Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes

eproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as “evolutionary bulge” during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants

Electronic Footprints in the Sand: Technologies for Assisting Domestic Violence Survivors

With the rapid growth and spread of Internet-based social support systems, the impact that these systems can make to society – be it good or bad – has become more significant and can make a real difference to people’s lives. As such, various aspects of these systems need to be carefully investigated and analysed, including their security/privacy issues. In this paper, we present our work in designing and implementing various technological features that can be used to assist domestic violence survivors in obtaining help without leaving traces which might lead to further violence from their abuser. This case study serves as the core of our paper, in which we outline our approach, various de- sign considerations – including difficulties in keeping browsing history private, our currently implemented solutions (single use URL, targeted history sanitita- tion agent, and secret graphical gateway), as well as novel ideas for future work (including location-based service advertising and deployment in the wild)

A feeding guild indicator to assess environmental change impacts on marine ecosystem structure and functioning.

Integrating food web indicators into ecological status assessments is central to developing effective management measures that can improve degraded ecosystems. This is because they can reveal how ecosystems respond to environmental change that cannot be inferred from studying habitat, species or assemblages alone. However, the substantial investment required to monitor food webs (e.g. via stomach contents analysis) and the lack of internationally agreed approaches to assessing them has hampered their development. Inventories of trophic interactions have been collated world-wide and across biomes, and can be applied to infer food web structure and energy flow. Here, we compile a new marine dataset containing 8,092 unique predator–prey interactions from 415,294 fish stomachs. We demonstrate how feeding guilds (i.e. groupings based on diet and life stage) could be defined systematically and in a way that is conducive to their application internationally across ecosystems; and apply them to the North Sea fish assemblage to demonstrate their responsiveness to anthropogenic pressures. We found evidence for seven distinct feeding guilds. Differences between guilds were related to predator size, which positively correlated with piscivory, phylogeny, with multiple size classes of a species often in the same guild, and habitat, as pelagic, benthic and shallow-coastal foraging was apparent. Guild biomasses were largely consistent through time at the North Sea-level and spatially aggregated at the regional level with change relating to changes in resource availability, temperature, fishing and the biomass of other guilds. This suggests that fish biomass was partitioned across broad feeding and environmental niches, and changes over time were governed partly by guild carrying capacities, but also by a combination of covariates with contrasting patterns of change. Management of the North Sea ecosystem could therefore be adaptive and focused towards specific guilds and pressures in a given area. Synthesis and applications. We propose a food web indicator which has been explicitly called for to inform policy via food web status assessment as part of the European Union's Marine Strategy Framework Directive and the indicator toolkit supporting The Convention for the Protection of the Marine Environment of the North-East Atlantic (the ‘OSPAR Convention’)

A preliminary investigation into the apparent abhesive effect of stearic acid on cured silicone elastomer

The effect of addition of small amounts of stearic acid on the adhesive properties of polydimethylsiloxane (PDMS) was investigated. Stearic acid reduced the peel strength of bonded aluminium samples with the joint weakening effect increasing with increased loadings. Surface analysis of the peeled surfaces was carried out using XPS, SSIMS and FTIR. This showed that stearic acid did not form a weak boundary layer at the metal-polymer interface as would traditionally be expected. Local Force Microscopy confirmed this, as the surface adhesion of the PDMS increased, rather than decreased, on addition of stearic acid

Relativistic Calculation of the Meson Spectrum: a Fully Covariant Treatment Versus Standard Treatments

A large number of treatments of the meson spectrum have been tried that consider mesons as quark - anti quark bound states. Recently, we used relativistic quantum "constraint" mechanics to introduce a fully covariant treatment defined by two coupled Dirac equations. For field-theoretic interactions, this procedure functions as a "quantum mechanical transform of Bethe-Salpeter equation". Here, we test its spectral fits against those provided by an assortment of models: Wisconsin model, Iowa State model, Brayshaw model, and the popular semi-relativistic treatment of Godfrey and Isgur. We find that the fit provided by the two-body Dirac model for the entire meson spectrum competes with the best fits to partial spectra provided by the others and does so with the smallest number of interaction functions without additional cutoff parameters necessary to make other approaches numerically tractable. We discuss the distinguishing features of our model that may account for the relative overall success of its fits. Note especially that in our approach for QCD, the resulting pion mass and associated Goldstone behavior depend sensitively on the preservation of relativistic couplings that are crucial for its success when solved nonperturbatively for the analogous two-body bound-states of QED.Comment: 75 pages, 6 figures, revised content

