Interdependence of Primary Metabolism and Xenobiotic Mitigation Characterizes the Proteome of Bjerkandera adusta during Wood Decomposition.

The aim of the current work was to identify key features of the fungal proteome involved in the active decay of beechwood blocks by the white rot fungus Bjerkandera adusta at 20°C and 24°C. A combination of protein and domain analyses ensured a high level of annotation, which revealed that while the variation in the proteins identified was high between replicates, there was a considerable degree of functional conservation between the two temperatures. Further analysis revealed differences in the pathways and processes employed by the fungus at the different temperatures, particularly in relation to nutrient acquisition and xenobiotic mitigation. Key features showing temperature-dependent variation in mechanisms for both lignocellulose decomposition and sugar utilization were found, alongside differences in the enzymes involved in mitigation against damage caused by toxic phenolic compounds and oxidative stress.IMPORTANCE This work was conducted using the wood decay fungus B. adusta, grown on solid wood blocks to closely mimic the natural environment, and gives greater insight into the proteome of an important environmental fungus during active decay. We show that a change in incubation temperature from 20°C to 24°C altered the protein profile. Proteomic studies in the field of white-rotting basidiomycetes have thus far been hampered by poor annotation of protein databases, with a large proportion of proteins simply with unknown function. This study was enhanced by extensive protein domain analysis, enabling a higher level of functional assignment and greater understanding of the proteome composition. This work revealed a strong interdependence of the primary process of nutrient acquisition and specialized metabolic processes for the detoxification of plant extractives and the phenolic breakdown products of lignocellulose.

Fungus wars: basidiomycete battles in wood decay.

Understanding the mechanisms underlying wood decay basidiomycete community dynamics is crucial for fully understanding decomposition processes, and for modelling ecosystem function and resilience to environmental change. Competition drives community development in decaying woody resources, with interactions occurring at a distance, following physical contact, and through specialised relationships such as mycoparasitism. Outcomes of combative interactions range from replacement, where one mycelium displaces another, to deadlock, where neither combatant captures territory from the other; and a spectrum of intermediate outcomes (i.e. partial or mutual replacement) lie between these extremes. Many wood decay basidiomycetes coexist within a resource, in a complex and dynamic community, and new research techniques are focussing on spatial orientation of interactions in 3 dimensions, as opposed to historical two-dimensional research. Not only do interactions drive changes in species composition and thus wood decomposition rate, they also may have industrial applications in biocontrol of pathogenic or nuisance fungi, enzyme production, and in the production of novel antifungals and antibiotics. Altogether, fungal interactions are a fascinating and important field of study.

Physical activity guidelines and cardiovascular risk in children: a cross sectional analysis to determine whether 60 minutes is enough.

BACKGROUND: Physical activity reduces cardiovascular mortality and morbidity. The World Health Organisation (WHO) recommends children engage in 60 min daily moderate-to-vigorous physical activity (MVPA). The effect of compliance with this recommendation on childhood cardiovascular risk has not been empirically tested. To evaluate whether achieving recommendations results in reduced composite-cardiovascular risk score (CCVR) in children, and to examine if vigorous PA (VPA) has independent risk-reduction effects. METHODS: PA was measured using accelerometry in 182 children (9-11 years). Subjects were grouped according to achievement of 60 min daily MVPA (active) or not (inactive). CCVR was calculated (sum of z-scores: DXA body fat %, blood pressure, VO2peak, flow mediated dilation, left ventricular diastolic function; CVR score ≥ 1SD indicated 'higher risk'). The cohort was further split into quintiles for VPA and odds ratios (OR) calculated for each quintile. RESULTS: Active children (92 (53 boys)) undertook more MVPA (38 ± 11 min, P < 0.001), had greater VO2peak (4.5 ± 0.8 ml/kg/min P < 0.001), and lower fat % (3.9 ± 1.1 %, P < 0.001) than inactive. No difference were observed between active and inactive for CCVR or OR (P > 0.05). CCVR in the lowest VPA quintile was significantly greater than the highest quintile (3.9 ± 0.6, P < 0.05), and the OR was 4.7 times higher. CONCLUSION: Achievement of current guidelines has positive effects on body composition and cardiorespiratory fitness, but not CCVR. Vigorous physical activity appears to have beneficial effects on CVD risk, independent of moderate PA, implying a more prescriptive approach may be needed for future VPA guidelines.

