A review of rhizosphere carbon flow modelling

Rhizosphere processes play a key role in nutrient cycling in terrestrial ecosystems. Plant rhizodeposits supply low-molecular weight carbon substrates to the soil microbial community, resulting in elevated levels of activity surrounding the root. Mechanistic compartmental models that aim to model carbon flux through the rhizosphere have been reviewed and areas of future research necessary to better calibrate model parameters have been identified. Incorporating the effect of variation in bacterial biomass physiology on carbon flux presents a considerable challenge to experimentalists and modellers alike due to the difficulties associated with differentiating dead from dormant cells. A number of molecular techniques that may help to distinguish between metabolic states of bacterial cells are presented. The calibration of growth, death and maintenance parameters in rhizosphere models is also discussed. A simple model of rhizosphere carbon flow has been constructed and a sensitivity analysis was carried out on the model to highlight which parameters were most influential when simulating carbon flux. It was observed that the parameters that most heavily influenced long-term carbon compartmentalisation in the rhizosphere were exudation rate and biomass yield. It was concluded that future efforts to simulate carbon flow in the rhizosphere should aim to increase ecological realism in model structure.

Edaphic factors affecting the toxicity and accumulation of arsenate in the earthworm Lumbricus terrestris

The toxicity and accumulation of arsenate was determined in the earthworm Lumbricus terrestris in soil from different layers of a forest profile. Toxicity increased fourfold between 2 and 10 d. Edaphic factors (pH, soil organic matter, and depth in soil profile) also affected toxicity with a three fold decrease in the concentration that causes 50% mortality with increasing depth in soil (from 0-70 mm to 500-700 mm). In a 4-d exposure study, there was no evidence of arsenic bioconcentration in earthworm tissue, although bioaccumulation was occurring. There was a considerable difference in tissue residues between living and dead earthworms, with dead worms having higher concentrations. This difference was dependent on both soil arsenate concentration and on soil type. Over a wide range of soil arsenate concentrations, earthworm arsenic residues are homeostatically maintained in living worms, but this homeostasis breaks down during death. Alternatively, equilibration with soil residues may occur via accumulation after death. In long-term accumulation studies in soils dosed with a sublethal arsenate concentration (40 μg/g dry weight), bioconcentration of arsenate did not occur until day 12, after which earthworm concentrations rose steadily above the soil concentration, with residues in worms three fold higher than soil concentrations by the termination of the study (23 d). This bioconcentration only occurred in depurated worms over the time period of the study. Initially, depurated worms had lower arsenic concentrations than undepurated until tissue concentrations were equivalent to the soil concentration. Once tissue concentration was greater than soil concentration, depurated worms had higher arsenic residues than undepurated.

Marine Biosilica as a Tool to Understand the Therapeutic Benefit of Silica in Bone Repair

It is widely accepted that silicon-substituted materials enhance bone formation, yet the mechanism by which this occurs is poorly understood. This work investigates the potential of using diatom frustules to answer on fundamental questions surrounding the role of silica in bone healing. Biosilica with frustules 20m were isolated from Cyclotella meneghiniana a unicellular microalgae that was sourced from the Mississippi River, USA. Silanisation chemistry was used to modify the surface of C. meneghiniana with amine (–NH2) and thiol (–SH) terminated silanes. Untreated frustules and both functionalised groups were soaked in culture medium for 24hrs. Following the culture period, frustules were separated from the conditioned medium by centrifugation and both were tested separately in vitro for cytotoxicity using murine-monocyte macrophage (J774) cell line. Cytotoxicity was measured using LDH release to measure damage to cell membrane, MTS to measure cell viability and live-dead staining. The expression and release of pro-inflammatory cytokines (IL-6 and TNF) were measured using ELISA. Our results found that diatom frustules and those functionalised with amino groups showed no cytotoxicity or elevated cytokine release. Diatom frustules functionalised with thiol groups showed higher levels of cytotoxicity. Diatom frustules and those functionalised with amino groups were taken forward to an in vivo mouse toxicity model, whereby the immunological response, organ toxicity and route of metabolism/excretion of silica were investigated. Histological results showed no organ toxicity in any of the groups relative to control. Analysis of blood Si levels suggests that modified frustules are metabolised quicker than functionalised frustules, suggesting that physiochemical attributes influence their biodistribution. Our results show that diatom frustules are non cytotoxic and are promising materials to better understand the role of silica in bone healing.