A general framework for combining ecosystem models

When making predictions about ecosystems, we often have available a number of different ecosystem models that attempt to represent their dynamics in a detailed mechanistic way. Each of these can be used as a simulator of large-scale experiments and make projections about the fate of ecosystems under different scenarios to support the development of appropriate management strategies. However, structural differences, systematic discrepancies and uncertainties lead to different models giving different predictions. This is further complicated by the fact that the models may not be run with the same functional groups, spatial structure or time scale. Rather than simply trying to select a “best” model, or taking some weighted average, it is important to exploit the strengths of each of the models, while learning from the differences between them. To achieve this, we construct a flexible statistical model of the relationships between a collection of mechanistic models and their biases, allowing for structural and parameter uncertainty and for different ways of representing reality. Using this statistical meta-model, we can combine prior beliefs, model estimates and direct observations using Bayesian methods and make coherent predictions of future outcomes under different scenarios with robust measures of uncertainty. In this study, we take a diverse ensemble of existing North Sea ecosystem models and demonstrate the utility of our framework by applying it to answer the question what would have happened to demersal fish if fishing was to stop

Nonapeptide influences on social behaviour: effects of vasotocin and isotocin on shoaling and interaction in zebrafish

Nonapeptides are important regulators of social behaviour across vertebrate taxa. While their role in simple grouping behaviour has been explored in estrildid finches, other taxa are understudied, prompting us to investigate nonapeptide influences on shoaling behaviour in zebrafish. Subjects received injections of isotocin, an isotocin antagonist, vasotocin, a vasotocin antagonist, or saline, followed by a test of grouping behaviour. Vasotocin decreased social interaction with the shoal. Unexpectedly, the vasotocin antagonist also reduced social interaction with the shoal, as well as general shoaling behaviour. Isotocin and its antagonist had minimal effects on grouping behaviours. These results suggest social interaction and shoaling are discrete aspects of sociality differentially influenced by vasotocin, although we cannot discount possible anxiogenic effects of vasotocin. Contrasting these results with studies in other systems demonstrates that each nonapeptide’s role in social behaviour varies across taxa, and cautions against a simplistic characterisation of nonapeptides as prosocial regulators of behaviour

Associations between Antiretrovirals and Cognitive Function in Women with HIV

Cognitive complications persist in antiretroviral therapy(ART)-treated people with HIV. However, the pattern and severity of domain-specific cognitive performance is variable and may be exacerbated by ART-mediated neurotoxicity. 929 women with HIV(WWH) from the Women’s Interagency HIV Study who were classified into subgroups based on sociodemographic and longitudinal behavioral and clinical data using semi-parametric latent class trajectory modelling. Five subgroups were comprised of: 1) well-controlled HIV with vascular comorbidities(n = 116); 2) profound HIV legacy effects(CD4 nadir <250 cells/μL; n = 275); 3) primarily <45 year olds with hepatitis C(n = 165); 4) primarily 35–55 year olds(n = 244), and 5) poorly-controlled HIV/substance use(n = 129). Within each subgroup, we fitted a constrained continuation ratio model via penalized maximum likelihood to examine adjusted associations between recent ART agents and cognition. Most drugs were not associated with cognition. However, among the few drugs, non-nucleoside reverse transcriptase inhibitor (NNRTIs) and protease inhibitors(PIs) were most commonly associated with cognition, followed by nucleoside reverse transcriptase inhibitors(NRTIs) and integrase inhibitors(IIs). Directionality of ART-cognition associations varied by subgroup. Better psychomotor speed and fluency were associated with ART for women with well-controlled HIV with vascular comorbidities. This pattern contrasts women with profound HIV legacy effects for whom poorer executive function and fluency were associated with ART. Motor function was associated with ART for younger WWH and primarily 35–55 year olds. Memory was associated with ART only for women with poorly-controlled HIV/substance abuse. Findings demonstrate interindividual variability in ART-cognition associations among WWH and highlight the importance of considering sociodemographic, clinical, and behavioral factors as an underlying contributors to cognition