The relationship between body mass index, aerobic performance and asthma in a pre-pubertal, population-level cohort.

PURPOSE: To assess the relationship between asthma, body mass index (BMI) and aerobic performance, as indicated by a shuttle test. METHODS: 20,577 participants (10,413 boys) from the SportsLinx serial cross-sectional study participated. Parental reports of asthma status and home postcode data were gathered from consent forms. Stature, sitting stature and body mass were measured and BMI, somatic maturity and indices of multiple deprivation scores (IMD) were derived. Performance on the 20 m multi-stage shuttle runs test (20mSRT) was used to estimate cardiorespiratory fitness (CRF). RESULTS: Asthma [F (1, 17,015) = 82.26, P < 0.01] and gender [F (1, 17,015) = 678.491, P < 0.001] significantly influenced 20mSRT. The addition of BMI, maturity and IMD to the model did not alter these significant effects. There was a significant interaction between 20mSRT and BMI [F (1, 16,723) = 132.80, P < 0.01], with a significant decrease in 20mSRT from the 50th BMI percentile upwards [t (16,699) = 36.88, P < 0.01]. Binary logistic regression revealed gender and 20mSRT to be significant predictors of asthma occurrence; BMI SDS just reached significance whilst maturity and IMD were not significant contributors to the model. CONCLUSIONS: This study demonstrates the negative influences of low CRF and high BMI on the risk of asthma occurrence in pre-pubertal children. Furthermore, it highlights the significant influence of BMI on CRF, revealing these effects to be manifest considerably below those BMI percentiles conventionally associated with being overweight or obese.

Assessment of biochemical liver markers, physical activity, fitness and body mass index for a cardiometabolic risk model in childhood.

AIM: The aim of this study was to investigate clustered cardiometabolic risk scores in healthy 10- to 12-year-olds using anthropometric characteristics, measurements of cardiorespiratory fitness (CRF) and physical activity and blood markers of metabolic disease. We also evaluated how including markers of liver cell injury would affect the clustered cardiometabolic risk assessment model. METHODS: This cross-sectional study focused on 99 children aged 10-12 years. The main outcome included assessing participants with increased and low cardiometabolic risk factors using a clustered risk score model that incorporated markers implicated in metabolic syndrome pathogenesis. Two clustered risk scores were calculated, one incorporating markers of liver cell injury. RESULTS: Children classified as 'increased risk' exhibited significantly lower CRF and higher body mass index Z-scores than their 'low-risk' peers. No significant differences in physical activity were observed. This trend remained unchanged when markers of liver injury were included in the clustered risk assessment model. CONCLUSION: The clustered risk score model is a scientifically robust method of cardiometabolic risk assessment, which reiterates the importance of weight reduction and CRF promotion in childhood. Our study did not show a significant contribution of liver injury markers, and further research is needed to evaluate their effect on cardiometabolic risk stratification in childhood.

Ten-year changes in positive and negative marker food, fruit, vegetables, and salad intake in 9-10 year olds: SportsLinx 2000-2001 to 2010-2011.

BACKGROUND: To investigate changes in intakes of 'negative' and 'positive' foods, fruit, vegetables, and salad in serial cohorts of 9-10-year-old children from 2000-2001 to 2010-2011. METHODS: For this serial, cross-sectional study, children in school year 5 (9-10 years of age) completed the SportsLinx Lifestyles Survey [n = 30,239 (15,336 boys and 14,903 girls)]. Changes in positive and negative food scores, and the proportion of boys and girls reportedly consuming fruit, vegetables and salad on the previous day to surveying, were investigated annually from 2000 to 2011. RESULTS: The consumption of negative foods declined and positive foods increased significantly compared to baseline. Positive changes in fruit, vegetables and salad consumption were observed over time, with the most recent cohort more likely to consume fruit, vegetables and salad compared to the 2000-2001 baseline. Girls displayed more favourable positive and negative food scores and were more likely to consume fruit, salad and vegetables across several study years compared to boys. CONCLUSIONS: The consumption of negative and positive foods, fruit, vegetables, and salad has improved over the last 10 years. In addition, girls appear to have better positive and negative food scores, and were more likely to consume fruit, vegetables and salad, across a number of study years or cohorts compared to boys. These encouraging findings suggest that children's food intake has improved since 2000. Furthermore, the data indicate that boys and girls may require separate or different healthy eating messages to further improve food intake.

Network traits predict ecological strategies in fungi.

