The Effects of Crop Type and Production Systems on the Activity of Beneficial Invertebrates

Beneficial invertebrate activity (13 groups) was assessed in five crop types on a split-plot experimental system in northern England using pitfall trapping and suction sampling in May-October 2005. Very significant differences were detected in activity between crop type, and in the preference of groups for individual crops. Within crop types, differences in fertiliser and crop protection approaches appeared to significantly affect activity, with preferences for either organic or conventional management differing between groups. In general, inorganic fertiliser application had more effect on activity than pesticide, herbicide and fungicide use

Sustainable intensification? Increased production diminishes omega-3 content of sheep milk

Intensifying agricultural production alters food composition, but this is often ignored when assessing system sustainability, yet it could compromise consumers’ health and the concept of ‘sustainable diets’. Here we consider milk composition from Mediterranean dairy sheep, finding inferior fatty acid (FA) profiles with respect to consumer health as a result of a more intensive system of production. Semi-intensive management did produce 57% more milk per ewe with 20% lower fat content, but inferior fat composition. Milk had a nutritionally poorer fatty acid (FA) profile, with 18% less omega-3 FA (n-3) (19% less long-chain n-3) and 7% less monounsaturated FA but 3% more saturated FA (9% higher in C14:0) concentrations compared with ewes under traditional, extensive management. Redundancy analysis identified close associations between fat composition and animal diets, particularly concentrate supplementation and grazing cultivated pasture - n-3 was associated with grazing diverse, native mountain pastures. The paper questions if identifying such key elements in traditional systems could be deployed for ‘sustainable intensification’ to maintain food quality whilst increasing output

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

The Surprising Power of Neighborly Advice

Two experiments revealed that (i) people can more accurately predict their affective reactions to a future event when they know how a neighbor in their social network reacted to the event than when they know about the event itself and (ii) people do not believe this. Undergraduates made more accurate predictions about their affective reactions to a 5-minute speed date (n = 25) and to a peer evaluation (n = 88) when they knew only how another undergraduate had reacted to these events than when they had information about the events themselves. Both participants and independent judges mistakenly believed that predictions based on information about the event would be more accurate than predictions based on information about how another person had reacted to it.Psycholog

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

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease

Copyright: © 2013 Eyre et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedClostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2–8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients’ first and last samples was 60 (29.5–118.5) [0–561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00–1.28) and within-host diversity was 0.28 SNVs/called genome (0.05–0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.Peer reviewe

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Increase in degraded collagen type II in synovial fluid early in the rabbit meniscectomy model of osteoarthritis

SummaryObjectiveThe objective of this study was to determine whether collagen type II breakdown products in synovial fluid (SF), detected by an enzyme-linked immunoassay, represent a useful marker for early events in osteoarthritis (OA) in the rabbit medial meniscectomy model.DesignComplete medial meniscectomy was performed on the right knee joints of 32 rabbits. Balanced groups of rabbits were then sacrificed at 2, 4, 8, and 12 weeks post-surgery. An additional 8 unoperated and 11 sham-operated animals served as controls. SF lavages were performed on right and left knee joints of the same animals at sacrifice. The proteolytic epitope of type II collagen was monitored using an enzyme-linked immunoassay.ResultsMacroscopically visible surface fibrillation and focal erosions appeared as early as 2 weeks after meniscectomy in the femorotibial joint (P<0.01). OA developed gradually during the later observation period, and then predominantly on the medial tibial plateau and medial femur. Significant histological alterations in cartilage, including a loss of proteoglycans, surface irregularities, and clefts, were detected at 2 weeks after meniscectomy (P<0.01). Collagen type II epitope levels in SF lavage samples were elevated peaking at 2 weeks after meniscectomy (P<0.02). Levels decreased at later time points, but they were still raised at 12 weeks (P≤0.05). Highly significant correlations were found between the SF collagen type II epitope levels and the macroscopic and microscopic scoring results (Spearman rho correlation coefficient, macroscopy—collagen type II epitope r=0.222, P=0.025; microscopy—collagen type II epitope r=0.436, P≤0.01).ConclusionIn this rabbit model of medial meniscectomy, levels of type II collagen fragments in SF appear to provide a useful marker of the early degenerative changes

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