RESUMEN
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.
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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.
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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.
Asunto(s)
Adaptación Biológica/genética , Basidiomycota/fisiología , Materiales de Construcción/microbiología , Ecosistema , Variación Genética , Madera/microbiología , Basidiomycota/genética , Humanos , Análisis de Secuencia de ADNRESUMEN
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.
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Coriolaceae/metabolismo , Proteínas Fúngicas/análisis , Lignina/metabolismo , Proteoma , Madera/microbiología , Proteínas Fúngicas/genética , Genoma Fúngico , Filogenia , Proteómica , Azúcares/metabolismo , Temperatura , Madera/metabolismo , XenobióticosRESUMEN
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.
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Conductas Relacionadas con la Salud , Propiedad , Obesidad Infantil/epidemiología , Aptitud Física , Animales , Peso Corporal , Niño , Perros , Femenino , Humanos , Masculino , Obesidad Infantil/etiología , Encuestas y Cuestionarios , CaminataRESUMEN
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.
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Enfermedades Cardiovasculares/epidemiología , Ejercicio Físico , Guías como Asunto , Acelerometría , Presión Sanguínea , Niño , Estudios Transversales , Femenino , Humanos , Masculino , Oportunidad Relativa , Aptitud Física , Factores de Riesgo , Conducta de Reducción del Riesgo , Factores de TiempoRESUMEN
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.
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Índice de Masa Corporal , Enfermedades Cardiovasculares/diagnóstico , Cintura Hipertrigliceridémica/complicaciones , Sobrepeso/complicaciones , Obesidad Infantil/complicaciones , Adolescente , Biomarcadores/sangre , Enfermedades Cardiovasculares/etiología , Niño , Estudios Transversales , Femenino , Humanos , Masculino , Fenotipo , Medición de Riesgo/métodos , Factores de Riesgo , Circunferencia de la CinturaRESUMEN
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.
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Índice de Masa Corporal , Enfermedades Cardiovasculares/etiología , Indicadores de Salud , Hepatopatías/diagnóstico , Síndrome Metabólico/etiología , Actividad Motora , Aptitud Física , Biomarcadores/sangre , Enfermedades Cardiovasculares/sangre , Enfermedades Cardiovasculares/diagnóstico , Niño , Estudios Transversales , Técnicas de Apoyo para la Decisión , Femenino , Humanos , Hepatopatías/sangre , Hepatopatías/complicaciones , Masculino , Síndrome Metabólico/sangre , Síndrome Metabólico/diagnóstico , Medición de Riesgo , Factores de RiesgoRESUMEN
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.
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Dieta/tendencias , Frutas , Verduras , Niño , Fenómenos Fisiológicos Nutricionales Infantiles , Estudios de Cohortes , Estudios Transversales , Conducta Alimentaria , Femenino , Preferencias Alimentarias , Promoción de la Salud , Humanos , Lactuca , Masculino , Factores SexualesRESUMEN
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.
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Asma/fisiopatología , Índice de Masa Corporal , Ejercicio Físico , Resistencia Física , Factores de Edad , Asma/epidemiología , Estudios de Casos y Controles , Niño , Estudios de Cohortes , Estudios Transversales , Femenino , Humanos , Masculino , Factores SexualesRESUMEN
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 Asunto(s)
Índice de Masa Corporal
, Ejercicio Físico
, Obesidad/epidemiología
, Sobrepeso/epidemiología
, Resistencia Física
, Aptitud Física
, Análisis de Varianza
, Niño
, Inglaterra/epidemiología
, Femenino
, Humanos
, Masculino
, Prevalencia
, Valores de Referencia
, Carrera
, Factores Sexuales
, Aumento de Peso
RESUMEN
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.
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Alimentos , Hongos/metabolismo , Procesamiento de Imagen Asistido por Computador/métodos , Microscopía Confocal/métodos , Microscopía Fluorescente/métodos , Microscopía por Video/métodos , Micelio/metabolismoRESUMEN
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'.
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Conducta Alimentaria , Preferencias Alimentarias , Niño , Estudios Transversales , Dieta , Inglaterra , Ambiente , Humanos , Encuestas y CuestionariosRESUMEN
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.
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Ecosistema , Cuerpos Fructíferos de los Hongos/crecimiento & desarrollo , Hongos/crecimiento & desarrollo , Micorrizas/crecimiento & desarrollo , Inglaterra , Estaciones del Año , Temperatura , Factores de Tiempo , Tracheophyta/microbiología , Árboles/microbiologíaRESUMEN
OBJECTIVE: To examine the changes over time in cardiorespiratory fitness and body mass index (BMI) of children. DESIGN: Serial cross-sectional, population-based study. SETTING: Primary schools in Liverpool, UK. PARTICIPANTS: A total of 15,621 children (50% boys), representing 74% of eligible 9-11-year olds in the annual school cohorts between 1998/9 and 2003/4, who took part in a 20m multi-stage shuttle run test (20mMST). MAIN OUTCOME MEASURES: Weight, height, BMI (kg/m(2)) and obesity using the International Obesity Taskforce definition. RESULTS: Median (95% confidence interval) 20mMST score (number of runs) fell in boys from 48.9 (47.9-49.9) in 1998/9 to 38.1 (36.8-39.4) in 2003/4, and in girls from 35.8 (35.0-36.6) to 28.1 (27.2-29.1) over the same period. Fitness scores fell across all strata of BMI (P<0.001). Moreover, BMI increased over the same 6-year period even among children in fittest third of 20mMST. CONCLUSION: In a series of uniform cross-sectional assessments of school-aged children, BMI increased whereas cardiorespiratory fitness levels decreased within a 6-year period. Even among lean children, fitness scores decreased. Public health measures to reduce obesity, such as increasing physical activity, may help raise fitness levels among all children - not just the overweight or obese.
