study. Expected heterogeneity in taste intensity across respondents is addressed with a mixed logit model in Willingness to Pay space. Our methodology is applied to value, in monetary terms, the landscape of the Sorrento Peninsula in Italy, an area that has faced increasing pressure from urbanization affecting its traditional horticultural, herbaceous, and arboreal structure, with loss of biodiversity, and an increasing risk of landslides. We find that residents of the Sorrento Peninsula would prefer landscapes characterized by large open views and natural features. Residents also appear to dislike heterogeneous landscapes and the presence of lemon orchards and farmers' stewardship, which are associated with the current failure of protecting the traditional landscape. The outcomes suggest that the use of landscape ecology metrics in a stated preferences model may be an effective way to move forward integrated methodologies to better understand and represent landscape and its complexity.

Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers

RATIONALE: The role bacteria play in the progression of COPD has increasingly been highlighted in recent years. However, the microbial community complexity in the lower airways of patients with COPD is poorly characterised.

OBJECTIVES: To compare the lower airway microbiota in patients with COPD, smokers and non-smokers.

METHODS: Bronchial wash samples from adults with COPD (n=18), smokers with no airways disease (n=8) and healthy individuals (n=11) were analysed by extended-culture and culture-independent Illumina MiSeq sequencing. We determined aerobic and anaerobic microbiota load and evaluated differences in bacteria associated with the three cohorts. Culture-independent analysis was used to determine differences in microbiota between comparison groups including taxonomic richness, diversity, relative abundance, 'core' microbiota and co-occurrence.

MEASUREMENT AND MAIN RESULTS: Extended-culture showed no difference in total load of aerobic and anaerobic bacteria between the three cohorts. Culture-independent analysis revealed that the prevalence of members of Pseudomonas spp. was greater in the lower airways of patients with COPD; however, the majority of the sequence reads for this taxa were attributed to three patients. Furthermore, members of Bacteroidetes, such as Prevotella spp., were observed to be greater in the 'healthy' comparison groups. Community diversity (α and β) was significantly less in COPD compared with healthy groups. Co-occurrence of bacterial taxa and the observation of a putative 'core' community within the lower airways were also observed.

CONCLUSIONS: Microbial community composition in the lower airways of patients with COPD is significantly different to that found in smokers and non-smokers, indicating that a component of the disease is associated with changes in microbiological status.

Paramountcy, family rights and contested adoption: does contact with birth relatives balance the scales?

This article combines practitioner insight and research evidence to chart how principles of partnership and paramountcy have led to birth family contact becoming the expected norm following contested adoption from care in Northern Ireland. The article highlights how practice has adapted to the delay in proposed reforms to adoption legislation resulting in the evolution of increasingly open adoption practices. Adoption represents an irrevocable transfer of parental responsibility from birth to adoptive parents and achieves permanence and legal security for children in care who cannot return to their birth family. Its enduring effect, however, makes public adoption a contentious field of child welfare practice, particularly when contested by birth parents. This article explores how post-adoption contact may be viewed as reconciling the uneasy interface between paramountcy principles and parental rights to respect for family life. The article highlights the complexity of adoptive kinship relationships following contested adoption from care, and how contact presents unique challenges that mitigate against meaningful and sustainable connections between the child and their birth relatives. In conclusion, a call is made for sensitive negotiation and support of contact arrangements, and the development of practice models that are informed by an understanding of the workings of adoptive kinship.

Rotational velocities of single and binary O-type stars in the Tarantula Nebula

Rotation is a key parameter in the evolution of massive stars, affecting their evolution, chemical yields, ionizing photon budget, and final fate. We determined the projected rotational velocity, υ e sin i, of ~330 O-type objects, i.e. ~210 spectroscopic single stars and ~110 primaries in binary systems, in the Tarantula nebula or 30 Doradus (30 Dor) region. The observations were taken using VLT/FLAMES and constitute the largest homogeneous dataset of multi-epoch spectroscopy of O-type stars currently available. The most distinctive feature of the υ e sin i distributions of the presumed-single stars and primaries in 30 Dor is a low-velocity peak at around 100 km s^-1. Stellar winds are not expected to have spun-down the bulk of the stars significantly since their arrival on the main sequence and therefore the peak in the single star sample is likely to represent the outcome of the formation process. Whereas the spin distribution of presumed-single stars shows a well developed tail of stars rotating more rapidly than 300 km s^-1, the sample of primaries does not feature such a high-velocity tail. The tail of the presumed-single star distribution is attributed for the most part - and could potentially be completely due - to spun-up binary products that appear as single stars or that have merged. This would be consistent with the lack of such post-interaction products in the binary sample, that is expected to be dominated by pre-interaction systems. The peak in this distribution is broader and is shifted toward somewhat higher spin rates compared to the distribution of presumed-single stars. Systems displaying large radial velocity variations, typical for short period systems, appear mostly responsible for these differences.