Age and microenvironment outweigh genetic influence on the Zucker rat microbiome

Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?

Impact of chronic neonicotinoid exposure on honeybee colony performance and queen supersedure

BACKGROUND: Honeybees provide economically and ecologically vital pollination services to crops and wild plants. During the last decade elevated colony losses have been documented in Europe and North America. Despite growing consensus on the involvement of multiple causal factors, the underlying interactions impacting on honeybee health and colony failure are not fully resolved. Parasites and pathogens are among the main candidates, but sublethal exposure to widespread agricultural pesticides may also affect bees. METHODOLOGY/PRINCIPAL FINDINGS: To investigate effects of sublethal dietary neonicotinoid exposure on honeybee colony performance, a fully crossed experimental design was implemented using 24 colonies, including sister-queens from two different strains, and experimental in-hive pollen feeding with or without environmentally relevant concentrations of thiamethoxam and clothianidin. Honeybee colonies chronically exposed to both neonicotinoids over two brood cycles exhibited decreased performance in the short-term resulting in declining numbers of adult bees (-28%) and brood (-13%), as well as a reduction in honey production (-29%) and pollen collections (-19%), but colonies recovered in the medium-term and overwintered successfully. However, significantly decelerated growth of neonicotinoid-exposed colonies during the following spring was associated with queen failure, revealing previously undocumented long-term impacts of neonicotinoids: queen supersedure was observed for 60% of the neonicotinoid-exposed colonies within a one year period, but not for control colonies. Linked to this, neonicotinoid exposure was significantly associated with a reduced propensity to swarm during the next spring. Both short-term and long-term effects of neonicotinoids on colony performance were significantly influenced by the honeybees' genetic background. CONCLUSIONS/SIGNIFICANCE: Sublethal neonicotinoid exposure did not provoke increased winter losses. Yet, significant detrimental short and long-term impacts on colony performance and queen fate suggest that neonicotinoids may contribute to colony weakening in a complex manner. Further, we highlight the importance of the genetic basis of neonicotinoid susceptibility in honeybees which can vary substantially.

Deconstructing the climate change response of the Northern Hemisphere wintertime storm tracks

There are large uncertainties in the circulation response of the atmosphere to climate change. One manifestation of this is the substantial spread in projections for the extratropical storm tracks made by different state-of-the-art climate models. In this study we perform a series of sensitivity experiments, with the atmosphere component of a single climate model, in order to identify the causes of the differences between storm track responses in different models. In particular, the Northern Hemisphere wintertime storm tracks in the CMIP3 multi-model ensemble are considered. A number of potential physical drivers of storm track change are identified and their influence on the storm tracks is assessed. The experimental design aims to perturb the different physical drivers independently, by magnitudes representative of the range of values present in the CMIP3 model runs, and this is achieved via perturbations to the sea surface temperature and the sea-ice concentration forcing fields. We ask the question: can the spread of projections for the extratropical storm tracks present in the CMIP3 models be accounted for in a simple way by any of the identified drivers? The results suggest that, whilst the changes in the upper-tropospheric equator-to-pole temperature difference have an influence on the storm track response to climate change, the large spread of projections for the extratropical storm track present in the northern North Atlantic in particular is more strongly associated with changes in the lower-tropospheric equator-to-pole temperature difference.

Can a computerised training paradigm assist people with intellectual disabilities to learn cognitive mediation skills? A randomised experiment

Aims: The aim was to examine whether specific skills required for cognitive behavioural therapy (CBT) could be taught using a computerised training paradigm with people who have intellectual disabilities (IDs). Training aimed to improve: a) ability to link pairs of situations and mediating beliefs to emotions, and b) ability to link pairs of situations and emotions to mediating beliefs. Method: Using a single-blind mixed experimental design, sixty-five participants with IDs were randomised to receive either computerised training or an attention-control condition. Cognitive mediation skills were assessed before and after training. Results: Participants who received training were significantly better at selecting appropriate emotions within situation beliefs pairs, controlling for baseline scores and IQ. Despite significant improvements in the ability of those who received training to correctly select intermediating beliefs for situation-feelings pairings, no between-group differences were observed at post-test. Conclusions: The findings indicated that computerised training led to a significant improvement in some aspects of cognitive mediation for people with IDs, but whether this has a positive effect upon outcome from therapy is yet to be established. (C) 2015 Elsevier Ltd. All rights reserved.

Regulation of early steps of GPVI signal transduction by phosphatases: a systems biology approach

We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.

Colour relationalism and the real deliverances of introspection

Colour relationalism holds that the colours are constituted by relations to subjects. Anti-relationalists have claimed that this view stands in stark contrast to our phenomenally-informed, pre-theoretic intuitions. Is this claim right? Cohen and Nichols��� recent empirical study suggests not, as about half of their participants seemed to be relationalists about colour. Despite Cohen and Nichols��� study, we think that the anti-relationalist���s claim is correct. We explain why there are good reasons to suspect that Cohen and Nichols��� experimental design skewed their results in favour of relationalism. We then run an improved study and find that most of our participants seem to be anti-relationalists. We find some other interesting things too. Our results suggest that the majority of ordinary people find it no less intuitive that colours are objective than that shapes are objective. We also find some evidence that when those with little philosophical training are asked about the colours of objects, their intuitions about colour and shape cases are similar, but when asked about people���s colour ascriptions, their intuitions about colour and shape cases differ.

Using computers to teach people with intellectual disabilities to perform some of the tasks used within cognitive behavioural therapy: a randomised experiment

Aims Training has been shown to improve the ability of people with intellectual disabilities (IDs) to perform some cognitive behavioural therapy (CBT) tasks. This study used a computerised training paradigm with the aim of improving the ability of people with IDs to: a) discriminate between behaviours, thoughts and feelings, and b) link situations, thoughts and feelings. Methods Fifty-five people with mild-to-moderate IDs were randomly assigned to a training or attention-control condition in a single-blind mixed experimental design. Computerised tasks assessed the participants��� skills in: (a) discriminating between behaviours, thoughts and feelings (separately and pooled together), and (b) cognitive mediation by selecting appropriate emotions as consequences to given thoughts, and appropriate thoughts as mediators of given emotions. Results Training significantly improved ability to discriminate between behaviours, thoughts and feelings pooled together, compared to the attention-control condition, even when controlling for baseline scores and IQ. Large within-group improvements in the ability to identify behaviours and feelings were observed for the training condition, but not the attention-control group. There were no significant between-group differences in ability to identify thoughts, or on cognitive mediation skills. Conclusions A single session of computerised training can improve the ability of people with IDs to understand and practise CBT tasks relating to behaviours and feelings. There is potential for computerised training to be used as a ���primer��� for CBT with people with IDs to improve engagement and outcomes, but further development on a specific computerised cognitive mediation task is needed.