Host genotype and age shape the leaf and root microbiomes of a wild perennial plant.

Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.

Weekday sunlight exposure, but not vitamin D intake, influences the association between vitamin D receptor genotype and circulating concentration 25-hydroxyvitamin D in a pan-European population: the Food4Me study

SCOPE: Little is known about diet- and environment-gene interactions on 25-hydroxyvitamin D (25(OH)D concentration. This cross-sectional study aimed to investigate (i) predictors of 25(OH)D concentration and relationships with vitamin D genotypes and (ii) whether dietary vitamin D intake and sunlight exposure modified these relationships.

METHODS AND RESULTS: Participants from the Food4Me study (n = 1312; age 18-79) were genotyped for vitamin D receptor (VDR) and vitamin D binding protein at baseline and a genetic risk score was calculated. Dried blood spot samples were assayed for 25(OH)D concentration and dietary and lifestyle information collected. Circulating 25(OH)D concentration was lower with increasing genetic risk score, lower in females than males, higher in supplement users than non-users and higher in summer than winter. Carriage of the minor VDR allele was associated with lower 25(OH)D concentration in participants with the least sunlight exposure. Vitamin D genotype did not influence the relationship between vitamin D intake and 25(OH)D concentration.

CONCLUSION: Age, sex, dietary vitamin D intake, country, sunlight exposure, season, and vitamin D genetic risk score were associated with circulating 25(OH)D concentration in a pan-European population. The relationship between VDR genotype and 25(OH)D concentration may be influenced by weekday sunlight exposure but not dietary vitamin D intake.

Comparison of multitemporal MODIS-EVI smoothing algorithms and its contribution to crop monitoring.

Crop monitoring and more generally land use change detection are of primary importance in order to analyze spatio-temporal dynamics and its impacts on environment. This aspect is especially true in such a region as the State of Mato Grosso (south of the Brazilian Amazon Basin) which hosts an intensive pioneer front. Deforestation in this region as often been explained by soybean expansion in the last three decades. Remote sensing techniques may now represent an efficient and objective manner to quantify how crops expansion really represents a factor of deforestation through crop mapping studies. Due to the special characteristics of the soybean productions' farms in Mato Grosso (area varying between 1000 hectares and 40000 hectares and individual fields often bigger than 100 hectares), the Moderate Resolution Imaging Spectroradiometer (MODIS) data with a near daily temporal resolution and 250 m spatial resolution can be considered as adequate resources to crop mapping. Especially, multitemporal vegetation indices (VI) studies have been currently used to realize this task [1] [2]. In this study, 16-days compositions of EVI (MODQ13 product) data are used. However, although these data are already processed, multitemporal VI profiles still remain noisy due to cloudiness (which is extremely frequent in a tropical region such as south Amazon Basin), sensor problems, errors in atmospheric corrections or BRDF effect. Thus, many works tried to develop algorithms that could smooth the multitemporal VI profiles in order to improve further classification. The goal of this study is to compare and test different smoothing algorithms in order to select the one which satisfies better to the demand which is classifying crop classes. Those classes correspond to 6 different agricultural managements observed in Mato Grosso through an intensive field work which resulted in mapping more than 1000 individual fields. The agricultural managements above mentioned are based on combination of soy, cotton, corn, millet and sorghum crops sowed in single or double crop systems. Due to the difficulty in separating certain classes because of too similar agricultural calendars, the classification will be reduced to 3 classes : Cotton (single crop), Soy and cotton (double crop), soy (single or double crop with corn, millet or sorghum). The classification will use training data obtained in the 2005-2006 harvest and then be tested on the 2006-2007 harvest. In a first step, four smoothing techniques are presented and criticized. Those techniques are Best Index Slope Extraction (BISE) [3], Mean Value Iteration (MVI) [4], Weighted Least Squares (WLS) [5] and Savitzky-Golay Filter (SG) [6] [7]. These techniques are then implemented and visually compared on a few individual pixels so that it allows doing a first selection between the five studied techniques. The WLS and SG techniques are selected according to criteria proposed by [8]. Those criteria are: ability in eliminating frequent noises, conserving the upper values of the VI profiles and keeping the temporality of the profiles. Those selected algorithms are then programmed and applied to the MODIS/TERRA EVI data (16-days composition periods). Tests of separability are realized based on the Jeffries-Matusita distance in order to see if the algorithms managed in improving the potential of differentiation between the classes. Those tests are realized on the overall profile (comprising 23 MODIS images) as well as on each MODIS sub-period of the profile [1]. This last test is a double interest process because it allows comparing the smoothing techniques and also enables to select a set of images which carries more information on the separability between the classes. Those selected dates can then be used to realize a supervised classification. Here three different classifiers are tested to evaluate if the smoothing techniques as a particular effect on the classification depending on the classifiers used. Those classifiers are Maximum Likelihood classifier, Spectral Angle Mapper (SAM) classifier and CHAID Improved Decision tree. It appears through the separability tests on the overall process that the smoothed profiles don't improve efficiently the potential of discrimination between classes when compared with the original data. However, the same tests realized on the MODIS sub-periods show better results obtained with the smoothed algorithms. The results of the classification confirm this first analyze. The Kappa coefficients are always better with the smoothing techniques and the results obtained with the WLS and SG smoothed profiles are nearly equal. However, the results are different depending on the classifier used. The impact of the smoothing algorithms is much better while using the decision tree model. Indeed, it allows a gain of 0.1 in the Kappa coefficient. While using the Maximum Likelihood end SAM models, the gain remains positive but is much lower (Kappa improved of 0.02 only). Thus, this work's aim is to prove the utility in smoothing the VI profiles in order to improve the final results. However, the choice of the smoothing algorithm has to be made considering the original data used and the classifier models used. In that case the Savitzky-Golay filter gave the better results.

