Evidence for variation in the effective population size of animal mitochondrial DNA

Background: It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant. Results: Here we present several lines of evidence that suggest, to the contrary, that the effective population size of mtDNA does vary, and that the variation can be substantial. First, we show that levels of mitochondrial and nuclear diversity are correlated within all groups of animals we surveyed. Second, we show that the effectiveness of selection on non-synonymous mutations, as measured by the ratio of the numbers of non-synonymous and synonymous polymorphisms, is negatively correlated to levels of mitochondrial diversity. Finally, we estimate the effective population size of mitochondrial DNA in selected mammalian groups and show that it varies by at least an order of magnitude. Conclusions: We conclude that there is variation in the effective population size of mitochondria. Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation

Assessment of the ergogenic effect of caffeine supplementation on mood, anticipation timing, and muscular strength in older adults

The effect of caffeine to promote improvements in mood, cognition, and exercise performance has been well established in young and athletic adults. However, little is known about whether such nutritional ergogenic aids are effective in enhancing psychological well-being, physiological or cognitive performance in older adults. This study assesses the ergogenic effect of caffeine on mood, perceptual-motor coupling, and muscular strength in an older human population. Following a familiarization session, 12 apparently healthy volunteers (nine females and three males; 69 ± 6 years) completed two laboratory visits. "Pre ingestion" trials of mood state Brunel Mood State Inventory (BRUMS) and coincidence anticipation performance (Bassin anticipation timer) at slow (3 mph) and fast (8 mph) stimulus speeds were completed on both visits. Using a randomized, double-blind, cross-over design, participants consumed either caffeine (3 mg/kg body mass) or a placebo. Sixty minutes postingestion participants repeated the trials before completing a set of 10 consecutive repetitions of maximal knee extension using isokinetic dynamometry. Rating of perceived exertion (RPE) was assessed following the fifth and final repetition. Caffeine ingestion significantly improved mood state scores for vigor by 17% (P = 0.009) and reduced absolute error by 35% (P = 0.045) during coincidence anticipation assessment at 8 mph compared to placebo. There were no other significant effects. Caffeine ingestion failed to augment maximal voluntary contraction of the knee extensors and RPE did not prove to be significantly different to from placebo (P > 0.33 in each case). Acute caffeine ingestion may not be an effective ergogenic aid for improving muscular strength in older adults but could possibly be used as a nutrition supplement for enhancing mood and improving cognitive performance in daily living tasks where interceptive timing skills are required

Association of the CCR5 gene with juvenile idiopathic arthritis

The CC chemokine receptor 5 (CCR5) has been shown to be important in the recruitment of T-helper cells to the synovium, where they accumulate, drive the inflammatory process and the consequent synovitis and joint destruction. A 32 base-pair insertion/deletion variant (CCR5Δ32) within the gene leads to a frame shift and a nonfunctional receptor. CCR5Δ32 has been investigated for its association with juvenile idiopathic arthritis (JIA), with conflicting results. The aim of this study was to investigate whether CCR5Δ32 is associated with JIA in an UK population. CCR5Δ32 was genotyped in JIA cases (n=1054) and healthy controls (n=3129) and genotype and allele frequencies were compared. A meta-analysis of our study combined with previously published studies was performed. CCR5Δ32 was significantly associated with protection from developing JIA, in this UK data set (P(trend)=0.006, odds ratio (OR) 0.79 95% confidence interval (95% CI): 0.66-0.94). The meta-analysis of all published case-control association studies confirmed the protective association with JIA (P=0.001 OR 0.82 95% CI: 0.73-0.93). CCR5Δ32 is a functional variant determining the number of receptors on the surface of T cells, and it is hypothesized that the level of CCR5 expression could influence the migration of proinflammatory T cells into the synovium and thus susceptibility to JIA

The impact of a school-based gardening intervention on intentions and behaviour related to fruit and vegetable consumption in children

A total of 77 children (34 boys, 43 girls, mean age ± standard deviation = 9 ± 1 years) participated in this study; 46 children (intervention) undertook a 12-week school gardening programme and 31 children acted as controls. Measures of the Theory of Planned Behaviour and fruit and vegetable consumption were taken pre- and post-intervention. Repeated measures analysis of variance and hierarchical regression analysis indicated that the intervention group increased daily consumption of fruits and vegetables and increased intentions, attitudes, norms, and perceived behavioural control related to fruit and vegetable consumption. Attitudes, norms and perceived behavioural control significantly predicted changes in fruit and vegetable consumption

Fluctuating selection models and Mcdonald-Kreitman type analyses

It is likely that the strength of selection acting upon a mutation varies through time due to changes in the environment. However, most population genetic theory assumes that the strength of selection remains constant. Here we investigate the consequences of fluctuating selection pressures on the quantification of adaptive evolution using McDonald-Kreitman (MK) style approaches. In agreement with previous work, we show that fluctuating selection can generate evidence of adaptive evolution even when the expected strength of selection on a mutation is zero. However, we also find that the mutations, which contribute to both polymorphism and divergence tend, on average, to be positively selected during their lifetime, under fluctuating selection models. This is because mutations that fluctuate, by chance, to positive selected values, tend to reach higher frequencies in the population than those that fluctuate towards negative values. Hence the evidence of positive adaptive evolution detected under a fluctuating selection model by MK type approaches is genuine since fixed mutations tend to be advantageous on average during their lifetime. Never-the-less we show that methods tend to underestimate the rate of adaptive evolution when selection fluctuates