Antibiofilm Activity of the Brown Alga Halidrys siliquosa against Clinically Relevant Human Pathogens

The marine brown alga Halidrys siliquosa is known to produce compounds with antifouling activity against several marine bacteria. The aim of this study was to evaluate the antimicrobial and antibiofilm activity of organic extracts obtained from the marine brown alga H. siliquosa against a focused panel of clinically relevant human pathogens commonly associated with biofilm-related infections. The partially fractionated methanolic extract obtained from H. siliquosa collected along the shores of Co. Donegal; Ireland; displayed antimicrobial activity against bacteria of the genus Staphylococcus; Streptococcus; Enterococcus; Pseudomonas; Stenotrophomonas; and Chromobacterium with MIC and MBC values ranging from 0.0391 to 5 mg/mL. Biofilms of S. aureus MRSA were found to be susceptible to the algal methanolic extract with MBEC values ranging from 1.25 mg/mL to 5 mg/mL respectively. Confocal laser scanning microscopy using LIVE/DEAD staining confirmed the antimicrobial nature of the antibiofilm activity observed using the MBEC assay. A bioassay-guided fractionation method was developed yielding 10 active fractions from which to perform purification and structural elucidation of clinically-relevant antibiofilm compounds.

Gender and Cosmopolitanism in Europe: A Feminist Perspective

Gender and Cosmopolitanism in Europe combines a feminist critique of contemporary and prominent approaches to cosmopolitanism with an in-depth analysis of historical cosmopolitanism and the manner in which gendered symbolic boundaries of national political communities in two European countries are drawn. Exploring the work of prominent scholars of new cosmopolitanism in Britain and Germany, including Held, Habermas, Beck and Bhabha, it delivers a timely intervention into current debates on globalisation, Europeanisation and social processes of transformation in and beyond specific national societies.

A rigorous examination of the emancipatory potential of current debates surrounding cosmopolitanism in Europe, this book will be of interest to sociologist and political scientists working on questions of identity, inclusion, citizenship, globalisation, cosmopolitanism and gender.
Contents: Introduction: gendered cosmopolitanism: the scope of this book; Who belongs? Who is the Other?; Recognition, social equality and the current EU anti-discrimination policy; Kulturnation and the homogenised notion of community belonging: Jürgen Habermas's and Ulrich Beck's approaches to 'European' cosmopolitanism; Global trade, the city and commercial cosmopolitanism: David Held's and Homi K. Bhabha's approaches to new cosmopolitanism; About dead-ends, one-way streets and critical crossroads; Transversal conversations on the scope of new cosmopolitanism beyond the Eurocentric framework; Bibliography; Index.

Vaccination and All Cause Child Mortality 1985-2011: Global Evidence from the Demographic and Health Surveys

Based on models with calibrated parameters for infection, case fatality rates, and vaccine efficacy, basic childhood vaccinations have been estimated to be highly cost effective. We estimate the association of vaccination with mortality directly from survey data. Using 149 cross-sectional Demographic and Health Surveys, we determine the relationship between vaccination coverage and under five mortality at the survey cluster level. Our data include approximately one million children in 68,490 clusters in 62 countries. We consider the childhood measles, Bacille Calmette-Guérin (BCG), Diphtheria-Pertussis-Tetanus (DPT), Polio, and maternal tetanus vaccinations. Using modified Poisson regression to estimate the relative risk of child mortality in each cluster, we also adjust for selection bias caused by the vaccination status of dead children not being reported. Childhood vaccination, and in particular measles and tetanus vaccination, is associated with substantial reductions in childhood mortality. We estimate that children in clusters with complete vaccination coverage have relative risk of mortality 0.73 (95% Confidence Interval: 0.68, 0.77) that of children in a cluster with no vaccination. While widely used, basic vaccines still have coverage rates well below 100% in many countries, and our results emphasize the effectiveness of increasing their coverage rates in order to reduce child mortality.