Colonization of terrestrial environments by filamentous fungi relies on their ability to form networks that can forage for and connect resource patches. Despite the importance of these networks, ecologists rarely consider network features as functional traits because their measurement and interpretation are conceptually and methodologically difficult. To address these challenges, we have developed a pipeline to translate images of fungal mycelia, from both micro- and macro-scales, to weighted network graphs that capture ecologically relevant fungal behaviour. We focus on four properties that we hypothesize determine how fungi forage for resources, specifically: connectivity; relative construction cost; transport efficiency; and robustness against attack by fungivores. Constrained ordination and Pareto front analysis of these traits revealed that foraging strategies can be distinguished predominantly along a gradient of connectivity for micro- and macro-scale mycelial networks that is reminiscent of the qualitative 'phalanx' and 'guerilla' descriptors previously proposed in the literature. At one extreme are species with many inter-connections that increase the paths for multidirectional transport and robustness to damage, but with a high construction cost; at the other extreme are species with an opposite phenotype. Thus, we propose this approach represents a significant advance in quantifying ecological strategies for fungi using network information.

Changes in fitness, body mass index and obesity in 9-10 year olds.

BACKGROUND: The prevalence of obesity in children has increased substantially in recent years and, paediatric obesity and poor fitness are risk factors for disease. The present study aimed to assess changes in body mass index (BMI), the prevalence of obesity and changes in aerobic endurance over time in 9-10-year-old schoolchildren. METHODS: Participants were recruited by the SportsLinx project from primary schools across Liverpool. Height and weight data were used to calculate BMI. The prevalence of obesity and overweight were estimated using age- and sex-specific cut-off points. Performance on the 20-m multi-stage shuttle runs test (20 mMST) was used as a marker of aerobic endurance. Data were available for 13,418 (6572 boys, 6846 girls) 9-10-year-old children. Analysis of covariance was completed to assess year-on-year changes in BMI controlling for deprivation (IMD) and 20 mMST performance, and 20 mMST performance controlling for IMD and BMI. RESULTS: No significant changes in BMI from baseline were observed (P > 0.05). Obesity prevalence reduced in girls (2005 = 10.3%, 2008 = 8.52% in 2008). The data for boys showed no reductions in prevalence (2005 = 6.77%, 2008 = 7.87%). The most recent cohort for boys and two most recent cohorts for girls had lower levels of aerobic endurance than baseline (2004-2005) (P

Imaging complex nutrient dynamics in mycelial networks.

Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier techniques shows that as the colony forms, it self-organizes into well demarcated domains that are identifiable by differences in the phase relationship of the pulses. On the centimetre to metre scale, we have begun to use techniques borrowed from graph theory to characterize the development and dynamics of the network, and used these abstracted network models to predict the transport characteristics, resilience, and cost of the network.

Mapping dietary habits may provide clues about the factors that determine food choice.

BACKGROUND: Food deserts are thought to be a barrier to making healthier food choices. This concept has been challenged. The interaction between the physical environment and children's food choice has received little attention. The present study used food intake data to generate hypotheses concerning the role of the physical environment in food choice. METHODS: A cross-sectional analysis was conducted of the dietary habits of Year 5 (9-10-year-old) children from 90 of Liverpool's 118 primary schools. Individuals with the 'best' and 'worst' food choices were mapped and two areas associated with these extreme choices located. RESULTS: One thousand five hundred and thirty-five children completed the dietary questionnaire and supplied a full and valid postcode. Two adjacent areas with relatively large numbers of children in the 'best' and 'worst' food choice groups were chosen. Both areas had very similar socio-economic profiles. The contrast in the physical environments was striking, even on visual inspection. CONCLUSIONS: Food deserts as a cause of poor food choice did not stand scrutiny; the area located by the worst food choices had a plethora of shops selling food (better termed a food prairie), whereas the area located by the best food choices had no shops in evidence but did have more 'space'.

The fungus that came in from the cold: dry rot's pre-adapted ability to invade buildings.

Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions. Adaptations in intracellular transport machineries promoting hyphal growth, and nutrient and water transport may explain why it is has become a successful invader of timber in houses. Further, we demonstrate that S. lacrymans has poor combative ability in our experimental setup, compared to other brown rot fungi. In sheltered indoor conditions, the dry rot fungus may have limited encounters with other wood decay fungi compared to its wild relatives. Overall, our analyses indicate that the dry rot fungus is an ecological specialist with poor combative ability against other fungi.