Socioeconomic differences in takeaway food consumption and their contribution to inequalities in dietary intakes

Background Takeaway consumption has been increasing and may contribute to socioeconomic inequalities in overweight/obesity and chronic disease. This study examined socioeconomic differences in takeaway consumption patterns, and their contributions to dietary intake inequalities. Method Cross-sectional dietary intake data from adults aged between 25 and 64 years from the Australian National Nutrition Survey (n= 7319, 61% response rate). Twenty-four hour dietary recalls ascertained intakes of takeaway food, nutrients and fruit and vegetables. Education was used as socioeconomic indicator. Data were analysed using logistic regression and general linear models. Results Thirty-two percent (n = 2327) consumed takeaway foods in the 24 hour period. Lower-educated participants were less likely than their higher-educated counterparts to have consumed total takeaway foods (OR 0.64; 95% CI 0.52, 0.80). Of those consuming takeaway foods, the lowest-educated group was more likely to have consumed “less healthy” takeaway choices (OR 2.55; 95% CI 1.73, 3.77), and less likely to have consumed “healthy” choices (OR 0.52; 95% CI 0.36, 0.75). Takeaway foods made a greater contribution to energy, total fat, saturated fat, and fibre intakes among lower than higher-educated groups. Lower likelihood of fruit and vegetable intakes were observed among “less healthy” takeaway consumers, whereas a greater likelihood of their consumption was found among “healthy” takeaway consumers. Conclusions Total and the types of takeaway foods consumed may contribute to socioeconomic inequalities in intakes of energy, total and saturated fats. However, takeaway consumption is unlikely to be a factor contributing to the lower fruit and vegetable intakes among socioeconomically-disadvantaged groups.

The citizen's voice : Albert Hirschman's Exit, Voice and Loyalty and its contribution to media citizenship debates

This paper analyses Albert Hirschman's Exit, Voice and Loyalty (Hirschman 1970) as a basis for understanding the relationship between media and citizenship. It considers the significance of Hirschman's concept of voice in relation to media policy, media participation through user-created content, and the rise of 'citizen media' and 'citizen journalism'. It associates these developments with a 'de-centering' of both media practice and media studies, as considered by Couldry (2006a, 2006b). It concludes by suggesting that voice and participation, rather than citizenship, may constitute a more suitable foundation for understanding new digital media initiatives.

The association between MC1R genotype and BRAF mutation status in cutaneous melanoma : findings from an Australian population

There is increasing epidemiological and molecular evidence that cutaneous melanomas arise through multiple causal pathways. The purpose of this study was to explore the relationship between germline and somatic mutations in a population-based series of melanoma patients to reshape and refine the divergent pathway model for melanoma. Melanomas collected from 123 Australian patients were analyzed for melanocortin-1 receptor (MC1R) variants and mutations in the BRAF and NRAS genes. Detailed phenotypic and sun exposure data were systematically collected from all patients. We found that BRAF-mutant melanomas were significantly more likely from younger patients and those with high nevus counts, and were more likely in melanomas with adjacent neval remnants. Conversely, BRAF-mutant melanomas were significantly less likely in people with high levels of lifetime sun exposure. We observed no association between germline MC1R status and somatic BRAF mutations in melanomas from this population. BRAF-mutant melanomas have different origins from other cutaneous melanomas. These data support the divergent pathways hypothesis for melanoma, which may require a reappraisal of targeted cancer prevention activities.