Salt-inducible kinase 2 regulates mitotic progression and transcription in prostate cancer

UNLABELLED: Salt-inducible kinase 2 (SIK2) is a multifunctional kinase of the AMPK family that plays a role in CREB1-mediated gene transcription and was recently reported to have therapeutic potential in ovarian cancer. The expression of this kinase was investigated in prostate cancer clinical specimens. Interestingly, auto-antibodies against SIK2 were increased in the plasma of patients with aggressive disease. Examination of SIK2 in prostate cancer cells found that it functions both as a positive regulator of cell-cycle progression and a negative regulator of CREB1 activity. Knockdown of SIK2 inhibited cell growth, delayed cell-cycle progression, induced cell death, and enhanced CREB1 activity. Expression of a kinase-dead mutant of SIK2 also inhibited cell growth, induced cell death, and enhanced CREB1 activity. Treatment with a small-molecule SIK2 inhibitor (ARN-3236), currently in preclinical development, also led to enhanced CREB1 activity in a dose- and time-dependent manner. Because CREB1 is a transcription factor and proto-oncogene, it was posited that the effects of SIK2 on cell proliferation and viability might be mediated by changes in gene expression. To test this, gene expression array profiling was performed and while SIK2 knockdown or overexpression of the kinase-dead mutant affected established CREB1 target genes; the overlap with transcripts regulated by forskolin (FSK), the adenylate cyclase/CREB1 pathway activator, was incomplete.

IMPLICATIONS: This study demonstrates that targeting SIK2 genetically or therapeutically will have pleiotropic effects on cell-cycle progression and transcription factor activation, which should be accounted for when characterizing SIK2 inhibitors.

Prying into the intimate secrets of animal lives; software beyond hardware for comprehensive annotation in 'Daily Diary' tags

BACKGROUND: Smart tags attached to freely-roaming animals recording multiple parameters at infra-second rates are becoming commonplace, and are transforming our understanding of the way wild animals behave. Interpretation of such data is complex and currently limits the ability of biologists to realise the value of their recorded information.

DESCRIPTION: This work presents Framework4, an all-encompassing software suite which operates on smart sensor data to determine the 4 key elements considered pivotal for movement analysis from such tags (Endangered Species Res 4: 123-37, 2008). These are; animal trajectory, behaviour, energy expenditure and quantification of the environment in which the animal moves. The program transforms smart sensor data into dead-reckoned movements, template-matched behaviours, dynamic body acceleration-derived energetics and position-linked environmental data before outputting it all into a single file. Biologists are thus left with a single data set where animal actions and environmental conditions can be linked across time and space.

CONCLUSIONS: Framework4 is a user-friendly software that assists biologists in elucidating 4 key aspects of wild animal ecology using data derived from tags with multiple sensors recording at high rates. Its use should enhance the ability of biologists to derive meaningful data rapidly from complex data.

A tool for the evaluation of slaughter horse welfare during unloading

This study aimed to develop a scientific and practical tool to be used to assess horse welfare after commercial transport over long journeys. A set of physical, behavioural and environmental measures was selected, covering welfare aspects of both transport and unloading procedures. The protocol was field-tested on 51 intra-EU commercial transports arriving at different sites in Italy. Univariate analysis was implemented to look for associations between the input variables (environmental hazards potentially affecting the animal well-being during long transports) and the outcome variables (direct evaluation of the animal condition). No severe welfare impairments were recorded (ie dead on arrival, severe injuries, non-ambulatory animals), while milder ones were more frequent at unloading (eg slipping; 36.7%, reluctance to move; 9.6%). Correlations emerged between ramp slope and falling; type of ramp floor and slipping; fast gait and the presence of gaps between the ramp and the floor. The horses' behaviour was also related to the type of handling procedure used. The measures were repeatable and practical to apply and score during real-time unloading. This work provides a sound basis for a new and practical welfare assessment tool for horses travelling over long journeys. Careful and constant application of this protocol would provide stakeholders with the opportunity to track and monitor changes in the industry over time, as well as to identify high risk areas in transport routines.