The association between dog ownership or dog walking and fitness or weight status in childhood.

BACKGROUND: Health benefits of dog walking are established in adults: dog owners are on average more physically active, and those walking their dogs regularly have lower weight status than those who do not. However, there has been little research on children. OBJECTIVES: This study aimed to examine the association between dog ownership or dog walking and childhood fitness or weight status. METHODS: A survey of pet ownership and involvement in dog walking was combined with fitness and weight status measurements of 1021 9 to 10-year-old children in the Liverpool SportsLinx study. RESULTS: We found little evidence to support that children who live with, or walk with, dogs are any fitter or less likely to be obese than those who do not. CONCLUSIONS: This is an important finding, as it suggests that the activity that children currently do with dogs is not sufficient enough to impact weight status or fitness.

Utility of the hypertriglyceridemic waist phenotype in the cardiometabolic risk assessment of youth stratified by body mass index.

BACKGROUND: It is unclear whether the hypertriglyceridemic waist phenotype (HTWP) can be used to identify those at most risk of cardiometabolic disorders. OBJECTIVES: The utility of the HTWP as a useful predictor of cardiometabolic risk in youth stratified by body mass index was assessed. METHODS: Three hundred and eighty-seven children (12-17.5 years) were used within this cross-sectional study. Participants were classified as normal weight or overweight/obese according to the International Obesity Task Force criteria. The HTWP phenotype was defined as having a waist circumference ≥90th percentile for age and gender with concomitant triglyceride concentrations ≥1.24 mmol L(-1) . Cardiometabolic risk profiles were compared using MANCOVA. RESULTS: Normal weight participants with the HTWP had significantly higher levels of C-reactive protein 2.6 ± 0.4 vs. 1.6 ± 0.3 mg L(-1) (P < 0.05) and cardiometabolic risk scores (1.3 ± 0.3 vs. -0.7 ± 0.2 and 2.1 ± 0.4 vs. -0.5 ± 0.2; both P < 0.05) compared with those of a normal weight without the HTWP. Overweight/obese participants with the HTWP had significantly higher C-reactive protein levels (3.5 ± 0.6 vs. 2.6 ± 0.5; P < 0.05) as well as both cardiometabolic risk scores (1.6 ± 0.6 vs. 0.9 ± 0.2 and 2.2 ± 0.6 vs. 0.8 ± 0.2; both P < 0.001) when compared with overweight/obese participants without the HTWP. CONCLUSIONS: The HTWP may serve as a simple and clinically useful approach to identify youth at increased cardiometabolic risk.

Effects of oxygen, pH and nitrate concentration on denitrification by Pseudomonas species.

The production of nitrogen-containing gases by denitrification in three organisms was examined using membrane inlet mass spectrometry. The effects of O2 (during both growth and maintenance) and of pH, nitrate concentration and carbon source were tested in non-proliferating cell suspensions. Two strains of Pseudomonas aeruginosa were capable of co-respiration of NO3- and O2 and, under controlled O2 supply, gave oscillatory denitrification. Variations in culture and assay conditions affected both the rate of denitrification and the ratio of end products (N2O:N2). Higher rates were seen following anaerobic growth. Optimum values of pH and nitrate concentration for denitrification are given. Generally, the optimum pH was 7.0-7.5, approximately that of the growth medium. Optimum nitrate concentration was generally 20 mM.

Training radial basis function neural networks: effects of training set size and imbalanced training sets.

Obtaining training data for constructing artificial neural networks (ANNs) to identify microbiological taxa is not always easy. Often, only small data sets with different numbers of observations per taxon are available. Here, the effect of both size of the training data set and of an imbalanced number of training patterns for different taxa is investigated using radial basis function ANNs to identify up to 60 species of marine microalgae. The best networks trained to discriminate 20, 40 and 60 species respectively gave overall percentage correct identification of 92, 84 and 77%. From 100 to 200 patterns per species was sufficient in networks trained to discriminate 20, 40 or 60 species. For 40 and 60 species data sets an imbalance in the number of training patterns per species always affected training success, the greater the imbalance the greater the effect. However, this could be largely compensated for by adjusting the networks using a posteriori probabilities, estimated as network output values.

Proportion estimation with confidence limits.