Integrase Inhibitors are Associated with Neuropsychiatric Symptoms in Women with HIV

Objective: Women with HIV(WWH) are more likely to discontinue/change antiretroviral therapy(ART) due to side effects including neuropsychiatric symptoms. Efavirenz and integrase strand transfer inhibitors(INSTIs) are particularly concerning. We focused on these ART agents and neuropsychiatric symptoms in previously developed subgroups of WWH that differed on key sociodemographic factors as well as longitudinal behavioral and clinical profiles. WWH from the Women’s Interagency HIV Study were included if they had ART data available, completed the Perceived Stress Scale-10 and PTSD Checklist-Civilian. Questionnaires were completed biannually beginning in 2008 through 2016. To examine ART-symptom associations, constrained continuation ratio model via penalized maximum likelihood were fit within 5 subgroups of WWH. Data from 1882 WWH contributed a total of 4598 observations. 353 women were previously defined as primarily having well-controlled HIV with vascular comorbidities, 463 with legacy effects(CD4 nadir < 250cells/mL), 274 aged ≤ 45 with hepatitis, 453 between 35–55 years, and 339 with poorly-controlled HIV/substance users. INSTIs, but not efavirenz, were associated with symptoms among key subgroups of WWH. Among those with HIV legacy effects, dolutegravir and elvitegravir were associated with greater stress/anxiety and avoidance symptoms(P’s < 0.01); dolutegravir was also associated with greater re-experiencing symptoms(P = 0.005). Elvitegravir related to greater re-experiencing and hyperarousal among women with well-controlled HIV with vascular comorbidities(P’s < 0.022). Raltegravir was associated with less hyperarousal, but only among women aged ≤ 45 years(P = 0.001). The adverse neuropsychiatric effects of INSTIs do not appear to be consistent across all WWH. Key characteristics (e.g., age, hepatitis positivity) may need consideration to fully weight the risk–benefit ratio of dolutegravir and elvitegravir in WWH

Starting or Switching to an Integrase Inhibitor-Based Regimen Affects PTSD Symptoms in Women with HIV

As the use of Integrase inhibitor (INSTI)-class antiretroviral medications becomes more common to maintain long-term viral suppression, early reports suggest the potential for CNS side-effects when starting or switching to an INSTI-based regimen. In a population already at higher risk for developing mood and anxiety disorders, these drugs may have significant effects on PTSD scale symptom scores, particularly in women with HIV (WWH). A total of 551 participants were included after completing ≥ 1 WIHS study visits before and after starting/switching to an INSTI-based ART regimen. Of these, 14% were ART naïve, the remainder switched from primarily a protease inhibitor (PI) or non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimen. Using multivariable linear mixed effects models, we compared PTSD Civilian Checklist subscale scores before and after a “start/switch” to dolutegravir (DTG), raltegravir (RAL), or elvitegravir (EVG). Start/switch to EVG improved re-experiencing subscale symptoms (P’s 0.08). In WWH, an EVG-based ART regimen is associated with improved PTSD symptoms, in both treatment naïve patients and those switching from other ART. While a RAL-based regimen was associated with better PTSD symptoms than in treatment naïve patients, switching onto a RAL-based regimen was associated with worse PTSD symptoms. DTG-based regimens either did not affect, or worsened symptoms, in both naïve and switch patients. Further studies are needed to determine mechanisms underlying differential effects of EVG, RAL and DTG on stress symptoms in WWH