Household food expenditure and its contribution to socioeconomic inequalities in purchasing foods consistent with Australian dietary guideline recommendations

Aim: To examine the amount of money spent on food by household income, and to ascertain whether food expenditure mediates the relationship between household income and the purchase of staple foods consistent with Australian dietary guideline recommendations. ----- ----- Methods: In face-to-face interviews (n = 1003, 66.4% response rate), households in Brisbane, Australia were asked about their purchasing choices for a range of staple foods, including grocery items, fruits and vegetables. For each participant, information was obtained about their total weekly household food expenditure, along with their sociodemographic and household characteristics. ----- ----- Results: Household income was significantly associated with food expenditure; participants residing in higher-income households spent more money on food per household member than those from lower-income households. Lower income households were less likely to make food purchasing choices of dietary staples that were consistent with recommendations. However, food expenditure did not attenuate the relationship between household income and the purchase of staple foods consistent with dietary guideline recommendations. ----- ----- Conclusions: The findings suggest that food expenditure may not contribute to income inequalities in purchasing staple foods consistent with dietary guideline recommendations: instead, other material or psychosocial factors not considered in the current study may be more important determinants of these inequalities. Further research should examine whether expenditure on non-staple items and takeaway foods is a larger contributor to socioeconomic inequalities in dietary behavior.

Structural inquiry, human agency and the contribution of Harre and Bhaskar : a case study of Wright’s “Classes”

This paper examines the contribution of aspects of critical and referential realism to the “logic” of structural explanation through an analysis of Erik Olin Wright’s Classes and the debate surrounding this work. Wright’s Classes has been selected as a case study because it offers an opportunity to examine issues pertaining to “objective” and “subjective” determinations of class and related questions of agency and structure at the level of actual methodological strategies. A close examination of the structure of Wright’s inquiry reveals a number of places where Harre’s and Bhaskar’s approaches may contribute to the prescription of methodological strategies which could overcome some of the antinomies on which the debate on Classes is based. As a case study, the paper underlines the important “underlabourer” role of critical and referential realism and their contribution to questions of agency and structure in the context of actual stages involved in structural explanation

My Victorian Waterway : Personal Connections with Rivers, Estuaries and Wetlands in Victoria. Report Commissioned by the Department of Sustainability and Environment

Victorians feel a strong connection to their local waterways and most have a good grasp of river health issues. The My Victorian Waterway report analyses how Victorians interact with their local waterways including rivers, lakes and estuaries. The report is based on the results of a survey completed by more than 7,000 Victorians who answered questions about how they use and care for their local waterways as well as their knowledge of river health issues and aspirations for the future of our waterways.

Stress and addiction : contribution of the corticotropin releasing factor (CRF) system in neuroplasticity

Corticotropin releasing factor (CRF) has been shown to induce various behavioral changes related to adaptation to stress. Dysregulation of the CRF system at any point can lead to a variety of psychiatric disorders, including substance use disorders (SUDs). CRF has been associated with stress-induced drug reinforcement. Extensive literature has identified CRF to play an important role in the molecular mechanisms that lead to an increase in susceptibility that precipitates relapse to SUDs. The CRF system has a heterogeneous role in SUDs. It enhances the acute effects of drugs of abuse and is also responsible for the potentiation of drug-induced neuroplasticity evoked during the withdrawal period. We present in this review the brain regions and circuitries where CRF is expressed and may participate in stress-induced drug abuse. Finally, we attempt to evaluate the role of modulating the CRF system as a possible therapeutic strategy for treating the dysregulation of emotional behaviors that result from the acute positive reinforcement of substances of abuse as well as the negative reinforcement produced by withdrawal.

The influence of neighbourhood disadvantage on smoking cessation and its contribution to inequalities in smoking status

Introduction and aims: Individual smokers from disadvantaged backgrounds are less likely to quit, which contributes to widening inequalities in smoking. Residents of disadvantaged neighbourhoods are more likely to smoke, and neighbourhood inequalities in smoking may also be widening because of neighbourhood differences in rates of cessation. This study examined the association between neighbourhood disadvantage and smoking cessation and its relationship with neighbourhood inequalities in smoking. Design and methods: A multilevel longitudinal study of mid-aged (40-67 years) residents (n=6915) of Brisbane, Australia, who lived in the same neighbourhoods (n=200) in 2007 and 2009. Neighbourhood inequalities in cessation and smoking were analysed using multilevel logistic regression and Markov chain Monte Carlo simulation. Results: After adjustment for individual-level socioeconomic factors, the probability of quitting smoking between 2007 and 2009 was lower for residents of disadvantaged neighbourhoods (9.0%-12.8%) than their counterparts in more advantaged neighbourhoods (20.7%-22.5%). These inequalities in cessation manifested in widening inequalities in smoking: in 2007 the between-neighbourhood variance in rates of smoking was 0.242 (p≤0.001) and in 2009 it was 0.260 (p≤0.001). In 2007, residents of the most disadvantaged neighbourhoods were 88% (OR 1.88, 95% CrI 1.41-2.49) more likely to smoke than residents in the least disadvantaged neighbourhoods: the corresponding difference in 2009 was 98% (OR 1.98 95% CrI 1.48-2.66). Conclusion: Fundamentally, social and economic inequalities at the neighbourhood and individual-levels cause smoking and cessation inequalities. Reducing these inequalities will require comprehensive, well-funded, and targeted tobacco control efforts and equity based policies that address the social and economic determinants of smoking.