The Promise of Peace:Revisiting the Northern Irish Model

The Northern Ireland peace process is often eulogized as a successful model of conflict transformation. Although the process exhibited many of the problems that beset other societies seeking to move from conflict to a negotiated peace (including disagreements over the functioning of institutions and the meanings of cultural symbols, unresolved issues relating to the effects of political violence on victims and survivors and society at large; and the residual presence of violent and political ‘spoiler’ groups), the resilience of political dialogue has proven remarkable.
This collection revisits the promise of ‘a truly historic opportunity for a new beginning’ a decade and a half on from the signing of the Belfast/Good Friday Agreement in 1998. The book will bring together academics from across a number of disciplines, including management and organizational behaviour, law, politics, sociology, archaeology and literature.

The different contributions aim to assess what impact it has made in the legal, policy, and institutional areas it specifically targeted: political reform, human rights and equality provision, working through legacies of the past (including police reform, prisoner release and victims' rights) and the building of new relationships within the island of Ireland and between Ireland and Britain. With the emergence of first-time voters who had no direct experience of the violence the book explores what the Agreement offers for future generations.

The book is the culmination of a 12-month research project sponsored by the British Academy and Leverhulme that addressed the following aspects of the peace process:
Peace walls: The euphemistically named peace walls remain one of the most visible reminders of Northern Ireland’s divisions and they are famously the only material manifestations of the conflict that have grown in number and extent since the 1998 Agreement. They were originally placed between antagonistic neighbouring communities – often at their request – at times of heightened tensions. Research under this theme explored the lack of ongoing engagement with their continuing presences, evolving meanings and impact on the communities that reside beside them needs to be overtly addressed.
Cultural division: Cultural differences have often been seen as lying at the heart of the ‘Irish problem’. Despite this, art and artists have increasingly been seen as having the potential to develop new discourses. Research explored the following questions: What role can the arts play in re-imagining the spaces opened up by the promises of the 1998 Agreement? What implication does the confrontation with the legacies of conflict have for artistic practices? What impact do the arts have on constructions of identity, on narratives of history, and on electoral politics?
Institutional transformation: This strand of research explored the significance of the process of organizational change which followed the establishment of the 1998 on political and other public policy institutions such as the police and prison services. It suggested that the experience and lessons learned from such periods of transition have much to contribute to how Northern Ireland begins to address political polarization in other areas of public service infrastructure, chiefly around the sectarian monoliths of education and housing.
Working through the past: ‘Legacy’ issues have gained increasing prominence since 1998: issues to do with public symbolism (particularly relating to the flying of flags and parading), defining victimhood, securing victims’ rights, recovery of the ‘disappeared’, reintegrating ex- prisoners back into society, and the possibilities for truth recovery and reconciliation have all acquired salient and emotive force. Although the 1998 Agreement promised to ‘honour the dead’ through a ‘new beginning’, it is increasingly unclear as to whether an agreed narrative about the past is possible – or even worthwhile pursuing. Research under this theme looked at the complex relationship between memory, commemoration and violence; how commemorative events are performed, organized, policed and represented. It also addressed the fraught issue of how to come to terms with Northern Ireland’s divided and bloodied past.

The editors are in the process of guiding contributors to adapt their papers, which were presented to a series of workshops on the above themes, to the purposes of the book. In particular, the contributors will be guided to focus on the related aims of assessing the extent of change that has occurred and providing an assessment of what remains to be done. To that end, contributors are asked to engage directly with the questions that close the ‘Introduction’, namely: To what extent has the ‘promise’ of the 1998 Agreement been fulfilled? To what extent has the 1998 Agreement given rise to forms of exclusion? To what extent has the 1998 Agreement shaped new forms of debate, dispute and engagement? In the absence of that guidance having been sent out yet, the outlines below are, for the time being, the abstracts of their original papers.