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Índice de Masa Corporal , Obesidad/epidemiología , Obesidad/fisiopatología , Sobrepeso/epidemiología , Sobrepeso/fisiopatología , Aptitud Física , Fenómenos Fisiológicos Cardiovasculares , Niño , Estudios Transversales , Inglaterra/epidemiología , Femenino , Humanos , Masculino , Prevalencia , Fenómenos Fisiológicos Respiratorios , Factores de RiesgoRESUMEN
The effects of exudates from uncolonized and from partly decayed beech wood on the extension rates of 16 later stage decay fungi were investigated. The partly decayed wood had been colonized by the pyrenomycete Eutypa spinosa, or the basidiomycetes Fomes fomentarius, Stereum hirsutum, and Trametes versicolor, all known as common early decay agents in European beech forests. Sterilized wood pieces were placed onto 0.5% malt agar, opposite to small agar plugs containing the test fungi. The latter showed very variable and species-specific growth responses to the various wood types. The presence of uncolonized wood stimulated extension rates in many species, whereas the four previously decayed wood types had variable stimulatory or inhibitory effects. Wood decayed by S. hirsutum resulted in reduced extension rate, delayed growth, or total inhibition in the majority of species, thus it is suggested that this species uses secondary metabolites in a defensive strategy. A single species was, however, stimulated in the presence of S. hirsutum-decayed wood. In contrast, the presence of wood decayed by F. fomentarius was stimulatory to 45% of the species. The other previously decayed wood types generally resulted in more variable responses, depending upon species. The results are discussed in an ecological context and it is suggested that the exudates from the partly decayed wood that are responsible for the reported effects may function as infochemicals, structuring microbial communities in wood.
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Hongos/química , Hongos/crecimiento & desarrollo , Madera , Ecología , Fagus , Dinámica PoblacionalRESUMEN
Fungal community structure and diversity in two types of agricultural grassland soil were investigated by amplified 18S ribosomal DNA restriction analysis (ARDRA) and 18S ribosomal DNA sequence analysis. These two grassland sites represent a species-rich old hay meadow and an agriculturally improved site with low floristic diversity. Two primer sets were used in combination to amplify approximately 550 bp of rDNA from three major fungal groups, the zygomycetes, basidiomycetes, and ascomycetes, and clone libraries were created for each site. 18S ARDRA was used to analyze 170 rDNA clones, and three diversity indices were calculated. A small-scale culturing analysis was also carried out and the most common isolates analyzed using ARDRA and sequence analysis. The soil fungal community revealed by the rDNA approaches was significantly different from that produced by this limited culture-based analysis. Twenty-eight soil-derived clones were sequenced, and many represented fungal taxa rarely reported in culture-based studies. The PCR-based techniques detected differences in diversity between the two fungal communities and changes in patterns of dominance that paralleled higher plant diversity. The results suggest that 18S rDNA-based approaches are a useful tool for initial screening of fungal communities, and that they represent a more comprehensive picture of the community than plate culturing.
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Biodiversidad , Hongos/genética , Poaceae/microbiología , Microbiología del Suelo , Secuencia de Bases , Análisis por Conglomerados , ADN Ribosómico/genética , Datos de Secuencia Molecular , Filogenia , Mapeo Restrictivo/métodos , Análisis de Secuencia de ADN/métodos , Reino UnidoRESUMEN
BACKGROUND: Analytical flow cytometry (AFC), by quantifying sometimes more than 10 optical parameters on cells at rates of approximately 10(3) cells/s, rapidly generates vast quantities of multidimensional data, which provides a considerable challenge for data analysis. We review the application of multivariate data analysis and pattern recognition techniques to flow cytometry. METHODS: Approaches were divided into two broad types depending on whether the aim was identification or clustering. Multivariate statistical approaches, supervised artificial neural networks (ANNs), problems of overlapping character distributions, unbounded data sets, missing parameters, scaling up, and estimating proportions of different types of cells comprised the first category. Classic clustering methods, fuzzy clustering, and unsupervised ANNs comprised the second category. We demonstrate the state of the art by using AFC data on marine phytoplankton populations. RESULTS AND CONCLUSIONS: Information held within the large quantities of data generated by AFC was tractable using ANNs, but for field studies the problem of obtaining suitable training data needs to be resolved, and coping with an almost infinite number of cell categories needs further research.
Asunto(s)
Citometría de Flujo/métodos , Redes Neurales de la Computación , Fitoplancton/clasificaciónRESUMEN
BACKGROUND: Artificial neural networks (ANNs) have been shown to be valuable in the analysis of analytical flow cytometric (AFC) data in aquatic ecology. Automated extraction of clusters is an important first stage in deriving ANN training data from field samples, but AFC data pose a number of challenges for many types of clustering algorithm. The fuzzy k-means algorithm recently has been extended to address nonspherical clusters with the use of scatter matrices. Four variants were proposed, each optimizing a different measure of clustering "goodness." METHODS: With AFC data obtained from marine phytoplankton species in culture, the four fuzzy k-means algorithm variants were compared with each other and with another multivariate clustering algorithm based on critical distances currently used in flow cytometry. RESULTS: One of the algorithm variants (adaptive distances, also known as the Gustafson--Kessel algorithm) was found to be robust and reliable, whereas the others showed various problems. CONCLUSIONS: The adaptive distances algorithm was superior in use to the clustering algorithms against which it was tested, but the problem of automatic determination of the number of clusters remains to be addressed.
Asunto(s)
Algoritmos , Citometría de Flujo/métodos , Redes Neurales de la Computación , Fitoplancton/clasificación , Procesamiento Automatizado de Datos , Predicción , InvestigaciónRESUMEN
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.