Association of the AFF3 gene and IL2/IL21 gene region with juvenile idiopathic arthritis

Recent genetic studies have led to identification of numerous loci that are associated with susceptibility to autoimmune diseases. The strategy of using information from these studies has facilitated the identification of novel juvenile idiopathic arthritis (JIA) susceptibility loci, specifically, PTPN22 and IL2RA. Several novel autoimmune susceptibility loci have recently been identified, and we hypothesise that single-nucleotide polymorphisms (SNPs) within these genes may also be JIA susceptibility loci. Five SNPs within the genes AFF3, IL2/IL21, IL7R, CTLA4 and CD226, previously associated with multiple autoimmune diseases were genotyped, in a large data set of Caucasian JIA patients and controls, and tested for association with JIA. We identified two susceptibility loci for JIA, AFF3 and the IL2/IL21 region and additional weak evidence supporting an association with the CTLA4 and IL7R genes, which warrant further investigation. All results require validation in independent JIA data sets. Further characterisation of the specific causal variants will be required before functional studies can be performed

The assessment of science: the relative merits of post- publication review, the impact factor, and the number of citations

The assessment of scientific publications is an integral part of the scientific process. Here we investigate three methods of assessing the merit of a scientific paper: subjective post-publication peer review, the number of citations gained by a paper, and the impact factor of the journal in which the article was published. We investigate these methods using two datasets in which subjective post-publication assessments of scientific publications have been made by experts. We find that there are moderate, but statistically significant, correlations between assessor scores, when two assessors have rated the same paper, and between assessor score and the number of citations a paper accrues. However, we show that assessor score depends strongly on the journal in which the paper is published, and that assessors tend to over-rate papers published in journals with high impact factors. If we control for this bias, we find that the correlation between assessor scores and between assessor score and the number of citations is weak, suggesting that scientists have little ability to judge either the intrinsic merit of a paper or its likely impact. We also show that the number of citations a paper receives is an extremely error-prone measure of scientific merit. Finally, we argue that the impact factor is likely to be a poor measure of merit, since it depends on subjective assessment. We conclude that the three measures of scientific merit considered here are poor; in particular subjective assessments are an error-prone, biased, and expensive method by which to assess merit. We argue that the impact factor may be the most satisfactory of the methods we have considered, since it is a form of pre-publication review. However, we emphasise that it is likely to be a very error-prone measure of merit that is qualitative, not quantitative

The influence of organic and conventional fertilisation and crop protection practices, preceding crop, harvest year and weather conditions on yield and quality of potato (Solanum tuberosum) in a long-term management trial

The effects of organic versus conventional crop management practices (fertilisation, crop protection) and preceding crop on potato tuber yield (total, marketable, tuber size grade distribution) and quality (proportion of diseased, green and damaged tubers, tuber macro-nutrient concentrations) parameters were investigated over six years (2004–2009) as part of a long-term factorial field trial in North East England. Inter-year variability (the effects of weather and preceding crop) was observed to have a profound effect on yields and quality parameters, and this variability was greater in organic fertility systems. Total and marketable yields were significantly reduced by the use of both organic crop protection and fertility management. However, the yield gap between organic and conventional fertilisation regimes was greater and more variable than that between crop protection practices. This appears to be attributable mainly to lower and less predictable nitrogen supply in organically fertilised crops. Increased incidence of late blight in organic crop protection systems only occurred when conventional fertilisation was applied. In organically fertilised crops yield was significantly higher following grass/red clover leys than winter wheat, but there was no pre-crop effect in conventionally fertilised crops. The results highlight that nitrogen supply from organic fertilisers rather than inefficient pest and disease control may be the major limiting factor for yields in organic potato production systems

Nurturing the young shoots of talent: Using action research for exploration and theory building

This is an Author's Accepted Manuscript of an article published in European Early Childhood Education Research Journal, 19(4), 433-450, 2011, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/1350293X.2011.623515.This paper reports the outcomes of a set of action research projects carried out by teacher researchers in 14 local education authorities in England, working collaboratively with university tutors, over a period of three years. The common aim of all the projects was to explore practical ways of nurturing the gifts and talents of children aged four–seven years. The project was funded by the Department of Education and Skills in England as part of the government's gifted and talented programme. The project teachers felt that their understanding of issues relating to nurturing the gifts and talents of younger children was enhanced through their engagement in the project. It was possible to map the findings of the projects to the English government's National Quality Standards for gifted and talented education which include: (1) identification; (2) effective provision in the classroom; (3) enabling curriculum entitlement and choice; (4) assessment for learning; (5) engaging with community, families and beyond. The findings are also analysed within the framework of good practice in educating children in the first years of schooling. Participating practitioners felt that action research offered them a suitable methodology to explore the complexity of the topic of giftedness through cycles of planning, action and reflection and personal theory building