A common task in microbiology involves determining the composition of a mixed population of individuals by drawing a sample from the population and using some procedure to identify the individuals in the sample. There may be a significant probability that the identification procedure misidentifies some members of the sample (for example, because the available data are insufficient unambiguously to identify an individual) which makes finding the proportions in the underlying population non-trivial. A further complication arises where individuals are present in the population that do not belong to any of the subpopulations recognised by use of the identification procedure. A simple algorithm is presented to address these problems and construct a maximum likelihood estimate of the proportions, together with confidence limits. The technique is illustrated using an example drawn from flow cytometry in which phytoplankton cells are identified from flow cytometry data by an RBF neural network, and the limitations of the approach are discussed.

Encounter with New Resources Causes Polarized Growth of the Cord-Forming Basidiomycete Phanerochaete velutina on Soil.

Abstract The development and physiology of cord-forming saprotrophic basidiomycetes, which form extensive and persistent mycelial networks in woodland ecosystems, can be conveniently studied on non-sterile soil in laboratory microcosms mimicking field conditions. Morphological responses of Phanerochaete velutina mycelial systems to resource encounters, and decay partitioning following encounters, varied according to whether simulated woody litter was unsterile or autoclaved and on whether encounter took place at the mycelial foraging front or behind the margin (simulating litter fall onto established systems in the field). Results show that encounter of discrete resources by P. velutina is rapidly communicated to the entire mycelial system; that resource capture takes high priority at the expense of continued system extension and decay-derived carbon reallocation; and that polarized growth toward newly encountered resources, previously considered to occur infrequently with this species, may be readily detected using image analysis techniques. Potential advantages of polarized development of P. velutina are discussed.

Rates and quantities of carbon flux to ectomycorrhizal mycelium following 14C pulse labeling of Pinus sylvestris seedlings: effects of litter patches and interaction with a wood-decomposer fungus.

We used a novel digital autoradiographic technique that enabled, for the first time, simultaneous visualization and quantification of spatial and temporal changes in carbon allocation patterns in ectomycorrhizal mycelia. Mycorrhizal plants of Pinus sylvestris L. were grown in microcosms containing non-sterile peat. The time course and spatial distribution of carbon allocation by P. sylvestris to mycelia of its mycorrhizal partners, Paxillus involutus (Batsch) Fr. and Suillus bovinus (L.): Kuntze, were quantified following 14C pulse labeling of the plants. Litter patches were used to investigate the effects of nutrient resource quality on carbon allocation. The wood-decomposer fungus Phanerochaete velutina (D.C.: Pers.) Parmasto was introduced to evaluate competitive and territorial interactions between its mycelial cords and the mycelial system of S. bovinus. Growth of ectomycorrhizal mycelium was stimulated in the litter patches. Nearly 60% of the C transferred from host plant to external mycorrhizal mycelium (> 2 mm from root surfaces) was allocated to mycelium in the patches, which comprised only 12% of the soil area available for mycelial colonization. Mycelia in the litter patch most recently colonized by mycorrhizal mycelium received the largest investment of carbon, amounting to 27 to 50% of the total 14C in external mycorrhizal mycelium. The amount of C transfer to external mycelium of S. bovinus following pulse labeling was reduced from a maximum of 167 nmol in systems with no saprotroph to a maximum of 61 nmol in systems interacting with P. velutina. The 14C content of S. bovinus mycelium reached a maximum 24-36 h after labeling in control microcosms, but allocation did not reach a peak until 56 h after labeling, when S. bovinus interacted with mycelium of P. velutina. The mycelium of S. bovinus contained 9% of the total 14C in the plants (including mycorrhizae) at the end of the experiment, but this was reduced to 4% in the presence of P. velutina. The results demonstrate the dynamic manner in which mycorrhizal mycelia deploy C when foraging for nutrients. The inhibitory effect of the wood-decomposer fungus P. velutina on C allocation to external mycorrhizal mycelium has important implications for nutrient cycling in forest ecosystems.

Rapid and recent changes in fungal fruiting patterns.

Information on responses of higher organisms to climate change is dominated by events in spring. Far less is known about autumnal events and virtually nothing about communities of microorganisms. We analyzed autumnal fruiting patterns of macrofungi over the past 56 years and found that average first fruiting date of 315 species is earlier, while last fruiting date is later. Fruiting of mycorrhizal species that associate with both deciduous and coniferous trees is delayed in deciduous, but not in coniferous, forests. Many species are now fruiting twice a year, indicating increased mycelial activity and possibly greater decay rates in ecosystems.